Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring.

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.

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny.

We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.