Application of phylodynamics to support surveillance of bacterial enteric pathogens in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy, Massey University, Palmerston North, New Zealand. EMBARGOED until 8 October 2027.

Abstract

Salmonella enterica subsp. enterica serovar Enteritidis (particularly sequence types ST11 and ST183) and Yersinia enterocolitica ST12 are major contributors to morbidity from enteric bacterial infections in New Zealand (NZ). Despite their public health importance, critical gaps remain in understanding their reservoirs, transmission pathways, evolutionary histories, and drivers of recent increases in incidence. In particular, the ecological niches of these pathogens and the relative contributions of animal, environmental, and food sources to human infection are poorly defined, limiting the effectiveness of surveillance and control strategies. This thesis integrates whole-genome sequencing with phylodynamic and comparative genomic analyses to investigate the emergence, transmission, and persistence of S. Enteritidis ST11 and ST183 and Y. enterocolitica ST12 in NZ. Genomic evidence demonstrated that the outbreak strain S. Enteritidis SE-19C01 (ST11) was introduced into the NZ poultry industry only months before the first detected human case, followed by multiple transmission and amplification events within poultry production environments. The rapid expansion in effective bacterial population size coincided with increased human notifications and multiple point-source outbreaks. Importantly, a subsequent marked decline in effective population size aligned with interventions implemented by the NZ Ministry of Health, the NZ Ministry for Primary Industries, and the NZ poultry industry, indicating the effectiveness of these control measures. Previous literature suggests that European hedgehogs (Erinaceus europaeus) are a major reservoir for S. Enteritidis ST183 in Great Britain and mainland Europe. Hedgehogs were introduced to NZ in the late 19th century; however, their role in the ecology of ST183 in NZ has not been formally evaluated. Phylodynamic analyses showed no temporal association of S. Enteritidis ST183 with the historical introduction of hedgehogs to NZ. Instead, my results showed that ST183 was introduced approximately a century later and is now widespread in the NZ environment. While limited sample size precludes definitive attribution of hedgehogs as a reservoir, evidence of interspecies transmission supports their role as environmental sentinels. Genomic analyses revealed differences between NZ and European ST183 strains, including loss of function of the idnT gene and presence of ydjG and clpV1_2, suggesting local adaptation to a distinct environmental reservoir. Finally, this study identified Y. enterocolitica ST12-SL1, a prolonged circulating lineage accounting for 39% of notified yersiniosis cases caused by Y. enterocolitica ST12 between mid-2024 and mid-2025. Overall, this work demonstrates the value of integrating genomics and phylodynamics into a One Health surveillance framework to inform timely, evidence-based public health action in NZ.