{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T04:44:30Z","timestamp":1789101870167,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012992","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000}}],"reference-count":93,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T00:00:00Z","timestamp":1742169600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Program on Key Research Project of China","award":["2022YFC2604201"],"award-info":[{"award-number":["2022YFC2604201"]}]},{"name":"European Union's Horizon 2020 Research and Innovation Programme","award":["861917 \u2013 SAFFI"],"award-info":[{"award-number":["861917 \u2013 SAFFI"]}]},{"name":"Zhejiang Provincial Key R&D Program of China","award":["2023C03045"],"award-info":[{"award-number":["2023C03045"]}]},{"name":"Zhejiang Provincial Natural Science Foundation of China","award":["LZ24C180002"],"award-info":[{"award-number":["LZ24C180002"]}]},{"name":"Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City","award":["2021JJLH0083"],"award-info":[{"award-number":["2021JJLH0083"]}]},{"name":"Henan Provincial Science and Technology Research and Development Program","award":["252102110032"],"award-info":[{"award-number":["252102110032"]}]},{"name":"Scientific Research Fund of Zhejiang Provincial Education Department","award":["Y202250872"],"award-info":[{"award-number":["Y202250872"]}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p><jats:italic>Salmonella<\/jats:italic>, a significant threat to public safety, inflicts substantial economic losses on the poultry industry. The unique \u201cparental feeding\u201d breeding model of pigeon farms, against the \u201call-in &amp; all-out\u201d biosecurity strategy, makes them susceptible to <jats:italic>Salmonella<\/jats:italic> infections and subsequent outbreaks of pigeon paratyphoid. This study initially studied three pigeon paratyphoid outbreak incidents in Henan, China, in which 53 strains of pigeon-origin <jats:italic>Salmonella<\/jats:italic> Typhimurium (STM) were identified. Whole-genome sequencing (WGS) and antimicrobial-resistant profile analysis revealed that the three outbreaks were caused by distinct STM clones (ST128-DT2, ST19-DT99). Global phylogenetic analysis suggested that the United States is a possible origin, indicating a risk of intercontinental transmission via pigeon eggs. Further bacterial virulence and invasion assays, including <jats:italic>in vitro<\/jats:italic> and <jats:italic>in vivo<\/jats:italic> assays, revealed that pigeon-host-adaptive STM, compared to broad-host-range STM, carried fewer resistance genes, exhibited higher invasion indices and pseudogene levels, displayed a non-rdar (red dry and rough) phenotype, and had strong biofilm formation capability. Additionally, they showed reduced virulence and invasiveness in mice but a pigeon-adaptive feature in cogent models. The collective results support the host adaptation for pigeons among DT2 and DT99 phage-type isolates.<\/jats:p>","DOI":"10.1371\/journal.ppat.1012992","type":"journal-article","created":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T17:30:47Z","timestamp":1742232647000},"page":"e1012992","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["A genomic and phenotypic investigation of pigeon-adaptive Salmonella"],"prefix":"10.1371","volume":"21","author":[{"given":"Zining","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zenghai","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianzhe","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenghao","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyang","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenghu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linlin","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingying","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6787-0794","authenticated-orcid":true,"given":"Min","family":"Yue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,3,17]]},"reference":[{"key":"ppat.1012992.ref001","doi-asserted-by":"crossref","first-page":"985","DOI":"10.3389\/fmicb.2019.00985","article-title":"Antibiotic resistance in salmonella typhimurium isolates recovered from the food chain through national antimicrobial resistance monitoring system between 1996 and 2016","volume":"10","author":"X Wang","year":"2019","journal-title":"Front Microbiol"},{"key":"ppat.1012992.ref002","doi-asserted-by":"crossref","first-page":"753085","DOI":"10.3389\/fmed.2022.753085","article-title":"Genomic investigation reveals a community typhoid outbreak caused by contaminated drinking water in China, 2016","volume":"9","author":"B Hu","year":"2022","journal-title":"Front Med (Lausanne)"},{"issue":"12","key":"ppat.1012992.ref003","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1016\/S1473-3099(19)30418-9","article-title":"The global burden of non-typhoidal salmonella invasive disease: a systematic analysis for the Global Burden of Disease Study 2017","volume":"19","author":"GBD 2017 Non-Typhoidal Salmonella Invasive Disease Collaborators","year":"2019","journal-title":"Lancet Infect Dis"},{"issue":"10369","key":"ppat.1012992.ref004","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1016\/S0140-6736(22)02185-7","article-title":"Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019","volume":"400","author":"GBD 2019 Antimicrobial Resistance Collaborators","year":"2022","journal-title":"Lancet"},{"issue":"1","key":"ppat.1012992.ref005","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid1701.P11101","article-title":"Foodborne illness acquired in the United States--major pathogens","volume":"17","author":"E Scallan","year":"2011","journal-title":"Emerg Infect Dis"},{"issue":"2","key":"ppat.1012992.ref006","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.it.2014.12.003","article-title":"Exploiting host immunity: the Salmonella paradigm","volume":"36","author":"J Behnsen","year":"2015","journal-title":"Trends Immunol"},{"issue":"2","key":"ppat.1012992.ref007","doi-asserted-by":"crossref","first-page":"e14417","DOI":"10.1111\/1751-7915.14417","article-title":"Climate change affects the spread of typhoid pathogens","volume":"17","author":"C Jia","year":"2024","journal-title":"Microb Biotechnol"},{"issue":"1","key":"ppat.1012992.ref008","doi-asserted-by":"crossref","first-page":"2372364","DOI":"10.1080\/22221751.2024.2372364","article-title":"Nationwide trends and features of human salmonellosis outbreaks in China","volume":"13","author":"Z Wang","year":"2024","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"ppat.1012992.ref009","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/s41597-024-03085-7","article-title":"Salmonellosis outbreak archive in China: data collection and assembly","volume":"11","author":"Z Wang","year":"2024","journal-title":"Sci Data"},{"key":"ppat.1012992.ref010","doi-asserted-by":"crossref","first-page":"180227","DOI":"10.1038\/sdata.2018.227","article-title":"Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010","volume":"5","author":"M Gilbert","year":"2018","journal-title":"Sci Data"},{"issue":"3","key":"ppat.1012992.ref011","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1111\/jpn.12869","article-title":"Expression analyses of candidate genes related to meat quality traits in squabs from two breeds of meat-type pigeon","volume":"102","author":"M Ye","year":"2018","journal-title":"J Anim Physiol Anim Nutr (Berl)"},{"issue":"7","key":"ppat.1012992.ref012","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1534\/g3.116.029793","article-title":"Transcriptomic analysis identifies candidate genes related to intramuscular fat deposition and fatty acid composition in the breast muscle of Squabs (Columba)","volume":"6","author":"M Ye","year":"2016","journal-title":"G3 (Bethesda)"},{"issue":"4","key":"ppat.1012992.ref013","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1111\/tbed.13891","article-title":"Can domestic pigeon be a potential carrier of zoonotic Salmonella?","volume":"68","author":"E Kaczorek-\u0141ukowska","year":"2021","journal-title":"Transbound Emerg Dis"},{"key":"ppat.1012992.ref014","doi-asserted-by":"crossref","first-page":"1390732","DOI":"10.3389\/fvets.2024.1390732","article-title":"Editorial: Zoonotic bacteria: genomic evolution, antimicrobial resistance, pathogenicity, and prevention strategies","volume":"11","author":"A Ed-Dra","year":"2024","journal-title":"Front Vet Sci"},{"issue":"8","key":"ppat.1012992.ref015","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1089\/fpd.2021.29015.int","article-title":"Impacts of microbial food safety in China and beyond","volume":"18","author":"M Yue","year":"2021","journal-title":"Foodborne Pathog Dis"},{"issue":"5","key":"ppat.1012992.ref016","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1089\/fpd.2012.1347","article-title":"Salmonella enterica isolated from pigeon (Columba livia) in Egypt","volume":"10","author":"KM Osman","year":"2013","journal-title":"Foodborne Pathog Dis"},{"issue":"24","key":"ppat.1012992.ref017","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1136\/vr.158.24.817","article-title":"Isolation of different serovars of Salmonella enterica from wild birds in Great Britain between 1995 and 2003","volume":"158","author":"TW Pennycott","year":"2006","journal-title":"Vet Rec"},{"issue":"4","key":"ppat.1012992.ref018","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1638\/2008-0166.1","article-title":"Prevalence of Salmonella spp. antibodies to Toxoplasma gondii, and Newcastle disease virus in feral pigeons (Columba livia) in the city of Jaboticabal, Brazil","volume":"41","author":"E de Sousa","year":"2010","journal-title":"J Zoo Wildl Med"},{"issue":"4","key":"ppat.1012992.ref019","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1089\/vbz.2011.0943","article-title":"Occurrence of enteropathogenic bacteria in urban pigeons (Columba livia) in Italy","volume":"14","author":"A Gargiulo","year":"2014","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"11","key":"ppat.1012992.ref020","doi-asserted-by":"crossref","first-page":"5600","DOI":"10.1128\/AEM.68.11.5600-5606.2002","article-title":"Molecular epidemiology of Salmonella enterica serovar typhimurium isolates determined by pulsed-field gel electrophoresis: comparison of isolates from avian wildlife, domestic animals, and the environment in Norway","volume":"68","author":"T Refsum","year":"2002","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"ppat.1012992.ref021","doi-asserted-by":"crossref","first-page":"e0155366","DOI":"10.1371\/journal.pone.0155366","article-title":"House sparrows do not constitute a significant salmonella typhimurium reservoir across urban gradients in Flanders, Belgium","volume":"11","author":"LO Rouffaer","year":"2016","journal-title":"PLoS One"},{"issue":"4","key":"ppat.1012992.ref022","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1007\/s10393-013-0868-9","article-title":"Causes of morbidity and mortality in free-living birds in an urban environment in Germany","volume":"10","author":"J Stenkat","year":"2013","journal-title":"Ecohealth"},{"issue":"5","key":"ppat.1012992.ref023","doi-asserted-by":"crossref","first-page":"896","DOI":"10.2460\/ajvr.1981.42.05.896","article-title":"Biotyping of Salmonella typhimurium strains isolated from animals and birds in northern Japan","volume":"42","author":"N Ishiguro","year":"1981","journal-title":"Am J Vet Res"},{"issue":"1","key":"ppat.1012992.ref024","doi-asserted-by":"crossref","first-page":"169","DOI":"10.2478\/pjvs-2014-0023","article-title":"Antimicrobial resistance in bacteria isolated from pigeons in Poland","volume":"17","author":"T Stenzel","year":"2014","journal-title":"Pol J Vet Sci"},{"issue":"2","key":"ppat.1012992.ref025","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1128\/AEM.03223-13","article-title":"Prevalence and fimbrial genotype distribution of poultry Salmonella isolates in China (2006 to 2012)","volume":"80","author":"J Gong","year":"2014","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"ppat.1012992.ref026","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1128\/MMBR.00015-13","article-title":"Salmonella pathogenicity and host adaptation in chicken-associated serovars","volume":"77","author":"SL Foley","year":"2013","journal-title":"Microbiol Mol Biol Rev"},{"issue":"5","key":"ppat.1012992.ref027","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1046\/j.1365-2958.2000.01907.x","article-title":"Host adaptation and the emergence of infectious disease: the Salmonella paradigm","volume":"36","author":"RA Kingsley","year":"2000","journal-title":"Mol Microbiol"},{"issue":"5","key":"ppat.1012992.ref028","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1128\/IAI.70.5.2249-2255.2002","article-title":"Salmonella enterica serotype Typhimurium and its host-adapted variants","volume":"70","author":"W Rabsch","year":"2002","journal-title":"Infect Immun"},{"issue":"3","key":"ppat.1012992.ref029","doi-asserted-by":"crossref","first-page":"e1009451","DOI":"10.1371\/journal.ppat.1009451","article-title":"Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host","volume":"17","author":"E Cohen","year":"2021","journal-title":"PLoS Pathog"},{"issue":"6","key":"ppat.1012992.ref030","doi-asserted-by":"crossref","first-page":"e0184722","DOI":"10.1128\/jcm.01847-22","article-title":"Whole-genome subtyping reveals population structure and host adaptation of salmonella typhimurium from wild birds","volume":"61","author":"Y Fu","year":"2023","journal-title":"J Clin Microbiol"},{"key":"ppat.1012992.ref031","doi-asserted-by":"crossref","first-page":"8754","DOI":"10.1038\/ncomms9754","article-title":"Allelic variation contributes to bacterial host specificity","volume":"6","author":"M Yue","year":"2015","journal-title":"Nat Commun"},{"issue":"5","key":"ppat.1012992.ref032","doi-asserted-by":"crossref","first-page":"e00565","DOI":"10.1128\/mBio.00565-13","article-title":"Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar","volume":"4","author":"RA Kingsley","year":"2013","journal-title":"mBio"},{"issue":"9","key":"ppat.1012992.ref033","doi-asserted-by":"crossref","first-page":"5158","DOI":"10.1093\/nar\/gkac302","article-title":"\u201cPseudo-pseudogenes\u201d in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica","volume":"50","author":"Y Feng","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"9835","key":"ppat.1012992.ref034","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1016\/S0140-6736(11)61752-2","article-title":"Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa","volume":"379","author":"NA Feasey","year":"2012","journal-title":"Lancet"},{"issue":"1","key":"ppat.1012992.ref035","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1002\/mlf2.12117","article-title":"Genomic investigation and nationwide tracking of pediatric invasive nontyphoidal Salmonella in China","volume":"3","author":"Y Ke","year":"2024","journal-title":"mLife"},{"key":"ppat.1012992.ref036","doi-asserted-by":"crossref","first-page":"1245416","DOI":"10.3389\/fmicb.2023.1245416","article-title":"Genomic characterization of dengue virus serotype 2 during dengue outbreak and endemics in Hangzhou, Zhejiang (2017-2019)","volume":"14","author":"H Sun","year":"2023","journal-title":"Front Microbiol"},{"key":"ppat.1012992.ref037","doi-asserted-by":"crossref","first-page":"110105","DOI":"10.1016\/j.ijfoodmicro.2023.110105","article-title":"Infant food production environments: A potential reservoir for vancomycin-resistant enterococci non-nosocomial infections","volume":"389","author":"Z Wang","year":"2023","journal-title":"Int J Food Microbiol"},{"issue":"10","key":"ppat.1012992.ref038","doi-asserted-by":"crossref","first-page":"nwad228","DOI":"10.1093\/nsr\/nwad228","article-title":"Genome degradation promotes Salmonella pathoadaptation by remodeling fimbriae-mediated proinflammatory response","volume":"10","author":"X Zhou","year":"2023","journal-title":"Natl Sci Rev"},{"key":"ppat.1012992.ref039","doi-asserted-by":"crossref","first-page":"110198","DOI":"10.1016\/j.foodres.2021.110198","article-title":"Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China","volume":"142","author":"Y Liu","year":"2021","journal-title":"Food Res Int"},{"key":"ppat.1012992.ref040","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.meegid.2014.05.013","article-title":"Salmonella Typhi shdA: pseudogene or allelic variant?","volume":"26","author":"IM Urrutia","year":"2014","journal-title":"Infect Genet Evol"},{"issue":"7","key":"ppat.1012992.ref041","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.tim.2010.04.002","article-title":"Impact of recombination on bacterial evolution","volume":"18","author":"X Didelot","year":"2010","journal-title":"Trends Microbiol"},{"key":"ppat.1012992.ref042","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.mib.2014.11.004","article-title":"The application of genomics to tracing bacterial pathogen transmission","volume":"23","author":"NJ Croucher","year":"2015","journal-title":"Curr Opin Microbiol"},{"issue":"12","key":"ppat.1012992.ref043","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1101\/gr.091017.109","article-title":"Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype","volume":"19","author":"RA Kingsley","year":"2009","journal-title":"Genome Res"},{"issue":"12","key":"ppat.1012992.ref044","doi-asserted-by":"crossref","first-page":"7338","DOI":"10.1128\/IAI.72.12.7338-7341.2004","article-title":"Pigeon-associated strains of Salmonella enterica serovar Typhimurium phage type DT2 have genomic rearrangements at rRNA operons","volume":"72","author":"RA Helm","year":"2004","journal-title":"Infect Immun"},{"issue":"6","key":"ppat.1012992.ref045","doi-asserted-by":"crossref","first-page":"e0088323","DOI":"10.1128\/msystems.00883-23","article-title":"Mobilome-driven partitions of the resistome in Salmonella","volume":"8","author":"C Jia","year":"2023","journal-title":"mSystems"},{"issue":"1","key":"ppat.1012992.ref046","doi-asserted-by":"crossref","first-page":"104646","DOI":"10.1016\/j.psj.2024.104646","article-title":"Genomic and virulent characterization of a duck-associated Salmonella serovar Potsdam from China","volume":"104","author":"H An","year":"2025","journal-title":"Poult Sci"},{"issue":"3","key":"ppat.1012992.ref047","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1128\/AAC.00575-07","article-title":"Induction of the carrier state in pigeons infected with Salmonella enterica subspecies enterica serovar typhimurium PT99 by treatment with florfenicol: a matter of pharmacokinetics","volume":"52","author":"F Pasmans","year":"2008","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"ppat.1012992.ref048","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1016\/j.cvex.2009.07.001","article-title":"Bacterial and parasitic diseases of Columbiformes","volume":"12","author":"R Harlin","year":"2009","journal-title":"Vet Clin North Am Exot Anim Pract"},{"issue":"5","key":"ppat.1012992.ref049","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1080\/03079457.2020.1845300","article-title":"New strategies to prevent and control avian pathogenic Escherichia coli (APEC)","volume":"50","author":"H Christensen","year":"2021","journal-title":"Avian Pathol"},{"key":"ppat.1012992.ref050","doi-asserted-by":"crossref","first-page":"105715","DOI":"10.1016\/j.envint.2020.105715","article-title":"Contaminated in-house environment contributes to the persistence and transmission of NDM-producing bacteria in a Chinese poultry farm","volume":"139","author":"R Zhai","year":"2020","journal-title":"Environ Int"},{"issue":"7","key":"ppat.1012992.ref051","doi-asserted-by":"crossref","first-page":"e0036224","DOI":"10.1128\/msphere.00362-24","article-title":"Integrated OMICs approach reveals energy metabolism pathway is vital for Salmonella Pullorum survival within the egg white","volume":"9","author":"X Kang","year":"2024","journal-title":"mSphere"},{"key":"ppat.1012992.ref052","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1186\/1471-2164-14-718","article-title":"Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types","volume":"14","author":"S Pang","year":"2013","journal-title":"BMC Genomics"},{"issue":"1","key":"ppat.1012992.ref053","first-page":"e000285","article-title":"Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont","volume":"6","author":"I Goodhead","year":"2020","journal-title":"Microb Genom"},{"issue":"3","key":"ppat.1012992.ref054","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1073\/pnas.1416707112","article-title":"Patterns of genome evolution that have accompanied host adaptation in Salmonella","volume":"112","author":"GC Langridge","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"ppat.1012992.ref055","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1093\/cid\/ciac035","article-title":"Invasive Non-typhoidal Salmonella (iNTS) infections","volume":"75","author":"J Fierer","year":"2022","journal-title":"Clin Infect Dis"},{"issue":"1","key":"ppat.1012992.ref056","doi-asserted-by":"crossref","DOI":"10.1186\/s44149-024-00145-8","article-title":"A dynamic platform for global pullorum disease and fowl typhoid","volume":"4","author":"X Kang","year":"2024","journal-title":"Animal Diseases"},{"issue":"1","key":"ppat.1012992.ref057","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/01652176.2025.2454473","article-title":"Developing a novel TaqMan qPCR assay for optimizing Salmonella Pullorum detection in chickens","volume":"45","author":"H Wang","year":"2025","journal-title":"Vet Q"},{"key":"ppat.1012992.ref058","doi-asserted-by":"crossref","first-page":"964823","DOI":"10.3389\/fmicb.2022.964823","article-title":"Prevalence and antimicrobial-resistant characterization of Bacillus cereus isolated from ready-to-eat rice products in Eastern China","volume":"13","author":"J Chen","year":"2022","journal-title":"Front Microbiol"},{"issue":"1","key":"ppat.1012992.ref059","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1080\/22221751.2020.1733439","article-title":"Emerging colistin resistance in Salmonella enterica serovar Newport isolates from human infections","volume":"9","author":"M Elbediwi","year":"2020","journal-title":"Emerg Microbes Infect"},{"issue":"10","key":"ppat.1012992.ref060","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.3390\/antibiotics10101156","article-title":"Antimicrobial resistance profiles and genetic typing of salmonella serovars from chicken embryos in China","volume":"10","author":"Y Xu","year":"2021","journal-title":"Antibiotics (Basel)"},{"issue":"5","key":"ppat.1012992.ref061","doi-asserted-by":"crossref","first-page":"625","DOI":"10.3390\/antibiotics11050625","article-title":"Prevalence and genomic investigation of multidrug-resistant salmonella isolates from companion animals in Hangzhou, China","volume":"11","author":"L Teng","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"ppat.1012992.ref062","doi-asserted-by":"crossref","first-page":"172","DOI":"10.3389\/fpubh.2019.00172","article-title":"Whole genome sequencing: bridging one-health surveillance of foodborne diseases","volume":"7","author":"P Gerner-Smidt","year":"2019","journal-title":"Front Public Health"},{"key":"ppat.1012992.ref063","doi-asserted-by":"crossref","first-page":"684400","DOI":"10.3389\/fmicb.2021.684400","article-title":"Genomic investigation of antimicrobial-resistant salmonella enterica isolates from dead chick embryos in China","volume":"12","author":"M Elbediwi","year":"2021","journal-title":"Front Microbiol"},{"key":"ppat.1012992.ref064","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.3389\/fmicb.2019.01513","article-title":"Antibiotic resistance profiles of salmonella recovered from finishing pigs and slaughter facilities in Henan, China","volume":"10","author":"Z Jiang","year":"2019","journal-title":"Front Microbiol"},{"key":"ppat.1012992.ref065","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ Screen: A tool for multi-genome mapping and quality control","volume":"7","author":"SW Wingett","year":"2018","journal-title":"F1000Res"},{"issue":"12","key":"ppat.1012992.ref066","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"D Kim","year":"2016","journal-title":"Genome Res"},{"issue":"20","key":"ppat.1012992.ref067","doi-asserted-by":"crossref","first-page":"3600","DOI":"10.1093\/bioinformatics\/bty350","article-title":"Snakemake-a scalable bioinformatics workflow engine","volume":"34","author":"J K\u00f6ster","year":"2018","journal-title":"Bioinformatics"},{"issue":"15","key":"ppat.1012992.ref068","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"7","key":"ppat.1012992.ref069","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btv688","article-title":"hybridSPAdes: an algorithm for hybrid assembly of short and long reads","volume":"32","author":"D Antipov","year":"2016","journal-title":"Bioinformatics"},{"issue":"9","key":"ppat.1012992.ref070","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1080\/14737159.2016.1217158","article-title":"Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis","volume":"16","author":"E Lavezzo","year":"2016","journal-title":"Expert Rev Mol Diagn"},{"issue":"1","key":"ppat.1012992.ref071","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/JCM.02452-13","article-title":"Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples","volume":"52","author":"H Hasman","year":"2014","journal-title":"J Clin Microbiol"},{"issue":"6","key":"ppat.1012992.ref072","doi-asserted-by":"crossref","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","article-title":"Multilocus sequence typing as a replacement for serotyping in Salmonella enterica","volume":"8","author":"M Achtman","year":"2012","journal-title":"PLoS Pathog"},{"issue":"23","key":"ppat.1012992.ref073","doi-asserted-by":"crossref","first-page":"e01746-19","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: rapid and improved salmonella serotype determination using whole-genome sequencing data","volume":"85","author":"S Zhang","year":"2019","journal-title":"Appl Environ Microbiol"},{"issue":"7","key":"ppat.1012992.ref074","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"A Carattoli","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"ppat.1012992.ref075","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"E Zankari","year":"2012","journal-title":"J Antimicrob Chemother"},{"issue":"D1","key":"ppat.1012992.ref076","doi-asserted-by":"crossref","first-page":"D694-7","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on","volume":"44","author":"L Chen","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"ppat.1012992.ref077","doi-asserted-by":"crossref","first-page":"e1007333","DOI":"10.1371\/journal.pgen.1007333","article-title":"Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica","volume":"14","author":"NE Wheeler","year":"2018","journal-title":"PLoS Genet"},{"issue":"14","key":"ppat.1012992.ref078","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ppat.1012992.ref079","article-title":"Building a BLAST database with your (local) sequences","volume-title":"BLAST\u00ae Command Line Applications User Manual","author":"C Camacho","year":"2024"},{"issue":"7","key":"ppat.1012992.ref080","doi-asserted-by":"crossref","first-page":"msac153","DOI":"10.1093\/molbev\/msac153","article-title":"Pseudofinder: detection of pseudogenes in prokaryotic genomes","volume":"39","author":"MJ Syberg-Olsen","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"1","key":"ppat.1012992.ref081","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Z Zhou","year":"2020","journal-title":"Genome Res"},{"issue":"8","key":"ppat.1012992.ref082","first-page":"000615","article-title":"Generalizable characteristics of false-positive bacterial variant calls","volume":"7","author":"SJ Bush","year":"2021","journal-title":"Microb Genom"},{"issue":"5","key":"ppat.1012992.ref083","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1093\/molbev\/mst028","article-title":"Hierarchical and spatially explicit clustering of DNA sequences with BAPS software","volume":"30","author":"L Cheng","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"22","key":"ppat.1012992.ref084","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"issue":"5","key":"ppat.1012992.ref085","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"W1","key":"ppat.1012992.ref086","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"I Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ppat.1012992.ref087","doi-asserted-by":"crossref","first-page":"vex042","DOI":"10.1093\/ve\/vex042","article-title":"TreeTime: Maximum-likelihood phylodynamic analysis","volume":"4","author":"P Sagulenko","year":"2018","journal-title":"Virus Evol"},{"issue":"3","key":"ppat.1012992.ref088","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"NJ Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ppat.1012992.ref089","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"MA Suchard","year":"2018","journal-title":"Virus Evol"},{"issue":"6","key":"ppat.1012992.ref090","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/ng.3281","article-title":"Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events","volume":"47","author":"VK Wong","year":"2015","journal-title":"Nat Genet"},{"issue":"5","key":"ppat.1012992.ref091","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in bayesian phylogenetics using tracer 1.7","volume":"67","author":"A Rambaut","year":"2018","journal-title":"Syst Biol"},{"issue":"8","key":"ppat.1012992.ref092","doi-asserted-by":"crossref","first-page":"3486","DOI":"10.1093\/molbev\/msab031","article-title":"Relax, keep walking - a practical guide to continuous phylogeographic inference with BEAST","volume":"38","author":"S Dellicour","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"4","key":"ppat.1012992.ref093","doi-asserted-by":"crossref","first-page":"2564","DOI":"10.1128\/AEM.72.4.2564-2572.2006","article-title":"Analyses of the red-dry-rough phenotype of an Escherichia coli O157:H7 strain and its role in biofilm formation and resistance to antibacterial agents","volume":"72","author":"GA Uhlich","year":"2006","journal-title":"Appl Environ Microbiol"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1012992","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012992","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T21:05:40Z","timestamp":1743455140000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012992"}},"subtitle":[],"editor":[{"given":"Andreas J","family":"Baumler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,3,17]]},"references-count":93,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1012992","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1012992","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,17]]}}}