Shifts in the Respiratory Microbiome and Clinical Outcomes of SARS-CoV-2

SARS-CoV-2 Infection Clinical Trial

— COVID-19  

Official title:

A Longitudinal Observational Study Identifying Shifts in the Respiratory Microbiome and Clinical Outcomes of SARS-CoV-2 in Nursing Home Residents

Clinical Trial Details — Status: Terminated

Administrative data

• NCT number: NCT04815018
• Other study ID #: 2020-rmcovid
• Status: Terminated
• Start date: October 7, 2020
• Est. completion date: May 30, 2021

Study information

• Verified date: June 2021
• Source: Pathnostics
• Contact: n/a
• Is FDA regulated: No
• Study type: Observational

Clinical Trial Summary

This is a longitudinal, prospective observational study focusing on health-related outcomes relative to potential changes in the respiratory microbiome seen with weekly SARS-CoV-2 testing in nursing home residents.

Description:

This study targets the influence of SARS-CoV-2, and the presence of mixed/co-infections on the respiratory microbiome. Their interrelationship will be characterized in a prospective observational study design. The observed changes will be correlated to medical (FEV1, CXR/CT, mortality, morbidity, symptoms) and clinical laboratory parameters (hematology, coagulation, bacterial/viral detection). The study aims at the detection of significant changes in microbiome in the respiratory tract following incidence of SARS-CoV-2 infection. These alterations in the respiratory microbiome will be determined by shotgun metagenomic sequencing. Ultimately, this can provide a better understanding of how SARS-CoV-2 and the presence of other bacteria and viruses affect the composition of the respiratory microbiome and a description of the microbiological etiology of these respiratory tract infections.

Recruitment information / eligibility

• Status: Terminated
• Enrollment: 185
• Est. completion date: May 30, 2021
• Est. primary completion date: May 30, 2021
• Accepts healthy volunteers: Accepts Healthy Volunteers
• Gender: All
• Age group: 60 Years and older

Eligibility

Inclusion Criteria:

• All residents of the nursing home facility, (M/F) 65 years or above, who have recently tested positive through Ohio's PARRT Program are eligible
• Resident must submit weekly nasal swab sample per nursing home COVID testing guidelines
• Clinical suspicion of a new episode of acute respiratory tract infection.
• Laboratory confirmed SARS-CoV-2 infection by either a laboratory test, PCR or any other commercial or public health test

Exclusion Criteria:

• Nursing home residents that are not taking part regularly in weekly screening for SARS-COV-2 or residents that test negative through Ohio's PARRT program cannot be included as part of study analyses
• Residents on hospice, residents currently intubated, residents with scheduled transfer to another nursing home facility will not be included in study analyses

Related Conditions & MeSH terms

• Bacterial Respiratory Tract Infection
• Communicable Diseases
• Infection
• Respiratory Tract Infections
• SARS-CoV-2 Infection
• Viral Respiratory Tract Infection

Locations

Country	Name	City	State
United States	Willow Brook Christian Village	Delaware	Ohio
United States	Willow Brook Delaware Run	Delaware	Ohio
United States	Kendall at Granville	Granville	Ohio
United States	Inniswood Village	Westerville	Ohio

Sponsors (1)

Lead Sponsor	Collaborator
Pathnostics

Country where clinical trial is conducted

United States, 

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	Percent of SARS-CoV-2 infection	Examine prospective data to determine the change from baseline (week 1 of testing) in resident/bed ratio positive for SARS-CoV-2.	4-8 weeks
Primary	Percent of SARS-CoV-2 and bacterial co-infection	Examine prospective data to determine the change from baseline number of healthy [SARS-CoV-2 naïve] to number that develop respiratory tract infection. Percent of SARS-CoV-2 positives without a bacterial source of RTI compared to percent of SARS-CoV-2 positives with bacterial co-infection identified by either PCR, symptoms, CXR, CT, throat culture swab, RDT and documented in patient chart.	4-8 weeks
Primary	Percent of SARS-CoV-2 and viral co-infection	Examine prospective data to determine the change from baseline number of healthy [SARS-CoV-2 naïve] to number that develop respiratory tract infection. Percent of SARS-CoV-2 positives without an additional viral cause identified compared to percent of SARS-CoV-2 positives with viral co-infection identified.	4-8 weeks
Primary	Mortality rate due to SARS-CoV-2 infection with bacterial/viral co-infection	Examine prospective data to determine the mortality rate (outpatient and inpatient) due to SARS-CoV-2 with additional bacteria and/or virus identified at any time during SARS-Cov-2 PCR positivity prior to death.	12 months
Primary	Mortality rate due to SARS-CoV-2 infection	Examine prospective data to determine the mortality rate (outpatient and inpatient) due to SARS-CoV-2 only (no additional bacteria and/or virus identified on PCR at any time during SARS-CoV-2 PCR positivity prior to death.	12 months
Primary	Symptoms of SARS-CoV-2 infection, bacterial co-infection, viral co-infection	Any changes in symptom severity will be captured by monitoring the patient's chart for any updates in clinical progress notes. Any symptoms compatible with SARS-CoV-2 infection will be captured such as high temperature, dyspnea, diarrhea, vomiting, myalgia, pharynx pain, abdominal pain, anosmia, cough etc.	Up to 12 weeks post-PCR confirmation for a SARS-CoV-2 positive diagnosis
Primary	Percent of SARS-Cov-2 positives and/or bacterial/viral infection with full resolution by 30 days	Examine prospective data to determine the percent of SARS-Cov-2 positives and/or bacterial/viral infection with full resolution by 30 days after respiratory symptom onset [full resolution defined as resolution of acute onset clinical symptoms].	Up to 30 days after respiratory symptom onset
Primary	Percent of SARS-Cov-2 positives and/or bacterial/viral infection that develop pneumonia-like symptoms	Examine prospective data to determine the percent of SARS-Cov-2 positives and/or bacterial/viral infection that develop pneumonia-like symptoms during SARS-CoV-2 PCR positivity	4-8 weeks
Primary	Percent of asymptomatic SARS-Cov-2 positives and/or bacterial/viral infection	Examine prospective data to determine the percent of asymptomatic SARS-Cov-2 positives and/or bacterial/viral infection that never develop symptoms throughout infectious period and are alive/healthy at end of study.	4-8 weeks
Primary	Percent of pre-symptomatic SARS-Cov-2 positives and/or bacterial/viral infection	Examine prospective data to determine the percent of pre-symptomatic SARS-CoV-2 positives and/or bacterial/viral infection. This is the asymptomatic period PRIOR to a symptomatic period all during time of PCR positivity.	4-8 weeks
Primary	Percent of all acute medical complications	Examine prospective data to determine the prevalence of all medical usual complications and geriatric acquired complications, such as delirium, falls, pressure sores, new infectious disease (UTI), cardiovascular, incidence of acute heart failure [elevated BNP presence of new ECG abnormalities (ST elevation and/or T-wave inversion), myocardial injury [reflected by elevation in cardiac troponin levels above the 99th percentile upper reference limit on admission, cerebrovascular disease [Stroke, stroke subtype (ischemic, cryptogenic , metabolic disease manifestations DKA, hyperosmolar hyperglycemic state (HHS), and severe insulin resistance, Neurological Manifestations [Anosmia/dysgeusia, Guillen Barre Syndrome, Meningoencephalitis, Encephalomyelitis, myoclonus (generalized), Rhabdomyolysis, VTE, DIC, PE, acute limb ischemia	4-8 weeks
Primary	Pulmonary function	Examine prospective data to determine the the percent change in forced vital capacity (FVC), forced expiratory volume (FEV1), peak expiratory flow (PEF) in patients	Baseline to any timepoint for 4 to 8 weeks
Primary	Chest CT X-ray	Examine prospective data to determine the percent of lung CT containing consolidation, percent of patients showing reticular patterns, percent containing pure ground-glass opacification, percent containing honeycomb appearance, percent containing Bronchiectasis	Baseline to any timepoint for 4 to 8 weeks
Primary	Changes in hematology	Examine prospective data to identify changes in patient hematology through analysis of complete blood routines for CBC and WBC.	Baseline to any timepoint for 4 to 8 weeks
Secondary	ALPHA Diversity (determined by NGS)	Defined as intra-community diversity as measured by the total number of detected taxa and distribution of those taxa.	6-12 months
Secondary	Taxon Identification (determined by NGS)	Defined as intra-community diversity as measured by the total number of detected taxa and distribution of those taxa.	6-12 months
Secondary	BETA Diversity (determined by NGS)	Defined as inter-community diversity as measured by the total number of detected taxa and distribution of those taxa.	6-12 months
Secondary	Frequency of Detection (Determined by NGS)	Frequency of detection of the total amount of bacterial DNA/RNA that corresponds to specific bacterial taxa found within nasal swab/ exhaled breath	6-12 months