Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism

Abstract

Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.

Fig. 1.

—Prevalence of clinical and agricultural C. jejuni within ST-21 and ST-45 CCs in a public archive repository. The prevalence of clinical (black) and poultry/livestock (gray) isolation sources in pubMLST for each ST in our data set with more than ten isolate records in the pubMLST database (https://pubmlst.org/campylobacter/; last accessed February 07, 2018). There were a total of 17,107 archived public isolate records.

Fig. 2.

—Population structure of 601 C. jejuni ST-21 and ST-45 complex isolates. Isolates are labeled by KPAX group labels (integers) and colored by their source distribution within KPAX groups: Isolates from chicken and clinical sources (yellow), cattle and clinical sources (blue), chicken, cattle and clinical sources (pink), or clinical only (red). Polyphyletic KPAX groups, reflecting isolates in the same KPAX group but in multiple lineages on the tree, are indicated with an asterisk. The phylogenetic tree was reconstructed from a whole-genome gene-by-gene amino acid alignment, translated in-frame, using an approximation of the maximum-likelihood algorithm implemented in FastTree2, and using a general time reversible model.

Fig. 3.

—Genes associated with clinical-only C. jejuni KPAX groups. (A) GWAS results visualized on a circular reference genome. The outer circle indicates genes from the C. jejuni NCTC1168 reference genome, with core genes shared by all isolates in our data set (black) and accessory genes (gray) indicated. Genes found to contain characteristic amino acid sites defining KPAX groups are represented (red ticks) along with a quantitative visualization of the number of these sites per gene (red dots; scale of the quantification from 0 to 420). Genes found to contain k-mers associated with clinical-only KPAX groups using SEER are represented (blue ticks) along with a quantitative visualization of the number of these k-mers mapped per gene (blue dots; scale of the quantification from 0 to 25). Black ticks indicate genes containing both KPAX group characteristic sites and associated k-mers using SEER. (B) Difference in COGs prevalence (%) among genes containing KPAX characteristic sites (red) and genes containing associated k-mers inferred by SEER (blue) with COGs prevalence in the C. jejuni NCTC11168 reference genome annotation.