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ORIGINAL ARTICLE Table of Contents  
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Secondary infections in COVID-19: Antemortem and Postmortem culture study

1 Department of Microbiology, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi, India
2 PhD Scholar, Division of Forensic Pathology and Molecular DNA, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi, India
3 Division of Clinical Microbiology, Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi, India
4 Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences, New Delhi, India
5 Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India
6 Division of Forensic Pathology and Molecular DNA, JPNATC, AIIMS, New Delhi, India

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Date of Submission06-Feb-2022
Date of Decision19-Mar-2022
Date of Acceptance20-Mar-2022
Date of Web Publication14-Apr-2023


Background: Secondary bacterial infections during COVID-19 hospitalization have been reported in about 6–15% of patients.
Aims: To study the secondary bacterial infections that affected the COVID-19 patients during their hospitalisation and to unearth the bacteriological profile of samples obtained after their demise.
Settings and Design: This prospective study was carried out at a COVID-19 dedicated, apex tertiary care centre in North India from July 2020 to April 2021.
Methods and Material: Samples of 268 patients were considered for the study. Nasopharyngeal swab specimen, blood, and tissue (lung) were collected from the deceased body as early as possible and processed.
Statistical Analysis: Statistical analyses were performed using STATA version 11.1 (Stata Corp., College Station, TX, USA).
Results: A total of 170 samples were received from patients before their death, which included blood, urine, respiratory samples, pus, and cerebrospinal fluid. Forty-four pathogens were isolated, which consisted of Acinetobacter baumannii (43.1%), Klebsiella pneumoniae (36.3%), Escherichia coli (11.3%), and Pseudomonas aeruginosa (4.5%), Enterococcus faecium (4.5%). Two hundred fifty-eight samples were collected from the deceased bodies wherein the nasopharyngeal sample was highest, followed by tissue and blood. A total of 43 pathogens were isolated among them which included A. baumannii (44.1%), followed by K. pneumoniae (25.5%), E. coli (20.9%), P. aeruginosa (6.97%) and Enterobacter cloacae (2.3%). All these isolates were highly resistant to antimicrobials.
Conclusions: In our study, bacterial profiles in antemortem and postmortem samples were found to be similar, suggesting that resistant pathogens may be the cause of mortality in COVID-19 infected hospitalised patients.

Keywords: Antemortem, COVID-19, multidrug-resistant, postmortem, secondary infections

How to cite this URL:
Kiro VV, Sharma M, Srivastava S, Lalwani P, Aggarwal R, Soni KD, Malhotra R, Lalwani S, Mathur P, Trikha A. Secondary infections in COVID-19: Antemortem and Postmortem culture study. Indian J Pathol Microbiol [Epub ahead of print] [cited 2023 Jun 1]. Available from:

   Introduction Top

SARS-CoV-2, the notorious cause of Coronavirus disease (COVID-19) has globally infected 38,65,48,962 and has led to 57,05,754 deaths, as of 5 February 2022.[1] The clinical syndrome of COVID-19 varies from mild upper respiratory symptoms to severe acute respiratory distress syndrome (ARDS) requiring prolonged support with mechanical ventilation. To date, many studies investigating secondary bacterial infections (SBIs) in COVID-19 patients have put their trust in cohorts that include these heterogeneous populations of patients.[2] However, of the available data, bacterial infection (prominently diagnosed as secondary pneumonia or bacteremia) at some point during COVID-19 hospitalization has been reported in about 6–15% of patients where the bacterial infection was assessed.[2] In a meta-analysis of bacterial infection in people hospitalized with COVID-19, it was found that an average of 8% of patients in all included studies were found to have co-infections or secondary bacterial infections.[3] Here, in this study, we present the profile of bacterial infections in COVID-19 patients diagnosed through postmortem and its correlation with antemortem microbiological diagnosis.

   Material and Methods Top

This prospective study was carried out at an apex tertiary care centre in North India, dedicated to COVID-19 care. From July 2020 to April 2021 (the first wave of COVID-19), a total of 1521 patients succumbed due to COVID-19 in our hospital. Among them, 268 deceased have been included in this study.

Their ante-mortem report for SARS-CoV-2 was tested positive on applying reverse transcription-polymerase chain reaction (RT-PCR), Cartridge Based Nucleic Acid Amplification Test, Rapid Antigen test, or a combination of these. All the documents available at the centre concerning the deaths were evaluated descriptively. The subjects were selected randomly and collection was done according to the availability of personnel under the challenging pandemic situation. All the deceased bodies were shifted from the ward to the mortuary and preserved at a standardized temperature of 4°C. Nasopharyngeal swab specimen, blood and tissue (lung) were collected using the recommended personal protective equipment. This was done only after taking informed consent from the legally authorized representative of the deceased, ensuring the protection of privacy and confidentiality, other cultural or religious sentiments.[4]

Thereafter the samples were cultured onto MacConkey and Blood agar plates. The organisms isolated from cultures were processed for identification and antibiotic susceptibility using Vitek 2 system (bioMérieux Inc., France). There was no delay in disposal or handover of the deceased body because of the study. Culture and sensitivity of the samples obtained from these subjects (if any) during their period of hospitalisation was also studied.

Isolates were considered to be causing distinct infections for each new body site from which they were isolated. In patients, from whom a given species was repeatedly isolated from one type of sample several times, were considered only once.

The Institution ethics committee approved the study (Ref. No.: RP-22/2020)

Statistical analysis

Descriptive statistics were calculated and interpreted as mean (standard deviation) or median (Interquartile range) with range for continuous variables and frequency with proportions for categorical variables. Statistical analyses were performed using STATA version 11.1 (Stata Corp., College Station, TX, USA).

   Results Top

A total of 268 deceased subjects were taken into consideration.

The mean age of the deceased was 51 years (± 18.4). The average length of stay (LOS) was 6 days ranging from 2 to 12 days, which is described in [Figure 1]. Among them, male were 185 (69%) and female were 83 (35%). 241 (90.3%) were Non Medico-legal cases (MLC) with proper history while 26 (9.7%) were MLC cases with no history. The most common symptom observed was dyspnoea (n = 145, 54.1%) followed by fever (n = 99, 36.9%), gastrointestinal symptoms (n = 64, 23.9%), cough (n = 63, 23.5%), neurological symptoms (n = 46, 17.2%) and anorexia (n = 7, 2.6%). The major comorbidities observed were hypertension and diabetes followed by cardiovascular complications, chronic kidney disease, chronic liver disease, and cancer. The cause of death was mainly attributable to septic shock, ARDS, pneumonia, acute kidney injury, cardiogenic shock, multiple organ dysfunction syndromes (MODS), and others as described in [Table 1].
Figure 1: Distribution of length of stay of hospitalisation

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Table 1: Demography and clinical details

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A total of 170 samples were received from the considered subjects before their death. These included blood (n = 90, 52.9%), urine (n = 36, 21.1%), respiratory samples (n = 25, 14.7%), pus (n = 6, 3.5%), and CSF (n = 5, 2.9%), miscellaneous samples like ascitic fluid, bile, and tips (n = 8, 4.7%). The pathogens isolated from these samples were Acinetobacter baumannii (n = 19, 43.1%), Klebsiella pneumoniae (n = 16, 36.3%), Escherichia coli (n = 5, 11.3%), Pseudomonas aeruginosa (n = 2, 4.5%), and Enterococcus faecium (n = 2, 4.5%). With regard to the antibiotic susceptibility, A. baumannii was sensitive to Amikacin (36%), Ceftazidime (14%), Tigecycline (59%), and Colistin (32%). K. pneumoniae was sensitive to Amikacin (10%), Ceftazidime (20%), Tigecycline (35%), and Colistin (5%). E. coli was sensitive to Amikacin (50%), Ceftazidime (25%), Tigecycline (75%), and Piperacillin-Tazobactam (25%). All isolates of P. aeruginosa were multi-drug resistant. E. faecium were sensitive to Vancomycin (100%), Teicoplanin (100%), and Linezolid (100%).

A total of 258 samples were collected from COVID-19 deceased bodies preserved at the mortuary. Among these, highest was nasopharyngeal swab (n = 236, 91.4%) followed by tissue sample (n = 13, 5.03%) and blood (n = 9, 3.48%). The number of pathogens detected were 43; of which maximum were A. baumannii (n = 19, 44.1%), followed by K. pneumoniae (n = 11, 25.5%), E. coli (n = 9, 20.9%), P. aeruginosa (n = 3, 6.97%), and Enterobacter cloacae (n = 1, 2.3%). Pure cultures of A. baumannii (n = 1), K. pneumoniae (n = 1), E. coli (n = 2), and Enterobacter cloacae (n = 1) were obtained from tissues. Pure isolates of Klebsiella pneumoniae (n = 1) and Escherichia coli (n = 2) were recovered in blood. In majority of the nasopharyngeal swabs, cultures grew greater than three organisms so only pure single growths were processed. Among them were A. baumannii (18), followed by K. pneumoniae (9), E. coli (5) and P. aeruginosa (3). All these isolates were highly drug resistant. A. baumannii was sensitive to Amikacin (15.7%), and Tigecycline (78.9%). K. pneumoniae was sensitive to Amikacin (11.1%), Imipenem (11.1%), and Tigecycline (27.2%). E. coli was sensitive to Amikacin (66.6%), Imipenem (22.2%), and Tigecycline (100%). P. aeruginosa was sensitive only to Amikacin (33.3%). They were all resistant to Piperacillin-Tazobactam, Ceftazidime, and Ciprofloxacin. Enterobacter cloacae was pan drug resistant. [Table 2] describes the above findings.
Table 2: Antibiotic susceptibility pattern of organisms isolated from the postmortem samples

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With regard to secondary bacterial infections (SBIs), 18.2% (n = 42) were observed in Non-MLC cases with proper history while in medico-legal cases it was 7.1% (n = 2). The rate of infection with respect to LOS of patients when calculated as greater and less than 2 days; it was observed that, out of 229 patients; 6.5% (n = 3) of SBIs developed before 2 days while 22.4% (n = 41) developed after 2 days with P value of 0.012. Thus, 22.4% (n = 41) of SBIs were hospital acquired. The graph depicting SBIs associated with samples along with LOS is depicted in [Figure 2].
Figure 2: Length of stay and associated secondary infectionsUTI- Urinary tract infections, RTI- Respiratory tract infections, BSI- Blood stream infections

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Another comparison was done on steroid administration and associated SBIs. Out of 233 patients, 31.7% (n = 74) received steroid treatment. Among them, 14.8% (n = 11) developed SBIs while 85.1% (n = 63) acquired none. Among the 159 patients who did not receive steroid treatment, 11.8% (n = 19) suffered from SBIs.

   Discussion Top

SBIs appear in individuals who already have a pre-existing infection. The presence of one infection often provides a favourable environment for other microbes to grow, which eventually leads to secondary infections.

Studies reveal that such SBIs have led to severe disease and worse health outcomes.[5] Another study, suggests that SBIs often occur in people with influenza and other viral respiratory illnesses. This happens most probably due to alteration in the epithelial surfaces of the lungs and respiratory tracts by these viral infections which result in modulation of the immune responses resulting in severe inflammation and the contracting of secondary infections.[6],[7]

In our study, we investigated the bacteriological profile of samples collected before the demise of the included subjects as well as samples collected after their death. One hundred seventy samples were received prior to the death of these patients, from which 44 pathogens were isolated and reported. All the isolates recovered were poorly sensitive to drugs.

Samples collected post death were 258, of which 43 pure isolates were processed. Again all isolates were highly resistant to drugs. This reiterates that multidrug-resistant (MDR) organisms frequently caused a fatal outcome in COVID-19 cases.

In a retrospective study of secondary infections in patients admitted in 10 hospitals under the Indian Council of Medical Research antimicrobial resistance surveillance network, out of 17,534 patients, 3.6% of patients developed secondary bacterial or fungal infections.[8] In their study, 10.6% mortality was observed in total admitted patients, while among those patients who developed secondary infections it was noted to be 56.7%.[8]

The observations in our study are consistent with the above study as our centre was also a part of it. In another multicentre retrospective cohort study,[9] out of 126 patients, 61% (n = 77) had positive bacterial cultures that met inclusion criteria, resulting in a total of 174 unique infections. Respiratory infections were the most common followed by bacteremia and urinary tract infection. Contrary to our study, Gram-positive were dominant organisms implicated in secondary infection in the above study.

In another study, a review was done on infections occurring in admitted patients and their frequency and risk factors for secondary bacterial infections were assessed. It included several studies and a minimum of 100 patients were evaluated in each.[10],[11],[12],[13],[14],[15],[16],[17] Secondary bacterial infections occurred in 3.7–21.9% of patients admitted with COVID-19.

Among the aforementioned studies, two of them had evaluated patients admitted at ICU only in which 38.6% and 47.5% of patients developed secondary bacterial infection, respectively.[13],[17] The median time from admission till the development of secondary bacterial infection was typically 1–2 weeks. Pneumonia and bloodstream infections (BSIs) were the most common sources of these bacterial infections.

Three of the four studies that compared outcomes of patients with and without secondary bacterial infections found an increased mortality rate in the former group.[10],[13],[15],[17] Contrary to the above finding, in our study, Gram negative were the dominant organisms and secondary bloodstream infection was the most common source of infection followed by respiratory tract infections and others as described in [Figure 2]. Infections acquired after 2 days of hospitalization has been described as hospital acquired infections. In this study, all infections were associated with hospital acquired infections except three infections in the bloodstream.

Corticosteroids, as an anti-inflammatory and anti-fibrotic agent has been used in severe pneumonia and complicated cases of COVID-19. In a retrospective analysis done on 226 patients in order to investigate steroids and their effect, Obata et al.[18] found that the steroid group developed higher rates of SBIs (25%) than the non-steroid group (13.1%) with P value of 0.001. The now deceased in our study were also treated with steroids (methylprednisolone and dexamethasone) during their hospital stay before death. A total of 14.8% (n = 11) acquired SBIs in steroid group while 11.8% (n = 19) suffered in non-steroid group. Thus in this study also SBIs were more common in steroid group with P value of 0.020.

Our study is unique as we have studied the secondary infections on deceased and have also evaluated the bacterial profile of organisms isolated post-death from the subjects included. In our study, we have found almost the same bacterial profile in antemortem and postmortem samples.

   Conclusion Top

COVID -19 primarily affects the lungs, but in some patients, it also causes severe complications like hypoxia, ARDS, thromboembolic disease, cytokine storm, and multiorgan failure, which leads to the administration of several antibacterial therapies and prolonged hospitalisation, that often require mechanical ventilation exposing them to secondary infections. So it is not surprising if MDR organisms are reported. Therefore, infection control practices, strict adherence to antimicrobial stewardship, and diagnostic stewardship are the need of the hour.

   Declarations Top

Ethical statement

The local/institution ethics committee approved the study (Ref. No.: RP-22/2020).

Data availability statement

The datasets used and analysed during the current study are available from the corresponding author on reasonable request.


The authors would like to thank The All India Institute of Medical Sciences, India, for funding this study and all participating employees from the JPNATC, AIIMS, Delhi for their help.

Financial support and sponsorship

The All India Institute of Medical Sciences supported this work's intramural research grant theme: research on SARS-Cov-2 and COVID-19 (Code no. A-COVID-59).

Conflicts of interest

There are no conflicts of interest.

   References Top

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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;26:1622-9.  Back to cited text no. 3
Centres for Disease Control and prevention (CDC), Updated Interim guidelines for collecting, handling and testing clinical specimens from persons for coronavirus disease 2019 (COVID-19). Available from: [Last accessed on 2022 Jan 05].  Back to cited text no. 4
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Risa E, Roach D, Budak JZ, Hebert C, Chan JD, Mani NS, et al. Characterization of secondary bacterial infections and antibiotic use in mechanically ventilated patients with COVID-19 induced acute respiratory distress syndrome. J Intensive Care Med 2021;36:1167-75.  Back to cited text no. 9
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Cheng LS, Chau SK, Tso EY, Tsang SW, Li IY, Wong BK, et al. Bacterial co-infections and antibiotic prescribing practice in adults with COVID-19: Experience from a single hospital cluster. Ther Adv Infect Dis 2020;7:2049936120978095. doi: 10.1177/2049936120978095.  Back to cited text no. 11
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 2021;40:859-69.  Back to cited text no. 12
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Correspondence Address:
Purva Mathur,
Division of Clinical Microbiology, Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi- 110 029
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijpm.ijpm_141_22


  [Figure 1], [Figure 2]

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