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.
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.
Study Type
OBSERVATIONAL
Enrollment
185
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, United States
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.
Time frame: 4-8 weeks
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.
Time frame: 4-8 weeks
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.
Time frame: 4-8 weeks
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.
Time frame: 12 months
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.
Time frame: 12 months
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.
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Time frame: Up to 12 weeks post-PCR confirmation for a SARS-CoV-2 positive diagnosis
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 \[full resolution defined as resolution of acute onset clinical symptoms\].
Time frame: Up to 30 days after respiratory symptom onset
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
Time frame: 4-8 weeks
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.
Time frame: 4-8 weeks
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.
Time frame: 4-8 weeks
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
Time frame: 4-8 weeks
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
Time frame: Baseline to any timepoint for 4 to 8 weeks
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
Time frame: Baseline to any timepoint for 4 to 8 weeks
Changes in hematology
Examine prospective data to identify changes in patient hematology through analysis of complete blood routines for CBC and WBC.
Time frame: Baseline to any timepoint for 4 to 8 weeks
ALPHA Diversity (determined by NGS)
Defined as intra-community diversity as measured by the total number of detected taxa and distribution of those taxa.
Time frame: 6-12 months
Taxon Identification (determined by NGS)
Defined as intra-community diversity as measured by the total number of detected taxa and distribution of those taxa.
Time frame: 6-12 months
BETA Diversity (determined by NGS)
Defined as inter-community diversity as measured by the total number of detected taxa and distribution of those taxa.
Time frame: 6-12 months
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
Time frame: 6-12 months