Genomic global epidemiology and evolution of Escherichia coli ST131 clade A

Abstract

During the 2010s, Escherichia coli ST131 clade A tested sensitive to most antibiotics. In the 2020s, Europe experienced outbreaks of fluoroquinolone-resistant ST131-A that contained CTX-M β-lactamases and OXA-48-like carbapenemases. We investigated the acquisition of different antimicrobial resistance determinants in the emergence of multidrug-resistant (MDR) ST131-A. Phylogenetic analysis and Bayesian inference were utilized to define subclades and clusters (within subclades) and investigate the evolutionary history of ST131-A, using sequenced genomes and publicly available genomic data ( n =2,905). ST131-A consisted of five dominant subclades and ten frequent clusters, representing 93 and 83% of the total population, respectively. The sampled most recent common ancestors of the dominant subclades dated mainly to the 1990s. Several MDR clusters linked with diverse quinolone resistance-determining region mutations, CTX-M and OXA-48-like genes diversified during the 2000s. The distribution and mobile genetic elements linked with bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-27 differed among ST131-A subclades and clusters across geographic locations. Three ST131-A clusters belonging to different subclades and carrying bla OXA-48 and bla OXA-244 in distinct genetic contexts were associated with the recent European dissemination. The identification of MDR ST131-A subclades and clusters with divergent molecular architectures emerging independently across regions highlights the challenges for public health surveillance and control efforts.

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BibTeX RIS

BibTeX

@article{matsumura2026genomic,
  title = {{Genomic global epidemiology and evolution of Escherichia coli ST131 clade A}},
  author = {Yasufumi Matsumura and Gisele Peirano and Pierre Bogaerts and Te-Din Huang and Bogdan I. Iorga and Miki Nagao and Johann D.D. Pitout},
  journal = {Microbial Genomics},
  year = {2026},
  month = oct,
  doi = {10.1099/mgen.0.001858},
  url = {https://hal.science/hal-05787188v1},
  note = {CC BY 4.0},
}

RIS

TY  - JOUR
TI  - Genomic global epidemiology and evolution of Escherichia coli ST131 clade A
AU  - Yasufumi Matsumura
AU  - Gisele Peirano
AU  - Pierre Bogaerts
AU  - Te-Din Huang
AU  - Bogdan I. Iorga
AU  - Miki Nagao
AU  - Johann D.D. Pitout
PY  - 2026
DA  - 2026/10/07
JO  - Microbial Genomics
DO  - 10.1099/mgen.0.001858
UR  - https://hal.science/hal-05787188v1
AB  - During the 2010s, Escherichia coli ST131 clade A tested sensitive to most antibiotics. In the 2020s, Europe experienced outbreaks of fluoroquinolone-resistant ST131-A that contained CTX-M β-lactamases and OXA-48-like carbapenemases. We investigated the acquisition of different antimicrobial resistance determinants in the emergence of multidrug-resistant (MDR) ST131-A. Phylogenetic analysis and Bayesian inference were utilized to define subclades and clusters (within subclades) and investigate the evolutionary history of ST131-A, using sequenced genomes and publicly available genomic data ( n =2,905). ST131-A consisted of five dominant subclades and ten frequent clusters, representing 93 and 83% of the total population, respectively. The sampled most recent common ancestors of the dominant subclades dated mainly to the 1990s. Several MDR clusters linked with diverse quinolone resistance-determining region mutations, CTX-M and OXA-48-like genes diversified during the 2000s. The distribution and mobile genetic elements linked with bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-27 differed among ST131-A subclades and clusters across geographic locations. Three ST131-A clusters belonging to different subclades and carrying bla OXA-48 and bla OXA-244 in distinct genetic contexts were associated with the recent European dissemination. The identification of MDR ST131-A subclades and clusters with divergent molecular architectures emerging independently across regions highlights the challenges for public health surveillance and control efforts.
SN  - 2057-5858
SN  - 2057-5858
ER  -

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