ESBL gene abundance in gut microbiome, H. pylori therapy
53 fecal samples from adults with gastrointestinal infection/diarrhoea undergoing H. pylori eradication (antibiotic) therapy, studied longitudinally for ESBL-coding gene abundance and prevalence. machine-written summary
53 samples · 53 runs · LV · Adult · 2022 · 5.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 53 sample values (timepoint) |
| ✓ Abstract / description | 106 sample values (health condition, health condition detail) |
| ✓ Full text | 106 sample values (antibiotic exposure, country) · PMC10414638 |
| ○ 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
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · H. pylori eradication therapy, pre- vs post-treatment fecal samples
“patients undergoing H. pylori eradication therapy” — abstract:37561723 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Each patient sampled twice: once pre-eradication and once post-eradication H. pylori therapy (therapy duration 10 days); exact day offsets not stated” (time origin: start of H. pylori eradication therapy).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 53 | 100% | ||||
| country | 53 | 100% | 53 | |||
| health_condition | 53 | 100% | 53 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 53 | 100% | 53 | |||
| health_condition_detail | 53 | 100% | 53 | |||
| timepoint_label | 53 | 100% | 53 |
- Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori. 2023 PMID 37561723 PMC10414638 own_data
Archive description
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0289879 The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.
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 · “in the human gut microbiome”
- body site study.description · “profiles of the gut microbiome. To assess”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA11350185 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods | clarithromycinum 500 mg and amoxicillinum 1000 mg |
| SAMEA11350185 | country | LV | R3 | 0.70 | paper.fulltext.methods | Biomedical Ethics Committee of the Riga East University Hospital |
| SAMEA11350185 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | paper.abstract | patients undergoing H. pylori eradication therapy |
| SAMEA11350185 | health_condition_detail | All subjects have H. pylori infection requiring eradication therapy | R4 | 0.50 | paper.abstract | patients undergoing H. pylori eradication therapy |
| SAMEA11350185 | timepoint_label | post-eradication | R1 | 0.85 | biosample.attribute:description | post-eradication |
Sequencing
53 runs over 53 samples · mean 5.66 Gbp per run (median 5.46 Gbp, total 299.89 Gbp; 53 runs with a base count) · layout PAIRED 53 · platform DNBSEQ 53 · models DNBSEQ-G400 (53) · 0% of runs with a Sandpiper profile · first public 2022-01-05
Authors (11)
Gudra D first · Silamikelis I · Pjalkovskis J · Danenberga I · Pupola D · Skenders G · Ustinova M · Megnis K · Leja M · Vangravs R · Fridmanis D last
Downloads
PRJEB48983.csv.gz (2.0 KB) · parquet (71.1 KB) — all 53 samples, every field with route and confidence · PRJEB48983_determinations.csv.gz (1.8 KB) — 265 evidence rows