Extended spectrum beta-lactamase producing Escherichia coli and antimicrobial resistance gene sharing at the interface of human, poultry and environment: results of ESBL tricycle surveillance in Kathmandu, Nepal.

Background: The spread of antimicrobial resistant pathogens, including extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae is a global health threat and can be addressed only through a One Health approach. We aimed to characterize ESBL producing Escherichia coli isolates from World Health Organization Tricycle surveillance using data from whole genome sequencing (WGS) to decipher the potential dynamics of their circulation at the human, poultry and environment interface.

Methods: WGS was performed on 100 non-duplicate representative ESBL E. coli isolates including 28 isolates from humans, 36 from poultry caeca, and 36 from water samples. Minimum Inhibitory Concentration (MIC) was determined using Vitek 2 Compact. WGS was performed on Illumina NextSeq 2000 platform and open-source bioinformatics pipelines were used to analyze WGS data for genomic characterization including phylogenetic analysis and in silico multi-locus sequence typing and, serotyping and, ESBL gene detection.

Results: Most isolates were susceptible to imipenem (98%), meropenem (94%) and tigecycline (94%). Six ESBL E. coli isolates from poultry were resistant to colistin (MIC ≥ 4 μg/ml). WGS revealed high genetic diversity representing 56 sequence types (ST) including three novel STs. ST131 (7 isolates) was the most prevalent comprising human and environment isolates, followed by ST2179 (6 isolates, all poultry) and ST155 (5 isolates across the three sectors). All eight recognized E. coli phylogroups were observed, with majority (86%) of the isolates belonging to A, B1, B2 and D phylogroups. Of the100 isolates, 98 carried bla_CTX-M gene, with bla_CTX-M-15 the most prevalent allele (76%). AmpC type ESBL genes were found in four and OXA type β lactamases in six isolates. In our study, bla_NDM-5 was detected in two imipenem resistant isolates from human. Coexistence of more than one β-lactamase genes was seen in 26% isolates.

Conclusion: Our findings indicate high genetic diversity among ESBL E. coli strains from all three sectors and sharing of identical strains and resistance genes within and between sectors. ST131, the globally dominant ESBL E. coli clade is gaining prevalence in Nepal with bla_CTX-M being the most common ESBL gene across the phylogroups and all source groups. Antimicrobial stewardship should be promoted in one health approach to combat antimicrobial resistance.