Emergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infection

Lachlan L. Walker, Minh-Duy Phan, Budi Permana, Zheng Jie Lian, Nguyen Thi Khanh Nhu, Thom Cuddihy, Kate M. Peters, Kay A. Ramsay, Chelsea Stewart, Niels Pfennigwerth, Timothy J. Kidd, Patrick N. A. Harris, David L. Paterson, Matthew J. Sweet, Brian M. Forde () and Mark A. Schembri ()
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Lachlan L. Walker: The University of Queensland
Minh-Duy Phan: The University of Queensland
Budi Permana: The University of Queensland
Zheng Jie Lian: The University of Queensland
Nguyen Thi Khanh Nhu: The University of Queensland
Thom Cuddihy: The University of Queensland
Kate M. Peters: The University of Queensland
Kay A. Ramsay: The University of Queensland
Chelsea Stewart: The University of Queensland
Niels Pfennigwerth: Ruhr-University Bochum
Timothy J. Kidd: Queensland Health
Patrick N. A. Harris: The University of Queensland
David L. Paterson: National University of Singapore
Matthew J. Sweet: The University of Queensland
Brian M. Forde: The University of Queensland
Mark A. Schembri: The University of Queensland

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Carbapenem-resistant Enterobacterales pose a critical global health threat, exemplified by increasing resistance of uropathogenic E. coli (UPEC) that cause urinary tract infections (UTIs). Here, we investigate the publicly available EnteroBase dataset and identify a signal of increasing UTI caused by phylogroup A E. coli sequence type 167 (ST167). Phylogenetic analysis of ST167 based on whole genome sequence data reveal three major clades (A, B, C), with clade C further resolving into several subclades, notably subclade C2 that possessed high carriage rates of carbapenem and cephalosporin resistance genes. Hierarchical clustering of core genome multi-locus sequence typing reveals ~77% of subclade C2 strains contain

Date: 2025
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DOI: 10.1038/s41467-025-63477-0

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