Detection of SARS-CoV-2 and Other Infectious Agents in Lower Respiratory Tract Samples Belonging to Patients Admitted to Intensive Care Units of a Tertiary-Care Hospital, Located in an Epidemic Area, during the Italian Lockdown

Abstract

The aim of this study was the detection of infectious agents from lower respiratory tract (LRT) samples in order to describe their distribution in patients with severe acute respiratory failure and hospitalized in intensive care units (ICU) in an Italian tertiary-care hospital. LRT samples from 154 patients admitted to ICU from 27 February to 10 May 2020 were prospectively examined for respiratory viruses, including SARS-CoV-2, bacteria and/or fungi. SARS-CoV-2 was revealed in 90 patients (58.4%, 72 males, mean age 65 years). No significant difference was observed between SARS-CoV-2 positives and SARS-CoV-2 negatives with regard to sex, age and bacterial and/or fungal infections. Nonetheless, fungi were more frequently detected among SARS-CoV-2 positives (44/54, 81.4%, p = 0.0053). Candida albicans was the overall most frequently isolated agent, followed by Enterococcus faecalis among SARS-CoV-2 positives and Staphylococcus aureus among SARS-CoV-2 negatives. Overall mortality rate was 40.4%, accounting for 53 deaths: 37 among SARS-CoV-2 positives (mean age 69 years) and 16 among SARS-CoV-2 negatives (mean age 63 years). This study highlights the different patterns of infectious agents between the two patient categories: fungi were prevalently involved among SARS-CoV-2-positive patients and bacteria among the SARS-CoV-2-negative patients. The different therapies and the length of the ICU stay could have influenced these different patterns of infectious agents.

Epidemiology of Systemic Mycoses in the COVID-19 Pandemic

“…Co-infections by Candida have been observed in both women and men, but predominantly in men over the age of 40 [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. The predisposing factors of candidiasis were multiple, including mechanical ventilation, placement of a central venous catheter, diabetes mellitus, antibiotics treatment, hospitalization time, anti-inflammatory treatment, and cancer [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , …”

“…The predisposing factors of candidiasis were multiple, including mechanical ventilation, placement of a central venous catheter, diabetes mellitus, antibiotics treatment, hospitalization time, anti-inflammatory treatment, and cancer [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. Other less common risk factors were asthma, HIV, and surgery, among others [ 34 , 35 , 36 , 38 , 41 , 45 , 47 , 48 , 49 , 50 , 52 , 56 , 60 ]. The diagnosis was performed through culture, PCR, sequencing, and MALDI-TOF [ 33 , 34 , 35 , 36 , 37 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , …”

“…Other less common risk factors were asthma, HIV, and surgery, among others [ 34 , 35 , 36 , 38 , 41 , 45 , 47 , 48 , 49 , 50 , 52 , 56 , 60 ]. The diagnosis was performed through culture, PCR, sequencing, and MALDI-TOF [ 33 , 34 , 35 , 36 , 37 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. The most identified pathogen was C. albicans , followed by C. glabrata , C. parapsilosis , C. tropicalis , C. auris , C. krusei , C. lusitaniae , C. inconspicua , C. dubliniensis , C. orthopsilosis , Candida spp.…”

“…The most identified pathogen was C. albicans , followed by C. glabrata , C. parapsilosis , C. tropicalis , C. auris , C. krusei , C. lusitaniae , C. inconspicua , C. dubliniensis , C. orthopsilosis , Candida spp. and non- albicans Candida [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. Patient treatment included azole antifungal agents (fluconazole, voriconazole, isavuconazole), echinocandins (caspofungin, anidulafungin, micafungin), and polyenes (amphotericin B, nystatin) [ 33 , 34 , 35 , 40 , 42 , 43 , 44 , 46 , 47 , 48 , 51 , 52 , 53 , 54 , 56 , 59 ].…”

“…It should be noted that nystatin was used for the treatment of a patient with oropharyngeal candidiasis [ 43 ]. Despite antifungal treatment, the fatality rate among patients with COVID-19 and candidiasis oscillated between 11 and 100% [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ].…”