Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia

Abstract

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 blaCTX-M variants were observed, dominated by blaCTX-M-27 (n = 12), blaCTX-M-65 (n = 10), and blaCTX-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.

Genomic epidemiology and mechanisms of antibiotic resistance in Pseudomonas aeruginosa isolated from children’s hospital in Shenzhen, China

“…We report that bla CTX-M-15 is the predominant ESBL encoding gene present in P. aeruginosa and is highly disseminated in the reported '23' STs. Similar resistance encoding genes were reported globally including in China, but our study is in contrast with some reports in China [32,33,34,35]. No bla OXA-48 gene was reported in this study.…”

“…P. aeruginosa strains show a similar resistance phenotype globally and in other provinces of China such as Zhejiang and rates of resistance are increasing rapidly which is particularly alarming in the healthcare sector [31,32]. In addition to this 42% ESBL producers were observed by VITEK ® 2 compact system (BioMerieux, France) and DDDM which is lower compared to Chinese data but is similar to other Asian countries such as Malaysia [33,34]. We have proven that both methods are potentially good for the detection of the ESBL enzyme in P. aeruginosa.…”

Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia

“…Opportunistic pathogens such as E. coli have been associated with bacterial infections (e.g., gastroenteritis 70 , urinary tract infection 71 , inflammatory bowel disease 72 ) and non-communicable diseases (e.g., type II diabetes 73 and hypertension 70 ). In our previous study, we reported on the frequent carriage of multiple plasmid groups among ESBL-producing E. coli , with a phenotypic multidrug resistance rate of 90.29% in Segamat 25 . The observed correlation between E. coli abundance and resistome diversity reported in this study therefore corroborated our previous finding.…”

“…In our previous research, we examined the 16 S rRNA-based gut microbial composition of community dwellers in Segamat, a district in Southern Malaysia 24 , and profiled the colonisation burden of ESBL-producing E. coli using whole-genome sequencing 25 . This study expands upon our previous findings by utilizing shotgun metagenomic sequencing to relate the resistome profiles of community members to their microbiota and lifestyle behaviours.…”

Genomic heterogeneity of Multidrug Resistance E.coli recovered from diarrheagenic children under five years from Mukuru Informal Settlement, Nairobi, Kenya

“…Fluoroquinolones are resisted in bacterial species due to point mutations in the quinolone-resistance-determining region, gryA, and parC gene. The co-existence of the quinoloneresistance-determining region and plasmid-mediated quinolone-resistance, such as qnrS and qnrB, aggravates resistance to this class of antimicrobial agents [14]. Plasmids can mobilize and transmit multiple antimicrobial resistance genes with and across bacterial species.…”