Wild birds, including migratory species, are understudied reservoirs of enterococci in South Africa. This study investigated the resistome, mobilome, virulome and genetic diversity of enterococci from wild birds frequenting water bodies during the migratory season in Gauteng, South Africa. Faecal samples were collected from five sites between November 2023 and March 2024. Enterococci were isolated on selective media and identified with polymerase chain reaction and Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry, with 48 isolates undergoing whole-genome sequencing analysis: Enterococcus faecalis (E. faecalis) (56. 3% (27/48) ), Enterococcus faecium (E. faecium) (18. 8% (9/48) ) and other enterococci (25. 0% (12/48) ). Aminoglycoside resistance genes aph (3') -III (11. 1% (3/27) ) and ant (6') -Ia (7. 4% (2/27) ) were detected in E. faecalis and linked to Inc18 and RepAN plasmids. Linezolid resistance was confirmed in an E. faecalis (MIC = 24 μg/mL) and E. faecium (MIC = 8 μg/mL) isolate carrying optrA and rplDN130K, respectively, with optrA linked to plasmid-derived sequences. A daptomycin resistance-associated liaSE192G mutation was identified in one E. faecium isolate (MIC = 4μg/mL). Five potential multidrug-resistant E. faecalis and E. faecium isolates belonged to infrequently described strains. Clinically relevant virulence genes in E. faecalis included: gelE (100%), asa1 25. 9% (7/27), hylA 59. 3% (16/27), hylB 74. 1% (20/27) and sex-pheromone genes (100%). Phylogenetic analysis revealed wild bird-adapted strains, alongside One Health-relevant E. faecalis ST16 and ST21 and E. faecium ST54 and ST800 lineages, with limited clustering with global isolates. Wild birds harbour enterococcal lineages carrying antimicrobial resistance genes, underscoring surveillance within a One Health framework in low- and middle-income countries.
Govender et al. (Fri,) studied this question.