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Massa B, Vervaeke S, Van Hoecke F. Semi-quantitative assessment of gastrointestinal viruses in stool samples with Seegene Allplex gastrointestinal panel assays: a solution to the interpretation problem of multiple pathogen detection? Eur J Clin Microbiol Infect Dis 2024; 43:435-443. [PMID: 38147237 DOI: 10.1007/s10096-023-04739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
PURPOSE The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections. METHODS The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined. RESULTS After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting. CONCLUSION By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.
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Affiliation(s)
- Bo Massa
- Department of Laboratory Medicine, AZ Delta, Roeselare, Belgium.
| | - Steven Vervaeke
- Department of Laboratory Medicine, AZ Delta, Roeselare, Belgium
| | - Frederik Van Hoecke
- Department of Laboratory Medicine, AZ Delta, Roeselare, Belgium
- Department of Laboratory Medicine, Sint-Andries Hospital, Tielt, Belgium
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Yi HW, Wang XM, Tan X, Ding CZ, Zhang CL, Wu JH, Li Q, Xin CQ, Fan W. Simultaneous detection of human norovirus GI, GII and SARS-CoV-2 by a quantitative one-step triplex RT-qPCR. Front Microbiol 2024; 14:1269275. [PMID: 38260899 PMCID: PMC10800780 DOI: 10.3389/fmicb.2023.1269275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Background There are many similarities in the clinical manifestations of human norovirus and SARS-CoV-2 infections, and nucleic acid detection is the gold standard for diagnosing both diseases. In order to expedite the identification of norovirus and SARS-CoV-2, a quantitative one-step triplex reverse transcription PCR (RT-qPCR) method was designed in this paper. Methods A one-step triplex RT-qPCR assay was developed for simultaneous detection and differentiation of human norovirus GI (NoV-GI), GII (NoV-GII) and SARS-CoV-2 from fecal specimens. Results The triplex RT-qPCR assay had high detection reproducibility (CV < 1%) and sensitivity. The lower limits of detection (LLOD95) of the triplex RT-qPCR assay for each target site were 128.5-172.8 copies/mL, and LLOD95 of the singleplex RT-qPCR assay were 110.3-142.0 copies/mL. Meanwhile, among the detection of clinical oropharyngeal swabs and fecal specimens, the results of the singleplex and triplex RT-qPCR assay showed high agreement. Conclusion The triplex RT-qPCR assay for simultaneous detection of NoV-GI, NoV-GII and SARS-CoV-2 from fecal specimens has high clinical application value.
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Affiliation(s)
- Hua-Wei Yi
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Xian-Mo Wang
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Xin Tan
- Health Science Center of Yangtze University, Jingzhou, Hubei, China
| | - Cai-Zhi Ding
- The People's Hospital of Songzi, Jingzhou, Hubei, China
| | - Chang-Li Zhang
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Jia-Hao Wu
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Qi Li
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Chen-Qi Xin
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Wen Fan
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
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Ketabi K, Meshkat Z, Soleimanjahi H, Teimoori A, Tanzadepanah H, Bakhshi F. Distribution of group a Rotavirus circulating in Mashhad, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2023; 15:796-802. [PMID: 38156307 PMCID: PMC10751614 DOI: 10.18502/ijm.v15i6.14160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Background and Objectives Group A Rotavirus (RVA) is the most important causative agent of acute diarrheal disease in pediatrics 5 years and below. This study aimed to determine the distribution of circulating RVA in Mashhad, Iran to develop health improvement strategies and vaccine decision making. Materials and Methods A total of 106 fecal specimens were collected from children admitted to Akbar and Dr. Sheikh referral pediatric hospitals of Mashhad City during the December 2020 to March 2021 and December 2021 to March 2022. All specimens were tested for specific bacterial, parasitic, and amoebic infections. Negative samples were analyzed for RVA infections using the RT-PCR method. Results RVA was detected in 31.3% of the specimens, indicating no statistical significance in gender distribution or between fall and winter positivity rates. The number of RVA-positive specimens increased following age increasing in the range of 1 to 60 months. Conclusion Today, acute diarrheal disease (ADD) is still caused mostly by Rotavirus infections in pediatrics in Mashhad. Comprehensive studies are needed to determine the genetic diversity of circulating Rotavirus strains in this era.
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Affiliation(s)
- Kiana Ketabi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Teimoori
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Tanzadepanah
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Bakhshi
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran
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Omotade TI, Babalola TE, Anyabolu CH, Japhet MO. Rotavirus and bacterial diarrhoea among children in Ile-Ife, Nigeria: Burden, risk factors and seasonality. PLoS One 2023; 18:e0291123. [PMID: 37699036 PMCID: PMC10497142 DOI: 10.1371/journal.pone.0291123] [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: 08/08/2022] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Diarrhoea is a leading cause of death among under-five children globally, with sub-Saharan Africa alone accounting for 1/3 episodes yearly. Viruses, bacteria and parasites may cause diarrhoea. Rotavirus is the most common viral aetiology of diarrhoea in children less than five years globally. In Nigeria, there is scarce data on the prevalence/importance, burden, clinical/risk factors and seasonality of rotavirus and bacteria and this study aims to determine the role of rotavirus and bacteria on diarrhoea cases in children less than five years in Ile-Ife, Nigeria. METHODS Socio-demographic data, environmental/risk factors and diarrhoiec stool samples were collected from children less than five years presenting with acute diarrhoea. Rotavirus was identified using ELISA. Bacteria pathogens were detected using cultural technique and typed using PCR. Diarrhoeagenic E. coli (DEC) isolates were subjected to antimicrobial susceptibility testing. Pathogen positive and negative samples were compared in terms of gender, age-group, seasonal distribution, and clinical/risk factors using chi-square with two-tailed significance. SPSS version 20.0.1 for Windows was used for statistical analysis. RESULTS At least one pathogen was detected from 63 (60.6%) children having gastroenteritis while 28 (44.4%) had multiple infections. Rotavirus was the most detected pathogen. Prevalence of rotavirus mono-infection was 22%, multiple infection with bacteria was 45%. Mono-infection prevalence of DEC, Shigella spp., and Salmonella spp. were 5.8% (6/104), 5.8% (6/104), and 2.9% (3/104) and co-infection with RVA were 23.1% (24/104), 21.2% (22/104) and 10.6% (11/104) respectively. All rotaviral infections were observed in the dry season. The pathotypes of DEC detected were STEC and EAEC. Parent earnings and mid-upper arm circumference measurement have statistical correlation with diarrhoea (p = 0.034; 0.035 respectively). CONCLUSION In this study, rotavirus was more prevalent than bacteria and occurred only in the dry season. Among bacteria aetiologies, DEC was the most common detected. Differences in seasonal peaks of rotavirus and DEC could be employed in diarrhoea management in Nigeria and other tropical countries to ensure optimal limited resources usage in preventing diarrhoea transmission and reducing indiscriminate use of antibiotics.
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Affiliation(s)
| | - Toluwani Ebun Babalola
- Department of Paediatrics, Obafemi Awolowo University Teaching Hospital (OAUTHC), Ile-Ife, Osun State, Nigeria
| | - Chineme Henry Anyabolu
- Department of Paediatrics, Obafemi Awolowo University Teaching Hospital (OAUTHC), Ile-Ife, Osun State, Nigeria
| | - Margaret Oluwatoyin Japhet
- Faculty of Science, Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
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Chadwick PR, Trainor E, Marsden GL, Mills S, Chadwick C, O'Brien SJ, Evans CM, Mullender C, Strazds P, Turner S, Weston V, Toleman MS, de Barros C, Kontkowski G, Bak A. Guidelines for the management of norovirus outbreaks in acute and community health and social care settings. J Hosp Infect 2023:S0195-6701(23)00043-9. [PMID: 36796728 DOI: 10.1016/j.jhin.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 02/17/2023]
Affiliation(s)
| | - Eamonn Trainor
- Northern Care Alliance NHS Foundation Trust, Greater Manchester, UK.
| | - Gemma L Marsden
- Healthcare Infection Society, London, UK; Royal College of General Practitioners, London, UK
| | - Samuel Mills
- British Infection Association, Seafield, West Lothian, UK; Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Cariad M Evans
- Sheffield Teaching Hospital NHS Foundation Trust, Sheffield, UK
| | | | - Pixy Strazds
- Infection Prevention Society, London, UK; St Andrew's Healthcare, Northampton, UK
| | - Sarah Turner
- Infection Prevention Society, London, UK; Stockport Council, Stockport, UK
| | - Valya Weston
- Healthcare Infection Society, London, UK; Infection Prevention Society, London, UK; NHS England, London, UK
| | - Michelle S Toleman
- Healthcare Infection Society, London, UK; Cambridge University Hospitals NHS Trust, Cambridge, UK
| | | | | | - Aggie Bak
- Healthcare Infection Society, London, UK
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Ligero-López J, García-Rodríguez J, Ruiz-Carrascoso G. Diagnosis of gastrointestinal infections: comparison between traditional microbiology and a commercial syndromic molecular-based panel. FEMS Microbiol Lett 2023; 370:fnad122. [PMID: 37960927 DOI: 10.1093/femsle/fnad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023] Open
Abstract
Traditional diagnosis of infectious gastroenteritis is based on culture, microscopy and antigen detection. The development of gastrointestinal syndromic panels based on molecular techniques have allowed rapid and simultaneous identification of multiple pathogens. The objective was to evaluate the implementation of Allplex™ Gastrointestinal Panel Assays (AGPA): Allplex™ GI-Virus, Allplex™ GI-Bacteria (I) and Allplex™ GI-Parasite by comparing with traditional diagnosis. A retrospective comparative study was conducted at Hospital Universitario La Paz, between the first year of implementation of the AGPA (April 1, 2018 to March 31, 2019) and the results obtained during the previous year with traditional methods (April 1, 2017 to March 31, 2018). With the implementation of AGPA we obtained an increase in the detection of rotavirus and adenovirus, being statistically significant for rotavirus ([CI95%:3.60-6.79]; P < 0.05) and an increase in the positivity rates of all the bacteria tested, with the exception of Salmonella spp. ([CI95%:3.60-6.79]; P < 0.05). Comparing the bacteria recovered by culture, we obtained an increase in the case of Shigella spp. cultivation during the AGPA period. Regarding protozoa, we achieved a significant increase in the positivity rates for Cryptosporidium spp. ([CI95%:1.98-3.01] P < 0.05), Giardia intestinalis ([CI95%:3.94-5.25]; P < 0.05) and Blastocystis spp. ([CI95%:9.44-11.36]; P < 0.05). There was an improvement in report turnaround time when comparing molecular diagnosis to bacterial culture and concentration plus microscopy for parasites; but not compared with antigen detection. The molecular diagnosis approach with AGPA were more sensitive and had a faster turnaround time for some targets, and in our setting, enabled an increased diagnostic capacity for viruses and protozoa.
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Affiliation(s)
- Jorge Ligero-López
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, 28046 - Madrid, Spain
| | - Julio García-Rodríguez
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, 28046 - Madrid, Spain
| | - Guillermo Ruiz-Carrascoso
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, 28046 - Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029 -Madrid, Spain
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Bonacorsi S, Visseaux B, Bouzid D, Pareja J, Rao SN, Manissero D, Hansen G, Vila J. Systematic Review on the Correlation of Quantitative PCR Cycle Threshold Values of Gastrointestinal Pathogens With Patient Clinical Presentation and Outcomes. Front Med (Lausanne) 2021; 8:711809. [PMID: 34631732 PMCID: PMC8496934 DOI: 10.3389/fmed.2021.711809] [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: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 02/04/2023] Open
Abstract
Background: Quantitative (q) polymerase chain reaction (PCR) cycle threshold (Ct) values represent the number of amplification cycles required for a positive PCR result and are a proxy of pathogen quantity in the tested sample. The clinical utility of Ct values remains unclear for gastrointestinal infections. Objectives: This systematic review assesses the global medical literature for associations between Ct values of gastrointestinal pathogens and patient presentation and clinical outcomes. Data Sources: MEDLINE, EMBASE, Cochrane library databases: searched January 14-17, 2020. Study Eligibility Criteria: Studies reporting on the presence or absence of an association between Ct values and clinical outcomes in adult and pediatric populations were included. Animal studies, reviews, meta-analyses, and non-English language studies were excluded. Participants: Humans infected with gastrointestinal pathogens, detected with qPCR. Interventions: Diagnostics assessing Ct values. Extracted data were reported narratively. Results: Thirty-three eligible studies were identified; the most commonly studied pathogens were Clostridioides difficile (n = 15), norovirus (n = 10), and rotavirus (n = 9). Statistically significant associations between low C. difficile Ct values and increased symptom severity or poor outcome were reported in 4/8 (50%) studies, and increased risk of death in 1/2 (50%) studies; no significant associations were found between Ct value and duration of symptoms or length of hospital stay. Among studies of norovirus, 5/7 (71%), mainly genogroup II, reported symptomatic cases with significantly lower median Ct values than controls. Significantly lower rotavirus Ct values were also observed in symptomatic cases vs. controls in 3/7 (43%) studies, and associated with more severe symptoms in 2/2 studies. Contradictory associations were identified for non-C. difficile bacterial and parasitic pathogens. Conclusions: In conclusion, some studies reported clinically useful associations between Ct values and patient or healthcare outcomes; additional, well-designed, large-scale trials are warranted based on these findings. Systematic Review Registration: [PROSPERO], identifier [CRD42020167239].
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Affiliation(s)
- Stéphane Bonacorsi
- Department of Microbiology, Robert Debré University Hospital, AP-HP, Paris, France
| | - Benoit Visseaux
- Université de Paris, IAME, INSERM, Paris, France
- Université de Paris, Laboratoire de Virologie, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Donia Bouzid
- Université de Paris, IAME, INSERM, Paris, France
- Université de Paris, Service d'Accueil des Urgences, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Josep Pareja
- STAT-Dx Life, S.L. (a QIAGEN Company), Medical Affairs, Barcelona, Spain
| | - Sonia N. Rao
- QIAGEN Inc., Medical Affairs, Germantown, MD, United States
| | - Davide Manissero
- QIAGEN Manchester Ltd, Medical Affairs, Manchester, United Kingdom
| | - Glen Hansen
- Microbiology and Molecular Diagnostics, Hennepin County Medical Center, Department of Infectious Diseases, School of Medicine, University of Minnesota, Minneapolis, MN, United States
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jordi Vila
- Biomedical Diagnostic Centre, Department of Clinical Microbiology, Institute of Global Health, School of Medicine, Hospital Clinic, University of Barcelona, Barcelona, Spain
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Molecular detection of Mycobacterium tuberculosis in blood stained sputum samples using GeneXpert PCR assay. Diagn Microbiol Infect Dis 2021; 100:115363. [PMID: 33743471 DOI: 10.1016/j.diagmicrobio.2021.115363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022]
Abstract
This study investigated the possibility of detecting Mycobacterium tuberculosis (MTB) in blood-stained sputa with GeneXpert assay (Xpert MTB/Rif G4 v.5) using appropriate blood lysing (distilled water and distilled water/carbon tetrachloride) and protein denaturing (guanidinium chloride and heat) agents. Blood free sputa were collected from individuals infected with MTB. Various levels of blood-spiked sputa (0%-50%) were prepared and subsequently assayed with GeneXpert analyzer. GeneXpert was found to be reproducible at less than 2% blood contamination. However, beyond 5% blood contamination, GeneXpert was unreliable with absolute PCR inhibition at 20% of blood contamination. Boiling at 95°C for 5 minutes was able to recover MTB DNA in previously undetectable levels as well as in 57% of patients' sputa with blood stains with previous negative GeneXpert results.
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Darton TC, Thi Hong Chau T, Parry CM, Campbell JI, Minh Ngoc N, Le Chau Ngoc T, Thanh Tuyen H, Thuy Duong V, Thanh Hoang Nhat L, van Minh P, Kestelyn E, Thwaites GE, Huu Tung T, Baker S. The CIPAZ study protocol: an open label randomised controlled trial of azithromycin versus ciprofloxacin for the treatment of children hospitalised with dysentery in Ho Chi Minh City, Vietnam. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16093.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Diarrhoeal disease remains a common cause of illness and death in children <5 years of age. Faecal-oral infection by Shigella spp. causing bacillary dysentery is a leading cause of moderate-to-severe diarrhoea, particularly in low and middle-income countries. In Southeast Asia, S. sonnei predominates and infections are frequently resistant to first-line treatment with the fluoroquinolone, ciprofloxacin. While resistance to all antimicrobials is increasing, there may be theoretical and clinical benefits to prioritizing treatment of bacillary dysentery with the azalide, azithromycin. In this study we aim to measure the efficacy of treatment with azithromycin compared with ciprofloxacin, the current standard of care, for the treatment of children with bacillary dysentery. Methods and analysis: We will perform a multicentre, open-label, randomized controlled trial of two therapeutic options for the antimicrobial treatment of children hospitalised with dysentery. Children (6–60 months of age) presenting with symptoms and signs of dysentery at Children’s Hospital 2 in Ho Chi Minh City will be randomised (1:1) to treatment with either oral ciprofloxacin (15mg/kg/twice daily for 3 days, standard-of-care) or oral azithromycin (10mg/kg/daily for 3 days). The primary endpoint will be the proportion of treatment failure (defined by clinical and microbiological parameters) by day 28 (+3 days) and will be compared between study arms by logistic regression modelling using treatment allocation as the main variable. Ethics and dissemination: The study protocol (version 1.2 dated 27th December 2018) has been approved by the Oxford Tropical Research Ethics Committee (47–18) and the ethical review boards of Children's Hospital 2 (1341/NĐ2-CĐT). The study has also been approved by the Vietnamese Ministry of Health (5044/QĐ-BYT). Trial registration: Clinicaltrials.gov: NCT03854929 (February 26th 2019).
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Jiang C, Yang H, Chen X, Qiu S, Wu C, Zhang B, Jin L. Macleaya cordata extracts exert antiviral effects in newborn mice with rotavirus-induced diarrhea via inhibiting the JAK2/STAT3 signaling pathway. Exp Ther Med 2020; 20:1137-1144. [PMID: 32742353 PMCID: PMC7388234 DOI: 10.3892/etm.2020.8766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Accumulating evidence demonstrates that Macleaya cordata extract exerts antiviral and anti-inflammatory effects in various diseases. The present study aimed to investigate the potential effects of M. cordata on rotavirus SA11-induced diarrhea in mice. Diarrhea severity, levels of inflammatory cytokines, histological changes in the small intestine and the underlying mechanisms were evaluated in rotavirus-stimulated mice treated with 1, 2 and 4 mg/kg/day M. cordata or 4 mg/kg/day ribavirin (positive control). M. cordata treatment effectively ameliorated rotavirus-induced diarrhea in a dose-dependent manner by decreasing viral RNA levels. In addition, M. cordata reduced the release of pro-inflammatory cytokines including migration inhibitory factor, interleukin (IL)-8, IL-β, interferon-γ and tumor necrosis factor-α, and elevated the secretion of the anti-inflammatory cytokine IL-10 following rotavirus infection. M. cordata inhibited intestinal epithelial cell apoptosis and improved intestinal inflammation after rotavirus infection. The study also revealed that M. cordata exerted antiviral and anti-inflammatory effects on rotavirus-induced diarrhea by suppressing the Janus kinase 2 (JAK2)/STAT3 pathway, as reflected by decreased protein expression of phosphorylated (p)-JAK2 and p-STAT3. Overall, M. cordata effectively inhibited the inflammation caused by rotavirus, which was closely associated with the suppression of JAK2/STAT3 phosphorylation. These data suggested that M. cordata may be applied as a treatment for rotavirus-induced diarrhea.
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Affiliation(s)
- Chunmao Jiang
- School of Veterinary Medicine, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Haifeng Yang
- School of Animal Pharmaceutical Sciences, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Xiaolan Chen
- School of Animal Pharmaceutical Sciences, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Shulei Qiu
- School of Veterinary Medicine, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Caihong Wu
- School of Veterinary Medicine, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Bin Zhang
- School of Pet Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
| | - Liqin Jin
- School of Animal Pharmaceutical Sciences, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, P.R. China
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De Grazia S, Bonura F, Bonura C, Mangiaracina L, Filizzolo C, Martella V, Giammanco GM. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation. J Clin Virol 2020; 129:104513. [PMID: 32575023 DOI: 10.1016/j.jcv.2020.104513] [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: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy. METHODS A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses. RESULTS At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients. CONCLUSIONS Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.
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Affiliation(s)
- Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy.
| | - Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
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12
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Hong NTT, Anh NT, Mai NTH, Nghia HDT, Nhu LNT, Thanh TT, Phu NH, Deng X, van Doorn HR, Chau NVV, Delwart E, Thwaites G, Tan LV. Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting. Open Forum Infect Dis 2020; 7:ofaa046. [PMID: 32158774 PMCID: PMC7051036 DOI: 10.1093/ofid/ofaa046] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious diseases diagnosis, but few studies have been conducted in resource-limited settings. Methods We assessed the performance of mNGS in the cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral-specific polymerase chain reaction (PCR). As a complementary analysis, 6 viral PCR-positive samples were analyzed using MinION-based metagenomics. Results Routine diagnosis could identify a virus in 15 (22.7%) patients, including herpes simplex virus (HSV; n = 7) and varicella zoster virus (VZV; n = 1) by PCR, and mumps virus (n = 4), dengue virus (DENV; n = 2), and Japanese encephalitis virus (JEV; n = 1) by serological diagnosis. mNGS detected HSV, VZV, and mumps virus in 5/7, 1/1, and 1/4 of the CSF positive by routine assays, respectively, but it detected DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in 7 patients of unknown cause. Metagenomic MinION-Nanopore sequencing could detect a virus in 5/6 PCR-positive CSF samples, including HSV in 1 CSF sample that was negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR. Conclusions In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in the CSF of meningoencephalitis patients. Further studies are needed to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.
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Affiliation(s)
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | | | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Department of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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13
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Li Z, Zhao F, Tang T, Wang M, Yu X, Wang R, Li Y, Xu Y, Tang L, Wang L, Zhou H, Jiang Y, Cui W, Qiao X. Development of a Colloidal Gold Immunochromatographic Strip Assay for Rapid Detection of Bovine Rotavirus. Viral Immunol 2019; 32:393-401. [PMID: 31596683 DOI: 10.1089/vim.2019.0071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bovine rotavirus (BRV) is one of main pathogens responsible for diarrhea, fever, and vomiting. In this study, we developed a colloidal gold immunochromatographic test strip for detecting BRV according to the principle of double-antibody sandwich. The monoclonal antibodies (mAbs) and polyclonal antibodies (pAbs) were prepared and purified. On the strip, the purified mAbs labeled with the colloidal gold were used as the detector, and the goat anti-mouse antibodies and purified pAbs were coated on the nitrocellulose membranes as the control line and the test line, respectively. We optimized different reaction conditions, including the amount of mAbs, the pH of colloidal gold solution, coating solution, blocking solution, sample pad treatment solution, antibody concentration in control line, and antibody concentration in detection line. In specificity assay, the strip had high specificity in detecting BRV. No cross-reaction was observed in detecting other viruses. The detection sensitivity of the strip was found to be 1 × 103 TCID50/0.1 mL. Two hundred twenty clinical samples were detected with the strip compared to reverse transcription-polymerase chain reaction. No false-negative or false-positive results were found, and the results obtained by the two methods were similar. In conclusion, we developed a novel immunochromatographic strip to rapidly detect BRV. The strip developed exhibited high sensitivity and specificity for BRV detection. It could be a rapid, convenient, and effective method for the rapid diagnosis of BRV infection in the fields.
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Affiliation(s)
- Zhenxue Li
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Feipeng Zhao
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Tingting Tang
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Mengmeng Wang
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiaoli Yu
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Ruichong Wang
- Heilongjiang Province Center for Disease Control and Prevention, Department of Radiological Protection, Harbin, China
| | - Yijing Li
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yigang Xu
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Lijie Tang
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Li Wang
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Han Zhou
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yanping Jiang
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wen Cui
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xinyuan Qiao
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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14
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Nirwati H, Donato CM, Mawarti Y, Mulyani NS, Ikram A, Aman AT, Peppelenbosch MP, Soenarto Y, Pan Q, Hakim MS. Norovirus and rotavirus infections in children less than five years of age hospitalized with acute gastroenteritis in Indonesia. Arch Virol 2019; 164:1515-1525. [PMID: 30887229 DOI: 10.1007/s00705-019-04215-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 02/18/2019] [Indexed: 01/19/2023]
Abstract
Rotaviruses and noroviruses are the most important viral causes of acute gastroenteritis in children. While previous studies of acute gastroenteritis in Indonesia mainly focused on rotavirus, here, we investigated the burden and epidemiology of norovirus and rotavirus disease. Children less than five years of age hospitalized with acute gastroenteritis were enrolled in this study from January to December 2015 at three participating hospitals. Rotavirus was detected by enzyme immunoassay (EIA), followed by genotyping by reverse transcription PCR (RT-PCR). Norovirus genogroups were determined by TaqMan-based quantitative RT-PCR. Among 406 enrolled children, 75 (18.47%), 223 (54.93%) and 29 (7.14%) cases were positive for norovirus, rotavirus and both viruses (mixed infections), respectively. Most cases clinically presented with fever, diarrhea, vomiting and some degree of dehydration. The majority (n = 69/75 [92%]) of the noroviruses identified belonged to genogroup II, and several genotypes were identified by sequencing a subset of samples. Among 35 samples tested for rotavirus genotype, the most prevalent genotype was G3P[8] (n = 30/35 [85.6%]). Our study suggests that the burden of norovirus diseases in Indonesian children should not be underestimated. It also shows the emergence of rotavirus genotype G3P[8] in Indonesia.
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Affiliation(s)
- Hera Nirwati
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Celeste M Donato
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Enteric Virus Group, Murdoch Children's Research Institute, Melbourne, Australia
| | - Yuli Mawarti
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nenny S Mulyani
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Aqsa Ikram
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.,Atta-Ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Abu T Aman
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Yati Soenarto
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mohamad S Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia. .,Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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15
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Bentes GA, Guimarães JR, Volotão EDM, Fialho AM, Hooper C, Ganime AC, Gardinali NR, Lanzarini NM, da Silva ADS, Pitcovski J, Leite JP, Pinto MA. Cynomolgus Monkeys ( Macaca fascicularis) as an Experimental Infection Model for Human Group A Rotavirus. Viruses 2018; 10:v10070355. [PMID: 29973483 PMCID: PMC6071073 DOI: 10.3390/v10070355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 12/25/2022] Open
Abstract
Group A rotaviruses (RVA) are one of the most common causes of severe acute gastroenteritis in infants worldwide. Rotaviruses spread from person to person, mainly by faecal–oral transmission. Almost all unvaccinated children may become infected with RVA in the first two years of life. The establishment of an experimental monkey model with RVA is important to evaluate new therapeutic approaches. In this study, we demonstrated viral shedding and viraemia in juvenile–adult Macaca fascicularis orally inoculated with Wa RVA prototype. Nine monkeys were inoculated orally: seven animals with human RVA and two control animals with saline solution. During the study, the monkeys were clinically monitored, and faeces and blood samples were tested for RVA infection. In general, the inoculated animals developed an oligosymptomatic infection pattern. The main clinical symptoms observed were diarrhoea in two monkeys for three days, associated with a reduction in plasmatic potassium content. Viral RNA was detected in seven faecal and five sera samples from inoculated animals, suggesting virus replication. Cynomolgus monkeys are susceptible hosts for human Wa RVA infection. When inoculated orally, they presented self-limited diarrhoea associated with presence of RVA infectious particles in faeces. Thus, cynomolgus monkeys may be useful as animal models to evaluate the efficacy of new antiviral approaches.
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Affiliation(s)
- Gentil Arthur Bentes
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Juliana Rodrigues Guimarães
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Eduardo de Mello Volotão
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Alexandre Madi Fialho
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Cleber Hooper
- Serviço de Controle da Qualidade Animal, Instituto de Ciência e Tecnologia em Biomodelos, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Ana Carolina Ganime
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Noemi Rovaris Gardinali
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Natália Maria Lanzarini
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Alexandre Dos Santos da Silva
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Jacob Pitcovski
- Virology and Vaccine Development Laboratory, MIGAL Technology Center, Kiryat Shmona 11016, Israel.
| | - José Paulo Leite
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
| | - Marcelo Alves Pinto
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro/RJ 21.040-360, Brazil.
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16
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Jiang N, Shi L, Lin J, Zhang L, Peng Y, Sheng H, Wu P, Pan Q. Comparison of two different combined test strips with fluorescent microspheres or colored microspheres as tracers for rotavirus and adenovirus detection. Virol J 2018. [PMID: 29534739 PMCID: PMC5851252 DOI: 10.1186/s12985-018-0951-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Rotavirus (RV) and enteric adenovirus (AdV) mainly cause infantile infectious gastroenteritis. Several separate test methods for the detection of RV or AdV are currently available, but few tests are able to simultaneously detect both RV and AdV viruses, especially in primary medical institutions. Methods The present study was mainly designed to compare the performance of two combined test strips for the detection of RV and AdV: a rotavirus–adenovirus strip with fluorescent microspheres for tracers (FMT); and the CerTest rotavirus–adenovirus blister strip with colored microspheres for tracers (CMT). To test the strips cultures of RV, AdV and from other enteric pathogens were used, in addition to 350 stool specimens from 45 symptomatic patients with gastrointestinal infections. Results Detection thresholds for RV and AdV cultures using serial dilutions showed that the sensitivity of FMT was significantly higher than that of CMT (both P < 0.05). Specificity evaluation demonstrated that with culture mixtures of Coxsackie (A16), ECHO (type30), and entero- (EV71) viruses there was no detection of cross reaction using the two test strips, i.e., all the results were negative. With regard to the detection of RV in 350 clinical specimens, the total coincidence rate was 92.9%, the positive coincidence rate was 98.2%, and the negative coincidence rate was 90.8%. With regard to AdV detection, the total coincidence rate was 95.4%, the positive coincidence rate was 95.2%, and the negative coincidence rate was 95.5%. Conclusions FMT performed better than CMT with regard to the combined detection of RV and AdV.
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Affiliation(s)
- Na Jiang
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Lei Shi
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jieping Lin
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Lifang Zhang
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yanxia Peng
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Huiying Sheng
- Division of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Centre, Guangzhou, Guangdong, China
| | - Ping Wu
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.
| | - Qingjun Pan
- Clinical Research Center, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.
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17
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Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Ccirculating
in Ahvaz, Iran in 2016. IRANIAN BIOMEDICAL JOURNAL 2018; 22:107-16. [PMID: 28915725 PMCID: PMC5786656 DOI: 10.22034/ibj.22.2.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023]
Abstract
Background Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines. Methods A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping. Results Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%). Conclusion A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
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Affiliation(s)
- Azarakhsh Azaran
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeedeh Ebrahimi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farzad Heydari
- Cukurova University, Medicine Faculty, Medical Microbiology Department, Adana, Turkey
| | - Roya Nikfar
- Department of Infectious Diseases, Aboozar Children’s Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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18
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Chau TTH, Chau NNM, Le NTH, The HC, Vinh PV, To NTN, Ngoc NM, Tuan HM, Ngoc TLC, Kolader ME, Farrar JJ, Wolbers M, Thwaites GE, Baker S. A Double-blind, Randomized, Placebo-controlled Trial of Lactobacillus acidophilus for the Treatment of Acute Watery Diarrhea in Vietnamese Children. Pediatr Infect Dis J 2018; 37:35-42. [PMID: 28787388 PMCID: PMC5681247 DOI: 10.1097/inf.0000000000001712] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Probiotics are the most frequently prescribed treatment for children hospitalized with diarrhea in Vietnam. We were uncertain of the benefits of probiotics for the treatment of acute watery diarrhea in Vietnamese children. METHODS We conducted a double-blind, placebo-controlled, randomized trial of children hospitalized with acute watery diarrhea in Vietnam. Children meeting the inclusion criteria (acute watery diarrhea) were randomized to receive either 2 daily oral doses of 2 × 10 CFUs of a local probiotic containing Lactobacillus acidophilus or placebo for 5 days as an adjunct to standard of care. The primary end point was time from the first dose of study medication to the start of the first 24-hour period without diarrhea. Secondary outcomes included the total duration of diarrhea and hospitalization, daily stool frequency, treatment failure, daily fecal concentrations of rotavirus and norovirus, and Lactobacillus colonization. RESULTS One hundred and fifty children were randomized into each study group. The median time from the first dose of study medication to the start of the first 24-hour diarrhea-free period was 43 hours (interquartile range, 15-66 hours) in the placebo group and 35 hours (interquartile range, 20-68 hours) in the probiotic group (acceleration factor 1.09 [95% confidence interval, 0.78-1.51]; P = 0.62). There was also no evidence that probiotic treatment was efficacious in any of the predefined subgroups nor significantly associated with any secondary end point. CONCLUSIONS This was a large double-blind, placebo-controlled trial in which the probiotic underwent longitudinal quality control. We found under these conditions that L. acidophilus was not beneficial in treating children with acute watery diarrhea.
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Affiliation(s)
- Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Minh Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhat Thanh Hoang Le
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Nguyen To
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ha Manh Tuan
- Children’s Hospital 2 (CH2), Ho Chi Minh City, Vietnam
| | | | | | - Jeremy J. Farrar
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Marcel Wolbers
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Guy E. Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom,The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom,Corresponding Author: Professor Stephen Baker, the Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam. Tel: +84 89241761; Fax: +84 89238904;
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19
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Japhet MO, Famurewa O, Iturriza-Gomara M, Adesina OA, Opaleye OO, Niendorf S, Bock CT, Mas Marques A. Group A rotaviruses circulating prior to a national immunization programme in Nigeria: Clinical manifestations, high G12P[8] frequency, intra-genotypic divergence of VP4 and VP7. J Med Virol 2017; 90:239-249. [PMID: 28906005 DOI: 10.1002/jmv.24949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/06/2017] [Indexed: 12/24/2022]
Abstract
Nigeria having approximately 50 000 Rotavirus A (RVA) deaths annually is yet to introduce RVA vaccine into routine national immunization; therefore surveillance of RVA strains circulating before vaccine introduction is essential in evaluating impact of the intervention. Stool samples and sociodemographic data of diarrhoeic children, <5 years were collected between August 2012 and December 2013. While a high prevalence of RVA infection (47.6%; 49/103) was observed by quantitative reverse transcription real time PCR, only 25% (26/103) had high RVA genome concentrations and were antigen positive. G and P types were obtained for 31 and 37 samples respectively. G12P[8] strains were predominant (30.6%; 16/31); Other genotypes found included G9, G3, G2 and P[4], P[6], P[8]. A G12 + G2/P[8] + P[6] mixed infection was detected. The P[8] genotype showed divergence with strains distributed in lineage III and IV. Compared to the vaccines, changes in antigenic sites of VP8* and VP7 were found. The finding of the G2P[6] genotype combination and emergence of G12 strains support observations in most of the recent RVA studies from Africa. P[6] is common in many African countries, in contrast to countries in Europe and the Americas. In conclusion, this study shows the circulation of other RVA genotypes compared to the common RVA genotypes in Nigeria. PCR results should be interpreted with caution to avoid significant bias from samples with low RVA genome concentrations. These findings provide important information on the detection and molecular epidemiology of RVA prior to vaccination and contribute as a baseline for future evaluations after possible vaccine introduction.
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Affiliation(s)
- Margaret O Japhet
- Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria.,Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria.,Department of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch-Institute, Berlin, Germany
| | - Oladiran Famurewa
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria.,Department of Biological Sciences, Microbiology Unit, Kings University, Ode-omu, Osun State
| | | | - Olufisayo A Adesina
- Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Oluyinka O Opaleye
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University, Osogbo, Osun state, Nigeria
| | - Sandra Niendorf
- Department of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch-Institute, Berlin, Germany
| | - C Thomas Bock
- Department of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch-Institute, Berlin, Germany
| | - Andreas Mas Marques
- Department of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch-Institute, Berlin, Germany
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20
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Shioda K, Barclay L, Becker-Dreps S, Bucardo-Rivera F, Cooper PJ, Payne DC, Vinjé J, Lopman BA. Can Use of Viral Load Improve Norovirus Clinical Diagnosis and Disease Attribution? Open Forum Infect Dis 2017; 4:ofx131. [PMID: 32455144 PMCID: PMC7236086 DOI: 10.1093/ofid/ofx131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/31/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Real-time reverse-transcriptase polymerase chain reaction (RT-PCR) is the state-of-the-art diagnostic for norovirus. Cycle threshold (Ct), an indicator of viral load, may be associated with symptomatic disease as well as demographic and outbreak characteristics. METHODS Data on (1) outbreak and sporadic cases and (2) asymptomatic controls in the United States and Latin America were analyzed. With multivariate regression models, we assessed relationships between various factors and Ct values, and we calculated odds ratios (ORs) for the presence of symptoms and attributable fractions of norovirus. Receiver-operating characteristic analysis was performed to define an optimal Ct cutoff to identify disease-causing infections. RESULTS Cycle threshold values were lower (ie, higher viral loads) among symptomatic cases (model-adjusted mean ± standard error: 25.3 ± 1.2) compared with asymptomatic controls (28.5 ± 1.4). Cycle threshold values were significantly different across age groups, norovirus genogroups, timing of specimen collection, outbreak settings, and transmission modes. Genogroup II (GII) Ct values were associated with presence of symptoms (OR = 1.1), allowing us to estimate that 16% of diarrheal disease was attributable to norovirus. The optimized Ct cutoff led to poor sensitivity and specificity for genogroup I and GII. CONCLUSIONS Cycle threshold values were associated with host, pathogen, and outbreak factors. Cycle threshold values may not effectively distinguish disease-causing infection for individual patients, but they are useful for epidemiological studies aiming to attribute disease.
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Affiliation(s)
- Kayoko Shioda
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Leslie Barclay
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Philip J Cooper
- Facultad de Ciencias Médicas, de la Salud y de la Vida, Universidad Internacional del Ecuador Quito; Institute of Infection and Immunity, St George's University of London, United Kingdom
| | - Daniel C Payne
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin A Lopman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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21
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Dung TTN, Duy PT, Sessions OM, Sangumathi UK, Phat VV, Tam PTT, To NTN, Phuc TM, Hong Chau TT, Chau NNM, Minh NN, Thwaites GE, Rabaa MA, Baker S. A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection. BMC Genomics 2017; 18:324. [PMID: 28438140 PMCID: PMC5404283 DOI: 10.1186/s12864-017-3714-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. Methods To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. Results Our approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct < 30). Conclusions This method provides a novel, reproducible and comparatively simple approach for genomic RoV characterization and could be scaled-up for use in global RoV surveillance systems. Trial registration (prospectively registered) Current Controlled Trials ISRCTN88101063. Date of registration: 14/06/2012 Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3714-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tran Thi Ngoc Dung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Pham Thanh Duy
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | | | | | - Voong Vinh Phat
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Nguyen To
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Tran My Phuc
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Minh Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | | | - Guy E Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Oxford University, Oxford, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Oxford University, Oxford, UK.,The London School of Hygiene and Tropical Medicine, London, UK
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22
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Evaluation of an Assay Based On Multiple Detection Temperature Technique for Simultaneous Detection of Viral Gastroenteritis-Causing Pathogens. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.43548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G, Woolhouse M, Kellam P, Rabaa MA, Cotten M. Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evol 2016; 2:vew027. [PMID: 28748110 PMCID: PMC5522372 DOI: 10.1093/ve/vew027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.
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Affiliation(s)
- My V T Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bas B Oude Munnink
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Phuc Tran My
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tue Ngo Tri
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,London School of Tropical Medicine and Hygiene, London, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark Woolhouse
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Kymab Inc., Cambridge, UK.,Imperial College, London, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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24
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Liu J, Platts-Mills JA, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Blackwelder WC, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Toema D, Wu Y, Zaidi A, Nataro JP, Kotloff KL, Levine MM, Houpt ER. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet 2016; 388:1291-301. [PMID: 27673470 PMCID: PMC5471845 DOI: 10.1016/s0140-6736(16)31529-x] [Citation(s) in RCA: 543] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). METHODS GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. FINDINGS We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. INTERPRETATION A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jashim Uddin
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Pedro L Alonso
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain
| | | | - Stephen M Becker
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - William C Blackwelder
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert F Breiman
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | | | - Sheikh Jarju
- Medical Research Council Unit, Banjul, The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Deanna Toema
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yukun Wu
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anita Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - James P Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Myron M Levine
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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25
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Optimization of Quantitative PCR Methods for Enteropathogen Detection. PLoS One 2016; 11:e0158199. [PMID: 27336160 PMCID: PMC4918952 DOI: 10.1371/journal.pone.0158199] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen's extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease.
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26
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Leung JM, Hong CTT, Trung NHD, Thi HN, Minh CNN, Thi TV, Hong DT, Man DNH, Knowles SCL, Wolbers M, Hoang NLT, Thwaites G, Graham AL, Baker S. The impact of albendazole treatment on the incidence of viral- and bacterial-induced diarrhea in school children in southern Vietnam: study protocol for a randomized controlled trial. Trials 2016; 17:279. [PMID: 27266697 PMCID: PMC4896038 DOI: 10.1186/s13063-016-1406-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/25/2016] [Indexed: 11/14/2022] Open
Abstract
Background Anthelmintics are one of the more commonly available classes of drugs to treat infections by parasitic helminths (especially nematodes) in the human intestinal tract. As a result of their cost-effectiveness, mass school-based deworming programs are becoming routine practice in developing countries. However, experimental and clinical evidence suggests that anthelmintic treatments may increase susceptibility to other gastrointestinal infections caused by bacteria, viruses, or protozoa. Hypothesizing that anthelmintics may increase diarrheal infections in treated children, we aim to evaluate the impact of anthelmintics on the incidence of diarrheal disease caused by viral and bacterial pathogens in school children in southern Vietnam. Methods/design This is a randomized, double-blinded, placebo-controlled trial to investigate the effects of albendazole treatment versus placebo on the incidence of viral- and bacterial-induced diarrhea in 350 helminth-infected and 350 helminth-uninfected Vietnamese school children aged 6–15 years. Four hundred milligrams of albendazole, or placebo treatment will be administered once every 3 months for 12 months. At the end of 12 months, all participants will receive albendazole treatment. The primary endpoint of this study is the incidence of diarrheal disease assessed by 12 months of weekly active and passive case surveillance. Secondary endpoints include the prevalence and intensities of helminth, viral, and bacterial infections, alterations in host immunity and the gut microbiota with helminth and pathogen clearance, changes in mean z scores of body weight indices over time, and the number and severity of adverse events. Discussion In order to reduce helminth burdens, anthelmintics are being routinely administered to children in developing countries. However, the effects of anthelmintic treatment on susceptibility to other diseases, including diarrheal pathogens, remain unknown. It is important to monitor for unintended consequences of drug treatments in co-infected populations. In this trial, we will examine how anthelmintic treatment impacts host susceptibility to diarrheal infections, with the aim of informing deworming programs of any indirect effects of mass anthelmintic administrations on co-infecting enteric pathogens. Trial registration ClinicalTrials.gov: NCT02597556. Registered on 3 November 2015. Electronic supplementary material The online version of this article (doi:10.1186/s13063-016-1406-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacqueline M Leung
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Chau Tran Thi Hong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Nghia Ho Dang Trung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Department of Infectious Diseases, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Hoa Nhu Thi
- Department of Parasitology and Mycology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Chau Nguyen Ngoc Minh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Thuy Vu Thi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Dinh Thanh Hong
- Cu Chi Preventive Medicine Centre, Ho Chi Minh City, Vietnam
| | | | - Sarah C L Knowles
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hertfordshire, UK
| | - Marcel Wolbers
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Nhat Le Thanh Hoang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine, University of Oxford, Oxford, UK. .,The London School of Hygiene and Tropical Medicine, London, UK.
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27
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Evaluation of Luminex xTAG Gastrointestinal Pathogen Panel Assay for Detection of Multiple Diarrheal Pathogens in Fecal Samples in Vietnam. J Clin Microbiol 2016; 54:1094-100. [PMID: 26865681 PMCID: PMC4809950 DOI: 10.1128/jcm.03321-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/02/2016] [Indexed: 12/17/2022] Open
Abstract
Diarrheal disease is a complex syndrome that remains a leading cause of global childhood morbidity and mortality. The diagnosis of enteric pathogens in a timely and precise manner is important for making treatment decisions and informing public health policy, but accurate diagnosis is a major challenge in industrializing countries. Multiplex molecular diagnostic techniques may represent a significant improvement over classical approaches. We evaluated the Luminex xTAG gastrointestinal pathogen panel (GPP) assay for the detection of common enteric bacterial and viral pathogens in Vietnam. Microbiological culture and real-time PCR were used as gold standards. The tests were performed on 479 stool samples collected from people admitted to the hospital for diarrheal disease throughout Vietnam. Sensitivity and specificity were calculated for the xTAG GPP for the seven principal diarrheal etiologies. The sensitivity and specificity for the xTAG GPP were >88% for Shigellaspp.,Campylobacterspp., rotavirus, norovirus genotype 1/2 (GI/GII), and adenovirus compared to those of microbiological culture and/or real-time PCR. However, the specificity was low (∼60%) for Salmonella species. Additionally, a number of important pathogens that are not identified in routine hospital procedures in this setting, such as Cryptosporidiumspp. and Clostridium difficile, were detected with the GPP. The use of the Luminex xTAG GPP for the detection of enteric pathogens in settings, like Vietnam, would dramatically improve the diagnostic accuracy and capacity of hospital laboratories, allowing for timely and appropriate therapy decisions and a wider understanding of the epidemiology of pathogens associated with severe diarrheal disease in low-resource settings.
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Fumian TM, Leite JPG, Rocha MS, de Andrade JS, Fioretti JM, de Assis RM, Assis MR, Fialho AM, Miagostovich MP. Performance of a one-step quantitative duplex RT-PCR for detection of rotavirus A and noroviruses GII during two periods of high viral circulation. J Virol Methods 2016; 228:123-9. [DOI: 10.1016/j.jviromet.2015.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 01/27/2023]
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Otto PH, Rosenhain S, Elschner MC, Hotzel H, Machnowska P, Trojnar E, Hoffmann K, Johne R. Detection of rotavirus species A, B and C in domestic mammalian animals with diarrhoea and genotyping of bovine species A rotavirus strains. Vet Microbiol 2015. [DOI: 10.1016/j.vetmic.2015.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Thanh TT, Anh NT, Tham NT, Van HMT, Sabanathan S, Qui PT, Ngan TT, Van TTM, Nguyet LA, Ny NTH, Thanh LTM, Chai OK, Perera D, Viet DC, Khanh TH, Ha DQ, Tuan HM, Wong KT, Hung NT, Chau NVV, Thwaites G, van Doorn HR, Van Tan L. Validation and utilization of an internally controlled multiplex Real-time RT-PCR assay for simultaneous detection of enteroviruses and enterovirus A71 associated with hand foot and mouth disease. Virol J 2015; 12:85. [PMID: 26050791 PMCID: PMC4464700 DOI: 10.1186/s12985-015-0316-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/30/2015] [Indexed: 11/12/2022] Open
Abstract
Background Hand foot and mouth disease (HFMD) is a disease of public health importance across the Asia-Pacific region. The disease is caused by enteroviruses (EVs), in particular enterovirus A71 (EV-A71). In EV-A71-associated HFMD, the infection is sometimes associated with severe manifestations including neurological involvement and fatal outcome. The availability of a robust diagnostic assay to distinguish EV-A71 from other EVs is important for patient management and outbreak response. Methods We developed and validated an internally controlled one-step single-tube real-time RT-PCR in terms of sensitivity, linearity, precision, and specificity for simultaneous detection of EVs and EV-A71. Subsequently, the assay was then applied on throat and rectal swabs sampled from 434 HFMD patients. Results The assay was evaluated using both plasmid DNA and viral RNA and has shown to be reproducible with a maximum assay variation of 4.41 % and sensitive with a limit of detection less than 10 copies of target template per reaction, while cross-reactivity with other EV serotypes was not observed. When compared against a published VP1 nested RT-PCR using 112 diagnostic throat and rectal swabs from 112 children with a clinical diagnosis of HFMD during 2014, the multiplex assay had a higher sensitivity and 100 % concordance with sequencing results which showed EVs in 77/112 (68.8 %) and EV-A71 in 7/112 (6.3 %). When applied to clinical diagnostics for 322 children, the assay detected EVs in throat swabs of 257/322 (79.8 %) of which EV-A71 was detected in 36/322 (11.2 %) children. The detection rate increased to 93.5 % (301/322) and 13.4 % (43/322) for EVs and EV-A71, respectively, when rectal swabs from 65 throat-negative children were further analyzed. Conclusion We have successfully developed and validated a sensitive internally controlled multiplex assay for rapid detection of EVs and EV-A71, which is useful for clinical management and outbreak control of HFMD. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0316-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tran Tan Thanh
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.
| | - Nguyen To Anh
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Tham
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | | | - Saraswathy Sabanathan
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Phan Tu Qui
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Thuy Ngan
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | | | - Lam Anh Nguyet
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Han Ny
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | | | - Ong Kien Chai
- Facuty of Medicine, University of Malaya, Lumpur, Malaysia
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Do Chau Viet
- Children Hospital Number Two, Ho Chi Minh City, Vietnam
| | | | - Do Quang Ha
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Ha Manh Tuan
- Children Hospital Number Two, Ho Chi Minh City, Vietnam
| | - Kum Thong Wong
- Facuty of Medicine, University of Malaya, Lumpur, Malaysia
| | | | | | - Guy Thwaites
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford University Clinical Research Unit in partnership with the Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
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Anders KL, Thompson CN, Thuy NTV, Nguyet NM, Tu LTP, Dung TTN, Phat VV, Van NTH, Hieu NT, Tham NTH, Ha PTT, Lien LB, Chau NVV, Baker S, Simmons CP. The epidemiology and aetiology of diarrhoeal disease in infancy in southern Vietnam: a birth cohort study. Int J Infect Dis 2015; 35:3-10. [PMID: 25813553 PMCID: PMC4508461 DOI: 10.1016/j.ijid.2015.03.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 01/11/2023] Open
Abstract
The diarrhoeal disease burden in a large, prospective infant cohort in Vietnam is defined. Minimum incidence of clinic-based diarrhoea in infants: 271/1000 infant-years. Rotavirus was most commonly identified, followed by norovirus and bacterial pathogens. Frequent repeat infections with the same pathogen within 1 year. Inclusion of rotavirus in the immunization schedule for Vietnam is warranted.
Objectives Previous studies indicate a high burden of diarrhoeal disease in Vietnamese children, however longitudinal community-based data on burden and aetiology are limited. The findings from a large, prospective cohort study of diarrhoeal disease in infants in southern Vietnam are presented herein. Methods Infants were enrolled at birth in urban Ho Chi Minh City and a semi-rural district in southern Vietnam, and followed for 12 months (n = 6706). Diarrhoeal illness episodes were identified through clinic-based passive surveillance, hospital admissions, and self-reports. Results The minimum incidence of diarrhoeal illness in the first year of life was 271/1000 infant-years of observation for the whole cohort. Rotavirus was the most commonly detected pathogen (50% of positive samples), followed by norovirus (24%), Campylobacter (20%), Salmonella (18%), and Shigella (16%). Repeat infections were identified in 9% of infants infected with rotavirus, norovirus, Shigella, or Campylobacter, and 13% of those with Salmonella infections. Conclusions The minimum incidence of diarrhoeal disease in infants in both urban and semi-rural settings in southern Vietnam was quantified prospectively. A large proportion of laboratory-diagnosed disease was caused by rotavirus and norovirus. These data highlight the unmet need for a rotavirus vaccine in Vietnam and provide evidence of the previously unrecognized burden of norovirus in infants.
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Affiliation(s)
- Katherine L Anders
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia.
| | - Corinne N Thompson
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; The London School of Hygiene and Tropical Medicine, London, UK
| | - Nguyen Thi Van Thuy
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Minh Nguyet
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam; The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Thi Phuong Tu
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Dung
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
| | - Voong Vinh Phat
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Hong Van
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam
| | | | | | | | - Le Bich Lien
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; The London School of Hygiene and Tropical Medicine, London, UK
| | - Cameron P Simmons
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
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Abstract
OBJECTIVES Because rotavirus gastroenteritis is associated with high morbidity and mortality especially in developing countries, it is necessary to develop antirotavirus drugs for the treatment of rotavirus infection. Previous studies have demonstrated that cyclosporin A (CsA) has antiviral properties against rotavirus. Its effect has not yet been evaluated against rotavirus diarrheal disease. The aim of this study was to assess the anti-rotavirus efficacy of CsA in neonatal mice after induction of rotavirus diarrhea. METHODS Suckling mice were inoculated with murine rotavirus. On the onset of diarrhea, mice were given different concentrations of CsA. To evaluate the effects of CsA on reduction of rotavirus diarrhea, diarrhea score, fecal virus shedding, and pathological lesion change in the small intestine, messenger RNA (mRNA) expression levels in the small intestine and spleen of mice were measured for type I interferon (IFN-α and IFN-β), inflammation-related cytokines (interleukin [IL]-8, IL-10, IFN-γ, and tumor necrosis factor-α), and inflammatory signaling pathways (p38, c-Jun N-terminal kinase, activator protein-1, and nuclear factor-kappa B). RESULTS Among virus-inoculated and CsA-treated groups, a dose of 5 mg · kg⁻¹ · day⁻¹ of CsA inhibited diarrhea and improved fecal virus shedding and intestinal lesion changes. IFN-β mRNA expression was significantly increased in rotavirus-induced diarrhea mice treated with 5 mg · kg⁻¹ · day⁻¹ of CsA, whereas the mRNA expression levels of inflammation-related cytokines (IL-8, IL-10, IFN-γ, and tumor necrosis factor-α) and inflammatory signaling pathways (p38, c-Jun N-terminal kinase, activator protein-1, and nuclear factor-kappa B) were markedly decreased. Antiviral effects of CsA were dose dependent. CONCLUSIONS CsA can inhibit rotavirus infection in neonatal mice through its antiviral properties. The mechanism for this may be through CsA suppression of inflammation by viral inhibition in animal models.
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Thompson CN, Anders KL, Nhi LTQ, Tuyen HT, Van Minh P, Tu LTP, Nhu TDH, Nhan NTT, Ly TTT, Duong VT, Vi LL, Van Thuy NT, Hieu NT, Van Chau NV, Campbell JI, Thwaites G, Simmons C, Baker S. A cohort study to define the age-specific incidence and risk factors of Shigella diarrhoeal infections in Vietnamese children: a study protocol. BMC Public Health 2014; 14:1289. [PMID: 25514820 PMCID: PMC4300998 DOI: 10.1186/1471-2458-14-1289] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/12/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Shigella spp. are one of the most common causes of paediatric dysentery globally, responsible for a substantial proportion of diarrhoeal disease morbidity and mortality, particularly in industrialising regions. Alarming levels of antimicrobial resistance are now reported in S. flexneri and S. sonnei, hampering treatment options. Little is known, however, about the burden of infection and disease due to Shigella spp. in the community. METHODS/DESIGN In order to estimate the incidence of this bacterial infection in the community in Ho Chi Minh City, Vietnam we have designed a longitudinal cohort to follow up approximately 700 children aged 12-60 months for two years with active and passive surveillance for diarrhoeal disease. Children will be seen at 6 month intervals for health checks where blood and stool samples will be collected. Families will also be contacted every two weeks for information on presence of diarrhoea in the child. Upon report of a diarrhoeal disease episode, study nurses will either travel to the family home to perform an evaluation or the family will attend a study hospital at a reduced cost, where a stool sample will also be collected. Case report forms collected at this time will detail information regarding disease history, risk factors and presence of disease in the household.Outcomes will include (i) age-specific incidence of Shigella spp. and other agents of diarrhoeal disease in the community, (ii) risk factors for identified aetiologies, (iii) rates of seroconversion to a host of gastrointestinal pathogens in the first few years of life. Further work regarding the longitudinal immune response to a variety of Shigella antigens, host genetics and candidate vaccine/diagnostic proteins will also be conducted. DISCUSSION This is the largest longitudinal cohort with active surveillance designed specifically to investigate Shigella infection and disease. The study is strengthened by the active surveillance component, which will likely capture a substantial proportion of episodes not normally identified through passive or hospital-based surveillance. It is hoped that information from this study will aid in the design and implementation of Shigella vaccine trials in the future.
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Affiliation(s)
- Corinne N Thompson
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- />The London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine L Anders
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- />Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Le Thi Quynh Nhi
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Van Minh
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Le Thi Phuong Tu
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Do Hoang Nhu
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Thanh Nhan
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Thi Thao Ly
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Lu Lan Vi
- />Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | | | | | | | - James I Campbell
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy Thwaites
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cameron Simmons
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- />Department of Microbiology & Immunology, University of Melbourne, Melbourne, Australia
| | - Stephen Baker
- />Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- />Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- />The London School of Hygiene & Tropical Medicine, London, UK
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Real-time PCR identification of agents causing diarrhea in Rwandan children less than 5 years of age. Pediatr Infect Dis J 2014; 33:1037-42. [PMID: 25037040 DOI: 10.1097/inf.0000000000000448] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Knowledge about causes of acute diarrhea among children in developing countries is insufficient. Molecular methods might improve diagnostics of infectious gastroenteritis, but due to the high sensitivity, findings may be difficult to interpret. METHODS Feces samples from Rwandan children 0.5-5.0 years of age, with diarrhea for <96 hours (patients, n = 544) or without diarrhea for 14 days (controls, n = 162), were analyzed by real-time polymerase chain reaction targeting 17 pathogens. RESULTS At least 1 agent was detected in 94% of patients and in 79% of controls, with higher rates in sick children for rotavirus (42% vs. 2%, P < 0.0001) and enterotoxigenic Escherichia coli (ETEC)-estA (21% vs. 9%, P = 0.0006). Detection rates did not differ significantly for adenovirus (39% vs. 36%), ETEC-eltB (29% vs. 30%), Campylobacter (14% vs. 17%) or Shigella (13% vs. 10%), but for Shigella the threshold cycle (Ct) values were lower (pathogen loads were higher) in sick children than in controls. By multivariate analysis, including gender and age, detection of rotavirus (P < 0.0001), ETEC-estA (P = 0.001), Shigella (P = 0.004) and norovirus genogroup II (P = 0.009) was associated with symptomatic infection, and a Ct value below a cutoff (in the range 28-29) improved identification of ETEC-estA, Shigella and norovirus genogroup II. CONCLUSION Real-time polymerase chain reaction can detect essentially all diarrheagenic agents, and provides Ct values that improve identification of clinically relevant infections.
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Kabayiza JC, Andersson ME, Nilsson S, Baribwira C, Muhirwa G, Bergström T, Lindh M. Diarrhoeagenic microbes by real-time PCR in Rwandan children under 5 years of age with acute gastroenteritis. Clin Microbiol Infect 2014; 20:O1128-35. [PMID: 24890572 DOI: 10.1111/1469-0691.12698] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/20/2014] [Accepted: 05/26/2014] [Indexed: 11/29/2022]
Abstract
Acute gastroenteritis is a main cause of disease and death among children in low-income countries. The causality rates and pathogenic characteristics of putative aetiological agents remain insufficiently known. We used real-time PCR targeting 16 diarrhoeagenic agents to analyse stool samples from children ≤5.0 years old with acute diarrhoea in Rwanda. Among the 880 children (median age 14.2 months; 41% female) at least one pathogen was detected in 92% and two or more agents in 63% of cases. Rotavirus was detected in 36.9%, adenovirus in 39.7%, enterotoxigenic Escherichia coli (ETEC) with genes for labile (eltB) or stable (estA) toxin in 31.3% and 19.0%, E. coli with eae or bfpA genes in 25.2% and 14.2%, Shigella in 17.5% and Cryptosporidium in 7.8%. Rotavirus and ETEC-estA were associated with more severe dehydration than diarrhoea due to other causes. Shigella was associated with bloody stools and higher CRP. Microbial loads (Ct values) of rotavirus, ETEC-estA and Shigella were associated with severity of symptoms. Rotavirus, ETEC-estA and E. coli with bfpA were associated with younger age, Shigella with older age. Antibiotic treatment was given to 42% and was associated with dehydration, fever and CRP, but not with pathogen. We conclude that rotavirus and ETEC-estA were the most important causes of diarrhoea with dehydration, that Shigella caused bloody diarrhoea but less severe dehydration, that microbial loads of rotavirus, ETEC-estA and Shigella were associated with severity of symptoms, and that antibiotic use was frequent and in poor agreement with microbiological findings.
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Affiliation(s)
- J-C Kabayiza
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Department of Paediatrics, National University of Rwanda, Kigali, Rwanda
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Development and evaluation of new primers for PCR-based identification of Prevotella intermedia. Anaerobe 2014; 28:126-9. [PMID: 24875331 DOI: 10.1016/j.anaerobe.2014.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 04/14/2014] [Accepted: 05/16/2014] [Indexed: 02/05/2023]
Abstract
The aim of this study was to develop new Prevotella intermedia-specific PCR primers based on the 16S rRNA. The new primer set, Pi-192 and Pi-468, increased the accuracy of PCR-based P. intermedia identification and could be useful in the detection of P. intermedia as well as epidemiological studies on periodontal disease.
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A two-tube multiplex reverse transcription PCR assay for simultaneous detection of viral and bacterial pathogens of infectious diarrhea. BIOMED RESEARCH INTERNATIONAL 2014; 2014:648520. [PMID: 24711998 PMCID: PMC3966319 DOI: 10.1155/2014/648520] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/26/2014] [Accepted: 02/02/2014] [Indexed: 12/20/2022]
Abstract
Diarrhea caused by viral and bacterial infections is a major health problem in developing countries. The purpose of this study is to develop a two-tube multiplex PCR assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial Centers for Diseases Control and Prevention, China. The assay was designed to detect rotavirus A, norovirus genogroups GI and GII, human astrovirus, enteric adenoviruses, and human bocavirus (tube 1), and Salmonella, Vibrio parahaemolyticus, diarrheagenic Escherichia coli, Campylobacter jejuni, Shigella, Yersinia, and Vibrio cholera (tube 2). The analytical specificity was examined with positive controls for each pathogen. The analytical sensitivity was evaluated by performing the assay on serial tenfold dilutions of in vitro transcribed RNA, recombinant plasmids, or bacterial culture. A total of 122 stool samples were tested by this two-tube assay and the results were compared with those obtained from reference methods. The two-tube assay achieved a sensitivity of 20–200 copies for a single virus and 102-103 CFU/mL for bacteria. The clinical performance demonstrated that the two-tube assay had comparable sensitivity and specificity to those of reference methods. In conclusion, the two-tube assay is a rapid, cost-effective, sensitive, specific, and high throughput method for the simultaneous detection of enteric bacteria and virus.
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Pham HA, Carrique-Mas JJ, Nguyen VC, Ngo TH, Nguyet LA, Do TD, Vo BH, Phan VTM, Rabaa MA, Farrar J, Baker S, Bryant JE. The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam. Vet Microbiol 2014; 170:258-65. [PMID: 24679960 PMCID: PMC4003349 DOI: 10.1016/j.vetmic.2014.02.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/10/2014] [Accepted: 02/17/2014] [Indexed: 12/15/2022]
Abstract
Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children worldwide and the cause of approximately 45% of pediatric hospitalizations for acute diarrhea in Vietnam. ARoVs are known to cause significant economic losses to livestock producers by reducing growth performance and production efficiencies, however little is known about the implications of asymptomatic endemic circulation of ARoV. We aimed to determine the prevalence and predominant circulating genotypes of ARoVs on pig farms in a southern province of Vietnam. We found overall animal-level and farm-level prevalence of 32.7% (239/730) and 74% (77/104), respectively, and identified six different G types and 4 P types in various combinations (G2, G3, G4, G5, G9, G11 and P[6], P[13], P[23], and P[34]). There was no significant association between ARoV infection and clinical disease in pigs, suggesting that endemic asymptomatic circulation of ARoV may complicate rotavirus disease attribution during outbreaks of diarrhea in swine. Sequence analysis of the detected ARoVs suggested homology to recent human clinical cases and extensive genetic diversity. The epidemiological relevance of these findings for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study.
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Affiliation(s)
- Hong Anh Pham
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Juan J Carrique-Mas
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Van Cuong Nguyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Thi Hoa Ngo
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | | | - Be Hien Vo
- Sub-Department of Animal Health, Dong Thap, Viet Nam
| | - Vu Tra My Phan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; University of Edinburgh, London, United Kingdom
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom
| | - Stephen Baker
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom; The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom.
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Le VT, de Jong MD, Nguyen VK, Nguyen VT, Taylor W, Wertheim HFL, van der Ende A, van der Hoek L, Canuti M, Crusat M, Sona S, Nguyen HU, Giri A, Nguyen TTCB, Ho DTN, Farrar J, Bryant JE, Tran TH, Nguyen VVC, van Doorn HR. Limited geographic distribution of the novel cyclovirus CyCV-VN. Sci Rep 2014; 4:3967. [PMID: 24495921 PMCID: PMC3913916 DOI: 10.1038/srep03967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/17/2014] [Indexed: 01/03/2023] Open
Abstract
A novel cyclovirus, CyCV-VN, was recently identified in cerebrospinal fluid (CSF) from patients with central nervous system (CNS) infections in central and southern Vietnam. To explore the geographic distribution of this novel virus, more than 600 CSF specimens from patients with suspected CNS infections in northern Vietnam, Cambodia, Nepal and The Netherlands were screened for the presence of CyCV-VN but all were negative. Sequence comparison and phylogenetic analysis between CyCV-VN and another novel cyclovirus recently identified in CSF from Malawian patients indicated that these represent distinct cycloviral species, albeit phylogenetically closely related. The data suggest that CyCV-VN has a limited geographic distribution within southern and central Vietnam. Further research is needed to determine the global distribution and diversity of cycloviruses and importantly their possible association with human disease.
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Affiliation(s)
- Van Tan Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Menno D de Jong
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Van Kinh Nguyen
- 1] National Hospital for Tropical Diseases, Hanoi, Vietnam [2] Hanoi Medical University, Hanoi, Vietnam
| | - Vu Trung Nguyen
- 1] National Hospital for Tropical Diseases, Hanoi, Vietnam [2] Hanoi Medical University, Hanoi, Vietnam
| | - Walter Taylor
- 1] Oxford University Clinical Research Unit, Hanoi, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heiman F L Wertheim
- 1] Oxford University Clinical Research Unit, Hanoi, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Arie van der Ende
- 1] Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands [2] The Netherlands National Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marta Canuti
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Martin Crusat
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Soeng Sona
- Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia
| | - Hanh Uyen Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Abhishek Giri
- Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal
| | | | - Dang Trung Nghia Ho
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam [3] Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juliet E Bryant
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tinh Hien Tran
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - H Rogier van Doorn
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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40
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Real-time PCR threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in Zanzibar. J Clin Microbiol 2014; 52:916-23. [PMID: 24403298 DOI: 10.1128/jcm.02697-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular assays might improve the identification of causes of acute diarrheal disease but might lead to more frequent detection of asymptomatic infections. In the present study, real-time PCR targeting 14 pathogens was applied to rectal swabs from 330 children aged 2 to 59 months in Zanzibar, including 165 patients with acute diarrhea and 165 asymptomatic control subjects. At least one pathogen was detected for 94% of the patients and 84% of the controls, with higher rates among patients for norovirus genogroup II (20% versus 2.4%; P<0.0001), rotavirus (10% versus 1.8%; P=0.003), and Cryptosporidium (30% versus 11%; P<0.0001). Detection rates did not differ significantly for enterotoxigenic Escherichia coli (ETEC)-estA (33% versus 24%), ETEC-eltB (44% versus 46%), Shigella (35% versus 33%), and Campylobacter (35% versus 33%), but for these agents threshold cycle (CT) values were lower (pathogen loads were higher) in sick children than in controls. In a multivariate analysis, CT values for norovirus genogroup II, rotavirus, Cryptosporidium, ETEC-estA, and Shigella were independently associated with diarrhea. We conclude that this real-time PCR allows convenient detection of essentially all diarrheagenic agents and provides CT values that may be critical for the interpretation of results for pathogens with similar detection rates in patients and controls. The results indicate that the assessment of pathogen loads may improve the identification of agents causing gastroenteritis in children.
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41
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Miura T, Parnaudeau S, Grodzki M, Okabe S, Atmar RL, Le Guyader FS. Environmental detection of genogroup I, II, and IV noroviruses by using a generic real-time reverse transcription-PCR assay. Appl Environ Microbiol 2013; 79:6585-92. [PMID: 23956397 PMCID: PMC3811514 DOI: 10.1128/aem.02112-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/13/2013] [Indexed: 01/16/2023] Open
Abstract
Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups.
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Affiliation(s)
- Takayuki Miura
- Laboratoire de Microbiologie, IFREMER, Nantes, France
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | | | - Marco Grodzki
- Laboratoire de Microbiologie, IFREMER, Nantes, France
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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Kolader ME, Vinh H, Ngoc Tuyet PT, Thompson C, Wolbers M, Merson L, Campbell JI, Ngoc Dung TT, Manh Tuan H, Vinh Chau NV, Farrar J, van Doorn HR, Baker S. An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial. Trials 2013; 14:27. [PMID: 23356823 PMCID: PMC3563448 DOI: 10.1186/1745-6215-14-27] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/27/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Diarrhoeal disease is a major global health problem, particularly affecting children under the age of 5 years. Besides oral rehydration solution, probiotics are also commonly prescribed to children with acute watery diarrhoea in some settings. Results from randomised clinical trials (RCTs) in which investigators studied the effect of probiotics on diarrhoeal symptoms have largely shown a positive effect; yet, the overall quality of the data is limited. In Vietnam, probiotics are the most frequently prescribed treatment for children hospitalised with acute watery diarrhoea, but there is little justification for this treatment in this location. We have designed a RCT to test the hypothesis that an oral preparation of Lactobacillus acidophilus is superior to placebo in the treatment of acute watery diarrhoea in Vietnamese children. METHODS This RCT was designed to study the effect of treatment with L. acidophilus (4 × 109 colony-forming units/day) for 5 days for acute watery diarrhoea against a placebo in 300 children ages 9 to 60 months admitted to hospitals in Vietnam. Clinical and laboratory data plus samples will be collected on admission, daily during hospitalisation, at discharge, and at follow-up visits for a subset of participants. The primary end point will be defined as the time from the first dose of study medication to the start of the first 24-hour period without diarrhoea as assessed by the on-duty nurse. Secondary endpoints include the time to cessation of diarrhoea as recorded by parents or guardians in an hourly checklist, stool frequency over the first 3 days, treatment failure, rotavirus and norovirus viral loads, and adverse events. DISCUSSION The existing evidence for the use of probiotics in treating acute watery diarrhoea seems to favour their use. However, the size of the effect varies across publications. An array of different probiotic organisms, doses, treatment durations, study populations, designs, settings, and aetiologies have been described. In this trial, we will investigate whether probiotics are beneficial as an adjuvant treatment for children with acute watery diarrhoea in Vietnam, with the aim of guiding clinical practice through improved regional evidence. TRIAL REGISTRATION Current Controlled Trials ISRCTN88101063.
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Affiliation(s)
- Marion-Eliëtte Kolader
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Medical Microbiology, Academic Medical Centre, Amsterdam, the Netherlands
| | - Ha Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Corinne Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Marcel Wolbers
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Laura Merson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Tran Thi Ngoc Dung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Manh Tuan
- Children’s Hospital 2, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Jeremy Farrar
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - H Rogier van Doorn
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- The London School of Hygiene and Tropical Medicine, London, UK
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43
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Kolader ME, Vinh H, Ngoc Tuyet PT, Thompson C, Wolbers M, Merson L, Campbell JI, Ngoc Dung TT, Manh Tuan H, Vinh Chau NV, Farrar J, van Doorn HR, Baker S. An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial. Trials 2013. [PMID: 23356823 DOI: 10.1186/1745-6215-14-27.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diarrhoeal disease is a major global health problem, particularly affecting children under the age of 5 years. Besides oral rehydration solution, probiotics are also commonly prescribed to children with acute watery diarrhoea in some settings. Results from randomised clinical trials (RCTs) in which investigators studied the effect of probiotics on diarrhoeal symptoms have largely shown a positive effect; yet, the overall quality of the data is limited. In Vietnam, probiotics are the most frequently prescribed treatment for children hospitalised with acute watery diarrhoea, but there is little justification for this treatment in this location. We have designed a RCT to test the hypothesis that an oral preparation of Lactobacillus acidophilus is superior to placebo in the treatment of acute watery diarrhoea in Vietnamese children. METHODS This RCT was designed to study the effect of treatment with L. acidophilus (4 × 109 colony-forming units/day) for 5 days for acute watery diarrhoea against a placebo in 300 children ages 9 to 60 months admitted to hospitals in Vietnam. Clinical and laboratory data plus samples will be collected on admission, daily during hospitalisation, at discharge, and at follow-up visits for a subset of participants. The primary end point will be defined as the time from the first dose of study medication to the start of the first 24-hour period without diarrhoea as assessed by the on-duty nurse. Secondary endpoints include the time to cessation of diarrhoea as recorded by parents or guardians in an hourly checklist, stool frequency over the first 3 days, treatment failure, rotavirus and norovirus viral loads, and adverse events. DISCUSSION The existing evidence for the use of probiotics in treating acute watery diarrhoea seems to favour their use. However, the size of the effect varies across publications. An array of different probiotic organisms, doses, treatment durations, study populations, designs, settings, and aetiologies have been described. In this trial, we will investigate whether probiotics are beneficial as an adjuvant treatment for children with acute watery diarrhoea in Vietnam, with the aim of guiding clinical practice through improved regional evidence. TRIAL REGISTRATION Current Controlled Trials ISRCTN88101063.
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Affiliation(s)
- Marion-Eliëtte Kolader
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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