Molecular Epidemiology of Escherichia coli Sequence Type 131

The worldwide dissemination of Escherichia coli sequence type 131 (ST131) has reshaped the epidemiology of extra-intestinal pathogenic E. coli infections. Defined by multilocus sequence typing, ST131 comprises several phylogenetic clades—A, B and the predominant clade C with subclades C1/H30R and C2/H30Rx—each distinguished by unique resistance and virulence traits. The emergence of fluoroquinolone resistance in the mid-1980s, followed by acquisition of extended-spectrum β-lactamase (ESBL) genes, most notably blaCTX-M variants, drove rapid clonal expansion. Whole-genome sequencing and pangenome analyses have uncovered complex patterns of horizontal gene transfer, plasmid reshuffling and compensatory mutations that mitigate fitness costs. ST131 has demonstrated the capacity to colonise diverse reservoirs, including the human gut, clinical settings, wastewater and riverine environments. High-resolution molecular surveillance has elucidated global and local transmission networks, informing targeted mitigation strategies. The lineage’s adaptability to antibiotic selection pressure, coupled with metabolic and colonisation advantages, underpins its persistence as a major public health threat.

Research from Nature Portfolio

Recent genomic surveillance of bloodstream isolates across a national cohort revealed that all major ST131 clades circulate within the population, with clade C/H30 accounting for the majority of third-generation cephalosporin-resistant infections through blaCTX-M-1 group ESBLs. Phylogeographic reconstruction pinpointed the emergence of a region-specific sublineage in the late 1990s that seeded a localised cluster by the late 2000s, underscoring the value of high-resolution genomics for detecting microevolutionary events and guiding public health interventions. In parallel, community carriage studies have documented a paradoxical rise in ciprofloxacin-resistant E. coli despite a substantial reduction in prescriptions. This trend was driven by both the expansion of multi-drug resistant ST1193 and ST131 subclones bearing fewer chromosomal mutations but increased co-resistance to third-generation cephalosporins, illustrating the complex interplay between antibiotic use and clonal success.

Molecular Epidemiology of Escherichia coli Sequence Type 131 publication trend

The graph below shows the total number of articles in molecular epidemiology of escherichia coli sequence type 131 across all publications each year (not limited to Nature Index journals).

Technical terms

Sequence type (ST): A classification of bacterial isolates based on the allelic profiles of multiple housekeeping genes.

Clade: A monophyletic group within a phylogenetic tree sharing a common ancestor, used to subdivide ST131 lineages.

Extended-spectrum β-lactamase (ESBL): An enzyme capable of hydrolysing a broad spectrum of β-lactam antibiotics, conferring resistance to penicillins and cephalosporins.

Quinolone resistance determining region (QRDR): Specific chromosomal loci where point mutations reduce susceptibility to quinolone antibiotics.

References

1. Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales. Nature Communications (2024).
2. Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. The Lancet Microbe (2024).
3. Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland. Environmental Pollution (2023).
4. Increase in the community circulation of ciprofloxacin-resistant Escherichia coli despite reduction in antibiotic prescriptions. Communications Medicine (2023).
5. Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLOS Biology (2023).
6. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. mBio (2016).
7. Escherichia coli ST131: a multidrug-resistant clone primed for global domination. F1000Research (2017).
8. Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131. mBio (2016).
9. Dissemination of Clonally Related Escherichia coli Strains Expressing Extended-Spectrum β-Lactamase CTX-M-15 - Volume 14, Number 2—February 2008 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases (2008).
10. Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms. PLOS ONE (2011).