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dbGaP phs001260 Metagenomic Epidemiology of Antibiotic Resistance in Infectious Diarrhea - pht006054.v1.p1

- 5/5/23 - 5 forms, 1 itemgroup, 15 items, 1 language
Itemgroup: pht006054
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=phs001260 The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens. We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.

Eligibility

1 itemgroup 20 items

pht006051.v1.p1

1 itemgroup 5 items

pht006052.v1.p1

1 itemgroup 5 items

pht006053.v1.p1

1 itemgroup 16 items

dbGaP phs001352 Metagenomics-Guided Pathogen Discovery in Travelers' Diarrhea - Eligibility

- 2/28/23 - 5 forms, 1 itemgroup, 21 items, 1 language
Itemgroup: IG.elig
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.

pht007064.v1.p1

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pht007065.v1.p1

1 itemgroup 5 items

pht007066.v1.p1

1 itemgroup 2 items

pht007067.v1.p1

1 itemgroup 6 items

Efficacy, Safety and Immunogenicity of Oral HRV Vaccine NCT00241644 - HIV Repeat Test

- 1/9/19 - 1 form, 2 itemgroups, 5 items, 1 language
Itemgroups: Administrative Data, HIV repeat test
Study ID: 102248 Clinical Study ID: 102248 Study Title: Multi-Center Study to Assess the Efficacy, Safety and Immunogenicity of 2 or 3 Doses of GSK Biologicals' Oral Live Attenuated Human Rotavirus (HRV) Vaccine Given Concomitantly With Routine EPI Vaccinations in Healthy Infants Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00241644 Study Link: https://clinicaltrials.gov/ct2/show/NCT00241644 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Infections, Rotavirus The visits are defined as follows: Visit 1: (Study/Participation) Day 0, Age: 5-10 weeks, Dose 1 Visit 2: (Study/Participation) Month 1, 30-48 days after Visit 1, Dose 2 Visit 3: (Study/Participation) Month 2, 30-48 days after Visit 2, Dose 3 Visit 4: (Study/Participation) Month 3, 30-48 days after Visit 3, Visit 5: (Study/Participation) 1 year of age, 343-391 days of age For amendment 5: Visit 5: (Study/Participation) 21-48 days after Visit 4 Visit 6: (Study/Participation) 1 year of age, 343-391 days of age This form contains information about the HIV repeat test, that should be performed at visit 6 and is part of amendment 1

Efficacy, Safety and Immunogenicity of Oral HRV Vaccine NCT00241644 - HIV Confirmation Testing

- 11/1/18 - 1 form, 2 itemgroups, 5 items, 1 language
Itemgroups: Administrative Data, HIV Confirmatory Test
Study ID: 102248 Clinical Study ID: 102248 Study Title: Multi-Center Study to Assess the Efficacy, Safety and Immunogenicity of 2 or 3 Doses of GSK Biologicals' Oral Live Attenuated Human Rotavirus (HRV) Vaccine Given Concomitantly With Routine EPI Vaccinations in Healthy Infants Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00241644 Study Link: https://clinicaltrials.gov/ct2/show/NCT00241644 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Infections, Rotavirus The visits are defined as follows: Visit 1: (Study/Participation) Day 0, Age: 5-10 weeks, Dose 1 Visit 2: (Study/Participation) Month 1, 30-48 days after Visit 1, Dose 2 Visit 3: (Study/Participation) Month 2, 30-48 days after Visit 2, Dose 3 Visit 4: (Study/Participation) Month 3, 30-48 days after Visit 3, Visit 5: (Study/Participation) 1 year of age, 343-391 days of age For amendment 5: Visit 5: (Study/Participation) 21-48 days after Visit 4 Visit 6: (Study/Participation) 1 year of age, 343-391 days of age This form contains information about the confirmation testing of the subject for HIV. It should be checked at Visit 4 and is part of study amendment 1.

Efficacy, Safety and Immunogenicity of Oral HRV Vaccine NCT00241644 - HIV Testing

- 11/1/18 - 1 form, 2 itemgroups, 9 items, 1 language
Itemgroups: Administrative Data, HIV Testing
Study ID: 102248 Clinical Study ID: 102248 Study Title: Multi-Center Study to Assess the Efficacy, Safety and Immunogenicity of 2 or 3 Doses of GSK Biologicals' Oral Live Attenuated Human Rotavirus (HRV) Vaccine Given Concomitantly With Routine EPI Vaccinations in Healthy Infants Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00241644 Study Link: https://clinicaltrials.gov/ct2/show/NCT00241644 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Infections, Rotavirus The visits are defined as follows: Visit 1: (Study/Participation) Day 0, Age: 5-10 weeks, Dose 1 Visit 2: (Study/Participation) Month 1, 30-48 days after Visit 1, Dose 2 Visit 3: (Study/Participation) Month 2, 30-48 days after Visit 2, Dose 3 Visit 4: (Study/Participation) Month 3, 30-48 days after Visit 3, Visit 5: (Study/Participation) 1 year of age, 343-391 days of age For amendment 5: Visit 5: (Study/Participation) 21-48 days after Visit 4 Visit 6: (Study/Participation) 1 year of age, 343-391 days of age This form contains information about testing the subject for HIV. It should be checked at Visit 3 and is part of study amendment 1.

Efficacy, Safety and Immunogenicity of Oral HRV Vaccine NCT00241644 - Gastroenteritis Episodes, HIV Testing

- 11/9/18 - 1 form, 3 itemgroups, 5 items, 1 language
Itemgroups: Administrative Data, Gastroenteritis Episodes, HIV Test
Study ID: 102248 Clinical Study ID: 102248 Study Title: Multi-Center Study to Assess the Efficacy, Safety and Immunogenicity of 2 or 3 Doses of GSK Biologicals' Oral Live Attenuated Human Rotavirus (HRV) Vaccine Given Concomitantly With Routine EPI Vaccinations in Healthy Infants Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00241644 Study Link: https://clinicaltrials.gov/ct2/show/NCT00241644 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Infections, Rotavirus The visits are defined as follows: Visit 1: (Study/Participation) Day 0, Age: 5-10 weeks, Dose 1 Visit 2: (Study/Participation) Month 1, 30-48 days after Visit 1, Dose 2 Visit 3: (Study/Participation) Month 2, 30-48 days after Visit 2, Dose 3 Visit 4: (Study/Participation) Month 3, 30-48 days after Visit 3, Visit 5: (Study/Participation) 1 year of age, 343-391 days of age For amendment 5: Visit 5: (Study/Participation) 21-48 days after Visit 4 Visit 6: (Study/Participation) 1 year of age, 343-391 days of age This form asks if the patient had any episodes of gastroenteritis between visits. It should be checked on visit 2-5. The HIV-Test itemgroup is part of amendment 4.

Efficacy, Safety and Immunogenicity of Oral HRV Vaccine NCT00241644 - Gastroenteritis Episode Form

- 11/1/18 - 1 form, 3 itemgroups, 23 items, 1 language
Itemgroups: Administrative Data, Gastroenteritis Episodes, Documentation of Gastroenteritis Episode
Study ID: 102248 Clinical Study ID: 102248 Study Title: Multi-Center Study to Assess the Efficacy, Safety and Immunogenicity of 2 or 3 Doses of GSK Biologicals' Oral Live Attenuated Human Rotavirus (HRV) Vaccine Given Concomitantly With Routine EPI Vaccinations in Healthy Infants Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00241644 Study Link: https://clinicaltrials.gov/ct2/show/NCT00241644 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Infections, Rotavirus The visits are defined as follows: Visit 1: (Study/Participation) Day 0, Age: 5-10 weeks, Dose 1 Visit 2: (Study/Participation) Month 1, 30-48 days after Visit 1, Dose 2 Visit 3: (Study/Participation) Month 2, 30-48 days after Visit 2, Dose 3 Visit 4: (Study/Participation) Month 3, 30-48 days after Visit 3, Visit 5: (Study/Participation) 1 year of age, 343-391 days of age For amendment 5: Visit 5: (Study/Participation) 21-48 days after Visit 4 Visit 6: (Study/Participation) 1 year of age, 343-391 days of age This form contains information about gastroenteritis episodes and should be filled out if the subject has experienced an episode of GE between visits.

GSK Biologicals' oral HRV vaccine given with OPV in infants NCT00139334 - Gastroenteritis stools collection

- 10/17/18 - 1 form, 2 itemgroups, 4 items, 1 language
Itemgroups: Administrative Data, Gastroenteritis stools samples
Study ID: 103992 Clinical Study ID: 103992 Study Title: Evaluate immunogenicity, reactogenicity & safety of 2 doses of GSK Biologicals’ oral live attenuated HRV vaccine (RIX4414 at 106.5 CCID50) when given concomitantly with OPV versus given alone (HRV vaccine dose given 15 days after the OPV dose) in healthy infants in Bangladesh Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00139334 https://clinicaltrials.gov/ct2/show/NCT00139334 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 2 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Haemophilus influenzae type b; Neisseria Meningitidis This form is only for documentation of unplanned stool samples in case of gastroenteritis epidoseds during the trial. Planned stool samples at pre-defined timepoints need to be recorded in the "planned stool sample" form for visits 3 and 5.

GSK Biologicals' oral HRV vaccine given with OPV in infants NCT00139334 - Gastroenteritis episodes

- 10/17/18 - 1 form, 2 itemgroups, 4 items, 1 language
Itemgroups: Administrative Data, Gastroenteritis episodes
Study ID: 103992 Clinical Study ID: 103992 Study Title: Evaluate immunogenicity, reactogenicity & safety of 2 doses of GSK Biologicals’ oral live attenuated HRV vaccine (RIX4414 at 106.5 CCID50) when given concomitantly with OPV versus given alone (HRV vaccine dose given 15 days after the OPV dose) in healthy infants in Bangladesh Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00139334 https://clinicaltrials.gov/ct2/show/NCT00139334 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 2 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Haemophilus influenzae type b; Neisseria Meningitidis This form is for documentation of gastroenteritis episodes between visits 3 and 4, 4 and 5 as well as 5 and 6, starting 1 week after dose 1 of HRV/Placebo in Visit 3). To be assessed at Visits 4, 5 and 6. Visit 4 -> Timing: Day 60, Age: 14 weeks +/- 1 week Visit 5 -> Timing: Day 75, Age: 16 weeks +/- 1 week Visit 6 -> Timing: Day 105, Age: 20 weeks +/- 1 week

GSK Biologicals' oral HRV vaccine given with OPV in infants NCT00139334 - Planned stool samples

- 10/16/18 - 1 form, 2 itemgroups, 9 items, 1 language
Itemgroups: Administrative Data, Laboratory tests: Planned stool Samples
Study ID: 103992 Clinical Study ID: 103992 Study Title: Evaluate immunogenicity, reactogenicity & safety of 2 doses of GSK Biologicals’ oral live attenuated HRV vaccine (RIX4414 at 106.5 CCID50) when given concomitantly with OPV versus given alone (HRV vaccine dose given 15 days after the OPV dose) in healthy infants in Bangladesh Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00139334 https://clinicaltrials.gov/ct2/show/NCT00139334 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 2 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: Rotarix Study Indication: Haemophilus influenzae type b; Neisseria Meningitidis This form is for documentation of planned stool samples for the "stool subset". To be filled in at visit 3 (prior to and after first dose of study vaccine) and at visit 5 (prior and after second dose of study vaccine). Visit 3, Vaccination 1 -> Timing: Day 45, Age: 12 weeks +/- 1 week Visit 5, Vaccination 2 -> Timing: Day 75, Age: 16 weeks +/- 1 week This is not for documentation of stool samples in case of a gastroenteritis episode. Please use the Stool Collection form in that case.

Rotavirus Vaccine RIX4414 Study NCT00289172 - gastroenteritis, concomitant vaccination, medication and non-serious adverse events

- 4/13/18 - 1 form, 8 itemgroups, 38 items, 2 languages
Itemgroups: Header, Gastroenteritis Episodes, Gastroenteritis protocol, Concomitant Vaccination, Concomitant Vaccination, Medication, Medication, Non-serious Adverse Events
A multicenter study of the immunogenicity & safety of 2 doses of GSK Biologicals’oral live attenuated human rotavirus vaccine (RIX4414) as primary dosing of healthy infants in India aged approximately 8 wks at the time of the first dose Study ID:103792 Clinical Study ID:103792 Study Title: A multicenter study of the immunogenicity & safety of 2 doses of GSK Biologicals’oral live attenuated human rotavirus vaccine (RIX4414) as primary dosing of healthy infants in India aged approximately 8 wks at the time of the first dose Patient Level Data:Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier:NCT00289172 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: BIO ROTA; Rotarix Study Indication: Infections, Rotavirus CRF Seiten: 375-430

GSK Biologicals' oral live attenuated human rotavirus vaccine (RIX4414) as primary dosing of healthy infants; NCT00289172 - Visit 3

- 4/28/19 - 1 form, 5 itemgroups, 11 items, 1 language
Itemgroups: Administrative documentation, Continuation status, Clinical Trials, Collection of blood specimen for laboratory procedure, Post-vaccination precautions, Gastroenteritis, Episode of, Body Height, Body Weight
Study ID: 103792 Clinical Study ID: 103792 Study Title: A multicenter study of the immunogenicity & safety of 2 doses of GSK Biologicals’ oral live attenuated human rotavirus vaccine (RIX4414) as primary dosing of healthy infants in India aged approximately 8 wks at the time of the first dose Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00289172 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: phase 3 Study Recruitment Status: Completed Generic Name: Rotavirus Vaccine Trade Name: BIO ROTA; Rotarix Study Indication: Infections, Rotavirus

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