Virulence genes, antibiotic resistome, and mobile genetic elements in the genome of multi-drug resistant Escherichia coli migula isolated from Philippine native swine (Sus scrofa L.) raised in backyard farm

Microorganisms have been shown to acquire extraneous genetic elements via horizontal gene transfer for virulence factors and antimicrobial resistance (AMR) genes thereby increasing their pathogenicity. This increase in pathogenicity is particular concerning in backyard grown Philippine Native Swine (PNS) where management practices and antibiotic use are mostly unregulated. Previous studies revealed the presence of multidrug resistant (MDR) pathogenic bacteria in PNS, particularly, Shiga-toxin producing Escherichia coli (STEC). However, the genes conferring these phenotypes and potential vehicles of transfer have not been identified. In this study, and MDR STEC isolate (I116 obtained from PNS grown in a backyard farm from Quezon Province was sent for whole genome sequencing (WGS) and subjected to bioinformatic analysis, to determine the AMR genes and mobile genetic elements the isolate carriers. The sequence reads were assembled into a draft genome and analyzed for phylogeny, virulence, AMR genes and MGEs. Phylogenetic analysis of the MDR STEC isolate (I116) revealed that it is most closely related to E. coli INSRA6015, a clinical isolate, with no largely nonhomologous regions between their genomes; however, the larger genome size of I116 and presence of genetic rearrangements imply that is distinct from INSRA6015. Present the genome are several virulence genes, namely, yehBADC, fimAICDFGH, IpfA, csgA, hra, fdeC, hlyE/cytA, gad, terC, and iss, which code for various virulence factors for colonization, toxins and fitness; and several AMR genes that code for resistance to tetracycline, trimethoprim/sulfonamides, quinolone, phenicols, penicilin and aminoglycoside. The detected although their phenotypic expression has not been confirmed in the laboratory. Several MGEs such as insertion sequences, a composite transposin (cn_5129_ISVa3) carrying the phenicol resistance gene, floR, nonconjugative plasmids, and two prophage regions harboring AMR genes for resistance to amnoglycosides, sulfonamide, phenicol, and beta-lactamase were also found, along with an integron carrying the aada5 and qace delta 1 resistance genes in proximity yo other AMR and virulence genes. The findings in studies have shown the antibiotic use can confer competency in bacterial cells, making it viable for transformation to obtain resistance genes. More stringent management practices in rearing PNS are also recommended to prevent the spread of pathogenic bacteria, which can occur through a number of ways especially through direct contact of the farmer with the animal and its carcass.