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 (n = 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 Morganella morganii, Providencia alcalifaciens, Stenotrophomonas pavanii, Klebsiella aerogenes, Proteus mirabilis, Providencia huaxiensis, Proteus terrae, Stenotrophomonas maltophilia and Klebsiella pneumoniae. The carbapenemase genotypes detected were blaNDM-114.7 % (51/347), blaKPC-3 5.4 % (19/347) and blaOXA-48-like 7.2 % (25/347). Two isolates were found to co-produce blaNDM-1 and blaOXA-48-like, while three isolates co-produced blaNDM-1 and blaKPC-3.The majority of the PCR positive isolates were confirmed to produce carbapenemase in the Hodge test (n = 54/95). Two K. pneumoniae isolates (ST15 and ST16) carried resistance genes including blaNDM-1, blaCTX-M, blaSHV and blaOXA-232; virulence factors identified were fep, ent, fyu, ybt, irp and OmpA, alongside yag/ ecp and ykg/ecp complexes. This study highlights the need for the molecular surveillance studies in prominent poultry producing countries like India.