Extensively drug-resistant and extended spectrum β-lactamase-producing Raoultella terrigena from the reproductive tract of a mare in Australia.

Raoultella terrigena is a bacterium commonly isolated from environmental sources, with rare reports of isolation from clinical samples. Multidrug resistance is also rare. In this study, R. terrigena was obtained from the uterine lavage of a thoroughbred mare. Broth microdilution and disc diffusion methods were used to determine susceptibility to antimicrobials. Whole genome sequencing was performed to identify and characterise the presence of mobile genetic elements, antimicrobial resistance and virulence genes. Pan-genome analysis allowed comparison of the genome of this isolate with other R. terrigena isolates. Phenotypic resistance was detected to cefazolin, ceftiofur, cefotaxime, ticarcillin/clavulanic acid, tetracycline, doxycycline, gentamicin, sulfamethoxazole/trimethoprim and chloramphenicol. The genome included two plasmids (IncQ1/IncU and IncFII/rep_cluster_2078 types). Also identified in the IncQ1/IncU plasmid were genes conferring resistance to aminoglycosides, fluoroquinolones, rifamycin, phenicols, cephalosporins, diaminopyrimidines, sulfonamides and tetracycline. Except for enrofloxacin susceptibility, the presence of resistance genes was consistent with observed phenotypes. Genes conferring resistance to antiseptics, biocides and metals were also detected. Phylogenetic analysis of the combined dataset, including the isolate in this study and publicly available genomes, revealed two distinct clades, with equine isolates clustering together with other animal-derived isolates. The emergence of antimicrobial resistance in rare opportunistic pathogens underlines the importance of continuous monitoring of such bacteria and emphasizing the need for developing antimicrobial stewardship programs in veterinary settings.