Prevalence and clinical outcomes of viral and bacterial coinfections in hospitalized COVID-19 patients

By Dr. Chinta SidharthanMar 7 2023Reviewed by Aimee Molineux

In a recent study published in Influenza and Other Respiratory Viruses, researchers analyzed the occurrence of bacterial and viral infections in adults hospitalized with coronavirus disease 2019 (COVID-19) to determine the clinical and demographic features, outcomes, and microbial spectrums associated with bacterial coinfections and the prevalence of viral coinfections.

Background

Respiratory infections are often associated with bacterial or viral coinfections due to alterations in the immune system during the initial respiratory infection or damage to the lung mucosa. While sometimes these coinfections increase the severity and mortality rates, often these infections are incidental.

Severe influenza infections have been known to result in complications such as bacterial coinfections. Still, secondary infections or co-infections with bacteria have been generally rare in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Therefore, there is a paucity of information on the risk factors, prevalence, and clinical outcomes associated with viral and bacterial coinfections in COVID-19 patients.

About the study

In the present study, the researchers used data from a surveillance platform based on a geographically diverse large population from the United States (U.S.) known as Coronavirus Disease 2019-Associated Hospitalization Surveillance Network (COVID-NET), which comprises data from 250 hospitals from 14 U.S. states. The data from this platform consists of all COVID-19-associated hospitalizations, symptoms of SARS-CoV-2 infections, demographic characteristics, comorbidities, results from bacterial and viral testing, chest imaging, and a wide range of outcomes, including critical care, need for mechanical ventilation, and death.

A cross-sectional analysis included all adults above the age of 18 that were hospitalized with SARS-CoV-2 infections and were tested for bacterial pathogens from respiratory or sterile sites. The sites in individuals that tested positive for bacterial infection were classified as sputum, blood, deep respiratory (bronchoalveolar lavage fluid, endotracheal aspirate, lung tissue, or pleural fluid), and other sterile sites, which included bone, cerebrospinal fluid, and peritoneal fluid.

Polymerase chain reaction (PCR) was used to test for viral coinfections such as rhinovirus or enterovirus, respiratory syncytial virus, influenza A, B or of unspecified subtypes, human metapneumovirus, parainfluenza, adenovirus, and human coronaviruses that were seasonal.

Associations between having bacterial coinfections with SARS-CoV-2 infections and worse clinical outcomes, such as the need for mechanical ventilation, admission to intensive care units, or death, were analyzed. Furthermore, the study also compared demographic and clinical characteristics between patients who had and did not have bacterial coinfections. Additionally, the prevalence of viral coinfections or secondary infections was also calculated.

Results

The results reported that out of the 36,490 hospitalized COVID-19 patients, a little more than half (53.3%) has available bacterial cultures within a week of hospital admission, and of these 6% had coinfections with clinically relevant bacteria. Furthermore, bacterial coinfections within one week of hospitalization due to SARS-CoV-2 infection were associated with a 2.3 times higher risk of mortality as compared to patients who had negative bacterial pathogen test cultures.

The findings indicated that while bacterial infections were not detected frequently in the first week following hospital admission due to COVID-19, among the patients that did test positive for bacterial co-infections, close to one-third died in the hospital. The most frequently detected bacterial pathogens were Gram-negative rod-shaped bacteria and Staphylococcus aureus. Among the Gram-negative rods, the most frequently identified bacteria in sputum samples were Pseudomonas aeruginosa and Klebsiella pneumoniae. In the deep respiratory samples, Escherichia coli were also detected, while in blood samples the two most frequently detected bacteria were S. aureus and E. coli.

Demographic characteristics such as age, sex, race, and ethnicity were not associated with an increased risk of bacterial coinfections. Still, comorbidities such as renal disease, diabetes, chronic lung disease, gastrointestinal or liver disease, obesity, and cardiovascular disease were linked to a higher risk of having bacterial coinfections.

Among the 25.5% of the COVID-19 patients tested for other respiratory viruses, 0.1% tested positive for influenza, while 0.01% tested positive for the respiratory syncytial virus. The other most frequently detected virus was rhinovirus or enterovirus. Two hospitalized COVID-19 patients tested positive for another viral and bacterial infection within one week of admission.

Conclusions

Overall, the results suggested that while the prevalence of bacterial coinfections among individuals hospitalized with COVID-19 was low (6%), and the prevalence of viral coinfections in the group was lower (0.9%), there was an increased risk of mortality associated with developing a bacterial coinfection within one week of hospitalization. Individuals with comorbidities were also more susceptible to bacterial coinfections.