Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

Abstract

Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla _CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla _CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla _CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.

Keywords: ESBL; Escherichia coli; antimicrobial resistance; freshwater.

Fig. 1.

Sample site location. (a) New Zealand map showing the sample site location and (b) a topographical map illustrating the three sample sites.

Fig. 2.

Core SNP comparison of the ST131 isolates from humans, dogs and water. Maximum-likelihood trees of New Zealand ST131 isolates (n=245), reconstructed using 14 296 core SNPs (a) and clade A ST131 isolates (n=66), reconstructed using 4 132 core SNPs (b). The genomes sequenced in this study are indicated in bold.

Fig. 3.

Core SNP comparison of the ST69 isolates from humans, animals (bovine and avian) and water. Maximum-likelihood trees of New Zealand ST69 isolates (n=27) reconstructed using 15 812 SNPs. The genome sequenced in this study is indicated in bold.

Fig. 4.

Comparison of the IncF plasmids with their closest relatives. A neighbour-joining tree was reconstructed using a core-genome alignment generated by Roary (v.3.8.2) (a). Genetic maps and degree of homology between the IncF plasmids (b). Genetic maps and degree of homology between the resistance gene cassettes of AGR4587, AGR5151 and AGR6128 (c). Genes coloured in grey are hypothetical proteins, bla _CTX-M-27 is coloured in red, other resistance genes are coloured in blue and the qacE gene is coloured in yellow.