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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa</title><author><name sortKey="Wong, Vanessa K" sort="Wong, Vanessa K" uniqKey="Wong V" first="Vanessa K." last="Wong">Vanessa K. Wong</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Holt, Kathryn E" sort="Holt, Kathryn E" uniqKey="Holt K" first="Kathryn E." last="Holt">Kathryn E. Holt</name><affiliation><nlm:aff id="aff003"><addr-line>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name><affiliation><nlm:aff id="aff005"><addr-line>The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff006"><addr-line>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff007"><addr-line>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Pickard, Derek J" sort="Pickard, Derek J" uniqKey="Pickard D" first="Derek J." last="Pickard">Derek J. Pickard</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name><affiliation><nlm:aff id="aff008"><addr-line>International Vaccine Institute, Department of Epidemiology, Kwanak, Seoul, Republic of Korea</addr-line></nlm:aff></affiliation></author><author><name sortKey="Page, Andrew J" sort="Page, Andrew J" uniqKey="Page A" first="Andrew J." last="Page">Andrew J. Page</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Olanipekun, Grace" sort="Olanipekun, Grace" uniqKey="Olanipekun G" first="Grace" last="Olanipekun">Grace Olanipekun</name><affiliation><nlm:aff id="aff009"><addr-line>International Foundation Against Infectious Diseases in Nigeria, Abuja, Nigeria</addr-line></nlm:aff></affiliation></author><author><name sortKey="Munir, Huda" sort="Munir, Huda" uniqKey="Munir H" first="Huda" last="Munir">Huda Munir</name><affiliation><nlm:aff id="aff010"><addr-line>Department of Medical Microbiology, Aminu Kano Teaching Hospital, Kano, Nigeria</addr-line></nlm:aff></affiliation></author><author><name sortKey="Alter, Roxanne" sort="Alter, Roxanne" uniqKey="Alter R" first="Roxanne" last="Alter">Roxanne Alter</name><affiliation><nlm:aff id="aff011"><addr-line>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Fey, Paul D" sort="Fey, Paul D" uniqKey="Fey P" first="Paul D." last="Fey">Paul D. Fey</name><affiliation><nlm:aff id="aff011"><addr-line>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Feasey, Nicholas A" sort="Feasey, Nicholas A" uniqKey="Feasey N" first="Nicholas A." last="Feasey">Nicholas A. Feasey</name><affiliation><nlm:aff id="aff012"><addr-line>Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="Francois-Xavier" last="Weill">Francois-Xavier Weill</name><affiliation><nlm:aff id="aff013"><addr-line>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Le Hello, Simon" sort="Le Hello, Simon" uniqKey="Le Hello S" first="Simon" last="Le Hello">Simon Le Hello</name><affiliation><nlm:aff id="aff013"><addr-line>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hart, Peter J" sort="Hart, Peter J" uniqKey="Hart P" first="Peter J." last="Hart">Peter J. Hart</name><affiliation><nlm:aff id="aff014"><addr-line>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff015"><addr-line>St George’s University of London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation></author><author><name sortKey="Breiman, Robert F" sort="Breiman, Robert F" uniqKey="Breiman R" first="Robert F." last="Breiman">Robert F. Breiman</name><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff017"><addr-line>Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff018"><addr-line>Emory Global Health Institute, Atlanta, Georgia, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gordon, Melita A" sort="Gordon, Melita A" uniqKey="Gordon M" first="Melita A." last="Gordon">Melita A. Gordon</name><affiliation><nlm:aff id="aff019"><addr-line>Institute of Infection and Global Health, University of Liverpool, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff020"><addr-line>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</addr-line></nlm:aff></affiliation></author><author><name sortKey="Heyderman, Robert S" sort="Heyderman, Robert S" uniqKey="Heyderman R" first="Robert S." last="Heyderman">Robert S. Heyderman</name><affiliation><nlm:aff id="aff020"><addr-line>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff021"><addr-line>Division of Infection and Immunity, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name><affiliation><nlm:aff id="aff022"><addr-line>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff023"><addr-line>KU Leuven, University of Leuven, Department of Microbiology and Immunology, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lunguya, Octavie" sort="Lunguya, Octavie" uniqKey="Lunguya O" first="Octavie" last="Lunguya">Octavie Lunguya</name><affiliation><nlm:aff id="aff024"><addr-line>National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff025"><addr-line>University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</addr-line></nlm:aff></affiliation></author><author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name><affiliation><nlm:aff id="aff021"><addr-line>Division of Infection and Immunity, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff026"><addr-line>Microbiology Department, College of Medicine, University of Malawi, Malawi</addr-line></nlm:aff></affiliation></author><author><name sortKey="Maclennan, Calman A" sort="Maclennan, Calman A" uniqKey="Maclennan C" first="Calman A." last="Maclennan">Calman A. Maclennan</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff014"><addr-line>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff027"><addr-line>The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Keddy, Karen H" sort="Keddy, Karen H" uniqKey="Keddy K" first="Karen H." last="Keddy">Karen H. Keddy</name><affiliation><nlm:aff id="aff028"><addr-line>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</addr-line></nlm:aff></affiliation></author><author><name sortKey="Smith, Anthony M" sort="Smith, Anthony M" uniqKey="Smith A" first="Anthony M." last="Smith">Anthony M. Smith</name><affiliation><nlm:aff id="aff028"><addr-line>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</addr-line></nlm:aff></affiliation></author><author><name sortKey="Onsare, Robert S" sort="Onsare, Robert S" uniqKey="Onsare R" first="Robert S." last="Onsare">Robert S. Onsare</name><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation></author><author><name sortKey="De Pinna, Elizabeth" sort="De Pinna, Elizabeth" uniqKey="De Pinna E" first="Elizabeth" last="De Pinna">Elizabeth De Pinna</name><affiliation><nlm:aff id="aff029"><addr-line>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name><affiliation><nlm:aff id="aff029"><addr-line>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Amos, Ben" sort="Amos, Ben" uniqKey="Amos B" first="Ben" last="Amos">Ben Amos</name><affiliation><nlm:aff id="aff030"><addr-line>St Augustine’s Hospital, Muheza, Tanzania</addr-line></nlm:aff></affiliation></author><author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name><affiliation><nlm:aff id="aff031"><addr-line>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff032"><addr-line>University of Abuja Teaching Hospital, Gwagwalada, Nigeria</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff033"><addr-line>Bingham University, Karu, Nassarawa State, Nigeria</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27657909</idno><idno type="pmc">5033494</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033494</idno><idno type="RBID">PMC:5033494</idno><idno type="doi">10.1371/journal.pntd.0004781</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">002913</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002913</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa</title><author><name sortKey="Wong, Vanessa K" sort="Wong, Vanessa K" uniqKey="Wong V" first="Vanessa K." last="Wong">Vanessa K. Wong</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Holt, Kathryn E" sort="Holt, Kathryn E" uniqKey="Holt K" first="Kathryn E." last="Holt">Kathryn E. Holt</name><affiliation><nlm:aff id="aff003"><addr-line>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Okoro, Chinyere" sort="Okoro, Chinyere" uniqKey="Okoro C" first="Chinyere" last="Okoro">Chinyere Okoro</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name><affiliation><nlm:aff id="aff005"><addr-line>The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff006"><addr-line>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff007"><addr-line>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Pickard, Derek J" sort="Pickard, Derek J" uniqKey="Pickard D" first="Derek J." last="Pickard">Derek J. Pickard</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Marks, Florian" sort="Marks, Florian" uniqKey="Marks F" first="Florian" last="Marks">Florian Marks</name><affiliation><nlm:aff id="aff008"><addr-line>International Vaccine Institute, Department of Epidemiology, Kwanak, Seoul, Republic of Korea</addr-line></nlm:aff></affiliation></author><author><name sortKey="Page, Andrew J" sort="Page, Andrew J" uniqKey="Page A" first="Andrew J." last="Page">Andrew J. Page</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Olanipekun, Grace" sort="Olanipekun, Grace" uniqKey="Olanipekun G" first="Grace" last="Olanipekun">Grace Olanipekun</name><affiliation><nlm:aff id="aff009"><addr-line>International Foundation Against Infectious Diseases in Nigeria, Abuja, Nigeria</addr-line></nlm:aff></affiliation></author><author><name sortKey="Munir, Huda" sort="Munir, Huda" uniqKey="Munir H" first="Huda" last="Munir">Huda Munir</name><affiliation><nlm:aff id="aff010"><addr-line>Department of Medical Microbiology, Aminu Kano Teaching Hospital, Kano, Nigeria</addr-line></nlm:aff></affiliation></author><author><name sortKey="Alter, Roxanne" sort="Alter, Roxanne" uniqKey="Alter R" first="Roxanne" last="Alter">Roxanne Alter</name><affiliation><nlm:aff id="aff011"><addr-line>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Fey, Paul D" sort="Fey, Paul D" uniqKey="Fey P" first="Paul D." last="Fey">Paul D. Fey</name><affiliation><nlm:aff id="aff011"><addr-line>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Feasey, Nicholas A" sort="Feasey, Nicholas A" uniqKey="Feasey N" first="Nicholas A." last="Feasey">Nicholas A. Feasey</name><affiliation><nlm:aff id="aff012"><addr-line>Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="Francois-Xavier" last="Weill">Francois-Xavier Weill</name><affiliation><nlm:aff id="aff013"><addr-line>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Le Hello, Simon" sort="Le Hello, Simon" uniqKey="Le Hello S" first="Simon" last="Le Hello">Simon Le Hello</name><affiliation><nlm:aff id="aff013"><addr-line>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hart, Peter J" sort="Hart, Peter J" uniqKey="Hart P" first="Peter J." last="Hart">Peter J. Hart</name><affiliation><nlm:aff id="aff014"><addr-line>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff015"><addr-line>St George’s University of London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation></author><author><name sortKey="Breiman, Robert F" sort="Breiman, Robert F" uniqKey="Breiman R" first="Robert F." last="Breiman">Robert F. Breiman</name><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff017"><addr-line>Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff018"><addr-line>Emory Global Health Institute, Atlanta, Georgia, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gordon, Melita A" sort="Gordon, Melita A" uniqKey="Gordon M" first="Melita A." last="Gordon">Melita A. Gordon</name><affiliation><nlm:aff id="aff019"><addr-line>Institute of Infection and Global Health, University of Liverpool, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff020"><addr-line>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</addr-line></nlm:aff></affiliation></author><author><name sortKey="Heyderman, Robert S" sort="Heyderman, Robert S" uniqKey="Heyderman R" first="Robert S." last="Heyderman">Robert S. Heyderman</name><affiliation><nlm:aff id="aff020"><addr-line>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff021"><addr-line>Division of Infection and Immunity, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Jacobs, Jan" sort="Jacobs, Jan" uniqKey="Jacobs J" first="Jan" last="Jacobs">Jan Jacobs</name><affiliation><nlm:aff id="aff022"><addr-line>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff023"><addr-line>KU Leuven, University of Leuven, Department of Microbiology and Immunology, Belgium</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lunguya, Octavie" sort="Lunguya, Octavie" uniqKey="Lunguya O" first="Octavie" last="Lunguya">Octavie Lunguya</name><affiliation><nlm:aff id="aff024"><addr-line>National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff025"><addr-line>University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</addr-line></nlm:aff></affiliation></author><author><name sortKey="Msefula, Chisomo" sort="Msefula, Chisomo" uniqKey="Msefula C" first="Chisomo" last="Msefula">Chisomo Msefula</name><affiliation><nlm:aff id="aff021"><addr-line>Division of Infection and Immunity, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff026"><addr-line>Microbiology Department, College of Medicine, University of Malawi, Malawi</addr-line></nlm:aff></affiliation></author><author><name sortKey="Maclennan, Calman A" sort="Maclennan, Calman A" uniqKey="Maclennan C" first="Calman A." last="Maclennan">Calman A. Maclennan</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff014"><addr-line>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff027"><addr-line>The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Keddy, Karen H" sort="Keddy, Karen H" uniqKey="Keddy K" first="Karen H." last="Keddy">Karen H. Keddy</name><affiliation><nlm:aff id="aff028"><addr-line>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</addr-line></nlm:aff></affiliation></author><author><name sortKey="Smith, Anthony M" sort="Smith, Anthony M" uniqKey="Smith A" first="Anthony M." last="Smith">Anthony M. Smith</name><affiliation><nlm:aff id="aff028"><addr-line>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</addr-line></nlm:aff></affiliation></author><author><name sortKey="Onsare, Robert S" sort="Onsare, Robert S" uniqKey="Onsare R" first="Robert S." last="Onsare">Robert S. Onsare</name><affiliation><nlm:aff id="aff016"><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></nlm:aff></affiliation></author><author><name sortKey="De Pinna, Elizabeth" sort="De Pinna, Elizabeth" uniqKey="De Pinna E" first="Elizabeth" last="De Pinna">Elizabeth De Pinna</name><affiliation><nlm:aff id="aff029"><addr-line>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Nair, Satheesh" sort="Nair, Satheesh" uniqKey="Nair S" first="Satheesh" last="Nair">Satheesh Nair</name><affiliation><nlm:aff id="aff029"><addr-line>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Amos, Ben" sort="Amos, Ben" uniqKey="Amos B" first="Ben" last="Amos">Ben Amos</name><affiliation><nlm:aff id="aff030"><addr-line>St Augustine’s Hospital, Muheza, Tanzania</addr-line></nlm:aff></affiliation></author><author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name><affiliation><nlm:aff id="aff001"><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Obaro, Stephen" sort="Obaro, Stephen" uniqKey="Obaro S" first="Stephen" last="Obaro">Stephen Obaro</name><affiliation><nlm:aff id="aff031"><addr-line>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff032"><addr-line>University of Abuja Teaching Hospital, Gwagwalada, Nigeria</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff033"><addr-line>Bingham University, Karu, Nassarawa State, Nigeria</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Neglected Tropical Diseases</title><idno type="ISSN">1935-2727</idno><idno type="eISSN">1935-2735</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="sec001"><title>Background</title><p>The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with <italic>Salmonella enterica</italic> serovar Typhi (<italic>S</italic>. Typhi) as an important cause of bacteremia in children.</p></sec><sec id="sec002"><title>Methods</title><p>A total of 128 <italic>S</italic>. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance.</p></sec><sec id="sec003"><title>Results</title><p>Several distinct <italic>S</italic>. Typhi genotypes were identified in Nigeria that were related to other clusters of <italic>S</italic>. Typhi isolates from north, west and central regions of Africa. The rapidly expanding <italic>S</italic>. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with <italic>S</italic>. Typhi.</p></sec><sec id="sec004"><title>Conclusions</title><p>These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Crump, Ja" uniqKey="Crump J">JA Crump</name></author><author><name sortKey="Luby, Sp" uniqKey="Luby S">SP Luby</name></author><author><name sortKey="Mintz, Ed" uniqKey="Mintz E">ED Mintz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crump, Ja" uniqKey="Crump J">JA Crump</name></author><author><name sortKey="Mintz, Ed" uniqKey="Mintz E">ED Mintz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mogasale, V" uniqKey="Mogasale V">V Mogasale</name></author><author><name sortKey="Maskery, B" uniqKey="Maskery B">B 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Negl Trop Dis</journal-id><journal-id journal-id-type="iso-abbrev">PLoS Negl Trop Dis</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosntds</journal-id><journal-title-group><journal-title>PLoS Neglected Tropical Diseases</journal-title></journal-title-group><issn pub-type="ppub">1935-2727</issn><issn pub-type="epub">1935-2735</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27657909</article-id><article-id pub-id-type="pmc">5033494</article-id><article-id pub-id-type="doi">10.1371/journal.pntd.0004781</article-id><article-id pub-id-type="publisher-id">PNTD-D-16-00463</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Mammals</subject><subj-group><subject>Cats</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Infectious Diseases</subject><subj-group><subject>Bacterial Diseases</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Typhi</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Medical Microbiology</subject><subj-group><subject>Microbial Pathogens</subject><subj-group><subject>Bacterial Pathogens</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Typhi</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Pathology and Laboratory Medicine</subject><subj-group><subject>Pathogens</subject><subj-group><subject>Microbial Pathogens</subject><subj-group><subject>Bacterial Pathogens</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Typhi</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Bacteria</subject><subj-group><subject>Enterobacteriaceae</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Typhi</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>People and Places</subject><subj-group><subject>Geographical Locations</subject><subj-group><subject>Africa</subject><subj-group><subject>Nigeria</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Infectious Diseases</subject><subj-group><subject>Bacterial Diseases</subject><subj-group><subject>Typhoid</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial Control</subject><subj-group><subject>Antimicrobial Resistance</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Antimicrobial Resistance</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Public and Occupational Health</subject><subj-group><subject>Global Health</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>People and places</subject><subj-group><subject>Geographical locations</subject><subj-group><subject>Europe</subject><subj-group><subject>United Kingdom</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa</article-title><alt-title alt-title-type="running-head">Surveillance Identifies Transmissions of Typhoid in West Africa</alt-title></title-group><contrib-group><contrib contrib-type="author"><collab>International Typhoid Consortium</collab><xref ref-type="author-notes" rid="fn001"><sup>¶</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wong</surname><given-names>Vanessa K.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="author-notes" rid="currentaff001"><sup>¤</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib><contrib contrib-type="author"><name><surname>Holt</surname><given-names>Kathryn E.</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Okoro</surname><given-names>Chinyere</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Baker</surname><given-names>Stephen</given-names></name><xref ref-type="aff" rid="aff005"><sup>5</sup></xref><xref ref-type="aff" rid="aff006"><sup>6</sup></xref><xref ref-type="aff" rid="aff007"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Pickard</surname><given-names>Derek J.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Marks</surname><given-names>Florian</given-names></name><xref ref-type="aff" rid="aff008"><sup>8</sup></xref></contrib><contrib contrib-type="author"><name><surname>Page</surname><given-names>Andrew J.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Olanipekun</surname><given-names>Grace</given-names></name><xref ref-type="aff" rid="aff009"><sup>9</sup></xref></contrib><contrib contrib-type="author"><name><surname>Munir</surname><given-names>Huda</given-names></name><xref ref-type="aff" rid="aff010"><sup>10</sup></xref></contrib><contrib contrib-type="author"><name><surname>Alter</surname><given-names>Roxanne</given-names></name><xref ref-type="aff" rid="aff011"><sup>11</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fey</surname><given-names>Paul D.</given-names></name><xref ref-type="aff" rid="aff011"><sup>11</sup></xref></contrib><contrib contrib-type="author"><name><surname>Feasey</surname><given-names>Nicholas A.</given-names></name><xref ref-type="aff" rid="aff012"><sup>12</sup></xref></contrib><contrib contrib-type="author"><name><surname>Weill</surname><given-names>Francois-Xavier</given-names></name><xref ref-type="aff" rid="aff013"><sup>13</sup></xref></contrib><contrib contrib-type="author"><name><surname>Le Hello</surname><given-names>Simon</given-names></name><xref ref-type="aff" rid="aff013"><sup>13</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hart</surname><given-names>Peter J.</given-names></name><xref ref-type="aff" rid="aff014"><sup>14</sup></xref><xref ref-type="aff" rid="aff015"><sup>15</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kariuki</surname><given-names>Samuel</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff016"><sup>16</sup></xref></contrib><contrib contrib-type="author"><name><surname>Breiman</surname><given-names>Robert F.</given-names></name><xref ref-type="aff" rid="aff016"><sup>16</sup></xref><xref ref-type="aff" rid="aff017"><sup>17</sup></xref><xref ref-type="aff" rid="aff018"><sup>18</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gordon</surname><given-names>Melita A.</given-names></name><xref ref-type="aff" rid="aff019"><sup>19</sup></xref><xref ref-type="aff" rid="aff020"><sup>20</sup></xref></contrib><contrib contrib-type="author"><name><surname>Heyderman</surname><given-names>Robert S.</given-names></name><xref ref-type="aff" rid="aff020"><sup>20</sup></xref><xref ref-type="aff" rid="aff021"><sup>21</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jacobs</surname><given-names>Jan</given-names></name><xref ref-type="aff" rid="aff022"><sup>22</sup></xref><xref ref-type="aff" rid="aff023"><sup>23</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lunguya</surname><given-names>Octavie</given-names></name><xref ref-type="aff" rid="aff024"><sup>24</sup></xref><xref ref-type="aff" rid="aff025"><sup>25</sup></xref></contrib><contrib contrib-type="author"><name><surname>Msefula</surname><given-names>Chisomo</given-names></name><xref ref-type="aff" rid="aff021"><sup>21</sup></xref><xref ref-type="aff" rid="aff026"><sup>26</sup></xref></contrib><contrib contrib-type="author"><name><surname>MacLennan</surname><given-names>Calman A.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff014"><sup>14</sup></xref><xref ref-type="aff" rid="aff027"><sup>27</sup></xref></contrib><contrib contrib-type="author"><name><surname>Keddy</surname><given-names>Karen H.</given-names></name><xref ref-type="aff" rid="aff028"><sup>28</sup></xref></contrib><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Anthony M.</given-names></name><xref ref-type="aff" rid="aff028"><sup>28</sup></xref></contrib><contrib contrib-type="author"><name><surname>Onsare</surname><given-names>Robert S.</given-names></name><xref ref-type="aff" rid="aff016"><sup>16</sup></xref></contrib><contrib contrib-type="author"><name><surname>De Pinna</surname><given-names>Elizabeth</given-names></name><xref ref-type="aff" rid="aff029"><sup>29</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nair</surname><given-names>Satheesh</given-names></name><xref ref-type="aff" rid="aff029"><sup>29</sup></xref></contrib><contrib contrib-type="author"><name><surname>Amos</surname><given-names>Ben</given-names></name><xref ref-type="aff" rid="aff030"><sup>30</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dougan</surname><given-names>Gordon</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Obaro</surname><given-names>Stephen</given-names></name><xref ref-type="aff" rid="aff031"><sup>31</sup></xref><xref ref-type="aff" rid="aff032"><sup>32</sup></xref><xref ref-type="aff" rid="aff033"><sup>33</sup></xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia</addr-line></aff><aff id="aff004"><label>4</label><addr-line>Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia</addr-line></aff><aff id="aff005"><label>5</label><addr-line>The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</addr-line></aff><aff id="aff006"><label>6</label><addr-line>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom</addr-line></aff><aff id="aff007"><label>7</label><addr-line>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom</addr-line></aff><aff id="aff008"><label>8</label><addr-line>International Vaccine Institute, Department of Epidemiology, Kwanak, Seoul, Republic of Korea</addr-line></aff><aff id="aff009"><label>9</label><addr-line>International Foundation Against Infectious Diseases in Nigeria, Abuja, Nigeria</addr-line></aff><aff id="aff010"><label>10</label><addr-line>Department of Medical Microbiology, Aminu Kano Teaching Hospital, Kano, Nigeria</addr-line></aff><aff id="aff011"><label>11</label><addr-line>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></aff><aff id="aff012"><label>12</label><addr-line>Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom</addr-line></aff><aff id="aff013"><label>13</label><addr-line>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</addr-line></aff><aff id="aff014"><label>14</label><addr-line>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</addr-line></aff><aff id="aff015"><label>15</label><addr-line>St George’s University of London, London, United Kingdom</addr-line></aff><aff id="aff016"><label>16</label><addr-line>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</addr-line></aff><aff id="aff017"><label>17</label><addr-line>Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></aff><aff id="aff018"><label>18</label><addr-line>Emory Global Health Institute, Atlanta, Georgia, United States of America</addr-line></aff><aff id="aff019"><label>19</label><addr-line>Institute of Infection and Global Health, University of Liverpool, United Kingdom</addr-line></aff><aff id="aff020"><label>20</label><addr-line>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</addr-line></aff><aff id="aff021"><label>21</label><addr-line>Division of Infection and Immunity, University College London, London, United Kingdom</addr-line></aff><aff id="aff022"><label>22</label><addr-line>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</addr-line></aff><aff id="aff023"><label>23</label><addr-line>KU Leuven, University of Leuven, Department of Microbiology and Immunology, Belgium</addr-line></aff><aff id="aff024"><label>24</label><addr-line>National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</addr-line></aff><aff id="aff025"><label>25</label><addr-line>University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</addr-line></aff><aff id="aff026"><label>26</label><addr-line>Microbiology Department, College of Medicine, University of Malawi, Malawi</addr-line></aff><aff id="aff027"><label>27</label><addr-line>The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom</addr-line></aff><aff id="aff028"><label>28</label><addr-line>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</addr-line></aff><aff id="aff029"><label>29</label><addr-line>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</addr-line></aff><aff id="aff030"><label>30</label><addr-line>St Augustine’s Hospital, Muheza, Tanzania</addr-line></aff><aff id="aff031"><label>31</label><addr-line>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</addr-line></aff><aff id="aff032"><label>32</label><addr-line>University of Abuja Teaching Hospital, Gwagwalada, Nigeria</addr-line></aff><aff id="aff033"><label>33</label><addr-line>Bingham University, Karu, Nassarawa State, Nigeria</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Ryan</surname><given-names>Edward T.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Massachusetts General Hospital, UNITED STATES</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p><list list-type="simple"><list-item><p><bold>Analyzed the data:</bold> VKW KEH AJP CO SO.</p></list-item><list-item><p><bold>Contributed reagents/materials/analysis tools:</bold> DJP KEH AJP CO SO GD GO HM RA PDF SB NAF FXW PJH SLH SK RFB JJ OL CM FM MAG RSH CAM KHK AMS RSO EDP SA BA.</p></list-item><list-item><p><bold>Wrote the paper:</bold> VKW SO KEH GD.</p></list-item><list-item><p><bold>Project oversight:</bold> SO GD.</p></list-item><list-item><p><bold>Study design:</bold> SO KEH GD.</p></list-item><list-item><p><bold>Isolate acquisition and processing and clinical data collection:</bold> DJP KEH AJP CO SO GD GO HM RA PDF SB NAF FXW PJH SLH SK RFB JJ OL CM FM MAG RSH CAM KHK AMS RSO EDP SA BA.</p></list-item><list-item><p><bold>Sequencing data generation:</bold> AJP.</p></list-item><list-item><p><bold>Contributed to manuscript editing:</bold> DJP KEH AJP CO SO GD GO HM RA PDF SB NAF FXW PJH SLH SK RFB JJ OL CM FM MAG RSH CAM KHK AMS RSO EDP SA BA.</p></list-item></list></p></fn><fn fn-type="current-aff" id="currentaff001"><label>¤</label><p>Current address: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK</p></fn><fn fn-type="other" id="fn001"><p>¶ Membership of the International Typhoid Consortium is listed in the Members of International Typhoid Consortium section.</p></fn><corresp id="cor001">* E-mail: <email>vw1@sanger.ac.uk</email>; <email>vanessawong@doctors.org.uk</email></corresp></author-notes><pub-date pub-type="epub"><day>22</day><month>9</month><year>2016</year></pub-date><pub-date pub-type="collection"><month>9</month><year>2016</year></pub-date><volume>10</volume><issue>9</issue><elocation-id>e0004781</elocation-id><history><date date-type="received"><day>19</day><month>3</month><year>2016</year></date><date date-type="accepted"><day>25</day><month>5</month><year>2016</year></date></history><permissions><license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/publicdomain/zero/1.0/">Creative Commons CC0</ext-link> public domain dedication.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pntd.0004781.pdf"></self-uri><abstract><sec id="sec001"><title>Background</title><p>The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with <italic>Salmonella enterica</italic> serovar Typhi (<italic>S</italic>. Typhi) as an important cause of bacteremia in children.</p></sec><sec id="sec002"><title>Methods</title><p>A total of 128 <italic>S</italic>. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance.</p></sec><sec id="sec003"><title>Results</title><p>Several distinct <italic>S</italic>. Typhi genotypes were identified in Nigeria that were related to other clusters of <italic>S</italic>. Typhi isolates from north, west and central regions of Africa. The rapidly expanding <italic>S</italic>. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with <italic>S</italic>. Typhi.</p></sec><sec id="sec004"><title>Conclusions</title><p>These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.</p></sec></abstract><abstract abstract-type="summary"><title>Author Summary</title><p>Typhoid fever, a serious bloodstream infection caused by the bacterium <italic>Salmonella</italic> Typhi, is a major cause of disease and death around the world. There have been limited data on the epidemiology of typhoid in many countries in sub-Saharan African, including Nigeria. Recent evidence, however, showed that typhoid was an important cause of bacteraemia in children residing in two regions of Nigeria. Here, we analyzed the whole genome sequences of 128 <italic>S</italic>. Typhi isolates from two studies in order to elucidate the population structure and characterize the genetic components of antimicrobial resistance. We found that the multiple <italic>S</italic>. Typhi genotypes identified were closely related to other <italic>S</italic>. Typhi from neighboring regions of Africa and that multidrug resistance (MDR) was common among these isolates, and in many cases was associated with the IncHI1 plasmid known to cause MDR typhoid. These results provide evidence that typhoid was established in Nigeria as a result of several independent introductions into the country and that there has been extensive exchange of <italic>S</italic>. Typhi in and around the region of West Africa. This study emphasizes the importance of surveillance to improve our understanding of the epidemiology of typhoid, which is needed to underpin public health measures to reduce the spread of disease and facilitate patient management.</p></abstract><funding-group><funding-statement>This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award 098051; NAF was supported by the Wellcome Trust Research Fellowship WT092152MA. NAF, RSH and this work were supported by a strategic award from the Wellcome Trust for the MLW Clinical Research Programme (101113/Z/13/Z). KEH was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI) (grant #VR0082). CAM was supported by a Clinical Research Fellowship from GlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-driven vaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire, and by the French Government “Investissement d'Avenir” program (Integrative Biology of Emerging Infectious Diseases” Laboratory of Excellence, grant no. ANR-10-LABX-62-IBEID). CO was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. JJ was supported by the antibiotic resistance surveillance project in DR Congo, funded by Project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine, Antwerp, Belgium. FM was supported by a research grant from the Bill & Melinda Gates Foundation. The findings and conclusions contained within this publication are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation. SK was supported by the NIH Grant Number R01 AI099525-02. SB is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). SO was supported by the National Institute Of Allergy And Infectious Diseases (NIAID) of the National Institutes of Health (#R01AI097493). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><fig-count count="3"></fig-count><table-count count="2"></table-count><page-count count="22"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All sequence read files are available from European Nucleotide Archive under accession number ERP005877.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All sequence read files are available from European Nucleotide Archive under accession number ERP005877.</p></notes></front><body><sec sec-type="intro" id="sec005"><title>Introduction</title><p>Typhoid fever is a systemic infection caused by the Gram-negative bacterium <italic>Salmonella enterica</italic> serovar Typhi (<italic>S</italic>. Typhi) that continues to be a serious global health problem and a major cause of morbidity and mortality in low-middle income countries [<xref rid="pntd.0004781.ref001" ref-type="bibr">1</xref>]. It is estimated that the yearly incidence of typhoid fever exceeds 20 million cases, with over 200,000 deaths [<xref rid="pntd.0004781.ref002" ref-type="bibr">2</xref>, <xref rid="pntd.0004781.ref003" ref-type="bibr">3</xref>]. Defining the burden of typhoid fever is a challenge in settings where there are few diagnostic microbiology facilities, with diagnosis often based on clinical history of fever, malaise, and abdominal pain. Unfortunately, these symptoms have considerable overlap with several other febrile illnesses and clinical diagnosis is therefore inaccurate [<xref rid="pntd.0004781.ref004" ref-type="bibr">4</xref>].</p><p>Nigeria is one of the most densely populated countries in Africa with large areas of urban development. Thus, it is perhaps surprising that little reliable data are available on microbial culture of the etiologic agents of bacteremia in children or adults. This poses a challenge for data comparison with other regions, including other sub-Saharan African countries where such data are available [<xref rid="pntd.0004781.ref005" ref-type="bibr">5</xref>–<xref rid="pntd.0004781.ref007" ref-type="bibr">7</xref>]. In general, febrile illnesses among children in Nigeria are presumed by clinicians to be caused by malaria, which is still very common in many parts of the country. Only if fever persists following an empiric course of anti-malarials, is typhoid then considered as a potential cause of infection [<xref rid="pntd.0004781.ref008" ref-type="bibr">8</xref>]. In studies from central and northwest Nigeria [<xref rid="pntd.0004781.ref009" ref-type="bibr">9</xref>], we found that <italic>S</italic>. Typhi was the commonest cause of bloodstream infections in children, particularly in those living in the proximity of Abuja city located in central Nigeria.</p><p>Until recently, molecular epidemiological studies on <italic>S</italic>. Typhi were compromised by a lack of genetic resolution, limiting the ability to define the population structure of the bacteria and identify transmission patterns. This is because <italic>S</italic>. Typhi is a relatively monomorphic pathogen with limited genome variation [<xref rid="pntd.0004781.ref010" ref-type="bibr">10</xref>]. However, sequencing-based approaches have facilitated the stratification of <italic>S</italic>. Typhi into multiple genotypes [<xref rid="pntd.0004781.ref011" ref-type="bibr">11</xref>] (see Wong <italic>et al</italic>. 2016, under review in <italic>Nature Communications</italic>, NCOMMS-15-25823, manuscript included). Whole genome sequencing in particular can unequivocally identify phylogenetic relationships with important genetic traits such as antimicrobial resistance [<xref rid="pntd.0004781.ref012" ref-type="bibr">12</xref>]. Here we report whole genome-based analysis of 128 bloodstream isolates of <italic>S</italic>. Typhi from children residing in two regions of Nigeria, and compared these with data from other countries in Africa, including the West African subregion.</p></sec><sec sec-type="materials|methods" id="sec006"><title>Methods</title><sec id="sec007"><title>Settings</title><p>Nigeria has a population of approximately 177 million people making it the most populous country in sub-Saharan Africa [<xref rid="pntd.0004781.ref013" ref-type="bibr">13</xref>]. The two study sites in Nigeria were the Federal Capital Territory (FCT) and Kano. The FCT is a federal territory in central Nigeria and covers a land area of 8,000 square kilometers. It is the home of the capital city Abuja, a “planned” city, built in the 1980s. It was officially made Nigeria’s capital in 1991 replacing the previous capital in Lagos. In 2006, the population was estimated at 1.7 million [<xref rid="pntd.0004781.ref014" ref-type="bibr">14</xref>]. The FCT continue to experience rapid population growth; it has been reported that some areas around Abuja have been growing at an annual rate of 20–30%, and the current population may be as high as 5.7 million [<xref rid="pntd.0004781.ref014" ref-type="bibr">14</xref>]. The rapid spread of squatter settlements and shantytowns in and around the city limits contribute to this rapid growth. The rainy season begins in April and ends in October. Within this period there is a brief interlude of Harmattan, occasioned by the Northeast Trade Wind, with the main features of dust haze, intensified coldness and dryness. The annual total rainfall for the FCT is in the range of 1,100 to 1,600 mm. The population is diverse, with increasing representation from the major ethnic groups of Hausa, Yoruba, and Igbos following the development of the FCT and relocation of the federal capital [<xref rid="pntd.0004781.ref015" ref-type="bibr">15</xref>]. Of note, there is also perennial malaria transmission, mostly due to <italic>Plasmodium falciparum</italic>, and the HIV prevalence is 7.5% amongst pregnant women attending antenatal clinics [<xref rid="pntd.0004781.ref016" ref-type="bibr">16</xref>].</p><p>Kano is the capital of Kano state in northwest Nigeria. According to the 2006 census, Kano state has a population of 9.38 million, which is comprised predominantly of Hausa and Fulani ethnic groups [<xref rid="pntd.0004781.ref017" ref-type="bibr">17</xref>]. It is recognized as one of the fastest growing cities in Nigeria with a population density of about 1,000 inhabitants per km<sup>2</sup>. It lies within the Sahel savannah region with daily mean temperature of about 30–33°C during the dry months of March to May and 10°C during the autumn months of September to February. Rainy season varies from year to year, but typically commences in May and ends in October, with an average annual rainfall of 600mm. The dry season starts from November to April [<xref rid="pntd.0004781.ref018" ref-type="bibr">18</xref>]. The entire state is within the meningococcal disease belt and malarial transmission is seasonal [<xref rid="pntd.0004781.ref017" ref-type="bibr">17</xref>]. HIV prevalence among women attending antenatal clinic is 1.3% [<xref rid="pntd.0004781.ref016" ref-type="bibr">16</xref>].</p></sec><sec id="sec008"><title>Enrolment sites</title><p>The enrolment sites at FCT are as previously described [<xref rid="pntd.0004781.ref009" ref-type="bibr">9</xref>, <xref rid="pntd.0004781.ref015" ref-type="bibr">15</xref>]. Briefly, children aged less than 5 years were enrolled from primary, secondary and tertiary healthcare facilities on presentation with an acute febrile illness and symptoms suggestive of sepsis. In Kano, we enrolled children from Aminu Kano Teaching Hospital (AKTH), Hasiya Bayero Pediatric Hospital and Murtala Specialist Hospital. While AKTH serves as a tertiary referral center, the other two facilities provide primary and secondary healthcare services. The combined outpatient attendance for children at these three facilities is about 1,000 daily. Both study sites included patients from the newer settlements on the outskirt of Abuja and around Kano where the level of sanitation is poor and access to potable water limited.</p></sec><sec id="sec009"><title>Data collection</title><p>A structured questionnaire was used to collate the clinical information. Study data were collected and managed using REDCap electronic data capture tools hosted at the University of Nebraska Medical Center [<xref rid="pntd.0004781.ref019" ref-type="bibr">19</xref>]. IBM SPSS for statistics was used for data analysis. Dichotomous variables were analyzed using <italic>χ</italic><sup><italic>2</italic></sup> or <italic>χ</italic><sup><italic>2</italic></sup> for trend tests [<xref rid="pntd.0004781.ref020" ref-type="bibr">20</xref>].</p></sec><sec id="sec010"><title>Ethics statement</title><p>Clinical information was collected using a structured questionnaire after obtaining a signed informed consent from the child’s parent or legal guardian. This study was approved by the ethics committees of the FCT, National Hospital Abuja, Zankli Medical Center, Federal Medical Center Keffi, Aminu Kano Teaching Hospital, and UNMC, Omaha Institutional Review Board.</p></sec><sec id="sec011"><title>Blood culture processing</title><p>Blood sampling and processing were as previously described [<xref rid="pntd.0004781.ref009" ref-type="bibr">9</xref>, <xref rid="pntd.0004781.ref015" ref-type="bibr">15</xref>]. Briefly, we utilized only aerobic blood culture bottles and held cultures in the Bactec 9050 incubator for a maximum of 5 days. Bacteria were identified by a combination of colony morphology and biochemical assays. For example, the API 20E system (bioMérieux, France) was used to identify <italic>Enterobacteriacae</italic>. Antimicrobial susceptibility profiles of the bacteria were determined by the Kirby-Bauer disk diffusion test using standard interpretative criteria [<xref rid="pntd.0004781.ref021" ref-type="bibr">21</xref>] for locally available antimicrobials (amoxicillin, co-amoxiclav, ceftazidime, ceftriaxone, nalidixic acid, ciprofloxacin, ofloxacin, sulfamethoxazole, trimethoprim-sulfamethoxazole, chloramphenicol, tetracycline, streptomycin, gentamicin, kanamycin, azithromycin, imipenem) in order to provide immediate management of patients. Bacterial isolates were stored in skimmed milk at -70°C and further characterized at the Clinical Microbiology Laboratory of the University of Nebraska Medical Center (UNMC).</p></sec><sec id="sec012"><title>Antimicrobial susceptibility testing</title><p>Antimicrobial susceptibility testing was performed at the UNMC Microbiology laboratory using the Epsilometer test (Etest; bioMérieux, France) according to standard methods. Minimum inhibitory concentration (MIC) values were interpreted according to Clinical Laboratory Standards Institute (CLSI) standards [<xref rid="pntd.0004781.ref021" ref-type="bibr">21</xref>]. Due to the lack of CLSI standards, a streptomycin MIC of ≥16 mg/L was considered resistant in these studies.</p></sec><sec id="sec013"><title><italic>Salmonella</italic> serotyping</title><p>All <italic>Salmonella</italic> isolates were identified to the serotype level using the Bioplex 200 (Bio-Rad) as previously described using the CDC standard <italic>Salmonella</italic> molecular serotyping protocol [<xref rid="pntd.0004781.ref022" ref-type="bibr">22</xref>–<xref rid="pntd.0004781.ref024" ref-type="bibr">24</xref>]. A total of 128 <italic>S</italic>. Typhi isolates were identified in these studies for whole genome sequencing.</p></sec><sec id="sec014"><title>DNA sequencing</title><p><italic>S</italic>. Typhi DNA was prepared using the Wizard Genomic DNA Kit (Promega, Madison, WI, USA) as per manufacturer’s instructions. Index-tagged paired end Illumina sequencing libraries were prepared as previously described [<xref rid="pntd.0004781.ref025" ref-type="bibr">25</xref>]. These were combined into pools each containing 96 uniquely tagged libraries and sequenced on the Illumina Hiseq2000 or Miseq platforms (Illumina, San Diego, CA, USA) according to manufacturer’s protocols to generate tagged 100 or 150 base pair (bp) paired-end reads with an insert size of 300–400 bp. Sequence reads were deposited in the European Nucleotide Archive under accession ERP005877 and a full list of accession numbers for each sample is available in <xref ref-type="supplementary-material" rid="pntd.0004781.s002">S1 Table</xref>. Sequence data from 1,831 additional <italic>S</italic>. Typhi isolates from 63 countries, generated previously in the same manner (Wong <italic>et al</italic>. 2015) [<xref rid="pntd.0004781.ref012" ref-type="bibr">12</xref>], were also included in the study (reads are available in the European Read Archive under accession ERP001718).</p></sec><sec id="sec015"><title>Read alignment and SNP detection</title><p>For analysis of single nucleotide polymorphisms (SNPs), the paired-end reads were mapped to the reference genome of <italic>S</italic>. Typhi CT18 (accession number AL513382), including the chromosome and plasmids pHCM1 and pHCM2 [<xref rid="pntd.0004781.ref026" ref-type="bibr">26</xref>], using SMALT (version 0.7.4) (<ext-link ext-link-type="uri" xlink:href="http://www.sanger.ac.uk/resources/software/smalt/">http://www.sanger.ac.uk/resources/software/smalt/</ext-link>). SNPs were identified as previously described, using <italic>samtools mpileup</italic> [<xref rid="pntd.0004781.ref027" ref-type="bibr">27</xref>] and filtering with a minimum mapping quality of 30 and a quality ratio cut-off of 0.75 [<xref rid="pntd.0004781.ref025" ref-type="bibr">25</xref>]. The allele at each locus in each isolate was determined by reference to the consensus base in that genome, using <italic>samtools mpileup</italic> [<xref rid="pntd.0004781.ref027" ref-type="bibr">27</xref>] and removing low confidence alleles with consensus base quality ≤20, read depth ≤5 or a heterozygous base call. SNPs called in phage regions, repetitive sequences (354 kbp; ~7.4% of bases in the <italic>S</italic>. Typhi CT18 reference chromosome, as defined previously [<xref rid="pntd.0004781.ref010" ref-type="bibr">10</xref>]) or recombinant regions (~180 kbp; <4% of CT18 reference chromosome, identified using an approach described previously [<xref rid="pntd.0004781.ref025" ref-type="bibr">25</xref>, <xref rid="pntd.0004781.ref028" ref-type="bibr">28</xref>]) were excluded, resulting in a final set of 23,300 chromosomal SNPs.</p></sec><sec id="sec016"><title>Phylogenetic analysis</title><p>The maximum likelihood (ML) phylogenetic tree was built from 23,300 SNP alignment of 1,961 isolates, including one <italic>S</italic>. Paratyphi A (accession number ERR326600) to provide an outgroup for tree rooting. We used RAxML (version 7.0.4) [<xref rid="pntd.0004781.ref029" ref-type="bibr">29</xref>] with the generalized time-reversible model and a Gamma distribution to model site-specific rate variation (the GTR+ substitution model; GTRGAMMA in RAxML). Support for the ML phylogeny was assessed via 100 bootstrap pseudo-replicate analyzes of the alignment data. The ML trees were displayed and annotated using iTOL [<xref rid="pntd.0004781.ref030" ref-type="bibr">30</xref>, <xref rid="pntd.0004781.ref031" ref-type="bibr">31</xref>].</p></sec><sec id="sec017"><title><italic>In silico</italic> resistance plasmid and resistance gene analysis</title><p>Plasmids and acquired antimicrobial resistance genes were detected, and their precise alleles determined, using the mapping-based allele typer SRST2 [<xref rid="pntd.0004781.ref032" ref-type="bibr">32</xref>] together with the ARG-Annot database of antimicrobial resistance genes [<xref rid="pntd.0004781.ref033" ref-type="bibr">33</xref>] and the PlasmidFinder database of plasmid replicons [<xref rid="pntd.0004781.ref034" ref-type="bibr">34</xref>]. SRST2 was also used to identify mutations in the <italic>gyrA</italic>, <italic>gyrB</italic>, <italic>parC</italic> and <italic>parE</italic> genes that have been associated with resistance to quinolones in <italic>Salmonella</italic> and other Gram-negative bacteria [<xref rid="pntd.0004781.ref035" ref-type="bibr">35</xref>–<xref rid="pntd.0004781.ref038" ref-type="bibr">38</xref>].</p></sec></sec><sec sec-type="results" id="sec018"><title>Results</title><sec id="sec019"><title>Typhoid surveillance</title><p>Blood cultures were performed for the evaluation of 10,133 acutely ill children, aged 0–60 months, from September 2008 until April 2015, in the FCT (including Abuja) and Kano located in central and northwest Nigeria, respectively [<xref rid="pntd.0004781.ref009" ref-type="bibr">9</xref>]. At FCT 6,082 children were enrolled between June 2012 and March 2015, of whom 457 (8%) had clinically significant bacteremia. Of these 110 (24%) had invasive salmonellosis, consisting of <italic>S</italic>. Typhi in 84 cases and non-typhoidal salmonellae (NTS) in 26 cases. In Kano from January 2014 until April 2015 clinically significant bacteremia was detected in 609 (15%) of 4,051 children: salmonellae accounted for 364 (60%) of 609 cases, of which 296 were <italic>S</italic>. Typhi and 68 were NTS. Across both regions <italic>Salmonella</italic> species accounted for 24–60% of bacteremia with <italic>S</italic>. Typhi being the most common serovar isolated with a total of 380 isolates (76–79%) [<xref rid="pntd.0004781.ref009" ref-type="bibr">9</xref>].</p></sec><sec id="sec020"><title>Phylogenetic analysis of Nigerian <italic>S</italic>. Typhi</title><p>A selection of one hundred and twenty-two <italic>S</italic>. Typhi from the FCT and six from Kano, all isolated between 2008–2013, were randomly selected and sequenced via Illumina HiSeq and MiSeq (see <xref ref-type="sec" rid="sec006">Methods</xref>). The genomes of the Nigerian isolates were compared to that of the <italic>S</italic>. Typhi CT18 reference strain and a previously published global collection of approximately 2,000 <italic>S</italic>. Typhi isolates [<xref rid="pntd.0004781.ref012" ref-type="bibr">12</xref>]. A phylogeny was built by extracting single nucleotide polymorphisms (SNPs) from the whole genome sequences, excluding likely recombination events and repetitive sequences that could confound phylogenetic analysis as described in Methods. The SNP data were also used to assign each isolate to one of 62 previously defined genotypes; details of the source and genotype of all Nigerian isolates is given in <xref ref-type="table" rid="pntd.0004781.t001">Table 1</xref> and <xref ref-type="supplementary-material" rid="pntd.0004781.s002">S1 Table</xref>. The distribution of the 128 Nigerian <italic>S</italic>. Typhi within the global phylogenetic tree is shown in <xref ref-type="supplementary-material" rid="pntd.0004781.s001">S1 Fig</xref>. This global phylogeny includes 238 isolates from other countries in Africa, and the Nigerian isolates all cluster with other African isolates. Detailed phylogenetic relationships amongst the 366 African isolates are shown in <xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>, and an interactive version of the phylogeny and map are available for exploration online at <ext-link ext-link-type="uri" xlink:href="http://microreact.org/project/styphi_nigeria">http://microreact.org/project/styphi_nigeria</ext-link>.</p><fig id="pntd.0004781.g001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0004781.g001</object-id><label>Fig 1</label><caption><title>Distribution of Nigerian <italic>S</italic>. Typhi isolates in Africa in this study.</title><p>A maximum likelihood tree of 366 <italic>S</italic>. Typhi isolates constructed using 9,352 SNPs from whole genome sequence from 128 Nigerian isolates and 238 isolates from other regions of Africa is shown on the left. The geographical location of isolation is highlighted on the maps of Africa displayed on the right (<ext-link ext-link-type="uri" xlink:href="http://microreact.org/showcase/">http://microreact.org/showcase/</ext-link>). <italic>S</italic>. Typhi isolates from Abuja (122 isolates) and Kano (6) are denoted using red and orange squares, respectively. Colored circles on both the tree and maps represent isolates from other regions of Africa. The common genotypes of the Nigerian isolate are highlighted by a grey ring surrounding the tree with the corresponding geographical location marked on the map. Branch lengths are indicative of the estimated substitution rate per variable site.</p></caption><graphic xlink:href="pntd.0004781.g001"></graphic></fig><table-wrap id="pntd.0004781.t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0004781.t001</object-id><label>Table 1</label><caption><title>Summary of genotypes of Nigerian <italic>S</italic>. Typhi.</title></caption><alternatives><graphic id="pntd.0004781.t001g" xlink:href="pntd.0004781.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="center" rowspan="1" colspan="1">Laboratory name</th><th align="center" rowspan="1" colspan="1">Year of isolation</th><th align="center" rowspan="1" colspan="1">Location</th><th align="center" rowspan="1" colspan="1">Roumagnac haplotype<xref ref-type="table-fn" rid="t001fn001">*</xref></th><th align="center" rowspan="1" colspan="1">Primary clade</th><th align="center" rowspan="1" colspan="1">Clade</th><th align="center" rowspan="1" colspan="1">Subclade</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">PO_30</td><td align="left" rowspan="1" colspan="1">2008</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_601</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_132</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_107</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1057</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1060</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1063</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_187</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_227</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_293</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_351</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_355</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_771</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_812</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_919</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_575</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_260</td><td align="left" rowspan="1" colspan="1">2009</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1102</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1131</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861198</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861206</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861239</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861254</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.1</td><td align="left" rowspan="1" colspan="1">2.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1255</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1098</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1101</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1210</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1242</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1265</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861190</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861230</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861262</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861271</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861184</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861208</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861216</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861224</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861232</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861183</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H42</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">3.3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1232</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861222</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861246</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861270</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861199</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861247</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1110</td><td align="left" rowspan="1" colspan="1">2010</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1256</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861272</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.1</td><td align="left" rowspan="1" colspan="1">2.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861209</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861248</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861256</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861264</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861193</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861201</td><td align="left" rowspan="1" colspan="1">2011</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861233</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861241</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861273</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861217</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861225</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861195</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861211</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861235</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861243</td><td align="left" rowspan="1" colspan="1">2012</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861210</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861226</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861202</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861234</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861242</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861218</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Kano</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861196</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861244</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0.0.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861359</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861290</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861298</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861350</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861287</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861280</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861289</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861337</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861353</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861361</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861369</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861253</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">2.2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861342</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861334</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">2.3.2</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861294</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861312</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861320</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861268</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861276</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861229</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861237</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861245</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861314</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861330</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861197</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861338</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861351</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861282</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861306</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861322</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861326</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861366</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861279</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861303</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861319</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861327</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861335</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861343</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861367</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861304</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861328</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861336</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861344</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861260</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861189</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861213</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861278</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861286</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861251</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861259</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861212</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861220</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861228</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861252</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861236</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H56</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861368</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">Untypeable</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861205</td><td align="left" rowspan="1" colspan="1">2013</td><td align="left" rowspan="1" colspan="1">Abuja</td><td align="left" rowspan="1" colspan="1">H52</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">4.1.0</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t001fn001"><p>* Reference [<xref rid="pntd.0004781.ref011" ref-type="bibr">11</xref>]</p></fn></table-wrap-foot></table-wrap><p>The majority of Nigerian <italic>S</italic>. Typhi (84/128, 66%) belonged to genotype 3.1.1 (these isolates were assigned to H56 under the old typing scheme of Roumagnac <italic>et al</italic> (2006) [<xref rid="pntd.0004781.ref011" ref-type="bibr">11</xref>]). This dominant genotype is relatively common across Africa, predominantly western and central countries (<xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>). The Nigerian isolates formed a tight phylogenetically clustered subgroup within the 3.1.1 subclade (<xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>), suggesting recent local expansion, and included isolates from both Abuja and Kano, suggesting intra-country transmission. Interestingly, in the wider African collection genotype 3.1.1 was represented by isolates from neighboring Cameroon and across West Africa (Benin, Togo, Ivory Coast, Burkina Faso, Mali, Guinea and Mauritania) suggesting long-term inter-country exchange within the region (<xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>). Most of the remaining isolates belonged to four other genotypes, indicating that these are also established genotypes in circulation at the study sites in Nigeria. These genotypes, highlighted in <xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>, are 2.2.0 (n = 13), 2.3.1 (n = 8), 4.1.0 (n = 8, H52 under the old scheme) and 0.0.3 (n = 7, H12). Nigerian isolates of genotypes 2.2.0 and 2.3.1 were closely related to isolates from neighboring Cameroon and West African countries and not found elsewhere, supporting regional transmission similar to the dominant genotype 3.1.1 (see map in <xref ref-type="fig" rid="pntd.0004781.g001">Fig 1</xref>), while genotype 4.1.0 was more widespread across Africa. Interestingly genotype 0.0.3 (previously identified in India and Malaysia), which accounted for >5% of Nigerian isolates, maps very close to the root of the global <italic>S</italic>. Typhi tree, suggestive of older circulating isolates. A further six other genotypes were also detected amongst the Nigerian isolates, represented by 1–2 isolates each (<xref ref-type="table" rid="pntd.0004781.t001">Table 1</xref>). Of note, genotype 4.3.1 (H58), which has become dominant elsewhere in sub-Saharan Africa and accounts for the majority of antimicrobial resistant typhoid globally, was not detected in the Nigerian studies.</p></sec><sec id="sec021"><title>Antimicrobial resistant <italic>S</italic>. Typhi in Nigeria</title><p><xref ref-type="fig" rid="pntd.0004781.g002">Fig 2</xref> shows the proportion of <italic>S</italic>. Typhi isolates that were resistant to one or more antimicrobials, and the proportion that were multidrug-resistant (MDR; defined as resistance to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole), each year from 2008–2013. The majority of isolates were MDR throughout this period (<xref ref-type="fig" rid="pntd.0004781.g002">Fig 2</xref>).</p><fig id="pntd.0004781.g002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0004781.g002</object-id><label>Fig 2</label><caption><title>Presence of antimicrobial resistance of <italic>S</italic>. Typhi in the study areas.</title><p>The proportion of <italic>S</italic>. Typhi isolates that were resistant to one or more antimicrobials (red line) and were multidrug-resistant (MDR; defined as resistance to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole, blue line) are shown. Percentages are of the total <italic>S</italic>. Typhi isolated per year.</p></caption><graphic xlink:href="pntd.0004781.g002"></graphic></fig><p><xref ref-type="fig" rid="pntd.0004781.g003">Fig 3</xref> and <xref ref-type="table" rid="pntd.0004781.t002">Table 2</xref> show the distribution of antimicrobial resistance determinants in the Nigerian isolates. Most of the 3.1.1 (H56) isolates carried genes encoding resistance to ampicillin, chloramphenicol, tetracycline and sulfamethoxazole (<italic>bla</italic><sub>TEM-1</sub>, <italic>catA1</italic>, <italic>tetB</italic>, <italic>dfrA15</italic>, <italic>sul1</italic>). These were located on an IncHI1 plasmid, similar to that commonly found in MDR <italic>S</italic>. Typhi 4.3.1 (H58). The same profile was identified in a single isolate of 0.0.3, indicative of local plasmid transfer between the co-circulating genotypes. Genotype 2.3.1 isolates were found to carry IncHI1 plasmids encoding these resistance genes, as well as resistance determinants <italic>sul2</italic> and <italic>strAB</italic>. An IncHI1 plasmid carrying <italic>bla</italic><sub>TEM</sub> and <italic>tetB</italic> was also identified in one 2.2.0 isolate. Interestingly, nine genotype 3.1.1 isolates lacked the IncHI1 plasmid. However, four of these carried plasmids of other incompatibility groups. Three isolates (3135STDY5861338; 3135STDY5861351; 3135STDY5861282) harbored a novel IncY plasmid (<italic>bla</italic><sub>TEM-198</sub>, <italic>catA1</italic>, <italic>tetB</italic>, <italic>dfrA14</italic>, <italic>sul1</italic>) and one (3135STDY5861242) harbored a plasmid-related to the Kpn3 plasmid (<italic>bla</italic><sub>TEM-198</sub>, <italic>tetAR</italic>, <italic>dfrA14</italic>, <italic>sul1</italic>, <italic>sul2</italic>, <italic>strAB</italic> and also <italic>qnr-S</italic>, which mediates fluoroquinolone resistance). Thus, plasmid-mediated MDR is common in Nigerian <italic>S</italic>. Typhi from the regions under study.</p><fig id="pntd.0004781.g003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0004781.g003</object-id><label>Fig 3</label><caption><title>Acquired multidrug-resistance in Nigerian <italic>S</italic>. Typhi isolates.</title><p>Maximum likelihood tree of 128 Nigerian <italic>S</italic>. Typhi isolates from 2,541 SNPs is shown on the left. On the right is a heatmap which shows, for each isolate, its multidrug-resistant (MDR) status (purple), the presence of <italic>gyrA</italic> mutations (dark green S83Y; light green S83F), resistance genes <italic>cat</italic>, <italic>blaTEM</italic>, <italic>dfrA</italic>, <italic>sul1/2</italic>, <italic>strAB</italic>, <italic>tetB/AR</italic>, <italic>qnr</italic> (red) and plasmids, including IncHI1 (dark blue), Kpn3 (light blue), IncY (orange), IncQ1 (light pink), IncFIIs (yellow) and Col(RNAI) (magenta). Different colored bars within the plasmid column show isolates that harbor multiple plasmids with each bar representing a plasmid type. The absence of a genotype or plasmid was displayed in grey. Branch lengths are indicative of the estimated substitution rate per variable site.</p></caption><graphic xlink:href="pntd.0004781.g003"></graphic></fig><table-wrap id="pntd.0004781.t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pntd.0004781.t002</object-id><label>Table 2</label><caption><title>Summary of drug resistance of Nigerian <italic>S</italic>. Typhi.</title></caption><alternatives><graphic id="pntd.0004781.t002g" xlink:href="pntd.0004781.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="center" rowspan="1" colspan="1">Laboratory name</th><th align="center" rowspan="1" colspan="1">Subclade</th><th align="center" rowspan="1" colspan="1">Plasmids</th><th align="center" colspan="2" rowspan="1">Resistance genes</th><th align="center" rowspan="1" colspan="1"><italic>gyrA</italic> mutations</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">3135STDY5861196</td><td align="left" rowspan="1" colspan="1">0.0.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861244</td><td align="left" rowspan="1" colspan="1">0.0.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_601</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1102</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1131</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861198</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861206</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861239</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1256</td><td align="left" rowspan="1" colspan="1">0.0.3</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861254</td><td align="left" rowspan="1" colspan="1">2.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861272</td><td align="left" rowspan="1" colspan="1">2.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861209</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861359</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861290</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861298</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861350</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861287</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861280</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861289</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861337</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861353</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861361</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861369</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861253</td><td align="left" rowspan="1" colspan="1">2.2.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_132</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, sul1, tetB, strA, strB, sul2, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_107</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, tetB, strA, strB, sul2, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861233</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, sul1, bla-TEM, tetB, strA, strB, sul2, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861241</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, sul1, bla-TEM, tetB, strA, strB, sul2, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861273</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, sul1, bla-TEM, tetB, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861210</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861195</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861342</td><td align="left" rowspan="1" colspan="1">2.3.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">dfrA, sul1, bla-TEM, tetB, strA, strB, sul2, aad</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861334</td><td align="left" rowspan="1" colspan="1">2.3.2</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861294</td><td align="left" rowspan="1" colspan="1">3.1.0</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_30</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1057</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1060</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1063</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_187</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">S83Y</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_227</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_293</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_351</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_355</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_771</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_812</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_919</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_575</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1255</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1098</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1101</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1210</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1242</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1265</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861190</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861230</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">S83Y</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861262</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861271</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861184</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861208</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861216</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861224</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861232</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861248</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861256</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861264</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861193</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861201</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861217</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861225</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861226</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861202</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861234</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861242</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">Kpn3</td><td align="left" colspan="2" rowspan="1">bla-TEM, strA, strB, sul1, sul2, dfrA, tetA, tetR, qnrS</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861218</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">S83F</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861211</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1, IncFIIs</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861235</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861243</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861312</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861320</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861268</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861276</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861229</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861237</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861245</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861314</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861330</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861197</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" colspan="2" rowspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861338</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncY</td><td align="left" colspan="2" rowspan="1">bla-TEM, strA, strB, sul1, dfrA, tetA, tetR</td><td align="left" rowspan="1" colspan="1">S83Y</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861351</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncY</td><td align="left" colspan="2" rowspan="1">bla-TEM, strA, strB, sul1, dfrA, tetA, tetR</td><td align="left" rowspan="1" colspan="1">S83Y</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861282</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncY</td><td align="left" colspan="2" rowspan="1">bla-TEM, strA, strB, sul1, dfrA, tetA, tetR</td><td align="left" rowspan="1" colspan="1">S83Y</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861306</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861322</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861326</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861366</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861279</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861303</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861319</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861327</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861335</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861343</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861367</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861304</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861328</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861336</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861344</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861260</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861189</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861213</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861278</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" colspan="2" rowspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861286</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861251</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861259</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861212</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861220</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861228</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861252</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861236</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM,</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861368</td><td align="left" rowspan="1" colspan="1">3.1.1</td><td align="left" rowspan="1" colspan="1">IncHI1, IncQ1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">cat, dfrA, sul1, bla-TEM, tetB</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861183</td><td align="left" rowspan="1" colspan="1">3.3.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_260</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1232</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861222</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861246</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861270</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861199</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861247</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">3135STDY5861205</td><td align="left" rowspan="1" colspan="1">4.1.0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr><tr><td align="left" rowspan="1" colspan="1">PO_1110</td><td align="left" rowspan="1" colspan="1">4.1.1</td><td align="left" rowspan="1" colspan="1">Col(RNAI)</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1">-</td></tr></tbody></table></alternatives></table-wrap><p>We identified only six <italic>S</italic>. Typhi isolates with quinolone resistance-associated mutations in <italic>gyrA</italic> (one with S83F; five with S83Y). The affected isolates were all of the dominant genotype 3.1.1, including the three that carried IncY plasmids and three that carried IncHI1 plasmids. No other polymorphisms were detected in the quinolone resistance determining regions of the <italic>gyrA</italic> or <italic>parC</italic> genes of Nigerian <italic>S</italic>. Typhi isolates.</p></sec></sec><sec sec-type="conclusions" id="sec022"><title>Discussion</title><p>Here, <italic>S</italic>. Typhi is shown to be a common cause of bacteremia and fever among children living in two geographically distinct regions of Nigeria. Studies on typhoid within Nigeria have been relatively rare, even though it is a country with a large population and extensive urbanization. Indeed, <italic>S</italic>. Typhi is the most common bacterial cause of bloodstream infections. Phylogenetic analysis identified distinct clusters of <italic>S</italic>. Typhi, with isolates of genotype 3.1.1 representing 66% of all isolates. Other common genotypes included 2.2.0 and 2.3.1, which have been previously reported in Africa, and genotypes 4.1.0 and 0.0.3, which were previously reported in Asia. The presence of multiple genotypes in these comparatively small regions suggests typhoid has been established for some time and that different waves of disease have entered the regions at different times. It is also interesting that the different clades of Nigerian isolates distributed across the phylogeny frequently map adjacent to other <italic>S</italic>. Typhi isolates from other African countries. For example, genotype 3.1.1 maps adjacent to <italic>S</italic>. Typhi isolates from both west and north Africa, with the Nigerian isolates located on a more recent phylogenetic branch. Similarly, genotypes 2.2.0 and 2.3.1 also map close to other African isolates. This general distribution indicates substantial exchange of <italic>S</italic>. Typhi between Nigeria and other parts of Africa. However, the phylogenetic analysis was limited to two sites within Nigeria, with only six <italic>S</italic>. Typhi isolates included in the analysis from Kano, over a five- year period, resulting in a selection bias towards strains from a single study site in Nigeria (Abuja). Therefore, a more comprehensive analysis involving a larger number of strains from multiple regions across Nigeria and surrounding countries over a wider time span would be required to further investigate transmission within the region.</p><p>It is notable that none of the Nigerian isolates were of the genotype 4.3.1 (H58), which is now expanding across many other regions with endemic typhoid and is associated with a MDR phenotype. This suggests that the recent expansion of H58 <italic>S</italic>. Typhi, estimated to date from the mid-1980s, has not yet reached Nigeria, unlike other African countries including Kenya, Tanzania, Malawi and South Africa. The absence of H58 isolates in the sampled area of Nigeria is an important finding. It has been postulated that H58 <italic>S</italic>. Typhi originally emerged in Asia, but subsequently entered Africa on a number of distinct occasions where they have gone on to cause large typhoid outbreaks [<xref rid="pntd.0004781.ref012" ref-type="bibr">12</xref>]. Thus, it is likely that H58 <italic>S</italic>. Typhi will reach Nigeria in the future, potentially changing the epidemiology of the disease in the region and molecular surveillance could be used to monitor for this.</p><p>Nevertheless, MDR <italic>S</italic>. Typhi are common in the regions of study despite the absence of H58 microorganisms. This is an important observation, as the MDR phenotype in other regions of the world has been driven by the spread of MDR <italic>S</italic>. Typhi H58. Many of the Nigerian <italic>S</italic>. Typhi, including those of genotype 3.1.1, harbored IncHI1 plasmids that have been previously associated with <italic>S</italic>. Typhi of other genotypes, particularly H58 [<xref rid="pntd.0004781.ref012" ref-type="bibr">12</xref>, <xref rid="pntd.0004781.ref039" ref-type="bibr">39</xref>]. This is consistent with a genetic compatibility between <italic>S</italic>. Typhi and such plasmids. Interestingly, genetic analysis indicates that an IncHI1 plasmid recently transferred between 3.1.1 and 0.0.3 Typhi within the study region. However, several other plasmids of distinct incompatibility types were also detected within the sampled <italic>S</italic>. Typhi and it will be interesting to see if any of these are common elsewhere in Nigeria or whether they solely persist within these study sites.</p><p>Mutations associated with resistance to quinolones were relatively rare within the sample set. This could be because fluoroquinolones are not commonly used to treat typhoid in these regions, or alternatively, it may be that such mutations have not become fixed in these non-H58 isolates. Further studies on the use of fluoroquinolones are warranted.</p><p>In conclusion, it is clear that typhoid associated with MDR <italic>S</italic>. Typhi is common in these parts of Nigeria and that the MDR phenotype is evolving independently of haplotype H58, which has emerged elsewhere in the world where typhoid is endemic.</p><sec id="sec023"><title>Members of International Typhoid Consortium</title><p>Vanessa K. Wong<sup>1,2</sup>, Stephen Baker<sup>3,4,5</sup>, Derek Pickard<sup>1</sup>, Julian Parkhill<sup>1</sup>, Andrew J Page<sup>1</sup>, Nicholas A. Feasey<sup>6</sup> Robert A. Kingsley<sup>1,7</sup>, Nicholas R. Thomson<sup>1,5</sup>, Jacqueline A. Keane<sup>1</sup>, François-Xavier Weill<sup>8</sup>, Simon Le Hello<sup>8</sup>, Jane Hawkey<sup>9,10,11</sup>, David J. Edwards<sup>9,11</sup>, Zoe A. Dyson<sup>9,11</sup>, Simon R. Harris<sup>1</sup>, Amy K. Cain<sup>1</sup>, James Hadfield<sup>1</sup>, Peter J. Hart<sup>12,13</sup>, Nga Tran Vu Thieu<sup>3</sup>, Elizabeth J. Klemm<sup>1</sup>, Robert F. Breiman<sup>14,15,16</sup>, Conall H. Watson<sup>17</sup>, Samuel Kariuki<sup>1,14</sup>, Melita A. Gordon<sup>18,19</sup>, Robert S. Heyderman<sup>20,19,</sup> Chinyere Okoro<sup>1,2</sup>, Jan Jacobs<sup>21,22</sup>, Octavie Lunguya<sup>23,24</sup>, W. John Edmunds<sup>17</sup>, Chisomo Msefula<sup>19,25</sup>, Jose A. Chabalgoity<sup>26</sup>, Mike Kama<sup>27</sup>, Kylie Jenkins<sup>28</sup>, Shanta Dutta<sup>29</sup>, Florian Marks<sup>30</sup>, Josefina Campos<sup>31</sup>, Corinne Thompson<sup>3,4</sup>, Stephen Obaro<sup>32,33,34</sup>, Calman A. MacLennan<sup>1,12,35</sup>, Christiane Dolecek<sup>3,4</sup>, Karen H. Keddy<sup>36</sup>, Anthony M. Smith<sup>36</sup>, Christopher M. Parry<sup>37,38</sup>, Abhilasha Karkey<sup>39</sup>, E. Kim Mulholland<sup>5,40</sup>, James I. Campbell<sup>3,4</sup>, Sabina Dongol<sup>39</sup>, Buddha Basnyat<sup>39</sup>, Amit Arjyal<sup>39</sup>, Muriel Dufour<sup>41</sup>, Don Bandaranayake<sup>42</sup>, Take N. Toleafoa<sup>43</sup>, Shalini Pravin Singh<sup>44</sup>, Mochammad Hatta<sup>45</sup>, Robert S. Onsare<sup>14</sup>, Lupeoletalalelei Isaia<sup>46</sup>, Guy Thwaites<sup>3,4</sup>, Paul Turner<sup>4,47,48</sup>, Sona Soeng<sup>48</sup>, John A. Crump<sup>49</sup>, Elizabeth De Pinna<sup>50</sup>, Satheesh Nair<sup>50</sup>, Eric J Nille<sup>51</sup>, Duy Pham Thanh<sup>3</sup>, Mary Valcanis<sup>52</sup>, Joan Powling<sup>52</sup>, Karolina Dimovski<sup>52</sup>, Geoff Hogg<sup>52</sup>, Thomas R. Connor<sup>53</sup>, Jayshree Dave<sup>54</sup>, Niamh Murphy<sup>54</sup>, Richard Holliman<sup>54</sup>, Armine Sefton<sup>55</sup>, Michael Millar<sup>55</sup>, Jeremy Farrar<sup>3,4</sup>, Alison E. Mather<sup>56</sup>, Ben Amos<sup>57</sup>, Grace Olanipekun<sup>58</sup>, Huda Munir<sup>59</sup>, Roxanne Alter<sup>60</sup>, Paul D. Fey<sup>60</sup>, Kathryn E Holt<sup>9,11</sup> and Gordon Dougan<sup>1</sup></p><list list-type="order"><list-item><p>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom</p></list-item><list-item><p>Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, United Kingdom</p></list-item><list-item><p>The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam</p></list-item><list-item><p>Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK</p></list-item><list-item><p>Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom</p></list-item><list-item><p>Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom</p></list-item><list-item><p>Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom</p></list-item><list-item><p>Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France</p></list-item><list-item><p>Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia</p></list-item><list-item><p>Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia</p></list-item><list-item><p>Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia</p></list-item><list-item><p>Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom</p></list-item><list-item><p>St George’s University of London, London, United Kingdom</p></list-item><list-item><p>Kenya Medical Research Institute (KEMRI), Nairobi, Kenya</p></list-item><list-item><p>Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</p></list-item><list-item><p>Emory Global Health Institute, Atlanta, Georgia, United States of America</p></list-item><list-item><p>Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom</p></list-item><list-item><p>Institute of Infection and Global Health, University of Liverpool, United Kingdom</p></list-item><list-item><p>Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi</p></list-item><list-item><p>Division of Infection and Immunity, University College London, London, United Kingdom</p></list-item><list-item><p>Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium</p></list-item><list-item><p>KU Leuven, University of Leuven, Department of Microbiology and Immunology, Belgium</p></list-item><list-item><p>National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo</p></list-item><list-item><p>University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo</p></list-item><list-item><p>Microbiology Department, College of Medicine, University of Malawi, Malawi</p></list-item><list-item><p>Departamento de Desarrollo Biotecnologico, Instituto de Higiene, Facultad de Medicina, Avda A Navarro 3051, Montevideo, Uruguay</p></list-item><list-item><p>Ministry of Health, Toorak, Suva, Fiji</p></list-item><list-item><p>Fiji Health Sector Support Program, Suva, Fiji</p></list-item><list-item><p>National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India</p></list-item><list-item><p>International Vaccine Institute, Department of Epidemiology, Kwanak, Republic of Korea</p></list-item><list-item><p>Enteropathogen Division, ANLIS-Carlos G Malbran Institute, CABA, Argentina</p></list-item><list-item><p>Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</p></list-item><list-item><p>University of Abuja Teaching Hospital, Gwagwalada, FCT, Nigeria</p></list-item><list-item><p>Bingham University, Karu, Nassarawa State, Nigeria</p></list-item><list-item><p>The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom</p></list-item><list-item><p>Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa</p></list-item><list-item><p>Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom</p></list-item><list-item><p>Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan</p></list-item><list-item><p>Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal</p></list-item><list-item><p>Murdoch Childrens Research Institute, Melbourne, Australia</p></list-item><list-item><p>Enteric and <italic>Leptospira</italic> Reference Laboratory, Institute of Environmental Science and Research Limited (ESR), New Zealand</p></list-item><list-item><p>National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand</p></list-item><list-item><p>Samoa Ministry of Health, Apia, Samoa</p></list-item><list-item><p>National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji</p></list-item><list-item><p>Department of Microbiology, Hasanuddin University, Makassar, Indonesia</p></list-item><list-item><p>National Health Services, Tupua Tamasese Meaole Hospital, Samoa</p></list-item><list-item><p>Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand</p></list-item><list-item><p>Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia</p></list-item><list-item><p>Centre for International Health, University of Otago, Dunedin, New Zealand</p></list-item><list-item><p>Salmonella Reference Service, Public Health England, Colindale, London, United Kingdom</p></list-item><list-item><p>Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji</p></list-item><list-item><p>Microbiological Diagnostic Unit—Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia</p></list-item><list-item><p>Cardiff University School of Biosciences, Cardiff University, Cardiff, United Kingdom</p></list-item><list-item><p>Public Health Laboratory London, Public Health England, London, United Kingdom</p></list-item><list-item><p>Division of Infection, Barts Health NHS Trust, London, United Kingdom</p></list-item><list-item><p>Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom</p></list-item><list-item><p>St Augustine’s Hospital, Muheza, Tanzania</p></list-item><list-item><p>International Foundation Against Infectious Diseases in Nigeria, Abuja, Nigeria</p></list-item><list-item><p>Department of Medical Microbiology, Aminu Kano Teaching Hospital, Kano, Nigeria</p></list-item><list-item><p>Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America</p></list-item></list></sec></sec><sec sec-type="supplementary-material" id="sec024"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pntd.0004781.s001"><label>S1 Fig</label><caption><title>Global distribution of African <italic>S</italic>. Typhi isolates analyzed in this study.</title><p>A maximum likelihood tree of 1,960 <italic>S</italic>. Typhi isolates from 23,300 SNPs surrounded by colored rings representing the geographic origin of 502 African isolates, according to the legend. 128 Nigerian isolates are highlighted in black (122 = Abuja) and grey (6 = Kano); neighboring African countries labeled by black arrows. The genotypes of the Nigerian isolates are labeled in red with the old Roumagnac haplotypes [<xref rid="pntd.0004781.ref011" ref-type="bibr">11</xref>] in parentheses (red * denotes untypeable Nigerian strains). The 4.3.1 (H58) subclade is indicated in red italics. Branch lengths are indicative of the estimated substitution rate per variable site.</p><p>(TIF)</p></caption><media xlink:href="pntd.0004781.s001.tif"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pntd.0004781.s002"><label>S1 Table</label><caption><title>Details of the 128 Nigerian <italic>Salmonella</italic> Typhi isolates used in the study (see excel sheet).</title><p>(XLS)</p></caption><media xlink:href="pntd.0004781.s002.xls"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ack><p>We would like to thank the members of the Pathogen Informatics Team and the core sequencing teams at the Wellcome Trust Sanger Institute (Cambridge, UK). 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