Observational Study on Secondary Bacterial Infection and the Use of Antibiotics in COVID-19 Patients Treated in a Tertiary Referral Hospital

Khie Chen Lie, Sharifah Shakinah, Adeline Pasaribu, Robert Sinto, Leonard Nainggolan


Background: Data on secondary bacterial infection in patients with COVID-19 in Indonesia are still limited, while the use of empirical antibiotics continues to increase. This study aims to determine the secondary bacterial infection rate in hospitalized COVID-19 patients and factors related to secondary bacterial infection. Methods: This is a retrospective cohort study on hospitalized COVID-19 patients undergoing treatment at Cipto Mangunkusumo Hospital from March 2020 to September 2020. Secondary bacterial infection is defined as the identification of a bacterial pathogen from a microbiological examination. Results: From a total of 255 subjects, secondary infection was identified in 14.5%. Predictors of secondary infection were early symptoms of shortness of breath (OR 5.31, 95% CI 1.3 – 21.5), decreased consciousness (OR 4.81, 95% CI 1.77 – 13.0), length of stay > 12 days (OR 8.2, 95% CI 2.9 – 23.3), and central venous catheter placement (OR 3.0, 95% CI 1.1 – 8.0) The most common pathogen of secondary bacterial infection is Acinetobacter sp. (n=9; 28%). Empirical antibiotics were administered to 82.4% of subjects with predominant use of macrolides (n=141; 32.4%). Conclusion: The secondary bacterial infection rate in COVID-19 was 14.5% and is associated with dyspnea, decreased consciousness, length of stay >12 days, and central venous catheter placement. The use of antibiotics in COVID-19 reaches 82.4% and requires special attention to prevent the occurrence of antibiotic resistance.


COVID-19; secondary bacterial infection; antibiotics; antibiotic stewardship


Coronavirus disease (COVID-19) – World Health Organization [Internet]. [cited 2022 Feb 14]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019

Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–13.

WHO Coronavirus (COVID-19) Dashboard [Internet]. [cited 2022 Feb 3]. Available from: https://covid19.who.int/table

Langford BJ, So M, Raybardhan S, et al. Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis. Clin Microbiol Infect. 2020;26(12):1622–9.

Elabbadi A, Turpin M, Gerotziafas GT, et al. Bacterial coinfection in critically ill COVID-19 patients with severe pneumonia. Infection. 2021;49(3):559–62.

Rawson TM, Moore LSP, Zhu N, et al. Bacterial and fungal coinfection in individuals with Coronavirus: A rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis. 2020;71(9):2459–68.

Elemraid MA, Rushton SP, Thomas MF, et al. Utility of inflammatory markers in predicting the aetiology of pneumonia in children. Diag Microbiol Infect Dis. 2014;79(4):458–62.

Cleland DA, Eranki AP. Procalcitonin. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 [cited 2022 Feb 4]. Available from: http://www.ncbi.nlm.nih.gov/books/NBK539794/

Lambden S, Laterre PF, Levy MM, et al. The SOFA score—development, utility and challenges of accurate assessment in clinical trials. Critical Care. 2019;23(1):374.

Wolkewitz M, Schumacher M, Rücker G, et al. Estimands to quantify prolonged hospital stay associated with nosocomial infections. BMC Med Res Methodol. 2019;19(1):111.

Asmarawati TP, Rosyid AN, Suryantoro SD, et al. The clinical impact of bacterial co-infection among moderate, severe and critically ill COVID-19 patients in the second referral hospital in Surabaya. F1000Res. 2021;10:113.

Manna S, Baindara P, Mandal SM. Molecular pathogenesis of secondary bacterial infection associated to viral infections including SARS-CoV-2. J Infect Publ Health. 2020;13(10):1397–404.

Mirzaei R, Goodarzi P, Asadi M, et al. Bacterial co-infections with SARS-CoV-2. IUBMB Life. 2020;72(10):2097–111.

SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? EMBO Mol Med. 2020;12(7):e12560.

He S, Liu W, Jiang M, et al. Clinical characteristics of COVID-19 patients with clinically diagnosed bacterial co-infection: A multi-center study. PLOS ONE. 2021;16(4):e0249668.

Attia AS, Hussein M, Aboueisha MA, et al. Altered mental status is a predictor of poor outcomes in COVID-19 patients: A cohort study. PLOS ONE. 2021;16(10):e0258095.

Mao L, Jin H, Wang M, et al. Neurologic manifestations of hospitalized patients with Coronavirus disease 2019 in Wuhan, China. JAMA Neurology. 2020;77(6):683–90.

Rees EM, Nightingale ES, Jafari Y, et al. COVID-19 length of hospital stay: a systematic review and data synthesis. BMC Medicine. 2020;18(1):270.

Vekaria B, Overton C, Wiśniowski A, et al. Hospital length of stay for COVID-19 patients: Data-driven methods for forward planning. BMC Infect Dis. 2021;21(1):700.

Zhou Q, Fan L, Lai X, et al. Estimating extra length of stay and risk factors of mortality attributable to healthcare-associated infection at a Chinese university hospital: a multi-state model. BMC Infect Dis. 2019;19(1):975.

Peleg AY, Hooper DC. Hospital-acquired infections due to gram-negative bacteria. N Engl J Med. 2010;362(19):1804–13.

Sharifipour E, Shams S, Esmkhani M, et al. Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU. BMC Infect Dis. 2020;20(1):646.

Rothe K, Feihl S, Schneider J, et al. Rates of bacterial co-infections and antimicrobial use in COVID-19 patients: a retrospective cohort study in light of antibiotic stewardship. Eur J Clin Microbiol Infect Dis. 2021;40(4):859–69.

Fakih MG, Bufalino A, Sturm L, et al. Coronavirus disease 2019 (COVID-19) pandemic, central-line–associated bloodstream infection (CLABSI), and catheter-associated urinary tract infection (CAUTI): The urgent need to refocus on hardwiring prevention efforts. Infect Control Hosp Epidemiol;1–6.

Ong CCH, Farhanah S, Linn KZ, et al. Nosocomial infections among COVID-19 patients: an analysis of intensive care unit surveillance data. Antimicrobial Resistance & Infection Control. 2021;10(1):119.

Gaynes R, Edwards JR, National Nosocomial Infections Surveillance System. Overview of nosocomial infections caused by gram-negative bacilli. Clin Infect Dis. 2005;41(6):848–54.

Burhan E, Susanto AD, Isbaniah F, et al. Pedoman Tatalaksana COVID-19. 3rd ed. Jakarta: PDPI, PERKI, PAPDI, PERDATIN, IDAI; 2020.

Metlay JP, Waterer GW, Long AC, et al. Diagnosis and treatment of adults with community-acquired pneumonia. An official clinical practice guideline of the American Thoracic Society and Infectious Diseases Society of America. Am J Respir Crit Care Med. 2019;200(7):e45–67.

Kalil AC, Metersky ML, Klompas M, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clinical Infectious Diseases. 2016;63(5):e61–111.

Feldman C, Anderson R. The role of co-infections and secondary infections in patients with COVID-19. Pneumonia. 2021;13(1):5.

O’Toole RF. The interface between COVID-19 and bacterial healthcare-associated infections. Clin Microbiol Infect. 2021;27(12):1772–6.

Abdela SG, Liesenborghs L, Tadese F, et al. Antibiotic Overuse for COVID-19: Are we adding insult to injury? The American Journal of Tropical Medicine and Hygiene. 2021;105(6):1519–20.

Founou RC, Blocker AJ, Noubom M, et al. The COVID-19 pandemic: a threat to antimicrobial resistance containment. Future Sci OA. 7(8):FSO736.

Full Text: PDF


  • There are currently no refbacks.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.