Evaluating sub-typing methods for pathogenic Yersinia enterocolitica to support outbreak investigations in New Zealand

Abstract

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 pathogenic Yersinia enterocolitica isolates is provided, in order to support epidemiological linking of connected cases. Subtyping of 227 Y. enterocolitica isolates 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 between Y. enterocolitica biotype 2 and biotype 3. For this reason, we propose that these biotypes should be reported as a single type namely: Y. enterocolitica biotype 2/3 and that the serotype should be prioritised as an indicator of prevalence.

Keywords: Outbreaks; Yersinia enterocolitica; surveillance.

Fig. 1.

Minimum spanning tree of 227 pathogenic Y. enterocolitica generated with BioNumerics v 7.6. Each circle represents a MLVA profile and its size is proportional to the number of isolates. Each colour represents a different geographical region. Partitioning grouped MLVA profiles that vary in one or less loci. Branches link those MLVA profiles that vary in two or less loci.

Fig. 2.

Core SNP analysis performed using Snippy version 3.1 and SnapperDB 1.4. A maximum likelihood tree was inferred on the 12 819 core SNP alignment using FastTree and visualised in conjunction with the corresponding DHB, serotype, biotype, MLST type, MLVA profile and core SNP cluster as well as using Phandango (these data should be interpreted in conjunction with Fig. S2).