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

Abstract

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 (1860-1979) 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.