EC Microbiology

Background: Bacterial co-infections are common complications of many viral respiratory tract diseases, such as influenza, and the same is presumed to be true in Corona Virus Disease-19 (COVID-19). Co-pathogens of other viral diseases are predominantly bacteria, followed by fungus. These co-infections play an important role in the progression of COVID-19 infections by escalating the severity and mortality rate. Antibiotics are therapeutic agents to combat these microbial infections. But their irrational use can promote antimicrobial resistance (AMR). During the COVID-19 pandemic, empiric antibiotic therapy was observed throughout the globe without any prior knowledge of bacterial co-infection patterns and their antimicrobial susceptibility.

Materials and Methods: This was a prospective study conducted in the microbiology diagnostic laboratory of Sylhet Women's Medical College and Hospital in collaboration with the COVID-19 isolation unit of this institute. The study period was from June 2021 to November 2021 (six months). A total of 535 RT-PCR-positive confirmed COVID-19 cases were enrolled in the study. Sputum samples were collected from them for microbiological analysis. The culture and sensitivity patterns of the isolated microbes from the samples were evaluated through standard microbiological procedures.

Results: Out of 535 samples, 150 samples were culture positive (28%). Male to female ratio among culture-positive patients was 1.3:1. Patients in the 60 to 69 years age group showed the highest culture-positivity rates (22.67%). About 24.5% of the isolates were pathogenic bacteria. Among them, Klebsiella pneumoniae had the highest positivity rates (38.7%) followed by Staphylococcus aureus (30.0%), Streptococcus species (11.3%), and Pseudomonas spp (7.3%). Growth of fungus and normal flora was found in 10.7% and 2% of the samples respectively. The top sensitive antimicrobials for Klebsiella pneumoniae were amikacin (89.7%), colistin (91.4%), amoxicillin and clavulanic acid (72.4%), meropenem (94.8%), imipenem (89.7%), piperacillin and tazobactam (91.4%) levofloxacin (79.3%) and ciprofloxacin (77.6%). Most of the organisms are resistant to azithromycin, cefixime, cefuroxime, ceftazidime, linezolid, ceftriaxone, vancomycin, and doxycycline.

Conclusion: Regular microbiological evaluation should be done for COVID-19 pneumonia infection in order to develop an effective therapeutic guideline.

Keywords: Sputum; Microbial Culture Growth; COVID-19; Antibiotic Sensitivity; Klebsiella pneumoniae

1. Ahmed N., et al. “Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients”. Antibiotics2 (2022): 276.
2. Kumar A., et al. SA-SS, 2020 undefined. Clinical features of COVID-19 and factors associated with the severe clinical course: a systematic review and meta-analysis (2022).
3. Liu HH., et al. “Bacterial and fungal growth in sputum cultures from 165 COVID-19 pneumonia patients requiring intubation: evidence for antimicrobial resistance development and analysis of risk factors”. Annals of Clinical Microbiology and Antimicrobials 1 (2021).
4. Zeshan B., et al. The usage of antibiotics by COVID-19 patients with comorbidities: the risk of increased antimicrobial resistance (2021).
5. Kariyawasam RM., et al. “Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta analysis”. Antimicrobial Resistance and Infection Control 1 (2021).
6. Rizvi A., et al. Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients in Lahore, Pakistan (2022).
7. Zhou F., et al. “Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study”. Lancet 10229 (2020): 1054.
8. Varga Z., et al. “Endothelial cell infection and endotheliitis in COVID-19”. Lancet10234 (2020): 1417.
9. Bradley BT., et al. “Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series”. Lancet10247 (2020): 320.
10. Dalton KR., et al. “One Health in hospitals: how understanding the dynamics of people, animals, and the hospital built-environment can be used to better inform interventions for antimicrobial-resistant gram-positive infections”. Antimicrobial Resistance and Infection Control 1 (2020): 1-17.
11. Bazaid AS., et al. Bacterial coinfection and antibiotic resistance profiles among hospitalized COVID-19 patients (2022).
12. Lucien MAB., et al. “Antibiotics and antimicrobial resistance in the COVID-19 era: Perspective from resource-limited settings”. The International Journal of Infectious Diseases 104 (2021): 250.
13. Haque M., et al. Potential ways to address antimicrobial resistance across India and wider exacerbated by COVID-19: AMR and COVID-19 11.10 (2021).
14. Organization WH. COVID-19 clinical management: living guidance (2021).
15. Karami Z., et al. Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands (2020).
16. Awad M., et al. Secondary bacterial infection in Adult Patients with COVID-19 in Iraq (2022): 349.
17. Shehabi A and Journal LB--EMH. Microbial infection and antibiotic resistance patterns among Jordanian intensive care patients 3.2 (1996).
18. Clancy C. PRO: The COVID-19 pandemic will result in increased antimicrobial resistance rates (2020).
19. Martín Llaca-Díaz J., et al. “One-year surveillance of ESKAPE pathogens in an intensive care unit of Monterrey”. Mexico 58 (2012): 475-481.
20. Hanson KE., et al. “Infectious Diseases Society of America Guidelines on the Diagnosis of Coronavirus Disease 2019”. Clinical Infectious Diseases (2020).
21. Talbot GH., et al. Bad bugs need drugs: an update on the development pipeline from the Antimicrobial Availability Task Force of the Infectious Diseases Society of America 42 (2006): 657-668.
22. Rawson TM., et al. “Bacterial and Fungal Coinfection in Individuals with Coronavirus: A Rapid Review To Support COVID-19 Antimicrobial Prescribing”. Clinical Infectious Diseases 9 (2020): 2459-2468.
23. Wang Z., et al. Clinical features of 69 cases of coronavirus disease 2019 in Wuhan, China (2020).
24. Zhou F., et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study (2022).
25. Zhu N., et al. “A Novel Coronavirus from Patients with Pneumonia in China, 2019”. The New England Journal of Medicine 8 (2020): 727-733.
26. Musuuza JS., et al. “Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis”. PLoS One 16 (2021).
27. Zhu X., et al. “Co-infection with respiratory pathogens among COVID-2019 cases”. Elsevier (2022).
28. Verroken A., et al. “Co-infections in COVID-19 critically ill and antibiotic management: A prospective cohort analysis”. Critical Care 1 (2020).
29. Huttner B “COVID-19: don’t neglect antimicrobial stewardship principles!” Clinical Microbiology and infection ... (2020).
30. Vincent J., et al. The prevalence of nosocomial infection in intensive care units in Europe: results of the European Prevalence of Infection in Intensive Care (EPIC) Study (2022).
31. Chastre J and Fagon JY. “Ventilator-associated pneumonia”. American Journal of Respiratory and Critical Care Medicine 7 (2002): 867-903.
32. Radji M., et al. Antibiotic sensitivity pattern of bacterial pathogens in the intensive care unit of Fatmawati Hospital, Indonesia (2011).
33. Bhaumik P V., et al. “Bacteriological profile and antibiogram of gram-negative organisms isolated from medical and neurology intensive care unit with special reference to multi-drug”. National Journal of Medical Research 2 (2012): 3.
34. Vincent J., et al. The international study of the prevalence and outcomes of infection in intensive care units (2009).
35. Zahra N., et al. Phenotypic and genotypic evaluation of antibiotic resistance of Acinetobacter baumannii bacteria isolated from surgical intensive care unit patients in Pakistan (2021).
36. A BH. Resistant gram-negative bacilli and antibiotic consumption in Zarqa, Jordan (2007).
37. Ahmed N., et al. “COVID-19 and public awareness”. The Professional Courier 8 (2020): 1710-1716.
38. Dalton KR., et al. “One Health in hospitals: How understanding the dynamics of people, animals, and the hospital built-environment can be used to better inform interventions for antimicrobial-resistant gram-positive infections”. Antimicrobial Resistance and Infection Control 1 (2020).
39. De With K., et al. “Strategies to enhance rational use of antibiotics in hospital: a guideline by the German Society for Infectious Diseases”. Infection3 (2016): 395.
40. Vagdalkar D., et al. “Bacteriological profile and the sensitivity patterns of culture positive organisms in COVID-19 positive patients”. Indian Journal of Microbiology Research 4 (2021): 285-290.
41. Ramadan HKA., et al. “Predictors of Severity and Co-Infection Resistance Profile in COVID-19 Patients: First Report from Upper Egypt”. Infection and Drug Resistance 13 (2020): 3409.
42. Gurung K., et al. Evaluation of Bacterial Co-infections of the Respiratory Tract in COVID-19 Patients 19.2 (2021).
43. Liu HH., et al. “Bacterial and fungal growth in sputum cultures from 165 COVID-19 pneumonia patients requiring intubation: evidence for antimicrobial resistance development and analysis of risk factors”. Annals of Clinical Microbiology and Antimicrobials 1 (2021): 1-13.
44. Soto A., et al. “Detection of Viral and Bacterial Respiratory Pathogens Identified by Molecular Methods in COVID-19 Hospitalized Patients and Its Impact on Mortality and Unfavorable Outcomes”. Infection and Drug Resistance 14 (2021): 2795.
45. Cheng LS kuen., et al. Bacterial co-infections and antibiotic prescribing practice in adults with COVID-19: experience from a single hospital cluster (2020): 7.
46. Fattorini L., et al. Bacterial coinfections in COVID-19: an underestimated adversary 56.3 (2022): 359-364.