Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline
Identifieur interne : 002C37 ( Pmc/Curation ); précédent : 002C36; suivant : 002C38Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline
Auteurs : Violette Da Cunha [France] ; Mark R. Davies [Royaume-Uni, Australie] ; Pierre-Emmanuel Douarre [France] ; Isabelle Rosinski-Chupin [France] ; Immaculada Margarit [Italie] ; Sebastien Spinali [France] ; Tim Perkins [Italie] ; Pierre Lechat [France] ; Nicolas Dmytruk [France] ; Elisabeth Sauvage [France] ; Laurence Ma [France] ; Benedetta Romi [Italie] ; Magali Tichit [France] ; Maria-José Lopez-Sanchez [France] ; Stéphane Descorps-Declere [France] ; Erika Souche [France] ; Carmen Buchrieser [France] ; Patrick Trieu-Cuot [France] ; Ivan Moszer [France] ; Dominique Clermont [France] ; Domenico Maione [Italie] ; Christiane Bouchier [France] ; David J. Mcmillan [Australie] ; Julian Parkhill [Royaume-Uni] ; John L. Telford [Italie] ; Gordan Dougan [Royaume-Uni] ; Mark J. Walker [Australie] ; Matthew T. G. Holden [Royaume-Uni] ; Claire Poyart [France] ; Philippe Glaser [France]Source :
- Nature communications [ 2041-1723 ] ; 2014.
Abstract
Url:
DOI: 10.1038/ncomms5544
PubMed: 25088811
PubMed Central: 4538795
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PMC:4538795Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>Streptococcus agalactiae</italic>
clones infecting humans were selected and fixed through the extensive use of tetracycline</title>
<author><name sortKey="Da Cunha, Violette" sort="Da Cunha, Violette" uniqKey="Da Cunha V" first="Violette" last="Da Cunha">Violette Da Cunha</name>
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<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
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<author><name sortKey="Davies, Mark R" sort="Davies, Mark R" uniqKey="Davies M" first="Mark R." last="Davies">Mark R. Davies</name>
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<author><name sortKey="Douarre, Pierre Emmanuel" sort="Douarre, Pierre Emmanuel" uniqKey="Douarre P" first="Pierre-Emmanuel" last="Douarre">Pierre-Emmanuel Douarre</name>
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<author><name sortKey="Rosinski Chupin, Isabelle" sort="Rosinski Chupin, Isabelle" uniqKey="Rosinski Chupin I" first="Isabelle" last="Rosinski-Chupin">Isabelle Rosinski-Chupin</name>
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<author><name sortKey="Margarit, Immaculada" sort="Margarit, Immaculada" uniqKey="Margarit I" first="Immaculada" last="Margarit">Immaculada Margarit</name>
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<author><name sortKey="Spinali, Sebastien" sort="Spinali, Sebastien" uniqKey="Spinali S" first="Sebastien" last="Spinali">Sebastien Spinali</name>
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<author><name sortKey="Perkins, Tim" sort="Perkins, Tim" uniqKey="Perkins T" first="Tim" last="Perkins">Tim Perkins</name>
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<author><name sortKey="Lechat, Pierre" sort="Lechat, Pierre" uniqKey="Lechat P" first="Pierre" last="Lechat">Pierre Lechat</name>
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<author><name sortKey="Dmytruk, Nicolas" sort="Dmytruk, Nicolas" uniqKey="Dmytruk N" first="Nicolas" last="Dmytruk">Nicolas Dmytruk</name>
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<author><name sortKey="Sauvage, Elisabeth" sort="Sauvage, Elisabeth" uniqKey="Sauvage E" first="Elisabeth" last="Sauvage">Elisabeth Sauvage</name>
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<author><name sortKey="Ma, Laurence" sort="Ma, Laurence" uniqKey="Ma L" first="Laurence" last="Ma">Laurence Ma</name>
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<author><name sortKey="Romi, Benedetta" sort="Romi, Benedetta" uniqKey="Romi B" first="Benedetta" last="Romi">Benedetta Romi</name>
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<author><name sortKey="Tichit, Magali" sort="Tichit, Magali" uniqKey="Tichit M" first="Magali" last="Tichit">Magali Tichit</name>
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<author><name sortKey="Lopez Sanchez, Maria Jose" sort="Lopez Sanchez, Maria Jose" uniqKey="Lopez Sanchez M" first="Maria-José" last="Lopez-Sanchez">Maria-José Lopez-Sanchez</name>
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<author><name sortKey="Descorps Declere, Stephane" sort="Descorps Declere, Stephane" uniqKey="Descorps Declere S" first="Stéphane" last="Descorps-Declere">Stéphane Descorps-Declere</name>
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<author><name sortKey="Buchrieser, Carmen" sort="Buchrieser, Carmen" uniqKey="Buchrieser C" first="Carmen" last="Buchrieser">Carmen Buchrieser</name>
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<affiliation wicri:level="1"><nlm:aff id="A9">Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris 75015, France.</nlm:aff>
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<author><name sortKey="Trieu Cuot, Patrick" sort="Trieu Cuot, Patrick" uniqKey="Trieu Cuot P" first="Patrick" last="Trieu-Cuot">Patrick Trieu-Cuot</name>
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<affiliation wicri:level="1"><nlm:aff id="A10">CNRS ERL3526, Paris 75015, France.</nlm:aff>
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<wicri:regionArea>CNRS ERL3526, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Moszer, Ivan" sort="Moszer, Ivan" uniqKey="Moszer I" first="Ivan" last="Moszer">Ivan Moszer</name>
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<author><name sortKey="Clermont, Dominique" sort="Clermont, Dominique" uniqKey="Clermont D" first="Dominique" last="Clermont">Dominique Clermont</name>
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</author>
<author><name sortKey="Maione, Domenico" sort="Maione, Domenico" uniqKey="Maione D" first="Domenico" last="Maione">Domenico Maione</name>
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<author><name sortKey="Bouchier, Christiane" sort="Bouchier, Christiane" uniqKey="Bouchier C" first="Christiane" last="Bouchier">Christiane Bouchier</name>
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<wicri:regionArea>Institut Pasteur Genomic platform, Paris 75015</wicri:regionArea>
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<author><name sortKey="Mcmillan, David J" sort="Mcmillan, David J" uniqKey="Mcmillan D" first="David J." last="Mcmillan">David J. Mcmillan</name>
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<affiliation wicri:level="1"><nlm:aff id="A13">Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland, Australia.</nlm:aff>
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<wicri:regionArea>Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland</wicri:regionArea>
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</author>
<author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name>
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<author><name sortKey="Telford, John L" sort="Telford, John L" uniqKey="Telford J" first="John L." last="Telford">John L. Telford</name>
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<author><name sortKey="Dougan, Gordan" sort="Dougan, Gordan" uniqKey="Dougan G" first="Gordan" last="Dougan">Gordan Dougan</name>
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<author><name sortKey="Walker, Mark J" sort="Walker, Mark J" uniqKey="Walker M" first="Mark J." last="Walker">Mark J. Walker</name>
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<author><name sortKey="Holden, Matthew T G" sort="Holden, Matthew T G" uniqKey="Holden M" first="Matthew T. G." last="Holden">Matthew T. G. Holden</name>
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<author><name sortKey="Poyart, Claire" sort="Poyart, Claire" uniqKey="Poyart C" first="Claire" last="Poyart">Claire Poyart</name>
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<affiliation wicri:level="1"><nlm:aff id="A14">Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014, France.</nlm:aff>
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<wicri:regionArea>Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="A15">INSERM, U1016, Paris 75014, France.</nlm:aff>
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<author><name sortKey="Glaser, Philippe" sort="Glaser, Philippe" uniqKey="Glaser P" first="Philippe" last="Glaser">Philippe Glaser</name>
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</affiliation>
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<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>Streptococcus agalactiae</italic>
clones infecting humans were selected and fixed through the extensive use of tetracycline</title>
<author><name sortKey="Da Cunha, Violette" sort="Da Cunha, Violette" uniqKey="Da Cunha V" first="Violette" last="Da Cunha">Violette Da Cunha</name>
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</affiliation>
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<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
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</affiliation>
</author>
<author><name sortKey="Davies, Mark R" sort="Davies, Mark R" uniqKey="Davies M" first="Mark R." last="Davies">Mark R. Davies</name>
<affiliation wicri:level="1"><nlm:aff id="A4">The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A5">Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Australie</country>
<wicri:regionArea>Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Douarre, Pierre Emmanuel" sort="Douarre, Pierre Emmanuel" uniqKey="Douarre P" first="Pierre-Emmanuel" last="Douarre">Pierre-Emmanuel Douarre</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Rosinski Chupin, Isabelle" sort="Rosinski Chupin, Isabelle" uniqKey="Rosinski Chupin I" first="Isabelle" last="Rosinski-Chupin">Isabelle Rosinski-Chupin</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Margarit, Immaculada" sort="Margarit, Immaculada" uniqKey="Margarit I" first="Immaculada" last="Margarit">Immaculada Margarit</name>
<affiliation wicri:level="1"><nlm:aff id="A6">Novartis Vaccines and Diagnostics, Siena 53100, Italy.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Italie</country>
<wicri:regionArea>Novartis Vaccines and Diagnostics, Siena 53100</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Spinali, Sebastien" sort="Spinali, Sebastien" uniqKey="Spinali S" first="Sebastien" last="Spinali">Sebastien Spinali</name>
<affiliation wicri:level="1"><nlm:aff id="A7">Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Perkins, Tim" sort="Perkins, Tim" uniqKey="Perkins T" first="Tim" last="Perkins">Tim Perkins</name>
<affiliation wicri:level="1"><nlm:aff id="A6">Novartis Vaccines and Diagnostics, Siena 53100, Italy.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Italie</country>
<wicri:regionArea>Novartis Vaccines and Diagnostics, Siena 53100</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lechat, Pierre" sort="Lechat, Pierre" uniqKey="Lechat P" first="Pierre" last="Lechat">Pierre Lechat</name>
<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Bioinformatics platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Dmytruk, Nicolas" sort="Dmytruk, Nicolas" uniqKey="Dmytruk N" first="Nicolas" last="Dmytruk">Nicolas Dmytruk</name>
<affiliation wicri:level="1"><nlm:aff id="A7">Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Sauvage, Elisabeth" sort="Sauvage, Elisabeth" uniqKey="Sauvage E" first="Elisabeth" last="Sauvage">Elisabeth Sauvage</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ma, Laurence" sort="Ma, Laurence" uniqKey="Ma L" first="Laurence" last="Ma">Laurence Ma</name>
<affiliation wicri:level="1"><nlm:aff id="A8">Institut Pasteur Genomic platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur Genomic platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Romi, Benedetta" sort="Romi, Benedetta" uniqKey="Romi B" first="Benedetta" last="Romi">Benedetta Romi</name>
<affiliation wicri:level="1"><nlm:aff id="A6">Novartis Vaccines and Diagnostics, Siena 53100, Italy.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Italie</country>
<wicri:regionArea>Novartis Vaccines and Diagnostics, Siena 53100</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Tichit, Magali" sort="Tichit, Magali" uniqKey="Tichit M" first="Magali" last="Tichit">Magali Tichit</name>
<affiliation wicri:level="1"><nlm:aff id="A8">Institut Pasteur Genomic platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur Genomic platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lopez Sanchez, Maria Jose" sort="Lopez Sanchez, Maria Jose" uniqKey="Lopez Sanchez M" first="Maria-José" last="Lopez-Sanchez">Maria-José Lopez-Sanchez</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Descorps Declere, Stephane" sort="Descorps Declere, Stephane" uniqKey="Descorps Declere S" first="Stéphane" last="Descorps-Declere">Stéphane Descorps-Declere</name>
<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Bioinformatics platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Souche, Erika" sort="Souche, Erika" uniqKey="Souche E" first="Erika" last="Souche">Erika Souche</name>
<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Bioinformatics platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Buchrieser, Carmen" sort="Buchrieser, Carmen" uniqKey="Buchrieser C" first="Carmen" last="Buchrieser">Carmen Buchrieser</name>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A9">Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Trieu Cuot, Patrick" sort="Trieu Cuot, Patrick" uniqKey="Trieu Cuot P" first="Patrick" last="Trieu-Cuot">Patrick Trieu-Cuot</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A10">CNRS ERL3526, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS ERL3526, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Moszer, Ivan" sort="Moszer, Ivan" uniqKey="Moszer I" first="Ivan" last="Moszer">Ivan Moszer</name>
<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Bioinformatics platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Clermont, Dominique" sort="Clermont, Dominique" uniqKey="Clermont D" first="Dominique" last="Clermont">Dominique Clermont</name>
<affiliation wicri:level="1"><nlm:aff id="A11">Institut Pasteur, Collection de l’Institut Pasteur (CIP), Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Collection de l’Institut Pasteur (CIP), Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Maione, Domenico" sort="Maione, Domenico" uniqKey="Maione D" first="Domenico" last="Maione">Domenico Maione</name>
<affiliation wicri:level="1"><nlm:aff id="A6">Novartis Vaccines and Diagnostics, Siena 53100, Italy.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Italie</country>
<wicri:regionArea>Novartis Vaccines and Diagnostics, Siena 53100</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bouchier, Christiane" sort="Bouchier, Christiane" uniqKey="Bouchier C" first="Christiane" last="Bouchier">Christiane Bouchier</name>
<affiliation wicri:level="1"><nlm:aff id="A8">Institut Pasteur Genomic platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur Genomic platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mcmillan, David J" sort="Mcmillan, David J" uniqKey="Mcmillan D" first="David J." last="Mcmillan">David J. Mcmillan</name>
<affiliation wicri:level="1"><nlm:aff id="A12">QIMR Berghofer Medical Research Institute, Brisbane, 7006 Queensland, Australia.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Australie</country>
<wicri:regionArea>QIMR Berghofer Medical Research Institute, Brisbane, 7006 Queensland</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A13">Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland, Australia.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Australie</country>
<wicri:regionArea>Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name>
<affiliation wicri:level="1"><nlm:aff id="A4">The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Telford, John L" sort="Telford, John L" uniqKey="Telford J" first="John L." last="Telford">John L. Telford</name>
<affiliation wicri:level="1"><nlm:aff id="A6">Novartis Vaccines and Diagnostics, Siena 53100, Italy.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Italie</country>
<wicri:regionArea>Novartis Vaccines and Diagnostics, Siena 53100</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Dougan, Gordan" sort="Dougan, Gordan" uniqKey="Dougan G" first="Gordan" last="Dougan">Gordan Dougan</name>
<affiliation wicri:level="1"><nlm:aff id="A4">The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Walker, Mark J" sort="Walker, Mark J" uniqKey="Walker M" first="Mark J." last="Walker">Mark J. Walker</name>
<affiliation wicri:level="1"><nlm:aff id="A5">Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Australie</country>
<wicri:regionArea>Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Holden, Matthew T G" sort="Holden, Matthew T G" uniqKey="Holden M" first="Matthew T. G." last="Holden">Matthew T. G. Holden</name>
<affiliation wicri:level="1"><nlm:aff id="A4">The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Poyart, Claire" sort="Poyart, Claire" uniqKey="Poyart C" first="Claire" last="Poyart">Claire Poyart</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A7">Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A14">Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A15">INSERM, U1016, Paris 75014, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>INSERM, U1016, Paris 75014</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Glaser, Philippe" sort="Glaser, Philippe" uniqKey="Glaser P" first="Philippe" last="Glaser">Philippe Glaser</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">CNRS UMR3525, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>CNRS UMR3525, Paris 75015</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A3">Institut Pasteur, Bioinformatics platform, Paris 75015, France.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">France</country>
<wicri:regionArea>Institut Pasteur, Bioinformatics platform, Paris 75015</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Nature communications</title>
<idno type="eISSN">2041-1723</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P6"><italic>Streptococcus agalactiae</italic>
(Group B <italic>Streptococcus</italic>
, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Edwards, Ms" uniqKey="Edwards M">MS Edwards</name>
</author>
<author><name sortKey="Baker, Cj" uniqKey="Baker C">CJ Baker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edmond, Km" uniqKey="Edmond K">KM Edmond</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Eickhoff, Tc" uniqKey="Eickhoff T">TC Eickhoff</name>
</author>
<author><name sortKey="Klein, Jo" uniqKey="Klein J">JO Klein</name>
</author>
<author><name sortKey="Daly, Ak" uniqKey="Daly A">AK Daly</name>
</author>
<author><name sortKey="Ingall, D" uniqKey="Ingall D">D Ingall</name>
</author>
<author><name sortKey="Finland, M" uniqKey="Finland M">M Finland</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kexel, G" uniqKey="Kexel G">G Kexel</name>
</author>
<author><name sortKey="Schoenbohm, S" uniqKey="Schoenbohm S">S Schoenbohm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jones, N" uniqKey="Jones N">N Jones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tazi, A" uniqKey="Tazi A">A Tazi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brochet, M" uniqKey="Brochet M">M Brochet</name>
</author>
<author><name sortKey="Couve, E" uniqKey="Couve E">E Couve</name>
</author>
<author><name sortKey="Bercion, R" uniqKey="Bercion R">R Bercion</name>
</author>
<author><name sortKey="Sire, Jm" uniqKey="Sire J">JM Sire</name>
</author>
<author><name sortKey="Glaser, P" uniqKey="Glaser P">P Glaser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nocard, M" uniqKey="Nocard M">M Nocard</name>
</author>
<author><name sortKey="Mollereau, H" uniqKey="Mollereau H">H Mollereau</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sorensen, Ub" uniqKey="Sorensen U">UB Sorensen</name>
</author>
<author><name sortKey="Poulsen, K" uniqKey="Poulsen K">K Poulsen</name>
</author>
<author><name sortKey="Ghezzo, C" uniqKey="Ghezzo C">C Ghezzo</name>
</author>
<author><name sortKey="Margarit, I" uniqKey="Margarit I">I Margarit</name>
</author>
<author><name sortKey="Kilian, M" uniqKey="Kilian M">M Kilian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brochet, M" uniqKey="Brochet M">M Brochet</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lindahl, G" uniqKey="Lindahl G">G Lindahl</name>
</author>
<author><name sortKey="Stalhammar Carlemalm, M" uniqKey="Stalhammar Carlemalm M">M Stalhammar-Carlemalm</name>
</author>
<author><name sortKey="Areschoug, T" uniqKey="Areschoug T">T Areschoug</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Drummond, Aj" uniqKey="Drummond A">AJ Drummond</name>
</author>
<author><name sortKey="Suchard, Ma" uniqKey="Suchard M">MA Suchard</name>
</author>
<author><name sortKey="Xie, D" uniqKey="Xie D">D Xie</name>
</author>
<author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="He, M" uniqKey="He M">M He</name>
</author>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101528555</journal-id>
<journal-id journal-id-type="pubmed-jr-id">37539</journal-id>
<journal-id journal-id-type="nlm-ta">Nat Commun</journal-id>
<journal-id journal-id-type="iso-abbrev">Nat Commun</journal-id>
<journal-title-group><journal-title>Nature communications</journal-title>
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<issn pub-type="epub">2041-1723</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25088811</article-id>
<article-id pub-id-type="pmc">4538795</article-id>
<article-id pub-id-type="doi">10.1038/ncomms5544</article-id>
<article-id pub-id-type="manuscript">EMS64295</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title><italic>Streptococcus agalactiae</italic>
clones infecting humans were selected and fixed through the extensive use of tetracycline</article-title>
</title-group>
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<given-names>Pierre-Emmanuel</given-names>
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<given-names>Isabelle</given-names>
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<xref ref-type="aff" rid="A1">1</xref>
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<given-names>Pierre</given-names>
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<given-names>Nicolas</given-names>
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<contrib contrib-type="author"><collab>The DEVANI Consortium</collab>
<xref ref-type="author-notes" rid="FN2">‡</xref>
</contrib>
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<given-names>Matthew T. G.</given-names>
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<xref ref-type="aff" rid="A4">4</xref>
<xref ref-type="author-notes" rid="FN1">†</xref>
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<given-names>Philippe</given-names>
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</contrib-group>
<aff id="A1"><label>1</label>
Institut Pasteur, Unité de Biologie des Bacteries Pathogènes à Gram-positif, Paris 75015, France.</aff>
<aff id="A2"><label>2</label>
CNRS UMR3525, Paris 75015, France.</aff>
<aff id="A3"><label>3</label>
Institut Pasteur, Bioinformatics platform, Paris 75015, France.</aff>
<aff id="A4"><label>4</label>
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 15A, UK.</aff>
<aff id="A5"><label>5</label>
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia.</aff>
<aff id="A6"><label>6</label>
Novartis Vaccines and Diagnostics, Siena 53100, Italy.</aff>
<aff id="A7"><label>7</label>
Centre National de Référence des Streptocoques, Hôpitaux Universitaires, Paris Centre Cochin–Hôtel Dieu-Broca, Paris 75014, France.</aff>
<aff id="A8"><label>8</label>
Institut Pasteur Genomic platform, Paris 75015, France.</aff>
<aff id="A9"><label>9</label>
Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris 75015, France.</aff>
<aff id="A10"><label>10</label>
CNRS ERL3526, Paris 75015, France.</aff>
<aff id="A11"><label>11</label>
Institut Pasteur, Collection de l’Institut Pasteur (CIP), Paris 75015, France.</aff>
<aff id="A12"><label>12</label>
QIMR Berghofer Medical Research Institute, Brisbane, 7006 Queensland, Australia.</aff>
<aff id="A13"><label>13</label>
Inflammation and Healing Research Cluster, University of the Sunshine Coast, Sippy Downs, 4556 Queensland, Australia.</aff>
<aff id="A14"><label>14</label>
Institut Cochin, Université Sorbonne Paris Descartes, Paris 75014, France.</aff>
<aff id="A15"><label>15</label>
INSERM, U1016, Paris 75014, France.</aff>
<author-notes><corresp id="CR1">Correspondence and requests for materials should be addressed to P.G. (<email>pglaser@pasteur.fr</email>
)</corresp>
<fn fn-type="present-address" id="FN1"><label>†</label>
<p id="P3">Present address: School of Medicine, University of St Andrews, St Andrews KY16 9TF, Scotland, UK</p>
</fn>
<fn id="FN2"><label>‡</label>
<p id="P4">Pierette Melin<sup>16</sup>
, Antoaneta Decheva<sup>17</sup>
, Bogdan Petrunov<sup>17</sup>
, Paula Kriz<sup>18</sup>
, Reinhard Berner<sup>19</sup>
, Anna Büchele<sup>19</sup>
, Markus Hufnagel<sup>19</sup>
, Mirjam Kunze<sup>19</sup>
, Roberta Creti<sup>20</sup>
, Lucilla Baldassarri<sup>20</sup>
, Graziella Orefici<sup>20</sup>
, Alberto Berardi<sup>21</sup>
, Javier Rodriguez Granger<sup>22</sup>
, Manuel De La Rosa Fraile<sup>22</sup>
, Baharak Afshar<sup>23</sup>
& Androulla Efstratiou<sup>23</sup>
</p>
<p id="P5"><sup>16</sup>
National Reference Centre for Group B Streptococci, University Hospital of Liege 4000, Belgium. <sup>17</sup>
National Center of Infectious and Parasitic Diseases, Sofia 1504, Bulgaria. <sup>18</sup>
National Institute of Public Health, Prague 10042, Czech Republic. <sup>19</sup>
University Hospital Freiburg, Freiburg 79106, Germany. <sup>20</sup>
Istituto Superiore di Sanità, Rome 00161, Italy. <sup>21</sup>
Azienda Ospedaliero-Universitaria Policlinico, Modena 41124, Italy. <sup>22</sup>
Hospital Universitario Virgen de las Nieves, Granada 18014, Spain. <sup>23</sup>
Health Protection Agency Centre for Infections, London NW9 5EQ, UK</p>
</fn>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>27</day>
<month>7</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>04</day>
<month>8</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>17</day>
<month>8</month>
<year>2015</year>
</pub-date>
<volume>5</volume>
<fpage>4544</fpage>
<lpage>4544</lpage>
<pmc-comment>elocation-id from pubmed: 10.1038/ncomms5544</pmc-comment>
<permissions><license license-type="permissions-link"><license-p><bold>Reprints and permission</bold>
information is available online at <ext-link ext-link-type="uri" xlink:href="http://npg.nature.com/reprintsandpermissions/">http://npg.nature.com/reprintsandpermissions/</ext-link>
</license-p>
</license>
<license license-type="open-access"><license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
</license-p>
</license>
</permissions>
<abstract><p id="P6"><italic>Streptococcus agalactiae</italic>
(Group B <italic>Streptococcus</italic>
, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.</p>
</abstract>
</article-meta>
</front>
<floats-group><fig id="F1" orientation="portrait" position="float"><label>Figure 1</label>
<caption><title>Population structure of human GBS is driven by tetracycline resistance acquisition</title>
<p>(<bold>a</bold>
) Whole-genome-based phylogeny of 229 sequenced GBS isolates and strain SS1219 isolated from fish<sup><xref rid="R48" ref-type="bibr">48</xref>
</sup>
. Maximum Likelihood (ML) using MEGA was used to infer phylogenetic relationships. The major clonal complexes (CC) 1, 10, 17, 19, 23 and 26 as defined on the GBS MLST web site (<ext-link ext-link-type="uri" xlink:href="http://pubmlst.org/sagalactiae/">http://pubmlst.org/sagalactiae/</ext-link>
) correspond to well-defined branches. Isolates are indicated by dots coloured according to their geographical origin. Flanking the whole-genome phylogeny, are four Bayesian maximum clade credibility phylogenies (<bold>b–e</bold>
) based on the non-recombinogenic genome for the GBS CC17 (<bold>b</bold>
), CC23 (<bold>c</bold>
), CC19 (<bold>d</bold>
) and CC1 strains (<bold>e</bold>
). Divergence dates (median estimates with 95% highest posterior density dates in brackets) are provided in blue for the major nodes. Coloured branches relate to the major tetracycline-resistant clones. Arrows indicate the predicted time of insertion of the ICE carrying the <italic>tet</italic>
(M) resistance determinant within the major clones. Capsular serotypes are indicated on the right of each tree according to the indicated colour code.</p>
</caption>
<graphic xlink:href="emss-64295-f0001"></graphic>
</fig>
<fig id="F2" orientation="portrait" position="float"><label>Figure 2</label>
<caption><title>Distribution of SNPs and recombination across all GBS isolates from the six major CCs</title>
<p>The maps were generated by using the SyntView software. Isolates were ordered according to the distance from the reference genome depicted at the inner circle. CC numbers are indicated in the centre. Recombined regions compared with the reference genome correspond to regions with a higher density of SNPs indicated by short lines on each circle corresponding to one strain. Around the outside circle are the relative positions of selected antigenic loci. The reference genomes were BG-NI-011 for CC1, DK-NI-008 for CC10, COH1 for CC17, RBH11 for CC19, CCH210801006 for CC23 and Bangui-IP-105 for CC26.</p>
</caption>
<graphic xlink:href="emss-64295-f0002"></graphic>
</fig>
<fig id="F3" orientation="portrait" position="float"><label>Figure 3</label>
<caption><title>Phylogeny of the ‘hypervirulent’ CC17 lineage</title>
<p>(<bold>a</bold>
) ML phylogeny based on the alignment of 3,922 polymorphic positions. Six independent ICE insertions (indicated on the right and by blue arrows) corresponding to six different lineages (indicated by different colours) were identified and are numbered from 11 to 16 (<xref ref-type="table" rid="T4">Table 4</xref>
). A star indicates that Tn<italic>5801</italic>
has been lost by this isolate. Following the loss of Tn<italic>5801</italic>
, strains CCH210160764 and CCH207800974 have acquired unrelated ICE expressing <italic>tet</italic>
(M) and <italic>erm</italic>
(B), and <italic>tet</italic>
(O) and <italic>erm</italic>
(B), respectively. Nodes with >90% bootstrap support are indicated by black dots. (<bold>b</bold>
) Genetic maps and alignment of Tn<italic>916</italic>
and Tn<italic>5801</italic>
. Comparisons were performed by BLASTn. The <italic>tet</italic>
(M) gene is coloured in yellow, genes encoding type 4 secretion system components are in blue and the integrase and excisionase genes which are not conserved between the two transposons in red. Percentages of identities are shown in blue scale and range between 68 and 98% for the <italic>tet</italic>
(M) region.</p>
</caption>
<graphic xlink:href="emss-64295-f0003"></graphic>
</fig>
<fig id="F4" orientation="portrait" position="float"><label>Figure 4</label>
<caption><title>Phylogeny of clonal complex CC1</title>
<p>(<bold>a</bold>
) ML phylogeny from the alignment of pseudosequences of the 1,244 polymorphic positions in 914 interrogated kbases. The five independent Tn<italic>916</italic>
or Tn<italic>5801</italic>
insertions are indicated in blue and numbers from 1 to 5 refer to their description in <xref ref-type="table" rid="T4">Table 4</xref>
. The two TcR lineages with more than one isolate are coloured in blue and red. Three sub-lineages have acquired an <italic>erm</italic>
resistance gene. Within lineage Tn<italic>916</italic>
-1, 40% of the isolates (12) carry Tn<italic>3872</italic>
(dark-blue branch and strain Bangui-IP-30). The four observed serotypes (<italic>cps</italic>
) II, IV, V and VI are indicated in violet. A star indicates that Tn<italic>916</italic>
has been lost by the isolate. Antibiotic resistance genes other than <italic>tet</italic>
(M) are indicated in red. Nodes with >90% bootstrap support are indicated by black dots. (<bold>b</bold>
) Genetic map of Tn<italic>3872</italic>
. Tn<italic>917</italic>
carrying the <italic>erm</italic>
(B) gene is in grey the <italic>erm</italic>
(B) gene being in orange, Tn<italic>916</italic>
genes are coloured as in <xref ref-type="fig" rid="F3">Fig. 3</xref>
. The location of 13 out of the 15 SNPs between strain CZ-NI-006 Tn<italic>916</italic>
and strain DE-NI-001 Tn<italic>3872</italic>
, indicated by black bars are located between positions 10,407 and 13,659 (Tn<italic>916</italic>
coordinates) and the 76 SNPs between strain Bangui-IP-50 and strain CZ-NI-006, all located between position 10,407 and 13,497 are in blue.</p>
</caption>
<graphic xlink:href="emss-64295-f0004"></graphic>
</fig>
<fig id="F5" orientation="portrait" position="float"><label>Figure 5</label>
<caption><title>Correlation of isolation date with maximum likelihood root-to-tip branch length for the five major TcR lineages calculated with Path-O-Gen</title>
<p>These analyses predict the origin of these clones in agreement with the BEAST analysis except for the CC23 lineage where there was a lack of temporal sampling to support tree root estimates. <italic>X</italic>
axis, time in years; <italic>Y</italic>
axis root-to-tip branch length in SNP per Mb. (<bold>a</bold>
) CC1 lineage Tn<italic>916</italic>
-1; (<bold>b</bold>
) CC19 lineage Tn<italic>916</italic>
-17; (<bold>c</bold>
) CC17 lineage Tn<italic>5801</italic>
-11; (<bold>d</bold>
) CC17 lineage Tn<italic>916</italic>
-12; (<bold>e</bold>
) CC23 lineage Tn<italic>5801</italic>
-23.</p>
</caption>
<graphic xlink:href="emss-64295-f0005"></graphic>
</fig>
<table-wrap id="T1" position="float" orientation="landscape"><label>Table 1</label>
<caption><title>Summary of global multi-locus sequence typing studies<xref ref-type="table-fn" rid="TFN2">*</xref>
.</title>
</caption>
<table frame="below" rules="groups"><thead><tr><th align="left" valign="middle" rowspan="1" colspan="1">Study<xref ref-type="table-fn" rid="TFN3">†</xref>
</th>
<th align="left" valign="middle" rowspan="1" colspan="1">Origin<xref ref-type="table-fn" rid="TFN4">‡</xref>
</th>
<th align="left" valign="middle" rowspan="1" colspan="1">Clinical origin<xref ref-type="table-fn" rid="TFN5">§</xref>
</th>
<th align="right" valign="middle" rowspan="1" colspan="1">Number of<break></break>
isolates</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC1 (ST1)<xref ref-type="table-fn" rid="TFN6">∥</xref>
</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC10<xref ref-type="table-fn" rid="TFN7">¶</xref>
</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC17</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC19 (ST19, 28)<xref ref-type="table-fn" rid="TFN6">∥</xref>
</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC23</th>
<th align="center" valign="middle" rowspan="1" colspan="1">CC26</th>
<th align="center" valign="middle" rowspan="1" colspan="1">Other</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="middle" rowspan="1" colspan="1">Jones<sup><xref rid="R5" ref-type="bibr">5</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">World</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca, Ninv, Ainv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">152</td>
<td align="center" valign="middle" rowspan="1" colspan="1">16% (14%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">18%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">30%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">17% (13%–2%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">12%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">5%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Luan<sup><xref rid="R55" ref-type="bibr">55</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Sweden (1988–1997)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ninv, Ainv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">158</td>
<td align="center" valign="middle" rowspan="1" colspan="1">15% (9%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">13%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">24%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">29% (16%–1%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">14%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">0</td>
<td align="center" valign="middle" rowspan="1" colspan="1">4%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Manning<sup><xref rid="R56" ref-type="bibr">56</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Canada Alberta (1993–2002)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca, Ninv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">413</td>
<td align="center" valign="middle" rowspan="1" colspan="1">23% (19%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">14%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">16%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">20% (19%–NA)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">22%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">NA</td>
<td align="center" valign="middle" rowspan="1" colspan="1">5%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Bohnsack<sup><xref rid="R57" ref-type="bibr">57</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">USA (1995–1999)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca, Ninv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">899</td>
<td align="center" valign="middle" rowspan="1" colspan="1">16% (15%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">9%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">13%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">17% (12%–2%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">40%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">0</td>
<td align="center" valign="middle" rowspan="1" colspan="1">5%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Sadowi<sup><xref rid="R58" ref-type="bibr">58</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Poland (1996–2005)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca, Ninv, Ainv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">114</td>
<td align="center" valign="middle" rowspan="1" colspan="1">17% (13%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">18%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">14%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">12% (9–2%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">37%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Huber<sup><xref rid="R59" ref-type="bibr">59</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Kenya (2007–2010)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca, Ainv</td>
<td align="right" valign="middle" rowspan="1" colspan="1">169</td>
<td align="center" valign="middle" rowspan="1" colspan="1">12% (9%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">17%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">21%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">14% (5%–4%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">27%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">7%</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Brochet<sup><xref rid="R7" ref-type="bibr">7</xref>
</sup>
</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Dakar Bangui (2006–2007)</td>
<td align="left" valign="middle" rowspan="1" colspan="1">Ca</td>
<td align="right" valign="middle" rowspan="1" colspan="1">163</td>
<td align="center" valign="middle" rowspan="1" colspan="1">20% (9%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">6%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">12%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">28% (4%–15%)</td>
<td align="center" valign="middle" rowspan="1" colspan="1">17%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">15%</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2%</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="TFN1"><p id="P26">NA, Not available.</p>
</fn>
<fn id="TFN2"><label>*</label>
<p id="P27">As percentage in each clonal complex.</p>
</fn>
<fn id="TFN3"><label>†</label>
<p id="P28">First author of the publication and reference.</p>
</fn>
<fn id="TFN4"><label>‡</label>
<p id="P29">In parenthesis the years of isolation if known.</p>
</fn>
<fn id="TFN5"><label>§</label>
<p id="P30">The epidemiological origin: Ca, carriage, Ninv, neonatal invasive disease, Ainv, adults invasive disease.</p>
</fn>
<fn id="TFN6"><label>∥</label>
<p id="P31">In parenthesis, the percentage corresponding to the indicated sequence types (STs).</p>
</fn>
<fn id="TFN7"><label>¶</label>
<p id="P32">Corresponds to strains from the closely related clonal complexes (CC) CC6, CC8 and CC10.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap id="T2" position="float" orientation="portrait"><label>Table 2</label>
<caption><title>Diversity within the six clonal complexes.</title>
</caption>
<table frame="below" rules="groups"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1"></th>
<th align="center" valign="top" rowspan="1" colspan="1">CC1</th>
<th align="center" valign="top" rowspan="1" colspan="1">CC10</th>
<th align="center" valign="top" rowspan="1" colspan="1">CC17</th>
<th align="center" valign="top" rowspan="1" colspan="1">CC19</th>
<th align="center" valign="top" rowspan="1" colspan="1">CC23</th>
<th align="center" valign="top" rowspan="1" colspan="1">CC26</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">Strain name</td>
<td align="center" valign="top" rowspan="1" colspan="1">BG-NI-011</td>
<td align="center" valign="top" rowspan="1" colspan="1">DK-NI-008</td>
<td align="center" valign="top" rowspan="1" colspan="1">COH1</td>
<td align="center" valign="top" rowspan="1" colspan="1">RBH11</td>
<td align="center" valign="top" rowspan="1" colspan="1">CCH210801006</td>
<td align="center" valign="top" rowspan="1" colspan="1">Bangui-IP-105</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Genome size<xref ref-type="table-fn" rid="TFN8">*</xref>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,078 (25)</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,080 (34)</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,065 (1)</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,180 (34)</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,055 (17)</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,054 (45)</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">No. of isolates</td>
<td align="center" valign="top" rowspan="1" colspan="1">39</td>
<td align="center" valign="top" rowspan="1" colspan="1">18</td>
<td align="center" valign="top" rowspan="1" colspan="1">79</td>
<td align="center" valign="top" rowspan="1" colspan="1">39</td>
<td align="center" valign="top" rowspan="1" colspan="1">36</td>
<td align="center" valign="top" rowspan="1" colspan="1">6</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Interrogated regions<xref ref-type="table-fn" rid="TFN9">†</xref>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">914 kb</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,069 kb</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,860 kb</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,427 kb</td>
<td align="center" valign="top" rowspan="1" colspan="1">980 kb</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,582 kb</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Polymorphic positions</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,244</td>
<td align="center" valign="top" rowspan="1" colspan="1">971</td>
<td align="center" valign="top" rowspan="1" colspan="1">3,922</td>
<td align="center" valign="top" rowspan="1" colspan="1">2,016</td>
<td align="center" valign="top" rowspan="1" colspan="1">1,329</td>
<td align="center" valign="top" rowspan="1" colspan="1">263</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Recombination<xref ref-type="table-fn" rid="TFN10">‡</xref>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">987 kb<break></break>
<italic>pil1, pil2, cps</italic>
, R5,<break></break>
<italic>alp, srr</italic>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">914 kb<break></break>
<italic>pil1, pil2, cps</italic>
, R5,<break></break>
<italic>alp, srr</italic>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">68 kb<break></break>
<italic>cps</italic>
, R5</td>
<td align="center" valign="top" rowspan="1" colspan="1">532 kb<break></break>
<italic>cps</italic>
, R5, <italic>pil2,</italic>
<break></break>
<italic>srr, alp</italic>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">875 kb<break></break>
<italic>pil1, pil2, cps</italic>
, R5,<break></break>
<italic>alp, srr</italic>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">398 kb<break></break>
Tn<italic>916</italic>
/CRISPR,<break></break>
R5, <italic>alp</italic>
</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Depth<xref ref-type="table-fn" rid="TFN11">§</xref>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">174±23</td>
<td align="center" valign="top" rowspan="1" colspan="1">126±7</td>
<td align="center" valign="top" rowspan="1" colspan="1">129±16</td>
<td align="center" valign="top" rowspan="1" colspan="1">97±21</td>
<td align="center" valign="top" rowspan="1" colspan="1">169±16</td>
<td align="center" valign="top" rowspan="1" colspan="1">74±34</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Mutation rate<xref ref-type="table-fn" rid="TFN12">∥</xref>
</td>
<td align="center" valign="top" rowspan="1" colspan="1">0.64</td>
<td align="center" valign="top" rowspan="1" colspan="1">—
</td>
<td align="center" valign="top" rowspan="1" colspan="1">0.56</td>
<td align="center" valign="top" rowspan="1" colspan="1">0.93</td>
<td align="center" valign="top" rowspan="1" colspan="1">0.75</td>
<td align="center" valign="top" rowspan="1" colspan="1">—
</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="TFN8"><label>*</label>
<p id="P33">Total contig size in kb, in parenthesis, the number of contigs.</p>
</fn>
<fn id="TFN9"><label>†</label>
<p id="P34">Cumulative size in kb of regions not predicted to have recombined.</p>
</fn>
<fn id="TFN10"><label>‡</label>
<p id="P35">Cumulative size in kb of the recombined regions and the exchanged antigenic loci.</p>
</fn>
<fn id="TFN11"><label>§</label>
<p id="P36">Expressed as the average number of single-nucleotide polymorphism (SNP) per Mb from the root to the tips of the tree for strains isolated after 2005.</p>
</fn>
<fn id="TFN12"><label>∥</label>
<p id="P37">As estimated by dividing the depth of each lineage by its age predicted by the BEAST analysis, in SNPs per Mb per year (<xref ref-type="fig" rid="F1">Fig. 1b–e</xref>
).</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap id="T3" position="float" orientation="portrait"><label>Table 3</label>
<caption><title>Distribution of antibiotic resistance genes among the 229 sequenced isolates.</title>
</caption>
<table frame="below" rules="groups"><thead><tr><th align="left" valign="middle" rowspan="1" colspan="1">Antibiotic resistance</th>
<th align="center" valign="middle" rowspan="1" colspan="1">Gene</th>
<th colspan="7" align="right" valign="middle" rowspan="1">Number of isolates<hr></hr>
</th>
<th align="right" valign="middle" rowspan="1" colspan="1">Total</th>
</tr>
<tr><th align="left" valign="middle" rowspan="1" colspan="1"></th>
<th align="center" valign="middle" rowspan="1" colspan="1"></th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC1</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC10</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC17</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC19</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC23</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC26</th>
<th align="right" valign="middle" rowspan="1" colspan="1">Other</th>
<th align="right" valign="middle" rowspan="1" colspan="1"></th>
</tr>
</thead>
<tbody><tr><td align="left" valign="middle" rowspan="1" colspan="1">Tetracycline</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>tet</italic>
(M)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">34</td>
<td align="right" valign="middle" rowspan="1" colspan="1">13</td>
<td align="right" valign="middle" rowspan="1" colspan="1">77</td>
<td align="right" valign="middle" rowspan="1" colspan="1">27</td>
<td align="right" valign="middle" rowspan="1" colspan="1">27</td>
<td align="right" valign="middle" rowspan="1" colspan="1">5</td>
<td align="right" valign="middle" rowspan="1" colspan="1">7</td>
<td align="right" valign="middle" rowspan="1" colspan="1">190</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>tet</italic>
(O)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">6</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">11</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>tet</italic>
(L)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">4</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Erythromycin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>erm</italic>
(B)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">13</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">4</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>erm</italic>
(TR)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">6</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">12</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>erm</italic>
(T)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>mefE</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Streptomycin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>aadE</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">4</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">6</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Kanamycin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>aph3’</italic>
-III</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">3</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">4</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Streptothrycin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>sta</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">3</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">4</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Chloramphenicol</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>cat</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Lincosamides</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>lnuB</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Lincosamide—streptogramin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>lsa</italic>
(C)</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">6</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Spectinomycin</td>
<td align="center" valign="middle" rowspan="1" colspan="1"><italic>spcR</italic>
</td>
<td align="right" valign="middle" rowspan="1" colspan="1">3</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1">0</td>
<td align="right" valign="middle" rowspan="1" colspan="1">8</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">Total number of isolates</td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">39</td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
<td align="right" valign="middle" rowspan="1" colspan="1">78</td>
<td align="right" valign="middle" rowspan="1" colspan="1">39</td>
<td align="right" valign="middle" rowspan="1" colspan="1">36</td>
<td align="right" valign="middle" rowspan="1" colspan="1">6</td>
<td align="right" valign="middle" rowspan="1" colspan="1">12</td>
<td align="right" valign="middle" rowspan="1" colspan="1">229</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="T4" position="float" orientation="portrait"><label>Table 4</label>
<caption><title>Characteristics of clones deriving from Tn<italic>916</italic>
and Tn<italic>5801</italic>
insertions.</title>
</caption>
<table frame="below" rules="groups"><thead><tr><th colspan="4" align="left" valign="middle" rowspan="1">Clone<hr></hr>
</th>
<th align="center" valign="middle" rowspan="1" colspan="1">No. of isolates per clone</th>
<th align="center" valign="middle" rowspan="1" colspan="1">Integrative and conjugative element<break></break>
and site<xref ref-type="table-fn" rid="TFN14">*</xref>
of insertion</th>
<th align="center" valign="middle" rowspan="1" colspan="1">Recombination events<break></break>
within the clone<xref ref-type="table-fn" rid="TFN15">†</xref>
</th>
</tr>
<tr><th align="left" valign="middle" rowspan="1" colspan="1"><italic>N</italic>
</th>
<th align="right" valign="middle" rowspan="1" colspan="1">CC</th>
<th align="right" valign="middle" rowspan="1" colspan="1">Sequence type</th>
<th align="center" valign="middle" rowspan="1" colspan="1"><italic>cps</italic>
</th>
<th align="center" valign="middle" rowspan="1" colspan="1"></th>
<th align="center" valign="middle" rowspan="1" colspan="1"></th>
<th align="center" valign="middle" rowspan="1" colspan="1"></th>
</tr>
</thead>
<tbody><tr><td align="left" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="right" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">V</td>
<td align="center" valign="middle" rowspan="1" colspan="1">27 (2)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
GI 624 kb<xref ref-type="table-fn" rid="TFN17">§</xref>
,,<xref ref-type="table-fn" rid="TFN18">∥</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">92 kb <italic>alp</italic>
; 100 kb</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">2</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">196, 459</td>
<td align="center" valign="middle" rowspan="1" colspan="1">IV</td>
<td align="center" valign="middle" rowspan="1" colspan="1">6</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
GI 624 kb<xref ref-type="table-fn" rid="TFN17">§</xref>
,,<xref ref-type="table-fn" rid="TFN18">∥</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">80 kb <italic>alp</italic>
: 35kb</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">3</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">IV</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
<xref ref-type="table-fn" rid="TFN20">#</xref>
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">4</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">IV</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">5</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
726 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">3<xref ref-type="table-fn" rid="TFN21">**</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">6</td>
<td align="right" valign="middle" rowspan="1" colspan="1">10</td>
<td align="right" valign="middle" rowspan="1" colspan="1">10</td>
<td align="center" valign="middle" rowspan="1" colspan="1">V-II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">5</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">347 kb <italic>cps</italic>
operon</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">7</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">8</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Ib</td>
<td align="center" valign="middle" rowspan="1" colspan="1">4</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
846 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">8</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">12</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
260 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">9</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">10</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Ib</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
626 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">10</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">10</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1,255 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">5<xref ref-type="table-fn" rid="TFN21">**</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">11</td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">42 (3)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">12</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">23</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
241 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">13</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">6</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
950 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">14</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1,928 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">15</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">17</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1,928 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">16</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">291</td>
<td align="center" valign="middle" rowspan="1" colspan="1">IV</td>
<td align="center" valign="middle" rowspan="1" colspan="1">5</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
52 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">17</td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III V</td>
<td align="center" valign="middle" rowspan="1" colspan="1">20 (3)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
923 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">253 kb <italic>cps</italic>
operon 36 kb R5 protein</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">18</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">4 (1)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
GI 557 kb<xref ref-type="table-fn" rid="TFN18">∥</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">19</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">19</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
2,005 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">20</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">28</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
395 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">21</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">28</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">3</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1,445 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">22</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">28</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
2,005 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">8<xref ref-type="table-fn" rid="TFN21">**</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">23</td>
<td align="right" valign="middle" rowspan="1" colspan="1">23</td>
<td align="right" valign="middle" rowspan="1" colspan="1">23</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Ia</td>
<td align="center" valign="middle" rowspan="1" colspan="1">18 (1)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">107 kb <italic>alp</italic>
; 56 kb R5 protein; 93 kb</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">24</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">23, 144</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Ia–V</td>
<td align="center" valign="middle" rowspan="1" colspan="1">8 (1)<xref ref-type="table-fn" rid="TFN16">‡</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1,928 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">91 kb <italic>alp</italic>
; 193 kb <italic>cps</italic>
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">25</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">23</td>
<td align="center" valign="middle" rowspan="1" colspan="1">III</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">26</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">23</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Ia</td>
<td align="center" valign="middle" rowspan="1" colspan="1">1</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>5801</italic>
972 kb<xref ref-type="table-fn" rid="TFN19">¶</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">8<xref ref-type="table-fn" rid="TFN21">**</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1"></td>
<td align="center" valign="middle" rowspan="1" colspan="1">n.a.</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">27</td>
<td align="right" valign="middle" rowspan="1" colspan="1">26</td>
<td align="right" valign="middle" rowspan="1" colspan="1">26</td>
<td align="center" valign="middle" rowspan="1" colspan="1">V</td>
<td align="center" valign="middle" rowspan="1" colspan="1">3</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
GI 1,023 kb<xref ref-type="table-fn" rid="TFN18">∥</xref>
</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">28</td>
<td align="right" valign="middle" rowspan="1" colspan="1"></td>
<td align="right" valign="middle" rowspan="1" colspan="1">26</td>
<td align="center" valign="middle" rowspan="1" colspan="1">V</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
923 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">77 kb R5 protein</td>
</tr>
<tr><td align="left" valign="middle" rowspan="1" colspan="1">29</td>
<td align="right" valign="middle" rowspan="1" colspan="1">22</td>
<td align="right" valign="middle" rowspan="1" colspan="1">22</td>
<td align="center" valign="middle" rowspan="1" colspan="1">II</td>
<td align="center" valign="middle" rowspan="1" colspan="1">2</td>
<td align="center" valign="middle" rowspan="1" colspan="1">Tn<italic>916</italic>
1787 kb</td>
<td align="center" valign="middle" rowspan="1" colspan="1">—
</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="TFN13"><p id="P38">n.a., Not applicable.</p>
</fn>
<fn id="TFN14"><label>*</label>
<p id="P39">Position relative to the completely sequenced 2603 V/R genome<sup><xref rid="R45" ref-type="bibr">45</xref>
</sup>
.</p>
</fn>
<fn id="TFN15"><label>†</label>
<p id="P40">Size of the recombined regions and antigenic loci.</p>
</fn>
<fn id="TFN16"><label>‡</label>
<p id="P41">In parenthesis are indicated the number of strains predicted to have lost Tn<italic>916</italic>
or Tn<italic>5801</italic>
.</p>
</fn>
<fn id="TFN17"><label>§</label>
<p id="P42">Tn<italic>916</italic>
is inserted in the opposite orientation at the same site.</p>
</fn>
<fn id="TFN18"><label>∥</label>
<p id="P43">Tn<italic>916</italic>
is inserted within genomic islands inserted at the reported locations relative to the 2603 V/R genome.</p>
</fn>
<fn id="TFN19"><label>¶</label>
<p id="P44">972 kb correspond to a hot spot of insertion of Tn<italic>5801</italic>
at the 5′ end of the <italic>guaA</italic>
gene.</p>
</fn>
<fn id="TFN20"><label>#</label>
<p id="P45">A dash indicates no recombination event.</p>
</fn>
<fn id="TFN21"><label>**</label>
<p id="P46">Number of isolates in clonal complex (CC)1, 10, 19 and 23 predicted not to have acquired Tn<italic>916</italic>
or Tn<italic>5801</italic>
.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</floats-group>
</pmc>
</record>
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