Hugo Strydom

Salmonella enterica subsp. enterica serovar Enteritidis ( S . Enteritidis) is the second most common serovar causing human salmonellosis in Aotearoa New Zealand (NZ). Sequence type (ST)183, which includes phage types 9a and 11, was the second most frequently isolated S . Enteritidis strain from human cases between 2020 and 2023. This ST is considered endemic in NZ as well as in mainland Europe and Great Britain, where the European hedgehog ( Erinaceus europaeus ) is a recognized wildlife reservoir. 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. The aim of this study was to investigate whether hedgehogs act as a reservoir for S . Enteritidis ST183 in NZ and to assess the evolutionary history and epidemiology of this strain across human, animal and environmental contexts. We analysed human, animal and environmental ST183 isolates, including hedgehog carcasses opportunistically sampled in NZ, using Bayesian phylogenetic methods integrated with national epidemiological data. Although S . Enteritidis ST183 was isolated from three of 45 hedgehog carcasses during our study, consistent with recent prior detections of ST183 in NZ hedgehogs, Bayesian phylogenetic analysis supports a most recent common ancestor for currently circulating ST183 strains in the late 20th century, ~100 years after the introduction of hedgehogs into NZ, providing no evidence that the strain was introduced concomitantly with hedgehogs. Epidemiological analysis revealed that, unlike in Europe, ST183 infections in NZ are more common in people aged over 60 years compared with non-ST183 S . Enteritidis infections, with rural residence and contact with farm animals identified as key risk factors. Together, these findings suggest that S . Enteritidis ST183 is established within the NZ rural environment, with evidence of interspecies transmission. While hedgehogs may contribute to the maintenance of ST183, they are unlikely to represent the original source of introduction, indicating a complex, multi-host ecology.

A Gram-negative bacillus isolated from human clinical cases in Aotearoa | New Zealand (NZ) and Australia was identified as a new species within the genus Yersinia based on genetic and phenotypic characteristics. This species demonstrated distinct biochemical differences in comparison to those typically reported for Yersinia enterocolitica (biotypes 1A, 1B, 2, 3, 4 and 5), including the ability to utilise raffinose and melibiose. Whole-genome sequencing data identified a total of 11 strains as a novel multi locus sequence type 598 (using the seven-gene McNally scheme). A closed genome for this species was obtained using Oxford Nanopore long-read sequencing, polished with high-accuracy Illumina short-read sequence data. Analysis of the 16S rRNA showed the closest similarity (98.36%) to Yersinia hibernica and Yersinia artesiana . Average nucleotide identity (ANI) values were below the threshold of ≤95% ANI when compared to the type strains of other Yersinia species, with Y. enterocolitica subsp. enterocolitica (94.1%) identified as the closest relative, thereby providing evidence that these strains should be considered as a novel species. The type strain is NZRM 4767 ^T = DSM 120367 ^T .

A corrigendum of this article has been published full details can be found at 10.1099/mgen.0.001594. Outbreaks caused by Salmonella Enteritidis are commonly linked to eggs and poultry meat internationally, but this serovar had never been detected in Aotearoa New Zealand (NZ) poultry prior to 2021. Locally designated genomic cluster Salmonella Enteritidis_2019_C_01, was implicated in a 2019 outbreak associated with a restaurant in Auckland. Four Enteritidis_2019_C_01 sub-clusters have since been identified, two retrospectively, in the Auckland region. Authorities initiated a formal outbreak investigation after genomically indistinguishable S . Enteritidis was isolated from the NZ poultry production environment. This study analysed 231 S . Enteritidis genomes obtained from the outbreak using Bayesian phylodynamic tools to gain insight into the outbreak’s dynamics and origin. We used Bayesian integrated coalescent epoch plots to estimate the change of the Enteritidis ST11 population size over time and marginal structured coalescent approximation to estimate transmission between poultry producers. We investigated human and poultry isolates to elucidate the time and location of the most recent common ancestor of the outbreak and transmission pathways. The median most recent common ancestor was estimated to be February 2019. We found evidence of amplification and spread of strain Enteritidis_2019_C_01 within the poultry industry, as well as transmission events throughout the production chain. The intervention by the public health and food safety authorities coincided with a drop in the effective population size of the S . Enteritidis ST11 as well as notified human cases. This information is crucial for understanding and preventing the transmission of S . Enteritidis in NZ poultry to ensure poultry meat and eggs are safe for consumption.

The rate of yersiniosis in New Zealand (NZ) is high compared with other developed countries, and rates have been increasing over recent years. Typically, >99% of human cases in NZ are attributed to Yersinia enterocolitica (YE), although in 2014, a large outbreak of 220 cases was caused by Yersinia pseudotuberculosis. Up until 2012, the most common NZ strain was YE biotype 4. The emergent strain since this time is YE biotype 2/3 serotype O:9. The pathogenic potential of some YE biotypes remains unclear. Most human cases of yersiniosis are considered sporadic without an identifiable source. Key restrictions in previous investigations included insufficient sensitivity for the isolation of Yersinia spp. from foods, although foodborne transmission is the most likely route of infection. In NZ, YE has been isolated from a variety of sick and healthy domestic and farm animals but the pathways from zoonotic reservoir to human remain unproven. Whole-genome sequencing provides unprecedented discriminatory power for typing Yersinia and is now being applied to NZ epidemiological investigations. A “One-Health” approach is necessary to elucidate the routes of transmission of Yersinia and consequently inform targeted interventions for the prevention and management of yersiniosis in NZ

Incidence of human yersiniosis in New Zealand has increased between 2013 and 2017. For surveillance and outbreak investigations it is essential that an appropriate level of discrimination between pathogenicYersinia enterocoliticaisolates is provided, in order to support epidemiological linking of connected cases. Subtyping of 227Y. enterocoliticaisolates was performed using a range of different typing methods, including biotyping, serotyping and seven loci multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, core genome single-nucleotide polymorphism (core SNP) analysis and multi-locus sequence typing were performed on a subset of 69 isolates. Sixty-seven different MLVA types were identified. One MLVA profile was associated with an outbreak in the Bay of Plenty region, supported by epidemiological data. Core SNP analysis showed that all the outbreak-related isolates clustered together. The subtyping and epidemiological evidence suggests that the outbreak of yersiniosis in the Bay of Plenty region between October and December 2016 could be attributed to a point source. However, subtyping results further suggest that the same clone was isolated from several regions between August 2016 and March 2017. Core SNP analysis and MLVA typing failed to differentiate betweenY. enterocoliticabiotype 2 and biotype 3. For this reason, we propose that these biotypes should be reported as a single type namely:Y. enterocoliticabiotype 2/3 and that the serotype should be prioritised as an indicator of prevalence.

Summary: This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed‐field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory ability of PFGE was so low as to severely limit its usefulness (DI Y. enterocolitica biotypes 2, 3 and 4, and inferences based on finding indistinguishable PFGE profiles among cases or between cases and sources need to be substantiated using alternative typing tools, or strong epidemiological evidence.