The microbial ecology of Campylobacter jejuni in New Zealand within a spatial-temporal framework : a thesis presented in partial fulfilment of requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatu, New Zealand

Campylobacter jejuni (C. jejuni) is an important cause of gastroenteritis internationally; it is a complex bacterium carried by multiple hosts, showing phenotypic and genotypic variation. This thesis systematically examines the molecular ecology and evolution of C. jejuni in New Zealand from the levels of population movement, phenotype, genome and metabolism. First, the demographic history of cattle, sheep and poultry importations into New Zealand (18601979) was quantified. Australia was the most common reported source of cattle sheep and poultry, with large numbers of cattle and sheep being imported in the 1860s, and large numbers of poultry imported from the 1960s onwards. This suggests the population structure of cattle and sheep and the microbial organisms they carried may exhibit a founder effect. The second level investigated the phenotypes of related sequence types (ST) with generalist and specialist lifestyles and compared them at 42°C and 22°C on the basis of carbon source utilisation in Biolog phenotypic microarrays. The isolates utilised a total of 29 carbon sources in a pattern that clustered them together on the basis of ST at 42°C more than lifestyle and host. At 22°C they utilised a limited palette of carbon sources (9) related to the tricarboxylic acid cycle (TCA). The third level, used genomic comparisons to identify a putative new species C. sp. nov. 4 spp. in the Australian purple swamphen (Porphyrio porphyrio melanotus). Overall, the pattern of relationship between isolates associated with the pukeko (Porphyrio porphyrio melanotus), takahe (Porphyrio hochstetteri) and the Australian swamphen isolates suggested a recent common ancestor and then divergence after separation. Despite high levels of recombination in C.jejuni, the genomes grouped by clonal complex and ST, this suggests there are factors restricting regular recombination between more distant C. jejuni STs. The draft genomes for the wild-bird and agricultural-related isolates clustered by lineages in a host(s). The fourth level involved the comparison of C. jejuni metabolic pathways (subsystems) to identify host association. Type VI secretion system, Coenzyme A biosynthesis and Campylobacter spp. iron metabolism were identified as important pathways in distinguishing between wild-bird and livestock associated isolates. We stand on the shoulders of giants. used by Sir Isaac Newton Acknowledgements My Supervisors: Professor Nigel French, Dr Patrick Biggs, Associate Professor Barbara Holland, Dr Phil Carter, and Dr Jonathan Marshall. The mEpiLab team: Angie Reynolds, Dr Anne Midwinter, Dr Julie Collins-Emmerson, Anthony Pita, Neville Hack, Sarah Moore, Rukhshana Nahid Akhter and Lynn Rogers. Helpers from across the Tasman: Dr Mary Valcanis of the Microbiological Diagnostic Unit (MDU) at Melbourne University and Dr Carl Mulnickel of the ASAP Lab. The volunteers who collected samples: Will Steele, Katrina Lee, Christine Hurring, Sandra Martig, Dorothy Dhaeze,Michael Tarburton, Tiffany Miller-Scott, Peter Dann and James O’Connor of Birdlife Australia. Massey University Support Staff: Jacque Mackenzie, Wendy Maharey, Christine Cunningham and Debbie Hill, and Noelene White. Software and IT help: Simon Verschaffelt, Xavier Didelot (ClonalFrame), Marco Galardini (Ductape), Bruno Contreras Moreira (Get Homologues), Markus Goker (opm), Korbinian Strimmer (binda), Vladimir Minin (rbrothers), Michael Woodhams (ADD), Sajia Akhter (Phispy) and Maulik Shukla (PATRIC). Friends and family: I wish to thank the postgrads of the Hopkirk for their help and comradeship especially Anja Friedrich, Hamid Ishad, Fang Fang and Patricia Jaros. The TTP team including Lesley Stringer, Debbie Leader, Jackie Benshop, Chris Jewell, Becky Frost and many more. Edward George Binney for his warmth and companionship that enriched my life. Funding: This research was made possible by funding from Massey University, the Marsden fund, and IVABs funding. I have met and been inspired by many people in my life, which has helped me to and through my journey, too many to list here, so I apologise to those I have not directly mentioned.