Host-Dependent Clustering of Campylobacter Strains From Small Mammals in Finland

Abstract

Small mammals are known to carry Campylobacter spp.; however, little is known about the genotypes and their role in human infections. We studied intestinal content from small wild mammals collected in their natural habitats in Finland in 2010-2017, and in close proximity to 40 pig or cattle farms in 2017. The animals were trapped using traditional Finnish metal snap traps. Campylobacter spp. were isolated from the intestinal content using direct plating on mCCDA. A total of 19% of the captured wild animals (n = 577) and 41% of the pooled farm samples (n = 227) were positive for C. jejuni, which was the only Campylobacter species identified. The highest prevalence occurred in yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) which carried Campylobacter spp. in 66.3 and 63.9% of the farm samples and 41.5 and 24.4% of individual animals trapped from natural habitats, respectively. Interestingly, all house mouse (Mus musculus) and shrew (Sorex spp.) samples were negative for Campylobacter spp. C. jejuni isolates (n = 145) were further characterized by whole-genome sequencing. Core genome multilocus sequence typing (cgMLST) clustering showed that mouse and vole strains were separated from the rest of the C. jejuni population (636 and 671 allelic differences, 94 and 99% of core loci, respectively). Very little or no alleles were shared with C. jejuni genomes described earlier from livestock or human isolates. FastANI results further indicated that C. jejuni strains from voles are likely to represent a new previously undescribed species or subspecies of Campylobacter. Core-genome phylogeny showed that there was no difference between isolates originating from the farm and wild captured animals. Instead, the phylogeny followed the host species-association. There was some evidence (one strain each) of livestock-associated C. jejuni occurring in a farm-caught A. flavicollis and a brown rat (Rattus norvegicus), indicating that although small mammals may not be the original reservoir of Campylobacter colonizing livestock, they may sporadically carry C. jejuni strains occurring mainly in livestock and be associated with disease in humans.

Keywords: Campylobacter jejuni; comparative genomics; mouse; phylogeny; rodent; shrew; vole.

FIGURE 1

Maximum likelihood phylogenetic tree based on the alignment of 864 core genes of 1,406 C. jejuni strains from various sources. The tree was rooted at mid-point. The clade associated with voles is shown in yellow and the clades associated with mice in green. Color in the external ring indicates the source of the strain (see legend).

FIGURE 2

Genealogy of vole-associated Campylobacter lineage (left) with associated metadata, i.e., taxon (M. glareolus in light yellow, M. rutilus in orange, M. agrestis in violet, and M. mystacinus in turquoise), geographical area (north Finland in orange and south in purple), location, farm number (if applicable), habitat (field in blue, forest in orange, and farm in green), time (spring in orange and fall in purple) and year (2015 in purple and 2017 in orange), displayed alongside the gene presence (blue)/absence (white) plot from the Roary pangenome analysis. The figure was drawn using the phandango.net web application (Hadfield et al., 2017). The phylogeny based on 1,238 core genes was reconstructed using ClonalFrameML (Didelot and Wilson, 2015) and rooted at mid-point.

FIGURE 3

Genealogy of mice-associated Campylobacter lineage (left) with associated metadata, i.e., taxon (A. flavicollis in purple and M. minutus in orange), location, farm (if applicable) and year (2017 in orange, 2015 in dark orange, 2014 in light red, 2013 in dark red, 2011 in violet, and 2010 in blue), displayed alongside the gene presence (blue)/absence (white) plot from the Roary pangenome analysis. The figure was drawn using the phandango.net web application (Hadfield et al., 2017). The phylogeny based on 1,402 core genes was reconstructed using ClonalFrameML (Didelot and Wilson, 2015) and rooted at mid-point.