Viral-bacterial codetection among patients with pneumonia during the COVID-19 pandemic in Jakarta, Indonesia

Pneumonia is a leading cause of death worldwide, especially among children and the elderly, mainly due to viral and bacterial infections. During the COVID-19 pandemic, cases rose as SARS-CoV-2 also causes pneumonia. This study investigates viral and bacterial detection among SARS-CoV-2 suspected patients with pneumonia admitted to the health care facilities in Jakarta, Indonesia. Of the 245 pneumonia cases, 80 (33%) were confirmed positive for SARS-CoV-2. Among other viruses, paramyxovirus and herpesvirus were the predominant viruses identified (each 7%) followed by influenza virus (5%) and enterovirus (2%). Bacterial screening of nasopharyngeal swab specimens detected 21 (9%) and 14 (6%) positive for Haemophilus influenzae and Streptococcus pneumoniae respectively. Overall, the higher rate of viral-bacterial codetection was observed in the SARS-CoV-2 positive cases than in the negative cases. We found that viral-bacterial codetection without any significant association with clinical manifestation, patient outcome or severity.Pneumonia is a leading cause of death worldwide, especially among children and the elderly, mainly due to viral and bacterial infections. During the COVID-19 pandemic, cases rose as SARS-CoV-2 also causes pneumonia. This study investigates viral and bacterial detection among SARS-CoV-2 suspected patients with pneumonia admitted to the health care facilities in Jakarta, Indonesia. Of the 245 pneumonia cases, 80 (33%) were confirmed positive for SARS-CoV-2. Among other viruses, paramyxovirus and herpesvirus were the predominant viruses identified (each 7%) followed by influenza virus (5%) and enterovirus (2%). Bacterial screening of nasopharyngeal swab specimens detected 21 (9%) and 14 (6%) positive for Haemophilus influenzae and Streptococcus pneumoniae respectively. Overall, the higher rate of viral-bacterial codetection was observed in the SARS-CoV-2 positive cases than in the negative cases. We found that viral-bacterial codetection without any significant association with clinical manifestation, patient outcome or severity.