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Garcia Bardales PF, Schiaffino F, Huynh S, Paredes Olortegui M, Peñataro Yori P, Pinedo Vasquez T, Manzanares Villanueva K, Curico Huansi GE, Shapiama Lopez WV, Cooper KK, Parker CT, Kosek MN. "Candidatus Campylobacter infans" detection is not associated with diarrhea in children under the age of 2 in Peru. PLoS Negl Trop Dis 2022; 16:e0010869. [PMID: 36251729 PMCID: PMC9612815 DOI: 10.1371/journal.pntd.0010869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/27/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
A working hypothesis is that less common species of Campylobacter (other than C. jejuni and C. coli) play a role in enteric disease among children in low resource settings and explain the gap between the detection of Campylobacter using culture and culture independent methods. "Candidatus Campylobacter infans" (C. infans), was recently detected in stool samples from children and hypothesized to play a role in Campylobacter epidemiology in low- and middle-income countries (LMIC). This study determined the prevalence of C. infans in symptomatic and asymptomatic stool samples from children living in Iquitos, Peru. Stool samples from 215 children with diarrhea and 50 stool samples from children without diarrhea under the age of two were evaluated using a multiplex qPCR assay to detect Campylobacter spp. (16S rRNA), Campylobacter jejuni / Campylobacter coli (cadF gene), C. infans (lpxA), and Shigella spp. (ipaH). C. infans was detected in 7.9% (17/215) symptomatic samples and 4.0% (2/50) asymptomatic samples. The association between diarrhea and the presence of these targets was evaluated using univariate logistic regressions. C. infans was not associated with diarrhea. Fifty-one percent (75/146) of Campylobacter positive fecal samples were negative for C. jejuni, C. coli, and C. infans via qPCR. Shotgun metagenomics confirmed the presence of C. infans among 13 out of 14 positive C. infans positive stool samples. C infans explained only 20.7% of the diagnostic gap in stools from children with diarrhea and 16.7% of the gap in children without diarrhea. We posit that poor cadF primer performance better explains the observed gap than the prevalence of atypical non-C. jejuni/coli species.
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Affiliation(s)
| | - Francesca Schiaffino
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Steven Huynh
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | | | - Pablo Peñataro Yori
- Asociacion Benefica Prisma, Iquitos, Peru
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
| | | | | | | | | | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (KKC); (MNKI)
| | - Craig T. Parker
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | - Margaret N. Kosek
- Asociacion Benefica Prisma, Iquitos, Peru
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail: (KKC); (MNKI)
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Parker CT, Schiaffino F, Huynh S, Paredes Olortegui M, Peñataro Yori P, Garcia Bardales PF, Pinedo Vasquez T, Curico Huansi GE, Manzanares Villanueva K, Shapiama Lopez WV, Cooper KK, Kosek MN. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLoS Negl Trop Dis 2022; 16:e0010815. [PMID: 36194603 PMCID: PMC9565744 DOI: 10.1371/journal.pntd.0010815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/14/2022] [Accepted: 09/13/2022] [Indexed: 12/11/2022] Open
Abstract
Campylobacter spp. are a major cause of bacterial 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 Campylobacter coli are most often the causative agents of enteric disease among children in LMICs. However, previous work on a collection of stool samples from children under 2 years of age, living in a low resource community in Peru with either acute diarrheal disease or asymptomatic, were found to be 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 demonstrate 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. Analysis of shotgun metagenomic data obtained from fecal samples of children living in a low resource tropical community of Peru revealed multiple Campylobacter species. Co-infections with more than one Campylobacter species within the same sample was a common finding. A potential new species of Campylobacter was also detected within these samples.
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Affiliation(s)
- Craig T. Parker
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | - Francesca Schiaffino
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Steven Huynh
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | | | - Pablo Peñataro Yori
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Iquitos, Peru
| | | | | | | | | | | | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (KKC); (MNK)
| | - Margaret N. Kosek
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Iquitos, Peru
- * E-mail: (KKC); (MNK)
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