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In this study, PCRs were used to detect <jats:italic>mcr<\/jats:italic> genes (<jats:italic>mcr-1<\/jats:italic>, <jats:italic>mcr-2<\/jats:italic>, <jats:italic>mcr-3<\/jats:italic>) in 213 anal and 1,339 nasal swabs from pigs (n\u2009=\u20091,454) in nine provinces of China, and 1,696 cloacal and 1,647 oropharyngeal samples from poultry (n\u2009=\u20091,836) at live-bird markets in 24 provinces. The <jats:italic>mcr-1<\/jats:italic> prevalences in pigs (79.2%) and geese (71.7%) were significantly higher than in chickens (31.8%), ducks (34.6%) and pigeons (13.1%). The <jats:italic>mcr-2<\/jats:italic> prevalence in pigs was 56.3%, significantly higher than in chickens (5.5%), ducks (2.3%), geese (5.5%) and pigeons (0%). The <jats:italic>mcr-3<\/jats:italic> prevalences in pigs (18.7%), ducks (13.8%) and geese (11.9%) were significantly higher than in chickens (5.2%) and pigeons (5.1%). In total, 173 pigs and three chickens were positive for all three <jats:italic>mcr<\/jats:italic> genes. The prevalences of the <jats:italic>mcr<\/jats:italic> were significantly higher in nasal\/oropharyngeal swabs than in the anal \/cloacal swabs. Phylogenetic studies identified 33 new <jats:italic>mcr-2<\/jats:italic> variants and 12 new <jats:italic>mcr-3<\/jats:italic> variants. This study demonstrates high prevalences of <jats:italic>mcr<\/jats:italic> in pigs and poultry in China, and indicates there is need for more thorough surveillance and control programs to prevent further selection of colistin resistance.<\/jats:p>","DOI":"10.1038\/s41598-018-22084-4","type":"journal-article","created":{"date-parts":[[2018,2,21]],"date-time":"2018-02-21T11:50:17Z","timestamp":1519213817000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":76,"title":["Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal\/oropharyngeal and anal\/cloacal swabs from pigs and poultry"],"prefix":"10.1038","volume":"8","author":[{"given":"Jilei","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiawei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afrah Kamal","family":"Yassin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Butaye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiansen","family":"Gong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weina","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhixing","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunlian","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaoyao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfeng","family":"You","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart","family":"Price","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kezong","family":"Qi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7874-8340","authenticated-orcid":false,"given":"Chengming","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,2,27]]},"reference":[{"key":"22084_CR1","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.cmi.2014.12.025","volume":"21","author":"JM Pogue","year":"2015","unstructured":"Pogue, J. 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