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El Zakhem A, Mahmoud O, Bou Fakhreddine H, Mahfouz R, Bouakl I. Patterns and predictors of positive multiplex polymerase chain reaction respiratory panel among patients with acute respiratory infections in a single center in Lebanon. Mol Biol Rep 2024; 51:346. [PMID: 38401017 DOI: 10.1007/s11033-023-09133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/08/2023] [Indexed: 02/26/2024]
Abstract
BACKGROUND Infectious agents associated with community-acquired acute respiratory infections (ARIs) remain understudied in Lebanon. We aim to assess the microbiological profiles of ARIs by employing polymerase chain reaction (PCR) and identifying predictors of positive PCR results among patients admitted for ARI. METHODS AND RESULTS We conducted a retrospective single-center study at the American University of Beirut Medical Center, including all respiratory PCR panels performed on pediatric (< 18) and adult (≥ 18) patients presenting with an ARI from January 2015 to March 2018, prior to the onset of the COVID-19 pandemic. We aimed to identify the epidemiological patterns of ARIs and the factors associated with positive PCRs in both adult and pediatric patients. Among 281 respiratory PCRs, 168 (59.7%) were positive for at least one pathogen, with 54.1% positive PCR for viruses, 7.8% for bacteria species, and 3.9% with virus-bacteria codetection. Almost 60% of the patients received antibiotics prior to PCR testing. PCR panels yielded more positive results in pediatric patients than in adults (P = 0.005). Bacterial detection was more common in adults compared to pediatrics (P < 0.001). The most common organism recovered in the entire population was Human Rhinovirus (RhV) (18.5%). Patients with pleural effusion on chest CT were less likely to have a positive PCR (95% Cl: 0.22-0.99). On multivariate analysis, pediatric age group (P < 0.001), stem cell transplant (P = 0.006), fever (P = 0.03) and UTRI symptoms (P = 0.004) were all predictive of a positive viral PCR. CONCLUSION Understanding the local epidemiology of ARI is crucial for proper antimicrobial stewardship. The identification of factors associated with positive respiratory PCR enhances our understanding of clinical characteristics and potential predictors of viral detection in our population.
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Affiliation(s)
- Aline El Zakhem
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, 110236, Lebanon
| | - Omar Mahmoud
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, 110236, Lebanon
| | - Hisham Bou Fakhreddine
- Division of Pulmonary and Critical Care, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Imad Bouakl
- Division of Pulmonary and Critical Care, American University of Beirut Medical Center, Beirut, Lebanon.
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Rafeek RAM, Divarathna MVM, Noordeen F. A review on disease burden and epidemiology of childhood parainfluenza virus infections in Asian countries. Rev Med Virol 2020; 31:e2164. [PMID: 32996257 DOI: 10.1002/rmv.2164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Human parainfluenza viruses (HPIVs) are an important cause of acute respiratory tract infections (ARTIs) in children less than 5 years, second only to human respiratory syncytial viruses (HRSVs). Generally, patients infected with HPIVs are treated in outpatient clinics, yet also contribute to ARTI-associated hospitalization in children. Although HPIV infections are well studied in developed countries, these infections remain under-investigated and not considered in the routine laboratory diagnosis of childhood ARTI in many developing countries in Asia. We performed an extensive literature search on the prevalence, epidemiology, and burden of HPIV infections in children less than 5 years in Asia using PubMed and PubMed Central search engines. Based on the literature, the prevalence of HPIV infection in Asia ranges from 1% to 66%. According to many studies, HPIV-3 is the major virus circulating among children; however, several studies failed to detect HPIV-4 due to unavailability of diagnostic tools. In Asian countries, HPIV contributes a substantial disease burden in children. The data in this review should assist researchers and public health authorities to plan preventive measures, including accelerating research on vaccines and antiviral drugs.
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Affiliation(s)
- Rukshan A M Rafeek
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
| | - Maduja V M Divarathna
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
| | - Faseeha Noordeen
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
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Hatem A, Mohamed S, Abu Elhassan UE, Ismael EAM, Rizk MS, El-Kholy A, El-Harras M. Clinical characteristics and outcomes of patients with severe acute respiratory infections (SARI): results from the Egyptian surveillance study 2010-2014. Multidiscip Respir Med 2019; 14:11. [PMID: 30976418 PMCID: PMC6442424 DOI: 10.1186/s40248-019-0174-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background Respiratory viral and atypical bacterial infections data in Egyptian patients are sparse. This study describes the clinical features and outcomes of patients with severe acute respiratory infections (SARI) in hospitalized patients in Egypt. Methods SARI surveillance was implemented at Cairo University Hospital (CUH) during the period 2010–2014. All hospitalized patients meeting the WHO case definition for SARI were enrolled. Nasopharyngeal/oropharyngeal (NP/OP) swabs were collected and samples were tested using RT-PCR for influenza A, B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza virus (PIV 1,2,3,4), adenovirus, bocavirus, coronavirus, enterovirus, rhinovirus, and atypical bacteria. Data were analyzed to calculate positivity rates for viral pathogens and determine which pathogens related to severe outcomes or resulted in death. Results Overall, 1,075/3,207 (33.5%) cases had a viral etiology, with a mean age of 5.74 (±13.87) years. The highest rates were reported for RSV (485 cases, 45.2%), PIV (125, 11.6%), and adenovirus (105, 9.8%). Children had a higher viral rate (981, 91.2%) compared to 94 (8.8%) cases in adults. Patients with identified viruses had significantly lower rates for ICU admission, hospital stay, mechanical ventilation, and overall mortality than those without identified viruses. No infections were independently associated with severe outcomes. Conclusions Viral pathogens were encountered in one-third of hospitalized adult and pediatric Egyptian patients with SARI, while atypical bacteria had a minor role. Highest rates of viral infections were reported for RSV, PIV, and adenovirus. Viral infections had neither negative impacts on clinical features nor outcomes of patients with SARI in our locality.
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Affiliation(s)
- Ashraf Hatem
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sherif Mohamed
- 2Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Assiut University, Assiut, 71516 Egypt
| | - Usama E Abu Elhassan
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eman A M Ismael
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Magda S Rizk
- 3Department of Anesthesia and Intensive Care, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amany El-Kholy
- 4Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed El-Harras
- Department of Clinical Pathology, Faculty of Medicine, Mansura University, Mansura, Egypt
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Horton KC, Dueger EL, Kandeel A, Abdallat M, El-Kholy A, Al-Awaidy S, Kohlani AH, Amer H, El-Khal AL, Said M, House B, Pimentel G, Talaat M. Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014. PLoS One 2017; 12:e0180954. [PMID: 28704440 PMCID: PMC5509236 DOI: 10.1371/journal.pone.0180954] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/23/2017] [Indexed: 11/19/2022] Open
Abstract
Introduction Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. Methods Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1–3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. Results At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens–influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. Conclusions Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest.
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Affiliation(s)
- Katherine C. Horton
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
- * E-mail:
| | - Erica L. Dueger
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
- Global Disease Detection Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Mohamed Abdallat
- Communicable Disease Department, Ministry of Health, Amman, Jordan
| | - Amani El-Kholy
- Clinical Pathology Department, Cairo University Hospitals, Cairo, Egypt
| | - Salah Al-Awaidy
- Communicable Disease Department, Ministry of Health, Muscat, Oman
| | | | - Hanaa Amer
- Clinical Pathology Department, Ain Shams University, Cairo, Egypt
| | | | - Mayar Said
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Brent House
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Guillermo Pimentel
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
| | - Maha Talaat
- Global Disease Detection Center, U.S. Centers for Disease Control and Prevention, Cairo, Egypt
- Global Disease Detection and Response Program, U.S. Naval Medical Research Unit, No.3, Cairo, Egypt
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Janahi I, Abdulkayoum A, Almeshwesh F, Alkuwari M, Al Hammadi A, Alameri M. Viral aetiology of bronchiolitis in hospitalised children in Qatar. BMC Infect Dis 2017; 17:139. [PMID: 28193180 PMCID: PMC5307797 DOI: 10.1186/s12879-017-2225-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/27/2017] [Indexed: 01/16/2023] Open
Abstract
Background Bronchiolitis is considered one of the earliest and most common causes of hospitalisation in young children. Development of molecular technologies allowed a better understanding of bronchiolitis aetiology. Results from cohort studies evaluating the association between single, multiple viral infections and clinical outcomes are conflicting. Data on viral bronchiolitis in children were found to be limited in Qatar. This study aimed to determine frequency and seasonal trends of viral pathogens causing acute bronchiolitis, and to explore association between viral pathogens, disease severity and length of stay (LOS). Methods This is a retrospective descriptive study, including children admitted in 2010 and 2011 with acute bronchiolitis. Presenting history, physical examination and respiratory viral co-infections as detected by molecular assays were analysed. Results At least one virus was detected in 315/369 (85.4%) of included children with single and multiple viruses in 67 and 33% of cases respectively. Respiratory syncytial virus (RSV) was the most detected virus, accounting for 51.2% followed by rhinovirus (RV) in 25.5% of cases. Fall and summer admissions were associated with longer LOS. On multivariate logistic regression analysis, retraction (OR 3.96; 95% CI 1.64,9.59) and age group 1–3 months (OR 3.09; 95% CI 1.06,9.05) were associated with longer LOS. Crepitation (OR 9.15; 95% CI 1.58,53.13), retraction (OR 4.10; 95% CI 1.05,16.12) and respiratory rate (OR 1.46; 95% CI 1.28,1.66) were associated with moderate to severe bronchiolitis. Identifying the viral agent did not influence disease severity or LOS. Conclusion Clinical presentation is of more relevance to LOS and disease severity than the detected viruses. Future studies should investigate the interplay between climate characteristics, population’s factors and the most detectable circulating viruses. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2225-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ibrahim Janahi
- Paediatric Pulmonology Unit, Hamad Medical Corporation, P. O. Box 3050, Doha, Qatar.
| | | | - Fawziya Almeshwesh
- Paediatric Pulmonology Unit, Hamad Medical Corporation, P. O. Box 3050, Doha, Qatar
| | - Mohamed Alkuwari
- Paediatric Pulmonology Unit, Hamad Medical Corporation, P. O. Box 3050, Doha, Qatar
| | - Ahmed Al Hammadi
- Paediatric Pulmonology Unit, Hamad Medical Corporation, P. O. Box 3050, Doha, Qatar
| | - Marwah Alameri
- Paediatric Pulmonology Unit, Hamad Medical Corporation, P. O. Box 3050, Doha, Qatar
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Al-Turab M, Chehadeh W, Al-Mulla F, Al-Nakib W. Human metapneumovirus in patients with respiratory tract infection in Kuwait. J Med Virol 2012; 83:1811-7. [PMID: 21837799 PMCID: PMC7166577 DOI: 10.1002/jmv.22193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Human metapneumovirus (hMPV) has been recognized as an important cause of respiratory tract infections in all age groups and in all geographical area. The role of hMPV in causing respiratory tract infections in Kuwait was not yet investigated. The aim of this study was to determine the prevalence of hMPV infection in Kuwait among patients with respiratory tract infection with respect to other respiratory viruses. During January–December 2009, 460 respiratory samples from 388 patients with respiratory tract infection were collected from different hospitals. They were tested for hMPV RNA by real‐time PCR, and for other respiratory viruses by conventional PCR. Out of 388 patients, 110 (28%) were positive for viral respiratory infections; 21 (5.4%) were positive for hMPV, 29 (7.5%) were positive for rhinovirus, 13 (4%) were positive for respiratory syncytial virus, and 10 (3%) were positive for adenovirus. Most (n = 19, 90.5%) of hMPV‐positive patients were admitted to the intensive care unit, 76% of them were of age 2 years and below, and 24% of age 59 years and above. All hMPV‐positive elderly patients had pneumonia while 50% of hMPV‐positive infants had bronchopneumonia. Children with hMPV/rhinovirus co‐infection (n = 3, 1%) had recurrent chest infection and frequent intensive care unit admission. The hMPV infection was mostly detected between December and May, and genotype B was more prevalent than genotype A. This is the first study demonstrating the prevalence of hMPV infection in Kuwait, and suggests that hMPV infection is prevalent in infants and elderly patients with lower respiratory tract infection. J. Med. Virol. 83:1811–1817, 2011. © 2011 Wiley‐Liss, Inc.
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Affiliation(s)
- Mariam Al-Turab
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait.
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