# Genomic epidemiology of strains currently and formerly classified as Enterobacter spp. recovered from equine necropsy samples

## TL;DR

This study uses genomic methods to identify and analyze bacteria from horse necropsies, revealing antibiotic resistance and virulence factors in some strains.

## Contribution

The study demonstrates that rMLST is more reliable than MALDI-TOF for identifying less-studied bacterial genera in equine samples.

## Key findings

- Enterobacter spp. strains showed high sequence diversity and antibiotic resistance genes.
- rMLST identified diverse genera like Huaxiibacter and Rahnella, which MALDI-TOF failed to detect.
- High-risk clones like E. hormaechei ST114 and ST171 were found to carry resistance and virulence genes.

## Abstract

Enterobacteriaceae are opportunistic pathogens responsible for local or systemic infections in both human and veterinary medicine. To monitor circulating strains in stud farms in Normandy (France), we investigated a collection of Enterobacteriaceae isolated from necropsied equids performed in the region between 1997 and 2020. These strains were initially identified using MALDI-TOF; however, as this method failed to identify some isolates, whole genome sequencing followed by rMLST analysis was subsequently performed. Different genera were identified: Enterobacter spp., Huaxiibacter spp., Lelliottia spp., Rahnella spp.. MALDI-TOF and rMLST identifications were concordant for only 26.5% of the strains studied, leading us to conclude that rMLST is a more reliable method for both genus- and species-level identification, particularly for less-studied genera such as Huaxiibacter spp. and Rahnella spp.. The genus Enterobacter spp. (E. hormaechei and E. ludwigii) accounted for 53% of the strains with a high degree of sequence type (ST) diversity. These include E. hormaechei ST114 and ST171, known as high-risk clone in human clinical medicine. These clones, containing plasmids and acquired resistance genes such as blaOXA-1, blaSHV-12 or blaTEM-1B, are resistant to at least four classes of antibiotics. The presence of genes encoding the enteroaggregative heat-stable enterotoxin 1 or the bacteriocin colicin, probably carried by plasmids, implies that Enterobacter spp. form a reservoir of antibiotic resistance and virulence factors. Conversely, strains of the genera Huaxiibacter spp., Lelliottia spp. and Rahnella spp. naturally found in the environment, showed a lean resistome and virulome. This analysis shows that genomic studies are essential to obtain precise species identification, monitor and detect high-risk clones, and to highlight the circulation of resistance and virulence genes through mobile genetic elements.