301. Use of a multiplex PCR assay for detection of respiratory co-infections in COVID-19 hospitalized non-ICU patients: an ace up a clinician’s sleeve (original) (raw)
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Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU
BMC Infectious Diseases
Background COVID-19 is known as a new viral infection. Viral-bacterial co-infections are one of the biggest medical concerns, resulting in increased mortality rates. To date, few studies have investigated bacterial superinfections in COVID-19 patients. Hence, we designed the current study on COVID-19 patients admitted to ICUs. Methods Nineteen patients admitted to our ICUs were enrolled in this study. To detect COVID-19, reverse transcription real-time polymerase chain reaction was performed. Endotracheal aspirate samples were also collected and cultured on different media to support the growth of the bacteria. After incubation, formed colonies on the media were identified using Gram staining and other biochemical tests. Antimicrobial susceptibility testing was carried out based on the CLSI recommendations. Results Of nineteen COVID-19 patients, 11 (58%) patients were male and 8 (42%) were female, with a mean age of ~ 67 years old. The average ICU length of stay was ~ 15 days and at...
Infection and Drug Resistance, 2021
The purpose of this study is to evaluate the frequency of viral and bacterial respiratory pathogens detected by molecular methods in sputum samples of patients hospitalized for COVID-19 and to evaluate its impact on mortality and unfavorable outcomes (inhospital death or mechanical ventilation). Patients and Methods: The prospective cohort included patients with diagnosis of COVID-19 hospitalized at Hospital Nacional Hipólito Unanue. Sociodemographic and clinical data were collected from clinical records. Sputum samples were analyzed with the Biofire Filmarray Pneumonia plus ® respiratory panel. Crude and adjusted associations with unfavorable outcomes were evaluated using logistic regression models. Results: Ninety-three patients who were able to collect sputum samples were recruited between September 8 and December 28, 2020. The median age was 61.7 years (IQR 52.3-69-8) and 66 (71%) were male. The most frequent symptoms were dyspnea, cough, fever, and general malaise found in 80 (86%), 76 (82%), 45 (48%), and 34 (37%) patients, respectively. Fifty-three percent of patients had comorbidities. Seventy-six (82%) patients received antibiotics prior to admission and 29 (31%) developed unfavorable outcome. Coinfection was evidenced in 38 (40.86%) cases. The most frequently found bacteria were Staphylococcus aureus, Streptococcus agalactiae, Haemophilus influenzae and Klebsiella pneumoniae in 11 (11.83%), 10 (10.75%), 10 (10.75%), and 8 (8.6%) cases, respectively. Streptococcus pneumoniae was found in one case (1.08%). We neither identify atypical bacteria nor influenza virus. No association was found between the presence of viral or bacterial microorganisms and development of unfavorable outcomes (OR 1.63; 95% CI 0.45-5.82). Conclusion: A high frequency of respiratory pathogens was detected by molecular methods in patients with COVID-19 pneumonia but were not associated with unfavorable outcomes. No atypical agents or influenza virus were found. The high use antibiotics before admission is a concern. Our data suggest that the use of drug therapy against atypical bacteria and viruses would not be justified in patients hospitalized for COVID-19.
Evaluation of Bacterial Co-infections of the Respiratory Tract in COVID-19 Patients
Journal of Nepalgunj Medical College, 2021
Introduction: The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2. The co-evolution of viral and bacterial respiratory pathogens has created an environment in which a viral infection allows concurrent or secondary bacterial co-infections. Aims: This study was carried out to isolate the different respiratory bacterial pathogens from COVID patients and evaluate their antibiotic sensitivity pattern. Methods: Hospital based descriptive cross sectional study was conducted over a period of between 2nd Jestha to 5th Shrawan 2078 (16th May to 20th July 2021) in Nepalgunj Medical college, Kohalpur during the second wave of COVID-19 in Nepal. The sputum was inoculated onto different culture plates such as Blood Agar (BA) and MacConkey Agar (MA) and incubated at 37 oC. After overnight growth and in Gram staining, different Gram’s positive and negative bacteria were observed. Antibiotic sensitivity test was performed by Kirby-Bauer Disk ...
Respiratory co-infections in COVID-19-positive patients
European Journal of Medical Research
Background Opportunistic respiratory infections may complicate critically ill patients with COVID-19. Early detection of co-infections helps to administrate the appropriate antimicrobial agent, to guard against patient deterioration. This study aimed at estimating co-infections in COVID-19-positive patients. Methods Eighty-nine COVID-19-positive patients confirmed by SARS-COV-2 PCR were tested for post-COVID-19 lower respiratory tract co-infections through bacterial culture, fungal culture and galactomannan (GM) testing. Results Fourteen patients showed positive coinfection with Klebsiella, nine with Acinetobacter, six with Pseudomonas and three with E. coli. As for fungal infections, nine showed coinfection with Aspergillus, two with Zygomycetes and four with Candida. Galactomannan was positive among one patient with Aspergillus coinfection, one with Zygomycetes coinfection and three with Candida, 13 samples with negative fungal culture were positive for GM. Ten samples showed posi...
Journal of Advances in Medicine and Medical Research, 2021
Aims: We aimed to evaluate the burden of bacterial co-infections in patients with COVID-19 and to ensure judicious use of antibiotics. Study Design: Hospital based, cross sectional study. Place and Duration of Study: Postgraduate department of Microbiology, Government Medical College, Srinagar, and associated hospitals, between July 2020 and February 2021. Methodology: A total of 70 patients diagnosed with COVID-19 by RT PCR of nasopharyngeal/oropharyngeal samples were included in the study. Lower respiratory specimen like endotracheal aspirate (ETA), sputum, and bronchoalveolar lavage (BAL) from COVID-19 patients admitted in the ICU were collected as per standard protocol and subjected to quantitative cultures in the laboratory. Antimicrobial susceptibility testing was carried out in line with CLSI recommendations. Results: Of the 70 lower respiratory tract specimens (Endotracheal aspirate n=53, sputum n=15, and Bronchoalveolar lavage n=02) taken from RT-PCR confirmed COVID-19 pati...
Co-infections observed in SARS-CoV-2 positive patients using a rapid diagnostic test
Scientific Reports
Rapid diagnostic tests are tools of paramount impact both for improving patient care and in antimicrobial management programs. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens, be they bacteria or viruses, while obtaining information about the presence/absence of a genetic target of resistance to modulate antibiotic therapy. In this paper, we present our experiences with the use of the Biofire® FilmArray® Pneumonia Panel Plus (FAPP; bioMérieux; Marcy l’Etoile, France) to assess coinfection in COVID-19 patients. A total of 152 respiratory samples from consecutive patients were examined, and 93 (61%) were found to be FAPP positive, with the detection of bacteria and/or viruses. The patients were 93 males and 59 females with an average age of 65 years who were admitted to our hospital due to moderate/severe acute respiratory symptoms. Among the positive samples were 52 from sputum (SPU) and 41 from bro...
Microorganisms, 2021
Background: The role of bacterial co-infection and superinfection among critically ill COVID-19 patients remains unclear. The aim of this study was to assess the rates and characteristics of pulmonary infections, and associated outcomes of ventilated patients in our facility. Methods: This was a retrospective study of ventilated COVID-19 patients between March 2020 and March 2021 that underwent BioFire®, FilmArray® Pneumonia Panel, testing. Community-acquired pneumonia (CAP) was defined when identified during the first 72 h of hospitalization, and ventilator-associated pneumonia (VAP) when later. Results: 148 FilmArray tests were obtained from 93 patients. With FilmArray, 17% of patients had CAP (16/93) and 68% had VAP (64/93). Patients with VAP were older than those with CAP or those with no infection (68.5 vs. 57–59 years), had longer length of stay and higher mortality (51% vs. 10%). The most commonly identified FilmArray target organisms were H. influenzae, S. pneumoniae, M. cat...
2020
ABSTRACTThere is scarce information on the frequency of co-detection of respiratory pathogens (RP) in patients with Covid-19. Documentation of coinfections in Covid-19 pneumonia patients may be relevant for appropriate clinical and therapeutic management of patients. Between March 4th and March 28th, 2020, a total of 183 adult patients testing positive by SARS CoV-2 RT-PCR on respiratory specimens were hospitalized with interstitial pneumonia at our center, of whom 103 were tested for other RP by a multiplexed PCR assay. Three patients had a positive result for either one (n=2; Coronavirus HKU1 or Mycoplasma pneumoniae) or two targets (n=1; Influenza virus A (H3) and Respiratory syncytial virus B). Twenty-three patients testing negative by SARS CoV-2 RT-PCR and presentig with clinical, laboratory findings and imaging compatibe with Covid-19 pneumonia underwent RP screening. Of these, 6 (26%) had a positive result for a single RP. Our data indicate that despite the apparent rarity of...
Microbial Co-infections in Covid Patients: A Mini Review
European Journal of Biology and Biotechnology
In this review, we highlight the complications of COVID-19 affected patients due to microbial infections, which increase the severity of the disease. Nearly 50% of COVID-19 affected patients among non-survivors were either co-infected with bacterial, fungal, or viral pathogens. During ongoing COVID-19 pandemic, it has been a challenge for developing and under developing countries to identify co-infections in patients due to limited healthcare facilities and high cost for the diagnostic tests. Since several microbial co-infections are associated with COVID-19, there is need to diagnose such co-infections in early stage so that required control measures would be taken to avoid the further health risks. People with severe COVID-19, COVID-19 patients in intensive care units (ICU), are susceptible to bacterial and fungal infections. Bacterial pathogens, representing less than 14% of patients with reported infections include Mycoplasma pneumoniae, Haemophilus influenzae and Pseudomonas ae...
Bacterial Pneumonia Co-Infection in COVID-19 Patients
Asian Journal of Medicine and Biomedicine
The objective of this study was to highlight the emergence of COVID-19 bacteria pneumonia co-infections in patients infected with SARS-Cov-2 and risk factors related to its incidence and outcomes. We reported two cases of elderly patients with multiple comorbidities infected with SARS-Cov-2 and developed COVID-19 bacterial pneumonia requiring admission to intensive care unit (ICU) with one mortality preceded by septicemic shock and multi-organ failures. Observing the potential risk factors for being infected with SARS-Cov-2 and developing COVID-19 bacterial pneumonia we strongly advocate for rapid detection of COVID-19 bacterial pneumonia in SARS-Cov-2 infected patients and rapidly characterized the bacterial involved for a better outcome and importantly for efficient antimicrobial stewardship. COVID-19 bacterial pneumonia is an emerging disease requiring rapid detection and bacterial characterization with the ongoing management for severe acute respiratory syndrome coronavirus 2 (S...