Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1⁺). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1⁺ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1⁺ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.

中文翻译：

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携带来自母猪及其后代的1类整合素的猪粪便共生大肠杆菌的全基因组测序分析。

集约化养猪生产系统通常依靠使用抗菌剂和重金属饲料添加剂来维持动物健康和福祉。为了深入了解商业饲养的健康猪的粪便菌群中抗微生物抗性基因（ARG）的携带情况，我们鉴定了携带1类整合酶基因（intI1 ⁺）的117头猪共生大肠杆菌的基因组序列。2017年来自澳大利亚一家商业繁育场的42头健康母猪及其后代中获得了分离株。在28/42（67％）母猪和90/126（71％）仔猪中检测到intI1 ⁺大肠杆菌。Phylogroup A，特别是克隆复合体10和phylogroup B1在 研究收藏。ST10，ST20，ST48和ST361是主要序列类型。值得注意的是，有113/117株（占96％）带有三个或更多ARG。编码对-内酰胺，氨基糖苷，甲氧苄啶，磺酰胺，四环素和重金属的抗性的基因占主导。未检测到编码对最后一线药物（如碳青霉烯类药物和第三代头孢菌素）有抗药性的ARG。IS 26是在108/117（92％）intI1 ⁺分离物中存在的一种插入序列，因其具有捕获和动员ARG的能力而着称，在确定1类整合子结构中发挥了作用。我们的数据表明，健康的澳大利亚猪粪是耐多药大肠杆菌的重要储藏库 携带编码对多种第一代抗生素和毒力相关基因具有抗性的基因。