Home › Studies › PRJNA682246

PRJNA682246 SRP297100

Gut metagenomes in UTI patients, USA, longitudinal

The gut reservoir facilitates UPEC persistence and in-host adaptation in UTIs

644 stool metagenome samples from UTI patients in the USA, studying gut reservoir persistence and in-host adaptation of uropathogenic E. coli; longitudinal design. machine-written summary

644 samples · 644 runs · US · Age unknown · 2022 · 1.51 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 3,712✓Abstract / description 313✓Full text 28✓Supplementary tables 1,306–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	3,712 sample values (collection date, country, latitude, location region, longitude, timepoint)
✓ Abstract / description	313 sample values (health condition)
✓ Full text	28 sample values (collection date) · PMC10365138, PMC11133793
✓ Supplementary tables	1,306 sample values (health condition, health condition detail, subject id)
– 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

Samples at a glance

4 sampling locations · 1 country

Age

unknown644

Condition

other_infection331

gi_infection_or_diarrhoea313

Country

US644

Body site

primary644

Collected 2016–2019

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

106 of 106 people sampled more than once (644 samples; median 5, up to 13 per person) · follow-up median 6 mo (max 12 mo) · median interval between samples 11 d (time from collection dates). Schedule stated by the source: “Each subject_id sampled at repeated timepoints labeled E1, E2, E3 (episode-based); exact day offsets not given in available evidence”.

Each row is one person (36 shown of 106); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 24.8%Phocaeicola 11.4%Parabacteroides 4.0%Blautia_A 3.9%Roseburia 3.8%Alistipes 3.7%Faecalibacterium 2.4%Mediterraneibacter 2.0%Ruminococcoides 1.8%Prevotella 1.5%Anaerostipes 1.4%Escherichia 1.3%not assigned to a genus 8.9%other genera 29.1%

Genera, mean relative abundance over 596 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R2	R3	R4
age_category	0	0%
country	644	100%	644
health_condition	644	100%		331		313
subject_id	644	100%		644
collection_date	644	100%	616		28
latitude	644	100%	644
longitude	644	100%	644
timepoint_label	644	100%	644
detailed_location	520	81%
location_region	520	81%	520
health_condition_detail	331	51%		331

Papers (2)

Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements. 2022 PMID 35545083 PMC10365138 own_data
Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study. 2024 PMID 38813445 PMC11133793 unsure

Details

Archive description

Here, we investigate 976 drug-resistant E. coli genomes recovered from 1,752 symptomatic and asymptomatic stool and urine specimens collected from 123 UTI patients, along with 642 corresponding stool metagenomes.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site study.description · “stool and urine specimens collected from 123 UTI patients”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN17049462	collection_date	2017-06-01	R1	0.90	biosample.attribute:collection_date	2017-06-01
SAMN17049492	collection_date	2016-07/2019-05	R3	0.70	paper.fulltext.methods	recruited between July 2016 and May 2019
SAMN17049462	country	US	R1	0.90	sample.attr.geo_loc_name	USA
SAMN17049483	health_condition	other_infection	R2	0.85	paper.supp.mmc5.xlsx[Accession_group_study][group]	rUTI
SAMN17049462	health_condition	gi_infection_or_diarrhoea	R4	0.30	study.description	123 UTI patients
SAMN17049483	health_condition_detail	rUTI	R2	0.85	paper.supp.mmc5.xlsx[Accession_group_study][group]	rUTI
SAMN17049462	latitude	36.0000	R1	0.90	biosample.attribute:lat_lon	36 N 78.94 W
SAMN17049585	location_region	Pennsylvania	R1	0.60	biosample.attribute:lat_lon	39.95 N 75.19 W
SAMN17049462	longitude	-78.9400	R1	0.90	biosample.attribute:lat_lon	36 N 78.94 W
SAMN17049462	subject_id	DK-1	R2	0.85	paper.supp.mmc5.xlsx[Accession_group_study][Patient_ID]	DK-1
SAMN17049462	timepoint_label	E1	R1	0.70	sample.name_rule:alias	DK-1-E1-S1

Sequencing

644 runs over 644 samples · mean 1.77 Gbp per run (median 1.51 Gbp, total 1,138.94 Gbp; 644 runs with a base count) · layout PAIRED 644 · platform ILLUMINA 644 · models NextSeq 500 (644) · 93% of runs with a Sandpiper profile · first public 2022-01-07 – 2023-02-01

Authors (28)

Thänert R first · Choi J · Reske KA · Hink T · Thänert A · Wallace MA · Wang B · Seiler S · Cass C · Bost MH · Struttmann EL · Iqbal ZH · Sax SR · Fraser VJ · Baker AW · Foy KR · Williams B · Xu B · Capocci-Tolomeo P · Lautenbach E · Burnham CD · Dubberke ER · Kwon JH · Dantas G · CDC Prevention Epicenters Program last · Nickel KB · Olsen MA · Barlet MH

Downloads

PRJNA682246.csv.gz (18.0 KB) · parquet (96.1 KB) — all 644 samples, every field with route and confidence · PRJNA682246_determinations.csv.gz (38.4 KB) — 5,359 evidence rows

Samples (644 · every field this project has values for · hover a cell for its source)

Loading the sample table…