Genome sequencing of E. coli and Salmonella sp. from AMR surveillance pilot study in tilapia and shrimp from wet-markets, Bangladesh. Bacterial pathogens

Escherichia coli and Salmonella sp. were recovered from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon) purchased from wet markets, Bangladesh. Bacterial species were confirmed by culture and PCR, then tested against a panel of antibiotics using the disc diffusion method for antibiotic susceptibility testing. The genomic DNA of each isolate was extracted and subjected to whole genome sequencing using Oxford Nanopore Technology. The complete or near-complete genomic sequences of E. coli and salmonella sp. were used to run a k-mer based species confirmation using the taxonomic classification from kraken2; multi-locus sequence typing (MLST), molecular serotyping, phylogroup and antimicrobial resistant genes (ARGs) from E. coli were determined so as the serovar, MLST, ARGs, salmonella pathogenicity islands (SPIs) and plasmids for Salmonella sp. E. coli isolates belong to the commensal phylogroups B1 and A. Absence of shiga-toxin genes confirms their status of commensal/normal E coli. The Salmonella kentucky strains all have the K variant of SPI-1 carrying the same resistance genes all on the same contig in each genome.