Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls

Abstract

Escherichia coli ST216, including those that carry blaKPC-2, blaFOX-5, blaCTX-M-15 and mcr-1, have been linked to wild and urban-adapted birds and the colonisation of hospital environments causing recalcitrant, carbapenem-resistant human infections. Here we sequenced 22 multiple-drug resistant ST216 isolates from Australian silver gull chicks sampled from Five Islands, of which 21 carried nine or more antibiotic resistance genes including blaIMP-4 (n = 21), blaTEM-1b (n = 21), aac(3)-IId (n = 20), mph(A) (n = 20), catB3 (n = 20), sul1 (n = 20), aph(3”)-Ib (n = 18) and aph(6)-Id (n = 18) on FIB(K) (n = 20), HI2-ST1 (n = 11) and HI2-ST3 (n = 10) plasmids. We show that (i) all HI2 plasmids harbour blaIMP-4 in resistance regions containing In809 flanked by IS26 (HI2-ST1) or IS15DI (HI2-ST3) and diverse metal resistance genes; (ii) HI2-ST1 plasmids are highly related to plasmids reported in diverse Enterobacteriaceae sourced from humans, companion animals and wildlife; (iii) HI2 were a feature of the Australian gull isolates and were not observed in international ST216 isolates. Phylogenetic analyses identified close relationships between ST216 from Australian gull and clinical isolates from overseas. E. coli ST216 from Australian gulls harbour HI2 plasmids encoding resistance to clinically important antibiotics and metals. Our studies underscore the importance of adopting a one health approach to AMR and pathogen surveillance.

F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses

“…We also observed shared IncF RSTs across ST95 isolates from different sources and across phylogenetic backgrounds, suggesting intersource plasmid transmission events. These findings are also consistent with those of other studies showing that closely related plasmids are shared between humans, food animals, and urban-adapted wild birds ( 12 , 17 , 72 , 73 ).…”

Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance

“…The collection contained 96 sequence types (STs), represented all the major E. coli phylogroups, and was predominantly comprised of commensal phylogroups A and B1. The collection also included examples of nearly clonal populations (e.g., ST1139); known ExPEC lineages such as ST38, ST58, ST69, and ST131 ( 32 ); emerging E. coli pathogens of ST457 ( 12 ) and ST216 ( 11 ); and a range of multiple-antibiotic-resistant “commensal” lineages that are also potential ExPEC lineages (e.g., ST10 [ 33 ]). Isolate summaries are provided in Table S1 in the supplemental material.…”

“…Previous studies of gull E. coli isolates have performed sampling at sites associated with human activity, e.g., where gulls congregate on beaches ( 9 ) and an island close to Australia’s populated coast where gulls are known to feed almost entirely on human refuse ( 8 ). These studies have described (i) a rich diversity of drug-resistant E. coli lineages, (ii) complete sequences of resistance plasmids carrying genes encoding resistance to CIAs and evidence of their mobility ( 11 ), and (iii) emerging MDR ( 12 ). Evidence of nearly clonal E. coli isolates from gulls and humans is suggestive of interspecies transmission.…”

Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany

“…ST216 was detected most frequently, with nine of the 19 isolates belonging to this ST. E. coli ST216 is known to carry resistance genes to a variety of antibiotics and has been detected several times in nosocomial infections [ 45 , 46 ]. In particular, in the context of carbapenem resistance, this ST has appeared several times both in humans [ 47 ] and animals [ 48 ]. However, we did not detect phenotypic or genotypic carbapenem resistance.…”

“…However, we did not detect phenotypic or genotypic carbapenem resistance. Nevertheless, ST216 E. coli seems to be particularly capable of capturing and transmitting genes encoding beta-lactamases and carbapenemases [ 48 ]. The detection of this ST in more than half of our ESBL isolates is therefore a matter of concern.…”