Emerging zoonotic risks: whole-genome sequencing reveals antimicrobial resistance and genomic diversity in Providencia stuartii isolated from broiler chickens in Noakhali, Bangladesh.

Abstract

Providencia stuartii is emerging as an Extensively Drug-Resistant (XDR) pathogen commonly found in animals, insects, and in burned and immunocompromised conditions. The misuse of antibiotics in poultry feed causes the emergence of XDR bacteria in the poultry industry. The knowledge of zoonotic transmissibility of poultry-derived P. stuartii remains elusive in Noakhali, Bangladesh. Poultry fecal and rectal swab samples were collected from selected farms in Noakhali, Bangladesh. Bacterial isolation and identification were performed using MacConkey agar, biochemical tests, and 16S rRNA Sanger sequencing. Antimicrobial susceptibility was assessed by the Kirby-Bauer disk diffusion method, and isolates with high multiple antibiotic resistance (MAR) indices were selected for whole-genome sequencing (WGS). Quality control, genome assembly, annotation, gene identification, pan-genome analysis, pathogenicity profiling, and comparative proteome analyses were subsequently conducted. Antibiogram analysis showed that ps_nstu_001 and ps_nstu_002 were resistant to 17 and 13 tested antibiotics, respectively. Furthermore, whole-genome sequencing revealed that both strains harbored resistance determinants to aminoglycosides, tetracyclines, sulfonamides, cephalosporins, β-lactams, and carbapenems. Additionally, mobile genetic elements (MGEs) and plasmids were identified, which represent the horizontal gene transfer capability. Moreover, pangenome analysis revealed ongoing gene acquisition and substantial genomic diversity among the isolates. The isolate ps_nstu_001 was identified as a putative human pathogen and clustered closely with a clinical strain isolated in the United States. In contrast, ps_nstu_002 was predicted to be a non-human pathogen; however, it exhibited a clear evolutionary relationship with a clinical isolate obtained from a diarrheal patient in Bangladesh, suggesting potential pathogenic relevance. Global pathogenic potential of the studied strains and key proteomic similarities between pathogenic and non-pathogenic strains revealed by pathogenicity profiling and proteome comparison. To conclude, these XDR isolates indicate the potential for zoonotic transmission and the spread of resistant genes to other animals, posing a significant public health risk.