Clinical mNGS pathogen detection study, Barcelona
199 clinical samples (serum, cerebrospinal fluid, amniotic fluid, feces) from Barcelona, Spain, analyzed by shotgun metagenomic sequencing to detect pathogens while addressing contamination in low-biomass clinical diagnostics. machine-written summary
199 samples · 199 runs · ES · Age unknown · 2026 · 32.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,516 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 103 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC13083213 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “17 longitudinal plasma samples from a single chronic HEV patient; otherwise mostly single clinical samples” (time origin: diagnosis).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 199 | 100% | 199 | |||
| health_condition | 125 | 63% | 125 | |||
| subject_id | 101 | 51% | 101 | |||
| collection_date | 199 | 100% | 199 | |||
| detailed_location | 199 | 100% | ||||
| health_condition_detail | 199 | 100% | 96 | 103 | ||
| latitude | 199 | 100% | 199 | |||
| location_locality | 199 | 100% | 199 | |||
| location_region | 199 | 100% | 199 | |||
| longitude | 199 | 100% | 199 |
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics. 2026 PMID 42005844 PMC13083213 own_data
Archive description
Metagenomics sequencing from serum, cerebrospinal fluid, amniotic fluid and feces.
How this project entered the registry
Classified as human blood / tissue / internal fluids / other human site / gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- host study.title · “refining metagenomics for clinical diagnostics”
- body site study.description · “serum, cerebrospinal fluid, amniotic fluid and feces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN55386486 | collection_date | 2022-08-17 | R1 | 0.90 | biosample.attribute:collection_date | 2022-08-17 |
| SAMN55386486 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Barcelona |
| SAMN55386486 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:alias | ALZ_CSF_1 |
| SAMN55386486 | health_condition_detail | ALZ | R1 | 0.70 | sample.name_rule:alias | ALZ_CSF_1 |
| SAMN55386525 | health_condition_detail | mixed_case_control: chronic infections, acute infections, respiratory co-infections | R4 | 0.50 | paper.abstract | chronic infections, acute infections, and respiratory co-infections |
| SAMN55386486 | latitude | 41.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 41.42 N 2.13 E |
| SAMN55386486 | location_locality | Barcelona | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Barcelona |
| SAMN55386486 | location_region | Catalonia | R1 | 0.60 | biosample.attribute:lat_lon | 41.42 N 2.13 E |
| SAMN55386486 | longitude | 2.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 41.42 N 2.13 E |
| SAMN55386486 | subject_id | ALZ_1 | R1 | 0.70 | sample.name_rule:alias | ALZ_CSF_1 |
Sequencing
199 runs over 199 samples · mean 35.40 Gbp per run (median 32.99 Gbp, total 7,043.70 Gbp; 199 runs with a base count) · layout PAIRED 199 · platform ILLUMINA 199 · models Illumina NovaSeq 6000 (120), NextSeq 2000 (79) · 0% of runs with a Sandpiper profile · first public 2026-04-19
Authors (26)
Ibañez-Lligoña M first · Colomer-Castell S · Campos C · González-Camuesco · González-Camuesco Á · Llauradó A · Garcia-Larroy J · Sánchez-Tejerina D · Rando-Segura A · Andrés C · Esperalba J · Nadal P · Ferrer R · Cortese MF · Tabernero D · Gregori J · Riveiro-Barciela M · Ruiz-Cobo JC · Ruiz A · Del Barco E · Buti M · Goya M · Antón A · Cano A · Juntas-Morales R · Quer J last
Downloads
PRJNA1424541.csv.gz (7.3 KB) · parquet (79.5 KB) — all 199 samples, every field with route and confidence · PRJNA1424541_determinations.csv.gz (13.7 KB) — 1,619 evidence rows