Genomic Diversity and Coexistence of Multidrug-Resistance Mechanisms of Klebsiella pneumoniae in Poultry Farms

Abstract

Klebsiella pneumoniae is an opportunistic pathogen and poses a serious threat to the livestock industry and human health. Therefore, it is necessary to investigate the prevalence of K. pneumoniae in agricultural settings. In this study, fecal and environmental samples from poultry farms were collected, and the antibiotic resistance prevalence and genetic diversity of K. pneumoniae were determined through antimicrobial susceptibility testing, whole-genome sequencing (WGS), and bioinformatics analysis. Resistance phenotype analysis of 99 strains indicated that all of them exhibited resistance to most of the tested antimicrobials. Genome data analysis revealed the coexistence of the tmexCD-toprJ efflux pump gene cluster along with either bla_NDM or mcr genes on IncFIB(Mar)/HI1B plasmids in four isolates. Phylogenetic analysis of the tmexCD-toprJ-positive K. pneumoniae isolates revealed a predominance of sequence types (STs) ST2185 and ST15. These isolates were characterized by the presence of key virulence factors, including the aerobactin siderophore gene iutA and the salmochelin siderophore gene iroE, which are associated with enhanced invasiveness and pathogenicity. In addition, conjugation experiments showed that tmexCD-toprJ and bla_NDM could be transferred to Escherichia coli J53, while mcr is impervious to interspecies transfer. Although avian-derived K. pneumoniae differs from human-derived K. pneumoniae, the spread of multidrug-resistant (MDR) plasmids encoding both tmexCD-toprJ and bla_NDM among different bacteria has raised significant public health concerns. Our analysis indicates that this MDR plasmid harboring critical resistance genes is widely disseminated in chicken farms, and it is necessary to conduct further epidemiological surveillance of such plasmids on a global scale to mitigate the threat to global public health.