Andrew Platt, MD, PhD,
Clinical Fellow
National Institutes of Health Clinical Center
Bethesda, MD
Disclosure information not submitted.
Nadia Nasir, MD
Fellow
National Cancer Institute, United States
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Bradley Ben, MD
Resident
University of Washington, United States
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James Dickey, n/a
Medical Research Scholar
National Institutes of Health Clinical Center, United States
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Madeleine Purcell, n/a
Medical Student
University of Maryland School of Medicine, United States
Disclosure information not submitted.
Jocelyn Wu, n/a
Medical Student
University of Maryland School of Medicine, United States
Disclosure information not submitted.
Shreya Singireddy, n/a
Medical Student
University of Maryland School of Medicine, United States
Disclosure information not submitted.
Stephen Salipante, MD, PhD
Pathologist
University of Washington, United States
Disclosure information not submitted.
Claire Chisholm, MS, M(ASCP)
Technician
University of Washington, United States
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Alison Grazioli, MD
Staff Clinician
National Institute of Diabetes and Digestive and Kidney Diseases, United States
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Ronson Madathil, MD
Assistant Professor of Surgery
University of Maryland School of Medicine, United States
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Joseph Rabin, MD
Assistant Professor
University of Maryland School of Medicine, United States
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Kapil Saharia, MD, MPH
Assistant Professor
University of Maryland School of Medicine, United States
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David Kleiner, MD, PhD
Senior Research Physician
National Cancer Institute, United States
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Stephen Hewitt, MD, PhD
Associate Research Physician
National Cancer Institute, United States
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Joshua Leiberman, MD, PhD
Pathologist
University of Washington, United States
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Daniel Chertow, MD, FCCM
Tenure Track Investigator
National Institutes of Health Clinical Center, United States
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Title: Prevalence of Bacterial and Fungal Co-Infections in a COVID-19 Autopsy Case Series
Introduction: Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2, has caused a global pandemic. Secondary bacterial and fungal infections have been reported as complications of COVID-19 and contribute to overall mortality. Secondary infections have been well studied in other viral pneumonias such as influenza, but post-mortem prevalence in fatal COVID-19 cases has not been established.
Methods: Autopsies were performed on 44 fatal COVID-19 cases recruited from 8 hospitals in Maryland and the District of Columbia from April 2020 to March 2021. Medical charts were reviewed for diagnoses of pulmonary or extra-pulmonary infections. Histopathological assessment of all lung lobes, including bacterial and fungal stains, was performed. In cases with evidence of bronchopneumonia PCR with broad range 16S ribosomal DNA primers was performed followed by sequencing. If a Gomori methamine silver (GMS) stain was positive PCR with 28S ribosomal and Internal Transcribed Spacer sequence (ITS) DNA primers followed by sequencing was performed.
Results: Pre-mortem pulmonary infections were diagnosed in 30% (13/44) of cases and extra-pulmonary infections were diagnosed in 36% (16/44) of cases during each patients’ hospital admission, of these 11 had both pulmonary and extra-pulmonary infections. Pseudomonas aeruginosa and Staphylococcus aureus were the most identified pathogens. Post-mortem bronchopneumonia was detected in 75% (33/44) of cases with a positive bacterial stain in 72% (24/33). Bacterial PCR and sequencing identified a putative pathogen in 6 cases. In five cases (11%) a previously unrecognized invasive fungal infection was detected by GMS stain (3 mold, 2 invasive yeast), none of which were PCR positive.
Conclusions: Systematic histopathological and molecular evaluation of fatal COVID-19 cases revealed a higher prevalence of invasive bacterial and fungal infections than was detected premortem. These finding suggests that both bacterial and invasive fungal pneumonias in critically ill patients with COVID-19 may be under-recognized, and thus a high index of suspicion is needed among treating providers.