published_or_final_version / Microbiology / Master / Master of Medical Sciences

Ingestion of contaminated chicken meat is a major cause of Campylobacteriosis in Europe and the USA. The environment, including wild birds, is considered to be an important reservoir for chicken colonization. The aims of this study were to determine the population structure of Campylobacter amongst chicken and wild bird sources on a single farm, and to establish the extent to which genotypes flow between them and ultimately infect humans, using MLST and antigen sequence typing. A pilot study amongst farm animals and wild birds in Lancashire demonstrated that Campylobacter genotypes from human disease were common on the farm and could be isolated from more than one animal source. Between 30-50% of wild geese and Starlings were shedding Campylobacter, with a seasonal peak in shedding rate in Spring. Genotypes were divergent from those previously isolated from human disease, retail meat and farm animal sources, with the majority being restricted to the host source. The carriage rate of Campylobacter was between 70- 100% amongst 78 free-range poultry flocks tested at 56 days of age. Up to seven genotypes were found to co-exist within a flock, and genotypes varied throughout the year on a random basis. Some Campylobacter strains were isolated from one farm site only, but a small percentage of them had spread nationally and were stable over a period of a decade. A total of 23% of Campylobacter isolates from free-range chickens were indistinguishable to those from human disease, and 5% were indistinguishable from wild birds. A total of 6% of genotypes isolated from wild birds were indistinguishable from those isolated from human disease. Wild birds could not be completely disregarded as a potential reservoir of Campylobacter for both humans and poultry, but their role is likely to be limited.

Bats and birds are known to be the reservoirs of a number of zoonotic diseases. The capacity of flight and the diversity of these animals may make them special in maintaining and disseminating diverse viruses leading to instances of emerging zoonoses. In particular bats are increasingly recognized to be reservoirs of a wide range of viruses, including Nipah, Ebola and severe acute respiratory syndrome (SARS) coronaviruses. In most instances these viruses appear to establish long-term persistence in bats. In this thesis I report the identification of novel astroviruses from different insectivorous species of apparently healthy bats sampled in Hong Kong and in 11 provinces of Mainland China with high positive rates. Astroviruses are important causes of diarrhea in many animal species, including humans. This study revealed a remarkably high genetic diversity of bat astroviruses, which form novel distinct phylogenetic groups in the genus Mamastrovirus. Evidence for varying degrees of host restriction for bats astroviruses has been found. The finding of diverse astroviruses in Miniopterus bats captured within a single cave habitat in Hong Kong illustrates a very unusual virus host relationship between astroviruses and these bats. Surveillance of astroviruses in rodents, the only mammal with species numbers surpassing that of bats, has revealed a novel astrovirus in only 1.6 % of the faecal samples of urban brown rat (Rattus norvegicus) in Hong Kong in marked contrast with the prevalence and diversity of astroviruses in bats. Rat astrovirus was phylogenetically related to human astroviruses MLB1 which was detected from clinical samples from diarrhoeal patients in Hong Kong in this study. The unusually high positive rates of astroviruses in bats have been again highlighted. Avastroviruses were detected in 7.1% of the aquatic wild bird samples. Avastrovirus have also been detected in doves in Hong Kong, pond herons and a less whistling duck in Cambodia. A phylogenetic analysis of these novel astroviruses together with other previously known astroviruses revealed that avastrovirus can be divided into 3 monophyletic groups. On the other hand, avian coronaviruses was detected in 12.5% of the aquatic wild bird samples. Phylogenetic analysis of these avian coronaviruses has led us to suggest taxonomic separation of these viruses into two groups as gammacoronaviruses and deltacoronaviruses. Frequent interspecies transmissions of gammacoronaviruses between duck species were demonstrated. Analysis of the avian viral sequences and host mitochondrial DNA sequences suggested that some coronaviruses may have coevolved with birds from the same order. With the discoveries of coronaviruses and astroviruses in mammalian and birds, we now have a better understanding on the diversity and ecology of these two virus families in wildlife. These findings provide new insights into the ecology and evolution of these viruses in nature and have revealed possible inter-species transmissions of these viruses. The role of bats as a reservoir of viruses with potential to pose zoonotic threats to human health was also reinforced. Studies of the virus ecology in wildlife as demonstrated in this thesis will help formulating better strategies for controlling emerging diseases in the future. / published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy