An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Abstract

Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131’s origin, adaptation and spread is essential. E. coli ST131’s ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131’s population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.

Whole Genome Sequencing and Characteristics of mcr-1–Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

“…The CG SNP-based phylogenetic tree of 84 human and animal ST131 isolates analyzed in this study showed (Figure 1) that they are mostly clustered into three well-defined clades (A, B, and C), and similarly to Petty et al (2014) study, we have observed that clade A is the most divergent from clades B and C. Our results also agree with those published by other authors (Ben Zakour et al, 2016;Matsumura et al, 2017;Liu C. M. et al, 2018;Decano and Downing, 2019) regarding that clade B isolates are displayed into multiple subclades. We identified the six subclades (B0, B1, B2, B3, B4, and B5) described by Ben Zakour et al (2016) and five new ones (B6, B6-like, B7, B8, and B9).…”

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

“…The seven ST131 assemblies above were from a set of 4,071 ST131 from Clades A, B and C [61] that were aligned here to pEK499 and pEK204 with BLAST. 837 (20.6%) had >10 Kb of regions similar to pEK204 (Figure S9), whereas 3,108 (76.3%) had >10 Kb like pEK499 ( Figure S10).…”

“…This implied blaCTX-M (via orf477) was common in C2 and blaTEM (via impB) in C1 due to different ancestral transposition of the 9.3 Kb region. To resolve the origin of pEK204-related pil HGT, we searched for the 14 pil operon genes (pilIJKMNOPQRSTUVI) individually in the 4,071 assemblies [61]. The entire pil operon was conserved in 376 (9%), including 61 from A (out of 414, 15%), 97 from B (out of 433, 22%), 17 from C0 (out of 52, 33%), 95 from C1 (out of 1,121, 8.5%) and 106 from C2 (out of 2,051, 5.2%) (Table 3) (see Data Access).…”

“…Some plasmids in ST131 encode genes for post-segregation killing and stable inheritance to ensure their propagation, but these genes can be lost or may recombine with other plasmids [58][59][60]. As a result of this mixing and their extensive array of MGEs, plasmids may rearrange extensively even within a clonal radiation [61][62]. Plasmids may also impair cell reproduction due to the energetic cost of their replication and maintenance, so conjugation and recombination could allow gene dosage optimisation and gene expression coordination.…”

“…This study focused on uropathogenic ST131 Clade C (fimH30) because of its high plasmid and AMR gene diversity [50,61] where the mobile resistome and how plasmids mediate AMR gene composition needs deeper scrutiny. Here, we found a large shared core preterm infant resistome and a smaller accessory one that varied between closely related isolates.…”