Pathogen spectrum in lower respiratory tracts of suspected case infected with SARS-CoV-2

Objective  To understand the pathogen spectrum in the lower respiratory tracts of 100 suspected cases infected with SARS-CoV-2 in Chaoyang district of Beijing from January to March, 2020. Methods  A total of 28 kinds of respiratory pathogens were detected by real-time fluorescent quantitative polymerase chain reaction (PCR), including 14 viruses and 11 bacteria, as well as Mycoplasma pneumoniae, Chlamydia pneumoniae and fungi. Results  The positive rate of nucleic acid of detected pathogens in 100 sputum samples of the suspected cases was 72.00% (72/100). The positive rate of SARS-CoV-2 was 15.00% (15/100). The positive rates of gram-negative bacteria, gram-positive bacteria, fungi, Mycoplasma pneumoniae and Chlamydia pneumoniae were 32.00% (32/100), 24.00% (24/100), 39.00% (39/100), 6.00% (6/100) and 3.00% (3/100), respectively. Influenza A virus, influenza B virus, adenovirus, respiratory syncytial virus and rhinovirus were also detected. A total of 13 samples were positive with both SARS-CoV-2 and other pathogens. Conclusion  The pathogens detected in the lower respiratory tracts of 100 suspected cases infected with SARS-CoV-2 in Chaoyang from January to March in 2020 was diverse. Fungi, SARS-CoV-2, Staphylococcus aureus and Haemophilus influenzae were the main pathogens. S. aureus and fungi were the main co-infected pathogens detected in the lower respiratory tracts of suspected SARS-CoV-2 infection cases.