Detection of Viral and Bacterial Respiratory Pathogens Identified by Molecular Methods in COVID-19 Hospitalized Patients and Its Impact on Mortality and Unfavorable Outcomes

Abstract

The purpose of this study is to evaluate the frequency of viral and bacterial respiratory pathogens detected by molecular methods in sputum samples of patients hospitalized for COVID-19 and to evaluate its impact on mortality and unfavorable outcomes (inhospital death or mechanical ventilation). Patients and Methods: The prospective cohort included patients with diagnosis of COVID-19 hospitalized at Hospital Nacional Hipólito Unanue. Sociodemographic and clinical data were collected from clinical records. Sputum samples were analyzed with the Biofire Filmarray Pneumonia plus ® respiratory panel. Crude and adjusted associations with unfavorable outcomes were evaluated using logistic regression models. Results: Ninety-three patients who were able to collect sputum samples were recruited between September 8 and December 28, 2020. The median age was 61.7 years (IQR 52.3-69-8) and 66 (71%) were male. The most frequent symptoms were dyspnea, cough, fever, and general malaise found in 80 (86%), 76 (82%), 45 (48%), and 34 (37%) patients, respectively. Fifty-three percent of patients had comorbidities. Seventy-six (82%) patients received antibiotics prior to admission and 29 (31%) developed unfavorable outcome. Coinfection was evidenced in 38 (40.86%) cases. The most frequently found bacteria were Staphylococcus aureus, Streptococcus agalactiae, Haemophilus influenzae and Klebsiella pneumoniae in 11 (11.83%), 10 (10.75%), 10 (10.75%), and 8 (8.6%) cases, respectively. Streptococcus pneumoniae was found in one case (1.08%). We neither identify atypical bacteria nor influenza virus. No association was found between the presence of viral or bacterial microorganisms and development of unfavorable outcomes (OR 1.63; 95% CI 0.45-5.82). Conclusion:A high frequency of respiratory pathogens was detected by molecular methods in patients with COVID-19 pneumonia but were not associated with unfavorable outcomes. No atypical agents or influenza virus were found. The high use antibiotics before admission is a concern. Our data suggest that the use of drug therapy against atypical bacteria and viruses would not be justified in patients hospitalized for COVID-19.

SARS-CoV-2–Legionella Co-Infections: A Systematic Review and Meta-Analysis (2020–2021)

“…After applying the inclusion and exclusion criteria ( Figure 1 ), a total of 38 articles were included in the qualitative synthesis [ 23 , 24 , 26 , 28 , 29 , 35 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 ]. More precisely, 27 observational studies (see Table 1 for details), 1 case series, and 10 case reports (see Appendix A for details) were included.…”

“…Overall, 18 cases of co-infections were retrieved (0.4% of total samples), with the majority of studies (18 out of 27, 66.7%) not reporting a single occurrence [ 23 , 24 , 26 , 42 , 44 , 46 , 48 , 50 , 53 , 54 , 55 , 56 , 58 , 59 , 61 , 63 ]. The majority of diagnoses was obtained from studies performed during the “first wave” (61.1%) and in European countries (50.0%).…”

“…Even the high lethality we were able to identify may represent a substantial overestimate. In fact, only half (i.e., 14 out 27) of the observational studies reported the overall mortality for the entirety of the patients sampled for Legionella [ 23 , 42 , 43 , 48 , 49 , 50 , 52 , 53 , 54 , 55 , 57 , 58 , 60 , 62 ]. Even in these reports, a specific analysis of mortality among co-infections of SARS-CoV-2– Legionella is lacking, eventually impairing a summary analysis.…”

“…The majority of the reports came from European countries (n = 17, 63.0%), followed by China (n = 4, 14.8%) and India (n = 2, 7.4%), while a single report was retrieved from Israel, Japan, Peru, and the USA, respectively (3.7% each). Overall, 18 cases of co-infections were retrieved (0.4% of total samples), with the majority of studies (18 out of 27, 66.7%) not reporting a single occurrence [23,24,26,42,44,46,48,50,[53][54][55][56]58,59,61,63]. The majority of diagnoses was obtained from studies performed during the "first wave" (61.1%) and in European countries (50.0%).…”

Methicillin-resistant Staphylococcus aureus lung infection in coronavirus disease 2019: how common?

“…Overall, S. aureus was the most frequent causative agent of respiratory infections in this large cohort (with early and late infections being considered together for this calculation) [ 27 ]. In a prospective, single center study conducted in Peru, among 93 hospitalized patients with COVID-19, 11 patients had sputum culture yielding S. aureus (12%), which was the most frequently isolated pathogen from sputum [ 21 ]. In a cross-sectional, multicenter study of 399 hospitalized patients with COVID-19 in Colombia, 18 of them had respiratory S. aureus infection (5%).…”