Frontiers in veterinary science · 2026
Shelter dogs and cats as a one health interface for phenotypic and genomic surveillance of antimicrobial-resistant Enterococcus Spp. in the United Arab Emirates.
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Habib Ihab, Mohteshamuddin Khaja, Mohamed Mohamed-Yousif Ibrahim, Bhagya Lakshmi Glindya, Antony Asha, Elbediwi Mohammed
Аннотация
BACKGROUND: Companion animal shelters represent underexplored settings for One Health antimicrobial resistance (AMR) surveillance. This study investigated the recovery, antimicrobial resistance, and genomic features of Enterococcus spp. from shelter dogs and cats in the United Arab Emirates (UAE).
METHODS: Rectal swabs were collected from 230 shelter animals, including 129 dogs and 101 cats, across five shelters in four UAE emirates/cities. Enterococcus isolates were recovered using selective culture and identified by MALDI-TOF MS. Confirmed Enterococcus faecalis and Enterococcus faecium isolates underwent antimicrobial susceptibility testing using Vitek-2. Multidrug-resistant (MDR) and linezolid-resistant isolates were subjected to whole-genome sequencing (WGS) for multilocus sequence typing, resistome analysis, single-nucleotide polymorphism-based phylogeny, phenotype-genotype concordance assessment, and virulence-associated gene profiling.
RESULTS: Enterococcus spp. were recovered from 122/230 animals (53.0%; 95% confidence interval: 46.6-59.4), with higher recovery in dogs (71.3% (92/129)) than cats (29.7% (30/101)). Overall, E. faecalis accounted for 63/122 isolates (51.6%) and E. faecium for 59/122 isolates (48.4%). Phenotypic resistance was most frequent for tetracycline (51.6%), erythromycin (30.3%), ciprofloxacin (27.2%), high-level streptomycin (20.5%), and high-level gentamicin (9.8%). All isolates were susceptible to ampicillin, vancomycin, teicoplanin, and tigecycline. MDR was detected in 25/122 isolates (20.5%) and was more frequent among E. faecalis than E. faecium. Linezolid resistance was detected in two isolates recovered from two dogs, one male and one female, housed in the same shelter. WGS of 25 MDR or linezolid-resistant isolates revealed diverse sequence types, including dominant E. faecalis ST16, shelter-associated SNP clusters, and multiple resistance determinants, including erm(B), tet(L), tet(M), aminoglycoside resistance genes, quinolone resistance-associated mutations, and plasmid-predicted optrA in three E. faecalis isolates. Virulence-associated genes were more prominent in E. faecalis, particularly the endocarditis- and biofilm-associated pilus genes involved in adhesion and biofilm formation, together with a putative exoenzyme-associated factor potentially contributing to host interaction and bacterial fitness.
CONCLUSIONS: Shelter dogs and cats in the UAE carried E. faecalis and E. faecium with phenotypic AMR, MDR profiles, and diverse genomic resistance determinants. The detection of linezolid resistance and plasmid-predicted optrA supports inclusion of shelter companion animals in regional One Health AMR surveillance.
METHODS: Rectal swabs were collected from 230 shelter animals, including 129 dogs and 101 cats, across five shelters in four UAE emirates/cities. Enterococcus isolates were recovered using selective culture and identified by MALDI-TOF MS. Confirmed Enterococcus faecalis and Enterococcus faecium isolates underwent antimicrobial susceptibility testing using Vitek-2. Multidrug-resistant (MDR) and linezolid-resistant isolates were subjected to whole-genome sequencing (WGS) for multilocus sequence typing, resistome analysis, single-nucleotide polymorphism-based phylogeny, phenotype-genotype concordance assessment, and virulence-associated gene profiling.
RESULTS: Enterococcus spp. were recovered from 122/230 animals (53.0%; 95% confidence interval: 46.6-59.4), with higher recovery in dogs (71.3% (92/129)) than cats (29.7% (30/101)). Overall, E. faecalis accounted for 63/122 isolates (51.6%) and E. faecium for 59/122 isolates (48.4%). Phenotypic resistance was most frequent for tetracycline (51.6%), erythromycin (30.3%), ciprofloxacin (27.2%), high-level streptomycin (20.5%), and high-level gentamicin (9.8%). All isolates were susceptible to ampicillin, vancomycin, teicoplanin, and tigecycline. MDR was detected in 25/122 isolates (20.5%) and was more frequent among E. faecalis than E. faecium. Linezolid resistance was detected in two isolates recovered from two dogs, one male and one female, housed in the same shelter. WGS of 25 MDR or linezolid-resistant isolates revealed diverse sequence types, including dominant E. faecalis ST16, shelter-associated SNP clusters, and multiple resistance determinants, including erm(B), tet(L), tet(M), aminoglycoside resistance genes, quinolone resistance-associated mutations, and plasmid-predicted optrA in three E. faecalis isolates. Virulence-associated genes were more prominent in E. faecalis, particularly the endocarditis- and biofilm-associated pilus genes involved in adhesion and biofilm formation, together with a putative exoenzyme-associated factor potentially contributing to host interaction and bacterial fitness.
CONCLUSIONS: Shelter dogs and cats in the UAE carried E. faecalis and E. faecium with phenotypic AMR, MDR profiles, and diverse genomic resistance determinants. The detection of linezolid resistance and plasmid-predicted optrA supports inclusion of shelter companion animals in regional One Health AMR surveillance.