Molecular and eco-epidemiology of Leptospira borgpetersenii serovar Ballum in wild invasive mammals in a farming environment in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand

Abstract

Leptospirosis is an important zoonosis in New Zealand where it has historically been associated with livestock. Formerly negligible in human cases notified, 𝘓𝘦𝘱𝘵𝘰𝘴𝘱𝘪𝘳𝘢 𝘣𝘰𝘳𝘨𝘱𝘦𝘵𝘦𝘳𝘴𝘦𝘯𝘪𝘪 serovar Ballum—associated with rodents and hedgehogs (𝘌𝘳𝘪𝘯𝘢𝘤𝘦𝘶𝘴 𝘦𝘶𝘳𝘰𝘱𝘢𝘦𝘶𝘴)—is now preponderant. The role of wild introduced mammals in the epidemiology of leptospirosis has been overlooked in New Zealand but remains a critical question. In this thesis, we determined the prevalence of 𝘓𝘦𝘱𝘵𝘰𝘴𝘱𝘪𝘳𝘢 serovars, renal colonisation and seroprevalence in wild mammals and sympatric livestock. During a cross-sectional and a longitudinal survey, house mice (𝘔𝘶𝘴 𝘮𝘶𝘴𝘤𝘶𝘭𝘶𝘴), ship rats (𝘙𝘢𝘵𝘵𝘶𝘴 𝘳𝘢𝘵𝘵𝘶𝘴) and hedgehogs were trapped in farms with a history of leptospirosis to collect sera and kidneys. Urine and sera from livestock (dairy or beef cattle, sheep) and dogs were also collected on the same farms. Sera were tested by microagglutination test to identify serovars/serogroups that circulate in wildlife for comparison with those circulating in livestock. Urine and kidney samples were used to determine prevalence by qPCR, to isolate circulating leptospires by culture and subject them to whole genome sequencing, in order to determine their phylogenetic relationships and compare them to other sequences locally, nationally and internationally. Capture-mark recapture (CMR) methods were used to investigate the population dynamics of mice naturally infected with Ballum. Finally, the level of lesions and bacterial load in kidneys were assessed visually by histopathology and put in perspective with other results to investigate reservoir dynamics. Direct or indirect presence of Ballum was found in all wild and domestic species investigated. Overall apparent prevalence in mice, rats and hedgehogs was respectively 46%, 95% CI [39, 52%], 44% [26, 62%] and 27% [11, 50%]. It varied greatly between seasons in mice, with a spring peak (83 to 86%) and minimum in autumn (31 to 37%). Mice densities reached up to 56 mice/ha and varied seasonally in the opposite way, resulting in a relatively constant density of infected mice, ranging 3-8 infected mice/ha. An extremely low rate of mutations hindered the investigation of transmission pathways using genomics. However, despite little or no lesions in all species, the bacterial load was markedly higher in mice, suggesting rats and hedgehogs are secondary hosts. Control strategies to mitigate exposure to 𝘓𝘦𝘱𝘵𝘰𝘴𝘱𝘪𝘳𝘢 in NZ should include wild mammals, and especially mice.