Wild birds as reservoirs of antimicrobial-resistant enterococci : genomic surveillance in Gauteng, South Africa, during the migratory season

Abstract

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 Ionization-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 RepA_N plasmids. Linezolid resistance was confirmed in an E. faecalis (MIC = 24 μg/mL) and E. faecium (MIC = 8 μg/mL) isolate carrying optrA and rplD_N130K, respectively, with optrA linked to plasmid-derived sequences. A daptomycin resistance-associated liaS_E192G mutation was identified in one E. faecium isolate (MIC = 4 μg/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.

HIGHLIGHTS • Aminoglycoside, linezolid and daptomycin resistance determinants detected. • Linezolid resistance expressed in E. faecalis (optrA) and E. faecium (rplD_N130K). • Mobile genetic elements linked to antimicrobial resistance genes. • Potentially virulent E. faecalis isolates harbouring asa1, gelE and hylAB genes. • Diverse and uncommon STs reflecting wild bird-adapted strains and genome plasticity.