Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Abstract

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.

Fig 1

(A) Location of study site in Santa Clara, near Iquitos in Peru. (B) Sequence types (STs) of isolates collected from children in the Peruvian Amazon ranked according to the frequency in our local dataset and how often they have been sampled from human disease isolates (data from pubMLST; https://pubmlst.org/). (C) Population structure of C. jejuni isolates used in this study. All core (present in ≥95% of isolates) genes from the reference pan-genome list (2,348 genes) were used to build alignments of the Peruvian isolates (n = 62) contextualized with 164 previously published genomes representing the known genetic diversity in C. jejuni (n = 234, alignment: 720,853 bp. A maximum-likelihood phylogeny was constructed with IQ-TREE, using a GTR model and ultrafast bootstrapping (1,000 bootstraps; version 1.6.8) [55,56]. Scale bar represents genetic distance of 0.001. Leaves from asymptomatic Peruvian isolates are colored green; symptomatic Peruvian isolates are red; and isolates from the reference dataset are grey. Common STs and clonal complexes (CC), based on four or more shared alleles in seven MLST housekeeping genes, are annotated [60]. Interactive visualization is available on Microreact [57]: https://microreact.org/project/CampyPeruContext. (D) Pairwise core and accessory genome distances were compared using PopPunk for the Peruvian pediatric genomes only and (E) with the global reference dataset (version 1.1.4) [70].

Fig 2

(A) Frequency of clonal complexes (CCs) identified among isolates collected from children in the Peruvian Amazon (grey bars) and the global reference dataset (red dotted line). Asymptomatic isolates are colored in green. (B) Average severity score of CCs represented by 3 or more genomes in our local dataset and how often they have previously been sampled from human disease (data from pubMLST; https://pubmlst.org/). Circle diameter represents how frequently they were sampled in our Peruvian Amazon pediatric collection. (C) A maximum-likelihood phylogeny was constructed with IQ-TREE, using a GTR model and ultrafast bootstrapping (1,000 bootstraps; version 1.6.8) [55,56] from an alignment of the Peruvian isolates only (n = 62, alignment: 772,794 bp. Scale bar represents genetic distance of 0.001. Leaves from asymptomatic isolates are colored green and symptomatic isolates are red. The tree is annotated with lipooligosaccharide classes, capsular types and disease severity scores. Colored bar charts indicate the frequency with which the corresponding sequence type has been isolated from non-human hosts in pubMLST. Black bars indicate the overall frequency that the corresponding ST profile has been sampled before. Interactive visualization is available on Microreact [57]: https://microreact.org/project/CampyPeruOnly.