Genomic comparisons of Escherichia coli ST131 from Australia

Abstract

Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron–integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462–1014 bp), highlighting the ongoing evolution of this element. The module intI1–dfrA17–aadA5–qacEΔ1–sul1–ORF–chrA–padR–IS1600–mphR–mrx–mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.

Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC

“…pUTI89-like plasmids were confined to phylogroups B2 and D and were most common in ST963 (8/9, 89%), ST95 (3/6, 66.7%), and ST131 (5/8, 62.5%) sequences. Their presence in these STs is indicative of sublineage partitioning, as has been recently described for ST131 and ST95 ( 22 , 23 ).…”

“…The major human ExPEC STs, particularly ST95 ( 22 ), ST131 ( 23 , 26 ), and ST73 ( 45 ), comprise sublineages that are often discernible by serotype and fimH allele variation. Lineage subdivision is also often accompanied by carriage of different F plasmid replicon sequence types belonging to ColV (various replicon types) and pUTI89-like (ColIa + /F29:A-:B10) genotypes ( 22 , 25 , 26 ).…”

“…Despite its vast commensal and pathogenic range, deciphering the zoonotic and zooanthroponotic potential of E. coli remains a challenge ( 20 , 21 ). Addressing this issue requires a deep understanding of genomic epidemiology of the dominant ExPEC sequence types (STs) as well as emerging ExPEC STs in both humans and animals ( 7 , 22 – 26 ). There are more than 11,000 E. coli sequence types, but the top 20 ExPEC sequence types are responsible for more than 85% of ExPEC infections in humans ( 13 ).…”

“…Despite the variety of plasmids that are found in E. coli , F plasmids dominate among a proportion of major and emerging ExPEC STs. For example, carriage of F plasmids is very common in ST131, ST95, ST58, and ST127, with separate plasmid lineages found to be characteristic of ST sublineages ( 7 , 22 , 23 , 25 ). F plasmids can be categorized genotypically by their accessory gene content, and plasmid lineages within those genotypes can be approximated by their F replicon sequence types (RSTs).…”

Antimicrobial-Resistant Escherichia coli Distribution and Whole-Genome Analysis of Sequence Type 131 Escherichia coli Isolates in Public Restrooms in Taiwan

“…Whole-genome analysis revealed a large cluster belonging to fimH41 ST131. A recent study in Austria also reported cross-species transmission (synanthropic birds and humans) in fimH41 ( Li et al, 2021 ). Our study supports the “one health” concept ( Murphy et al, 2010 ; Trinh et al, 2018 ; Collignon and McEwen, 2019 ) that the same clone of fimH41 ST131 circulates among humans, dogs, and the environment.…”