Genotyping Reveals Potential Sources of Human Leptospirosis Outbreaks in Aotearoa New Zealand

Abstract

Introduction: The introduction of PCR testing for leptospirosis in Aotearoa New Zealand has reduced the availability of serotyping data, and current diagnostic PCRs do not routinely genotype Leptospira. This study genotyped Leptospira from PCR-confirmed human cases between 2016 and 2023 and compared them with genotypes found in animals to identify potential sources of infection in a 2023 human leptospirosis outbreak.

Methods: Human samples were genotyped using glmU amplicon sequencing and compared to animal genotypes from previous studies. In addition, human national surveillance data were analysed to provide broader epidemiological context including regional distribution to reveal outbreak areas; diagnostic test usage to assess trends; serotyping results to evaluate consistency across methods; and demographic information to evaluate the representativeness of the genotyped dataset. Chi-squared and Poisson regression were used to assess host-genotype associations, and phylogenetics evaluated genetic relatedness.

Results: Surveillance data showed flood-associated outbreaks in several regions and a significant shift in diagnostic practice (p ≤ 0.001), with increased use of PCR. Genotyping of PCR-confirmed cases revealed a rise in Pomona infections in 2023 across rural flood-associated regions (Gisborne, Hawke's Bay, Manawatū-Whanganui, Waikato and Wairarapa). In contrast, the Auckland region—including Aotearoa's largest city which also experienced flooding—had infections linked to Ballum, Copenhageni and Balcanica NZ. In animals, Pomona was primarily detected in sheep (Ovis aries), followed by cattle, while Ballum, Copenhageni and Balcanica NZ were primarily detected in mice (Mus musculus), Norway rats (Rattus norvegicus) and brushtail possums (Trichosurus vulpecula), respectively.

Conclusions: Flooding-driven outbreaks in rural areas with pastoral livestock were predominantly linked to livestock-associated strains, while urban cases were associated with rodents and small wildlife. These findings highlight the need for tailored mitigation strategies addressing distinct epidemiological risks in rural and urban settings. Surveillance strategies should be adapted to preserve typing capabilities to better inform public health responses in future outbreaks.