Respiratory etiological surveillance among quarantined patients with suspected lower respiratory tract infection at a medical center in southern Taiwan during COVID-19 pandemic

Abstract

Background A comprehensive study of respiratory pathogens was conducted in an area with a low prevalence of COVID-19 among the adults quarantined at a tertiary hospital. Methods From March to May 2020, 201 patients suspected lower respiratory tract infection (LRTI) were surveyed for etiologies by multiplex polymerase chain reaction (PCR: FilmArray TM Respiratory Panel) test combination with cultural method, viral antigen detection and serologic surveys. Results Total 201 patients tested with FilmArray TM Respiratory Panel were enrolled, of which 68.2% had sputum bacterial culture, 86.1% had pneumococcus and Legionella urine antigen test. Their median age was 72.0 year-old with multiple comorbidities, and 11.4% were nursing home residents. Bacteria accounted for 59.7% of identified pathogens. Atypical pathogens were identified in 31.3% of total pathogens, of which viruses accounted for 23.9%. In comparison to patients with bacterial infection, patients with atypical pathogens were younger (median= 77.2 vs 67.1, years, P = 0.017) and had shorter length of hospital (8.0 vs 4.5, days, P = 0.007). Conclusions Patients with LRTI caused by atypical pathogens was indistinguishable from those with bacterial pathogens by clinical manifestations or biomarkers. Multiplex PCR providing rapid diagnosis of atypical pathogens enhance patient care and decision making when rate of sputum culture sampling was low in quarantine ward during pandemic.

The Assessment of Multiplex PCR in Identifying Bacterial Infections in Patients Hospitalized with SARS-CoV-2 Infection: A Systematic Review

“…Out of the nine studies included [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ], most studies were retrospective [ 35 , 37 , 38 , 39 , 40 , 41 ], one article was cross-sectional [ 36 ], and two articles were prospective [ 42 , 43 ]. Regarding the place where the studies were conducted, there was a heterogeneous result since each study took place in another country, as follows: Saudi Arabia [ 35 ], Romania [ 36 ], Israel [ 37 ], Italy [ 38 ], Taiwan [ 39 ], Austria [ 40 ], France [ 41 ], Germany and Switzerland together [ 42 ], and Peru [ 43 ]. Regarding the sample size, almost half of the studies (44.4%) had a sample size of less than 100 patients [ 35 , 37 , 40 , 43 ], while the others (55.6%) ranged from 178 to 489 patients [ 38 , 39 , 41 , 42 ].…”

“…Regarding the place where the studies were conducted, there was a heterogeneous result since each study took place in another country, as follows: Saudi Arabia [ 35 ], Romania [ 36 ], Israel [ 37 ], Italy [ 38 ], Taiwan [ 39 ], Austria [ 40 ], France [ 41 ], Germany and Switzerland together [ 42 ], and Peru [ 43 ]. Regarding the sample size, almost half of the studies (44.4%) had a sample size of less than 100 patients [ 35 , 37 , 40 , 43 ], while the others (55.6%) ranged from 178 to 489 patients [ 38 , 39 , 41 , 42 ]. Reported data can be found in Table 1 .…”

“…These patients could have been treated in a standard unit or in an intensive care unit, depending on their condition. The median ages of the study populations were 52 years [ 35 ], 67 years [ 37 ], 72 years [ 39 ], 62.5 years [ 40 ], 57 years [ 41 ], 58.5 years [ 42 ], and 61.7 years [ 43 ], with the majority of patients being male, as presented in Table 2 and Figure 2 . Two studies, [ 36 , 38 ], did not report the median age of the study sample.…”

Distribution of Viral Respiratory Infections during the COVID-19 Pandemic Using the FilmArray Respiratory Panel

“…SARS-CoV-2, first detected in Wuhan city, Hubei province, has now infected over one billion people, causing over two million deaths globally [ 1 ]. Multiple studies have shown the epidemiology of viral infection during the COVID-19 pandemic [ 2 , 3 , 4 , 5 ], and coexisting respiratory pathogens among COVID-19 patients [ 6 , 7 , 8 , 9 , 10 ]. The epidemiology of respiratory pathogens in regions with high prevalence may be different from that in regions with low prevalence of COVID-19.…”

“…The epidemiology of respiratory pathogens in regions with high prevalence may be different from that in regions with low prevalence of COVID-19. Recently, Huang CP et al conducted a comprehensive study of respiratory pathogens in a Taiwanese population using multiplex PCR [ 3 ]. They showed that 59.7% of identified organisms were bacteria, and viruses accounted for 23.9%.…”