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

Abstract

12Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated 13 by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase 14 (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131's origin, adaptation and 15 spread is essential. E. coli ST131's ESBL genes are typically embedded in mobile genetic elements (MGEs) that 16 aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and 17 recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We 18 used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available 19 high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 20 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene 21 screening to resolve ST131's population structure across three genetically distinct Clades (A, B, C) and 22 abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the 23 core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods 24 to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively 25 stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This 26 contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were 27 located at distinct locations across the chromosomes and plasmids between isolates. Within the three C 28 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 1 dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically 2 variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary 3 pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover 4 accessory genome changes linked to novel subtypes. 5 6 Background 10 11 Infections caused by multidrug-resistant (MDR) Escherichia coli sequence type (ST) 131 are increasing 12 worldwide [1,2]. ST131 are extraintestinal pathogenic E. coli (ExPEC) associated with bloodstream and urinary 13 tract infections and typically possessing extended-spectrum beta-lactamase (ESBL) genes [3-5], or more rarely 14 carbapenemase genes [6]. MDR ST131 is a major cause of ExPEC infection because it has an extensive range of 15 virulence factors [7-11] and may be highly pathogenic to hosts. ST131 has been reported in healthcare and 16 community settings around the globe, and its dominant lineage Clade C is fluoroquinolone-resistant (FQ-R) 17 [12,13]. Clade...

Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi

“…This is consistent with global trends that suggest that the highly drug-resistant E. coli ST131, associated with the bla CTX-M- 15 gene, has been increasing in prevalence. [9][10][11] [15][16][17][18] There is some subtle structure within ST131, with isolates from this study that are primarily localized on a branch with a longer internal branch length, which may suggest the seeding and expansion locally in central Malawi ( Figure 1 ). Another difference from previous work is the higher number of ST410 isolates in this study, which carried the bla CTX-M-15 gene at the highest frequency of all the sequence types.…”

“…Additionally, recent evidence suggests that the highly drug resistant E. coli sequence type (ST) 131 has been increasing in prevalence globally. [9][10][11] This sequence type is an extraintestinal pathogenic E. coli (ExPEC) that is associated with bloodstream and urinary tract infections, often possessing genes associated with extended-spectrum β-lactamases (ESBL). [12,13] The main mechanism of cephalosporin resistance is drug inactivation mediated by hydrolysis of the β-lactam ring by ESBL enzymes.…”

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

“…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.…”

Genomic network analysis of an environmental and livestock IncF plasmid population

“…This includes livestock [1][2][3][4][5] and water-borne [6] resistance. Frequent horizontal gene transfer (HGT) in Enterobacteriaceae populations results in a large and open pangenome, enabling the wide-spread transmission of the genes conferring AMR [7][8][9]. This includes AMR transmission between humans and the environment and vice versa [10].…”