1. Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?
- Author
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Piklu Roy Chowdhury, Priyanka Hastak, Matthew DeMaere, Ethan Wyrsch, Dmitriy Li, Paarthiphan Elankumaran, Monika Dolejska, Glenn F. Browning, Mark S. Marenda, Thomas Gottlieb, Elaine Cheong, John Merlino, Garry S. A. Myers, and Steven P. Djordjevic
- Subjects
enteroaggregative E. coli ,EAEC ,ST38 ,One Health ,bla CTX-M ,genomic surveillance ,Microbiology ,QR1-502 - Abstract
ABSTRACT We performed a comprehensive phylogenomic analysis of 925 extraintestinal pathogenic Escherichia coli (ExPEC) ST38 genomes from 38 countries and diverse hosts and sources. The phylogeny resolved two broad clades: A (593 strains; 91% human) and B (332 isolates; 42% human), each with distinct ST38 clusters linked to the carriage of specific bla CTX-M alleles, often in association with other antibiotic resistance genes, class 1 integrons and specific plasmid replicon types. Co-carriage of fyuA and irp2 virulence genes, a reliable proxy for carriage of the Yersinia high-pathogenicity island, featured in 580 (62.7%) genomes. ST38 lineages carrying combinations of ExPEC and intestinal pathogenic Escherichia coli virulence factors were also identified. The F plasmid replicon was identified in 536 (58%) genomes, and 112 of these (21%) carry cjrABC-senB, a virulence operon frequently identified in pandemic ExPEC sequence types. Most (108; 96.4%) cjrABC-senB+ ST38 isolates were from human and other sources, except food animals, and were associated with F5:A-:B10 (41 isolates), F1:A2:B20 (20 isolates), and F24:A-:B1 (15 isolates) F replicon types. ST38 genomes that were inferred to carry a ColV-F virulence plasmid (69; 7.4%) were mostly from human (12; 17.4%), avian (26; 37.7%), or poultry (10; 6.9%) sources. We identified multiple examples of putative inter-host and host-environment transmission events, where genomes differed by
- Published
- 2023
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