Microbiological Evaluation of Patients Admitted with Acute Respiratory Illness during First Wave of COVID-19 Pandemic in New Delhi, India

Abstract

Introduction: The Coronavirus Disease-2019 (COVID-19) is associated with damage of cells of both innate and adaptive immunity, which results in immune system’s impairment leading to secondary infections. Microbiological evaluation helps in diagnostic as well as antimicrobial stewardship leading to accurate treatment of COVID-19 infected patients. Aim: To evaluate superadded bacterial and fungal infections in COVID-19 infected patients and to evaluate bacterial and fungal infections in COVID-19 non infected patients admitted with Acute Respiratory Illness (ARI). Materials and Methods: This retrospective study was carried out in a tertiary care hospital in Delhi, India, over a period of eight months (May to December 2020). Respiratory samples, received from indoor patients with history of ARI, were processed for COVID-19 (TrueNat based real time polymerase chain reaction) as well as for bacterial and fungal cultures following Standard Operating Procedures (SOP). Identification and susceptibility pattern was evaluated by Vitek2 compact system (bioMérieux, Inc. Durham, North Carolina/USA). Quality control strains used were American Type Culture Collection (ATCC) Staphylococcus aureus 29213, Escherichia coli 25922 and Candida parapsilosis ATCC 22019. Minimum Inhibitory Concentration (MIC) levels were standardised as per Clinical and Laboratory Standards Institute (CLSI) guideline 2020. All statistical analysis was done by Chi-square test using Software Statistical Package for the Social Sciences (SPSS) version 22.0. Results: Total patients admitted with the history of ARI were 542; COVID-19 Positive Group (CPG) included 115 (21.22%) while COVID-19 Negative Group (CNG) included 427 (78.78%). Growth in bacterial and fungal cultures in CPG was 59.13% (68/115) while in CNG; it was 47.78% (204/427). Among the bacterial isolates, most common isolate was Klebsiella pneumoniae {CPG: 41.93% (26/62); CNG: 36.72% (76/207)}, followed by Pseudomonas aeruginosa {CPG: 33.87% (21/62); CNG: 31.88% (66/207)}. Fungal isolates in CPG was 19.48% (15/77) (p-value 0.0445). On comparing Antimicrobial Susceptibility (AST) pattern of Enterobacterales in both CPG (n=36) and CNG (n=102), no statistically significant difference was observed. Co-morbid conditions were found mostly in CNG 89% (140/158) with ARI while only 11% (18/158) was found in CPG. Conclusion: Secondary respiratory infections are quite common amongst COVID-19 positive patients. However, growth in culture, type of isolates, Antimicrobial Resistance (AMR) was almost similar with COVID-19 non infected patients admitted with ARI. Co-morbidity had the similar impact as COVID-19 infection with respect to co-infections.

Keywords

• co-infection
• coronavirus disease-2019 infection
• respiratory tract infection
• superinfection
• truenat real time polymerase chain reaction