Infant stool metagenomes, Campylobacter infans study, Loreto
14 stool samples from children in Loreto, Peru, examined for Campylobacter spp. (including C. infans) and Shigella spp. in a case-control study comparing diarrheal and diarrhea-free samples. machine-written summary
14 samples · 14 runs · PE · Infant / toddler · 2022 · 0.51 Gbp / sample · cohort Peru Loreto LMIC infant stool cohort
One study deposited as 2 BioProjects (97 catalog samples together): PRJNA834762 · PRJNA837236 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 28 sample values (collection date, country) |
| ✓ Abstract / description | 14 sample values (location locality) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 11 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 14 | 100% | 14 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 14 | 100% | 14 | |||
| detailed_location | 14 | 100% | ||||
| location_locality | 14 | 100% | 14 |
- (no title) curated
- (no title) curated
Archive description
A diagnostic gap exists in the detection of Campylobacter spp. using nucleic acid-based techniques in comparison to standard microbiological culture. A working hypothesis is that uncommon species of Campylobacter play a role in enteric disease among children in low resource settings. C. infans, was recently detected in stool samples from children and hypothesized to play a role in the epidemiology of this pathogen within highly endemic communities. This study aimed to determine the prevalence of C. infans in symptomatic and asymptomatic stool samples from children living in Iquitos, Peru, and to determine if the presence of this pathogen would explain the high discrepancy of the detection of Campylobacter between nucleic acid diagnostics and culture. Stool samples from 215 children with diarrhea and 50 stool samples from children in a diarrhea free interval under the age of two were queried using a Taqman based multiplex assay to detect Campylobacter spp. (16sRNA), Campylobacter jejuni/ Campylobacter coli (cadF gene), C. infans and Shigella spp.. Odds ratios and 95% confidence intervals of diarrhea were calculated based on the presence of these targets using univariate logistic regressions. C. infans was detected in 7.9% (17/215) symptomatic samples and 4.0% (2/50) asymptomatic samples. The presence of C. infans was not associated with higher odds of diarrhea. Twenty nine percent of Campylobacter positive fecal samples are not attributed to C. jejuni, C. coli or C. infans. Whole metagenomic DNA confirmed the presence of C. infans among 13 out 14 positive C. infans positive stool samples. Eight C. infans positive samples were co-infected with at least one additional Campylobacter species. A BLASTn analysis of the qPCR cadF pforward and reverse primers against 3076 C. jejuni and C. coli WGS in pubmlst determined that 41% of the strains (1254/3076) did not have 100% identity at both primer binding sites. Further studies are needed to determine if the targeted section of the cadF gene for the detection of C. jejuni and C. coli can be improved for the detection of strains present in LMICs.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by sonnet_x2 with confidence 0.69. Assay shotgun_dna.
- host study.title · “human infant stool whole-genome shotgun”
- body site study.title · “human infant stool”
- life stage study.description · “children in Iquitos, Peru”
- life stage study.description · “under the age of two”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28491927 | collection_date | 2019-10-14 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2019-10-14 |
| SAMN28491927 | country | PE | R1 | 0.90 | biosample_attr | Peru:Loreto |
| SAMN28491927 | location_locality | Iquitos | R4 | 0.50 | paper.abstract | children living in Iquitos, Peru |
Sequencing
14 runs over 14 samples · mean 0.80 Gbp per run (median 0.51 Gbp, total 11.17 Gbp; 14 runs with a base count) · layout PAIRED 14 · platform ILLUMINA 14 · models Illumina MiSeq (14) · 79% of runs with a Sandpiper profile · first public 2022-05-19
Authors (16)
Pinedo Vasquez T · Curico Huansi GE · Shapiama Lopez WV · Schiaffino F first · Parker CT · Garcia Bardales PF · Huynh S · Manzanares Villanueva K · Mourkas E · Pascoe B · Peñataro Yori P · Paredes Olortegui M · Houpt ER · Liu J · Cooper KK · Kosek MN last
Downloads
PRJNA837236.csv.gz (1.3 KB) · parquet (69.4 KB) — all 14 samples, every field with route and confidence · PRJNA837236_determinations.csv.gz (860 B) — 42 evidence rows