Genomic Characterization of Bat-Associated Escherichia coli from fecal samples of Fruit bats (Pteropus medius) in Bangladesh: A Whole Genome Sequencing Approach

Abstract

Antimicrobial resistance (AMR) is a major global public health threat, yet its occurrence in wildlife remains poorly understood, particularly in bats, increasing their potential exposure to resistant bacteria. E. coli serves as a sentinel organism in AMR research because of its public health importance and its ability to acquire and disseminate antimicrobial resistance genes. Although bat-associated AMR has been documented in several countries, genomic information on bat-associated E. coli is limited. Therefore, this study investigated E. coli isolated from Bat (Pteropus medius) using a whole-genome sequencing approach. A total of 60 freshly voided fecal samples were collected from two P. medius roosting sites in Chattogram, Bangladesh: Pahartoli (n = 40) and Halishahar (n = 20), and 11 confirmed E. coli isolates were analyzed by culture-based isolation and identification, AST, MIC for colistin, whole-genome sequencing (WGS), Multilocus Sequence Typing, serotyping, phylogrouping, AMR and virulence gene profiling, plasmid replicon typing, and MashTree-based phylogenetic analysis. The overall prevalence of E. coli was 18.3% (11/60), with a higher positivity rate in site 2 (25.0%) than site 1 (15.0%); no multidrug-resistant isolate was detected phenotypically, and all isolates remained below the colistin breakpoint, although reduced susceptibility to ampicillin was observed. Genomic analysis identified 5 AMR genes, with blaEC-19 as the most common, 6 plasmid replicons led by Col(pHAD28), and 28 virulence genes, among which nlpI, terC, fimH, and chuA were prominent. MLST revealed high sequence diversity, with ST1727 as the most frequent type and two isolates remaining unassigned, while O83 was the predominant serogroup and phylogroups B1 and B2 were equally dominant. Phylogenetic analysis showed that the isolates were distributed across multiple clades without clear roosting site-specific clustering. In conclusion, this study shows that P. medius in Bangladesh harbors genetically diverse E. coli carrying AMR genes, plasmids, and virulence-associated determinants, despite the absence of phenotypic multidrug resistance, and the findings suggest that fruit bats may be involved in the circulation of diverse E. coli lineages across human, animal, and environmental reservoirs, providing an important baseline for wildlife-inclusive One Health surveillance in Bangladesh.