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Tligui H, Hattoufi K, Jroundi I, Mahraoui C, Bassat Q. Dataset of acute respiratory infections: Epidemiological and etiological data from a cohort of 801 Moroccan children. Data Brief 2024; 54:110457. [PMID: 38725553 PMCID: PMC11079449 DOI: 10.1016/j.dib.2024.110457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Acute respiratory infections remain a leading cause of death among young children in low- and middle-income countries. The etiological diagnosis of these infections is challenging due to the similarity in clinical presentations and overlapping symptoms caused by various pathogens. This database provides comprehensive epidemiological, clinical, paraclinical, and biological data on 801 Moroccan children admitted to the Children's Hospital of Rabat for the management of Clinical Severe Pneumonia. Identification of the pathogens responsible of respiratory infections was carried out using blood samples for hemoculture, standard bacterial culture and multiplex RT-PCR using the TrueScience RespiFinder Pathogen Identification Panel (Applied Biosystems).
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Affiliation(s)
- Houssain Tligui
- Research Laboratory of Ibn Sina University Hospital, Rabat, Morocco
- Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Kenza Hattoufi
- Research Team on Health and Nutrition of Mother and Child, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Imane Jroundi
- National School of Public Health, Ministry of Health, Rabat, Morocco
| | - Chafiq Mahraoui
- Children's Hospital of Rabat (CHR), Ibn Sina University Hospital Center, Rabat, Morocco
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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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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Epidemiology of Respiratory Pathogens in Children with Severe Acute Respiratory Infection and Impact of the Multiplex PCR Film Array Respiratory Panel: A 2-Year Study. Int J Microbiol 2022; 2021:2276261. [PMID: 35003265 PMCID: PMC8741400 DOI: 10.1155/2021/2276261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
Sever acute respiratory infections (SARIs) are a public health issue that are common in children and are associated with an important morbidity and mortality rate worldwide. Although SARI are mainly caused by viruses, they are still a cause of antibiotic overuse. The use of molecular methods especially real-time multiplex PCR allowed to detect a wide range of respiratory viruses and their subtype as well as some atypical bacteria. The aim of this study was to investigate the epidemiology of respiratory pathogens detected in children admitted with SARI and to highlight the role of real-time multiplex PCR in the rapid diagnosis of viral and bacterial SARI. This work is a descriptive observational study from January 2018 to December 2019 including nasopharyngeal secretions collected from 534 children hospitalised in paediatric department. The detection of respiratory viruses and bacteria was performed by the FilmArray® Respiratory Panel. A total of 387 (72.5%) children were tested positive for at least one respiratory pathogen, and 23.3% of them were coinfected with more than one pathogen. Viral aetiology was found in 91.2% (n = 340). The most common viruses detected were HRV (n = 201) and RSV (n = 124), followed by PIV (n = 35) influenza A (n = 29) and human metapneumovirus (n = 27). Bacteria was found in 8.8% (n = 47), and Bordetella pertussis was the most detected. Respiratory syncytial virus and Bordetella pertussis were significantly higher in infants less than 6 months old. The detection of RSV and influenza A presented a pic in winter, and HMPV was statistically significant in spring (p < 0.01). This study described the epidemiology of respiratory pathogens involved in severe respiratory infections in children that were affected by several factors such as season and age group. It also highlighted the importance of multiplex PCR in confirming viral origin, thus avoiding irrational prescription of antibiotics in paediatric settings.
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Cytokine expression patterns in hospitalized children with Bordetella pertussis, Rhinovirus or co-infection. Sci Rep 2021; 11:10948. [PMID: 34040002 PMCID: PMC8154898 DOI: 10.1038/s41598-021-89538-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Mechanisms of interaction between Bordetella pertussis and other viral agents are yet to be fully explored. We studied the inflammatory cytokine expression patterns among children with both viral-bacterial infections. Nasopharyngeal aspirate (NPA) samples were taken from children, aged < 1 year, positive for Rhinovirus, Bordetella pertussis and for Rhinovirus and Bordetella pertussis. Forty cytokines were evaluated in NPA by using human cytokine protein arrays and a quantitative analysis was performed on significantly altered cytokines. Forty cytokines were evaluated in NPA by using human cytokine protein arrays and a quantitative analysis was performed on significantly altered cytokines. Our results show that co-infections display a different inflammatory pattern compared to single infections, suggesting that a chronic inflammation caused by one of the two pathogens could be the trigger for exacerbation in co-infections.
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Correlation between the Antibiotic Resistance Genes and Susceptibility to Antibiotics among the Carbapenem-Resistant Gram-Negative Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10030255. [PMID: 33806340 PMCID: PMC8001261 DOI: 10.3390/antibiotics10030255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
In this study, the correlation between the antibiotic resistance genes and antibiotic susceptibility among the carbapenem-resistant Gram-negative pathogens (CRGNPs) recovered from patients diagnosed with acute pneumonia in Egypt was found. A total of 194 isolates including Klebsiella pneumoniae (89; 46%), Escherichia coli (47; 24%) and Pseudomonas aeruginosa (58; 30%) were recovered. Of these, 34 (18%) isolates were multiple drug resistant (MDR) and carbapenem resistant. For the K. pneumoniae MDR isolates (n = 22), blaNDM (14; 64%) was the most prevalent carbapenemase, followed by blaOXA-48 (11; 50%) and blaVIM (4; 18%). A significant association (p value < 0.05) was observed between the multidrug efflux pump (AcrA) and resistance to β-lactams and the aminoglycoside acetyl transferase gene (aac-6’-Ib) gene and resistance to ciprofloxacin, azithromycin and β-lactams (except for aztreonam). For P. aeruginosa, a significant association was noticed between the presence of the blaSHV gene and the multidrug efflux pump (MexA) and resistance to fluoroquinolones, amikacin, tobramycin, co-trimoxazole and β-lactams and between the aac-6’-Ib gene and resistance to aminoglycosides. All P. aeruginosa isolates (100%) harbored the MexAB-OprM multidrug efflux pump while 86% of the K. pneumoniae isolates harbored the AcrAB-TolC pump. Our results are of great medical importance for the guidance of healthcare practitioners for effective antibiotic prescription.
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Rytter H, Jamet A, Coureuil M, Charbit A, Ramond E. Which Current and Novel Diagnostic Avenues for Bacterial Respiratory Diseases? Front Microbiol 2020; 11:616971. [PMID: 33362754 PMCID: PMC7758241 DOI: 10.3389/fmicb.2020.616971] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Bacterial acute pneumonia is responsible for an extremely large burden of death worldwide and diagnosis is paramount in the management of patients. While multidrug-resistant bacteria is one of the biggest health threats in the coming decades, clinicians urgently need access to novel diagnostic technologies. In this review, we will first present the already existing and largely used techniques that allow identifying pathogen-associated pneumonia. Then, we will discuss the latest and most promising technological advances that are based on connected technologies (artificial intelligence-based and Omics-based) or rapid tests, to improve the management of lung infections caused by pathogenic bacteria. We also aim to highlight the mutual benefits of fundamental and clinical studies for a better understanding of lung infections and their more efficient diagnostic management.
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Affiliation(s)
- Héloïse Rytter
- Université de Paris, Paris, France.,INSERM U1151, Institut Necker-Enfants Malades. Team 7, Pathogenesis of Systemic Infections, Paris, France.,CNRS UMR 8253, Paris, France
| | - Anne Jamet
- Université de Paris, Paris, France.,INSERM U1151, Institut Necker-Enfants Malades. Team 7, Pathogenesis of Systemic Infections, Paris, France.,CNRS UMR 8253, Paris, France.,Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Centre Université de Paris, Paris, France
| | - Mathieu Coureuil
- Université de Paris, Paris, France.,INSERM U1151, Institut Necker-Enfants Malades. Team 7, Pathogenesis of Systemic Infections, Paris, France.,CNRS UMR 8253, Paris, France
| | - Alain Charbit
- Université de Paris, Paris, France.,INSERM U1151, Institut Necker-Enfants Malades. Team 7, Pathogenesis of Systemic Infections, Paris, France.,CNRS UMR 8253, Paris, France
| | - Elodie Ramond
- Université de Paris, Paris, France.,INSERM U1151, Institut Necker-Enfants Malades. Team 7, Pathogenesis of Systemic Infections, Paris, France.,CNRS UMR 8253, Paris, France
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