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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Peterson A, Richins T, Houghton K, Mishina M, Sharma S, Sambhara S, Jacobson D, Qvarnstrom Y, Cama V. The limit of detection of the BioFire® FilmArray® gastrointestinal panel for the foodborne parasite Cyclospora cayetanensis. Diagn Microbiol Infect Dis 2023; 107:116030. [PMID: 37572510 PMCID: PMC10530562 DOI: 10.1016/j.diagmicrobio.2023.116030] [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: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/15/2023] [Indexed: 08/14/2023]
Abstract
Cyclosporiasis is a foodborne diarrheal illness caused by the parasite Cyclospora cayetanensis. The BioFire® FilmArray® gastrointestinal (FilmArray GI) panel is a common method for diagnosing cyclosporiasis from clinical stool samples. The currently published limit of detection (LOD) of this panel is in genome equivalents; however, it is unclear how this relates to the number of C. cayetanensis oocysts in a clinical sample. In this study, we developed a technique to determine the LOD in terms of oocysts, using a cell sorter to sort 1 to 50 C. cayetanensis oocyst(s) previously purified from three human stool sources. We found the FilmArray GI panel detected samples with ≥20 C. cayetanensis oocysts in 100% of replicates, with varying detection among samples with 1, 5, or 10 C. cayetanensis oocysts. This method provides a parasitologically relevant LOD that should enable comparison among C. cayetanensis detection techniques, including the FilmArray GI panel.
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Affiliation(s)
- Anna Peterson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA.
| | - Travis Richins
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Katelyn Houghton
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Margarita Mishina
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - Suresh Sharma
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - David Jacobson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Vitaliano Cama
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
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Carmon D, Rohana H, Azrad M, Peretz A. The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes. Diagnostics (Basel) 2023; 13:diagnostics13061094. [PMID: 36980402 PMCID: PMC10046972 DOI: 10.3390/diagnostics13061094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The gold standard diagnostic method for gastrointestinal infections is stool culture, which has limited sensitivity and long turnaround time. Infection diagnosis recently shifted to syndrome-based panel assays. This study employed the FilmArray® Gastrointestinal Panel, which detects 22 pathogens simultaneously, to investigate gastrointestinal infection and pathogen distribution in 91 stool samples of patients hospitalized at the Tzafon Medical Center, Israel, during 2020, and to compare the clinical and demographic data of negative vs. positive samples. Among the 61 positive samples (67%), the most common pathogen was Campylobacter (34.4%). Positive test results were associated with a slightly younger patient age (p = 0.012), significantly higher post-diagnosis use of antibiotics (63.9% vs. 36.7%; p = 0.014), and shorter length of stay and time to discharge (p = 0.035, p = 0.003, respectively) than negative test results. To conclude, the FilmArray® Gastrointestinal Panel enabled the early identification of causative infectious agents and enhanced clinical management and outcomes.
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Affiliation(s)
- David Carmon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Hanan Rohana
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
| | - Maya Azrad
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
| | - Avi Peretz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
- Correspondence: ; Tel.: +972-4-665-2322
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Cai H, Shao Y, Yu W. Prevalence and associated factors of acute gastroenteritis in children and adolescents aged from 6 to 17 years old: a cross-sectional study based on the National Health and Nutrition Examination Survey database 1999-2018. BMJ Open 2023; 13:e068319. [PMID: 36822803 PMCID: PMC9950896 DOI: 10.1136/bmjopen-2022-068319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
OBJECTIVE To explore the prevalence of acute gastroenteritis (AGE) and associated factors in children and adolescents in the USA from 1999 to 2018 using nationally representative data. DESIGN A retrospective cross-sectional study. SETTING The National Health and Nutrition Examination Survey (NHANES) database. PARTICIPANTS 25 361 children and adolescents aged 6-17 years old. PRIMARY AND SECONDARY OUTCOME MEASURES Whether the patient suffered from AGE. RESULTS Totally 1882 suffered from AGE. The overall monthly prevalence of AGE in children and adolescents was 7.69%. From 1999 to 2018, the prevalence of AGE in the USA had been decreasing over time. The decreasing trend was observed in all subgroups, including age, gender, body mass index (BMI), education level, poverty index and eating food at the restaurant. There were two small upticks from 2003 to 2007 and 2013 to 2015. AGE was negatively associated with male compared with female (OR=0.86, 95% CI: 0.73 to 0.99, p=0.035), Mexican American (OR=0.82, 95% CI: 0.70 to 0.97, p=0.018) and non-Hispanic Black (OR=0.80, 95% CI: 0.69 to 0.93, p=0.003) compared with non-Hispanic White. AGE was positively associated with obesity compared with underweight and normal weight (OR=1.37, 95% CI: 1.15 to 1.62, p<0.001). CONCLUSION The monthly prevalence of AGE was 7.69% and showed a downward trend from 1999 to 2018 in the USA.
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Affiliation(s)
- Hailun Cai
- Department of Pediatric, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanyan Shao
- Department of Pediatric, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weihao Yu
- Department of Pediatric, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Chiu SC, Hu SC, Liao LM, Chen YH, Liao HW, Cheng JC, Lin JH. Evaluation of a New Norovirus Genogroups GI and GII In Vitro Molecular Diagnostic Assay Using Clinical Specimens Collected from Acute Diarrheal Outbreaks. Foodborne Pathog Dis 2022; 19:311-315. [PMID: 35404143 DOI: 10.1089/fpd.2021.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Norovirus is a leading cause of acute gastroenteritis (AGE) in Taiwan. To improve diagnosis as part of laboratory surveillance, AGE surveillance was conducted using a new fluorescent probe hydrolysis-based insulated isothermal polymerase chain reaction (PCR) method, the POCKIT system, and the results were compared with those obtained from conventional methods. A total of 119 clinical stool samples from reported AGE outbreaks were collected for this study. From 83 real-time reverse transcription PCR (rRT-PCR) norovirus-positive cases, the POCKIT system identified 78 with a sensitivity of 90.3% in GI genogroup and 96.7% in GII genogroup. The specificity for both GI and GII genogroups was 100%. Overall, the POCKIT system is faster and easier to use than the conventional rRT-PCR method, and because of its high sensitivity and specificity, this system is a promising alternative for the detection of norovirus in patients with AGE, and would benefit public health laboratories for near real-time surveillance of AGE epidemic outbreaks.
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Affiliation(s)
- Shu-Chun Chiu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Szu-Chieh Hu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ling-Min Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Yu-Hua Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Hui-Wen Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jih-Hui Lin
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
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Teh R, Tee WD, Tan E, Fan K, Koh CJ, Tambyah PA, Oon J, Tee N, Soh AYS, Siah KTH. Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness. J Gastroenterol Hepatol 2021; 36:3286-3297. [PMID: 34129249 DOI: 10.1111/jgh.15581] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 01/25/2023]
Abstract
Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.
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Affiliation(s)
- Readon Teh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore
| | - Wei De Tee
- Division of Gastroenterology and Hepatology, Ng Teng Fong General Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eunice Tan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kristie Fan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Calvin Jianyi Koh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul Ananth Tambyah
- Division of Infectious Diseases, National University Hospital, Singapore.,Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jolene Oon
- Division of Infectious Diseases, National University Hospital, Singapore
| | - Nancy Tee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Alex Yu Sen Soh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kewin Tien Ho Siah
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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7
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Wang N, Pan G, Liu P, Rong S, Gao Z, Li Q. Advances and Future Perspective on Detection Technology of Human Norovirus. Pathogens 2021; 10:pathogens10111383. [PMID: 34832539 PMCID: PMC8618740 DOI: 10.3390/pathogens10111383] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Human norovirus (HuNoV) is a food-borne pathogen that causes acute gastroenteritis in people of all ages worldwide. However, no approved vaccines and antiviral drugs are available at present. Therefore, the development of accurate and rapid detection technologies is important in controlling the outbreak of HuNoVs. This paper reviewed the research progress on HuNoV detection, including immunological methods, molecular detection and biosensor technology. Immunological methods and molecular detection technologies are still widely used for HuNoV detection. Furthermore, biosensors will become an emerging developmental direction for the rapid detection of HuNoVs because of their high sensitivity, low cost, easy operation and suitability for onsite detection.
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Affiliation(s)
- Nan Wang
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai 201418, China; (N.W.); (G.P.); (P.L.); (S.R.)
| | - Guiying Pan
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai 201418, China; (N.W.); (G.P.); (P.L.); (S.R.)
| | - Ping Liu
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai 201418, China; (N.W.); (G.P.); (P.L.); (S.R.)
| | - Shaofeng Rong
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai 201418, China; (N.W.); (G.P.); (P.L.); (S.R.)
| | - Zhiyong Gao
- Beijing Research Center for Preventive Medicine, Beijing Center for Disease Prevention and Control, Beijing 100013, China;
| | - Qianqian Li
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai 201418, China; (N.W.); (G.P.); (P.L.); (S.R.)
- Correspondence: ; Tel.: +86-21-60873381
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8
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Ghapoutsa RN, Boda M, Gautam R, Ndze VN, Mugyia AE, Etoa FX, Bowen MD, Esona MD. Detection of diarrhoea associated rotavirus and co-infection with diarrhoeagenic pathogens in the Littoral region of Cameroon using ELISA, RT-PCR and Luminex xTAG GPP assays. BMC Infect Dis 2021; 21:614. [PMID: 34182936 PMCID: PMC8237514 DOI: 10.1186/s12879-021-06318-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Background Despite the global roll-out of rotavirus vaccines (RotaTeq/Rotarix / ROTAVAC/Rotasiil), mortality and morbidity due to group A rotavirus (RVA) remains high in sub-Saharan Africa, causing 104,000 deaths and 600,000 hospitalizations yearly. In Cameroon, Rotarix™ was introduced in March 2014, but, routine laboratory diagnosis of rotavirus infection is not yet a common practice, and vaccine effectiveness studies to determine the impact of vaccine introduction have not been done. Thus, studies examining RVA prevalence post vaccine introduction are needed. The study aim was to determine RVA prevalence in severe diarrhoea cases in Littoral region, Cameroon and investigate the role of other diarrheagenic pathogens in RVA-positive cases. Methods We carried out a study among hospitalized children < 5 years of age, presenting with acute gastroenteritis in selected hospitals of the Littoral region of Cameroon, from May 2015 to April 2016. Diarrheic stool samples and socio-demographic data including immunization and breastfeeding status were collected from these participating children. Samples were screened by ELISA (ProSpecT™ Rotavirus) for detection of RVA antigen and by gel-based RT-PCR for detection of the VP6 gene. Co-infection was assessed by multiplexed molecular detection of diarrheal pathogens using the Luminex xTAG GPP assay. Results The ELISA assay detected RVA antigen in 54.6% (71/130) of specimens, with 45, positive by VP6 RT-PCR and 54, positive using Luminex xTAG GPP. Luminex GPP was able to detect all 45 VP6 RT-PCR positive samples. Co-infections were found in 63.0% (34/54) of Luminex positive RVA infections, with Shigella (35.3%; 12/34) and ETEC (29.4%; 10/34) detected frequently. Of the 71 ELISA positive RVA cases, 57.8% (41/71) were fully vaccinated, receiving two doses of Rotarix. Conclusion This study provides insight on RVA prevalence in Cameroon, which could be useful for post-vaccine epidemiological studies, highlights higher than expected RVA prevalence in vaccinated children hospitalized for diarrhoea and provides the trend of RVA co-infection with other enteric pathogens. RVA genotyping is needed to determine circulating rotavirus genotypes in Cameroon, including those causing disease in vaccinated children.
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Affiliation(s)
- Rahinatou N Ghapoutsa
- Department of Biochemistry, Faculty of Science, The University of Yaoundé 1, Yaoundé, Cameroon
| | - Maurice Boda
- Department of Microbiology, Faculty of Science, The University of Yaoundé 1, Yaoundé, Cameroon.
| | - Rashi Gautam
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | | | - Akongnwi E Mugyia
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Francois-Xavier Etoa
- Department of Microbiology, Faculty of Science, The University of Yaoundé 1, Yaoundé, Cameroon
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Mathew D Esona
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
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9
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Atabakhsh P, Kargar M, Doosti A. Detection and evaluation of rotavirus surveillance methods as viral indicator in the aquatic environments. Braz J Microbiol 2021; 52:811-820. [PMID: 33599964 PMCID: PMC8105488 DOI: 10.1007/s42770-020-00417-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
Group A rotaviruses (RVAs) have been introduced as the most important causative agents of acute gastroenteritis in the young children. One of every 260 children born globally will die due to rotavirus (RV) before 5 years old. The RV is widely known as a viral indicator for health (fecal contamination) because this pathogen has a high treatment resistance nature, which has been listed as a relevant waterborne pathogen by the World Health Organization (WHO). Therefore, monitoring of environmental is important, and RV is one of the best-known indicators for monitoring. It has been proved that common standards for microbiological water quality do not guarantee the absence of viruses. On the other hand, in order to recover and determine RV quantity within water, standard methods are scarce. Therefore, dependable prediction of RV quantities in water sample is crucial to be able to improve supervision efficiency of the treatment procedure, precise quantitative evaluation of the microbial risks as well as microbiological water safety. Hence, this study aimed to introduce approaches to detecting and controlling RV in environmental waters, and discussed the challenges faced to enable a clear perception on the ubiquity of the RV within different types of water across the world.
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Affiliation(s)
- Paymaneh Atabakhsh
- Department of Microbiology, Isfahan Water and Wastewater Company, Isfahan, Iran
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mohammad Kargar
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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10
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Abstract
Viral acute gastroenteritis (AGE) is common and afflicts people of all ages. Nonviral causes of AGE are less common. Norovirus is a leading cause of sporadic cases and outbreaks of AGE across all ages. Universal rotavirus vaccination of infants has reduced frequency and severity of rotavirus AGE cases in children and indirectly reduced cases in older adults. Severe illness is more likely in persons at age extremes or with immunocompromising conditions. Viral causes of AGE can lead to protracted diarrheal illness in immunocompromised persons. Nucleic acid amplification tests are changing diagnostic testing algorithms.
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Affiliation(s)
- Jeffery L Meier
- Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City Veterans Affairs Healthcare System, SW34 GH, 200 Hawkins Dr., Iowa City, IA 52242, USA.
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11
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Incidence of enterovirus in patients with acute gastroenteritis. Eur J Clin Microbiol Infect Dis 2021; 40:2185-2190. [PMID: 33987803 DOI: 10.1007/s10096-021-04275-6] [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: 02/12/2021] [Accepted: 05/09/2021] [Indexed: 10/21/2022]
Abstract
Enteroviruses (EV) have been linked to lymphocytic meningitis and exanthems, but they may also be involved in acute gastroenteritis (AGE), a condition whose aetiological agent often remains unidentified. In this work 1214 samples from individuals with AGE were studied with the aim of establishing the incidence of EV. The samples were collected between September and December in three different years and subjected to real-time genomic amplification in order to determine the viral load (VL). Of the 1214 samples studied, infection by a single virus was found in 328 cases (27%) and coinfection in 69 (5.7%). While adenoviruses (AdV) were the most frequent (14.8% of total), EV were present in 126 (10.4%) of the individuals tested. Of the 126 EV-positive samples, this virus was found as a single infection and coinfection in 76 (6.3%) and 50 (4.1%) cases, respectively. VL for EV was 5.58±1.51 log copies/ml (range 3.73-9.69) in the former and 6.27±1.75 (range 3.73-10.5) (p=0.02) in the latter. EV were identified in 97 children under 5 (16.9%) and in 29 (4.5%) patients over 5. Patients less than 5 years showed a higher VL that those more than 5 years age [6.08±1.57 (range 3.82-9.69) vs. 5.07±1.53 (range 3.73-10.58); (p=0.002)]. There was a high incidence of EV in AGE patients, and they were more frequent in those under 5, where they were found to replicate more efficiently. These results therefore indicate that testing for EV should be included in the diagnosis of AGE.
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12
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Knee J, Sumner T, Adriano Z, Anderson C, Bush F, Capone D, Casmo V, Holcomb D, Kolsky P, MacDougall A, Molotkova E, Braga JM, Russo C, Schmidt WP, Stewart J, Zambrana W, Zuin V, Nalá R, Cumming O, Brown J. Effects of an urban sanitation intervention on childhood enteric infection and diarrhea in Maputo, Mozambique: A controlled before-and-after trial. eLife 2021; 10:e62278. [PMID: 33835026 PMCID: PMC8121544 DOI: 10.7554/elife.62278] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/03/2021] [Indexed: 12/12/2022] Open
Abstract
We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.
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Affiliation(s)
- Jackie Knee
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Trent Sumner
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | | | - Claire Anderson
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Farran Bush
- Georgia Institute of Technology, School of Chemical and Biomolecular EngineeringAtlantaUnited States
| | - Drew Capone
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | | | - David Holcomb
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of Environmental Sciences and EngineeringChapel HillUnited States
| | - Pete Kolsky
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Amy MacDougall
- London School of Hygiene & Tropical Medicine, Faculty of Epidemiology and Population Health, Department of Medical StatisticsLondonUnited Kingdom
| | - Evgeniya Molotkova
- Georgia Institute of Technology, School of Biological SciencesAtlantaUnited States
| | | | - Celina Russo
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Wolf Peter Schmidt
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Jill Stewart
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Winnie Zambrana
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Valentina Zuin
- Yale-NUS College, Division of Social ScienceSingaporeSingapore
| | | | - Oliver Cumming
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Joe Brown
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
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Chang LJ, Hsiao CJ, Chen B, Liu TY, Ding J, Hsu WT, Su-Ortiz V, Chen ST, Su KY, Wu HP, Lee CC. Accuracy and comparison of two rapid multiplex PCR tests for gastroenteritis pathogens: a systematic review and meta-analysis. BMJ Open Gastroenterol 2021; 8:bmjgast-2020-000553. [PMID: 33648983 PMCID: PMC7925250 DOI: 10.1136/bmjgast-2020-000553] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Objectives The primary aim is to provide a summary of evidence for the diagnostic accuracies of multiplex PCR gastrointestinal (GI) panels—BioFire FilmArray and Luminex xTAG on the detection of gastroenteritis pathogens. The secondary aim is to compare the performance of these GI panels head to head. Methods A comprehensive search up to 1 December 2019 was conducted on PubMed, Embase, Ovid Medline and Web of Science for studies that used FilmArray or Luminex xTAG Gastrointestinal Pathogen Panel (GPP) for diagnosis of acute gastroenteritis. A summary of diagnostic accuracies for the 16 pathogens were calculated by comparing the GI panels to the current gold standards (conventional standard microbiology techniques such as culture or PCR for bacteria, PCR or enzyme immunoassay (EIA) for viruses, microscopy or EIA for parasite). Hierarchical summary receiver operating characteristic (HSROC) curve analysis, pretest and post-test probabilities were used for estimating the pathogen detection performance. Results A total of 11 studies with 7085 stool samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with specificity ≧0.98 and area under the ROC curve (AUROC) ≧0.97 for all the pathogens except for Yersinia enterocolitica (AUROC 0.91). The FilmArray panel demonstrated a higher sensitivity than xTAG GPP for most of the pathogens with the exception of Rotavirus A (xTAG GPP and FilmArray were both 0.93). Conclusions This is the first meta-analysis that is a head-to-head comparison examining the performance of the novel multiplex PCR-based tests Luminex xTAG GPP and FilmArray GI panel in detecting each pathogen. Point estimates calculated from eligible studies showed that both GI panels are highly accurate and may provide important diagnostic information for early identification of gastroenteritis. In addition, although FilmArray has higher sensitivity and post-test probability than xTAG GPP for most of the pathogens, how this will translate to a clinical setting remains unclear.
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Affiliation(s)
- Li-Jun Chang
- Department of Medical Education, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Hsiao
- Department of Medical Education, National Taiwan University Hospital, Taipei, Taiwan
| | - Bing Chen
- Department of Medicine, Mount Sinai Morningside Hospital, New York, New York, USA
| | - Tzu-Yu Liu
- Department of Medicine, Brown University Warren Alpert Medical School, Providence, Rhode Island, USA
| | - Julia Ding
- Internal Medicine, Brown University Division of Biology and Medicine, Providence, Rhode Island, USA
| | - Wan-Ting Hsu
- Department of Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA.,Medical Wizdom, LLC, Brooklinw, MA, USA
| | - Victor Su-Ortiz
- Department of Medical Engineering, College of Engineering, Cornell University, Ithaca, New York, USA.,Department of Computer Science, College of Engineering, Cornell University, Ithaca, NY, USA
| | - Szu-Ta Chen
- Department of Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Ke-Ying Su
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Han-Ping Wu
- Department of Pediatric Emergency Medicine and Medical Research, China Medical University Children's Hospital, Taichung, Taiwan.,Department of Medicine, School of Medicine, China Medical University, Taichung, Taiwan
| | - Chien-Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan .,Center of Intelligent Healthcare, National Taiwan University Hospital, Taipei, Taiwan.,Byers Center for Biodesign, Stanford University, Stanford, CA, USA
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14
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Pedrosa de Macena LDG, Castiglia Feitosa R, Vieira CB, Araújo IT, Taniuchi M, Miagostovich MP. Microbiological assessment of an urban lagoon system in the coastal zone of Rio de Janeiro, Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:1170-1180. [PMID: 32839906 DOI: 10.1007/s11356-020-10479-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
This study aims to assess microbiological contamination using a molecular tool for detection of multiple enteropathogens in a coastal ecosystem area in Rio de Janeiro, Brazil. Ten litres of superficial water samples were obtained during the spring ebb tide from sampling sites along the Jacarepaguá watershed. Samples were concentrated using skimmed milk flocculation method for TaqMan array card (TAC), designed to identify 35 enteric pathogens simultaneously, and single TaqMan qPCR analysis for detecting human adenovirus (HAdV) and JC human polyomavirus (JCPyV) as faecal indicator viruses (FIV). TAC results identified 17 enteric pathogens including 4/5 viral species investigated, 8/15 bacteria, 4/6 protozoa and 1/7 helminths. Escherichia coli concentration was also measured as faecal indicator bacteria (FIB) using Colilert Quanti-Tray System with positivity in all samples studied. HAdV and JCPyV qPCR were detected in 8 and 4 samples, respectively, with concentration ranging from 8 × 102 to 2 × 106 genome copies/L. Partial nucleotide sequencing demonstrated the occurrence of species HAdV A, C, D, and F, present in faeces of individuals with enteric and non-enteric infections, and JCPyV type 3 (Af2), prevalent in a high genetically mixed population like the Brazilian. The diversity of enteropathogens detected by TAC emphasizes the utility of this methodology for quick assessment of microbiological contamination of the aquatic ecosystems, speeding up mitigation actions where the risk of the exposed population is detected, as well as pointing out the infrastructure gaps in areas where accelerated urban growth is observed.
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Affiliation(s)
- Lorena da Graça Pedrosa de Macena
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Helio e Peggy Pereira Pavilion, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil.
| | - Renato Castiglia Feitosa
- Department of Sanitation and Environmental Health, National School of Public Health (ENSP), Oswaldo Cruz Foundation (FIOCRUZ), Rua Leopoldo Bulhões, 1.480, Manguinhos, Rio de Janeiro, RJ, 21041-210, Brazil
| | - Carmen Baur Vieira
- Department of Microbiology and Parasitology (MIP), Biomedical Institute, Federal Fluminense University (UFF), Rua Professor Hernani Melo, 101, São Domingos, Niterói, RJ, 24210-130, Brazil
| | - Irene Trigueiros Araújo
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Helio e Peggy Pereira Pavilion, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, VA, 22903, USA
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Helio e Peggy Pereira Pavilion, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil
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15
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Chhabra P, Browne H, Huynh T, Diez-Valcarce M, Barclay L, Kosek MN, Ahmed T, Lopez MR, Pan CY, Vinjé J. Single-step RT-PCR assay for dual genotyping of GI and GII norovirus strains. J Clin Virol 2020; 134:104689. [PMID: 33260046 PMCID: PMC7816162 DOI: 10.1016/j.jcv.2020.104689] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Noroviruses are the major cause of acute gastroenteritis (AGE) in people of all ages globally. Standardized genotyping is key for outbreak investigations and surveillance networks. OBJECTIVE Here we describe the validation of a one-step conventional RT-PCR assay for sequence-based dual typing of GI and GII noroviruses. This polymerase (P) and capsid (C) dual typing assay uses a combination of previously published oligonucleotide primers amplifying a genomic region spanning the 3'-end of ORF1 and 5'end of ORF2 resulting in a 579 bp product for GI and 570 bp product for GII viruses. RESULTS The limit of detection of the assay ranged from 5 to 50 copies of viral RNA per reaction for GI and GII. To validate the assay, we tested 2,663 noroviruspositive stool samples from outbreaks and sporadic cases of AGE in Bangladesh, Guatemala, Peru, and USA collected between 2010-2019, of which 2,392 (90 %) were genotyped successfully. Most of the known genotypes infecting humans (GI (n = 9) and GII (n = 23)) and P types (GI (n = 15), GII, (n = 20)) could be detected. The remaining 270 samples had low viral load (Ct > 30) by real-time RT-PCR. A panel of 166 samples positive for other enteric viruses (rotavirus, astrovirus, sapovirus, adenovirus type 40/41) tested negative. CONCLUSION The use of broadly reactive genotyping assays greatly strengthens exchange of standardized genotype data globally to monitor trends in genotype diversity which is important for both the development of vaccines and to measure their impact.
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Affiliation(s)
- Preeti Chhabra
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Hannah Browne
- National Foundation for the Centers for Disease Control and Prevention Inc., Atlanta, GA, USA
| | - Thalia Huynh
- California Department of Public Health, Richmond, CA, USA
| | | | - Leslie Barclay
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Margaret N Kosek
- University of Virginia Division of Infectious Diseases and International Health, Charlottesville, VA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Jan Vinjé
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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16
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Cleland A, Malloy K, Donnelly MC, Davidson J, Simpson KJ, Petrik J. Design and evaluation of Taqman low density array for monitoring post-transplant viral infections. Transpl Infect Dis 2020; 23:e13499. [PMID: 33118224 DOI: 10.1111/tid.13499] [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: 01/02/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND The majority of transplant recipients undergo immunosuppressive treatment to prevent organ or tissue rejection. Consequently, they are more susceptible to infection agents including a number of viruses causing a significant morbidity and mortality. Only a limited number of viruses are currently tested for in transplant donors and recipients due to the cost and complexity. Taqman low density array (TLDA) may provide a suitable format to address more systematic testing approach. METHODS One hundred and one liver transplant recipient samples were retrospectively tested for 48 viral targets including two controls (bovine viral diarrhea virus and MS2) and two common viruses (TTV and HPgV), using a custom designed TLDA. Eight samples were analysed simultaneously on 384-well TLDA. Samples giving a signal considered positive/indeterminant were re-tested by different individual confirmatory assays. RESULTS Infections with six previously untested for viruses-EBV, HPIV3, HuPuV9, KIV, HMPV and HPV-were detected in fourteen patients. Previously detected HCV infections were also confirmed. These infections did not seem have an effect on 5 year post-transplant outcome. 55 of 79 and 17 of 87 samples available for confirmatory assays were positive for TTV and HPgV, included for the evaluation of the TLDA performance. CONCLUSIONS The custom viral TLDA can be successfully used for simultaneous detection of a range of post-transplant viral infections. To fully exploit its potential for monitoring and intervention, a whole blood testing should be applied in a prospective setting.
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Affiliation(s)
- Alexander Cleland
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Kristen Malloy
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Mhairi C Donnelly
- Department of Hepatology, Division of Health Sciences, Edinburgh Medical School, Edinburgh, UK
| | - Janice Davidson
- Scottish Liver Transplantation Unit, Royal Infirmary, Edinburgh, UK
| | - Kenneth J Simpson
- Department of Hepatology, Division of Health Sciences, Edinburgh Medical School, Edinburgh, UK
| | - Juraj Petrik
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
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17
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Zhang X, Das S, Dunbar S, Tang YW. Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis. Adv Clin Chem 2020; 99:49-85. [PMID: 32951639 DOI: 10.1016/bs.acc.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.
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Affiliation(s)
- Xin Zhang
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China; Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States; Weill Medical College of Cornell University, New York, NY, United States; Cepheid, Danaher Diagnostic Platform, Shanghai, China.
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18
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Zhan Z, Guo J, Xiao Y, He Z, Xia X, Huang Z, Guan H, Ling X, Li J, Diao B, Zhao H, Kan B, Zhang J. Comparison of BioFire FilmArray gastrointestinal panel versus Luminex xTAG Gastrointestinal Pathogen Panel (xTAG GPP) for diarrheal pathogen detection in China. Int J Infect Dis 2020; 99:414-420. [PMID: 32800862 DOI: 10.1016/j.ijid.2020.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To compare the performance of two syndromic panels: Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and FilmArray Gastrointestinal (GI) panel. METHODS A total of 243 diarrhea specimens were detected by two panels in parallel, and the inconsistent results were analyzed by real-time PCR or reverse transcription PCR (RT-PCR). The target concentration in specimens was examined by comparing the crossing point values of FilmArray, the median fluorescence intensity of xTAG and the cycle threshold values in any discrepancies. RESULTS For pathogens detected by both panels, the positive rates of FilmArray GI and xTAG GPP were 65.0% and 48.6%, respectively. The two panels showed high consistency (kappa ≥0.74) in detecting norovirus, rotavirus and Campylobacter, while there was low consistency (kappa ≤0.40) in detecting Cryptosporidium, Salmonella, Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic Escherichia coli (ETEC). Samples with low concentration targets were more often detected by FilmArray than with xTAG GPP. The xTAG GPP was more likely to be affected by amplification inhibitors. Several defects of xTAG GPP were found in detecting ETEC. CONCLUSIONS FilmArray was more sensitive. For specimens with low target concentrations or containing ETEC heat stable enterotoxin, the false negatives of xTAG GPP need to be considered.
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Affiliation(s)
- Zhifei Zhan
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Jiayin Guo
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Yong Xiao
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Zixiang He
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Xin Xia
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Zheng Huang
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Xia Ling
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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19
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Brown J, Cumming O. Stool-Based Pathogen Detection Offers Advantages as an Outcome Measure for Water, Sanitation, and Hygiene Trials. Am J Trop Med Hyg 2020; 102:260-261. [PMID: 31701856 PMCID: PMC7008332 DOI: 10.4269/ajtmh.19-0639] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most health impact trials of water, sanitation, and hygiene use caregiver-reported diarrhea in children as the primary outcome; this measure is known to be subject to considerable bias, especially when used in unblinded trials. Detection of enteric pathogens in stool or fecal waste via multiplex molecular methods may offer advantages over—and is complementary to—caregiver-reported diarrhea because these measures are objective, on the causal pathway from exposures of interest to disease outcomes, and increasingly feasible in high-burden countries.
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Affiliation(s)
- Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Oliver Cumming
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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20
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Higgins RR, Peci A, Cardona M, Gubbay JB. Validation of a Laboratory-Developed Triplex Molecular Assay for Simultaneous Detection of Gastrointestinal Adenovirus and Rotavirus in Stool Specimens. Pathogens 2020; 9:pathogens9050326. [PMID: 32349251 PMCID: PMC7281709 DOI: 10.3390/pathogens9050326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Enteric viral pathogens causing gastroenteritis include adenovirus and rotavirus, among others. Rotavirus is the leading cause of severe diarrhea in infants and young children worldwide. Among the adenoviruses known to cause gastroenteritis are those of species F (serotypes 40, 41). Here, we describe the development and validation of a laboratory-developed gastrointestinal triplex rRT-PCR (triplex) assay that targets adenovirus and rotavirus. Stool specimens were tested from patients across Ontario. Specimens were previously tested for adenovirus and/or rotavirus by electron microscopy (EM) or immunochromatographic test (ICT). Triplex sensitivity, specificity, positive and negative predictive values compared to Seegene assay (a commercial assay used here as the standard reference method) were 100%, 97.8%, 86.0%, 100% for adenovirus, and 99.1%, 98.4%, 96.3%. 99.6% for rotavirus, respectively. The triplex assay had a 95.2% and 97.3% overall percent agreements (OPAs) when compared to EM for adenovirus or rotavirus detection, respectively, and an OPA of 90.9% when compared to rotavirus ICT for rotavirus detection. Triplex assay exhibited similar performance to the Seegene assay for both adenovirus and rotavirus and detected more adenovirus and rotavirus than traditional testing methods. The high performance along with lower cost and reduced turnaround time makes the triplex assay a desirable testing method for a clinical microbiology laboratory.
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Affiliation(s)
- Rachel R. Higgins
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
- Correspondence: ; Tel.: +1-647-792-3440
| | - Adriana Peci
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
| | - Mark Cardona
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
| | - Jonathan B. Gubbay
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2V8, Canada
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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Abstract
Viral gastroenteritis (VGE) is an acute, self-limiting gastrointestinal infection caused by several viruses which most often trigger nausea, vomiting, abdominal pain and diarrhea. It is one of the most common human illnesses with its greatest impact on the very young and elderly. In the developing world, VGE can be life threatening whereas in most developed countries, it is self-limited and managed with hydration. Most agents of VGE are spread by the fecal oral route or may occur in explosive outbreaks due to food or water contamination. Control of these infections depends upon proper food handling, hand hygiene, clean water and the rotavirus vaccination of infants. This chapter will discuss the common viruses which cause this syndrome.
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Leli C, Di Matteo L, Gotta F, Vay D, Cavallo V, Mazzeo R, Busso S, Carrabba L, Rocchetti A. Evaluation of a multiplex gastrointestinal PCR panel for the aetiological diagnosis of infectious diarrhoea. Infect Dis (Lond) 2019; 52:114-120. [DOI: 10.1080/23744235.2019.1688861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Christian Leli
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Luigi Di Matteo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Franca Gotta
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Daria Vay
- Pathology Unit, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Valeria Cavallo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Roberta Mazzeo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Simone Busso
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Laura Carrabba
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Andrea Rocchetti
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
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Redli PM, Wanzenried A, Huder JB, Berger C, Berlinger L, Capaul R, Böni J, Zbinden A. Evaluation of the RIDA®GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland. Diagn Microbiol Infect Dis 2019; 96:114924. [PMID: 31757559 DOI: 10.1016/j.diagmicrobio.2019.114924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/05/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
Abstract
Sapovirus (SaV) and astrovirus (AstV) increasingly are recognized as cause of acute viral gastroenteritis (AGE). We evaluated the real-time RT-PCR assays RIDA®GENE SaV and viral stool panel II (RGN RT-PCR) for detection of SaV, AstV, adenovirus (AdV) F40/41 and rotavirus (RoV) in clinical stool samples (n = 69). Results were compared with reference singleplex RT-PCRs. The sensitivity for SaV, AstV and RoV are 100%, the specificity ranges from 98.1% to 100%. In 10 out of 11 AdV (all types) samples, the RGN RT-PCR for AdV F40/41 displayed negative results. Retrospectively, 196 stool specimens from adult patients previously tested negative for norovirus (NoV) were analyzed. In about 10% of NoV-negative stool samples, AdV (n = 9), RoV (n = 6), AstV (n = 3) or SaV (n = 3) were found. The RGN RT-PCR assays are useful for detection of enteric viruses other than NoV. This study emphasizes the need for further testing of NoV-negative stool samples in patients with AGE.
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Affiliation(s)
- Patrick M Redli
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Adrian Wanzenried
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Zurich, Switzerland.
| | | | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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Enteropathogens in paediatric gastroenteritis: comparison of routine diagnostic and molecular methods. Clin Microbiol Infect 2019; 25:1519-1524. [PMID: 31374260 DOI: 10.1016/j.cmi.2019.07.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Studies of acute gastroenteritis (AGE) are hampered by the lack of routine diagnostic methods with good sensitivity and specificity. Molecular methods are increasingly used for clinical purposes, but the clinical significance of a positive result remains a challenge. In this study we aimed to compare results of routine diagnostic methods and molecular methods in symptomatic children and asymptomatic controls. METHODS Patients presenting to the pediatric emergency departments of two university hospitals in Brussels with AGE were recruited prospectively from May 2015 to October 2016; asymptomatic controls were recruited from the same hospitals. Stool analyses were performed for all participants for common pathogenic bacteria (culture), virus (immunochromatography) and parasites (microscopy). Stools were also analysed with the Luminex Gastrointestinal Pathogen Panel, a multiplex-PCR for common enteropathogens. RESULTS Stools from 178 patients and 165 controls were analysed. An enteropathogen was detected in 62.4% (111/178) of cases when combining the two methods (56.2% (100/178) by Luminex, 42.7% (76/178) with routine methods) and 29.1% (48/165) of controls (24.2% (40/165) by Luminex and 10.3% (17/165) by routine methods). Some pathogens were detected more often with Luminex than with routine methods, such as Salmonella (16.3% (29/178) with Luminex and 3.9% (7/178) with routine method, p < 0.05), whereas others identified by culture methods, such as Campylobacter, Shigella, Yersinia, were missed by Luminex. CONCLUSIONS Molecular tools seem attractive methods, providing high positivity and a rapid turn-around time for the diagnosis of AGE. However, high rates of positivity in both cases and controls highlight the difficulty in interpreting results. Pathogens missed by Luminex but detected by culture methods raise more questions about the true clinical interest of the technique for our patients.
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Abstract
PURPOSE OF REVIEW Noroviruses are a major cause of gastroenteritis. This review summarizes new information on noroviruses that may lead to the development of improved measures for limiting their human health impact. RECENT FINDINGS GII.4 strains remain the most common human noroviruses causing disease, although GII.2 and GII.17 strains have recently emerged as dominant strains in some populations. Histo-blood group antigen (HBGA) expression on the gut mucosa drives susceptibility to different norovirus strains. Antibodies that block virus binding to these glycans correlate with protection from infection and illness. Immunocompromised patients are significantly impacted by norovirus infection, and the increasing availability of molecular diagnostics has improved infection recognition. Human noroviruses can be propagated in human intestinal enteroid cultures containing enterocytes that are a significant primary target for initiating infection. Strain-specific requirements for replication exist with bile being essential for some strains. Several vaccine candidates are progressing through preclinical and clinical development and studies of potential antiviral interventions are underway. SUMMARY Norovirus epidemiology is complex and requires continued surveillance to track the emergence of new strains and recombinants, especially with the continued progress in vaccine development. Humans are the best model to study disease pathogenesis and prevention. New in-vitro cultivation methods should lead to better approaches for understanding virus-host interactions and ultimately to improved strategies for mitigation of human norovirus-associated disease.
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Performance evaluation of gastrointestinal viral ELIte panel multiplex RT-PCR assay for the diagnosis of rotavirus, adenovirus and astrovirus infection. J Virol Methods 2019; 268:48-52. [DOI: 10.1016/j.jviromet.2019.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/22/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023]
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Epidemiology and etiology of diarrhea in UK military personnel serving on the United Nations Mission in South Sudan in 2017: A prospective cohort study. Travel Med Infect Dis 2019; 28:34-40. [DOI: 10.1016/j.tmaid.2018.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023]
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Yoo J, Park J, Lee HK, Yu JK, Lee GD, Park KG, Oak HC, Park YJ. Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens. Arch Pathol Lab Med 2019; 143:999-1005. [PMID: 30763118 DOI: 10.5858/arpa.2018-0002-oa] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Infectious gastroenteritis is caused by various pathogens, including bacteria, viruses, and parasites. OBJECTIVE.— To compare the performance of Seegene Allplex Gastrointestinal (24 targets: 13 bacteria, 5 viruses, and 6 parasites in 4 panels), Luminex xTAG Gastrointestinal Pathogen Panel (15 targets: 9 bacteria, 3 viruses, and 3 parasites), and BD MAX Enteric panel (5 bacteria and 3 parasites). We estimated the agreement among 3 molecular assays. DESIGN.— A total of 858 stool samples (554 bacterial/parasite and 304 viral pathogens) were included. A consensus positive/negative was defined as concordant results from at least 2 tests. To evaluate the agreement among the assays, κ value was calculated. RESULTS.— The overall positive percentage agreements of Seegene, Luminex, and BD MAX were 94% (258 of 275), 92% (254 of 275), and 78% (46 of 59), respectfully. For Salmonella, Luminex showed low negative percentage agreement because of frequent false positives (n = 31) showing low median fluorescent intensity. For viruses, positive/negative percentage agreements of Seegene and Luminex were 99%/96% and 93%/99%, respectively. Compared with routine microbiology testing, Seegene, Luminex, and BD MAX additionally identified 39, 40, and 12 pathogens, respectively. Sixty-one cases (16 cases with Seegene, 51 cases with Luminex, and 1 case with BD MAX) showed positive results for multiple pathogens, but only 3 were consensus positive. CONCLUSIONS.— These multiplex molecular assays appear to be promising tools for the detection and identification of multiple gastrointestinal pathogens simultaneously. However, careful interpretation of positive results for multiple pathogens is required.
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Affiliation(s)
- Jaeeun Yoo
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Joonhong Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hae Kyung Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Jin Kyung Yu
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Gun Dong Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Kang Gyun Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hayeon Caitlyn Oak
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Yeon-Joon Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
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Zbinden A. [Acute Viral Gastroenteritis: Viruses Other Than Norovirus]. PRAXIS 2019; 108:335-339. [PMID: 30940042 DOI: 10.1024/1661-8157/a003182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Acute Viral Gastroenteritis: Viruses Other Than Norovirus Abstract. Norovirus is the leading cause of acute viral gastroenteritis. Norovirus is highly contagious, thus outbreaks of norovirus in hospitals and long-term care facilities are feared. Usually, stool samples of patients with a potentially viral gastroenteritis are first checked for the presence of norovirus. In recent years, sapovirus and astrovirus were increasingly reported as cause of acute gastroenteritis. Outbreaks of acute viral gastroenteritis caused by sapovirus or astrovirus are hardly distinguishable from those caused by norovirus because of a similar clinical presentation. Molecular analyses of stool specimen are needed for accurate diagnosis of the viral cause of acute gastroenteritis. It is worth to further investigate stool samples of patients suspected of acute viral gastroenteritis not only for norovirus, but also for sapovirus and astrovirus.
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Affiliation(s)
- Andrea Zbinden
- 1 Institut für Medizinische Virologie, Universität Zürich
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31
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Weinberg GA. Outbreak Epidemiology: One of Many New Frontiers of Norovirus Biology. J Infect Dis 2018; 219:1349-1352. [DOI: 10.1093/infdis/jiy570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, New York
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Yandle Z, Coughlan S, Drew RJ, Cleary J, De Gascun C. Diagnosis of rotavirus infection in a vaccinated population: Is a less sensitive immunochromatographic method more suitable for detecting wild-type rotavirus than real-time RT-PCR? J Clin Virol 2018; 109:19-21. [PMID: 30388662 DOI: 10.1016/j.jcv.2018.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Diagnosis of wild-type rotavirus disease may be complicated by the detection of vaccine-derived virus which can be detected in stool samples following immunisation. We evaluate an immunochromatographic assay and real-time RT-PCR to determine which is more suitable for the detection of wild-type rotavirus. OBJECTIVES To compare the Ct values of wild-type rotavirus and Rotarix determined by real-time RT-PCR. To establish the Ct value corresponding to the limit of detection of the immunochromatographic Combi-Strip method (Coris, BioConcept). STUDY DESIGN Retrospective review of real-time RT-PCR Ct values was performed on 100 samples tested by a pan-rotavirus assay (n = 50 wild-type, n = 50 Rotarix). Secondly the limit of detection of the Combi-Strip assay was determined by testing; wild-type rotavirus (n = 33, Ct range 6.85-34.26) samples, Rotarix (n = 9, Ct range 20.86-34.26) samples and rotavirus negative (n = 21) samples. RESULTS The median Ct of 50 wild-type rotavirus was Ct 12.43; range 6.11-32.66 compared with the median of 50 Rotarix, Ct 29.09; range 18.91-35.28, p=<0.0001. The limit of detection of the Combi-Strip method was approximately Ct 18. The 21 rotavirus negative samples were negative by real-time RT-PCR and Combi-Strip. CONCLUSIONS We found the Ct value was significantly lower, and therefore the viral load higher, for wild-type rotavirus compared to detectable Rotarix. The Combi-Strip assay detects most wild-type infections; however, it lacks sensitivity to detect low-level wild-type rotavirus and, beneficially, is unlikely to detect Rotarix. It is not a more suitable method than real-time RT-PCR when a definitive rotavirus result is required.
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Affiliation(s)
- Z Yandle
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland.
| | - S Coughlan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
| | - R J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - J Cleary
- Department of Microbiology, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - C De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin 4, Ireland
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Mattison CP, Cardemil CV, Hall AJ. Progress on norovirus vaccine research: public health considerations and future directions. Expert Rev Vaccines 2018; 17:773-784. [PMID: 30092671 DOI: 10.1080/14760584.2018.1510327] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Noroviruses are the leading cause of foodborne illness worldwide, account for approximately one-fifth of acute gastroenteritis (AGE) cases globally, and cause a substantial economic burden. Candidate norovirus vaccines are in development, but there is currently no licensed vaccine. AREAS COVERED Noroviruses cause approximately 684 million cases and 212,000 deaths per year across all age groups, though burden estimates vary by study and region. Challenges to vaccine research include substantial and rapidly evolving genetic diversity, short-term and homotypic immunity to infection, and the absence of a single, well-established correlate of protection. Nonetheless, several norovirus vaccine candidates are currently in development, utilizing virus-like particles (VLPs), P particles, and recombinant adenoviruses. Of these, a bivalent GI.1/GII.4 VLP-based intramuscular vaccine (Phase IIb) and GI.1 oral vaccine (Phase I) are in clinical trials. EXPERT COMMENTARY A norovirus vaccine should target high-risk populations, including the young and the elderly, and protect them against the most common circulating norovirus strains. A norovirus vaccine would be a powerful tool in the prevention and control of norovirus while lessening the burden of AGE worldwide. However, more robust burden and cost estimates are needed to justify investments in and guide norovirus vaccine development.
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Affiliation(s)
- Claire P Mattison
- a Oak Ridge Institute for Science and Education , Oak Ridge , TN , USA.,b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
| | - Cristina V Cardemil
- b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
| | - Aron J Hall
- b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
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McHugh MP, Guerendiain D, Hardie A, Kenicer J, MacKenzie L, Templeton KE. Detection of Norovirus by BD MAX™, Xpert ® Norovirus, and xTAG ® Gastrointestinal Pathogen Panel in stool and vomit samples. J Clin Virol 2018; 105:72-76. [PMID: 29908520 DOI: 10.1016/j.jcv.2018.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/09/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available. OBJECTIVES Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples. STUDY DESIGN 163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms. RESULTS In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus. CONCLUSIONS The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.
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Affiliation(s)
- Martin P McHugh
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Daniel Guerendiain
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alison Hardie
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Laura MacKenzie
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E Templeton
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK.
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Wang H, Liu M, Sugata K, Wang Y, Hull J, Foytich K, Jiang B. Development of a new enzyme immunoassay for improved detection of rotavirus in fecal specimens of vaccinated infants. J Clin Virol 2018; 99-100:44-49. [PMID: 29306770 DOI: 10.1016/j.jcv.2017.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Group A rotavirus is the most common cause of acute diarrhea in young children worldwide. A simple and rapid enzyme immunoassay (EIA) has been commonly used to detect rotavirus infection and evaluate rotavirus vaccines. Currently licensed commercial EIA kits have low sensitivity. A more sensitive detection of rotavirus can improve rotavirus diagnostics and vaccine efficacy studies. OBJECTIVE A biotin-avidin based sandwich EIA was developed and compared with commercial EIA kits for improved detection of viral shedding in fecal samples from infants who received human rotavirus vaccine Rotarix in Mexico. STUDY DESIGN A monoclonal antibody (mAb: 1D4) specific to human rotavirus group antigen VP6 was prepared and used to develop a biotin-avidin based sandwich EIA. This EIA was employed to test 128 fecal samples from vaccinated infants, in comparison with two commercial EIA kits using RT-PCR as a reference. RESULTS A new biotin-avidin based sandwich EIA showed specific reaction to group A rotaviruses, but not to other enteric viruses. This new EIA had a detection rate of 36.7% for rotavirus antigen shedding in fecal specimens, which was two times higher (16.4%, 18.0%) than those from two commercial EIA kits. CONCLUSION The new EIA had specificity and higher sensitivity than commercial kits. This new EIA has the potential to detect rotavirus at lower concentration in clinical specimens and thus should be further evaluated as a more sensitive kit for use in diagnostics and vaccine efficacy and effectiveness studies.
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Affiliation(s)
- Houping Wang
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA; IHRC Inc, Atlanta, USA
| | - Merry Liu
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, USA
| | - Ken Sugata
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Yuhuan Wang
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Jennifer Hull
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Baoming Jiang
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
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Affiliation(s)
- Mark D Gonzalez
- Department of Pathology, Children's Healthcare of Atlanta, 1405 Clifton Road, Northeast, Atlanta, GA 30322, USA
| | - Erin McElvania
- Department of Pathology, NorthShore University Health System, 2650 Ridge Avenue, Evanston, IL 60201, USA.
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