Microbiological profile of COVID-19 patients admitted in a tertiary care hospital Mathura, Uttar Pradesh, India

Anju Rani, Varuna Gupta, Kandhakumari Gandhi, Ashok Kumar Dhanvijay


Background: The pandemic due to severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) has drawn worldwide worst effect with diagnostic challenge. Every investigation has its own importance for diagnosis, care, treatment and for management of corona virus disease-2019 (COVID-19) patients. Here this prospective study aimed to investigate the microbiological profile, prevalence of co-infection, and antibiotic susceptibility pattern of patients with confirmed SARS-CoV-2.

Methods: A total of 336 samples were processed in COVID laboratory, Department of Microbiology. An array of serological investigations was done by rapid card screening test. C-Reactive protein (CRP) was analyzed by nephelometer. Blood culture was done by automated system and urine culture on Cystine-Lactose-Electrolyte-Deficient (CLED) Agar. Antibiotic susceptibility tests were done by Kirby Bauer disc diffusion method.

Results: Out of 336 samples tested 76%were male and 24%were female. All samples tested were negative for HIV, HBsAg, HCV, syphilis, malarial parasite. CRP and Typhi -dot with IgM and IgG antibody were positive in 89.28% and 11.42% respectively. About 27% of COVID-19 patients showed bacterial and fungal co-infections. The most prevalent organisms were MR-CoNS (26%), K. pneumoniae (19%) and less prevalent were P. aeruginosa (6%) and A. baumannii (4%).  C. albicans (11%) was the only isolated fungi. All gram positive isolates were 100% sensitive to Linezolid and vancomycin, among gram negative isolates, 100% were sensitive to colistin and polymyxin B.

Conclusions: Microbiological investigation for presence of other co-infecting agents among patients with COVID-19 infection should be considered, and prompt treatment should be carried out accordingly.


COVID-19, Co-infection, SARS-CoV-2, CRP

Full Text:



World Health Organization.2020. Available at Accessed on 7 May 2020.

Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents. 2020;55(3):105924.

Andrews MA, Areekal B, Rajesh KR, Krishnan J, Suryakala R, Krishnan B, First confirmed case of COVID-19 infection in India: a case report. Indian J Med Res. 2020;151(5):490-2.

Ko WC, Rolain JM, Lee NY, Chen PL, Huang CT, Lee PI, Arguments in favour of remdesivir for treating SARS-CoV-2 infections. Int J Antimicrob Agents. 2020;55(4):105933.

Beadling C, Slifka MK. How do viral infections predispose patients to bacterial infections? Curr Opin Infect Dis. 2004;17(3):185-91.

Cucchiari D, Pericàs JM, Riera J, Gumucio R, Md EC, Nicolás D, Pneumococcal super infection in COVID-19 patients: a series of 5 cases. Med Clin. 2020;155(11):502-5.

Adler H, Ball R, Fisher M, Mortimer K, Vardhan MS. Low rate of bacterial co-infection in patients with COVID-19. Lancet Microbe. 2020;1(2):e62.

Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, et al. Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet. 2020;395(10229):1054-62.

Zhu X, Ge Y, Wu T, Zhao K, Chen Y, Wu B, et al. Co-infection with respiratory pathogens among COVID-2019 cases. Virus Res. 2020;285:198005.

CLSI Performance standards for Antimicrobial Susceptibility Testing. 30th edition. CLSI Supplement M100. wayne, PA. Clinical and Laboratory Standards Institute. 2020.

Guan WJ, Ni ZY, Hu Y, Liang WH, Ou CQ, He JX, et al. China medical treatment expert group for Covid-19. Clinical characteristics of corona virus disease 2019 in China. N Engl J Med. 2020;382(18):1708-20.

Li LQ, Huang T, Wang YQ, Wang ZP, Liang Y, Huang TB, et al. COVID-19 patients' clinical characteristics, discharge rate, and fatality rate of meta-analysis. J Med Virol. 2020;92(6):577-83.

Kai Q, Yi D, Yong HT, Jun P, Hao P, Hong J, et al. Clinical characteristics of 2019 novel infected coronavirus pneumonia: a systemic review and meta- analysis. Virus Res.2020;8:96-8.

Klein SL, Huber S. Sex differences in susceptibility to viral infection. In: Klein S, Roberts C, eds. Sex hormones and immunity to infection.1st edition. Berlin, Springer-Verlag Berlin Heidelberg. 2010;93-122.

Baluku JB, Mwebaza S, Ingabire G, Nsereko C, Muwanga M. HIV and SARS-CoV-2 coinfection: A case report from Uganda. J Med Virol. 2020;92:2351-3.

Miah MA, Husna A. Co-infection, co-epidemics of COVID-19, and dengue in dengue-endemic countries: a serious health concern. J Med Virol. 2020;10:1002-9.

Haqqi A, Awan UA, Ali M, Saqib M, Ahmed H, Afzal MS. COVID-19 and dengue virus co-epidemics in Pakistan: a dangerous combination for an overburdened healthcare system. J Med Virol. 2020;10:1002-4.

Verduyn M, Allou N, Gazaille V, Andre M, Desroche T, Jaffar MC, et al. Co-infection of dengue and COVID-19: a case report. PLoS Negl Trop Dis. 2020;14(8):e0008476.

Lacour AG, Gervaix A, Zamora SA, Vadas L, Lombard PR, Dayer JM, et al. Procalcitonin, IL-6, IL-8, IL-1 receptor antagonist and C-reactive protein as identificators of serious bacterial infections in children with fever without localising signs. Eur J Pediatr. 2001;160(2):95-100.

Langford BJ, So M, Raybardhan S, Leung V, Westwood D, MacFadden DR, 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.

Chen X, Liao B, Cheng L, Peng X, Xu X, Li Y, et al. The microbial coinfection in COVID-19. Appl Microbiol Biotechnol. 2020;104(18):7777-85.

Rothe K, Feihl S, Schneider J, Wallnöfer F, Wurst M, Lukas M, 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. 2020;2:1-11.

Lansbury L, Lim B, Baskaran V, Lim WS. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect. 2020;81(2):266-75.

Rawson TM, Moore LSP, Zhu N, Ranganathan N, Skolimowska K, Gilchrist M, et al. Bacterial and fungal co- infection in individuals with corona virus: a rapid review to support covid-19 antimicrobial prescribing. Clin Infect Dis. 2020;71(9):2459-68.

Mahmoudi H. Bacterial co-infections and antibiotic resistance in patients with COVID-19. GMS Hyg Infect Control. 2020;15:35.