Genomic evidence for the emergence and evolution of pathogenicity and niche preferences in the genus Campylobacter

Abstract

The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology.

Keywords: Campylobacter; Campylobacter sputorum; comparative genomics; niche preferences; pathogenicity.

Fig. 1.—

Barplot and heatmap of virulence genes identified per genome. Established pathogens are displayed in violet, and putative pathogens are displayed in dark green. (A) The total number of virulence genes is displayed as bar lengths. Genomes are clustered based on the inferred consensus phylogeny for Campylobacter genus. (B) Genomes are clustered in established (top) and putative (bottom) pathogens based on the presence/absence patterns for virulence genes belonging to 12 functional categories. Colors (white to orange) represent the number of genes.

Fig. 2.—

Ancestral character reconstruction. The consensus phylogeny for Campylobacter is colored according to the average probability for the absence (P = 0, blue) or the presence (P = 1, red) of virulence genes. The probability densities using the inferred states for each genes are shown for the Campylobacter MRCA (A), the MRCA for putative pathogens (B), and the MCRA for established pathogens (C).

Fig. 3.—

GO analysis. Three GO graphs for (A) oral versus nonoral, (B) genital versus nongenital, and (C) established versus putative. Significant GO terms (P < 0.01) for each graph are colored in a yellow to red gradient. Numbers encode the name of significant functional categories, (A) 1-pathogenesis, 2-response to virus, 3-proteolysis, 4-response to oxygen species, 5-lactate metabolism, 6-sulfate metabolism, 7-antibiotic resistance; (B) 8-protein methylation, 9-response to external stimulus, 10-nitrogen utilization; (C) 11-response to antibiotics, 12-locomotion, 13-oxydative stress, 14-starvation, 15-nitrogen transport, 16-chromosome partition, 17-adhesion, 18-vitamin biosynthesis, and 19-pathogenesis.

Fig. 4.—

Distribution of genes belonging to oxidative stress and starvation. Red boxes show the presence of a gene in a certain genome whereas green boxes show its absence. Fractions at the bottom represent the counting of each gene in established and putative pathogens, respectively.

Fig. 5.—

Phylogeny of TBDTs. The phylogenetic tree was constructed using 98 TBDT orthologs recovered from Campylobacter genomes. The oral-exclusive cluster is highlighted in dark green.

Fig. 6.—

Correspondence analysis and whole-genome compositional features. Correspondence analysis using amino acids usage form secreted proteins (A) and linear correlation for genome size versus GC content (B). Small black circles represent each amino acid using the one-letter code. Big circles represent each genome colored according to niche preferences: gastrointestinal (red), genital (blue), and oral (green).

Fig. 7.—

Phylogeny of DsbA. The phylogenetic tree using DsbA protein clusters Campylobacter and related genomes according to their niche preferences.

Fig. 8.—

Main evolutionary processes in Campylobacter. This figure provides a phylogeny-based integrative view of the main evolutionary processes that have been shaping Campylobacter genomes in terms of pathogenicity and niche preferences. Species are highlighted in blue (genital), red (gastrointestinal), and green (oral). The species C. hominis is ticked off for not sharing the same genomic features than oral species, despite of belonging to the same phylogenetic group.