{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T19:14:24Z","timestamp":1790709264964,"version":"4.1.0"},"reference-count":52,"publisher":"Frontiers Media SA","funder":[{"DOI":"10.13039\/501100001501","name":"University Grants Commission","doi-asserted-by":"publisher","award":["F.4-2\/2006 (BSR)\/BL\/14-15\/0273"],"award-info":[{"award-number":["F.4-2\/2006 (BSR)\/BL\/14-15\/0273"]}],"id":[{"id":"10.13039\/501100001501","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2017.02120","type":"journal-article","created":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T08:28:27Z","timestamp":1510561707000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":79,"title":["Risk of Transmission of Antimicrobial Resistant Escherichia coli from Commercial Broiler and Free-Range Retail Chicken in India"],"prefix":"10.3389","volume":"8","author":[{"given":"Arif","family":"Hussain","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabiha","family":"Shaik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Ranjan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nishant","family":"Nandanwar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumeet K.","family":"Tiwari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Majid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramani","family":"Baddam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Insaf A.","family":"Qureshi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Semmler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lothar H.","family":"Wieler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad A.","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dipshikha","family":"Chakravortty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niyaz","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2017,11,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"B2","doi-asserted-by":"publisher","first-page":"4272","DOI":"10.1128\/JB.05413-11","article-title":"Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India.","volume":"193","author":"Avasthi","year":"2011","journal-title":"J. Bacteriol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-695X.2011.00797.x","article-title":"Escherichia coli from animal reservoirs as a potential source of human extraintestinal pathogenic E. coli.","volume":"62","author":"B\u00e9langer","year":"2011","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2463","DOI":"10.1128\/AEM.03893-12","article-title":"Frequent occurrence of extended-spectrum beta-lactamase- and transferable AmpC Beta-lactamase-producing Escherichia coli on domestic chicken meat in Sweden.","volume":"79","author":"Borjesson","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1289\/EHP292","article-title":"The prevalence of extended-spectrum Beta-lactamase-producing multidrug-resistant Escherichia Coli in poultry chickens and variation according to farming practices in Punjab, India.","volume":"125","author":"Brower","year":"2017","journal-title":"Environ. Health Perspect."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1128\/AAC.01099-13","article-title":"Widespread dissemination of CTX-M-15 genotype extended-spectrum-\u03b2-lactamase-producing enterobacteriaceae among patients presenting to community hospitals in the southeastern United States.","volume":"58","author":"Chen","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/agriculture4010001","article-title":"Microbiological safety of chicken litter or chicken litter-based organic fertilizers: a review.","volume":"4","author":"Chen","year":"2014","journal-title":"Agriculture"},{"key":"B9","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups.","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"B10","year":"2013","journal-title":"VET01-A4 Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2014.00005","article-title":"Is the concept of avian pathogenic Escherichia coli as a single pathotype fundamentally flawed?","volume":"1","author":"Collingwood","year":"2014","journal-title":"Front. Vet. Sci."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004776","article-title":"Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages.","volume":"10","author":"de Been","year":"2014","journal-title":"PLOS Genet."},{"key":"B13","first-page":"19","article-title":"Emerging & re-emerging infections in India: an overview.","volume":"138","author":"Dikid","year":"2013","journal-title":"Indian J. Med. Res."},{"key":"B14","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1128\/IAI.00585-12","article-title":"Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms.","volume":"81","author":"Dziva","year":"2013","journal-title":"Infect. Immun."},{"key":"B15","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/j.ijmm.2007.01.003","article-title":"Avian pathogenic, uropathogenic, and newborn meningitis-causing Escherichia coli: how closely related are they?","volume":"297","author":"Ewers","year":"2007","journal-title":"Int. J. Med. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"16","DOI":"10.3923\/ajbs.2015.16.29","article-title":"Chicken carcasses bacterial concentration at poultry slaughtering facilities.","volume":"8","author":"Firildak","year":"2015","journal-title":"Asian J. Biol. Sci."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1038\/srep14372","article-title":"Pathogenic Escherichia coli producing extended-spectrum \u03b2-Lactamases isolated from surface water and wastewater.","volume":"5","author":"Franz","year":"2015","journal-title":"Sci. Rep."},{"key":"B18","doi-asserted-by":"publisher","first-page":"6358","DOI":"10.1128\/AAC.01099-12","article-title":"Multiresistant uropathogenic Escherichia coli from a region in India where urinary tract infections are endemic: genotypic and phenotypic characteristics of sequence type 131 isolates of the CTX-M-15 extended-spectrum-\u03b2-lactamase-producing lineage.","volume":"56","author":"Hussain","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"B19","doi-asserted-by":"publisher","first-page":"7240","DOI":"10.1128\/AAC.03320-14","article-title":"Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India.","volume":"58","author":"Hussain","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018063","article-title":"Virulence characteristics and genetic affinities of multiple drug resistant uropathogenic Escherichia coli from a semi urban locality in India.","volume":"6","author":"Jadhav","year":"2011","journal-title":"PLOS ONE"},{"key":"B21","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1089\/fpd.2009.0409","article-title":"Escherichia coli isolates from broiler chicken meat, broiler chickens, pork, and pigs share phylogroups and antimicrobial resistance with community-dwelling humans and patients with urinary tract infection.","volume":"7","author":"Jakobsen","year":"2010","journal-title":"Foodborne Pathog. Dis."},{"key":"B22","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.1128\/AAC.47.7.2161","article-title":"Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli.","volume":"47","author":"Johnson","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"B23","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichia coli.","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1111\/jfs.12370","article-title":"Evaluation of genotypical antimicrobial resistance in ESBL producing Escherichia coli phylogenetic groups isolated from retail poultry meat.","author":"Klimien\u0117","year":"2017","journal-title":"J. Food Saf."},{"key":"B25","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1089\/fpd.2010.0726","article-title":"EcoR phylogenetic analysis and virulence genotyping of avian pathogenic Escherichia coli strains and Escherichia coli isolates from commercial chicken carcasses in Southern Brazil.","volume":"8","author":"Kobayashi","year":"2011","journal-title":"Foodborne Pathog. Dis."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/618752","article-title":"Comparison of antibiotic resistance and virulence factors among Escherichia coli isolated from conventional and free-range poultry.","volume":"2015","author":"Koga","year":"2015","journal-title":"Biomed. Res. Int."},{"key":"B27","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1177\/003335491212700103","article-title":"A review of antibiotic use in food animals: perspective, policy, and potential.","volume":"127","author":"Landers","year":"2012","journal-title":"Public Health Rep."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001974","article-title":"Antibiotic resistance in India: drivers and opportunities for action.","volume":"13","author":"Laxminarayan","year":"2016","journal-title":"PLOS Med."},{"key":"B29","doi-asserted-by":"publisher","first-page":"89","DOI":"10.3390\/ijerph7010089","article-title":"Avian colibacillosis and salmonellosis: a closer look at epidemiology, pathogenesis, diagnosis, control and public health concerns.","volume":"7","author":"Lutful Kabir","year":"2010","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"B30","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1089\/fpd.2013.1533","article-title":"Human and avian extraintestinal pathogenic Escherichia coli: infections, zoonotic risks, and antibiotic resistance trends.","volume":"10","author":"Mellata","year":"2013","journal-title":"Foodborne Pathog. Dis."},{"key":"B31","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1128\/AEM.03524-14","article-title":"Zoonotic potential of Escherichia coli isolates from retail chicken meat products and eggs.","volume":"81","author":"Mitchell","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.ijid.2016.02.741","article-title":"Population structure and molecular epidemiology of human clinical multi-drug resistant (MDR) Escherichia coli strains from Pune, India.","volume":"45","author":"Nandanwar","year":"2016","journal-title":"Int. J. Infect. Dis."},{"key":"B33","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/j.ijmm.2014.06.009","article-title":"Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features.","volume":"95","author":"Nandanwar","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"Escherichia coli st131, an intriguing clonal group.","volume":"27","author":"Nicolas-Chanoine","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"B35","doi-asserted-by":"publisher","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030619","article-title":"NGS QC toolkit: a toolkit for quality control of next generation sequencing data.","volume":"7","author":"Patel","year":"2012","journal-title":"PLOS ONE"},{"key":"B37","doi-asserted-by":"publisher","first-page":"e2305","DOI":"10.1128\/AEM.02305-16","article-title":"Genome dynamics and molecular infection epidemiology of multidrug-resistant Helicobacter pullorum isolates obtained from broiler and free-range chickens in India.","volume":"83","author":"Qumar","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"6087","DOI":"10.1128\/AAC.01447-15","article-title":"Genomic and functional portrait of a highly virulent, CTX-M-15-producing H30- Rx subclone of Escherichia coli sequence type (ST) 131.","volume":"59","author":"Ranjan","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B39","doi-asserted-by":"publisher","first-page":"6795","DOI":"10.1128\/AAC.01345-16","article-title":"Molecular epidemiology and genome dynamics of New Delhi metallo-beta-lactamase (NDM) producing extraintestinal pathogenic E. coli (ExPEC) strains from India.","volume":"60","author":"Ranjan","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"B40","doi-asserted-by":"publisher","first-page":"e01070","DOI":"10.1128\/mBio.01070-17","article-title":"Comparative genomics of Escherichia coli isolated from skin and soft tissue and other extraintestinal infections.","volume":"8","author":"Ranjan","year":"2017","journal-title":"MBio"},{"key":"B41","doi-asserted-by":"publisher","first-page":"146","DOI":"10.4315\/0362-028X-71.1.146","article-title":"Contamination of carcasses with Salmonella during poultry slaughter.","volume":"71","author":"Rasschaert","year":"2008","journal-title":"J. Food Prot."},{"key":"B42","doi-asserted-by":"publisher","first-page":"2097","DOI":"10.1099\/mic.0.27499-0","article-title":"Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis.","volume":"151","author":"Rodriguez-Siek","year":"2005","journal-title":"Microbiology"},{"key":"B43","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.5897\/AJMR2016.8251","article-title":"African journal of microbiology research comparison of the prevalence of antibiotic-resistant Escherichia coli isolates from commercial-layer and free-range chickens in Arusha district.","volume":"10","author":"Rugumisa","year":"2016","journal-title":"Tanzania"},{"key":"B44","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation.","volume":"16","author":"Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"B45","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1177\/104063870902100514","article-title":"Evaluation of Clinical Laboratory Standards Institute interpretive criteria for methicillin-resistant Staphylococcus pseudintermedius isolated from dogs.","volume":"21","author":"Schissler","year":"2009","journal-title":"J. Vet. Diagn. Invest."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0155459","article-title":"Contig-Layout-Authenticator (CLA): a combinatorial approach to ordering and scaffolding of bacterial contigs for comparative genomics and molecular epidemiology.","volume":"11","author":"Shaik","year":"2016","journal-title":"PLOS ONE"},{"key":"B47","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1637\/7569-033106R.1","article-title":"Potential impacts of antibiotic use in poultry production.","volume":"50","author":"Singer","year":"2006","journal-title":"Avian. Dis."},{"key":"B48","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.sbspro.2014.02.104","article-title":"Population and agro climatic zones in India: an analytical analysis.","volume":"120","author":"Singh","year":"2014","journal-title":"Procedia Soc. Behav. Sci."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0026578","article-title":"Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms.","volume":"6","author":"Totsika","year":"2011","journal-title":"PLOS ONE"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1186\/PREACCEPT-2573980311437212","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.","volume":"15","author":"Treangen","year":"2014","journal-title":"Genome Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1093\/JAC\/47.6.763","article-title":"Antibiotic resistance of faecal Escherichia coli in poultry, poultry farmers and poultry slaughterers.","volume":"47","author":"van den Bogaard","year":"2001","journal-title":"J. Antimicrob. Chemother."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1089\/fpd.2011.0852","article-title":"Contamination rates and antimicrobial resistance in Enterococcus spp., Escherichia coli, and Salmonella isolated from "no antibiotics added"-labeled chicken products.","volume":"8","author":"Zhang","year":"2011","journal-title":"Foodborne Pathog. Dis."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2017.02120\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T08:28:30Z","timestamp":1510561710000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2017.02120\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,13]]},"references-count":52,"alternative-id":["10.3389\/fmicb.2017.02120"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2017.02120","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,13]]},"article-number":"2120"}}