Bacterial co-infections and secondary bacterial infection in COVID-19 hospitalized patients with evaluation antimicrobial resistance patterns in the clinical isolates
Authors: Kumari Manisha , Bastola Anup , Poudel Ajit , Neupane Jenish , Maharjan Sushila , Rajbhandar Sagar Kumar , Chalise Bimal Sharma , Shrestha Anjana , Rijal Nisha , Acharya Jyoti , Jha Runa 
Published: August 2022

Abstract
Background:The current COVID-19 pandemic, previous several viral pandemics and seasonal influenza raise important questions about synergic interactions between the SARS-CoV-2 virus and bacterial co-infection. It is a needs time to determine if co-infection with antibiotic-resistant bacteria affects disease severity. Indeed, some of the pathogens detected in COVID-19 patients could be antibiotic-resistant, which could reduce the efficacy of treatments administered to patients. Unfortunately, there is no such study from Nepal which describes the specific co-infecting pathogens and no studies thus far have analyzed rates of co-infection by antibiotic-resistant bacteria. Thus, it is impossible to determine from the available data whether certain bacterial species or antibiotic-resistant strains correlate with outcome severity or mortality. However, the presence of antibiotic-resistant bacteria could potentially explain the high rates of bacterial co-infections in critically ill patients despite extensive antibiotic treatments in this study.Therefore, in the present study, we collected respiratory, blood, and urine samples from lab-confirmed cases of COVID-19 hospitalized patients. The study aims to identify co-infection and secondary bacterial infection to obtain the etiology and antimicrobial resistance for more accurate antimicrobial use.Objective:General Objectives:To detect the presence of co-infection and secondary bacterial infection in covid-19 hospitalized patients.Specific Objectives:1. To determine the antibiotic susceptibility pattern of clinical isolates from the covid-19 positive hospitalized patients.2. To determine the type of antimicrobial resistance in the clinical isolates from the covid-19 positive hospitalized patients.Materials and Methods:We performed a prospective descriptive study, in which we had received three different clinical specimens such as blood, urine, and respiratory samples (sputum, ETT aspirate, BAL, etc…) submitted for bacterial culture and sensitivity tests to the department of microbiology at the National Public Health Laboratory (NPHL) during the study period from January to July 2021. The clinical samples were received from 200 symptomatic, lab-confirmed COVID-19 hospitalized patients admitted at Sukraja Tropical and Infectious Diseases Hospital, Teku; Kathmandu, Nepal. The specimens were processed in two different phases. The first samples were collected within 48 hours of hospital admission which propose the bacterial co-infection. The second samples were taken after 48 hours of admission.Results:The findings were consistent with the national data as the majority of the infected patients were male (n=123) and most of the infected (n=145) belonged to the working-age group (21 to 70 years) (5). The mean age of infected patients was 53.24 years. 177 of the total patients in this study (88.5%) were admitted with either severe or moderate Covid symptoms. Additionally, this translated into 173 of 200 patients (86.5%) spending a week or more at the hospital with 18.5% being admitted for more than a month. The highlights the resistance to various antibiotics detected from either sputum, blood, or urine samples from patients with different co-morbidities. The ten most AMR-resistant antibiotics cultured from sputum were as follows - 328 were resistant to Ciprofloxacin, 304 each for Gentamycin, Levofloxacin, and Amikacin, 288 for Cotrimoxazole, 280 each for Cefotaxime and Piperacillin Tazobactum, 264 for Azithromycin, 256 for Ceftazidime, and 248 for Ampicillin.Conclusion:Covid-19 has had a devastating impact on population throughout the world and in a third world country like Nepal, this study provides a unique insight into multiple factors that exacerbate health conditions. Despite having limited data from one hospital, the findings of the study mimicked national data patterns regarding the demographics most affected (working population). It also highlighted the statistical significance among the impact of age and other respiratory co-illnesses have on further aggravating issues with Covid-19 infections. More importantly, the study also discovered the presence of MDR or even extremely drug-resistant (XDR) bacteria among patients admitted with a bacterial co-infection and secondary bacterial infection. It recommends Antimicrobial stewardship, strict infection control and prevention should be implicated in all health sections.