Integrative Genomic and Phenotypic Characterization of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae (ESBL-E) and Related Bacterial Species Isolated from Pediatric Diarrheal Cases in Bangladesh.
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Date
2025-12-15
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Abstract
Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) pose a major
global threat to antimicrobial therapy, particularly in pediatric populations where diarrheal
diseases remain a leading cause of morbidity and mortality. This study provides an integrative
genomic–phenotypic assessment of ESBL-producing pathogens isolated from diarrheal stool
samples of hospitalized children (<8 years) in Bangladesh. A total of 38 bacterial isolates
obtained from 32 samples were identified to the species level using MALDI-TOF MS, with
Escherichia coli (47.37%) and Klebsiella pneumoniae (10.53%) being predominant. Whole
genome sequencing (WGS) revealed genome sizes ranging from 3.36–6.63 Mb and 3,095–
6,056 annotated coding sequences. Genomic screening using ABRicate across five AMR
databases identified ESBL-associated genes in 55.3% (21/38) of isolates. The bla CTX-M-15 gene
was the most prevalent variant (76.19%), primarily among E. coli, followed by blaTEM and
blaSHV alleles. Phenotypic ESBL detection via CLSI-recommended double-disk synergy
testing confirmed ESBL activity in 39.5% of isolates. Genotype–phenotype concordance was
78.95%, with genotype-positive/phenotype-negative mismatches likely linked to silent gene
expression, masking by co-produced β-lactamases, or complex resistance mechanisms.
Plasmid replicon analysis identified diverse incompatibility groups, including IncF, IncI,
IncHI, IncX, IncR, and Col plasmids, supporting the mobility and dissemination of ESBL
genes. Virulence profiling showed substantial heterogeneity, with ESBL-positive isolates
carrying multiple adhesion, iron acquisition, and stress-response determinants that may
enhance pathogenic potential.
This study represents one of the first comprehensive genomic–phenotypic investigations of
ESBL-producing Enterobacteriaceae in pediatric diarrheal cases in Bangladesh. The
predominance of bla CTX-M-15, the complexity of plasmid-mediated gene dissemination, and
notable genotype–phenotype discrepancies underscore the need for integrated WGS-based
surveillance alongside refined phenotypic diagnostics. These findings offer critical insights
for early detection, infection control, and therapeutic decision-making in resource-limited
healthcare settings.