Longitudinal rectal swab metagenomes, MDRO patients, Lübeck
52 rectal swab samples from patients with two consecutive hospital admissions over four years in Lübeck, Germany, studying AMR gene detection and MDRO colonization via metagenomics versus culture-based methods; longitudinal design. machine-written summary
52 samples · 52 runs · DE · Age unknown · 2025 · 5.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 364 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11912604 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
26 of 26 people sampled more than once (52 samples; median 2, up to 2 per person). Schedule stated by the source: “two consecutive hospital admissions per patient over a four-year period (2016-2019); swab taken at admission, day 1 to 3” (time origin: admission).
Genera, mean relative abundance over 52 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 | 52 | 100% | 52 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 52 | 100% | 52 | |||
| collection_date | 52 | 100% | 52 | |||
| detailed_location | 52 | 100% | ||||
| latitude | 52 | 100% | 52 | |||
| location_locality | 52 | 100% | 52 | |||
| location_region | 52 | 100% | 52 | |||
| longitude | 52 | 100% | 52 |
- Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes. 2025 PMID 40097931 PMC11912604 own_data
Archive description
We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host study.description · “rectal swabs from 26 patients”
- host run.host_tax_id · “9606”
- body site study.description · “We analyzed rectal swabs”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41600881 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN41600881 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany:Luebeck |
| SAMN41600881 | latitude | 53.8600 | R1 | 0.90 | biosample.attribute:lat_lon | 53.86 N 10.69 E |
| SAMN41600881 | location_locality | Lübeck | R1 | 0.75 | biosample.attribute:geo_loc_name | Germany:Luebeck |
| SAMN41600881 | location_region | Schleswig-Holstein | R1 | 0.60 | biosample.attribute:lat_lon | 53.86 N 10.69 E |
| SAMN41600881 | longitude | 10.6900 | R1 | 0.90 | biosample.attribute:lat_lon | 53.86 N 10.69 E |
| SAMN41600881 | subject_id | P01 | R1 | 0.85 | biosample.attribute:isolation_source | Rectal swab P01 |
Sequencing
52 runs over 52 samples · mean 5.57 Gbp per run (median 5.63 Gbp, total 289.81 Gbp; 52 runs with a base count) · layout PAIRED 52 · platform ILLUMINA 52 · models NextSeq 2000 (52) · 100% of runs with a Sandpiper profile · first public 2025-03-01 – 2025-03-02
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1118222.csv.gz (2.2 KB) · parquet (71.4 KB) — all 52 samples, every field with route and confidence · PRJNA1118222_determinations.csv.gz (3.0 KB) — 364 evidence rows