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. 2023 Mar 2;17(3):e13107.
doi: 10.1111/irv.13107. eCollection 2023 Mar.

Bacterial and viral infections among adults hospitalized with COVID-19, COVID-NET, 14 states, March 2020-April 2022

Melisa M Shah  1   2 , Kadam Patel  2   3   4 , Jennifer Milucky  2   4 , Christopher A Taylor  2   4 , Arthur Reingold  5   6 , Isaac Armistead  7 , James Meek  8 , Evan J Anderson  9   10 , Andy Weigel  11 , Libby Reeg  12 , Kathryn Como-Sabetti  13 , Susan L Ropp  14 , Alison Muse  15 , Sophrena Bushey  16 , Eli Shiltz  17 , Melissa Sutton  18 , H Keipp Talbot  19 , Ryan Chatelain  20 , Fiona P Havers  2   4   21 ; CDC COVID‐NET Surveillance Team
Affiliations

Bacterial and viral infections among adults hospitalized with COVID-19, COVID-NET, 14 states, March 2020-April 2022

Melisa M Shah et al. Influenza Other Respir Viruses. .

Abstract

Background: Bacterial and viral infections can occur with SARS-CoV-2 infection, but prevalence, risk factors, and associated clinical outcomes are not fully understood.

Methods: We used the Coronavirus Disease 2019-Associated Hospitalization Surveillance Network (COVID-NET), a population-based surveillance system, to investigate the occurrence of bacterial and viral infections among hospitalized adults with laboratory-confirmed SARS-CoV-2 infection between March 2020 and April 2022. Clinician-driven testing for bacterial pathogens from sputum, deep respiratory, and sterile sites were included. The demographic and clinical features of those with and without bacterial infections were compared. We also describe the prevalence of viral pathogens including respiratory syncytial virus, rhinovirus/enterovirus, influenza, adenovirus, human metapneumovirus, parainfluenza viruses, and non-SARS-CoV-2 endemic coronaviruses.

Results: Among 36 490 hospitalized adults with COVID-19, 53.3% had bacterial cultures taken within 7 days of admission and 6.0% of these had a clinically relevant bacterial pathogen. After adjustment for demographic factors and co-morbidities, bacterial infections in patients with COVID-19 within 7 days of admission were associated with an adjusted relative risk of death 2.3 times that of patients with negative bacterial testing. Staphylococcus aureus and Gram-negative rods were the most frequently isolated bacterial pathogens. Among hospitalized adults with COVID-19, 2766 (7.6%) were tested for seven virus groups. A non-SARS-CoV-2 virus was identified in 0.9% of tested patients.

Conclusions: Among patients with clinician-driven testing, 6.0% of adults hospitalized with COVID-19 were identified to have bacterial coinfections and 0.9% were identified to have viral coinfections; identification of a bacterial coinfection within 7 days of admission was associated with increased mortality.

Keywords: COVID‐19; COVID‐NET; SARS‐CoV‐2; bacterial coinfection; viral coinfection.

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Conflict of interest statement

Ms. Leegwater and Ms. Reeg report grants from Michigan Department of Health and Human Services during the conduct of the study. Dr. Anderson reports grants from Pfizer, Merck, PaxVax, Micron, Sanofi‐Pasteur, Janssen, MedImmune, and GSK. Dr. Anderson reports personal fees from Sanofi‐Pasteur, Pfizer, Medscape, Kentucky Bioprocessing, Inc, Sanofi‐Pasteur, Janssen, GSK, WCG and ACI Clinical, and Moderna outside the submitted work. His institution has also received funding from NIH to conduct clinical trials of Moderna and Janssen COVID‐19 vaccines. Mr. Weigel reports grants from CDC/CSTE Cooperative Agreement, during the conduct of the study and grants from CDC/CSTE outside the submitted work. Mr. Teno reports grants from CDC/CSTE Cooperative Agreement during the conduct of the study and grants from CDC/CSTE outside the submitted work. Mrs. Billing reports grants from Council of State and Territorial Epidemiologists (CSTE) during the conduct of the study and grants from Centers for Disease Control and Prevention (CDC) outside the submitted work. Mr. Meek reports grants from CDC during the conduct of the study. Dr. Schaffner reports grants from CDC during the conduct of the study. Dr. Sutton reports grants from CDC Emerging Infections Program during the conduct of the study. Dr. Talbot reports grants from Centers for Disease Control and Prevention, during the conduct of the study. Ms. Yousey‐Hindes reports grants from CDC during the conduct of the study.

Figures

FIGURE 1
FIGURE 1
Flowchart of hospitalized adults in COVID‐NET with bacterial and viral infections. Unweighted counts and weighted percentages are reported. The seven viral groups include respiratory syncytial virus, rhinovirus/enterovirus, influenza (subtypes A, B, or unspecified), adenovirus, human metapneumovirus (HMPV), parainfluenza (serotypes 1–4), and common human coronaviruses (229E, HKU1, NL63, OC43).
FIGURE 2
FIGURE 2
Bacterial cultures from hospitalized sampled adults with COVID‐19 with bacterial pathogens detected in sputum, deep respiratory, or blood cultures within 7 days of admission from Coronavirus Disease 2019‐Associated Hospitalization Surveillance Network (COVID‐NET) from March 2020 to April 2022. This figure includes 1408 bacterial cultures with a clinically relevant organism from 1066 individuals. Deep respiratory sites include endotracheal aspirate, bronchoalveolar lavage fluid, pleural fluid, and lung tissue. Unweighted counts and percentages are reported in this figure.
See this image and copyright information in PMC

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