Identification and Speciation of Various Fungal Co-infections in COVID-19 Patients by Different Laboratory Diagnostic Methods: A Retrospective Observational Study

Abstract

Introduction: Respiratory illness caused by a novel coronavirus was first noted in December 2019 in Wuhan, Hubei Province, China. Later, the novel coronavirus was referred to as Severe and critical Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) by the International Committee on Taxonomy of Viruses (ICTV). However, the types of co-infected pathogens and the proportion of co-infection in SARS-CoV-2-positive patients were unclear. Co-infection with certain pathogens may also hinder accurate disease diagnosis. Aim: To determine the most suitable sample type for a better culture outcome and to identify the various opportunistic fungal infections related to Coronavirus Disease 2019 (COVID-19) patients. Materials and Methods: This retrospective observational study was conducted between November 2021 to January 2022 at Department of Microbiology, Government Medical College, Surat, Gujarat, India. The data collection was done in the month of November 2021 followed by data analysis in December 2021 to January 2022. A total of 252 suspected cases of fungal co-infection were sampled (including swabs, tissues, skin scrapings, Cerebrospinal fluid (CSF), sputum, pus, and drain) from different wards for fungal wet mount Potassium Hydroxide (KOH) and culture. The data was entered into Microsoft Excel (Windows 10), and analysis was performed using Microsoft Excel, including frequency distribution and percentage. Results: A total of 252 samples were received. Demographic details showed that individuals aged 41-50 years were more commonly affected, and males were affected more than females. Among the sample types, tissue samples showed the highest positivity 43 (17%), followed by scraping materials 14 (6%). Out of the total 252 cultures performed, 70 were positive. In terms of fungal speciation, Mucor species accounted for 24 (34.28%) isolates, while Aspergillus flavus accounted for 26 (37.14%), followed by other isolated fungal species. Conclusion: Fungal co-infection is observed in COVID-19 positive patients, which not only contributes to morbidity but also increases mortality. Tissue samples demonstrated the highest culture positivity. The culture results showed a higher frequency of Mucor species isolates and Aspergillus flavus compared to other isolates.