Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617

Abstract

Aquatic environments are recognized as one of the main reservoirs for the emergence and dissemination of high-risk lineages of multidrug-resistant (MDR) bacteria of public health concern. However, the genomic characteristics of antibiotic-resistant Escherichia coli isolates from aquatic origins remain limited. Herein, we examined the antibiotic resistance and virulence genomic profiles of three E. coli recovered from surface water in northwest Mexico. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and in-depth in silico analysis were performed. Two E. coli exhibited MDR phenotypes. WGS-based typing revealed genetic diversity, and phylogenetic analysis corroborated a notable divergent relationship among the studied E. coli. One E. coli strain, harboring enterotoxigenic and extraintestinal pathogenic-associated virulence genes, was assigned to the ST4 lineage. MDR E. coli, belonging to the international high-risk clones ST410 and ST617, carried genes and mutations conferring resistance to aminoglycosides, β-lactams, quinolones, sulfonamides, tetracyclines, and trimethoprim. This study describes, for the first time, the detection and genomic profiling of high-risk lineages of E. coli ST410 and ST617 from surface water in Mexico. Additionally, our results underscore the role of surface water as a reservoir for critical pathogenic and MDR E. coli clones and the need for the surveillance and monitoring of aquatic environments via WGS from the One Health perspective.

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings

“…Despite some environemtal isolates possibly losing some adhesion properties in vitro infection models, they still possess virulence properties according to our cytotoxicity assays. ST410 is a high-risk MDR clone of E. coli commonly associated with carbapenemase genes that carry blaOXA-181 and blaNDM-5 and with cross-sectorial Mexico's agricultural drainage(60). The ST410 isolates described in this study were not MDR, but carried the CS23 operon in combination with LT and STh.…”

“…ST410 was previously reported in soil samples from the Choqueyapu River and carried the bla OXA-1 gene (11). Studies have also found that E. coli ST410 is associated with vegetables on the municipal market in Ecuador (59) or surface water from Mexico’s agricultural drainage (60). The ST410 isolates described in this study were not MDR, but carried the CS23 operon in combination with LT and STh.…”

The First Report of Escherichia coli and Klebsiella pneumoniae Strains That Produce Both NDM-5 and OXA-181 in Jiangsu Province, China

“…), Asia (South Korea, 32 Singapore, 33 India, 34 China, 35 etc. ), Africa, 36 North America (United States, 37 Mexico, 38 etc.) and South America (Brazil, 39 Chile 40 et al), etc.…”

Genomic characterization of a multidrug-resistant uropathogenic <i>Escherichia coli</i> and evaluation of <i>Echeveria</i> plant extracts as antibacterials

“…DNA extraction and sequencing was performed as previously described [22] . A single E. coli colony was grown in Luria-Bertani (LB) broth overnight at 37 ± 2 °C under aerobic conditions.…”

“…A quality control assessment, filtering, and further assembly of raw sequencing data were performed as previously reported [22] . The FastQC program, version 0.11.9 ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), and Cutadapt, version 2.4 [23] , were employed to evaluate and process the raw genomic reads, respectively.…”