Gut resistome in pediatric HSCT patients, Bologna, Italy
32 gut metagenome samples from pediatric/adolescent HSCT patients in Bologna, Italy, studying antibiotic resistance gene dynamics linked to acute Graft-versus-Host Disease, case-control design. machine-written summary
32 samples · 32 runs · IT · Child · 2019 · 0.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 352 sample values (age, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6449395 |
| ○ 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population transplant_or_immunocompromised · Allogeneic hematopoietic stem cell transplantation, pre/post sampling
“pediatric patients undergoing allo-hematopoietic stem cell transplantation” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
8 of 8 people sampled more than once (32 samples; median 4, up to 7 per person).
Genera, mean relative abundance over 27 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 | 32 | 100% | ||||
| country | 32 | 100% | 32 | |||
| health_condition | 32 | 100% | 32 | |||
| subject_id | 32 | 100% | 32 | |||
| age_at_collection_days | 32 | 100% | 32 | |||
| detailed_location | 32 | 100% | ||||
| health_condition_detail | 32 | 100% | 32 | |||
| latitude | 32 | 100% | 32 | |||
| location_locality | 32 | 100% | 32 | |||
| location_region | 32 | 100% | 32 | |||
| longitude | 32 | 100% | 32 | |||
| sex | 32 | 100% | 32 | |||
| timepoint_label | 32 | 100% | 32 |
- Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation. 2019 PMID 30948795 PMC6449395 own_data
Archive description
The rate of infection by antibiotic-resistant bacteria (ARB) is continuously raising worldwide, particularly because of the selective pressure resulting from the increasing usage of broad-spectrum antibiotics. This burden of ARB is of particular relevance for hematological patients, who undergo frequent antimicrobial prophylaxis and treatments. The prolonged exposure to health care settings may indeed favor the progressive accumulation of antimicrobial resistance genes in the gut microbiome of patients. Consequently, opportunistic ARB can accumulate in intestinal niches, where they can take advantage of the chemotherapy-induced damage to the gut epithelium and the overlapping neutropenia, spreading through the gut wall and causing life-threatening systemic infections.The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome (i.e. the pattern of antibiotic resistance genes provided by the gut microbiome) in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “Gut resistome plasticity in”
- body site study.description · “genes in the gut microbiome of patients.”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “resistome plasticity in pediatric patients undergoing hematopoietic”
- life stage sample.attr.host_age · “12 (n=4/32)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11081373 | age_at_collection_days | 4383.0 | R1 | 0.85 | sample.attr.host_age | 12 |
| SAMN11081373 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy:Bologna |
| SAMN11081373 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | Acute Myeloid Leukemia |
| SAMN11081373 | health_condition_detail | aGvHD postive | R1 | 0.90 | sample.attr.gastrointest_disord | aGvHD postive |
| SAMN11081373 | latitude | 44.2900 | R1 | 0.90 | biosample.attribute:lat_lon | 44.29 N 11.21 E |
| SAMN11081373 | location_locality | Bologna | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy:Bologna |
| SAMN11081373 | location_region | Emilia-Romagna | R1 | 0.60 | biosample.attribute:lat_lon | 44.29 N 11.21 E |
| SAMN11081373 | longitude | 11.2100 | R1 | 0.90 | biosample.attribute:lat_lon | 44.29 N 11.21 E |
| SAMN11081373 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN11081373 | subject_id | Subject 4 | R1 | 0.85 | sample.attr.host_subject_id | Subject 4 |
| SAMN11081373 | timepoint_label | 18d post-HSCT | R1 | 0.85 | sample.attr.sampling_point | 18d post-HSCT |
Sequencing
32 runs over 32 samples · mean 0.42 Gbp per run (median 0.25 Gbp, total 13.35 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina Genome Analyzer IIx (32) · 84% of runs with a Sandpiper profile · first public 2019-03-08
Authors (14)
D'Amico F first · Soverini M · Zama D · Consolandi C · Severgnini M · Prete A · Pession A · Barone M · Turroni S · Biagi E · Brigidi P · Masetti R · Rampelli S · Candela M last
Downloads
PRJNA525982.csv.gz (1.8 KB) · parquet (71.8 KB) — all 32 samples, every field with route and confidence · PRJNA525982_determinations.csv.gz (3.0 KB) — 352 evidence rows