Antibiotic Resistome, Mobile Genetic Elements, and Virulence Profile of Multidrug-Resistant Enterobacteriaceae Isolated from Healthy Philippine Native Chicken as Revealed by Analysis of Whole Genome Sequence

Gram-negative bacteria, particularly Enterobacteriaceae, acquire antibiotic resistance via horizontal transmission of resistance genes in poultry farms that give rise to multidrug-resistant (MDR) strains. The presence of MDR strains that are potentially pathogenic and zoonotic poses a concern to animal and human health. The aims of this study were to isolate MDR, potentially pathogenic Enterobacteriaceae from Philippine native chicken (PNC) and to analyze the genome of a representative MDR isolate to gain insights into the mechanisms, acquisition, and transmissibility of antibiotic resistance genes (ARGs). Cloacal swabs from PNC were used to isolate putative Salmonella that were then tested for antimicrobial susceptibility. Twenty-six putative Salmonella isolates obtained from 13 chickens of PNC breeds exhibited diverse MDR phenotypes. Analysis of the whole genome of a representative MDR isolate, which was resistant to at least 10 antibiotic classes and exhibited atypical Salmonella phenotype, was identified as closest related to Enterobacter cloacae (E. cloacae) that is a known nosocomial pathogen frequently associated with MDR phenotype. The genome carries an abundance of ARGs, integrons, mobile genetic elements, toxin genes, and pathogenicity genes. This MDR E. cloacae isolate presents an infectious threat and a challenge to its control and management in humans and animals.