CRE-colonized patient rectal swab metagenomics, Baltimore
146 rectal swab samples from patients colonized with carbapenem-resistant Enterobacterales in Baltimore, USA, analyzed by Nanopore long-read metagenomic sequencing for microbiome and resistome characterization. machine-written summary
146 samples · 146 runs · US · Age unknown · 2024 · 0.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 765 sample values (collection date, country, latitude, location locality, longitude, subject id) |
| ✓ Abstract / description | 292 sample values (health condition, health condition detail) |
| ✓ Full text | 146 sample values (location site) · PMC12392892 |
| ✓ Supplementary tables | 111 sample values (subject id) |
| – 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
22 of 85 people sampled more than once (83 samples; median 2, up to 13 per person). Schedule stated by the source: “Admission and weekly thereafter for cohort-level patients; sequential swabs over multiple hospital encounters for longitudinal subset” (time origin: Hospital admission).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 146 | 100% | 146 | |||
| health_condition | 146 | 100% | 146 | |||
| subject_id | 146 | 100% | 35 | 111 | ||
| collection_date | 146 | 100% | 146 | |||
| detailed_location | 146 | 100% | ||||
| health_condition_detail | 146 | 100% | 146 | |||
| latitude | 146 | 100% | 146 | |||
| location_locality | 146 | 100% | 146 | |||
| location_site | 146 | 100% | 146 | |||
| longitude | 146 | 100% | 146 |
- Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs. 2025 PMID 40894237 PMC12392892 own_data
Archive description
Rectal swabs were sequenced with the Nanopore GridION X5 for microbiome and resistome analysis. All samples were multiplexed and human genomic sequences were removed prior to analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “patients colonized with carbapenem-resistant Enterobacterales”
- body site study.title · “rectal swabs”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40456997 | collection_date | 2019-06/2019-09 | R1 | 0.90 | biosample.attribute:collection_date | 2019-06/2019-09 |
| SAMN40456997 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Baltimore |
| SAMN40456997 | health_condition | other_infection | R4 | 0.45 | study.title | patients colonized with carbapenem-resistant Enterobacterales |
| SAMN40456997 | health_condition_detail | Carbapenem-resistant Enterobacterales colonization | R4 | 0.45 | study.title | patients colonized with carbapenem-resistant Enterobacterales |
| SAMN40456997 | latitude | 39.3000 | R1 | 0.90 | biosample.attribute:lat_lon | 39.30 N 76.59 W |
| SAMN40456997 | location_locality | Baltimore | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Baltimore |
| SAMN40456997 | location_site | The Johns Hopkins Hospital | R3 | 0.70 | paper.body.methods_results | Samples were collected as part of a larger surveillance study at The Johns Hopkins Hospital. |
| SAMN40456997 | longitude | -76.5900 | R1 | 0.90 | biosample.attribute:lat_lon | 39.30 N 76.59 W |
| SAMN40457004 | subject_id | P54 | R1 | 0.70 | biosample.attribute:P_ID | P54_4427 |
| SAMN40456997 | subject_id | P22 | R2 | 0.85 | paper.supp.dlaf152_supplementary_data.xlsx[Sheet1!Patient] | P22_6487 | P22 |
Sequencing
146 runs over 146 samples · mean 1.10 Gbp per run (median 0.88 Gbp, total 160.08 Gbp; 146 runs with a base count) · layout SINGLE 146 · platform OXFORD_NANOPORE 146 · models GridION (146) · 0% of runs with a Sandpiper profile · first public 2024-03-15
Authors (0)
No author record.
Downloads
PRJNA1088077.csv.gz (4.5 KB) · parquet (76.2 KB) — all 146 samples, every field with route and confidence · PRJNA1088077_determinations.csv.gz (10.5 KB) — 1,314 evidence rows