Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species

Authors: Parker, Craig; SCHIAFFINO, FRANCESCA - Universidad Peruana; Huynh, Steven; PAREDES OLORTEGUI, M - Prisma Charitable Association; PENATARO YORI, P - University Of Virginia School Of Medicine; GARCIA BARDALES, P - Prisma Charitable Association; PINEDO VASQUEZ, T - Prisma Charitable Association; CURICO HUANSI, G - Prisma Charitable Association; VILLANEUVA, K - Prisma Charitable Association; SHAPIAMA LOPEZ, W - Prisma Charitable Association; COOPER, KERRY - University Of Virginia; KOSEK, MARGARET - University Of Virginia

Submitted to: PLOS Neglected Tropical Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2022
Publication Date: 10/4/2022
Citation: Parker, C.T., Schiaffino, F., Huynh, S., Paredes Olortegui, M., Penataro Yori, P., Garcia Bardales, P.F., Pinedo Vasquez, T., Curico Huansi, G.E., Manzanares Villaneuva, K., Shapiama Lopez, W.V., Cooper, K.K., Kosek, M.N. 2022. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLOS Neglected Tropical Diseases. 16(10). Article e0010815. https://doi.org/10.1371/journal.pntd.0010815.
DOI: https://doi.org/10.1371/journal.pntd.0010815

Interpretive Summary: Campylobacter sp. are a major cause of diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and C. coli are most often the causative agents of enteric disease among children in LMICs. However, there are many stool samples from children under 2 years of age with acute diarrheal disease or asymptomatic carriers living in a low resource community in Peru that tested positive for Campylobacter species but negative for C. jejuni and C. coli by qPCR. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within such samples. A variety of Campylobacter species were identified in these stool samples included C. jejuni, C. coli, C. upsaliensis, C. concisus, and the potential new species of Campylobacter, "Candidatus Campylobacter infans". Moreover, our results demonstrated that over 65% of the samples represented co-infections with multiple Campylobacter species present in a single stool sample, a novel finding in human populations.

Technical Abstract: Campylobacter sp. are a major cause of diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and C. coli are most often the causative agents of enteric disease among children in LMICs. However, there are many stool samples from children under 2 years of age with acute diarrheal disease or asymptomatic carriers living in a low resource community in Peru that are qPCR positive for Campylobacter species but qPCR negative for C. jejuni and C. coli. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within these samples. The Campylobacter species identified in these stool samples included C. jejuni, C. coli, C. upsaliensis, C. concisus, and the potential new species of Campylobacter, "Candidatus Campylobacter infans". Moreover, WSMS results demonstrated that over 65% of the samples represented co-infections with multiple Campylobacter species present in a single stool sample, a novel finding in human populations.