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.

Keywords: H41; ST131; blaCTX-M-27; class 1 integrons; extraintestinal pathogenic Escherichia coli (ExPEC); one health; urinary tract infection (UTI).

Fig. 1.

Maximum-likelihood SNP-based phylogenetic tree of Australian ST131. Inferred using FastTree2, EC958 as a reference, and recombination filtering. Red and blue squares next to labels, denote presence of the characteristic fluoroquinolone resistance SNPs: gyrA-1AB (red) and parC-1aAB (blue). Coloured rings represent isolation dates (inner ring; colour gradient from light [2005] to dark [2019], serotype (second ring from centre), fimH type of isolate (third ring), host (fourth ring), virotype (fifth ring), fastBAPS groups (sixth ring) and bla _CTX-M variant (outer ring). Sections of the tree are coloured according to subclade (red=A, green=B, blue=C0, violet=C1 and black=C2). Inner tip label denotes isolate name, with names highlighted in purple representing previously unpublished genomes. Outer tip labels show which IncF plasmids are present in each isolate, with pMLSTs important for E. coli ST131 evolution highlighted. Tree scale bars represent the number of substitutions per site of alignment.

Fig. 2.

Closely related clade clusters. (a) Heatmap illustrating pairwise SNP distances for 35 isolates in clade A. Both axes have a maximum-likelihood phylogenetic tree presented as a cladogram, constructed using these 35 isolates and clade A reference strain SE15 (ASM1048v1) (98 % genome coverage; 4.73 Mbp; 970 SNPs total). (b) Heatmap illustrating pairwise SNP distances for 45 isolates from clade C1. Both axes have a maximum-likelihood phylogenetic tree presented as a cladogram, constructed using these 45 isolates and clade C1 reference strain 81 009 (ASM215724v1) (97 % genome coverage; 4.98 Mbp; 711 SNPs total). (c) Heatmap showing SNP distances of 13 closely related hospital isolates from subclade C2. Both axes have a maximum-likelihood phylogenetic tree presented as a cladogram, constructed using only these 13 isolates, with EC958 as the reference strain (96 % genome coverage; 5.02 Mbp; 133 SNPs total). All trees were constructed using recombination-filtered SNP alignments.

Fig. 3.

ARG, VAG and IncF pMLST abundances in Australian ST131 population. Heatmap based on clustering by fastBAPS (fastBAPS groups consisting of singular isolates omitted). Relative gene abundance presented as blue (VAGs), red (ARGs) and green (plasmid replicons) colour gradients ranging from 0 % (no colour) to 100 % (most opaque). Total numbers of isolates carrying a gene are shown in parentheses after the gene name.

Fig. 4.

Percentage of Australian ST131 isolates carrying ARGs conferring resistance to multiple antibiotics. (a) Percentage of isolates carrying one or more ARGs conferring resistance to various antibiotic classes across clades. Clade C0 isolates omitted due to the limited number (n=4). NSBL, narrow spectrum β-lactamase. (b) Box and whisker plot illustrating distribution of clade isolates carrying ARGs conferring resistance to antibiotic (AB) classes (c) Percentage of isolates carrying more than one ARG conferring resistance to various antibiotic class across hosts and in total. Environmental (n=5), porcine (n=1) and poultry (n=1) isolates omitted due to the limited numbers. Fluroquinolone mutation refers to the presence of parC and gyrA mutations. (d) Box and whisker plot illustrating distribution of host isolates carrying ARGs conferring resistance to AB classes. The presence of one or more genes counted as conferring resistance. Numbers in brackets are numbers of isolates.

Fig. 5.

Class 1 integron structures and bla _CTX-M-15, bla _CTX-M-27 genomic contexts. (a) Schematic map of class one integrons present in Australian ST131 isolates. (b) Schematic map of genomic context of bla _CTX-M-27. (c) Schematic map of genomic context of bla _CTX-M-15. In each panel, solid-coloured lines represent individual structures with dashed lines representing variations and connections between structures. Contig breaks denoted by ‘†’.

Fig. 6.

blast comparisons of three virulence plasmids using CGview. (a) Comparisons of pUTI89-like plasmids present in 43 Australian ST131 isolates. Rings coloured by isolate source and clade: red=wild bird, clade A; orange=human, clade A; green=canine, clade B; blue=human, clade B; purple=wild bird, clade C1; pink=human, clade C1; grey=wild bird, clade C2; black=human, clade C2. (b) Comparisons of pAPEC-O2-ColV-like plasmids present in ten isolates (c) Comparisons of pAA-like plasmids present in two isolates. VAGs are coloured in red, mobile elements in blue, tra region in scarlet, inner circle show GC skew.