Supporting data for "Molecular Epidemiology of Exotic Pet-Associated Pathogens and their Associations with Gut Microbiome"

The recent expansion of global wildlife trade contributes substantially to the emergence of zoonotic and epizootic diseases. In particular, the exotic pet trade plays a major role by allowing pathogen admixture and recombination among diverse, wild-sourced animals, increasing spillover risks to naive wildlife and human populations with risks accentuated in regions actively participating in trade. Yet, the epidemiology of many exotic pet-associated pathogens, including prevalence, transmission routes, and risk factors, remains understudied, especially in Asia. The primary aim of this study is to clarify epidemiological features, including prevalence, genetic diversity, risk factors, and/or antibiotic resistance (AMR) profiles of four critical pathogens associated with exotic pets (i.e., avian viruses Psittacine Beak and Feather Disease Virus (PBFDv) and Budgerigar Fledgling Disease Virus (BFDV); and zoonotic pathogens Chlamydia psittaci and Salmonella) in Hong Kong, a major hub of wildlife trade.

Using nested PCR assays, we identified low prevalences of PBFDv and BFDV (Chapter 2), in over five hundred captive birds from domestic, commercial, and veterinary settings. Phylogenetic analyses suggested potential contributions of international bird trade to disseminating PBFDv in Hong Kong. Notably, birds in commercial settings exhibited significantly higher PBFDv prevalence, with similar rates in psittacine and non-psittacine species, indicating a prominent role of trade in viral transmission and the potential for non-psittacine birds to serve as reservoirs. Considering that many feral bird populations live within urban areas, these findings highlight spillover risks of PBFDv to local wildlife, with trade being a key driver.

For zoonotic pathogens, this study surveyed C. psittaci, the major causative agent of psittacosis, among captive birds to identify its prevalence and genotypes (Chapter 3); and Salmonella, a widely distributed resilient pathogen, among pet reptiles and amphibians to clarify their prevalence and AMR profiles (Chapter 4). By detecting the ompa gene, a low prevalence of C. Psittaci was found with all strains belonging to genotype A, the most virulent genotype to humans. Identified strains clustered closely with those from diverse hosts (birds and mammals), suggesting generalist behavior and high zoonotic potential. Meanwhile, Salmonella was isolated from a majority of sampled pet herptiles, with prevalence comparable between reptiles and amphibians. Most isolates exhibited AMR with some being multi-drug resistant, adding to the limited evidence on AMR carriage by captive exotic pets within Asia.

Finally, to explore host-microbiota-pathogen dynamics in PBFDv infection (Chapter 5), this study investigated the associations of MHC functional diversity and gut microbiome with PBFDv levels in rosy-faced lovebirds (Agapornis roseicollis). Results revealed a negative association between MHC-I diversity and pathogenic bacteria abundance, which was positively linked to PBFDv load. In addition, findings suggest the presence of differential MHC-dependent mechanisms in the sculpture of pathogens and commensal compositions, offering insights into how MHC-I variations influence immune fitness in parrots.

Collectively, this study advances understanding of exotic pet-associated pathogens at the population (trade-driven spread, risk factors) and individual (host-microbiome interactions) levels. It emphasizes the need to integrate captive wildlife into One Health frameworks to mitigate zoonotic and conservation threats while providing insights for avian medicine and biosecurity policy.