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

Abstract

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 β-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.

The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes

“…The genes conferring resistance are frequently encoded on integrons and plasmids, as well as other mobile genetic elements, which can be passed between permissive APEC strains and other species (Hornsey et al, 2019;Cummins et al, 2019). Class 1 integrons in particular play a vital role in the capture and expression of gene islands that encode resistance to antimicrobials and heavy metals (Cummins et al, 2019;Zingali et al, 2020). These genetic features are considered markers of multidrug resistance and may serve as major drivers of AMR (Zingali et al, 2020).…”

“…Class 1 integrons in particular play a vital role in the capture and expression of gene islands that encode resistance to antimicrobials and heavy metals (Cummins et al, 2019;Zingali et al, 2020). These genetic features are considered markers of multidrug resistance and may serve as major drivers of AMR (Zingali et al, 2020). Therefore, determining the extent of class 1 integron presence in broiler production and other intensive farming settings is crucial to containing the impact of AMR.…”

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

“…Nonetheless, phenotypic and genotypic resistance to many first-generation antimicrobials is now widespread in commensal faecal E. coli populations in healthy Australian swine [ 7 , 8 ]. In intensive pig farming systems, antimicrobials are used to prevent the spread of diseases and animal loss [ 9 , 10 ]. Sows are an important reservoir of bacteria that carry antibiotic and heavy metal resistance genes which are readily transmitted to offspring [ 9 , 11 , 12 ].…”

Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups

“…There are multiple reports of IS26 class 1 integron variants in E. coli from animals in Australia, including cows and pigs (14,47,48) and Grey-headed flying foxes (Pteropus poliocephalus) (49), as well as in human clinical cases (50). The presence of class isolates from hospital patients and zoo and production animals in China.…”

“…There are multiple reports of IS26 class 1 integron variants in E. coli from animals in Australia, including cows and pigs (14,47,48) and Grey-headed flying foxes (Pteropus poliocephalus) (49), as well as in human clinical cases (50). The presence of class cassette is associated with human and domestic animal pathogens, the presence of this gene cassette in free-ranging pinnipeds provides further evidence to suggest that the Seal Rocks colony is exposed to anthropogenic microbial pollution.…”