1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.
2NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia.
Microb Genom. 2017 Dec;3(12). doi: 10.1099/mgen.0.000143.
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
猪粪是一种严重的环境污染物质。猪肠道共生的大肠杆菌携带的抗药性基因（ARGs）和毒力相关基因（VAGs），以及其对人类的潜在传染性，在很大程度上是未知的。此外，关于肠道共生大肠杆菌在促进食源性动物和环境之间的 ARGs 转移方面的作用，人们也知之甚少。在此，我们报告了对来自澳大利亚新南威尔士州两个商业养殖场的 103 株携带 1 类整合子的大肠杆菌的全基因组序列分析。大多数菌株属于 A 和 B1 群，并且携带与人类肠外感染相关的 VAGs。这 103 株菌属于 37 个多位点序列型和 10 个克隆群，其中以克隆群 10 最为突出。共检测到 17 个 ARGs，97%（100/103）的菌株携带 3 个或更多的 ARGs。重金属抗性基因 merA、cusA 和 terA 也很常见。98%（101/103）的菌株中存在 IS26，且通常与结构多样的 1 类整合子物理相关，这些整合子携带独特的遗传特征，可能被追踪。本研究提供了澳大利亚猪源肠道共生大肠杆菌的首次详细的基因组分析和参考点，有助于追踪特定的谱系及其携带的可移动抗性基因。
