ID

45625

Descrizione

Principal Investigator: Sarah Highlander, PhD, J Craig Venter Institute, La Jolla, CA, USA MeSH: Diarrhea,Escherichia coli,Salmonella,Campylobacter,Norovirus,Astroviridae,Adenoviridae,Gastroenteritis,Rotavirus https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001352 Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease.

collegamento

dbGaP study = phs001352

Keywords

versioni (1)
  1. 28/02/2023 28/02/2023 - Simon Heim
Titolare del copyright

Sarah Highlander, PhD, J Craig Venter Institute, La Jolla, CA, USA

Caricato su

28 de fevereiro de 2023

DOI

Per favore, per richiedere un accesso.

Licenza

Creative Commons BY 4.0
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dbGaP phs001352 Metagenomics-Guided Pathogen Discovery in Travelers' Diarrhea

Inglese

Eligibility Criteria

5 moduli  
Inclusion and exclusion criteria
Descrizione

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
Exclusion Criteria
Descrizione

Exclusion Criteria

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0680251
Fever > 100.3°F
Descrizione

Fever > 100.3°F

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0015967
Symptoms of acute gastroenteritis >/= 72 hours duration
Descrizione

Symptoms of acute gastroenteritis >/= 72 hours duration

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C1457887
UMLS CUI [1,2]
C0267446
Known or suspected infection or co-infection with a non-bacterial pathogen, such as viral or parasitic gastroenteritis
Descrizione

Known or suspected infection or co-infection with a non-bacterial pathogen, such as viral or parasitic gastroenteritis

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0205309
UMLS CUI [1,2]
C0332147
UMLS CUI [1,3]
C3714514
UMLS CUI [1,4]
C0275524
UMLS CUI [1,5]
C0450254
UMLS CUI [1,6]
C0521009
UMLS CUI [1,7]
C1518422
UMLS CUI [1,8]
C0521026
UMLS CUI [1,9]
C0521066
Bloody diarrhea
Descrizione

Bloody diarrhea

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0151594
History of inflammatory bowel disease
Descrizione

History of inflammatory bowel disease

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0262926
UMLS CUI [1,2]
C0021390
Treatment with an antimicrobial agent within 30 days prior to screening
Descrizione

Treatment with an antimicrobial agent within 30 days prior to screening

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0087111
UMLS CUI [1,2]
C1136254
UMLS CUI [1,3]
C4028326
UMLS CUI [1,4]
C0332152
UMLS CUI [1,5]
C0220908
Treatment with > 2 doses of an anti-diarrheal medicine within 24 hours prior to study entry, or the anticipated need for such therapy (including, but not limited to, bismuth subsalicylate, loperamide, and attapulgite) during study treatment
Descrizione

Treatment with > 2 doses of an anti-diarrheal medicine within 24 hours prior to study entry, or the anticipated need for such therapy (including, but not limited to, bismuth subsalicylate, loperamide, and attapulgite) during study treatment

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0087111
UMLS CUI [1,2]
C0718565
UMLS CUI [1,3]
C0332152
UMLS CUI [1,4]
C0439659
UMLS CUI [1,5]
C1830593
UMLS CUI [1,6]
C0053792
UMLS CUI [1,7]
C0023992
UMLS CUI [1,8]
C0052657
Concomitant need or use of any other oral, intramuscular or intravenous antibacterial with expected activities against enteric bacterial pathogens including a fluoroquinolone, macrolide, trimethoprim-sulfamethoxazole, doxycycline, or other potentially effective drug
Descrizione

Concomitant need or use of any other oral, intramuscular or intravenous antibacterial with expected activities against enteric bacterial pathogens including a fluoroquinolone, macrolide, trimethoprim-sulfamethoxazole, doxycycline, or other potentially effective drug

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C1707479
UMLS CUI [1,2]
C0279516
UMLS CUI [1,3]
C0442117
UMLS CUI [1,4]
C0442027
UMLS CUI [1,5]
C0348016
UMLS CUI [1,6]
C4316902
UMLS CUI [1,7]
C0450254
UMLS CUI [1,8]
C0041044
UMLS CUI [1,9]
C0013090
UMLS CUI [1,10]
C0282563
UMLS CUI [1,11]
C0949665
Participation in other clinical research studies utilizing an investigational agent within one month prior to screening or within five half-lives of the investigational agent, whichever is longer
Descrizione

Participation in other clinical research studies utilizing an investigational agent within one month prior to screening or within five half-lives of the investigational agent, whichever is longer

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0679823
UMLS CUI [1,2]
C0681814
UMLS CUI [1,3]
C0013223
UMLS CUI [1,4]
C4745138
UMLS CUI [1,5]
C0332152
UMLS CUI [1,6]
C0220908
UMLS CUI [1,7]
C0678761
Period of stay in the travel destination of < 72 hours
Descrizione

Period of stay in the travel destination of < 72 hours

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0023303
UMLS CUI [1,2]
C0079220
Unstable or clinically significant medical conditions, such as uncontrolled diabetes, cancer, etc.)
Descrizione

Unstable or clinically significant medical conditions, such as uncontrolled diabetes, cancer, etc.)

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0443343
UMLS CUI [1,2]
C4745084
UMLS CUI [1,3]
C2985739
UMLS CUI [1,4]
C0205318
UMLS CUI [1,5]
C0011849
UMLS CUI [1,6]
C0006826
Kidney disease
Descrizione

Kidney disease

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0022658
Seizure disorder
Descrizione

Seizure disorder

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0036572
Psychiatric condition requiring use of major tranquilizers, such as phenothiazines, butyrophenones, etc.
Descrizione

Psychiatric condition requiring use of major tranquilizers, such as phenothiazines, butyrophenones, etc.

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0033931
UMLS CUI [1,2]
C1514873
UMLS CUI [1,3]
C0040614
UMLS CUI [1,4]
C0031436
UMLS CUI [1,5]
C0006525
Concurrent treatment with Class 1a (e.g.: disopyramide, procainamide, quinidine) or Class III (e.g.: amiodarone, bretylium, ibutilide, sotalol) antiarrhythmic agents (medications that affect heartbeat)
Descrizione

Concurrent treatment with Class 1a (e.g.: disopyramide, procainamide, quinidine) or Class III (e.g.: amiodarone, bretylium, ibutilide, sotalol) antiarrhythmic agents (medications that affect heartbeat)

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0205420
UMLS CUI [1,2]
C0087111
UMLS CUI [1,3]
C0304503
UMLS CUI [1,4]
C0012702
UMLS CUI [1,5]
C0033216
UMLS CUI [1,6]
C0034414
UMLS CUI [1,7]
C0360703
UMLS CUI [1,8]
C0002598
UMLS CUI [1,9]
C0054040
UMLS CUI [1,10]
C0082966
UMLS CUI [1,11]
C0037707
Infection known or expected to be caused by a pathogen that is resistant to prulifloxacin
Descrizione

Infection known or expected to be caused by a pathogen that is resistant to prulifloxacin

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C3714514
UMLS CUI [1,2]
C1314792
UMLS CUI [1,3]
C0205309
UMLS CUI [1,4]
C1517001
UMLS CUI [1,5]
C0332325
UMLS CUI [1,6]
C0527129
History of allergy or serious adverse reaction to prulifloxacin or any other fluoroquinolone, such as ciprofloxacin
Descrizione

History of allergy or serious adverse reaction to prulifloxacin or any other fluoroquinolone, such as ciprofloxacin

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0262926
UMLS CUI [1,2]
C4684772
UMLS CUI [1,3]
C0013182
UMLS CUI [1,4]
C0527129
UMLS CUI [1,5]
C0949665
UMLS CUI [1,6]
C0008809
Failed therapy with a fluoroquinolone for any reason within the past three months
Descrizione

Failed therapy with a fluoroquinolone for any reason within the past three months

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0231175
UMLS CUI [1,2]
C0087111
UMLS CUI [1,3]
C0949665
UMLS CUI [1,4]
C4086725
Unable to tolerate oral therapy
Descrizione

Unable to tolerate oral therapy

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C1299582
UMLS CUI [1,2]
C0013220
UMLS CUI [1,3]
C0559681
Unable or unwilling to comply with the study protocol, including swallowing tablets, having blood drawn, and providing stool samples as scheduled
Descrizione

Unable or unwilling to comply with the study protocol, including swallowing tablets, having blood drawn, and providing stool samples as scheduled

Tipo di dati

boolean

Alias
UMLS CUI [1,1]
C0558080
UMLS CUI [1,2]
C1299582
UMLS CUI [1,3]
C0725694
UMLS CUI [1,4]
C2348563
UMLS CUI [1,5]
C0993159
UMLS CUI [1,6]
C1277698
UMLS CUI [1,7]
C1550661
UMLS CUI [1,8]
C0205539
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Similar models

Eligibility Criteria

5 moduli
Name
genere
Description | Question | Decode (Coded Value)
Tipo di dati
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
Exclusion Criteria
Item
Exclusion Criteria
boolean
C0680251 (UMLS CUI [1,1])
Fever > 100.3°F
Item
Fever > 100.3°F
boolean
C0015967 (UMLS CUI [1,1])
Symptoms of acute gastroenteritis >/= 72 hours duration
Item
Symptoms of acute gastroenteritis >/= 72 hours duration
boolean
C1457887 (UMLS CUI [1,1])
C0267446 (UMLS CUI [1,2])
Known or suspected infection or co-infection with a non-bacterial pathogen, such as viral or parasitic gastroenteritis
Item
Known or suspected infection or co-infection with a non-bacterial pathogen, such as viral or parasitic gastroenteritis
boolean
C0205309 (UMLS CUI [1,1])
C0332147 (UMLS CUI [1,2])
C3714514 (UMLS CUI [1,3])
C0275524 (UMLS CUI [1,4])
C0450254 (UMLS CUI [1,5])
C0521009 (UMLS CUI [1,6])
C1518422 (UMLS CUI [1,7])
C0521026 (UMLS CUI [1,8])
C0521066 (UMLS CUI [1,9])
Bloody diarrhea
Item
Bloody diarrhea
boolean
C0151594 (UMLS CUI [1,1])
History of inflammatory bowel disease
Item
History of inflammatory bowel disease
boolean
C0262926 (UMLS CUI [1,1])
C0021390 (UMLS CUI [1,2])
Treatment with an antimicrobial agent within 30 days prior to screening
Item
Treatment with an antimicrobial agent within 30 days prior to screening
boolean
C0087111 (UMLS CUI [1,1])
C1136254 (UMLS CUI [1,2])
C4028326 (UMLS CUI [1,3])
C0332152 (UMLS CUI [1,4])
C0220908 (UMLS CUI [1,5])
Treatment with > 2 doses of an anti-diarrheal medicine within 24 hours prior to study entry, or the anticipated need for such therapy (including, but not limited to, bismuth subsalicylate, loperamide, and attapulgite) during study treatment
Item
Treatment with > 2 doses of an anti-diarrheal medicine within 24 hours prior to study entry, or the anticipated need for such therapy (including, but not limited to, bismuth subsalicylate, loperamide, and attapulgite) during study treatment
boolean
C0087111 (UMLS CUI [1,1])
C0718565 (UMLS CUI [1,2])
C0332152 (UMLS CUI [1,3])
C0439659 (UMLS CUI [1,4])
C1830593 (UMLS CUI [1,5])
C0053792 (UMLS CUI [1,6])
C0023992 (UMLS CUI [1,7])
C0052657 (UMLS CUI [1,8])
Concomitant need or use of any other oral, intramuscular or intravenous antibacterial with expected activities against enteric bacterial pathogens including a fluoroquinolone, macrolide, trimethoprim-sulfamethoxazole, doxycycline, or other potentially effective drug
Item
Concomitant need or use of any other oral, intramuscular or intravenous antibacterial with expected activities against enteric bacterial pathogens including a fluoroquinolone, macrolide, trimethoprim-sulfamethoxazole, doxycycline, or other potentially effective drug
boolean
C1707479 (UMLS CUI [1,1])
C0279516 (UMLS CUI [1,2])
C0442117 (UMLS CUI [1,3])
C0442027 (UMLS CUI [1,4])
C0348016 (UMLS CUI [1,5])
C4316902 (UMLS CUI [1,6])
C0450254 (UMLS CUI [1,7])
C0041044 (UMLS CUI [1,8])
C0013090 (UMLS CUI [1,9])
C0282563 (UMLS CUI [1,10])
C0949665 (UMLS CUI [1,11])
Participation in other clinical research studies utilizing an investigational agent within one month prior to screening or within five half-lives of the investigational agent, whichever is longer
Item
Participation in other clinical research studies utilizing an investigational agent within one month prior to screening or within five half-lives of the investigational agent, whichever is longer
boolean
C0679823 (UMLS CUI [1,1])
C0681814 (UMLS CUI [1,2])
C0013223 (UMLS CUI [1,3])
C4745138 (UMLS CUI [1,4])
C0332152 (UMLS CUI [1,5])
C0220908 (UMLS CUI [1,6])
C0678761 (UMLS CUI [1,7])
Period of stay in the travel destination of < 72 hours
Item
Period of stay in the travel destination of < 72 hours
boolean
C0023303 (UMLS CUI [1,1])
C0079220 (UMLS CUI [1,2])
Unstable or clinically significant medical conditions, such as uncontrolled diabetes, cancer, etc.)
Item
Unstable or clinically significant medical conditions, such as uncontrolled diabetes, cancer, etc.)
boolean
C0443343 (UMLS CUI [1,1])
C4745084 (UMLS CUI [1,2])
C2985739 (UMLS CUI [1,3])
C0205318 (UMLS CUI [1,4])
C0011849 (UMLS CUI [1,5])
C0006826 (UMLS CUI [1,6])
Kidney disease
Item
Kidney disease
boolean
C0022658 (UMLS CUI [1,1])
Seizure disorder
Item
Seizure disorder
boolean
C0036572 (UMLS CUI [1,1])
Psychiatric condition requiring use of major tranquilizers, such as phenothiazines, butyrophenones, etc.
Item
Psychiatric condition requiring use of major tranquilizers, such as phenothiazines, butyrophenones, etc.
boolean
C0033931 (UMLS CUI [1,1])
C1514873 (UMLS CUI [1,2])
C0040614 (UMLS CUI [1,3])
C0031436 (UMLS CUI [1,4])
C0006525 (UMLS CUI [1,5])
Concurrent treatment with Class 1a (e.g.: disopyramide, procainamide, quinidine) or Class III (e.g.: amiodarone, bretylium, ibutilide, sotalol) antiarrhythmic agents (medications that affect heartbeat)
Item
Concurrent treatment with Class 1a (e.g.: disopyramide, procainamide, quinidine) or Class III (e.g.: amiodarone, bretylium, ibutilide, sotalol) antiarrhythmic agents (medications that affect heartbeat)
boolean
C0205420 (UMLS CUI [1,1])
C0087111 (UMLS CUI [1,2])
C0304503 (UMLS CUI [1,3])
C0012702 (UMLS CUI [1,4])
C0033216 (UMLS CUI [1,5])
C0034414 (UMLS CUI [1,6])
C0360703 (UMLS CUI [1,7])
C0002598 (UMLS CUI [1,8])
C0054040 (UMLS CUI [1,9])
C0082966 (UMLS CUI [1,10])
C0037707 (UMLS CUI [1,11])
Infection known or expected to be caused by a pathogen that is resistant to prulifloxacin
Item
Infection known or expected to be caused by a pathogen that is resistant to prulifloxacin
boolean
C3714514 (UMLS CUI [1,1])
C1314792 (UMLS CUI [1,2])
C0205309 (UMLS CUI [1,3])
C1517001 (UMLS CUI [1,4])
C0332325 (UMLS CUI [1,5])
C0527129 (UMLS CUI [1,6])
History of allergy or serious adverse reaction to prulifloxacin or any other fluoroquinolone, such as ciprofloxacin
Item
History of allergy or serious adverse reaction to prulifloxacin or any other fluoroquinolone, such as ciprofloxacin
boolean
C0262926 (UMLS CUI [1,1])
C4684772 (UMLS CUI [1,2])
C0013182 (UMLS CUI [1,3])
C0527129 (UMLS CUI [1,4])
C0949665 (UMLS CUI [1,5])
C0008809 (UMLS CUI [1,6])
Failed therapy with a fluoroquinolone for any reason within the past three months
Item
Failed therapy with a fluoroquinolone for any reason within the past three months
boolean
C0231175 (UMLS CUI [1,1])
C0087111 (UMLS CUI [1,2])
C0949665 (UMLS CUI [1,3])
C4086725 (UMLS CUI [1,4])
Unable to tolerate oral therapy
Item
Unable to tolerate oral therapy
boolean
C1299582 (UMLS CUI [1,1])
C0013220 (UMLS CUI [1,2])
C0559681 (UMLS CUI [1,3])
Unable or unwilling to comply with the study protocol, including swallowing tablets, having blood drawn, and providing stool samples as scheduled
Item
Unable or unwilling to comply with the study protocol, including swallowing tablets, having blood drawn, and providing stool samples as scheduled
boolean
C0558080 (UMLS CUI [1,1])
C1299582 (UMLS CUI [1,2])
C0725694 (UMLS CUI [1,3])
C2348563 (UMLS CUI [1,4])
C0993159 (UMLS CUI [1,5])
C1277698 (UMLS CUI [1,6])
C1550661 (UMLS CUI [1,7])
C0205539 (UMLS CUI [1,8])
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