CaPES: carbapenem-resistant bacterial infection samples
47 samples from a patient infected with carbapenem-resistant bacteria; no country or intervention specified. machine-written summary
47 samples · 50 runs · Age unknown · 2019 · 3.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 94 sample values (subject id, timepoint) |
| ✓ Abstract / description | 94 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10699202, PMC10782538 |
| ○ 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
14 of 14 people sampled more than once (47 samples; median 4, up to 6 per person). Schedule stated by the source: “Repeated stool sampling from a single hospitalised patient infected with carbapenem-resistant bacteria”.
Genera, mean relative abundance over 24 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 | 0 | 0% | ||||
| health_condition | 47 | 100% | 47 | |||
| subject_id | 47 | 100% | 47 | |||
| health_condition_detail | 47 | 100% | 47 | |||
| timepoint_label | 47 | 100% | 47 |
- metaFlye: scalable long-read metagenome assembly using repeat graphs. 2020 PMID 33020656 PMC10699202 own_data
- Comparative analysis of metagenomic classifiers for long-read sequencing datasets. 2024 PMID 38212694 PMC10782538 unsure
Archive description
Patient infected with carbapenem resistant bacteria
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host study.description · “Patient infected with carbapenem resistant bacteria”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5407421 | health_condition | other_infection | R4 | 0.50 | study.description | Patient infected with carbapenem resistant bacteria |
| SAMEA5407421 | health_condition_detail | Carbapenem-resistant bacterial infection | R4 | 0.50 | study.description | Patient infected with carbapenem resistant bacteria |
| SAMEA5407421 | subject_id | 0509 | R1 | 0.70 | sample.name_rule:project_alias | V00-S-0509-S01 |
| SAMEA5407421 | timepoint_label | V00 | R1 | 0.70 | sample.name_rule:project_alias | V00-S-0509-S01 |
Sequencing
50 runs over 47 samples · mean 3.62 Gbp per run (median 3.13 Gbp, total 181.04 Gbp; 50 runs with a base count) · layout SINGLE 26, PAIRED 24 · platform OXFORD_NANOPORE 26, ILLUMINA 24 · models Illumina HiSeq 2000 (24), GridION (17), MinION (9) · 48% of runs with a Sandpiper profile · first public 2019-03-08 – 2019-03-13
Authors (16)
Kolmogorov M first · Bickhart DM · Behsaz B · Gurevich A · Rayko M · Shin SB · Kuhn K · Yuan J · Polevikov E · Smith TPL · Pevzner PA last · Marić J first · Križanović K · Riondet S · Nagarajan N · Šikić M last
Downloads
PRJEB29152.csv.gz (2.1 KB) · parquet (70.4 KB) — all 47 samples, every field with route and confidence · PRJEB29152_determinations.csv.gz (1.8 KB) — 188 evidence rows