Detection of pneumococcus during hospitalization for SARS-CoV-2

Abstract

Background: Infections with respiratory viruses [e.g. influenza and respiratory syncytial virus (RSV)] can increase the risk of severe pneumococcal infections. Likewise, pneumococcal coinfection is associated with poorer outcomes in viral respiratory infection. However, there are limited data describing the frequency of pneumococcus and SARS-CoV-2 coinfection and the role of coinfection in influencing COVID-19 severity. We, therefore, investigated the detection of pneumococcus in COVID-19 inpatients during the early pandemic period.

Methods: The study included patients aged 18 years and older, admitted to the Yale-New Haven Hospital who were symptomatic for respiratory infection and tested positive for SARS-CoV-2 during March-August 2020. Patients were tested for pneumococcus through culture-enrichment of saliva followed by RT-qPCR (to identify carriage) and serotype-specific urine antigen detection (UAD) assays (to identify presumed lower respiratory tract pneumococcal disease).

Results: Among 148 subjects, the median age was 65 years; 54.7% were male; 50.7% had an ICU stay; 64.9% received antibiotics; and 14.9% died while admitted. Pneumococcal carriage was detected in 3/96 (3.1%) individuals tested by saliva RT-qPCR. Additionally, pneumococcus was detected in 14/127 (11.0%) individuals tested by UAD, and more commonly in severe than moderate COVID-19 [OR: 2.20; 95% CI: (0.72, 7.48)]; however, the numbers were small with a high degree of uncertainty. None of the UAD-positive individuals died.

Conclusions: Pneumococcal lower respiratory tract infection (LRTI), as detected by positive UAD, occurred in patients hospitalized with COVID-19. Moreover, pneumococcal LRTI was more common in those with more serious COVID-19 outcomes. Future studies should assess how pneumococcus and SARS-CoV-2 interact to influence COVID-19 severity in hospitalized patients.

Keywords: COVID-19; Streptococcus pneumoniae; saliva; urinary antigen detection.

Figure 1.

Pneumococcal detection in COVID-19 inpatients. Of the COVID-19 inpatients who tested positive for pneumococcus, detection was exclusively via PCR testing of culture-enriched saliva (indicating carriage; green) or urine antigen detection (UAD, indicating pneumococcal etiology; blue). For some individuals, multiple samples were tested, as shown by points connected by the solid line. Note: a positive UAD result that follows a negative UAD does not necessarily indicate a new acquisition, but can occur due to either imperfect UAD test sensitivity or low level infection or prior carriage that was insufficient to trigger a positive UAD result. Individuals are sorted by time from admission to first positive test for pneumococcus. The dashed line indicates separation of individuals with COVID-19 cases classified as severe (top) and moderate (bottom). All COVID-19 inpatients who tested positive for pneumococcus survived.

Figure 2.

Outcome measures of COVID-19 infection categorized by pneumococcal status. UAD-positive individuals are disproportionately categorized as severe disease, particularly in comparison to the other pneumococcal statuses (positive by culture of saliva or not detected). Despite this, no culture—nor UAD-positive individuals died while hospitalized for COVID-19.