Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26

Abstract

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.

Antimicrobial Resistance inEscherichia coli

“…Most of the dfrA and dfrB genes found in E. coli of animal origin are located on gene cassettes that are inserted into class 1 or class 2 integrons. Some examples are given for dfrA genes that have been identified in E. coli from dogs (dfrA1, dfrA12, dfrA17, dfrA29) (138,185,210), cats (dfrA1, dfrA12) (210), horses (dfrA1, dfrA9, dfrA12, dfrA17) (193,210), pigs (dfrA1, dfrA5, dfrA8, dfrA12, dfrA13, dfrA14, dfrA16, dfrA17) (144,156,210,228,229), cattle (dfrA1, dfrA8, dfrA12, dfrA17) (14,215,229), chickens (dfrA1, dfrA5, dfrA12, dfrA14, dfrA16) (144,229), and giant pandas (dfrA1, dfrA7, dfrA12, dfrA17) (128). In contrast to dfrA genes, dfrB genes have rarely been detected in E. coli from animals.…”

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

“…In Australia, restrictions on live animal imports, geographic isolation, and sound antibiotic stewardship have limited the incorporation and spread of genes encoding resistance to antibiotics used to treat serious human infections among Enterobacteriaceae circulating in food animals (Turner, 2011;Abraham et al, 2015;Reid et al, 2017;Kidsley et al, 2018). Australian porcine Escherichia coli are, albeit at low frequency, known to carry bla CMY−2 , bla CTX−M−14, and bla CTX−M−9 , possibly because of the use of ceftiofur as an off-label, last line antibiotic to treat serious disease (Abraham et al, 2015).…”

“…First generation antibiotics; commonly tetracyclines, penicillins, and sulphonamides are otherwise used for the therapeutic treatment of bacterial infections in swine (Jordan et al, 2009). Both pathogenic and commensal E. coli sourced from the feces of pig carry class 1 integrons and are often multiple drug resistant (MDR) (Abraham et al, 2015;Wyrsch et al, 2015;Reid et al, 2017). Notably, the insertion element IS26 has infiltrated the genomes of commensal E. coli of porcine origin, where it has played a role in altering the genetic context of clinical class 1 integrons and facilitated the acquisition of further resistances (Reid et al, 2017).…”

“…Both pathogenic and commensal E. coli sourced from the feces of pig carry class 1 integrons and are often multiple drug resistant (MDR) (Abraham et al, 2015;Wyrsch et al, 2015;Reid et al, 2017). Notably, the insertion element IS26 has infiltrated the genomes of commensal E. coli of porcine origin, where it has played a role in altering the genetic context of clinical class 1 integrons and facilitated the acquisition of further resistances (Reid et al, 2017). Furthermore, it is important to identify and characterize the genetic vehicles that can carry class 1 integrons and genes encoding resistance to first generation antibiotics which are widespread in commensal E. coli populations in Australian pigs (Abraham et al, 2015;Reid et al, 2017;Kidsley et al, 2018) because they are likely to acquire genes encoding resistance to clinically relevant antibiotics when resident in commensal enterobacterial populations in the gut of humans and companion animals.…”

Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58

“… E. coli ST58 belongs to a phylogroup B1 commensal lineage that has been isolated from diverse animal, environmental and human hosts [40–42], demonstrating links with human urinary tract infections and urosepsis, and it can carry a colV-like virulence resistance plasmid [40]. Recently we characterized an environmental ST58 isolate recovered from the faeces of a straw-necked ibis nest in inland wetlands, New South Wales, Australia [43].…”