Detecting Pathogenic Agents in Mechanically-Ventilated, Critically-Ill COVID-19 Patients with Ventilator-Associated Pneumonia


avatar Alireza Abdollahi ORCID 1 , avatar Mohammadreza Salehi ORCID 2 , avatar Ali Ahmadi 3 , avatar Sadegh Khodavaisy ORCID 3 , avatar Seyed Ali Dehghan Manshadi ORCID 2 , avatar Mehdi Norouzi 4 , 5 , avatar Pegah Afarinesh Khaki 6 , avatar Mahsa Norouzi Shadehi 2 , avatar Maryam Shadkam 6 , avatar Mahsa Abdorahimi 7 , avatar Reza Keikhaei 8 , avatar Ehsan Shiralipour 3 , avatar Ronak Bakhtiari 5 , 9 , *

Department of Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
Department of Virology, School Public Health, Tehran University of Medical Sciences, Tehran, Iran
Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
Central Laboratory, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

how to cite: Abdollahi A, Salehi M, Ahmadi A, Khodavaisy S, Dehghan Manshadi S A, et al. Detecting Pathogenic Agents in Mechanically-Ventilated, Critically-Ill COVID-19 Patients with Ventilator-Associated Pneumonia. Arch Clin Infect Dis. 2023;18(6):e134208.



The coronavirus disease 2019 (COVID-19) pandemic has been a global shock since its initial spread in 2019. Medically, patients with coronavirus disease, especially those with pneumonitis, face serious life-threatening risks and often require mechanical ventilation and intensive care. Ventilator-associated pneumonia (VAP) remains a significant concern for critical care providers. Recent reports have highlighted the susceptibility of patients with confirmed COVID-19 receiving mechanical ventilation to nosocomial pneumonia (NP).


This study was a cross-sectional study conducted in the intensive care unit (ICU) at Imam Khomeini Hospital Complex (IKHC) in Tehran, Iran, within April 2020 to April 2021. The study focused on critically ill COVID-19 patients who required mechanical ventilation and met the criteria for VAP. Standard biochemical assays were used to identify pure colonies in patients’ sample cultures, and antimicrobial susceptibility tests were conducted to assess antimicrobial resistance profiles. The findings were analyzed statistically using SPSS software (version 23.0).


Out of 93 endotracheal aspirate samples, 64 samples tested positive for bacteria. Among the 64 eligible patients with positive cultures, 42 (65.6%) and 22 (34.4%) patients were male and female, respectively, with a mean age of 60.56 ± 13.58 years. A total of 52 patients (81.25%) had underlying conditions, such as hypertension, diabetes, and kidney or heart diseases. According to the study results, the most common pathogens were extensively drug-resistant (XDR) Klebsiella pneumoniae (7%) and Acinetobacter baumannii (23%). Additionally, 80% of Klebsiella pneumoniae and 90% of Acinetobacter baumannii were observed to be multi-drug resistant (P < 0.05).


The COVID-19 pandemic has posed significant risks to critically ill patients, often necessitating mechanical ventilation and intensive care. Furthermore, VAP remains a serious challenge in this context, with high rates of XDR K. pneumoniae and A. baumannii. Effective infection control measures and surveillance are critical to mitigating the risk of NP in these vulnerable patients.

1. Background

The recent coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a global challenge since December 2019. Typically, 5 - 15% of patients require hospitalization, and in severe cases, intensive care with mechanical ventilation support becomes necessary due to the development of severe respiratory disease (1, 2). Consequently, intensive care units (ICUs) worldwide have been under significant strain.

Despite three years of dealing with the pandemic, ventilator-associated pneumonia (VAP), which occurs after 48 hours or longer of intubation (3), remains a critical technical issue for healthcare providers. Nearly 42.7% of VAP-related deaths are projected to occur in COVID-19 patients (4). Although COVID-19-related fatalities have predominantly affected the elderly with underlying health conditions, nosocomial pneumonia (NP) in ICUs, especially when patients are intubated, remains a significant risk factor. Furthermore, elderly individuals with underlying conditions, such as hypertension, diabetes, dyslipidemia, and cardiovascular disease (CVD), face a higher risk of mortality from COVID-19 (5). The situation can worsen in cases of lower respiratory tract infections (RTIs) (6, 7).

Studies have also indicated that patients with COVID-19 are more likely to develop community-acquired pneumonia (CAP); however, VAP-related mortality rates are nearly three times higher than those linked to CAP (8-10). Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, and Klebsiella pneumoniae are among the most significant microbial agents responsible for VAP, leading to high mortality rates worldwide (11-16). Numerous COVID-19 patients develop secondary bacterial infections (SBIs), which exacerbate disease severity and can result in death, particularly among those requiring invasive mechanical ventilation. In general, COVID-19 patients have low rates of bacterial coinfections and secondary infections; nevertheless, critically ill ICU patients exhibit higher rates (17).

Secondary bacterial infections are most common among critically ill patients (34.5%), followed by moderate and mild cases (3.9% and 8.3%, respectively) (18). Fast and accurate identification of bacteria as either resident or pathogenic microorganisms in COVID-19 patients should be a crucial step in managing these cases (19-21). However, the data on the rate of SBIs in hospitalized COVID-19 patients, especially those in critical condition, are limited (22).

2. Objectives

This study aimed to assess the frequencies and characteristics of SBIs and antimicrobial resistance (AMR) profiles in critically ill COVID-19 patients with VAP in ICUs.

3. Methods

This cross-sectional study aimed to identify microbial pathogens causing VAP in critically ill COVID-19 patients. The study included patients with confirmed COVID-19 who were admitted to the ICUs at Imam Khomeini Hospital Complex (IKHC) in Tehran, Iran, within April 2020 to April 2021.

3.1. Patients

The inclusion criteria consisted of patients with confirmed COVID-19, verified through SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) testing on respiratory secretions, who required mechanical ventilation (for more than 48 hours) and exhibited VAP criteria, which included new or persistent infiltrations in chest radiographs, fever exceeding 38°C or hypothermia below 36°C, a white blood cell count exceeding 10 000 or dropping below 5000 cells/mL, and a decrease in the ratio of arterial oxygen partial pressure/fractional inspired oxygen (PaO2/FiO2) or the presence of purulent tracheal secretions (23).

3.2. Sample Collection

Endotracheal aspirate (ETA) samples were collected using sterile tubes following standard clinical protocols (24). These samples were promptly transported to a microbiology laboratory and processed using conventional methods. Initially, the samples were cultured on blood, eosin methylene blue (EMB), and chocolate agars (Merck, Germany) and then incubated at 37°C for 24 - 72 hours in an environment with 5% CO2 under standard conditions. Plates with colony counts ≥ 104 colony-forming units (CFU/mL) were selected for further analysis. Pure colonies were identified through conventional biochemical assays.

3.3. Antimicrobial Susceptibility Testing

Antimicrobial susceptibility testing (AST) was conducted for various antibiotics, including cefoxitin (FOX, 30 μg), imipenem (IMP, 10 μg), ceftazidime (CAZ, 30 μg), amikacin (AK, 30 μg), azithromycin (AZM, 15 μg), gentamicin (GM, 10 μg), ceftriaxone (CRO, 30 μg), ciprofloxacin (CP, 5 μg), trimethoprim-sulfamethoxazole (SXT, 1.25/23.75 μg), levofloxacin (LEV, 5 μg), erythromycin (E, 15 μg), piperacillin-tazobactam (PIT, 100/10 μg), rifampicin (RIF, 5 μg), and ampicillin-sulbactam (AMS, 10/10 μg) (Rosco, Taastrup, Denmark). The testing was performed on Muller-Hinton media (Merck, Germany) using the Kirby-Bauer disk diffusion method, following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Additionally, E-tests (Liofilchem, Italy) were employed to determine bacterial susceptibilities to vancomycin and colistin, adhering to the manufacturer’s instructions. The plates were then incubated at 37°C for 18 hours. The interpretation of AST results was based on established protocols to identify multidrug-resistant (MDR) (25) and extensively drug-resistant (XDR) (26) bacteria. According to the criteria provided by the Centers for Disease Control and Prevention (CDC), bacterial isolates that exhibited resistance to three or more antimicrobials were classified as MDR isolates; nevertheless, XDR isolates were those susceptible to just one or a maximum of two categories of antimicrobials. Control strains of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923 were used for quality control purposes.

3.4. Statistical Analysis

For the statistical analysis, the data were imported into Microsoft Excel Plus 2019 Software and subsequently analyzed using SPSS software (version 23.0; IBM, USA). Continuous variables were presented as means ± standard deviation (SD), and comparisons between two groups were performed using Student’s t-test. Categorical variables were reported as counts (frequencies) and proportions (percentages), with multiple comparisons conducted using the chi-square test. Statistical significance was indicated when P < 0.05.

4. Results

Out of 241 COVID-19-verified patients, 93 met the criteria for diagnosing VAP. Among the 64 patients with positive cultures of ETA, 42 (65.6%) and 22 (34.4%) subjects were male and female, respectively, with a mean age of 60.56 ± 13.58 years. Furthermore, 52 patients (81.25%) had underlying diseases, including hypertension, diabetes, kidney, and heart diseases. Eventually, 55 patients (86%) died, with an average age of 62 ± 2 years, among whom 78.2% (43 patients) had a history of underlying diseases. Moreover, the length of hospitalization in K. pneumoniae-positive patients was longer than that in A. baumannii-positive patients. Demographic data of the patients, including age, gender, underlying disease, and length of hospitalization in ICUs, are reported in Table 1. No significant associations were observed between patients’ demographic data and VAP (P > 0.05).

Table 1.

Demographic and Clinical Characteristics of the Patients a

Total number of patients64 (100)
Male patients42 (65.6)
Female patients22 (34.4)
Patients’ ICU length of stay (days)22 ± 12.2
ICU length of stay for Acinetobacter baumannii-positive patients (days)20 ± 13.7
ICU length of stay for Klebsiella pneumonia-positive patients (days)25.2 ± 11
Mortality rates for Acinetobacter baumannii-positive patients24 (92.3)
Mortality rates for Klebsiella pneumonia-positive patients21 (75)
Patients with underlying diseases52 (81.25)
Expired patients55 (85.9)
Survived patients9 (14.1)
Mean age of the expired patients (y)62 ± 2

The three most prevalent bacteria included K. pneumoniae, A. baumannii, and P. aeruginosa, isolated from 28 (43.8%), 26 (40.6%), and 3 (4.7%) samples, respectively. The most prevalent isolated pathogens are listed in Tables 2 and 3. Significant associations were reported between infections with K. pneumoniae and A. baumannii in male and female subjects over 50 years (P < 0.001 and P < 0.01, respectively). However, these associations were not significant in male and female patients under 50 years (P < 0.1).

Table 2.

Type and Frequency of the Isolated Pathogens from Critically Ill Coronavirus Disease 2019 (COVID-19) Male Patients

BacteriaNo. (%) of PatientsAge < 50Age > 50P-Value
Klebsiella pneumonia28 (43.8)316< 0.001
Acinetobacter baumannii26 (40.6)410
Pseudomonas aeruginosa3 (4.7)-2
Klebsiella oxytoca1 (1.6)-1
Enterococcus faecalis1 (1.6)1-
Achromobacterdenitrificans1 (1.6)-1
Coagulase-negative staphylococci1 (1.6)-1
Stenotrophomonas maltophilia1 (1.6)-1
Klebsiella spp.1 (1.6)--
Mixed growth1 (1.6)-1
Table 3.

Type and Frequency of the Isolated Pathogens from Critically Ill Coronavirus Disease 2019 (COVID-19) Female Patients

BacteriaNo. (%) of PatientsAge < 50Age > 50P-Value
Klebsiella pneumonia9 (39.2)27
Acinetobacter baumannii12 (52.1)39
Pseudomonas aeruginosa1 (4.35)-10.002
Klebsiella spp.1 (4.35)-1

In this study, 75.4% of K. pneumoniae isolates were resistant to colistin; however, 88.46% of A. baumannii isolates were resistant to this antimicrobial. This high-level resistance to a last-resort antimicrobial could lead to increases in mortality rates in patients with MDR pathogens. As seen in Table 1, 92.3% (n = 24) and 75% (n = 21) of the patients with A. baumannii and K. pneumoniae-positive cultures died. The highest carbapenem-resistant (100%) rate belonged to A. baumannii, as bacteria showed resistance to meropenem. All strains of A. baumannii were also resistant to amikacin (100%). Table 4 shows the frequency of drug-resistance patterns in commonly isolated bacterial species. In general, resistance patterns of K. pneumoniae and A. baumannii isolates were not different between the non-survived and survived patients. The assessments of AST revealed that 80% of K. pneumonia and 90% of A. baumannii were MDR; nevertheless, 7% of K. pneumonia and 23% of A. baumannii were XDR with resistance to almost all the antimicrobials (P = 0.0012).

Table 4.

Frequency of Drug Resistance Patterns in Commonly Isolated Bacterial Species

Bacteria and Pattern aNo. (%)P-Value
Klebsiella pneumonia0.0012
XDR2 (7)
MDR23 (80)
MBL8 (29)
Acinetobacter baumannii
XDR6 (23)
MDR23 (90)
MBL21 (81)

5. Discussion

Coronavirus disease 2019, a viral pneumonia with a rapidly unique outbreak, is considered a novel public health hazard, posing a global threat to nations. Recent studies suggest that SARS-CoV-2 originated in animals and evolved into different variations, crossing species barriers to infect humans (27, 28). In previous epidemics of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), patients receiving invasive mechanical ventilation were susceptible to SBIs, leading to higher mortality rates (29, 30).

Traditionally, P. aeruginosa, Acinetobacter spp., and MRSA were identified as the most common causes of CAP and VAP. However, recent reports have highlighted K. pneumoniae and Acinetobacter spp. as the predominant pathogens in these patients (13, 15, 16). These findings align with a prior study by the current authors, which also identified K. pneumoniae and A. baumannii as the most prevalent pathogens. This study primarily focused on SBIs of the lower respiratory tract (RT) in critically ill COVID-19 patients intubated in ICUs. Surprisingly, microbiological examinations revealed that all collected specimens were contaminated by bacteria (64/64, 100%). These data suggested an association between VAP and increased patient mortality rates (55/64, 86%).

Similarly, a study in Egypt showed that specimens from critically ill COVID-19 patients under mechanical ventilation were positive for bacteria (197/197, 100%). Furthermore, significant relationships were observed between VAP and mortality rates (31). Nevertheless, studies in China and the UK reported that only 13.9% and 6.1% of COVID-19 ICU patients developed SBIs, respectively (32, 33). Differences in the results of these studies might be attributed to various variables affecting the quality of care and the frequency of ICU-acquired infections, including the type of ICUs, equipment quantity, admission/discharge criteria, and patient-to-nurse ratios.

In recent years, researchers have documented the occurrence of hypervirulent strains of both bacteria with resistance to various antimicrobial categories (34, 35). In a 2021 study in Egypt, the most frequently isolated bacteria from critically ill COVID-19 patients intubated in ICUs included K. pneumoniae and A. baumannii (33). Statistically, K. pneumoniae and Acinetobacter spp. exhibited the highest incidence rates in ICUs, as indicated by a 2019 study in Tehran, Iran (36). In a study conducted in India in 2018 (37), A. baumannii and Klebsiella spp. were the most prevalent bacteria isolated in Mysuru, India.

All bacterial isolates in the present study displayed high resistance to the highlighted antimicrobials. This resistance could be attributed to the scheduled administration of antimicrobials for COVID-19, which might have controlled other more susceptible pathogens, allowing resistant bacterial survivors to evade management protocols. Metallo-β-lactamase (MBL)-producing K. pneumoniae and A. baumannii were also identified as causative microorganisms of VAP in participants. Clinically, VAP was suspected after prolonged mechanical ventilation, similar to the scenario in the current study. This extended duration allowed for bacterial superinfections. The fatality rate of VAP in ICU patients typically varies from 20% to 50%, and it might be much higher when caused by antimicrobial-resistant bacteria (38).

The current study unexpectedly reported high rates of SBI VAP and significant (P < 0.001) mortality rates of 87.5% in ICUs. In some cases, mortality rates of patients in other studies exhibited significant differences between the two groups of A. baumannii and K. pneumoniae-positive patients. Overall, mortality rates were significantly higher in patients with A. baumannii infections (84.8%) than in those with K. pneumoniae infections (44.5%) (P < 0.001) (39, 40). In contrast to the current results, differences in the mortality rates of patients with A. baumannii and K. pneumoniae infections were insignificant in 37.5% and 32.8% of the patients, respectively.

Studies have generally shown that 75% of K. pneumoniae (41) and 86.3% of A. baumannii (42) strains were MDR. This trend was also observed in the current study, as AST revealed significant MDR rates of 80% for K. pneumoniae and 90% for A. baumannii isolates, respectively. Geographic distance, hygiene levels, specimen types, study dates, sample sizes, and antimicrobial use restrictions might account for these inconsistencies. In another study, 58% of K. pneumoniae (43) and 69.6% of A. baumannii (44) strains were reported as MDR.

Overall, the existing AMR situation is critical and must be addressed following CDC standards and recommendations. Adequate staffing is essential to improve infection control and reduce burnout among overworked healthcare workers. Additionally, medical equipment should be thoroughly disinfected before transferring between patients’ rooms in COVID-19 ICUs, and handwashing and hygiene facilities are crucial, preferably equipped with touchless sensors (45). Furthermore, the predicted increase in AMR is a result of inappropriate and extensive antimicrobial use, particularly during the COVID-19 pandemic. To prevent potentially fatal overuse of antimicrobials, patients should receive empirical treatments with the most appropriate antimicrobials based on clinical findings and global standards. In light of the current microbiological findings, empirical therapy should be promptly adjusted.

5.1. Study Limitations

The current study has certain limitations. It only included infections confirmed by cultures, potentially omitting some cases. Moreover, the study was confined to a single institution with its unique local epidemiology of AMR, which might limit the generalizability of the findings.

5.2. Conclusions

In conclusion, the COVID-19 pandemic poses a severe health risk to individuals, particularly those with pneumonitis who require critical care and mechanical ventilation. The present study has highlighted the significant problem of VAP in critically ill COVID-19 patients, particularly in the context of highly drug-resistant K. pneumoniae and A. baumannii. This finding underscores the urgent need for targeted antimicrobial strategies in such cases. These findings emphasize the crucial importance of stringent infection control protocols and surveillance programs to reduce the incidence of NP in vulnerable patients.

Overall, VAP remains a serious concern in critically ill COVID-19 patients, and as demonstrated in this study, there is an urgent need for action plans to enhance epidemic control efforts. Since the COVID-19 pandemic persists, exploring various solutions to address this critical issue is essential. One potential solution could involve the development of novel drugs targeting severe bacterial infections, particularly those caused by K. pneumoniae and A. baumannii. Such advancements can contribute to more effective treatment of emerging pandemics.



  • 1.

    Zu ZY, Jiang MD, Xu PP, Chen W, Ni QQ, Lu GM, et al. Coronavirus Disease 2019 (COVID-19): A perspective from China. Radiol. 2020;296(2):E15-25. [PubMed ID: 32083985]. [PubMed Central ID: PMC7233368].

  • 2.

    Mohlenkamp S, Thiele H. Ventilation of COVID-19 patients in intensive care units. Herz. 2020;45(4):329-31. [PubMed ID: 32313971]. [PubMed Central ID: PMC7169372].

  • 3.

    Kalanuria AA, Mirski M, Ziai W. Ventilator-associated Pneumonia in the ICU. Annual Update in Intensive Care and Emergency Medicine 2014. 2014. p. 65-77.

  • 4.

    Boyd S, Nseir S, Rodriguez A, Martin-Loeches I. Ventilator-associated pneumonia in critically ill patients with COVID-19 infection: A narrative review. ERJ Open Res. 2022;8(3). [PubMed ID: 35891621]. [PubMed Central ID: PMC9080287].

  • 5.

    Dadras O, SeyedAlinaghi S, Karimi A, Shamsabadi A, Qaderi K, Ramezani M, et al. COVID-19 mortality and its predictors in the elderly: A systematic review. Health Sci Rep. 2022;5(3). e657. [PubMed ID: 35620541]. [PubMed Central ID: PMC9125886].

  • 6.

    Velavan TP, Meyer CG. The COVID-19 epidemic. Trop Med Int Health. 2020;25(3):278-80. [PubMed ID: 32052514]. [PubMed Central ID: PMC7169770].

  • 7.

    Agaba P, Tumukunde J, Tindimwebwa JVB, Kwizera A. Nosocomial bacterial infections and their antimicrobial susceptibility patterns among patients in ugandan intensive care units: A cross sectional study. BMC Res Notes. 2017;10(1):349. [PubMed ID: 28754148]. [PubMed Central ID: PMC5534037].

  • 8.

    Corrado RE, Lee D, Lucero DE, Varma JK, Vora NM. Burden of adult community-acquired, health-care-associated, hospital-acquired, and ventilator-associated pneumonia: New York City, 2010 to 2014. Chest. 2017;152(5):930-42. [PubMed ID: 28455128].

  • 9.

    Koulenti D, Tsigou E, Rello J. Nosocomial pneumonia in 27 ICUs in Europe: Perspectives from the EU-VAP/CAP study. Eur J Clin Microbiol Infect Dis. 2017;36(11):1999-2006. [PubMed ID: 27287765].

  • 10.

    Torres A, Niederman MS, Chastre J, Ewig S, Fernandez-Vandellos P, Hanberger H, et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia: Guidelines for the management of hospital-acquired pneumonia (HAP)/ventilator-associated pneumonia (VAP) of the European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and Asociacion Latinoamericana del Torax (ALAT). Eur Respir J. 2017;50(3). [PubMed ID: 28890434].

  • 11.

    Gupta A, Agrawal A, Mehrotra S, Singh A, Malik S, Khanna A. Incidence, risk stratification, antibiogram of pathogens isolated and clinical outcome of ventilator associated pneumonia. Indian J Crit Care Med. 2011;15(2):96-101. [PubMed ID: 21814373]. [PubMed Central ID: PMC3145311].

  • 12.

    Djordjevic ZM, Folic MM, Jankovic SM. Distribution and antibiotic susceptibility of pathogens isolated from adults with hospital-acquired and ventilator-associated pneumonia in intensive care unit. J Infect Public Health. 2017;10(6):740-4. [PubMed ID: 28189513].

  • 13.

    Perez F, Endimiani A, Ray AJ, Decker BK, Wallace CJ, Hujer KM, et al. Carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae across a hospital system: impact of post-acute care facilities on dissemination. J Antimicrob Chemother. 2010;65(8):1807-18. [PubMed ID: 20513702]. [PubMed Central ID: PMC2904665].

  • 14.

    Vazquez Guillamet C, Kollef MH. Acinetobacter pneumonia: Improving outcomes with early identification and appropriate therapy. Clin Infect Dis. 2018;67(9):1455-62. [PubMed ID: 29741597].

  • 15.

    Quartin AA, Scerpella EG, Puttagunta S, Kett DH. A comparison of microbiology and demographics among patients with healthcare-associated, hospital-acquired, and ventilator-associated pneumonia: A retrospective analysis of 1184 patients from a large, international study. BMC Infect Dis. 2013;13:561. [PubMed ID: 24279701]. [PubMed Central ID: PMC4222644].

  • 16.

    Farag AM, Tawfick MM, Abozeed MY, Shaban EA, Abo-Shadi MA. Microbiological profile of ventilator-associated pneumonia among intensive care unit patients in tertiary Egyptian hospitals. J Infect Dev Ctries. 2020;14(2):153-61. [PubMed ID: 32146449].

  • 17.

    Pourajam S, Kalantari E, Talebzadeh H, Mellali H, Sami R, Soltaninejad F, et al. Secondary bacterial infection and clinical characteristics in patients With COVID-19 admitted to two intensive care units of an academic hospital in iran during the first wave of the pandemic. Front Cell Infect Microbiol. 2022;12:784130. [PubMed ID: 35281440]. [PubMed Central ID: PMC8904895].

  • 18.

    Bhat KA, Madi D, Bhat S, Mary T, Shenoy Mulki S, Kotian H. Profile of secondary bacterial and fungal infections in hospitalized COVID-19 patients in a tertiary care centre. Infect Drug Resist. 2022;15:5705-14. [PubMed ID: 36196428]. [PubMed Central ID: PMC9527002].

  • 19.

    Lai CC, Wang CY, Hsueh PR. Co-infections among patients with COVID-19: The need for combination therapy with non-anti-SARS-CoV-2 agents? J Microbiol Immunol Infect. 2020;53(4):505-12. [PubMed ID: 32482366]. [PubMed Central ID: PMC7245213].

  • 20.

    Sharifipour E, Shams S, Esmkhani M, Khodadadi J, Fotouhi-Ardakani R, Koohpaei A, 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. [PubMed ID: 32873235]. [PubMed Central ID: PMC7461753].

  • 21.

    Garcia-Vidal C, Sanjuan G, Moreno-Garcia E, Puerta-Alcalde P, Garcia-Pouton N, Chumbita M, et al. Incidence of co-infections and superinfections in hospitalized patients with COVID-19: A retrospective cohort study. Clin Microbiol Infect. 2021;27(1):83-8. [PubMed ID: 32745596]. [PubMed Central ID: PMC7836762].

  • 22.

    Zhou P, Liu Z, Chen Y, Xiao Y, Huang X, Fan XG. Bacterial and fungal infections in COVID-19 patients: A matter of concern. Infect Control Hosp Epidemiol. 2020;41(9):1124-5. [PubMed ID: 32317036]. [PubMed Central ID: PMC7184139].

  • 23.

    Koenig SM, Truwit JD. Ventilator-associated pneumonia: Diagnosis, treatment, and prevention. Clin Microbiol Rev. 2006;19(4):637-57. [PubMed ID: 17041138]. [PubMed Central ID: PMC1592694].

  • 24.

    Garcia LS. Clinical microbiology procedures handbook. 1. American Society for Microbiology Press; 2010.

  • 25.

    Catalano A, Iacopetta D, Ceramella J, Scumaci D, Giuzio F, Saturnino C, et al. Multidrug Resistance (MDR): A widespread phenomenon in pharmacological therapies. Molecules. 2022;27(3). [PubMed ID: 35163878]. [PubMed Central ID: PMC8839222].

  • 26.

    Basak S, Singh P, Rajurkar M. Multidrug resistant and extensively drug resistant bacteria: A study. J Pathog. 2016;2016:4065603. [PubMed ID: 26942013]. [PubMed Central ID: PMC4749793].

  • 27.

    Singhal T. A Review of Coronavirus Disease-2019 (COVID-19). Indian J Pediatr. 2020;87(4):281-6. [PubMed ID: 32166607]. [PubMed Central ID: PMC7090728].

  • 28.

    Li X, Geng M, Peng Y, Meng L, Lu S. Molecular immune pathogenesis and diagnosis of COVID-19. J Pharm Anal. 2020;10(2):102-8. [PubMed ID: 32282863]. [PubMed Central ID: PMC7104082].

  • 29.

    Zhu Z, Lian X, Su X, Wu W, Marraro GA, Zeng Y. From SARS and MERS to COVID-19: A brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses. Respir Res. 2020;21(1):224. [PubMed ID: 32854739]. [PubMed Central ID: PMC7450684].

  • 30.

    Yap FH, Gomersall CD, Fung KS, Ho PL, Ho OM, Lam PK, et al. Increase in methicillin-resistant Staphylococcus aureus acquisition rate and change in pathogen pattern associated with an outbreak of severe acute respiratory syndrome. Clin Infect Dis. 2004;39(4):511-6. [PubMed ID: 15356814]. [PubMed Central ID: PMC7204093].

  • 31.

    Meawed TE, Ahmed SM, Mowafy SMS, Samir GM, Anis RH. Bacterial and fungal ventilator associated pneumonia in critically ill COVID-19 patients during the second wave. J Infect Public Health. 2021;14(10):1375-80. [PubMed ID: 34420902]. [PubMed Central ID: PMC8349397].

  • 32.

    Fu Y, Yang Q, Xu M, Kong H, Chen H, Fu Y, et al. Secondary Bacterial Infections in Critical Ill Patients With Coronavirus Disease 2019. Open Forum Infect Dis. 2020;7(6):ofaa220. [PubMed ID: 32613024]. [PubMed Central ID: PMC7313762].

  • 33.

    Hughes S, Troise O, Donaldson H, Mughal N, Moore LSP. Bacterial and fungal coinfection among hospitalized patients with COVID-19: A retrospective cohort study in a UK secondary-care setting. Clin Microbiol Infect. 2020;26(10):1395-9. [PubMed ID: 32603803]. [PubMed Central ID: PMC7320692].

  • 34.

    Paczosa MK, Mecsas J. Klebsiella pneumoniae: Going on the offense with a strong defense. Microbiol Mol Biol Rev. 2016;80(3):629-61. [PubMed ID: 27307579]. [PubMed Central ID: PMC4981674].

  • 35.

    Wang M, Wei H, Zhao Y, Shang L, Di L, Lyu C, et al. Analysis of multidrug-resistant bacteria in 3223 patients with hospital-acquired infections (HAI) from a tertiary general hospital in China. Bosn J Basic Med Sci. 2019;19(1):86-93. [PubMed ID: 30579325]. [PubMed Central ID: PMC6387671].

  • 36.

    Sharifi A, Kavoosi F, Hosseini SMJ, Mosavat A, Ahmadi A. Prevalence of streptococcus pneumoniae in ventilator-associated pneumonia by Real-time PCR. Arch Clin Infectious Dis. 2019;14(3).

  • 37.

    Mahendra M, Jayaraj BS, Lokesh KS, Chaya SK, Veerapaneni VV, Limaye S, et al. Antibiotic prescription, organisms and its resistance pattern in patients admitted to respiratory ICU with respiratory infection in mysuru. Indian J Crit Care Med. 2018;22(4):223-30. [PubMed ID: 29743760]. [PubMed Central ID: PMC5930525].

  • 38.

    Chastre J, Fagon JY. Ventilator-associated pneumonia. Am J Respir Crit Care Med. 2002;165(7):867-903. [PubMed ID: 11934711].

  • 39.

    Russo A, Giuliano S, Ceccarelli G, Alessandri F, Giordano A, Brunetti G, et al. Comparison of septic shock due to multidrug-resistant acinetobacter baumannii or klebsiella pneumoniae carbapenemase-producing k. Pneumoniae in intensive care unit patients. Antimicrob Agents Chemother. 2018;62(6). [PubMed ID: 29555630]. [PubMed Central ID: PMC5971575].

  • 40.

    Salehi M, Jafari S, Ghafouri L, Malekafzali Ardakani H, Abdollahi A, Beigmohammadi MT, et al. Ventilator-associated pneumonia: Multidrug resistant acinetobacter vs. Extended spectrum beta lactamase-producing Klebsiella. J Infect Dev Ctries. 2020;14(6):660-3. [PubMed ID: 32683358].

  • 41.

    Indrajith S, Mukhopadhyay AK, Chowdhury G, Farraj DAA, Alkufeidy RM, Natesan S, et al. Molecular insights of Carbapenem resistance Klebsiella pneumoniae isolates with focus on multidrug resistance from clinical samples. J Infect Public Health. 2021;14(1):131-8. [PubMed ID: 33234410].

  • 42.

    Hosoglu S, Arslan E, Aslan E, Deveci O. Use of carbapenems and glycopepdides is significant risk for multidrug resistant Acinetobacter baumannii infections. J Infect Dev Ctries. 2018;12(2):67-72. [PubMed ID: 31825906].

  • 43.

    Farhadi M, Ahanjan M, Goli HR, Haghshenas MR, Gholami M. High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several beta-lactamase and integron genes collected from several hospitals in the north of Iran. Ann Clin Microbiol Antimicrob. 2021;20(1):70. [PubMed ID: 34583687]. [PubMed Central ID: PMC8479884].

  • 44.

    Blum CA, Nigro N, Briel M, Schuetz P, Ullmer E, Suter-Widmer I, et al. Adjunct prednisone therapy for patients with community-acquired pneumonia: A multicentre, double-blind, randomised, placebo-controlled trial. Lancet. 2015;385(9977):1511-8. [PubMed ID: 25608756].

  • 45.

    Sehulster L, Chinn RY; Cdc; Hicpac. Guidelines for environmental infection control in health-care facilities. Recommendations of CDC and the healthcare infection control practices advisory committee (HICPAC). MMWR Recomm Rep. 2003;52(RR-10):1-42. [PubMed ID: 12836624].