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

Parker, Craig T.; Schiaffino, Francesca; Huynh, Steven; Olórtegui, Maribel Paredes; Yori, Pablo Peñataro; Bardales, Paul F Garcia; Vasquez, Tackeshy Pinedo; Huansi, Greisi E. Curico; Villanueva, Katia Manzanares; Lopez, Wagner V. Shapiama; Cooper, Kerry K.; Kosek, Margaret

doi:10.1371/journal.pntd.0010815

Cited by 7 publications

(17 citation statements)

References 43 publications

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“…jejuni and C . coli in positive stool samples [ 5 ]. First, we identified genomic regions present in C .…”

Section: Resultsmentioning

confidence: 99%

“…However, for certain species, such as Campylobacter , the underrepresentation of whole genomes or extensive genomic data from different geographic areas impairs the development of effective primers and probes. After demonstrating the inadequate performance of the cadF assay [ 5 ], we developed a new qPCR assay for the detection C . jejuni / C .…”

Section: Discussionmentioning

confidence: 99%

“…jejuni/ C . coli using the single gene target cadF is not optimal [ 4 , 5 ]. Specifically, we demonstrated that within fecal samples that were positive for Campylobacter spp.…”

Section: Discussionmentioning

confidence: 99%

“…at levels lower than those required for culture based isolation [ 13 ]. The target for Campylobacter genus detection is usually the 16S rRNA gene [ 4 , 5 , 13 , 14 ] or the chaperonin protein cpn60 [ 1 , 15 , 16 ] that has been used to detect both common thermotolerant Campylobacters , such as C . jejuni and C .…”

Section: Introductionmentioning

confidence: 99%

“…jejuni or C . coli , and sometimes both [ 5 ]. This major underestimation of the overall prevalence of C .…”

Section: Introductionmentioning

confidence: 99%

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Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool

Schiaffino,

Parker,

Garcia Bardales

et al. 2024

PLoS Negl Trop Dis

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Campylobacter causes bacterial enteritis, dysentery, and growth faltering in children in low- and middle-income countries (LMICs). Campylobacter spp. are fastidious organisms, and their detection often relies on culture independent diagnostic technologies, especially in LMICs. Campylobacter jejuni and Campylobacter coli are most often the infectious agents and in high income settings together account for 95% of Campylobacter infections. Several other Campylobacter species have been detected in LMIC children at an increased prevalence relative to high income settings. After doing extensive whole genome sequencing of isolates of C. jejuni and C. coli in Peru, we observed heterogeneity in the binding sites for the main species-specific PCR assay (cadF) and designed an alternative rpsKD-based qPCR assay to detect both C. jejuni and C. coli. The rpsKD-based qPCR assay identified 23% more C.jejuni/ C.coli samples than the cadF assay among 47 Campylobacter genus positive cadF negative samples verified to have C. jejuni and or C. coli with shotgun metagenomics. This assay can be expected to be useful in diagnostic studies of enteric infectious diseases and be useful in revising the attribution estimates of Campylobacter in LMICs.

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“…jejuni and C . coli in positive stool samples [ 5 ]. First, we identified genomic regions present in C .…”

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…jejuni/ C . coli using the single gene target cadF is not optimal [ 4 , 5 ]. Specifically, we demonstrated that within fecal samples that were positive for Campylobacter spp.…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…jejuni or C . coli , and sometimes both [ 5 ]. This major underestimation of the overall prevalence of C .…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool

Schiaffino,

Parker,

Garcia Bardales

et al. 2024

PLoS Negl Trop Dis

Self Cite

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Geospatial Analysis of Multilevel Socio-environmental Factors Impacting theCampylobacterBurden Among Infants in Rural Eastern Ethiopia: A One Health Perspective

Li,

Chen,

Liang

et al. 2024

Preprint

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Increasing attention has focused on health outcomes ofCampylobacterinfections among children under five years in low-resource settings. Recent evidence suggests colonization ofCampylobacterspecies contributes to environmental enteric dysfunction, malnutrition, and growth faltering in young children.Campylobacterspecies are zoonotic, and factors from humans, animals, and the environment are involved in transmission. Few studies have assessed geospatial effects of environmental factors along with human and animal factors onCampylobacterinfections. Here, we leveragedCampylobacterGenomics and Environmental Enteric Dysfunction (CAGED) project data to model multiple socio-environmental factors onCampylobacterburden among infants in Eastern Ethiopia. Stool samples from 106 infants were collected monthly from birth through the first year of life (December 2020 – June 2022). Genus-specific Taqman real-time PCR was performed to detect and quantifyCampylobacterspp. and calculate cumulativeCampylobacterburden for each child as the outcome variable. Thirteen regional environmental covariates describing topography, climate, vegetation, soil, and human population density were combined with household demographics, livelihoods/wealth, livestock ownership, and child-animal interactions as explanatory variables. We dichotomized all continuous outcome and explanatory variables and built logistic regression models for the first and second half of the infant’s first year of life. Infants being female, living in households with cattle, reported to have physical contact with animals, or reported to have mouthed soil or animal feces had increased odds of higher cumulativeCampylobacterburden in Eastern Ethiopia. Future interventions should focus on infant-specific transmission pathways and create adequate separation of domestic animals from humans to prevent potential fecal exposures.

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Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project

Deblais,

Ojeda,

Brhane

et al. 2023

Appl Environ Microbiol

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A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth.

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

Cited by 7 publications

References 43 publications

Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool

Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool

Geospatial Analysis of Multilevel Socio-environmental Factors Impacting theCampylobacterBurden Among Infants in Rural Eastern Ethiopia: A One Health Perspective

Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project

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