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We tested the benefits of WGS using\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    collected from pig surveillance performed between 2013 to 2017. WGS was performed on 498\n                    <jats:italic>E. coli<\/jats:italic>\n                    producing ESBL and AmpC enzymes, recovered from pig caeca on MacConkey\u2009+\u2009cefotaxime (McC\u2009+\u2009CTX) agar, as recommended by the European Commission, or ESBL agar, used additionally by United Kingdom. Our results indicated WGS was extremely useful for monitoring trends for specific ESBL genes, as well as a plethora of AMR genotypes, helping to establish their prevalence and co-linkage to certain plasmids. Recovery of isolates with multi-drug resistance (MDR) genotypes was lower from McC\u2009+\u2009CTX than ESBL agar. The most widespread ESBL genes belonged to the\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M<\/jats:sub>\n                    family.\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-1<\/jats:sub>\n                    dominated all years, and was common in two highly stable IncI1 MDR plasmids harbouring (\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-1<\/jats:sub>\n                    ,\n                    <jats:italic>sul2<\/jats:italic>\n                    ,\n                    <jats:italic>tetA<\/jats:italic>\n                    ) or (\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-1<\/jats:sub>\n                    ,\n                    <jats:italic>aadA5<\/jats:italic>\n                    ,\n                    <jats:italic>sul2<\/jats:italic>\n                    ,\n                    <jats:italic>dfrA17<\/jats:italic>\n                    ), in isolates which were phylogenetically dissimilar, suggesting plasmid transmission. Therefore, WGS provided a wealth of data on prevalence of AMR genotypes and plasmid persistence absent from phenotypic data and, also, demonstrated the importance of culture media for detecting ESBL\n                    <jats:italic>E. coli<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1038\/s41598-020-76877-7","type":"journal-article","created":{"date-parts":[[2020,11,16]],"date-time":"2020-11-16T06:04:49Z","timestamp":1605506689000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":46,"title":["The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance"],"prefix":"10.1038","volume":"10","author":[{"given":"Nicholas","family":"Duggett","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manal","family":"AbuOun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke","family":"Randall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Horton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrizio","family":"Lemma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jon","family":"Rogers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derrick","family":"Crook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Teale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muna F.","family":"Anjum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,16]]},"reference":[{"key":"76877_CR1","first-page":"1","volume":"20","author":"J O\u2019Neill","year":"2014","unstructured":"O\u2019Neill, J. 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