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Claas ECJ, Rezek Y, Sterk L, Russcher A, Verhees FB, Heijne-Tol A, Smits PHM, Nijhuis RHT. Diagnosing viral gastro-enteritis using the fully automated sample-in, result-out STARlet All in one system (AIOS). J Virol Methods 2024; 329:114985. [PMID: 38878870 DOI: 10.1016/j.jviromet.2024.114985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
The STARlet All-In-One system is a modular platform that integrates the complete molecular diagnostic workflow from nucleic acid extraction of clinical samples to PCR set-up and amplification. The platform was evaluated in comparison with laboratory developed tests (LDT) on fecal samples from patients with suspected viral gastro-enteritis. In a retrospective study, 72 positive samples were analysed, including all pathogens detected by the Seegene Allplex™ GI-virus assay, adenovirus, astrovirus, norovirus GI and GII, sapovirus, and rotavirus. Concordant results were obtained for 69 samples (96 %). Three discordant results were observed, one norovirus GII positive that gave an invalid result in the AIOS and two samples that were negative in the AIOS. One adenovirus positive that was subtyped as a genotype 2 virus, which is not associated with gastro-enteritis, and a sapovirus. In the prospective part of the study, 661 fecal samples were included. A total of 61 positive samples were detected, of which 60 were also detected by the AIOS. One norovirus GII positive sample (CT 35.2) was tested negative in the AIOS. Two additional sapovirus positive samples, CT 37 and 38, were detected by the AIOS but not by the LDT. The STARlet All-In-One platforms results in an automated molecular workflow with reduced hands-on time and enables running assays during out of office hours. Application of the Seegene Allplex™ GI-virus assay showed excellent concordance to the current diagnostic LDT. In a prospective comparison, only three discordant results were observed, all with CT values over 35 and therefore unlikely of clinical relevance.
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Affiliation(s)
- Eric C J Claas
- Center for Infectious Diseases - Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, the Netherlands.
| | - Youssef Rezek
- Laboratory for Medical Microbiology and Immunology, Meander Medical Center, Amersfoort, the Netherlands
| | - Luuk Sterk
- Center for Infectious Diseases - Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne Russcher
- Laboratory for Medical Microbiology and Immunology, Meander Medical Center, Amersfoort, the Netherlands
| | - Fabienne B Verhees
- Center for Infectious Diseases - Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, the Netherlands
| | - Anja Heijne-Tol
- Laboratory for Medical Microbiology, Atal-medial, Amsterdam, the Netherlands
| | - Paul H M Smits
- Laboratory for Medical Microbiology, Atal-medial, Amsterdam, the Netherlands
| | - Roel H T Nijhuis
- Laboratory for Medical Microbiology and Immunology, Meander Medical Center, Amersfoort, the Netherlands
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Maldonado-Garza HJ, Garza-González E, Bocanegra-Ibarias P, Flores-Treviño S. Diagnostic syndromic multiplex approaches for gastrointestinal infections. Expert Rev Gastroenterol Hepatol 2021; 15:743-757. [PMID: 33682566 DOI: 10.1080/17474124.2021.1899807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: Gastrointestinal diseases due to infectious pathogens currently represent an important global health concern, especially in children and developing countries. Early and accurate detection of gastrointestinal pathogens is important to initiate the appropriate type of therapy. Multiplex molecular gastrointestinal panels rapidly detect several gastrointestinal pathogens at once with high sensitivity.Areas covered: We assess the scope and limitations of several multiplex gastrointestinal panels approved by the Food and Drug Administration or marked by Conformité Européenne-in vitro diagnostic. We compare 10 syndromic gastrointestinal panels, 14 bacteria-specific multiplex panels, seven parasite-specific multiplex panels, and eight virus-specific multiplex panels.Expert opinion: Thanks to the advances made in the diagnostic approaches for gastrointestinal infections, there are various panels to choose. The choice of a specific syndromic gastrointestinal multiplex panel should be made to improve patient care. Diagnostic syndromic multiplex approaches for gastrointestinal infections should be customized; each hospital should develop its diagnostic algorithm for gastrointestinal infections tailored to its setting, study population, and geographical site. Current multiplex gastrointestinal panels could be improved by including the detection of antimicrobial resistance, toxigenic Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus responsible for the COVID-19 pandemic).
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Affiliation(s)
- Héctor Jesús Maldonado-Garza
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Paola Bocanegra-Ibarias
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Samantha Flores-Treviño
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
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Singh S, Kumar V, Kapoor D, Dhanjal DS, Bhatia D, Jan S, Singh N, Romero R, Ramamurthy PC, Singh J. Detection and disinfection of COVID-19 virus in wastewater. ENVIRONMENTAL CHEMISTRY LETTERS 2021; 19:1917-1933. [PMID: 33642964 PMCID: PMC7898499 DOI: 10.1007/s10311-021-01202-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 05/20/2023]
Abstract
The coronavirus disease 2019, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, appears as a major pandemic having adverse impact on public health and economic activities. Since viral replication in human enterocytes results in its faecal shedding, wastewater surveillance is an ideal, non-invasive, cost-effective and an early warning epidemiological approach to detect the genetic material of SARS-CoV-2. Here, we review techniques for the detection of SARS-CoV-2 in municipal wastewater, and disinfectants used to control viral spread. For detection, concentration of ribonucleic acid involves ultrafiltration, ultracentrifugation and polyethylene glycol precipitation. Identification is done by reverse transcriptase amplification, nucleic acid sequence-based amplification, helicase dependent amplification, loop-mediated isothermal amplification, recombinase polymerase amplification, high throughput screening and biosensor assays. Disinfectants include ultraviolet radiations, ozone, chlorine dioxide, hypochlorites and hydrogen peroxide. Wastewater surveillance data indicates viral presence within longer detection window, and provides transmission dynamics earlier than classical methods. This is particularly relevant for pre-symptomatic and asymptomatic COVID-19 cases.
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Affiliation(s)
- Simranjeet Singh
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, 560012 India
| | - Vijay Kumar
- Regional Ayurveda Research Institute for Drug Development, Gwalior, MP 474009 India
| | - Dhriti Kapoor
- Department of Botany, Lovely Professional University, Phagwara, Punjab 144411 India
| | - Daljeet Singh Dhanjal
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab 144411 India
| | - Deepika Bhatia
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab 144411 India
| | - Sadaf Jan
- Department of Botany, Lovely Professional University, Phagwara, Punjab 144411 India
| | - Nasib Singh
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Himachal Pradesh 173101 India
| | - Romina Romero
- Laboratorio de Investigaciones Medioambientales de Zonas Áridas (LIMZA), Depto. Ingeniería Mecánica, Facultad de Ingeniería, Universidad de Tarapacá, Iquique, Chile
| | - Praveen C. Ramamurthy
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, 560012 India
| | - Joginder Singh
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab 144411 India
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Mitra S, Nayak MK, Majumdar A, Sinha A, Chatterjee S, Deb A, Chawla-Sarkar M, Dutta S. Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis. Diagn Microbiol Infect Dis 2020; 97:115061. [PMID: 32585545 DOI: 10.1016/j.diagmicrobio.2020.115061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/27/2020] [Accepted: 04/12/2020] [Indexed: 12/11/2022]
Abstract
Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.
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Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | | | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Avisek Sinha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Soumyadipta Chatterjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Alok Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
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Sciandra I, Piccioni L, Coltella L, Ranno S, Giannelli G, Falasca F, Antonelli G, Concato C, Turriziani O. Comparative analysis of 2 commercial molecular tests for the detection of gastroenteric viruses on stool samples. Diagn Microbiol Infect Dis 2019; 96:114893. [PMID: 31677959 DOI: 10.1016/j.diagmicrobio.2019.114893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/14/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Our purpose was to compare the performance of 2 recently introduced molecular tests for the identification of gastrointestinal viral infections. METHODS One hundred fecal samples from pediatric patients were analyzed using 2 workflows, each including nucleic acids extraction and multiplex Real-Time PCR: Allplex™ GI-Virus Assay and FTD Viral gastroenteritis. The agreement was evaluated calculating Cohen's kappa and applying McNemar's test. RESULTS AND CONCLUSION Allplex and FTD assays showed 100% overall agreement for Norovirus GI/GII and Sapovirus (κ: 1.00), and 99% for Astrovirus (κ: 0.66). A lower agreement was detected for Adenovirus (89%; κ: 0.72) and Rotavirus (91%, k: 0.53), owing to samples resulted positive only with FTD test. The discrepancies were attributed to a different efficiency of extraction/amplification and to the different Adenovirus serotype specificity of the tests since Allplex detects only AdVF40 and AdVF41. FTD test should be used when non enteric adenovirus could have a clinical significance.
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Affiliation(s)
- I Sciandra
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - L Piccioni
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - L Coltella
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - S Ranno
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - G Giannelli
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - F Falasca
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - G Antonelli
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - C Concato
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - O Turriziani
- Department of Molecular Medicine, Sapienza University, Rome, Italy.
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