Epidemiology and molecular characterization of CTX-M-type ESBLs producing Escherichia coli isolated from clinical settings

Objectives: Recently, bla(CTX-Ms) have become the dominant ESBLs for E. coli strains worldwide. We aim to provide a systematic study on the relationships between sequence types (STs), clinical origins, and the bla(CTX-Ms) genotypes of E. coli strains. Methods: Totally, 1005 complete sequences of clinical E. coli were collected from NCBI. Multilocus sequence typing (MLST) and antibiotic resistance genes screening were performed. Results: Faeces (26.27%), urine (16.02%), and blood (8.26%) were shown to be the main sources of clinical E. coli isolates. The isolates belong to 153 STs and 26 clonal complexes (CCs). The most prevalent STs were ST2 (11.3%), ST43 (8.6%), and ST8 (5.7%). The positive rate for bla(CTX-Ms) was 34.7%. Different samples showed significantly different bla(CTX-Ms) positive rates (P<0.05). The main genotypes were bla(CTX-M-55)(-like) (47.6%), bla(CTX-M-1)(-like) (31.8%), and bla(CTX-M-2)(-like) (22.1%). The majority of ST2 strains had bla(CTX-M-55)(-like) genes. In ST8 strains, there was a homogeneous distribution of bla(CTX-M-9), bla(CTX-M-65), bla(CTX-M-55), bla(CTX-M-2), and bla(CTX-M-1). Only ST43 strains exhibited the presence of bla(CTX-M-79). The bla(CTX-Ms) showed a pattern of cross-continental transmission with intra-regional spread. Among the 349 bla(CTX-Ms)-producing E. coli strains, 148 strains also carried carbapenem resistance genes, including bla(NDM) (119, 34.1%), bla(KPC) (16, 4.6%), bla(OXA-48) (9, 2.6%) and bla(IMP) (4, 1.1%). Also, 81 strains carried the mcr gene (23.2%). Conclusions: E. coli has become increasingly rich in bla(CTX-Ms) genotypes. Our findings about the connection between E. coli STs and bla(CTX-Ms) can be utilized to identify E. coli strains with high potential to spread drug resistance in the future. (c) 2023 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)