Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand

Background: Extended-spectrum Chi-lactamase producing Escherichia coli (ESBL-producing E. coli) have emerged, causing human and animal infections worldwide. This study was conducted to investigate the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant (MDR) E. coli in river water. Methods: A total of 172 E. coli samples were collected from the Kok River and Kham River in Chiang Rai, Thailand, during a 10-month period (2020-2021). Results: We detected 45.3% of E. coli to be MDR. The prevalence of ESBL-producers was 22%. Among those ESBL-producing strains, CTX-M-15 (44.7%) was predominantly found, followed by CTX-M-55 (26.3%), CTX-M-14 (18.4%), and CTX-M-27 (10.5%). The bla(TEM-1) and bla(TEM-116) genes were found to be co-harbored with the bla(CTX-M) genes. Mobile elements, i.e., ISEcp1 and Tn3, were observed. Twelve plasmid replicons were found, predominantly being IncF (76.3%) and IncFIB (52.6%). Whole genome sequencing of ten selected isolates revealed the co-existence of ESBL with mcr genes in two ESBL-producing E. coli. A wide diversity of MLST classifications was observed. An mcr-1.1-pap2 gene cassette was found to disrupt the PUF2806 domain-containing gene, while an mcr-3.4 contig on another isolate contained the nimC/nimA-mcr-3.4-dgkA core segment. Discussion: In conclusion, our data provides compelling evidence of MDR and ESBL-producing E. coli, co-existing with mcr genes in river water in northern Thailand, which may be disseminated into other environments and so cause increased risks to public health.

Automated summary

This study investigated the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant E. coli in river water in northern Thailand. The results showed that approximately 45.3% of E. coli were MDR, and 22% were ESBL producers. Among the ESBL-producing strains, CTX-M-15 was the predominant type. The study also revealed the presence of various plasmid replicons and mobile elements.