Abstract
IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related IncHI2 ST3 plasmids, pSDE-SvHI2 and pSDC-F2_12BHI2, from phylogenetically unrelated multiple-drug resistant Escherichia coli strains SvETEC (CC23:O157:H19) and F2_12B (ST93:O7:H4) from geographically disparate pig production operations in New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina) and long read (PacBio SMRT) nucleotide sequence data. The plasmids encoded three drug-resistance loci, two of which carried class 1 integrons. One integron, hosting drfA12-orfF-aadA2, was within a hybrid Tn1721/21, with the second residing within a copper/silver resistance transposon, comprising part of an atypical sul3-associated structure. The third resistance locus was flanked by IS15DI and encoded neomycin resistance (neoR). An oqx-encoding transposon (quinolone resistance), similar in structure to Tn6010, was identified only in pSDC-F2_12BHI2. Both plasmids showed high sequence identity to plasmid pSTM6-275, recently described in Salmonella enterica serotype 1,4,[5],12:i:- that has risen to prominence and become endemic in Australia. IncHI2 ST3 plasmids circulating in commensal and pathogenic E. coli from Australian swine belong to a lineage of plasmids often in association with sul3 and host multiple complex antibiotic and metal resistance structures, formed in part by IS26.
Highlights
IntroductionIn 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)
Based on the availability of metadata, plasmid sequences were from Enterobacteriaceae of different sources in the pacific region, including Australian porcine production operations and multiple human, agricultural and environmental sources in China
The most distant relative had 25 SNPs identified from conserved core sequence, suggesting a close evolutionary relationship between plasmid sequences reported from Australia and China
Summary
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). First generation antibiotics; commonly tetracyclines, Multiple Drug Resistant IncHI2:ST3 Plasmids 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). 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
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