Prevalence and characterization of carbapenem-resistant gram-negative bacteria from poultry in Tamil Nadu, India

Recent emergence of carbapenem-resistant bacteria in poultry has raised concerns on the potential transmission to humans. We aimed to investigate the molecular epidemiology, genotype and phenotype of the carbapenem-resistant gram-negative bacteria isolated from raw chicken meat samples from India and to evaluate resistance and virulence genes through whole genome sequencing (WGS). Poultry samples (<i>n</i> = 250) from local vendors in Coimbatore, Tamil Nadu, India were enriched in selective McConkey broth before culturing on McConkey agar (both containing 4 μg/ml meropenem). The isolates were screened for carbapenem resistance genes and carbapenemase production by PCR and Modified Hodge test respectively. Selected isolates underwent WGS for detailed analysis of the bacterial genomes. Carbapenem-resistant bacteria were identified in 36.8 % (92/250) of chicken meat samples, from which 347 isolates were selected for further testing. Common species were <i>Morganella morganii</i>, <i>Providencia alcalifaciens</i>, <i>Stenotrophomonas pavanii, Klebsiella aerogenes</i>, <i>Proteus mirabilis</i>, <i>Providencia huaxiensis</i>, <i>Proteus terrae</i>, <i>Stenotrophomonas maltophilia and Klebsiella pneumoniae.</i> The carbapenemase genotypes detected were <i>bla</i> _NDM-114.7 % (51/347), <i>bla</i> _KPC-3 5.4 % (19/347) and <i>bla</i> _OXA-48-like 7.2 % (25/347). Two isolates were found to co-produce <i>bla</i> _NDM-1 and <i>bla</i> _OXA-48-like<i>,</i> while three isolates co-produced <i>bla</i> _NDM-1 and <i>bla</i> _KPC-3 <i>.</i>The majority of the PCR positive isolates were confirmed to produce carbapenemase in the Hodge test (<i>n</i> = 54/95). Two <i>K. pneumoniae</i> isolates (ST15 and ST16) carried resistance genes including <i>bla</i> _NDM-1 <i>, bla</i> _CTX-M <i>, bla</i> _SHV and <i>bla</i> _OXA-232; virulence factors id<i>ent</i>ified were <i>fep, ent, fyu, ybt</i>, <i>irp and OmpA,</i> alongside <i>yag/ ecp</i> and <i>ykg/ecp</i> complexes. This study highlights the need for the molecular surveillance studies in prominent poultry producing countries like India.