# Genome-wide analysis of extended-spectrum beta-lactamase-producing Escherichia coli from seafood in Bangladesh: population structure, resistome, virulome, and global dissemination patterns

## TL;DR

This study analyzed E. coli from Bangladeshi seafood to understand their genetic makeup and resistance patterns, showing their potential role in spreading antibiotic resistance.

## Contribution

The study provides new insights into the population structure and global dissemination of beta-lactamase-producing E. coli from seafood in Bangladesh.

## Key findings

- Most isolates displayed unique sequence types, with some showing close genetic relatedness to global strains.
- Crab isolates carried the highest number of antimicrobial resistance genes and plasmids.
- ST345 in Bangladesh closely matched wastewater and human isolates from the Czech Republic and USA.

## Abstract

This study aimed to identify multilocus sequence type (MLST), serotype, average nucleotide identity (ANI), antimicrobial resistance genes (ARGs), virulence genes (VGs), and mobile genetic elements (MGEs) from whole-genome sequences of 10 Escherichia coli isolated from seafood in Bangladesh and compared them with the global datasets of beta-lactamase-producing E. coli.

Ten E. coli isolates (crab = 3, shrimp = 1, tuna = 6) were subjected to whole-genome sequencing using Oxford Nanopore Technologies (Oxford, UK). In-silico bioinformatics analyses were performed using online tools and Linux-based commands. A systematic advanced search in PubMed identified 722 global genomes of beta-lactamase-producing E. coli for comparative analysis. A population structure and global phylogeny were constructed to illustrate the current status of beta-lactamase-producing E. coli from diverse sources (seafood, human, aquatic, wastewater, and environmental) across countries, based on their STs, ARGs, VGs, MGEs, and serotypes.

Bioinformatics analysis revealed that most isolates displayed unique sequence types (STs) and core genome sequence types (cgSTs), while three isolates shared both ST1431 and cgST104784, indicating close genetic relatedness supported by ANI analysis. In shrimp and tuna isolates, both O and H antigens were detected, whereas crab isolates carried either O or H antigens. Pangenome analysis identified 56.4% strain-specific genes, 34.2% dispensable genes, and 9.4% core genes, with functions categorized into clusters of orthologous groups (COGs). Several ARGs, including beta-lactamase genes (CTX-M-15, AmpC, blaDHA-1), were detected across isolates, with crabs harboring the highest number. The VGs were more common in tuna isolates. Plasmids were only detected in crabs (Col440I, IncFIA, IncFIB(pHCM2), and ColRNAI) carrying qnrB4, dfrA17, qacE, mph(A), sul1, blaDHA-1 ARGs, but were absent in shrimp and tuna. Population structure analysis showed that ST345 in Bangladesh closely matched wastewater (Czech Republic) and human (USA) isolates. Some STs overlapped with international records, while others appeared novel, suggesting limited global distribution. Globally, wastewater and human isolates from the Czech Republic showed the greatest similarity to our strains.

These findings underscore the potential role of seafood in disseminating beta-lactamase-producing E. coli, highlighting the urgent need for integrated surveillance to mitigate antimicrobial resistance risks in humans, animals, and the food chain.