Gut microbiome dynamics in CPE-colonized adults, longitudinal
361 gut metagenome samples from adult subjects colonized by carbapenemase-producing Enterobacteriaceae (CPE) and family members, studied longitudinally across up to 12 timepoints to track microbiome ecological and strain-level dynamics. machine-written summary
361 samples · 361 runs · Adult · 2022 · 3.54 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 238 sample values (shared setting type) · PMC11790488, PMC9519440 |
| ✓ Supplementary tables | 1,925 sample values (antibiotic exposure, family id, health condition detail, shared setting id, subject id, timepoint) |
| – 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 |
longitudinal — not resolvedfamilieshouseholds
43 of 46 people sampled more than once (342 samples; median 8, up to 12 per person). Schedule stated by the source: “up to 12 visits, V00 to V11”; stated follow-up 12 mo.
29 families: 29 CPE-colonized index subjects + 17 non-colonized family members (home-environment-matched); kinship not stated · 11 families with 28 sampled people · 11 shared settings.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 11 families · 8 of 11 shared settings. 46 people in the project overall.
Families (11)
Genera, mean relative abundance over 323 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 | 361 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 345 | 96% | 345 | |||
| health_condition_detail | 361 | 100% | 361 | |||
| timepoint_label | 361 | 100% | 361 | |||
| family_id | 345 | 96% | 345 | |||
| antibiotic_exposure | 275 | 76% | 275 | |||
| shared_setting_id | 238 | 66% | 238 | |||
| shared_setting_type | 238 | 66% | 238 |
- Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects. 2022 PMID 36109646 PMC9519440 own_data
- Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations. 2025 PMID 39794474 PMC11790488 own_data
Archive description
Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n=46 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole genome sequencing data from CPE isolates (n=159) helped identify sub-strain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host study.description · “colonized by carbapenemase-producing Enterobacteriaceae”
- body site study.description · “gut microbiome by carbapenemase-producing Enterobacteriaceae”
- life stage study.description · “cohort of CPE-colonized subjects and family members”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12999963 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.41564_2022_1221_MOESM9_ESM.xlsx[1b!Antibiotics.since.last.visit] | Yes |
| SAMEA12999963 | family_id | fam0500 | R2 | 0.85 | paper.supp.41564_2022_1221_MOESM9_ESM.xlsx[1b!Family] | fam0500 Index V00 fam0500-T MBH038 |
| SAMEA12999963 | health_condition_detail | CPE_positive | R2 | 0.85 | paper.supp.41564_2022_1221_MOESM12_ESM.xlsx[1a!Status] | CPE_positive |
| SAMEA12999967 | shared_setting_id | fam0502 | R2 | 0.60 | paper.supp.41564_2022_1221_MOESM9_ESM.xlsx[1b!Family] | fam0502 Index V00 fam0502-T MBH042 |
| SAMEA12999967 | shared_setting_type | household | R3 | 0.60 | paper.body.Results[text] | non-CPE-colonized family members ( n = 17, home-environment-matched controls) |
| SAMEA12999963 | subject_id | fam0500-T | R2 | 0.85 | paper.supp.41564_2022_1221_MOESM9_ESM.xlsx[1b!Indiv.Code] | MBH038: fam0500-T |
| SAMEA12999963 | timepoint_label | V00 | R2 | 0.85 | paper.supp.41564_2022_1221_MOESM16_ESM.xlsx[abundances!timepoint] | V00 |
Sequencing
361 runs over 361 samples · mean 4.17 Gbp per run (median 3.54 Gbp, total 1,505.36 Gbp; 361 runs with a base count) · layout PAIRED 361 · platform ILLUMINA 361 · models Illumina HiSeq 2500 (361) · 89% of runs with a Sandpiper profile · first public 2022-02-17
Authors (18)
Kang JTL first · Teo JJY · Bertrand D · Ng A · Ravikrishnan A · Yong M · Ng OT · Marimuthu K · Chen SL · Chng KR · Gan YH · Nagarajan N last · Yin Q first · da Silva AC · Zorrilla F · Almeida AS · Patil KR · Almeida A last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, health_condition. Share metadata
Downloads
PRJEB49334.csv.gz (10.0 KB) · parquet (82.5 KB) — all 361 samples, every field with route and confidence · PRJEB49334_determinations.csv.gz (17.8 KB) — 2,163 evidence rows