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Su HC, Chang YC, Chen CH, Cheng MY, Hsih WH, Chen YJ, Chou CH, Lin YC, Hsiao CT, Shih HM, Ho MW, Hsueh PR. Unveiling the dynamics of respiratory infections revealed by multiplex PCR testing during the COVID-19 pandemic in Taiwan, 2020-2023. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00147-6. [PMID: 39179462 DOI: 10.1016/j.jmii.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND The emergence of SARS-CoV-2 in late 2019 sparked the global COVID-19 pandemic, leading to varied vaccine policies worldwide. The evolving patterns of respiratory pathogens, aside from SARS-CoV-2, during the pandemic have had a significant impact on the development of vaccine strategies. METHODS This study explores the landscape of respiratory pathogens, encompassing SARS-CoV-2, respiratory syncytial virus (RSV), and influenza viruses, through a retrospective analysis of data obtained from the BioFire Respiratory Panel 2.1 (RP 2.1) at China Medical University Hospital (Taichung, Taiwan) spanning from January 2020 to November 2023. RESULTS Among the 7950 respiratory samples studied, pediatric cases exhibited higher positivity (64.9%, 2488/3835) and mixed detection rates (43.8%, 1090/2488) than adults. Annual mixed detection rates increased (27.9-48%). Prevalence analysis revealed diverse patterns across age groups, with higher rates in pediatrics. Notably, human rhinovirus/enterovirus predominated (48.1%). Mixed detection illustrated viral co-detections, notably with parainfluenza viruses and adenovirus. Government policies and pandemic dynamics influenced infection patterns, with RSV resurgence after May 2022. Age-specific RSV detection demonstrated a shift, influencing vaccine considerations. Amid global vaccine initiatives, RSV's increasing trend in adults warrants attention. CONCLUSIONS This comprehensive analysis emphasizes the importance of multiplex PCR testing in shaping targeted vaccination strategies during evolving respiratory pathogen landscapes.
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Affiliation(s)
- Hung-Chieh Su
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Chang Chang
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chih-Hao Chen
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Meng-Yu Cheng
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Wen-Hsin Hsih
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yi-Jhen Chen
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chia-Huei Chou
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Chao Lin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan
| | - Chiung-Tzu Hsiao
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Hong-Mo Shih
- School of Medicine, China Medical University, Taichung, Taiwan; Department of Emergency Medicine, China Medical University Hospital, Taichung, Taiwan; Department of Public Health, China Medical University, Taichung, Taiwan
| | - Mao-Wang Ho
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan.
| | - Po-Ren Hsueh
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan.
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Merida Vieyra J, De Colsa Ranero A, Palacios Reyes D, Murata C, Aquino Andrade A. Chlamydophila pneumoniae-associated community-acquired pneumonia in paediatric patients of a tertiary care hospital in Mexico: molecular diagnostic and clinical insights. Sci Rep 2023; 13:21477. [PMID: 38052876 PMCID: PMC10698025 DOI: 10.1038/s41598-023-48701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023] Open
Abstract
Chlamydophila pneumoniae is a cause of community-acquired pneumonia (CAP) and responsible for 1-2% of cases in paediatric patients. In Mexico, information on this microorganism is limited. The aim of this study was to detect C. pneumoniae using two genomic targets in a real-time PCR and IgM/IgG serology assays in paediatric patients with CAP at a tertiary care hospital in Mexico City and to describe their clinical characteristics, radiological features, and outcomes. A total of 154 hospitalized patients with diagnosis of CAP were included. Detection of C. pneumoniae was performed by real-time PCR of the pst and arg genes. Complete blood cell count, C-reactive protein measurement and IgM and IgG detection were performed. Clinical-epidemiological and radiological data from the patients were collected. C. pneumoniae was detected in 25 patients (16%), of whom 88% had underlying disease (P = 0.014). Forty-eight percent of the cases occurred in spring, 36% in girls, and 40% in children older than 6 years. All patients had cough, and 88% had fever. Interstitial pattern on chest-X-ray was the most frequent (68%), consolidation was observed in 32% (P = 0.002). IgM was positive in 7% and IgG in 28.6%. Thirty-six percent presented complications. Four percent died. A high proportion showed co-infection with Mycoplasma pneumoniae (64%). This is the first clinical report of C. pneumoniae as a cause of CAP in Mexican paediatric patients, using two genomic target strategy and serology. We found a frequency of 16.2% with predominance in children under 6 years of age. In addition; cough and fever were the most common symptoms. Early detection of this pathogen allows timely initiation of specific antimicrobial therapy to reduce development of complications. This study is one of the few to describe the presence of C. pneumoniae in patients with underlying diseases.
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Affiliation(s)
- Jocelin Merida Vieyra
- Laboratory of Molecular Microbiology, Instituto Nacional de Pediatria, Insurgentes Sur 3700C, Insurgentes Cuicuilco, Coyoacan, 04530, Mexico City, Mexico
| | - Agustín De Colsa Ranero
- Department of Paediatric Infectious Diseases, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Deborah Palacios Reyes
- Department of Paediatric Infectious Diseases, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Chiharu Murata
- Department of Research Methodology, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Alejandra Aquino Andrade
- Laboratory of Molecular Microbiology, Instituto Nacional de Pediatria, Insurgentes Sur 3700C, Insurgentes Cuicuilco, Coyoacan, 04530, Mexico City, Mexico.
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Evaluation of the MAScIR SARS-CoV-2 M Kit 2.0 on the SARS-CoV-2 Infection. Adv Virol 2023; 2023:9313666. [PMID: 36816885 PMCID: PMC9929027 DOI: 10.1155/2023/9313666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 12/16/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 is a major public health problem worldwide. Since its emergence, several diagnostic kits have been developed to ensure rapid patient management. The aim of our study is to check the performance of the new Moroccan SARS-CoV-2 detection kit: MAScIR SARS-CoV-2 M 2.0. The following parameters were studied: repeatability, reproducibility, analytical specificity, analytical sensitivity, and comparison with the GeneFinder™ COVID-19 Plus RealAmp Kit. In addition, an external quality evaluation comprising five specimens was carried out as part of an international program for the external quality evaluation of sublaboratories of the WHO and the Laboratory Office of the National Institute of Hygiene of Morocco. The results of all parameters studied showed an analytical performance that complied with the requirements of the method verification/validation protocol adopted by the Central Laboratory of Virology and met the recommendations of COFRAC (French Accreditation Committee). During the current study, the sequencing of some randomly selected positive samples was performed, among which the carriers of the Alpha variant, the Delta variant, and the Omicron variant were detected. These results allowed us to deduce that this kit was valid for detecting these three variants.
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Distribution of Viral Respiratory Infections during the COVID-19 Pandemic Using the FilmArray Respiratory Panel. Biomedicines 2022; 10:biomedicines10112734. [DOI: 10.3390/biomedicines10112734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
This study was conducted to evaluate the distribution of respiratory viral pathogens in the emergency department during the coronavirus disease 2019 (COVID-19) pandemic. Between May 2020 and September 2022, patients aged between 0.1 and 98 years arrived at the emergency department of Asia University Hospital, and samples from nasopharyngeal swabs were tested by the FilmArrayTM Respiratory Panel (RP). SARS-CoV-2 positivity was subsequently retested by the cobas Liat system. There were 804 patients for whom the FilmArrayTM RP was tested, and 225 (27.9%) of them had positive results for respiratory viruses. Rhinovirus/enterovirus was the most commonly detected pathogen, with 170 (61.8%) cases, followed by adenovirus with 38 (13.8%), SARS-CoV-2 with 16 (5.8%) cases, and coronavirus 229E, with 16 (5.8%) cases. SARS-CoV-2 PCR results were positive in 16 (5.8%) cases, and there were two coinfections of SARS-CoV-2 with adenovirus and rhinovirus/enterovirus. A total of 43 (5.3%) patients were coinfected; the most coinfection was adenovirus plus rhinovirus/enterovirus, which was detectable in 18 (41.9%) cases. No atypical pathogens were found in this study. Intriguingly, our results showed that there was prefect agreement between the detection of SARS-CoV-2 conducted with the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test and the FilmArrayTM RP. Therefore, the FilmArrayTM RP assay is a reliable and feasible method for the detection of SARS-CoV-2. In summary, FilmArrayTM RP significantly broadens our capability to detect multiple respiratory infections due to viruses and atypical bacteria. It provides a prompt evaluation of pathogens to enhance patient care and clinical selection strategies in emergency departments during the COVID-19 pandemic.
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El‐Deeb AA, Zablotskaya SS, Rubel MS, Nour MAY, Kozlovskaya LI, Shtro AA, Komissarov AB, Kolpashchikov DM. Toward a Home Test for COVID-19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples. ChemMedChem 2022; 17:e202200382. [PMID: 36031581 PMCID: PMC9538286 DOI: 10.1002/cmdc.202200382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Indexed: 11/08/2022]
Abstract
Nucleic acid-based detection of RNA viruses requires an annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structures of folded viral RNA. In this study, we designed a protein-enzyme-free nano-construction, named four-armed DNA machine (4DNM), that requires neither an amplification stage nor a high-temperature annealing step for SARS-CoV-2 detection. It uses a binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with a total of four RNA-binding arms. Additional arms were found to improve the limit of detection at least 10-fold. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for the detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.
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Affiliation(s)
- Ahmed A. El‐Deeb
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Sofia S. Zablotskaya
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Maria S. Rubel
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Moustapha A. Y. Nour
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Liubov I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological ProductsRussian Academy of SciencesInstitute of PoliomyelitisMoscowRussia
| | - Anna A. Shtro
- Smorodintsev Research Institute of Influenza197376Saint PetersburgRussia
| | | | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
- Chemistry DepartmentUniversity of Central FloridaOrlandoFL 32816USA
- Burnett School of Biomedical SciencesUniversity of Central FloridaOrlandoFL 32827USA
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Calderaro A, Buttrini M, Farina B, Montecchini S, De Conto F, Chezzi C. Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays. Microorganisms 2022; 10:microorganisms10091856. [PMID: 36144458 PMCID: PMC9504108 DOI: 10.3390/microorganisms10091856] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in diagnostics to provide adequate and prompt management of patients. The current algorithm for the laboratory diagnosis of RTIs relies on multiple approaches including gold-standard conventional methods, among which the traditional culture is the most used, and innovative ones such as molecular methods, mostly used to detect viruses and atypical bacteria. The implementation of molecular methods with syndromic panels has the potential to be a powerful decision-making tool for patient management despite requiring appropriate use of the test in different patient populations. Their use radically reduces time-to-results and increases the detection of clinically relevant pathogens compared to conventional methods. Moreover, if implemented wisely and interpreted cautiously, syndromic panels can improve antimicrobial use and patient outcomes, and optimize laboratory workflow. In this review, a narrative overview of the main etiological, clinical, and epidemiological features of RTI is reported, focusing on the laboratory diagnosis and the potentialities of syndromic panels.
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Chang YC, Hsiao CT, Chen WL, Su YD, Hsueh PR. BioFire FilmArray respiratory panel RP2.1 for SARS-CoV-2 detection: The pitfalls. J Infect 2022; 85:e149-e151. [PMID: 35952904 PMCID: PMC9359754 DOI: 10.1016/j.jinf.2022.07.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Yu-Chang Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chiung-Tzu Hsiao
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Wan-Li Chen
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yang-Di Su
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan.
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