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Esmaeili B, Khoshnevis H, Alirezaee A, Shakoori A, Pourpak Z, Chegini H, Ahmadinejad Z. Cycle Threshold Values Predict COVID-19 Severity and Mortality but Are not Correlated with Laboratory Markers. Iran J Allergy Asthma Immunol 2023; 22:468-481. [PMID: 38085148 DOI: 10.18502/ijaai.v22i5.13996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/27/2023] [Indexed: 12/18/2023]
Abstract
Many studies have evaluated the possible utility of cycle threshold (Ct) values as a predictor of Coronavirus disease 2019 (COVID-19) severity and patient outcome. Given the inconsistent results, we aimed to evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Ct values and disease severity, inflammatory markers, and outcomes in Iranian patients with COVID-19. A retrospective study of 528 patients with COVID-19 hospitalized from September 2020 to October 2021 was conducted. Demographic, clinical, and laboratory data of patients were retrieved from electronic medical records. Ct values were analyzed as a continuous variable after subcategorizing into 3 groups: low (Ct values<20), medium (Ct values 20 to 30), and high (Ct values>30). Of the 528 patients (45.1% female) aged 13 to 97 years, 109 patients had low Ct values, 312 patients had medium, and 107 patients had high Ct values. Patients with low Ct values were more likely to present with critical COVID-19, require invasive mechanical ventilation and develop complications such as acute respiratory distress syndrome and pneumonia. Furthermore, patients with low or medium Ct values were more likely to die compared to patients with high Ct values. Multivariate analysis showed that patients with low or medium Ct values were more likely to have severe COVID-19 compared with patients with high Ct values. The multivariate analysis also showed a higher risk of mortality in patients with low Ct values compared to patients with high Ct values, although this was not statistically significant. Our findings revealed that Ct values were an independent predictor of COVID-19 severity. The risk of mortality was higher in patients with low Ct values. However, further investigation is needed to address the correlation between Ct values and inflammatory factors.
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Affiliation(s)
- Behnaz Esmaeili
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran.
| | - Hoda Khoshnevis
- Medical Genetic Ward, Imam Khomeini Hospital Complex (IKHC), School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Atefe Alirezaee
- Immunology, Asthma and Allergy Research Institute (IAARI), Tehran University of Medical Sciences, Tehran, Iran AND Pediatrics Center of Excellence, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Abbas Shakoori
- Medical Genetic ward, Imam Khomeini Hospital Complex (IKHC), School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zahra Pourpak
- Immunology, Asthma and Allergy Research Institute (IAARI), Tehran University of Medical Sciences, Tehran, Iran AND Pediatrics Center of Excellence, Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hamid Chegini
- Department of Medical Laboratory Science, School of Allied Medical Sciences, Shahid Beheshti University of Medical Science, Tehran, Iran.
| | - Zahra Ahmadinejad
- Department of Infectious Diseases, Liver Transplant Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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Mobarak-Qamsari M, Jenaghi B, Sahebi L, Norouzi-Shadehi M, Salehi MR, Shakoori-Farahani A, Khoshnevis H, Abdollahi A, Feizabadi MM. Evaluation of Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus respiratory tract superinfections among patients with COVID-19 at a tertiary-care hospital in Tehran, Iran. Eur J Med Res 2023; 28:314. [PMID: 37660109 PMCID: PMC10474718 DOI: 10.1186/s40001-023-01303-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/19/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND The emergence of healthcare-associated infections (HAIs) or superinfections in COVID-19 patients has resulted in poor prognosis and increased mortality. METHODS In a cross-sectional study, 101 respiratory samples were collected from ICU-admitted COVID-19 patients. The HAI rate, demographics, and antibiotic resistance were assessed. RESULTS The HAI rate was 83.16% (76.62% bacterial and 6.54% fungal). The prevalence of 3 major HAI-causing organisms included Klebsiella pneumoniae (41.5%), Acinetobacter baumannii (20.8%), and Staphylococcus aureus (4.9%). Mortality and intubation ventilation proportions of 90% (p = 0.027) and 92.2% (p = 0.02) were significant among patients with superinfection, respectively. Multiple logistic regression analysis showed SpO2 pressure (odds ratio 0.842; 95% CI 0.750-0.945; p = 0.004) as a predictive factor in the association between antibiotic usage and mortality. More than 50% of patients received carbapenems. The resistance rates to at least one antibiotic of third-generation cephalosporins, aminoglycosides, quinolones/fluoroquinolones, tetracyclines, and β-lactam inhibitors were 95.2%, 95.2%, 90%, 57.1%, and 100% among A. baumannii isolates and 71.4%, 55%, 69%, 61.9%, and 59.5% among K. pneumoniae isolates, respectively. A proportion of 60% was recorded for methicillin-resistant S. aureus isolates. CONCLUSION As a result, antibiotic treatment should be administered following the microbial resistance profile. Contact isolation and infection control measures should be implemented as needed.
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Affiliation(s)
- Maryam Mobarak-Qamsari
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bita Jenaghi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leyla Sahebi
- Family Health Research Institute. Maternal, Fetal, and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Norouzi-Shadehi
- Department of Infectious Disease, School of Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Salehi
- Department of Infectious Diseases, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori-Farahani
- Department of Medical Genetics, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hoda Khoshnevis
- Imam Khomeini Hospital Complex, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Thorax Research Center, Imam Khomeini Hospital Complex., Tehran University of Medical Sciences, Tehran, Iran.
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Abdollahi A, Salarvand S, Ghalehtaki R, Jafarzadeh B, Beigmohammadi MT, Ghiasvand F, Shakoori A, Khoshnevis H, Arabzadeh M, Nateghi S, Mehrtash V. The role of saliva PCR assay in the diagnosis of COVID-19. J Infect Dev Ctries 2022; 16:5-9. [PMID: 35192515 DOI: 10.3855/jidc.15239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/13/2021] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION The introduction of a self-collection sampling method with less discomfort would be of great benefit in reducing the risk of medical provider's contamination and patient's acceptance. The aim of the present study was to investigate saliva samples' diagnostic performance for the COVID-19 RT-PCR test compared to pharyngeal swabs. METHODOLOGY From individuals referred to a medical center with presentations compatible with COVID-19 who were eligible for molecular diagnostic tests, 80 cases were selected. Nasopharyngeal and oropharyngeal swabs (placed into the same transport tube) along with self-collected saliva sample were taken from each participant for COVID-19 RT-PCR assay. The results of pharyngeal swabs and saliva sample were compared. RESULTS Sixty-two (78%) infected cases were detected, of whom 31 (39%) cases tested positive for both pharyngeal swab and saliva samples. 24 (30%) and 7 (9%) cases tested positive only for pharyngeal or saliva samples, respectively. The overall percentage of agreement between pharyngeal swab and saliva sample was 61%, with a kappa value of 0.24 (p-value = 0.019, 95% CI: 0.04-0.44), showing a fair level of agreement. The diagnostic sensitivity of pharyngeal swabs was 88.71% (95% CI: 78.11-95.34), and the diagnostic sensitivity of saliva samples was 61.29% (95% CI: 48.07-73.40). Compared to pharyngeal swabs (oropharyngeal and nasopharyngeal swabs in the same collection tube), an important observation was that seven more positive cases were detected among saliva samples. CONCLUSIONS The findings of the present study indicated that self-collected saliva samples cannot replace pharyngeal swabs. Still, saliva samples significantly increased the case detection rate and can be used along with pharyngeal swabs.
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Affiliation(s)
- Alireza Abdollahi
- Department of pathology, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Salarvand
- Department of pathology, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Ghalehtaki
- Department of Radiation Oncology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran, Iran
| | - Bita Jafarzadeh
- Department of pathology, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghi Beigmohammadi
- Department of infectious diseases, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Ghiasvand
- Department of infectious diseases, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori
- Medical Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Hoda Khoshnevis
- Medical Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Arabzadeh
- Medical Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Nateghi
- Department of Cardiology, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Mehrtash
- Department of pathology, Imam Hospital Complex, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Abdollahi A, shakoori A, Khoshnevis H, Arabzadeh M, Dehghan Manshadi SA, Mohammadnejad E, Ghasemi D, Safari Aboksari M, Alizadeh S, Mehrtash V, Eftekhar-javadi A, Safaei M. Comparison of Patient-collected and Lab Technician-collected Nasopharyngeal and Oropharyngeal Swabs for Detection of COVID-19 by RT-PCR. Iran J Pathol 2020; 15:313-319. [PMID: 32944044 PMCID: PMC7477688 DOI: 10.30699/ijp.2020.127312.2387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND & OBJECTIVE A simple approach to prevent close contact in healthcare settings during the COVID-19 outbreak is to train patients to collect their own nasopharyngeal and oropharyngeal swabs and deliver them to medical laboratories to have them processed. The aim of our study was to compare lab technician- with patient- collected oropharyngeal and nasopharyngeal samples for detection of the coronavirus disease 2019 (COVID 19) using rapid real-time polymerase chain reaction (rRT-PCR). METHODS Fifty adult patients with flu-like symptoms and radiologic findings compatible with atypical pneumonia who were admitted to the infectious diseases ward of Imam Khomeini Hospital Complex, Tehran, Iran, with a clinical diagnosis of COVID-19 from February 28 to April 27 of 2020 were randomly selected and entered in our study. Two sets of naso- and oropharyngeal swabs were collected, one set by a lab technician and the other by the patients, and the COVID-19 rRT-PCR test was performed. RESULTS Of 50 selected cases, in seven patients all collected naso- and oropharyngeal swabs tested positive, and in 22 patients all samples tested negative for COVID-19 in rRT-PCR. Discrepancies between rRT-PCR results of lab technician- and patient-collected swabs were observed in 12 nasopharyngeal and 13 oropharyngeal specimens. Positive lab technician-collected and negative patient-collected samples were observed in 10 and 5 nasopharyngeal and oropharyngeal specimens, respectively. Negative lab technician-collected and positive patient-collected samples were observed in two and seven nasopharyngeal and oropharyngeal specimens, respectively. The overall percentage of agreement among both nasopharyngeal and oropharyngeal swabs taken by a lab technician and patients was 76% with a kappa value of 0.49 (P=0.001). CONCLUSION Based on our findings, lab technician-collected naso- and oropharyngeal swabs cannot be replaced by patient-collected ones with regard to COVID-19 rRT-PCR.
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Affiliation(s)
- Alireza Abdollahi
- Department of Pathology, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas shakoori
- Medical Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Hoda Khoshnevis
- Supervisor of Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Arabzadeh
- Laboratory Senior Technical Associate of Genetic Ward, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Dehghan Manshadi
- Department of Infectious Diseases and Tropical Medicine, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Esmaeil Mohammadnejad
- Department of Medical-Surgical Nursing, School of Nursing and Midwifery, Tehran University of Medical Sciences, Tehran, Iran
| | - Dorsa Ghasemi
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Safari Aboksari
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shaban Alizadeh
- Hematology Department, Allied medical school, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Mehrtash
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezoo Eftekhar-javadi
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoomeh Safaei
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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