Open AccessPan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia
Author(s) -
Jacky Dwiyanto,
Jia Wei Hor,
Daniel D. Reidpath,
Tin Tin Su,
Shaun Wen Huey Lee,
Qasim Ayub,
Faizah Binti Mustapha,
Sui Mae Lee,
Su Chern Foo,
Chun Wie Chong,
Sadequr Rahman
Publication year - 2022
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0265142
Subject(s) - resistome , replicon , biology , virulence , plasmid , escherichia coli , genome , microbiology and biotechnology , antibiotic resistance , whole genome sequencing , genetics , gene , antibiotics , mobile genetic elements
Objectives This study profiled the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) in the community and compared their resistome and genomic profiles with isolates from clinical patients through whole-genome sequencing. Methods Fecal samples from 233 community dwellers from Segamat, a town in southern Malaysia, were obtained between May through August 2018. Putative ESBL strains were screened and tested using antibiotic susceptibility tests. Additionally, eight clinical ESBL-EC were obtained from a hospital in the same district between June through October 2020. Whole-genome sequencing was then conducted on selected ESBL-EC from both settings (n = 40) for pan-genome comparison, cluster analysis, and resistome profiling. Results A mean ESBL-EC carriage rate of 17.82% (95% CI: 10.48%– 24.11%) was observed in the community and was consistent across demographic factors. Whole-genome sequences of the ESBL-EC (n = 40) enabled the detection of multiple plasmid replicon groups (n = 28), resistance genes (n = 34) and virulence factors (n = 335), with no significant difference in the number of genes carried between the community and clinical isolates (plasmid replicon groups, p = 0.13; resistance genes, p = 0.47; virulence factors, p = 0.94). Virulence gene marker analysis detected the presence of extraintestinal pathogenic E . coli (ExPEC), uropathogenic E . coli (UPEC), and enteroaggregative E . coli (EAEC) in both the community and clinical isolates. Multiple bla CTX-M variants were observed, dominated by bla CTX-M-27 (n = 12), bla CTX-M-65 (n = 10), and bla CTX-M-15 (n = 9). The clinical and community isolates did not cluster together based on the pan-genome comparison, suggesting isolates from the two settings were clonally unrelated. However, cluster analysis based on carried plasmids, resistance genes and phenotypic susceptibility profiles identified four distinct clusters, with similar patterns between the community and clinical isolates. Conclusion ESBL-EC from the clinical and community settings shared similar resistome profiles, suggesting the frequent exchange of genetic materials through horizontal gene transfer.