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Evaluation of the clinical sensitivity and specificity of the BD Max™ Enteric Bacterial Panel for molecular detection of pathogens for acute gastroenteritis in the Singaporean population. METHODS IN MICROBIOLOGY 2022; 197:106478. [DOI: 10.1016/j.mimet.2022.106478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022]
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Magwira CA, Steele D, Seheri ML. Norovirus diarrhea is significantly associated with higher counts of fecal histo-blood group antigen expressing Enterobacter cloacae among black South African infants. Gut Microbes 2022; 13:1979876. [PMID: 34586017 PMCID: PMC8489948 DOI: 10.1080/19490976.2021.1979876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The study tested the hypothesis that harboring high levels of histo-blood group antigen-expressing Enerobactero cloacae is a risk factor for norovirus diarrhea. The fecal E. cloacae abundance in diarrheic norovirus positive (DNP), non-diarrheic norovirus negative (NDNN), diarrhea norovirus negative (DNN), and non-diarrhea norovirus positive (NDNP) infants was determined by qPCR, and the risk of norovirus diarrhea was assessed by logistical regression. DNP infants contained significantly higher counts of E. cloacae than NDNN and DNN infants, p = .0294, and 0.0001, respectively. The risk of norovirus diarrhea was significantly high in infants with higher counts of E. cloacae than those with lower counts, p = .009. Harboring higher counts of E. cloacae is a risk factor for norovirus diarrhea.
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Affiliation(s)
- Cliff A Magwira
- Diarrheal Pathogens Research Unit (Dpru), Department of Medical Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa,CONTACT Cliff A Magwira ; Department of Medical Virology, School of Medicine, Sefako Makgatho Health Sciences University, Molotlegi St, Ga-Rankuwa, 0208, Pretoria, South Africa. (012) 521 3036
| | - Duncan Steele
- Diarrheal Pathogens Research Unit (Dpru), Department of Medical Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - ML Seheri
- Diarrheal Pathogens Research Unit (Dpru), Department of Medical Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
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Kebe O, Fernandez-Garcia MD, Zinsou BE, Diop A, Fall A, Ndiaye N, Vinjé J, Ndiaye K. Prevalence and genetic characterization of noroviruses in children with acute gastroenteritis in Senegal, 2007-2010. J Med Virol 2021; 94:2640-2644. [PMID: 34854097 DOI: 10.1002/jmv.27496] [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: 06/15/2021] [Revised: 10/23/2021] [Accepted: 11/30/2021] [Indexed: 11/06/2022]
Abstract
Norovirus is the leading cause of sporadic and epidemic acute gastroenteritis (AGE) in children and adults around the world. We investigated the molecular diversity of noroviruses in a pediatric population in Senegal between 2007 and 2010 before the rotavirus vaccine implementation. Stool samples were collected from 599 children under 5 years of age consulting for AGE in a hospital in Dakar. Specimens were screened for noroviruses using the Allplex™ GI-Virus Assay. Positive samples were genotyped after sequencing of conventional reverse transcription-polymerase chain reaction products. Noroviruses were detected in 79 (13.2%) of the children, with GII.4 (64%) and GII.6 (10%) as the most frequently identified genotypes. Our study describes the distribution of genotypes between 2007 and 2010 and should be a baseline for comparison with more contemporary studies. This could help decision-makers on possible choices of norovirus vaccines in the event of future introduction.
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Affiliation(s)
| | | | | | - Amadou Diop
- Pediatric Hospital Albert Royer, Dakar, Senegal
| | | | | | - Jan Vinjé
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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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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Gingras BA, Maggiore JA. Performance of a new molecular assay for the detection of gastrointestinal pathogens. Access Microbiol 2020; 2:acmi000160. [PMID: 33195974 PMCID: PMC7660239 DOI: 10.1099/acmi.0.000160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 02/04/2023] Open
Abstract
Introduction Conventional diagnostic laboratory algorithms for determining the cause of infectious gastroenteritis include culture, biochemical identification and immunoassays. In addition, multiplex PCR-based testing has advanced into the gastroenterology diagnostic arena in recent years. Aim The purpose of this study was to evaluate the performance of a new molecular test (Diagnostics Solutions Laboratory GI-MAP) for the detection of bacterial and parasitic pathogens in stool samples spiked with known organisms. Methodology Faeces from a healthy human subject were pooled into a standard matrix and screened for the absence of bacteria, parasites and Helicobacter pylori antigen. Once confirmed negative single faecal aliquots from the matrix were spiked with solely one pathogen-type from a panel of 14 bacterial pathogens or one of 2 parasitic pathogens at a density of 5×106 organisms ml−1. Sixteen spiked samples in appropriate transport media were sent to two testing labs, specifically a reference site using the PCR-based BioFire FilmArray Gastrointestinal Panel, and a second lab using the GI-MAP assay. Seven negative control samples comprised solely of stool matrix were also submitted. Results Significant variability was found when the GI-MAP assay was used to test normal stool matrix with and without known bacteria and parasites at densities well within the expected limits of detection. The GI-MAP assay displayed a sensitivity of 80 % and a specificity of only 26 % due to many false positive results. This assay also reported quantitative numbers for pathogens. The BioFire FilmArray Gastrointestinal Panel achieved a sensitivity and specificity of 100 %. Conclusion The highly variable results for the GI-MAP assay were unexpected due to the precise pre-spike analysis and the overall maturation of nucleic acid amplification methods within the industry. Problematic to this assay is the poor level of specificity displayed by this assay reporting the presence of several pathogens, which could cause clinicians to treat with antibacterial and/or antiparasitic agents in the absence of any true pathogens.
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Affiliation(s)
- Bruce A. Gingras
- IIT Research Institute, Chicago IL 60616, USA
- *Correspondence: Bruce A. Gingras,
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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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Kim GR, Kim SH, Jeon GW, Shin JH. Prevalence of Eleven Infectious Viruses Causing Diarrhea in Korea. Jpn J Infect Dis 2020; 73:427-430. [PMID: 32475874 DOI: 10.7883/yoken.jjid.2020.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rotavirus and norovirus are well-known causes of viral infectious diarrhea. There are few reports on diarrhea caused by other viruses in Korea, although cases of gastroenteritis attributable to other viruses are increasing worldwide. The aims of this study were to detect various causes of viral diarrhea and to investigate their prevalence. A total of 801 fecal specimens submitted to a clinical microbiology laboratory for the detection of diarrheal viruses were included. We sought to detect rotavirus A/B/C, adenovirus, astrovirus, norovirus GI/GII, sapovirus, Aichi virus, human parechovirus, enterovirus, human cosavirus, human bocavirus, and Saffold virus using multiplex reverse transcription polymerase chain reaction (RT-PCR). At least one diarrheal virus was detected in 223 (27.8%) fecal specimens. Among them, two viruses were detected in 11 specimens. Rotavirus A was most common (17.1%; N = 137), followed by norovirus GII (5.0%; N = 40), enterovirus (4.2%; N = 34), adenovirus (1.0%; N = 8), astrovirus (1.0%; N = 8), human parechovirus (0.6%; N = 5), and human bocavirus (0.2%; N = 2). Rotaviruses B and C, norovirus GI, sapovirus, Aichi virus, human cosavirus, and Saffold virus were not detected. We confirmed that various diarrheal viruses can be detected in fecal specimens. We must consider the possibility of viruses other than rotavirus and norovirus being present in cases of diarrhea.
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Affiliation(s)
- Gyu Ri Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Korea
| | - Ga Won Jeon
- Department of Pediatrics, Inje University College of Medicine, Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Korea
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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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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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Multicenter Clinical Validation of the Molecular BD Max Enteric Viral Panel for Detection of Enteric Pathogens. J Clin Microbiol 2019; 57:JCM.00306-19. [PMID: 31270179 PMCID: PMC6711915 DOI: 10.1128/jcm.00306-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/13/2019] [Indexed: 12/25/2022] Open
Abstract
The conventional methodology for gastrointestinal pathogen detection remains time-consuming, expensive, and of limited sensitivity. The objective of this study was to evaluate the performance of the BD Max enteric viral panel (Max EVP) assay for identification of viral pathogens in stool specimens from individuals with symptoms of acute gastroenteritis, enteritis, or colitis. Prospective and archival stool specimens from adult and pediatric patients with diarrhea were collected in Cary-Blair medium or unpreserved containers. The results for specimens tested by the Max EVP (on the BD Max platform) were compared to those obtained by the reference method (alternate PCR assays, followed by bidirectional sequencing). Positive percent agreement (PPA) and negative percent agreement (NPA) were calculated. A total of 2,239 specimens were collected, with 2,148 being included for analysis. In this population, 39.6% of specimens were from outpatients, 42.1% were from patients <21 years old, and 49.7% were from females. Prevalence rates for prospective specimens were 7.3%, 4.5%, 3.5%, 2.4%, and 1.2% for norovirus, sapovirus, astrovirus, rotavirus, and adenovirus, respectively. PPA was 92.8%, 84.9%, 93.0%, 100%, and 95.6%, for norovirus, sapovirus, astrovirus, rotavirus, and adenovirus, respectively. NPA was ≥99.4% for all targets. In conjunction with the clinical presentation, laboratory findings, and epidemiological information, the Max EVP assay is effective for the differential diagnosis of enteric disease caused by norovirus, sapovirus, astrovirus, rotavirus, and adenovirus. This assay can be used individually for patients at high risk for a viral enteropathogen (e.g., in outbreak settings) or as an adjunct to other enteric bacterial panels.
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Gao X, Wang Z, Wang Y, Liu Z, Guan X, Ma Y, Zhou H, Jiang Y, Cui W, Wang L, Xu Y. Surveillance of norovirus contamination in commercial fresh/frozen berries from Heilongjiang Province, China, using a TaqMan real-time RT-PCR assay. Food Microbiol 2019; 82:119-126. [PMID: 31027765 DOI: 10.1016/j.fm.2019.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/05/2018] [Accepted: 01/26/2019] [Indexed: 12/31/2022]
Abstract
Norovirus (NoV), a major food-borne virus, causes non-bacterial acute gastroenteritis in humans. Berries are generally harvested from low-growing bushes by hand and are minimally processed before being sold to consumers. Therefore, the consumption of berries has been linked to numerous food-borne gastroenteritis outbreaks caused by NoV in many countries. We performed a survey of NoV contamination in commercial fresh/frozen berry fruits collected from 2016 to 2017 in the Heilongjiang Province, the main berry-producing area in China, using a TaqMan-based real-time reverse transcription-PCR assay. Among 900 frozen and 900 fresh domestic retail berry samples, the prevalence of NoV was 9% (81/900) and 12.11% (109/900), including 35.80% (29/81) and 29.36% (32/109) of genotype GI alone, 54.32% (44/81) and 60.55% (66/109) of GII alone, and 9.88% (8/81) and 10.09% (11/109) of both GI and GII, respectively. No NoV was detected among the 677 frozen berry samples for export. Thus, the occurrence of NoV contamination was significantly higher in domestic berries than in exported berries and higher in fresh berries than in frozen berries. This study highlights the need for further risk surveillance for NoV contamination in berries produced in the Heilongjiang Province and recommends region-extended monitoring of retail berries for NoV.
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Affiliation(s)
- Xuwen Gao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Ziwei Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yixin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zhongmei Liu
- Technology Center, Heilongjiang Entry-Exit Inspection and Quarantine Bureau, Harbin, China
| | - Xueting Guan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yingying Ma
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, China.
| | - Yigang Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, China.
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Hirvonen JJ. Comparison of three multiplex real-time PCR assays for detection of enteric viruses in patients with diarrhea. Eur J Clin Microbiol Infect Dis 2018; 38:241-244. [DOI: 10.1007/s10096-018-3418-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023]
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Amrud K, Slinger R, Sant N, Desjardins M, Toye B. A comparison of the Allplex™ bacterial and viral assays to conventional methods for detection of gastroenteritis agents. BMC Res Notes 2018; 11:514. [PMID: 30055653 PMCID: PMC6064067 DOI: 10.1186/s13104-018-3645-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/24/2018] [Indexed: 01/28/2023] Open
Abstract
Objective Molecular methods to detect diarrheal pathogens are increasingly being used in place of conventional methods. We compared a new multiplex real-time PCR assay for detection of both bacterial and viral gastroenteritis agents, the Allplex™ Gastrointestinal Panel Assays (AGPA), to conventional methods (stool culture for bacterial pathogens and electron microscopy (EM) for viral pathogens). Results Gastrointestinal viruses, in particular norovirus genogroup II viruses, were detected by the AGPA in a high number of specimens that were negative by EM. For bacterial pathogens, the AGPA was able to detect the organisms grown in culture with high sensitivity and additionally detected several types of E. coli, such as enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and non-O157 Shiga toxin-producing E. coli (STEC), that could not be detected with conventional culture methods. Overall, the AGPA had a > 2-fold higher detection rate than the conventional methods, with 24/135 (17.8%) samples positive by conventional methods and 60/135 (44.4%) by AGPA. Thus, diarrhea pathogen detection rates increased substantially with the use of the AGPA as compared to conventional methods.
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Affiliation(s)
- Kelly Amrud
- Eastern Ontario Regional Laboratory Association, 401 Smyth Rd., Ottawa, ON, K1H 8L, Canada
| | - Robert Slinger
- Eastern Ontario Regional Laboratory Association, 401 Smyth Rd., Ottawa, ON, K1H 8L, Canada. .,Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.
| | - Nadia Sant
- Eastern Ontario Regional Laboratory Association, 401 Smyth Rd., Ottawa, ON, K1H 8L, Canada.,The Ottawa Hospital, Ottawa, ON, Canada
| | - Marc Desjardins
- Eastern Ontario Regional Laboratory Association, 401 Smyth Rd., Ottawa, ON, K1H 8L, Canada.,The Ottawa Hospital, Ottawa, ON, Canada
| | - Baldwin Toye
- Eastern Ontario Regional Laboratory Association, 401 Smyth Rd., Ottawa, ON, K1H 8L, Canada.,Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,The Ottawa Hospital, Ottawa, ON, Canada
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