Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

Abstract

Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes blaTEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.

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

“…The sul3 gene was first described in pigs (Perreten and Boerlin, 2003) and has since been reported widely in association with Enterobacteriaceae in humans, farm animals and their wasteparticularly swine (Antunes et al, 2007;Phuong Hoa et al, 2008;Byrne-Bailey et al, 2009;Curiao et al, 2011;Moran et al, 2016). In Australia and elsewhere, sul3 is identified frequently in commensal E. coli from the feces of swine (Guerra et al, 2004;Bischoff et al, 2005;Reid et al, 2017) but less frequently in avian pathogenic E. coli (APEC) from diverse poultry production systems in Australia (Cummins et al, 2019). These observations suggest that swine production, and food animal production more broadly, plays a major role in the evolution of IncHI2 ST3 plasmids that carry sul3.…”

Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic

“…Two isolates were assigned to ST117 (phylogenetic group F). Recent studies indicate that this sequence type comprises important APEC lineages that are repeatedly reported from colibacillosis outbreaks in different countries (25,37,(40)(41)(42), but are also highlighted as potential zoonotic pathogens for containing ExPEC-related virulence genes and being isolated from both retail poultry meat and human clinical urinary tract infections (43). The remaining phylogroup F isolate was ST354, another potentially zoonotic ST, reported particularly from human and animal healthcare facilities and characterized by common resistance to antimicrobials including fluoroquinolones (44,45).…”

Genomic analysis of avian-pathogenic Escherichia coli (APEC) isolated from diseased chicken

“…Two isolates were assigned to ST117 (phylogenetic group F). Recent studies indicate that this sequence type comprises an important APEC lineages that are repeatedly reported from colibacillosis outbreaks in different countries (25,37,(40)(41)(42), but are also highlighted as potential zoonotic pathogens for containing ExPEC-related virulence genes and being isolated from both retail poultry meat and human clinical urinary tract infections (43). The remaining phylogroup F isolate was ST354, another potentially zoonotic ST, reported particularly from human and animal healthcare facilities and characterized by common resistance to antimicrobials including fluoroquinolones (44,45).…”

“…Both ST429 and ST23 are considered as predominant APEC lineages that are frequently isolated from poultry with clinically manifested disease (35,37), but also poultry products (26). Although representing quite unrelated APEC clades, they both appear to be poultry-specific, with little pathogenic potential for humans (7,17).…”