Genomic epidemiology of strains currently and formerly classified as Enterobacter spp. recovered from equine necropsy samples.
Authors: Harel Blandine, Sévin Corinne, Le Hello Simon, Moreau Peggy, Giard Jean-Christophe, Petry Sandrine, Gravey François
Journal: PloS one
Summary
# Editorial Summary Between 1997 and 2020, French researchers examined Enterobacteriaceae isolated from necropsied equids in Normandy to understand which pathogenic strains were circulating in stud farms and assess their antimicrobial resistance profiles. Initial identification by MALDI-TOF mass spectrometry proved unreliable, prompting whole genome sequencing and rMLST (ribosomal multilocus sequence typing) analysis, which revealed critical discordance: only 26.5% of identifications matched between the two methods, with rMLST proving substantially more accurate for genus and species determination, particularly for less-commonly encountered genera. Enterobacter spp. dominated the collection at 53% of isolates, predominantly E. hormaechei and E. ludwigii, with concerning diversity in sequence types including high-risk clones (ST114 and ST171) previously associated with human clinical infections; these strains carried multiple antibiotic resistance genes (blaOXA-1, blaSHV-12, blaTEM-1B) conferring resistance to four or more antibiotic classes, alongside virulence factors including enteroaggregative heat-stable enterotoxin and colicin-encoding genes, whilst other genera (Huaxiibacter, Lelliottia, Rahnella) showed minimal resistance or virulence potential. For equine practitioners, this work underscores that phenotypic identification methods alone are insufficient for accurate diagnosis and resistance prediction; genomic approaches are necessary to identify high-risk clones, track resistance gene dissemination via plasmids, and inform evidence-based antimicrobial stewardship decisions, particularly in multi-animal environments where resistant pathogens pose significant infection control challenges.
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Practical Takeaways
- •Genomic sequencing should be used for reliable identification of Enterobacteriaceae in equine infections, particularly when MALDI-TOF results are inconclusive, to enable accurate epidemiological monitoring and infection control
- •High-risk antibiotic-resistant Enterobacter clones circulate in equine populations; clinicians should consider resistance patterns when selecting empirical antimicrobial therapy for suspected enterobacterial infections
- •Stud farm biosecurity protocols should address the circulation of resistance genes through mobile genetic elements, as Enterobacter spp. act as reservoirs that can spread resistance to other bacterial species
Key Findings
- •rMLST whole genome sequencing identified Enterobacteriaceae more reliably than MALDI-TOF, with concordance in only 26.5% of strains
- •Enterobacter spp. (E. hormaechei and E. ludwigii) represented 53% of isolates with high sequence type diversity, including high-risk clones ST114 and ST171
- •Identified Enterobacter strains carried multiple antibiotic resistance genes (blaOXA-1, blaSHV-12, blaTEM-1B) conferring resistance to at least four antibiotic classes
- •Enterobacter spp. harbour plasmid-borne virulence factors including enteroaggregative heat-stable enterotoxin 1 and colicin genes, functioning as a reservoir for resistance and virulence genes