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PRJNA486009 SRP157939

Diarrheagenic E. coli genomics, urban vs rural Ecuador

Genome diversity of pathogenic Escherichia coli in Ecuador

315 E. coli samples from individuals with or without diarrhea across urban and rural sites in Ecuador (e.g., Borbón, Esmeraldas, Quito), analyzed by whole genome sequencing in a case-control design to study genomic diversity, virulence, and resistance. machine-written summary

315 samples · 315 runs · EC · Age unknown · 2019 · 59.7 Mbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 2,539✓Abstract / description 204○Full text✓Supplementary tables 50✓External resources 254–User contribution–Human verified

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

what each source gave
✓ Sequence archive2,539 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region)
✓ Abstract / description204 sample values (health condition detail)
○ Full textread; no usable statement or table · PMC10484266, PMC10599324, PMC10730187, PMC6881795, PMC8105024, PMC8176484
✓ Supplementary tables50 sample values (health condition, health condition detail)
✓ External resources254 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
10 sampling locations · 1 country
Age
infant140
adult67
child65
adolescent18
neonate18
elderly7
Condition
healthy_control56
gi_infection_or_diarrhoea55
Sex
male175
female140
Country
EC315
Body site
primary315
Collected 2014–2015
2014: 177 samples2015: 138 samples20142015
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 89 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 86 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 19 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 8 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 93 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 20 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 0.06 Gbp per sample0130Gbp
! Self-contradictory metadata

age: sequence archive and curatedMetagenomicData disagree for 19 samples (e.g. 974.0 vs 730.5) — withheld.

The sources disagree on 19 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (19)
samplefieldvalueother valuehandling
SAMN09833089age974.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN09833095age487.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN09833119age669.6 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN09833120age669.6 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583209age487.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583215age456.6 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583217age700.1 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583218age487.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583219age639.2 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583221age517.4 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583227age639.2 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583228age639.2 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583229age974.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN12583232age943.6 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN12583233age456.6 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583234age639.2 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583237age547.9 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583240age487.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN12583241age547.9 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
Sampling design and relatedness

longitudinal

45 of 270 people sampled more than once (90 samples; median 2, up to 2 per person) · follow-up median 3 mo (max 12 mo) · median interval between samples 3 mo (time from age at collection).

B109B109: day 0B109: day 304B228B228: day 0B228: day 244B24B24: day 0B24: day 92B255B255: day 0B255: day 4B295B295: day 0B295: day 92B45B45: day 0B45: day 31B46B46: day 0B46: day 365B62B62: day 0B62: day 1B64B64: day 0B64: day 213E124E124: day 0E124: day 61E158E158: day 0E158: day 30E162E162: day 0E162: day 182E230E230: day 0E230: day 61E26E26: day 0E26: day 91Q132Q132: day 0Q132: day 213Q245Q245: day 0Q245: day 243Q249Q249: day 0Q249: day 244Q253Q253: day 0Q253: day 5Q282Q282: day 0Q282: day 183Q71Q71: day 0Q71: day 300 d3 mo6 mo9 mo12 mo

Each row is one person (20 shown of 45); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Prevotella 31.6%Bacteroides 11.0%Escherichia 4.3%Phocaeicola 3.4%Alloprevotella 2.8%Bifidobacterium 2.7%Veillonella 2.6%Succinivibrio 2.3%Alistipes 2.0%Faecalibacterium 1.9%Streptococcus 1.7%Roseburia 1.4%not assigned to a genus 4.8%other genera 27.4%

Genera, mean relative abundance over 103 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category315 100%
country315 100%315
health_condition111 35%4467
subject_id315 100%315
collection_date315 100%315
health_condition_detail315 100%4467204
latitude315 100%315
longitude315 100%315
sex315 100%27342
detailed_location311 99%
age_at_collection_days296 94%25442
location_locality235 75%235
location_region114 36%114
antibiotic_exposure86 27%86
Papers (6)
  • Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes. 2019 PMID 31585992 PMC6881795 own_data
  • The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. 2021 PMID 33452027 PMC8105024 own_data
  • Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. 2021 PMID 33872206 PMC8176484 own_data
  • Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador. 2023 PMID 37392822 PMC10599324 own_data
  • Distribution of Escherichia coli Pathotypes along an Urban-Rural Gradient in Ecuador. 2023 PMID 37549901 PMC10484266 own_data
1 more
  • Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic <i>E. coli</i> in northern Ecuador. 2023 PMID 37992406 PMC10730187
Details
Archive description

Here, we used whole genome sequencing to investigate the genome diversity, pangenomic gene function, virulence potential and antibiotic resistance profile of more than 200 pathogenic E. coli strains isolated from individuals with or without diarrhea living in urban and rural regions in Ecuador.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and child and infant / toddler by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “human gut metagenome”
  • life stage sample.attr.host_age · “1 (n=111/315)”
  • life stage sample.attr.host_age · “4 (n=61/315)”
  • life stage sample.attr.host_age · “2 (n=54/315)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN09833071age_at_collection_days1308.8R10.90sample.attr.host_age_months43
SAMN10908397age_at_collection_days365.25R20.75external.cmd sourceage: 1; age_unit: Year; age_group: Infant
SAMN09833071antibiotic_exposurenoR20.75external.cmd sourceantibiotics_current_use: No
SAMN09833071collection_date2014-09-03R10.90biosample.attribute:collection_date2014-09-03
SAMN09833071countryECR10.90sample.attr.geo_loc_nameEcuador: Quito
SAMN09833071health_conditionhealthy_controlR10.85biosample.attribute:host_diseaseasymptomatic
SAMN09833117health_conditiongi_infection_or_diarrhoeaR10.90biosample_attrdiarrhea
SAMN10908397health_conditionhealthy_controlR20.75external.cmd sourcedisease: Healthy
SAMN34233824health_conditionhealthy_controlR20.85paper.supp.KGMI_A_2281010_SM4493.docx_table3_[Supplementary Table 3. Supplemental meta...]B46: Control
SAMN09833071health_condition_detailasymptomaticR10.90sample.attr.host_diseaseasymptomatic
SAMN10908397health_condition_detailHealthyR20.75external.cmd sourcedisease: Healthy
SAMN34233824health_condition_detailControlR20.85paper.supp.KGMI_A_2281010_SM4493.docx_table3_[Supplementary Table 3. Supplemental meta...]B46: Control
SAMN34233842health_condition_detailmixed_case_control: diarrhea cases vs. controls without diarrheaR40.50study.descriptionindividuals with or without diarrhea
SAMN09833071latitude-0.1800R10.90biosample.attribute:lat_lon0.18 S 78.46 W
SAMN09833071location_localityQuitoR10.85biosample.attribute:geo_loc_nameEcuador: Quito
SAMN09833071location_regionPichinchaR10.60biosample.attribute:lat_lon0.18 S 78.46 W
SAMN12583211location_regionEsmeraldasR10.85biosample.attribute:geo_loc_nameEcuador:Esmeraldas
SAMN09833071longitude-78.4600R10.90biosample.attribute:lat_lon0.18 S 78.46 W
SAMN09833071sexmaleR10.90sample.attr.host_sexmale
SAMN10908397sexmaleR20.75external.cmd sourcesex: Male
SAMN09833071subject_idQ132R10.70sample.name_rule:aliasalias=Q132
SAMN10908397subject_idQ105R10.70sample.name_rule:TITLETITLE=Q105
SAMN12583207subject_idB001R10.85sample.attr.individual_idB001
Sequencing

315 runs over 315 samples · mean 0.93 Gbp per run (median 59.7 Mbp, total 293.53 Gbp; 315 runs with a base count) · layout PAIRED 315 · platform ILLUMINA 315 · models Illumina MiSeq (195), Illumina HiSeq 2000 (120) · 35% of runs with a Sandpiper profile · first public 2019-07-18 – 2025-06-23

Authors (21)

Meziti A first · Rodriguez-R LM · Hatt JK · Peña-Gonzalez A · Levy K · Konstantinidis KT last · Soto-Girón MJ first · Montero L · Páez M · Ortega E · Smith S · Cevallos W · Trueba G · Rothstein AP first · Jesser KJ · Feistel DJ · Smith SM · Paez M · Sánchez X · Puebla E · Endara P

Downloads

PRJNA486009.csv.gz (11.9 KB) · parquet (88.3 KB) — all 315 samples, every field with route and confidence · PRJNA486009_determinations.csv.gz (29.2 KB) — 3,047 evidence rows

Samples (315 · every field this project has values for · hover a cell for its source)
Loading the sample table…