Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion

Abstract

The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.

Keywords: Campylobacter jejuni; genomic epidemiology; monomorphic clones; whole-genome sequencing.

Fig. 1.

(a) Phylogram of RAxML tree based on non-recombined core genome. Semicircles from outside to inside represent genetic features listed in the legends. Branches are colored according to hierBAPS clustering. The two major clades (a and b) are indicated. (b) Inner phylogram: RAxML-tree as described for Fig. 1(a). Outer phylogram: RAxML-tree based on a binary matrix of presence–absence of accessory genes. Nodes with bootstrap values >50 % are indicated with a circle. Semicircles from outside to inside: ST, year and country of origin (see legends for indications). Branches are colored according to hierBAPS clustering.

Fig. 2.

Manhattan plots illustrating significant hits associated with UK (red, upper) or Baltic countries (blue, lower) mapped to C. jejuni M1 or C. jejuni 4031 genomes, respectively. The dots represent number of words (k-mers), and the regions with higher number of mapped words are indicated with arrows and letters. In the UK Manhattan plot, region A (11 k-mers) mapped to position 153 200–153 295 and region B (12 k-mers) to position 240 500–240 600 on M1. In the lower Baltic plot, region C (18 k-mers) mapped to position 1 276 300–1 277 300 on 4031.

Fig. 3.

Bayesian phylogenetic tree of Finnish BAPS 6 isolates inferred with BEAST based on non-recombined core genome of approximately 1.2 Mb. Year of isolation is indicated by the color of the bar: yellow: 2000, blue: 2001, purple: 2004, green: 2008, orange: 2012. Two subclusters of BAPS 6 are scaled up and presented as embedded illustrations. Predicted divergence times with confidence intervals given in years before present are given at their respective nodes. Single-nucleotide variant (SNV) numbers in a cluster are given in yellow and light green boxes near the most common recent ancestor of that cluster (when space allows, otherwise located between the involved leafs). Fewer than five SNVs were detected between epidemiologically linked isolates (two from 2008, two from 2012, two from 2004, three from 2012), indicating the usefulness of WGS in outbreak investigations.

Fig. 4.

Comparison of ST-45 of Canadian, Italian and barnacle geese origin and one representative of each hierBAPS cluster level 2 on the b-lineage. Purple open circle: BAPS 4 isolate, green open circles: BAPS 6 isolate, green triangles: barnacle geese isolate, red diamonds: Canadian strains, blue squares; Italian strains. BAPS 4 and 6 are highlighted. Genetic distance (nt substitutions per site) is indicated with a bar.