Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
Identifieur interne : 000444 ( Pmc/Curation ); précédent : 000443; suivant : 000445Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
Auteurs : Bradd J. Haley [États-Unis] ; Seon Woo Kim [États-Unis] ; James Pettengill [États-Unis] ; Yan Luo [États-Unis] ; Jeffrey S. Karns [États-Unis] ; Jo Ann S. Van Kessel [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Url:
DOI: 10.1371/journal.pone.0161225
PubMed: 27695032
PubMed Central: 5047448
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genomic and Evolutionary Analysis of Two <italic>Salmonella enterica</italic> Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America</title><author><name sortKey="Haley, Bradd J" sort="Haley, Bradd J" uniqKey="Haley B" first="Bradd J." last="Haley">Bradd J. Haley</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Seon Woo" sort="Kim, Seon Woo" uniqKey="Kim S" first="Seon Woo" last="Kim">Seon Woo Kim</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Pettengill, James" sort="Pettengill, James" uniqKey="Pettengill J" first="James" last="Pettengill">James Pettengill</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD</wicri:regionArea></affiliation></author><author><name sortKey="Luo, Yan" sort="Luo, Yan" uniqKey="Luo Y" first="Yan" last="Luo">Yan Luo</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD</wicri:regionArea></affiliation></author><author><name sortKey="Karns, Jeffrey S" sort="Karns, Jeffrey S" uniqKey="Karns J" first="Jeffrey S." last="Karns">Jeffrey S. Karns</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Van Kessel, Jo Ann S" sort="Van Kessel, Jo Ann S" uniqKey="Van Kessel J" first="Jo Ann S." last="Van Kessel">Jo Ann S. Van Kessel</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27695032</idno><idno type="pmc">5047448</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047448</idno><idno type="RBID">PMC:5047448</idno><idno type="doi">10.1371/journal.pone.0161225</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000445</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000445</idno><idno type="wicri:Area/Pmc/Curation">000444</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000444</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genomic and Evolutionary Analysis of Two <italic>Salmonella enterica</italic> Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America</title><author><name sortKey="Haley, Bradd J" sort="Haley, Bradd J" uniqKey="Haley B" first="Bradd J." last="Haley">Bradd J. Haley</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Seon Woo" sort="Kim, Seon Woo" uniqKey="Kim S" first="Seon Woo" last="Kim">Seon Woo Kim</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Pettengill, James" sort="Pettengill, James" uniqKey="Pettengill J" first="James" last="Pettengill">James Pettengill</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD</wicri:regionArea></affiliation></author><author><name sortKey="Luo, Yan" sort="Luo, Yan" uniqKey="Luo Y" first="Yan" last="Luo">Yan Luo</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD</wicri:regionArea></affiliation></author><author><name sortKey="Karns, Jeffrey S" sort="Karns, Jeffrey S" uniqKey="Karns J" first="Jeffrey S." last="Karns">Jeffrey S. Karns</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author><author><name sortKey="Van Kessel, Jo Ann S" sort="Van Kessel, Jo Ann S" uniqKey="Van Kessel J" first="Jo Ann S." last="Van Kessel">Jo Ann S. Van Kessel</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated <italic>S</italic>. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other <italic>Salmonella</italic> serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of <italic>S</italic>. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Foley, Sl" uniqKey="Foley S">SL Foley</name></author><author><name sortKey="Nayak, R" uniqKey="Nayak R">R Nayak</name></author><author><name sortKey="Hanning, Ib" uniqKey="Hanning I">IB Hanning</name></author><author><name sortKey="Johnson, Tj" uniqKey="Johnson T">TJ Johnson</name></author><author><name sortKey="Han, J" uniqKey="Han J">J Han</name></author><author><name sortKey="Ricke, Sc" uniqKey="Ricke S">SC Ricke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kessel, Js" uniqKey="Van Kessel J">JS Van Kessel</name></author><author><name sortKey="Karns, Js" uniqKey="Karns J">JS Karns</name></author><author><name sortKey="Wolfgang, Dr" uniqKey="Wolfgang D">DR Wolfgang</name></author><author><name sortKey="Hovingh, E" uniqKey="Hovingh E">E Hovingh</name></author><author><name sortKey="Schukken, Yh" uniqKey="Schukken Y">YH Schukken</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parveen, S" uniqKey="Parveen S">S Parveen</name></author><author><name sortKey="Taabodi, M" uniqKey="Taabodi M">M Taabodi</name></author><author><name sortKey="Schwarz, Jg" uniqKey="Schwarz J">JG Schwarz</name></author><author><name sortKey="Oscar, Tp" uniqKey="Oscar T">TP Oscar</name></author><author><name sortKey="Harter Dennis, J" uniqKey="Harter Dennis J">J Harter-Dennis</name></author><author><name sortKey="White, Dg" uniqKey="White D">DG White</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kessel, Js" uniqKey="Van Kessel J">JS Van Kessel</name></author><author><name sortKey="Karns, Js" uniqKey="Karns J">JS Karns</name></author><author><name sortKey="Wolfgang, Dr" uniqKey="Wolfgang D">DR Wolfgang</name></author><author><name sortKey="Hovingh, E" uniqKey="Hovingh E">E Hovingh</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Le Hello, S" uniqKey="Le Hello S">S Le Hello</name></author><author><name sortKey="Hendriksen, Rs" uniqKey="Hendriksen R">RS Hendriksen</name></author><author><name sortKey="Doublet, B" uniqKey="Doublet B">B Doublet</name></author><author><name sortKey="Fisher, I" uniqKey="Fisher I">I Fisher</name></author><author><name sortKey="Nielsen, Em" uniqKey="Nielsen E">EM Nielsen</name></author><author><name sortKey="Whichard, Jm" uniqKey="Whichard J">JM Whichard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Le Hello, S" uniqKey="Le Hello S">S Le Hello</name></author><author><name sortKey="Bekhit, A" uniqKey="Bekhit A">A Bekhit</name></author><author><name sortKey="Granier, S" uniqKey="Granier S">S Granier</name></author><author><name sortKey="Barua, H" uniqKey="Barua H">H Barua</name></author><author><name sortKey="Beutlich, J" uniqKey="Beutlich J">J Beutlich</name></author><author><name sortKey="Zaj C, M" uniqKey="Zaj C M">M Zając</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Le Hello, S" uniqKey="Le Hello S">S Le Hello</name></author><author><name sortKey="Harrois, D" uniqKey="Harrois D">D Harrois</name></author><author><name sortKey="Bouchrif, B" uniqKey="Bouchrif B">B Bouchrif</name></author><author><name sortKey="Sontag, L" uniqKey="Sontag L">L Sontag</name></author><author><name sortKey="Elhani, D" uniqKey="Elhani D">D Elhani</name></author><author><name sortKey="Guibert, V" uniqKey="Guibert V">V Guibert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Payne, Jb" uniqKey="Payne J">JB Payne</name></author><author><name sortKey="Santos, Fb" uniqKey="Santos F">FB Santos</name></author><author><name sortKey="Levine, Jf" uniqKey="Levine J">JF Levine</name></author><author><name sortKey="Anderson, Ke" uniqKey="Anderson K">KE Anderson</name></author><author><name sortKey="Sheldon, Bw" uniqKey="Sheldon B">BW Sheldon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Santos, Fb" uniqKey="Santos F">FB Santos</name></author><author><name sortKey="Dsouza, Dh" uniqKey="Dsouza D">DH Dsouza</name></author><author><name sortKey="Jaykus, L" uniqKey="Jaykus L">L Jaykus</name></author><author><name sortKey="Ferket, Pr" uniqKey="Ferket P">PR Ferket</name></author><author><name sortKey="Sheldon, Bw" uniqKey="Sheldon B">BW Sheldon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fricke, Wf" uniqKey="Fricke W">WF Fricke</name></author><author><name sortKey="Mcdermott, Pf" uniqKey="Mcdermott P">PF McDermott</name></author><author><name sortKey="Mammel, Mk" uniqKey="Mammel M">MK Mammel</name></author><author><name sortKey="Zhao, S" uniqKey="Zhao S">S Zhao</name></author><author><name sortKey="Johnson, Tj" uniqKey="Johnson T">TJ Johnson</name></author><author><name sortKey="Rasko, Da" uniqKey="Rasko D">DA Rasko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ladely, Sr" uniqKey="Ladely S">SR Ladely</name></author><author><name sortKey="Meinersmann, Rj" uniqKey="Meinersmann R">RJ Meinersmann</name></author><author><name sortKey="Ball, Ta" uniqKey="Ball T">TA Ball</name></author><author><name sortKey="Fedorka Cray, Pj" uniqKey="Fedorka Cray P">PJ Fedorka-Cray</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edrington, Ts" uniqKey="Edrington T">TS Edrington</name></author><author><name sortKey="Hume, Me" uniqKey="Hume M">ME Hume</name></author><author><name sortKey="Looper, Ml" uniqKey="Looper M">ML Looper</name></author><author><name sortKey="Schultz, Cl" uniqKey="Schultz C">CL Schultz</name></author><author><name sortKey="Fitzgerald, Ac" uniqKey="Fitzgerald A">AC Fitzgerald</name></author><author><name sortKey="Callaway, Tr" uniqKey="Callaway T">TR Callaway</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kessel, Js" uniqKey="Van Kessel J">JS Van Kessel</name></author><author><name sortKey="Karns, Js" uniqKey="Karns J">JS Karns</name></author><author><name sortKey="Lombard, Je" uniqKey="Lombard J">JE Lombard</name></author><author><name sortKey="Kopral, C" uniqKey="Kopral C">C Kopral</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Timme, Re" uniqKey="Timme R">RE Timme</name></author><author><name sortKey="Pettengill, Jb" uniqKey="Pettengill J">JB Pettengill</name></author><author><name sortKey="Allard, Mw" uniqKey="Allard M">MW Allard</name></author><author><name sortKey="Strain, E" uniqKey="Strain E">E Strain</name></author><author><name sortKey="Barrangou, R" uniqKey="Barrangou R">R Barrangou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name></author><author><name sortKey="Desai, Pt" uniqKey="Desai P">PT Desai</name></author><author><name sortKey="Den Bakker, Hc" uniqKey="Den Bakker H">HC den Bakker</name></author><author><name sortKey="Mikoleit, M" uniqKey="Mikoleit M">M Mikoleit</name></author><author><name sortKey="Tolar, B" uniqKey="Tolar B">B Tolar</name></author><author><name sortKey="Trees, E" uniqKey="Trees E">E Trees</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chun, J" uniqKey="Chun J">J Chun</name></author><author><name sortKey="Grim, Cj" uniqKey="Grim C">CJ Grim</name></author><author><name sortKey="Hasan, Na" uniqKey="Hasan N">NA Hasan</name></author><author><name sortKey="Lee, Jh" uniqKey="Lee J">JH Lee</name></author><author><name sortKey="Choi, Sy" uniqKey="Choi S">SY Choi</name></author><author><name sortKey="Haley, B" uniqKey="Haley B">B Haley</name></author><author><name sortKey="Taviani, E" uniqKey="Taviani E">E Taviani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Haley, Bj" uniqKey="Haley B">BJ Haley</name></author><author><name sortKey="Allard, M" uniqKey="Allard M">M Allard</name></author><author><name sortKey="Brown, E" uniqKey="Brown E">E Brown</name></author><author><name sortKey="Hovingh, E" uniqKey="Hovingh E">E Hovingh</name></author><author><name sortKey="Karns, Js" uniqKey="Karns J">JS Karns</name></author><author><name sortKey="Van Kessel, Js" uniqKey="Van Kessel J">JS Van Kessel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Herrera Leon, S" uniqKey="Herrera Leon S">S Herrera-Leon</name></author><author><name sortKey="Ramiro, R" uniqKey="Ramiro R">R Ramiro</name></author><author><name sortKey="Arroyo, M" uniqKey="Arroyo M">M Arroyo</name></author><author><name sortKey="Diez, R" uniqKey="Diez R">R Diez</name></author><author><name sortKey="Usera, Ma" uniqKey="Usera M">MA Usera</name></author><author><name sortKey="Echeita, Ma" uniqKey="Echeita M">MA Echeita</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karns, Js" uniqKey="Karns J">JS Karns</name></author><author><name sortKey="Haley, Bj" uniqKey="Haley B">BJ Haley</name></author><author><name sortKey="Van Kessel, Ja" uniqKey="Van Kessel J">JA Van Kessel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schmieder, R" uniqKey="Schmieder R">R Schmieder</name></author><author><name sortKey="Edwards, R" uniqKey="Edwards R">R Edwards</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bolger, Am" uniqKey="Bolger A">AM Bolger</name></author><author><name sortKey="Lohse, M" uniqKey="Lohse M">M Lohse</name></author><author><name sortKey="Usadel, B" uniqKey="Usadel B">B Usadel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bankevich, A" uniqKey="Bankevich A">A Bankevich</name></author><author><name sortKey="Nurk, S" uniqKey="Nurk S">S Nurk</name></author><author><name sortKey="Antipov, D" uniqKey="Antipov D">D Antipov</name></author><author><name sortKey="Gurevich, Aa" uniqKey="Gurevich A">AA Gurevich</name></author><author><name sortKey="Dvorkin, M" uniqKey="Dvorkin M">M Dvorkin</name></author><author><name sortKey="Kulikov, As" uniqKey="Kulikov A">AS Kulikov</name></author><author><name sortKey="Lesin, Vm" uniqKey="Lesin V">VM Lesin</name></author><author><name sortKey="Nikolenko, Si" uniqKey="Nikolenko S">SI Nikolenko</name></author><author><name sortKey="Pham, S" uniqKey="Pham S">S Pham</name></author><author><name sortKey="Prjibelski, Ad" uniqKey="Prjibelski A">AD Prjibelski</name></author><author><name sortKey="Pyshkin, Av" uniqKey="Pyshkin A">AV Pyshkin</name></author><author><name sortKey="Sirotkin, Av" uniqKey="Sirotkin A">AV Sirotkin</name></author><author><name sortKey="Vyahhi, N" uniqKey="Vyahhi N">N Vyahhi</name></author><author><name sortKey="Tesler, G" uniqKey="Tesler G">G Tesler</name></author><author><name sortKey="Alekseyev, Ma" uniqKey="Alekseyev M">MA Alekseyev</name></author><author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Albert, Mj" uniqKey="Albert M">MJ Albert</name></author><author><name sortKey="Obaid, K" uniqKey="Obaid K">K Obaid</name></author><author><name sortKey="Alfouzan, W" uniqKey="Alfouzan W">W Alfouzan</name></author><author><name sortKey="Sheikh, Ar" uniqKey="Sheikh A">AR Sheikh</name></author><author><name sortKey="Udo, E" uniqKey="Udo E">E Udo</name></author><author><name sortKey="Izumiya, H" uniqKey="Izumiya H">H Izumiya</name></author><author><name sortKey="Bulach, Dm" uniqKey="Bulach D">DM Bulach</name></author><author><name sortKey="Seemann, T" uniqKey="Seemann T">T Seemann</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Katz, Ls" uniqKey="Katz L">LS Katz</name></author><author><name sortKey="Petkau, A" uniqKey="Petkau A">A Petkau</name></author><author><name sortKey="Beaulaurier, J" uniqKey="Beaulaurier J">J Beaulaurier</name></author><author><name sortKey="Tyler, S" uniqKey="Tyler S">S Tyler</name></author><author><name sortKey="Antonova, Es" uniqKey="Antonova E">ES Antonova</name></author><author><name sortKey="Turnsek, Ma" uniqKey="Turnsek M">MA Turnsek</name></author><author><name sortKey="Guo, Y" uniqKey="Guo Y">Y Guo</name></author><author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name></author><author><name sortKey="Paxinos, Ee" uniqKey="Paxinos E">EE Paxinos</name></author><author><name sortKey="Orata, F" uniqKey="Orata F">F Orata</name></author><author><name sortKey="Gladney, Lm" uniqKey="Gladney L">LM Gladney</name></author><author><name sortKey="Stroika, S" uniqKey="Stroika S">S Stroika</name></author><author><name sortKey="Folster, Jp" uniqKey="Folster J">JP Folster</name></author><author><name sortKey="Rowe, L" uniqKey="Rowe L">L Rowe</name></author><author><name sortKey="Freeman, Mm" uniqKey="Freeman M">MM Freeman</name></author><author><name sortKey="Knox, N" uniqKey="Knox N">N Knox</name></author><author><name sortKey="Frace, M" uniqKey="Frace M">M Frace</name></author><author><name sortKey="Boncy, J" uniqKey="Boncy J">J Boncy</name></author><author><name sortKey="Graham, M" uniqKey="Graham M">M Graham</name></author><author><name sortKey="Hammer, Bk" uniqKey="Hammer B">BK Hammer</name></author><author><name sortKey="Boucher, Y" uniqKey="Boucher Y">Y Boucher</name></author><author><name sortKey="Bashir, A" uniqKey="Bashir A">A Bashir</name></author><author><name sortKey="Hanage, Wp" uniqKey="Hanage W">WP Hanage</name></author><author><name sortKey="Van Domselaar, G" uniqKey="Van Domselaar G">G Van 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sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Land, Sj" uniqKey="Land S">SJ Land</name></author><author><name sortKey="Lu, X" uniqKey="Lu X">X Lu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G. Stecher</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D. Peterson</name></author><author><name sortKey="Filipski, A" uniqKey="Filipski A">A. Filipski</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A Stamatakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cummings, Mp" uniqKey="Cummings M">MP Cummings</name></author><author><name sortKey="Neel, Mc" uniqKey="Neel M">MC Neel</name></author><author><name sortKey="Shaw, Kl" uniqKey="Shaw K">KL Shaw</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Pritchard, Jk" uniqKey="Pritchard J">JK Pritchard</name></author><author><name sortKey="Stephens, M" uniqKey="Stephens M">M Stephens</name></author><author><name sortKey="Donnelly, P" uniqKey="Donnelly P">P Donnelly</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Carattoli, A" uniqKey="Carattoli A">A Carattoli</name></author><author><name sortKey="Zankari, E" uniqKey="Zankari E">E Zankari</name></author><author><name sortKey="Garcia Fernandez, A" uniqKey="Garcia Fernandez A">A García-Fernández</name></author><author><name sortKey="Voldby Larsen, M" uniqKey="Voldby Larsen M">M Voldby Larsen</name></author><author><name sortKey="Lund, O" uniqKey="Lund O">O Lund</name></author><author><name sortKey="Villa, L" uniqKey="Villa L">L Villa</name></author><author><name sortKey="Aarestrup, F" uniqKey="Aarestrup F">F Aarestrup</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dhillon, Bk" uniqKey="Dhillon B">BK Dhillon</name></author><author><name sortKey="Laird, Mr" uniqKey="Laird M">MR Laird</name></author><author><name sortKey="Shay, Ja" uniqKey="Shay J">JA Shay</name></author><author><name sortKey="Winsor, Gl" uniqKey="Winsor G">GL Winsor</name></author><author><name sortKey="Lo, R" uniqKey="Lo R">R Lo</name></author><author><name sortKey="Nizam, F" uniqKey="Nizam F">F Nizam</name></author><author><name sortKey="Pereira, Sk" uniqKey="Pereira S">SK Pereira</name></author><author><name sortKey="Waglechner, N" uniqKey="Waglechner N">N Waglechner</name></author><author><name sortKey="Mcarthur, Ag" uniqKey="Mcarthur A">AG McArthur</name></author><author><name sortKey="Langille, Mg" uniqKey="Langille M">MG Langille</name></author><author><name sortKey="Brinkman, Fs" uniqKey="Brinkman F">FS Brinkman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wells, Sj" uniqKey="Wells S">SJ Wells</name></author><author><name sortKey="Fedorka Cray, Pj" uniqKey="Fedorka Cray P">PJ Fedorka-Cray</name></author><author><name sortKey="Dargatz, Da" uniqKey="Dargatz D">DA Dargatz</name></author><author><name sortKey="Ferris, K" uniqKey="Ferris K">K Ferris</name></author><author><name sortKey="Green, A" uniqKey="Green A">A Green</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blau, Dm" uniqKey="Blau D">DM Blau</name></author><author><name sortKey="Mccluskey, Bj" uniqKey="Mccluskey B">BJ McCluskey</name></author><author><name sortKey="Ladely, Sr" uniqKey="Ladely S">SR Ladely</name></author><author><name sortKey="Dargatz, Da" uniqKey="Dargatz D">DA Dargatz</name></author><author><name sortKey="Fedorka Cray, Pj" uniqKey="Fedorka Cray P">PJ Fedorka-Cray</name></author><author><name sortKey="Ferris, Ke" uniqKey="Ferris K">KE Ferris</name></author><author><name sortKey="Headrick, Ml" uniqKey="Headrick M">ML Headrick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Le Hello, S" uniqKey="Le Hello S">S Le Hello</name></author><author><name sortKey="Weill, Fx" uniqKey="Weill F">FX Weill</name></author><author><name sortKey="Guibert, V" uniqKey="Guibert V">V Guibert</name></author><author><name sortKey="Praud, K" uniqKey="Praud K">K Praud</name></author><author><name sortKey="Cloeckaert, A" uniqKey="Cloeckaert A">A Cloeckaert</name></author><author><name sortKey="Doublet, B" uniqKey="Doublet B">B Doublet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baucheron, S" uniqKey="Baucheron S">S Baucheron</name></author><author><name sortKey="Le Hello, S" uniqKey="Le Hello S">S Le Hello</name></author><author><name sortKey="Doublet, B" uniqKey="Doublet B">B Doublet</name></author><author><name sortKey="Giraud, E" uniqKey="Giraud E">E Giraud</name></author><author><name sortKey="Weill, Fx" uniqKey="Weill F">FX Weill</name></author><author><name sortKey="Cloeckaert, A" uniqKey="Cloeckaert A">A Cloeckaert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Achtman, M" uniqKey="Achtman M">M Achtman</name></author><author><name sortKey="Wain, J" uniqKey="Wain J">J Wain</name></author><author><name sortKey="Weill, Fx" uniqKey="Weill F">FX Weill</name></author><author><name sortKey="Nair, S" uniqKey="Nair S">S Nair</name></author><author><name sortKey="Zhou, Z" uniqKey="Zhou Z">Z Zhou</name></author><author><name sortKey="Sangal, V" uniqKey="Sangal V">V Sangal</name></author><author><name sortKey="Krauland, Mg" uniqKey="Krauland M">MG Krauland</name></author><author><name sortKey="Hale, Jl" uniqKey="Hale J">JL Hale</name></author><author><name sortKey="Harbottle, H" uniqKey="Harbottle H">H Harbottle</name></author><author><name sortKey="Uebeck, A" uniqKey="Uebeck A">A Uebeck</name></author><author><name sortKey="Dougan, J" uniqKey="Dougan J">J Dougan</name></author><author><name sortKey="Harrison, Lh" uniqKey="Harrison L">LH Harrison</name></author><author><name sortKey="Brisse, S" uniqKey="Brisse S">S Brisse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniels, Mj" uniqKey="Daniels M">MJ Daniels</name></author><author><name sortKey="Hutchings, Mr" uniqKey="Hutchings M">MR Hutchings</name></author><author><name sortKey="Greig, A" uniqKey="Greig A">A Greig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Callaway, Tr" 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Chang</name></author><author><name sortKey="Chuang, Yc" uniqKey="Chuang Y">YC Chuang</name></author><author><name sortKey="Jeang, Cl" uniqKey="Jeang C">CL Jeang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baida, Ge" uniqKey="Baida G">GE Baida</name></author><author><name sortKey="Kuzmin, Np" uniqKey="Kuzmin N">NP Kuzmin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Tj" uniqKey="Johnson T">TJ Johnson</name></author><author><name sortKey="Thorsness, Jl" uniqKey="Thorsness J">JL Thorsness</name></author><author><name sortKey="Anderson, C" uniqKey="Anderson C">C Anderson</name></author><author><name sortKey="Lynne, A" uniqKey="Lynne A">A Lynne</name></author><author><name sortKey="Foley, S" uniqKey="Foley S">S Foley</name></author><author><name sortKey="Han, J" uniqKey="Han J">J Han</name></author><author><name sortKey="Fricke, Wf" uniqKey="Fricke W">WF Fricke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levings, Rs" uniqKey="Levings R">RS Levings</name></author><author><name sortKey="Lightfoot, D" uniqKey="Lightfoot D">D Lightfoot</name></author><author><name sortKey="Partridge, Sr" uniqKey="Partridge S">SR Partridge</name></author><author><name sortKey="Hall, Rm" uniqKey="Hall R">RM Hall</name></author><author><name sortKey="Djordjevic, Sp" uniqKey="Djordjevic S">SP Djordjevic</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boyd, Da" uniqKey="Boyd D">DA Boyd</name></author><author><name sortKey="Shi, X" uniqKey="Shi X">X Shi</name></author><author><name sortKey="Hu, Qh" uniqKey="Hu Q">QH Hu</name></author><author><name sortKey="Ng, Lk" uniqKey="Ng L">LK Ng</name></author><author><name sortKey="Doublet, B" uniqKey="Doublet B">B Doublet</name></author><author><name sortKey="Cloeckaert, A" uniqKey="Cloeckaert A">A Cloeckaert</name></author><author><name sortKey="Mulvey, Mr" uniqKey="Mulvey M">MR Mulvey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hamidian, M" uniqKey="Hamidian M">M Hamidian</name></author><author><name sortKey="Holt, Ke" uniqKey="Holt K">KE Holt</name></author><author><name sortKey="Hall, Rm" uniqKey="Hall R">RM Hall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morgan, E" uniqKey="Morgan E">E Morgan</name></author><author><name sortKey="Campbell, Jd" uniqKey="Campbell J">JD Campbell</name></author><author><name sortKey="Rowe, Sc" uniqKey="Rowe S">SC Rowe</name></author><author><name sortKey="Bispham, J" uniqKey="Bispham J">J Bispham</name></author><author><name sortKey="Stevens, Mp" uniqKey="Stevens M">MP Stevens</name></author><author><name sortKey="Bowen, Aj" uniqKey="Bowen A">AJ Bowen</name></author><author><name sortKey="Barrow, Pa" uniqKey="Barrow P">PA Barrow</name></author><author><name sortKey="Maskell, Dj" uniqKey="Maskell D">DJ Maskell</name></author><author><name sortKey="Wallis, Ts" uniqKey="Wallis T">TS Wallis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Latasa, C" uniqKey="Latasa C">C Latasa</name></author><author><name sortKey="Roux, A" uniqKey="Roux A">A Roux</name></author><author><name sortKey="Toledo Arana, A" uniqKey="Toledo Arana A">A Toledo-Arana</name></author><author><name sortKey="Ghigo, Jm" uniqKey="Ghigo J">JM Ghigo</name></author><author><name sortKey="Gamazo, C" uniqKey="Gamazo C">C Gamazo</name></author><author><name sortKey="Penades, Jr" uniqKey="Penades J">JR Penadés</name></author><author><name sortKey="Lasa, I" uniqKey="Lasa I">I Lasa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gal Mor, O" uniqKey="Gal Mor O">O Gal-Mor</name></author><author><name sortKey="Gibson, Dl" uniqKey="Gibson D">DL Gibson</name></author><author><name sortKey="Baluta, D" uniqKey="Baluta D">D Baluta</name></author><author><name 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Bäumler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hensel, M" uniqKey="Hensel M">M Hensel</name></author><author><name sortKey="Shea, Je" uniqKey="Shea J">JE Shea</name></author><author><name sortKey="Waterman, Sr" uniqKey="Waterman S">SR Waterman</name></author><author><name sortKey="Mundy, R" uniqKey="Mundy R">R Mundy</name></author><author><name sortKey="Nikolaus, T" uniqKey="Nikolaus T">T Nikolaus</name></author><author><name sortKey="Banks, G" uniqKey="Banks G">G Banks</name></author><author><name sortKey="Vazquez Torres, A" uniqKey="Vazquez Torres A">A Vazquez-Torres</name></author><author><name sortKey="Gleeson, C" uniqKey="Gleeson C">C Gleeson</name></author><author><name sortKey="Fang, Fc" uniqKey="Fang F">FC Fang</name></author><author><name sortKey="Holden, Dw" uniqKey="Holden D">DW Holden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author><author><name sortKey="Santos, Rl" uniqKey="Santos R">RL Santos</name></author><author><name sortKey="Tsolis, Rm" uniqKey="Tsolis R">RM Tsolis</name></author><author><name sortKey="Stender, S" uniqKey="Stender S">S Stender</name></author><author><name sortKey="Hardt, Wd" uniqKey="Hardt W">WD Hardt</name></author><author><name sortKey="B Umler, Aj" uniqKey="B Umler A">AJ Bäumler</name></author><author><name sortKey="Adams, Lg" uniqKey="Adams L">LG Adams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcghie, Ej" uniqKey="Mcghie E">EJ McGhie</name></author><author><name sortKey="Brawn, Lc" uniqKey="Brawn L">LC Brawn</name></author><author><name sortKey="Hume, Pj" uniqKey="Hume P">PJ Hume</name></author><author><name sortKey="Humphreys, D" uniqKey="Humphreys D">D Humphreys</name></author><author><name sortKey="Koronakis, V" uniqKey="Koronakis V">V Koronakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Severi, E" uniqKey="Severi E">E Severi</name></author><author><name sortKey="Hood, Dw" uniqKey="Hood D">DW Hood</name></author><author><name sortKey="Thomas, Gh" uniqKey="Thomas G">GH Thomas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Almagro Moreno, S" uniqKey="Almagro Moreno S">S Almagro-Moreno</name></author><author><name sortKey="Boyd, Ef" uniqKey="Boyd E">EF Boyd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Almagro Moreno, S" uniqKey="Almagro Moreno S">S Almagro-Moreno</name></author><author><name sortKey="Boyd, Ef" uniqKey="Boyd E">EF Boyd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kroger, C" uniqKey="Kroger C">C Kröger</name></author><author><name sortKey="Fuchs, Tm" uniqKey="Fuchs T">TM Fuchs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chaudhuri, Rr" uniqKey="Chaudhuri R">RR Chaudhuri</name></author><author><name sortKey="Morgan, E" uniqKey="Morgan E">E Morgan</name></author><author><name sortKey="Peters, Se" uniqKey="Peters S">SE Peters</name></author><author><name sortKey="Pleasance, Sj" uniqKey="Pleasance S">SJ Pleasance</name></author><author><name sortKey="Hudson, Dl" uniqKey="Hudson D">DL Hudson</name></author><author><name sortKey="Davies, Hm" uniqKey="Davies H">HM Davies</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dobrindt, U" uniqKey="Dobrindt U">U Dobrindt</name></author><author><name sortKey="Hochhut, B" uniqKey="Hochhut B">B Hochhut</name></author><author><name sortKey="Hentschel, U" uniqKey="Hentschel U">U Hentschel</name></author><author><name sortKey="Hacker, J" uniqKey="Hacker J">J Hacker</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27695032</article-id><article-id pub-id-type="pmc">5047448</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0161225</article-id><article-id pub-id-type="publisher-id">PONE-D-15-43222</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject><subj-group><subject>Biological Databases</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Birds</subject><subj-group><subject>Fowl</subject><subj-group><subject>Gamefowl</subject><subj-group><subject>Chickens</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Birds</subject><subj-group><subject>Poultry</subject><subj-group><subject>Chickens</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Agriculture</subject><subj-group><subject>Livestock</subject><subj-group><subject>Poultry</subject><subj-group><subject>Chickens</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Birds</subject><subj-group><subject>Poultry</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Agriculture</subject><subj-group><subject>Livestock</subject><subj-group><subject>Poultry</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Molecular Biology Assays and Analysis Techniques</subject><subj-group><subject>Phylogenetic Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Molecular Biology Assays and Analysis Techniques</subject><subj-group><subject>Phylogenetic Analysis</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>DNA-binding proteins</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>People and places</subject><subj-group><subject>Geographical locations</subject><subj-group><subject>North America</subject><subj-group><subject>United States</subject><subj-group><subject>Kentucky</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>People and places</subject><subj-group><subject>Geographical locations</subject><subj-group><subject>North America</subject><subj-group><subject>United States</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Infectious Diseases</subject><subj-group><subject>Bacterial Diseases</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Enterica</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Medical Microbiology</subject><subj-group><subject>Microbial Pathogens</subject><subj-group><subject>Bacterial Pathogens</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Enterica</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Medicine and Health Sciences</subject><subj-group><subject>Pathology and Laboratory Medicine</subject><subj-group><subject>Pathogens</subject><subj-group><subject>Microbial Pathogens</subject><subj-group><subject>Bacterial Pathogens</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Enterica</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Bacteria</subject><subj-group><subject>Enterobacteriaceae</subject><subj-group><subject>Salmonella</subject><subj-group><subject>Salmonella Enterica</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genomic and Evolutionary Analysis of Two <italic>Salmonella enterica</italic> Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America</article-title><alt-title alt-title-type="running-head">Genomic Analysis from <italic>Salmonella</italic> Kentucky Recovered from Cattle and Poultry</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Haley</surname><given-names>Bradd J.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Seon Woo</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Pettengill</surname><given-names>James</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Luo</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Karns</surname><given-names>Jeffrey S.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Van Kessel</surname><given-names>Jo Ann S.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Cloeckaert</surname><given-names>Axel</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Institut National de la Recherche Agronomique, FRANCE</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p><list list-type="simple"><list-item><p><bold>Conceived and designed the experiments:</bold> BJH JP YL JSK JVK.</p></list-item><list-item><p><bold>Performed the experiments:</bold> BJH SWK JP YL.</p></list-item><list-item><p><bold>Analyzed the data:</bold> BJH SWK JP JSK JVK.</p></list-item><list-item><p><bold>Contributed reagents/materials/analysis tools:</bold> BJH JP YL JSK JVK.</p></list-item><list-item><p><bold>Wrote the paper:</bold> BJH JP JSK JVK.</p></list-item></list></p></fn><corresp id="cor001">* E-mail: <email>joann.vankessel@ars.usda.gov</email></corresp></author-notes><pub-date pub-type="epub"><day>3</day><month>10</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>10</issue><elocation-id>e0161225</elocation-id><history><date date-type="received"><day>30</day><month>9</month><year>2015</year></date><date date-type="accepted"><day>2</day><month>8</month><year>2016</year></date></history><permissions><license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/publicdomain/zero/1.0/">Creative Commons CC0</ext-link> public domain dedication.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pone.0161225.pdf"></self-uri><abstract><p><italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated <italic>S</italic>. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other <italic>Salmonella</italic> serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of <italic>S</italic>. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.</p></abstract><funding-group><funding-statement>This project was supported by internal USDA/ARS research funding.</funding-statement></funding-group><counts><fig-count count="12"></fig-count><table-count count="7"></table-count><page-count count="36"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>Accession numbers for genomic data in NCBI are available in the relevant Supporting Information file.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>Accession numbers for genomic data in NCBI are available in the relevant Supporting Information file.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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