Genomic Insights into Pluralibacter gergoviae Sheds Light on Emergence of a Multidrug-Resistant Species Circulating between Clinical and Environmental Settings

Pluralibacter gergoviae is a member of the Enterobacteriaceae family that has been reported sporadically. Although P. gergoviae strains exhibiting multidrug-resistant profiles have been identified an in-depth genomic analysis focusing on antimicrobial resistance (AMR) has been lacking, and was therefore performed in this study. Forty-eight P. gergoviae strains, isolated from humans, animals, foods, and the environment during 1970-2023, were analyzed. A large number of single-nucleotide polymorphisms were found, indicating a highly diverse population. Whilst P. gergoviae strains were found to be circulating at the One Health interface, only human and environmental strains exhibited multidrug resistance genotypes. Sixty-one different antimicrobial resistance genes (ARGs) were identified, highlighting genes encoding mobile colistin resistance, carbapenemases, and extended-spectrum beta-lactamases. Worryingly, the co-occurrence of mcr-9.1, bla(KPC-2), bla(CTX-M-9), and bla(SHV-12), as well as mcr-10.1, bla(NDM-5), and bla(SHV-7), was detected. Plasmid sequences were identified as carrying clinically important ARGs, evidencing IncX3 plasmids harboring bla(KPC-2), bla(NDM-5), or bla(SHV-12) genes. Virulence genotyping underlined P. gergoviae as being a low-virulence species. In this regard, P. gergoviae is emerging as a new multidrug-resistant species belonging to the Enterobacteriaceae family. Therefore, continuous epidemiological genomic surveillance of P. gergoviae is required.

Automated summary

This study conducted a genomic analysis of Pluralibacter gergoviae, a member of the Enterobacteriaceae family, and found a highly diverse population. While P. gergoviae strains were found in humans and the environment, only human and environmental strains exhibited multidrug-resistant profiles. Additionally, numerous antimicrobial resistance genes were identified, including those encoding mobile colistin resistance. The findings indicate that P. gergoviae is emerging as a new multidrug-resistant species, necessitating continuous epidemiological genomic surveillance.