1
|
Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
Collapse
Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
| |
Collapse
|
4
|
Xia H, Gravelsina S, Öhrmalm C, Ottoson J, Blomberg J. Development of single-tube nested real-time PCR assays with long internally quenched probes for detection of norovirus genogroup II. Biotechniques 2016; 60:28-34. [PMID: 26757809 DOI: 10.2144/000114370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/16/2015] [Indexed: 11/23/2022] Open
Abstract
The high sequence variation of RNA viruses necessitates use of degenerate primers and probes or multiple primers and probes in molecular diagnostic assays. We showed previously that PCR amplification in two rounds, first with long target-specific primers and then with short generic primers, followed by detection using long probes, can tolerate sequence variation. Here we demonstrate that long primers and probes of up to 56 nucleotides can also be applied in real-time PCR for the detection of norovirus genogroup II with improved sensitivity. Probe design (method of incorporating quenchers, use of Zen internal quencher or traditional quenchers) greatly affects the sensitivity of the real-time PCR assays.
Collapse
Affiliation(s)
- Hongyan Xia
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sabine Gravelsina
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden.,August Kirchenstein Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Christina Öhrmalm
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | - Jakob Ottoson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Risk and Benefit Assessment, National Food Administration, Uppsala, Sweden
| | - Jonas Blomberg
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| |
Collapse
|
5
|
Ukekwe FI, Nwajiobi C, Agbo MO, Ebede SO, Eni AO. Candidiasis, A Rare Cause of Gastric Perforation: A Case Report and Review of Literature. Ann Med Health Sci Res 2015; 5:314-6. [PMID: 26229723 PMCID: PMC4512127 DOI: 10.4103/2141-9248.160187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Fungi are unusually rare causes of gastric perforation, with most cases of gastric perforation occurring as complications of peptic ulcer disease (PUD), nonsteroidal anti-inflammatory drugs (NSAIDs) and gastric neoplasms. Here, we report the case of a 70-year-old Nigerian male who presented with severe epigastric pain, with no associated history of PUD, NSAIDs use or gastric neoplasm. An emergency exploratory laparotomy was performed and a gastric perforation was discovered and repaired. Histopathological examination of the gastric perforation edge biopsy revealed an intense Candida growth consisting of numerous fungal spores and hyphae invading and destroying the gastric wall. He was subsequently treated with fluconazole antifungal and discharged home after an uneventful postoperative period.
Collapse
Affiliation(s)
- F I Ukekwe
- Department of Morbid Anatomy, University of Nigeria, Enugu Campus, Enugu/University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| | - C Nwajiobi
- Division of General Surgery, Department of Surgery, University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| | - M O Agbo
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - S O Ebede
- Department of Medical Microbiology, University of Nigeria, Enugu Campus, Enugu/University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| | - A O Eni
- Department of Morbid Anatomy, University of Nigeria, Enugu Campus, Enugu/University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| |
Collapse
|
8
|
Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
Collapse
Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| |
Collapse
|
9
|
Di Carlo P, Di Vita G, Guadagnino G, Cocorullo G, D’Arpa F, Salamone G, Salvatore B, Gulotta G, Cabibi D. Surgical pathology and the diagnosis of invasive visceral yeast infection: two case reports and literature review. World J Emerg Surg 2013; 8:38. [PMID: 24067049 PMCID: PMC3849356 DOI: 10.1186/1749-7922-8-38] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/23/2013] [Indexed: 01/14/2023] Open
Abstract
Invasive mycoses are life-threatening opportunistic infections that have recently emerged as a cause of morbidity and mortality following general and gastrointestinal surgery.Candida species are the main fungal strains of gut flora. Gastrointestinal tract surgery might lead to mucosal disruption and cause Candida spp. to disseminate in the bloodstream.Here we report and discuss the peculiar clinical and morphological presentation of two cases of gastrointestinal Candida albicans lesions in patients who underwent abdominal surgery.Although in the majority of cases reported in the literature, diagnosis was made on the basis of microbiological criteria, we suggest that morphological features of fungi in histological sections of appropriate surgical specimens could help to detect the degree of yeast colonization and identify patients at risk of developing severe abdominal Candida infection.Better prevention and early antifungal treatments are highlighted, and relevant scientific literature is reviewed.
Collapse
Affiliation(s)
- Paola Di Carlo
- Department of Sciences for Health Promotion and Mother-Child Care “G. D’Alessandro”, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Gaetano Di Vita
- Department of Surgery and Oncology Sciences, General Surgery Unit, University of Study of Palermo, Italy, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Giuliana Guadagnino
- Department of Sciences for Health Promotion and Mother-Child Care “G. D’Alessandro”, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Gianfranco Cocorullo
- Department of General Surgery, Urgency and Organ Transplantation, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Francesco D’Arpa
- Department of General Surgery, Urgency and Organ Transplantation, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Giuseppe Salamone
- Department of General Surgery, Urgency and Organ Transplantation, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Buscemi Salvatore
- Department of Surgery and Oncology Sciences, General Surgery Unit, University of Study of Palermo, Italy, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Gaspare Gulotta
- Department of General Surgery, Urgency and Organ Transplantation, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| | - Daniela Cabibi
- Department of Sciences for Health Promotion and Mother-Child Care “G. D’Alessandro”, University of Palermo, Via del Vespro 127, I- 90127 Palermo, Italy
| |
Collapse
|
10
|
Weinberg GA, Schnabel KC, Erdman DD, Prill MM, Iwane MK, Shelley LM, Whitaker BL, Szilagyi PG, Hall CB. Field evaluation of TaqMan Array Card (TAC) for the simultaneous detection of multiple respiratory viruses in children with acute respiratory infection. J Clin Virol 2013; 57:254-60. [PMID: 23608639 PMCID: PMC7108303 DOI: 10.1016/j.jcv.2013.03.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/03/2022]
Abstract
Background Multipathogen reverse transcription real-time PCR (RT-qPCR) platforms have proven useful in surveillance for acute respiratory illness (ARI) and study of respiratory outbreaks of unknown etiology. The TaqMan® Array Card (TAC, Life Technologies™), can simultaneously test 7 clinical specimens for up to 21 individual pathogens (depending on arrangement of controls and use of duplicate wells) by arrayed singleplex RT-qPCR on a single assay card, using minimal amounts of clinical specimens. A previous study described the development of TAC for the detection of respiratory viral and bacterial pathogens; the assay was evaluated against well-characterized analytical materials and a limited collection of human clinical specimens. Objectives We wished to compare TAC assay performance against standard individual RT-qPCR assays for respiratory viral detection, focusing on 10 viruses (adenovirus, human metapneumovirus, human parainfluenza viruses 1–4, influenza viruses A and B, respiratory syncytial virus, and rhinovirus) from a larger collection of human specimens. Study design We used specimens from 942 children with ARI enrolled systematically in a population-based, ARI surveillance study (New Vaccine Surveillance Network, NVSN). Results Compared with standard individual RT-qPCR assays, the sensitivity of TAC for the targeted viruses ranged from 54% to 95% (54%, 56%, and 75% for adenovirus, human parainfluenza viruses-1 and -2, respectively, and 82%–95% for the other viruses). Assay specificity was 99%, and coefficients of variation for virus controls ranged from 1.5% to 4.5%. Conclusion The TAC assay should prove useful for multipathogen studies and rapid outbreak response.
Collapse
Affiliation(s)
- Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States.
| | | | | | | | | | | | | | | | | |
Collapse
|