CRE colonization & PPI use in ICU patients, South Korea
Case-control study of 98 stool samples from South Korean ICU patients (47 CRE carriers, 51 non-carriers), examining how proton pump inhibitor use affects gut microbiome composition and transfer of carbapenem resistance genes. machine-written summary
98 samples · 98 runs · KR · Age unknown · 2023 · 6.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 490 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 98 sample values (health condition detail) |
| ✓ Full text | 294 sample values (location locality, location site, subject id) · PMC11028007 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 85 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 | 98 | 100% | 98 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 98 | 100% | 98 | |||
| collection_date | 98 | 100% | 98 | |||
| detailed_location | 98 | 100% | ||||
| health_condition_detail | 98 | 100% | 98 | |||
| latitude | 98 | 100% | 98 | |||
| location_locality | 98 | 100% | 98 | |||
| location_region | 98 | 100% | 98 | |||
| location_site | 98 | 100% | 98 | |||
| longitude | 98 | 100% | 98 |
- Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome. 2024 PMID 38634770 PMC11028007 own_data
Archive description
The emergence of carbapenem-resistant Enterobacteriaceae (CRE) in recent decades has been a serious threat to global health. In patients treated with broad-spectrum antibiotics, the colonization of CRE is a serious problem to treat certain diseases. In the hospital, where many patients are treated not only with antibiotics but also with non-antibiotic drugs, the colonization of various antibiotic-resistant bacteria is occurring. So, it is necessary to study the risk factors of antibiotic-resistant bacteria colonized in the intestinal microflora of patients from multiple viewpoints. Here, we studied a total of 98 stool samples of patients including 47 CRE carriers and 51 CRE non-colonized patients. We performed not only a basic analysis of the microbial assemblage but also extended analyses including reconstructing 1,106 MAGs and prediction of horizontal gene transfer events. In the consequences, we notably found that the proton pump inhibitors increase the risk of colonization with multidrug-resistant pathogens by facilitating the transfer of mobile genetic elements.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “98 stool samples of patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112127999 | collection_date | 2020-08-21 | R1 | 0.90 | biosample.attribute:collection_date | 2020-08-21 |
| SAMEA112127999 | country | KR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | South Korea |
| SAMEA112127999 | health_condition_detail | mixed_case_control: CRE carriers vs CRE non-colonized patients; ICU patients with various conditions | R4 | 0.40 | study.description | 47 CRE carriers and 51 CRE non-colonized patients |
| SAMEA112127999 | latitude | 37.8841 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.88413372 127.73995339 |
| SAMEA112127999 | location_locality | Chuncheon | R3 | 0.70 | paper.fulltext.methods | Chuncheon Sacred Heart Hospital |
| SAMEA112127999 | location_region | Gangwon-do | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.88413372 127.73995339 |
| SAMEA112127999 | location_site | Hallym University Chuncheon Sacred Heart Hospital | R3 | 0.70 | paper.fulltext.methods | ICU of Hallym University Chuncheon Sacred Heart Hospital |
| SAMEA112127999 | longitude | 127.7400 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.88413372 127.73995339 |
| SAMEA112127999 | subject_id | SAMEA112127999 | R3 | 0.70 | design.one_sample_per_subject:fulltext | we were able to obtain fecal samples from 98 patients, including 47 with CRE colonization |
Sequencing
98 runs over 98 samples · mean 6.09 Gbp per run (median 6.27 Gbp, total 596.65 Gbp; 98 runs with a base count) · layout PAIRED 98 · platform ILLUMINA 98 · models Illumina NovaSeq 6000 (98) · 87% of runs with a Sandpiper profile · first public 2023-01-31
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB57404.csv.gz (4.0 KB) · parquet (76.1 KB) — all 98 samples, every field with route and confidence · PRJEB57404_determinations.csv.gz (6.7 KB) — 882 evidence rows