Antimicrobial resistance in the monotreme microbiome

Context Antimicrobial resistance (AMR) is a global health crisis requiring a One Health approach that recognises the interconnectedness of people, animals and the environment. Since wide adoption of the One Health framework, wildlife species have been identified as important potential reservoirs and vectors of antimicrobial-resistant bacteria. Studies have demonstrated that antimicrobial-resistant bacteria commonly found in human enteric microbiomes are present in ecologically and phylogenetically diverse wildlife species, with a higher frequency typically found in animals in closer proximity to anthropogenic activities. Aims This Australian study examined the role that anthropogenic environments (wildlife hospitals and zoological institutions) play in the carriage of AMR determinants in two native monotreme species, the short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus), which are both under increasing pressure from a growing human population and habitat loss. Key results The frequency and diversity of the clinical class 1 integron, a genetic element associated with AMR in enteric bacteria, was examined by extracting DNA from faecal and cloacal swab samples derived from the short-beaked echidna and platypus in wild, zoo and rehabilitation settings. The DNA samples were then screened for class 1 integron variants (qacEΔ and IS26). Overall, clinical class 1 integrons were detected in 41 of 156 (26.3%) short-beaked echidna samples and 7 of 49 (14.3%) platypus samples. DNA sequencing revealed the presence of antibiotic resistance genes for aminoglycosides (aadA genes) and trimethoprim (dfrA genes) drug classes in both monotremes. Conclusions The occurrence and the diversity of integrons and AMR genes were highest in samples derived from zoos, followed by animals in rehabilitation settings and then from the wild, suggesting that exposure to anthropogenic environments are an important predictor of class 1 integron occurrence and AMR gene diversity in both the short-beaked echidna and the platypus. Implications Better understanding of the types of antibiotic resistance genes common in monotremes will inform antimicrobial stewardship relative to veterinary care of monotremes in wildlife hospitals, rehabilitation settings, and captive breeding programs.