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.
Highlights
Escherichia coli (E. coli) comprises an important component of the commensal gastrointestinal flora of warm-blooded vertebrate species
The commensal E. coli from sows and their offspring had their phylogroup, Multilocus Sequence Typing (MLST) and serotype determined in silico
Our previous study showed that commensal E. coli belonged predominantly to phylogroup A and B1 and sequence types ST10, ST361 and ST542
Summary
Escherichia coli (E. coli) comprises an important component of the commensal gastrointestinal flora of warm-blooded vertebrate species. Antibiotic usage features prominently in efforts to curtail the impact of the pathogenic E. coli disease in livestock production systems and prevent animal loss. The application of manure as land fertiliser introduces faecal bacteria, antimicrobial and heavy metal residues into the environment beyond the farm [9,10,11]. The impact of composting on the carriage of multidrug resistant (MDR) bacteria is complex, and recent evidence suggests that the practice is not effective in reducing antimicrobial resistance gene (ARG) pollution in animal manure [11]. The precise ecological and molecular effects of livestock manure as a land fertiliser are poorly understood and undoubtedly complex [11,12,13], this practice may represent the driving force for AMR spread in the environment, wildlife and humans [9,14]
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