Gut ARGs in ICU healthcare workers vs controls, China
Cross-sectional study of 290 fecal samples from ICU healthcare workers and healthy controls across eight medical centers in China, comparing gut antibiotic resistance gene abundance and composition via metagenomic sequencing. machine-written summary
290 samples · 290 runs · CN · Adult · 2025 · 17.55 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 381 sample values (country, health condition) |
| ✓ Abstract / description | 290 sample values (subject id) |
| ✓ Full text | 580 sample values (antibiotic exposure, collection date) · PMC12042561 |
| ○ 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 |
Genera, mean relative abundance over 280 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 | 290 | 100% | ||||
| country | 290 | 100% | 290 | |||
| health_condition | 91 | 31% | 91 | |||
| subject_id | 290 | 100% | 290 | |||
| antibiotic_exposure | 290 | 100% | 290 | |||
| collection_date | 290 | 100% | 290 |
- Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study. 2025 PMID 40307838 PMC12042561 own_data
Archive description
Antibiotic resistance is a global public health threat, impacting human, animal, and environmental health. Healthcare settings, with their high antibiotic usage, are significant sources of antibiotic resistance genes (ARGs). Therefore, we plan to use deep metagenomic sequencing to assess the abundance of ARGs in healthcare workers, particularly those in ICUs, and compare it with healthy controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Differences in Gut Microbiome Antibiotics Resistance”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115973281 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | broad-spectrum antibiotic use within 6 months |
| SAMEA115973281 | collection_date | 2024-01/2024-02 | R3 | 0.70 | paper.fulltext.abstract | recruiting from January 2024 to February 2024 |
| SAMEA115973281 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA115973472 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | CK_HC1 |
| SAMEA115973281 | subject_id | SAMEA115973281 | R4 | 0.60 | design.one_sample_per_subject:abstract | Prospective, multicentre, cross-sectional study |
Sequencing
290 runs over 290 samples · mean 17.69 Gbp per run (median 17.55 Gbp, total 5,129.40 Gbp; 290 runs with a base count) · layout PAIRED 290 · platform ILLUMINA 290 · models Illumina NovaSeq X (290) · 97% of runs with a Sandpiper profile · first public 2025-02-13 – 2025-02-17
Authors (22)
Huang L first · Li K · Peng C · Gu S · Huang X · Gao C · Ren X · Cheng M · He G · Xu Y · Jiang Y · Wang H · Wang M · Shen P · Wang Q · He X · Zhong L · Wang S · Wang N · Zhang G · Cai H · Jiang C last
Downloads
PRJEB79317.csv.gz (8.1 KB) · parquet (81.8 KB) — all 290 samples, every field with route and confidence · PRJEB79317_determinations.csv.gz (7.5 KB) — 1,251 evidence rows