Microbial Profile and Antimicrobial Susceptibility Pattern of Pathogens Isolated from Long COVID-19 Patients and Their Correlation to Clinical Outcome: A Case Study of the a Tertiary Medical Institution in Eastern India

Aim: The study aimed to discuss about Microbial profile and antimicrobial susceptibility pattern of pathogens isolated from long COVID-19 patients and their correlation to clinical outcome.

Background: Despite being reverse transcriptase-polymerase chain reaction (RTPCR) negative for COVID infection, patients with persistent symptoms for at least four weeks are classified as long-term COVID-19 patients (pulmonary involvement is noted in a substantial number of cases). Patients who have a history of long-term use of corticosteroids, broad-spectrum antibiotics, and co-occurring illnesses are at a higher risk of contracting multidrug-resistant microbial strains. A worse prognosis could result from it, thus prompt microbiological assessment and treatment can improve the situation.

Methods: A retrospective observational study was carried out among long COVID patients admitted to the Kalinga Institute of Medical Sciences, Bhubaneswar, Odisha, India, a tertiary care hospital. Eighty-four patients admitted to the ICU or non-ICU ward in the hospital from April to October 2021 were included in the study. Antibiotics, as prescribed by our hospital antibiotic policy, were administered wherever required and were subsequently changed according to culture and sensitivity reports of the samples (sputum, endotracheal aspirates, or blood). An analysis of the antibiotic sensitivity patterns of the pathogens isolated was performed. The outcome after optimum medical management was assessed for survivors, discharge, or death.

Results: Out of the total of 84 patients, 41 samples (sputum, endotracheal aspirates or blood) were collected and sent for culture, of which 32 (78.1%) were found to be culture positive for pathogens. Among the pathogens isolated, there were 22 (69%) drug-resistant and 10 (31%) sensitive organisms. Among the 22 resistant pathogen isolates, 18 were Gram-negative species, the most common species being Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumanii; two were Gram-positive species, one each from Staphylococcus aureus and Enterococcus faecalis, and three were Candida tropicalis. Of five deaths reported among 22 cases with resistant isolates, extensively drug-resistant (XDR), multi-drug resistance (MDR), and pan drug resistance (PDR) strains were detected in three, one, and one cases, respectively, and were harboured by K. pneumoniae, P. aeruginosa, and A. baumanii. Of the total eight deaths, there were two deaths among the 43 patients who received an empiric antibiotic in the wards, and six deaths were reported in the ICU. Despite raised biomarkers of inflammation, comorbid illnesses, renal impairment, and immunocompromised states, there was 91% survival and discharge, which was statistically significant (p- value = 0.00).

Conclusion: To conclude, K. pneumoniae, P. aeruginosa, A. baumanii, C. tropicalis, S. aureus, and E. faecalis were the most commonly isolated organisms among long COVID pneumonia cases, of which some were MDR, PDR and XDR strains. Early microbiological evaluation with targeted, proper antimicrobial usage along with optimized medical management and, wherever needed, critical care support in the ICU may lead to a better prognostic outcome in those groups of patients. The survival advantage could be due to the better threshold of ICU care, judicious antimicrobial administration, and keeping antimicrobial stewardship as a priority. Death was noticed among ICU patients, those suffering from pneumonia, and those harbouring multi-drug-resistant Gram-negative organisms.