Assessing the Bacterial Zoonotic Risks Associated with the Pet Trade

Bates, Jodie (2021) Assessing the Bacterial Zoonotic Risks Associated with the Pet Trade. Doctoral thesis (PhD), Manchester Metropolitan University in collaboration with World Animal Protection.

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Abstract

Background. Zoonotic diseases can impart devastating consequences on social, medical, ecological and economical levels. An important driver of zoonotic disease is the pet trade; however, little is known about the presence of bacterial species across publicly accessible surfaces within pet shops. Furthermore, the increasing popularity of exotic pets can disproportionately affect some species over others; for example, Python regius, colloquially known as the Ball Python, is the most traded pet python species globally. The extent of the trade, along with the practice of ’ranching’, is potentially unsustainable. Aims/Objectives. This project aimed to i) develop a DNA extraction method suitable for retrieving data from low-biomass samples; ii) identify key bacterial zoonotic pathogens, referred to as target genera, within the literature to provide a foundation for microbial community analysis; iii) characterise bacterial communities associated with a range of surfaces - primarily publicly accessible - within a pet shop; iv) characterise bacterial microbiota associated with Python regius and feeder rodents within breeding farms in Africa; and v) use the information gathered from the wider literature to infer the presence of target genera within the pet shop and animal samples. Results. Phenol-chloroform extraction was found to be the most sensitive DNA extraction method, with a limit of detection of 28 cells. The systematic literature review found that: i) there were research biases at the genus and animal level, with Salmonella and fish and birds investigated the most respectively. Overall, nearly 10 % of genera isolated from the pet shop samples were target genera. Samples clustered based on animal type, inferring the presence of distinct animal-associated microbiomes. However, with one exception, these relationships became less distinct when clustering the target genera only. Multiple target genera were present across at least half of the samples, in addition to those accounting for more than 1 % of the sequencing reads. Finally, all of the sample types from Python regius and feeder rodents contained target genera, although feeder rodents contained a greater number of target genera for oral and rectal samples relative to the corresponding snake samples. Summary. The results are indicative of the presence of multiple potentially pathogenic genera within pet shops and the key animal species. More research is required using techniques capable of identification at the species and strain level to confirm the pathogenicity potential.