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

Authors: PASCOE, BEN - University Of Bath; SCHIAFFINO, FRANCESCA - Johns Hopkins University; MURRAY, SUSAN - Swansea University; BAYLISS, SION - University Of Bath; HITCHINGS, MATTHEW - Swansea University; MÉRIC, GUILLAUME - University Of Bath; MOURKAS, EVANGELOS - University Of Bath; CALLAND, JESSICA - University Of Bath; BURGA, ROSA - Naval Medical Research Center; PENATARO-YORI, PABLO - University Of Virginia; JOLLEY, KEITH - Oxford University; COOPER, KERRY - University Of Arizona; Parker, Craig; OLORTEGUI, MARIBEL - Johns Hopkins University; KOSEK, MARGARET - University Of Virginia; SHEPPARD, SAMUEL - University Of Bath

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2020
Publication Date: 8/10/2020
Citation: Pascoe, B., Schiaffino, F., Murray, S., Bayliss, S.C., Hitchings, M.D., Méric, G., Mourkas, E., Calland, J.K., Burga, R., Penataro-Yori, P., Jolley, K.A., Cooper, K.K., Parker, C., Olortegui, M., Kosek, M.N., Sheppard, S.K. 2020. Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS Pathogens. 14(8). Article e0008533. https://doi.org/10.1371/journal.pntd.0008533.
DOI: https://doi.org/10.1371/journal.pntd.0008533

Interpretive Summary: Campylobacter is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- to middle-income countries, where infection can be fatal, surveillance is rare and the genotypes responsible for disease have not been identified. The epidemiology of disease is different to the developed world, where infection is mostly associated with consumption of contaminated meat products. Infection is endemic among children and asymptomatic carriage is thought to be common. Widespread malnutrition encourages asymptomatic colonization stunting childhood growth, leading to poor cognitive and physical development. In this study, we sequence and characterize an archived collection from children under the age of 5 years in the Peruvian Amazon to investigate genetic differences between them and a global reference collection. In addition to common global disease lineages, we identified local genotypes rarely seen before. Asymptomatic isolates were not restricted to specific ecological groups or genotypes and chicken was the primary source of infection. Hidden reservoirs of bacterial diversity can help us understand the genetics underlying differences in the presentation of disease and will inform work to improve infant health globally.

Technical Abstract: Campylobacter is the leading bacterial cause of gastroenteritis worldwide and incidence is especially high in low- to middle- income countries. Disease epidemiology for low- to middle- income countries is different to that of the developed world and infection is prevalent even in the absence of symptoms and is associated with deficits in early childhood growth. In this study, we sequence and characterize an archived collection of Campylobacter jejuni isolates (n=62) from a longitudinal cohort study of children under the age of 5 years sampled from diarrheal episodes (n=31) and stools collected by protocol in the absence of diarrheal illness (n=28). We identify determinants associated with human symptomatic illness and attribute zoonotic origin of infecting strains. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of common global disease lineages, particularly notable is the paucity of the host generalist ST21 and ST45 clonal complexes. Half of local disease cases (15 of 31) could be attributed to sequence types not commonly isolated from other countries or reservoir sources. Phylogenetic analysis could not discriminate symptomatic and asymptomatic isolates, suggesting that asymptomatic carriage is not restricted to specific ecological groups or clonal complexes. Through comparison with large global repositories, we identify chicken as the primary source of infection. A better understanding of the genotypes underlying differences in disease epidemiology will facilitate targeted interventions to improve infant health.