151
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Cox C, McKenna JP, Watt AP, Coyle PV. New assay for Gardnerella vaginalis loads correlates with Nugent scores and has potential in the diagnosis of bacterial vaginosis. J Med Microbiol 2015; 64:978-984. [DOI: 10.1099/jmm.0.000118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ciara Cox
- Regional Virus Laboratory, Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
| | - James P. McKenna
- Regional Virus Laboratory, Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
| | - Alison P. Watt
- Regional Virus Laboratory, Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
| | - Peter V. Coyle
- Regional Virus Laboratory, Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
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152
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Noll LW, Shridhar PB, Shi X, An B, Cernicchiaro N, Renter DG, Nagaraja TG, Bai J. A Four-Plex Real-Time PCR Assay, Based on rfbE, stx1, stx2, and eae Genes, for the Detection and Quantification of Shiga Toxin-Producing Escherichia coli O157 in Cattle Feces. Foodborne Pathog Dis 2015; 12:787-94. [PMID: 26317538 DOI: 10.1089/fpd.2015.1951] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several real-time polymerase chain reaction (PCR) assays have been developed to detect and quantify Shiga toxin-producing Escherichia coli (STEC) O157:H7, but none have targeted the O-antigen specific gene (rfbEO157) in combination with the three major virulence genes, stx1, stx2, and eae. Our objectives were to develop and validate a four-plex, quantitative PCR (mqPCR) assay targeting rfbE(O157), stx1, stx2, and eae for the detection and quantification of STEC O157 in cattle feces, and compare the applicability of the assay to detect STEC O157 to a culture method and conventional PCR (cPCR) targeting the same four genes. Specificity of the mqPCR assay to differentially detect the four genes was confirmed with strains of O157 and non-O157 STEC with different profiles of target genes. In cattle feces spiked with pure cultures, detection limits were 2.8×10(4) and 2.8×10(0) colony-forming units/g before and after enrichment, respectively. Detection of STEC O157 in feedlot cattle fecal samples (n=278) was compared between mqPCR, cPCR, and a culture method. The mqPCR detected 48.9% (136/278) of samples as positive for E. coli O157. Of the 100 samples that were randomly picked from 136 mqPCR-positive samples, 35 and 48 tested positive by cPCR and culture method, respectively. Of the 100 samples randomly chosen from 142 mqPCR-negative samples, all were negative by cPCR, but 21 samples tested positive by the culture method. McNemar's chi-square tests indicated significant disagreement between the proportions of positive samples detected by the three methods. In conclusion, the mqPCR assay that targets four genes is a novel and more sensitive method than the cPCR or culture method to detect STEC O157 in cattle feces. However, the use of real-time PCR as a screening method to identify positive samples and then subjecting only positive samples to a culture method may underestimate the presence of STEC O157 in fecal samples.
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Affiliation(s)
- Lance W Noll
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Pragathi B Shridhar
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Xiaorong Shi
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Baoyan An
- 2 Department of Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
| | - Natalia Cernicchiaro
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - David G Renter
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Tiruvoor G Nagaraja
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Jianfa Bai
- 2 Department of Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
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153
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Heaney J, Rolfe K, Gleadall NS, Greatorex JS, Curran MD. Low-Density TaqMan® Array Cards for the Detection of Pathogens. METHODS IN MICROBIOLOGY 2015; 42:199-218. [PMID: 38620215 PMCID: PMC7172410 DOI: 10.1016/bs.mim.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Real-time PCR assays have revolutionised diagnostic microbiology over the past 15 years or more. Adaptations and improvements over that time frame have led to the development of multiplex assays. However, limitations in terms of available fluorophores has meant the number of assays which can be combined has remained in single figures. This latter limitation has led to the focus tending to be on individual pathogens and their detection. This chapter describes the development of TaqMan® Array Cards (TACs), technology which allows the detection of multiple pathogens (up to 48 targets) from a single nucleic acid extract, utilising small volumes and real-time PCR. This in turn lends itself to a syndromic approach to infectious disease diagnosis. Using the examples of TACs we have developed in our own laboratory, as well as others, we explain the design, optimisation and use of TACs for respiratory, gastrointestinal and liver infections. Refinement of individual assays is discussed as well as the incorporation of appropriate internal and process controls onto the array cards. Finally, specific examples are given of instances where the assays have had a direct, positive impact on patient care.
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Affiliation(s)
- Jude Heaney
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
| | - Kathryn Rolfe
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Nicholas S. Gleadall
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Jane S. Greatorex
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Martin D. Curran
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
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154
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Oketič K, Matijašić BB, Obermajer T, Radulović Z, Lević S, Mirković N, Nedović V. Evaluation of propidium monoazide real-time PCR for enumeration of probiotic lactobacilli microencapsulated in calcium alginate beads. Benef Microbes 2015; 6:573-81. [DOI: 10.3920/bm2014.0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aim of the study was to evaluate real-time PCR coupled with propidium monoazide (PMA) treatment for enumeration of microencapsulated probiotic lactobacilli microencapsulated in calcium alginate beads. Lactobacillus gasseri K7 (CCM 7710) and Lactobacillus delbrueckii subsp. bulgaricus (CCM 7712) were analysed by plate counting and PMA real-time PCR during storage at 4 °C for 90 days. PMA was effective in preventing PCR amplification of the target sequences of DNA released from heat-compromised bacteria. The values obtained by real-time PCR of non-treated samples were in general higher than those obtained by real-time PCR of PMA-treated samples or by plate counting, indicating the presence of sub-lethally injured cells. This study shows that plate count could not be completely replaced by culture independent method PMA real-time PCR for enumeration of probiotics, but may rather complement the well-established plate counting, providing useful information about the ratio of compromised bacteria in the samples.
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Affiliation(s)
- K. Oketič
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
| | - B. Bogovič Matijašić
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
| | - T. Obermajer
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
| | - Z. Radulović
- University of Belgrade, Faculty of Agriculture, Department of Food Technology, Nemanjina 6, 11080 Belgrade, Serbia
| | - S. Lević
- University of Belgrade, Faculty of Agriculture, Department of Food Technology, Nemanjina 6, 11080 Belgrade, Serbia
| | - N. Mirković
- University of Belgrade, Faculty of Agriculture, Department of Food Technology, Nemanjina 6, 11080 Belgrade, Serbia
| | - V. Nedović
- University of Belgrade, Faculty of Agriculture, Department of Food Technology, Nemanjina 6, 11080 Belgrade, Serbia
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155
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Guterres A, de Oliveira RC, Fernandes J, Schrago CG, de Lemos ERS. Detection of different South American hantaviruses. Virus Res 2015. [PMID: 26220480 DOI: 10.1016/j.virusres.2015.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hantaviruses are the etiologic agents of Hemorrhagic Fever with Renal Syndrome (HFRS) in Old World, and Hantavirus Pulmonary Syndrome (HPS)/Hantavirus Cardiopulmonary Syndrome (HCPS), in the New World. Serological methods are the most common approach used for laboratory diagnosis of HCPS, however theses methods do not allow the characterization of viral genotypes. The polymerase chain reaction (PCR) has been extensively used for diagnosis of viral infections, including those caused by hantaviruses, enabling detection of few target sequence copies in the sample. However, most studies proposed methods of PCR with species-specific primers. This study developed a simple and reliable diagnostic system by RT-PCR for different hantavirus detection. Using new primers set, we evaluated human and rodent hantavirus positive samples of various regions from Brazil. Besides, we performed computational analyzes to evaluate the detection of other South American hantaviruses. The diagnostic system by PCR proved to be a sensible and simple assay, allowing amplification of Juquitiba virus, Araraquara virus, Laguna Negra virus, Rio Mamore virus and Jabora virus, beyond of the possibility of the detecting Andes, Anajatuba, Bermejo, Choclo, Cano Delgadito, Lechiguanas, Maciel, Oran, Pergamino and Rio Mearim viruses. The primers sets designed in this study can detect hantaviruses from almost all known genetics lineages in Brazil and from others South America countries and also increases the possibility to detect new hantaviruses. These primers could easily be used both in diagnosis of suspected hantavirus infections in humans and also in studies with animals reservoirs.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Renata Carvalho de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Carlos Guerra Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elba Regina Sampaio de Lemos
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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156
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Brendish NJ, Schiff HF, Clark TW. Point-of-care testing for respiratory viruses in adults: The current landscape and future potential. J Infect 2015. [PMID: 26215335 PMCID: PMC7172689 DOI: 10.1016/j.jinf.2015.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Respiratory viruses are responsible for a large proportion of acute respiratory illness in adults as well as children, and are associated with a huge socio-economic burden worldwide. Development of accurate point-of-care tests (POCT) for respiratory viruses has been listed as a priority by the World Health Organisation and replacing the current paradigm of empirical antimicrobial use with directed use is a listed goal of the movement for reduction in antimicrobial resistance. POCTs for respiratory viruses have previously been limited by the poor sensitivity of antigen detection based tests and by a limited range of detectable viruses. Highly accurate molecular platforms are now able to test for a comprehensive range of viruses, can be operated by non-laboratory staff and can generate a result in approximately 1 h, making them potentially deployable as POCTs. The potential clinical benefits of POC testing for respiratory viruses in adults include a reduction in unnecessary antibiotic use, improved antiviral prescribing for influenza and rationalisation of isolation facilities. We review here the burden of disease, the currently available molecular platforms with potential for POCT use and the existing evidence for clinical and economic benefits of testing for respiratory viruses in adults. There is a large burden of respiratory virus infection in hospitalised adults. Replacing empirical antimicrobials with pathogen directed use is a global priority. Molecular platforms now exist with potential for use as point-of-care tests (POCT). Potential benefits of POCT include a reduction in unnecessary antibiotic use. High quality trials evaluating clinically relevant outcomes are urgently needed.
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Affiliation(s)
- Nathan J Brendish
- NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Hannah F Schiff
- Department of Respiratory Medicine, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK
| | - Tristan W Clark
- Department of Clinical and Experimental Sciences and Respiratory Biomedical Research Unit, University of Southampton, UK.
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157
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Tsuru A, Setoguchi T, Kawabata N, Hirotsu M, Yamamoto T, Nagano S, Yokouchi M, Kakoi H, Kawamura H, Ishidou Y, Tanimoto A, Komiya S. Enrichment of bacteria samples by centrifugation improves the diagnosis of orthopaedics-related infections via real-time PCR amplification of the bacterial methicillin-resistance gene. BMC Res Notes 2015; 8:288. [PMID: 26138214 PMCID: PMC4490765 DOI: 10.1186/s13104-015-1180-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/20/2015] [Indexed: 11/26/2022] Open
Abstract
Background To effectively treat orthopaedic infections by methicillin-resistant strains, an early diagnosis is necessary. Bacterial cultures and real-time polymerase chain reaction (PCR) have been used to define methicillin-resistant staphylococci. However, even when patients display clinical signs of infections, bacterial culture and real-time PCR often cannot confirm infection. The aim of this study was to prospectively compare the utility of real-time PCR for the mecA gene detection following centrifugation of human samples with suspected orthopaedic infections. Results In addition to the conventional real-time PCR method, we performed real-time PCR following centrifugation of the sample at 4,830×g for 10 min in a modified real-time PCR (M-PCR) method. We suspended cultured methicillin-resistant Staphylococcus aureus and generated standard dilution series for in vitro experiments. The in vitro detection sensitivity of the M-PCR method was approximately 5.06 times higher than that of the conventional real-time PCR method. We performed bacterial culture, pathological examination, real-time PCR, and M-PCR to examine the infectious fluids and tissues obtained from 36 surgical patients at our hospital. Of these, 20 patients who had undergone primary total hip arthroplasty were enrolled as negative controls. In addition, 15 patients were examined who were clinically confirmed to have an infection, including periprosthetic joint infection (eight patients), pyogenic spondylitis (two patients), infectious pseudoarthrosis (two patients), and after spine surgery (three patients). In one sample from a patient who developed infectious pseudoarthrosis and two samples from surgical site infections after spine surgery, the mecA gene was detected only by the M-PCR method. In one patient with infectious pseudoarthrosis, one patient with infection after arthroplasty, and two patients with purulent spondylitis, the detection sensitivity of the M-PCR method was increased compared with PCR (clinical sample average: 411.6 times). Conclusions These findings suggest that the M-PCR method is useful to detect methicillin-resistant strains infections. In addition, the centrifugation process only takes 10 min longer than conventional real-time PCR methods. We believe that the M-PCR method could be clinically useful to detect orthopaedic infections caused by methicillin-resistant strains. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1180-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arisa Tsuru
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Takao Setoguchi
- The Near-Future Locomotor Organ Medicine Creation Course (Kusunoki Kai), Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Naoya Kawabata
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Masataka Hirotsu
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Takuya Yamamoto
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Satoshi Nagano
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Masahiro Yokouchi
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Hironori Kakoi
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Hideki Kawamura
- Infection Control Team, Kagoshima University Hospital, Kagoshima, Japan.
| | - Yasuhiro Ishidou
- Department of Medical Joint Materials, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Akihide Tanimoto
- Molecular and Cellular Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Setsuro Komiya
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
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158
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Keeratijarut A, Lohnoo T, Yingyong W, Rujirawat T, Srichunrusami C, Onpeaw P, Chongtrakool P, Brandhorst TT, Krajaejun T. Detection of the oomycete Pythium insidiosum by real-time PCR targeting the gene coding for exo-1,3-β-glucanase. J Med Microbiol 2015; 64:971-977. [PMID: 26296566 DOI: 10.1099/jmm.0.000117] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pythiosis is a life-threatening infectious disease caused by Pythium insidiosum. Early and accurate diagnosis is the key to prompt treatment and an improved prognosis for patients with pythiosis. An alternative to microbiological and immunological approaches for facilitating diagnosis of pythiosis is the PCR-based assay. Until recently, the ribosomal DNA (rDNA) region was the only target available for PCR-based detection of P. insidiosum. Failure to detect P. insidiosum by PCR amplification using the rDNA-specific primers has been reported. PinsEXO1, encoding an exo-1,3-β-glucanase, is an alternative, novel and efficient target for identification of P. insidiosum by conventional PCR. In this study, we aimed to develop a real-time (RT)-PCR approach targeting PinsEXO1 and compare its performance with conventional PCR for the detection of P. insidiosum. Both conventional and RT-PCR assays were positive for all 35 P. insidiosum strains tested, whilst all 58 control fungi were negative. The turnaround time for conventional PCR was 10 h, whilst that for RT-PCR was 7.5 h. The lowest amounts of genomic DNA template required for successful amplification by conventional and RT-PCR were 1 and 1 × 10(-4) ng, respectively. In conclusion, the RT-PCR assay retained 100% sensitivity and 100% specificity for detection of P. insidiosum. It showed a substantially improved analytical sensitivity and turnaround time that could improve diagnosis of pythiosis. The assay could also facilitate quantitative DNA analysis and epidemiological studies of P. insidiosum.
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Affiliation(s)
- Angsana Keeratijarut
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Molecular Medicine Program, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tassanee Lohnoo
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wanta Yingyong
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chutatip Srichunrusami
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpit Onpeaw
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Piriyaporn Chongtrakool
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T Tristan Brandhorst
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin-Madison, Wisconsin, USA
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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159
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Rutschke N, Zimmermann J, Möller R, Klöck G, Winterhalter M, Leune A. Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance. J Anal Sci Technol 2015; 6:20. [PMID: 32226638 PMCID: PMC7099353 DOI: 10.1186/s40543-015-0063-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Reverse transcriptase is an indispensable enzyme for real-time reverse transcriptase (RT)-PCR, a standard method in molecular diagnostics for detection and quantification of defined RNA molecules. The prevention of non-specific products due to elongation of misprimed oligonucleotides by the enzyme at temperatures beneath the specific annealing temperature is one of the biggest challenges in real-time RT-PCR.In the present study, an aptamer directed against the reverse transcriptase was analyzed for its potential to attain a temperature-dependent reverse transcriptase ("hot start" RT). FINDINGS The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). Results with aptamer revealed a reduced RT activity at low temperatures while achieving full activity at the specific annealing temperature of 55 °C. Sensitivity (limit of detection (LoD) 95 %) of the MERS-CoV assay was increased by about two times in the presence of aptamer. CONCLUSIONS The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays.
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Affiliation(s)
- Nils Rutschke
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Jan Zimmermann
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
| | - Ronny Möller
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Gerd Klöck
- Institute of Environmental Biology and Biotechnology, University of Applied Sciences Bremen, Am Neustadtswall 30, 28199 Bremen, Germany
| | - Mathias Winterhalter
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Annika Leune
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
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160
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Lee CC, Liao YC, Lai YH, Lee CCD, Chuang MC. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus. Anal Chem 2015; 87:5410-6. [PMID: 25879394 DOI: 10.1021/acs.analchem.5b00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.
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Affiliation(s)
- Chun-Ching Lee
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Yu-Chieh Liao
- ‡Institute of Population Health Science, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
| | - Yu-Hsuan Lai
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | | | - Min-Chieh Chuang
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
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161
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Bergamaschi CC, Santamaria MP, Berto LA, Cogo-Müller K, Motta RHL, Salum EA, Nociti Júnior FH, Goodson JM, Groppo FC. Full mouth periodontal debridement with or without adjunctive metronidazole gel in smoking patients with chronic periodontitis: A pilot study. J Periodontal Res 2015; 51:50-9. [PMID: 25900347 DOI: 10.1111/jre.12278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE The evidence of effectiveness of metronidazole (Mtz) as an adjunct therapy to periodontal procedure in the treatment of patients with chronic periodontitis is not conclusive. The aim of this study was to compare the effect of Mtz (delivered locally as a gel or systemically as a tablet) as an adjunctive therapy with full mouth periodontal debridement (1 h of ultrasonic calculus/plaque removal) in smokers with chronic periodontitis. MATERIAL AND METHODS This pilot study involved 30 smokers with at least six teeth with a clinical attachment loss of ≥ 5 mm and probing pocket depth (PPD) of ≥ 5 mm. They were randomly assigned into one of three groups (n = 10): (i) 3 g daily of placebo gel applied topically (using a dental tray with the gel overnight) + periodontal debridement; (ii) 3 g daily of a 15% Mtz benzoate gel applied topically (using a dental tray with the gel overnight) + periodontal debridement; and (iii) a daily single dose of 750 mg Mtz (Flagyl(®)) + periodontal debridement. Clinical parameters (visible plaque index, gingival bleeding index [GBI], relative attachment level and PPD) and quantitative analysis (by real-time polymerase chain reaction) of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia were assessed at baseline and at 1, 3 and 6 mo after periodontal debridement. RESULTS There was no statistically significant difference in the average GBI and visible plaque index values at baseline between the groups (p ≥ 0.05). There was no significant difference between groups in all parameters evaluated (p ≥ 0.05). Significant reductions in GBI at 3 and 6 mo were observed in all groups (p < 0.05). Significant reductions in both PPD and relative attachment level at 1, 3 and 6 mo were observed in all groups (p < 0.05). Significant reductions in bacterial levels at 7 and 30 d were observed in all groups (p < 0.05). CONCLUSION Adjunctive use of Mtz (gel or tablet) to periodontal debridement had similar clinical and microbiological improvement compared to treatment with placebo + periodontal debridement in smokers with chronic periodontitis up to 6 mo post-treatment. Further studies are necessary to confirm the clinical relevance of these findings.
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Affiliation(s)
- C C Bergamaschi
- Department of Pharmaceutical Sciences, University of Sorocaba, Sorocaba, Brazil
| | - M P Santamaria
- Division of Periodontics, College of Dentistry, State University of São Paulo, São José dos Campos, Brazil
| | - L A Berto
- Department of Pharmacology, Anesthesiology and Therapeutics, Dental School of Piracicaba, State University of Campinas, Piracicaba, Brazil
| | - K Cogo-Müller
- Department of Dentistry, University of Santo Amaro, São Paulo, Brazil
| | - R H L Motta
- Department of Pharmacology, Anesthesiology and Therapeutics, São Leopoldo Mandic Dental School, Campinas, Brazil
| | - E A Salum
- Department of Prosthodontics and Periodontology, Dental School of Piracicaba, State University of Campinas, Piracicaba, Brazil
| | - F H Nociti Júnior
- Department of Prosthodontics and Periodontology, Dental School of Piracicaba, State University of Campinas, Piracicaba, Brazil
| | - J M Goodson
- Department of Clinical Research, The Forsyth Institute, Boston, MA, USA
| | - F C Groppo
- Department of Pharmacology, Anesthesiology and Therapeutics, Dental School of Piracicaba, State University of Campinas, Piracicaba, Brazil
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162
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Borysiak MD, Kimura KW, Posner JD. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification. LAB ON A CHIP 2015; 15:1697-707. [PMID: 25666345 DOI: 10.1039/c4lc01479k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications.
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Affiliation(s)
- Mark D Borysiak
- Chemical Engineering Department, University of Washington, Seattle, WA 98195, USA. E-mail:
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163
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García-Mazcorro JF, Garza-González E, Marroquín-Cardona AG, Tamayo JL. [Characterization, influence and manipulation of the gastrointestinal microbiota in health and disease]. GASTROENTEROLOGIA Y HEPATOLOGIA 2015; 38:445-66. [PMID: 25769877 DOI: 10.1016/j.gastrohep.2015.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 01/12/2015] [Accepted: 01/26/2015] [Indexed: 01/08/2023]
Abstract
The gastrointestinal tract harbors trillions of microorganisms that are indispensable for health. The gastrointestinal microbiota can be studied using culture and molecular methods. The applications of massive sequencing are constantly increasing, due to their high yield, increasingly accessible costs, and the availability of free software for data analysis. The present article provides a detailed review of a large number of studies on the gastrointestinal microbiota and its influence on human health; particular emphasis is placed on the evidence suggesting a relationship between the gastrointestinal microbial ecosystem and diverse physiological and immune/inflammatory processes. Discussion of the articles analyzed combines a medical approach and current concepts of microbial molecular ecology. The present revision aims to be useful to those interested in the gastrointestinal microbiota and its possible alteration to maintain, re-establish and enhance health in the human host.
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Affiliation(s)
- José F García-Mazcorro
- Facultad de Medicina Veterinaria, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo León, México; Grupo de investigación Ecobiología Médica, Facultad de Medicina Veterinaria, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo León, México.
| | - Elvira Garza-González
- Servicio de Gastroenterología y Departamento de Patología Clínica, Hospital Universitario «Dr. José Eleuterio González», Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Alicia G Marroquín-Cardona
- Facultad de Medicina Veterinaria, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo León, México; Grupo de investigación Ecobiología Médica, Facultad de Medicina Veterinaria, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo León, México; Departamento de Fisiología, Farmacología y Toxicología, Facultad de Medicina Veterinaria, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo León, México
| | - José L Tamayo
- Centro de Investigación y Docencia en Ciencias de la Salud, Hospital Civil de Culiacán, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
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164
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Wernike K, Hoffmann B, Beer M. Simultaneous detection of five notifiable viral diseases of cattle by single-tube multiplex real-time RT-PCR. J Virol Methods 2015; 217:28-35. [PMID: 25746154 DOI: 10.1016/j.jviromet.2015.02.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 12/25/2014] [Accepted: 02/24/2015] [Indexed: 12/28/2022]
Abstract
Multiplexed real-time PCR (qPCR) assays enable the detection of several target genes in a single reaction, which is applicable for simultaneous testing for the most important viral diseases in samples obtained from ruminants with unspecific clinical symptoms. Here, reverse transcription qPCR (RT-qPCR) systems for the detection of bovine viral diarrhoea virus (BVDV) and bluetongue virus (BTV) were combined with an internal control system based on the beta-actin gene. Additionally, a background screening for three further major pathogens of cloven-hoofed animals reportable to the World Organisation for Animal Health, namely foot-and-mouth disease virus, epizootic haemorrhagic disease virus, and Rift Valley fever virus, was integrated using the identical fluorophore for the respective RT-qPCR assays. Every pathogen-specific assay had an analytical sensitivity of at least 100 genome copies per reaction within the multiplex approach, and a series of reference samples and clinical specimens obtained from cattle, but also from small ruminants, were detected reliably. The qPCR systems integrated in the background screening were even not influenced by the simultaneous amplification of very high BVDV and BTV genome copy numbers. The newly developed multiplex qPCR allows the specific and sensitive detection of five of the most important diseases of ruminants and could be used in the context of monitoring programs or for differential diagnostics.
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Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald - Insel Riems, Germany.
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165
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Leffad M, Cousens R, Raoult D. CMI editorial report, 2015. Clin Microbiol Infect 2015; 21:207-13. [DOI: 10.1016/j.cmi.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 12/14/2022]
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166
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D AS, A MEH, L DS. Diagnostic approaches for tick-borne haemoparasitic diseases in livestock. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/jvmah2014.0345] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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167
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Janzen TW, Thomas MC, Goji N, Shields MJ, Hahn KR, Amoako KK. Rapid detection method for Bacillus anthracis using a combination of multiplexed real-time PCR and pyrosequencing and its application for food biodefense. J Food Prot 2015; 78:355-61. [PMID: 25710151 DOI: 10.4315/0362-028x.jfp-14-216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Bacillus anthracis, the causative agent of anthrax, has the capacity to form highly resilient spores as part of its life cycle. The potential for the dissemination of these spores using food as a vehicle is a huge public health concern and, hence, requires the development of a foodborne bioterrorism response approach. In this work, we address a critical gap in food biodefense by presenting a novel, combined, sequential method involving the use of real-time PCR and pyrosequencing for the rapid, specific detection of B. anthracis spores in three food matrices: milk, apple juice, and bottled water. The food samples were experimentally inoculated with 40 CFU ml(-1), and DNA was extracted from the spores and analyzed after immunomagnetic separation. Applying the combination of multiplex real-time PCR and pyrosequencing, we successfully detected the presence of targets on both of the virulence plasmids and the chromosome. The results showed that DNA amplicons generated from a five-target multiplexed real-time PCR detection using biotin-labeled primers can be used for single-plex pyrosequencing detection. The combined use of multiplexed real-time PCR and pyrosequencing is a novel, rapid detection method for B. anthracis from food and provides a tool for accurate, quantitative identification with potential biodefense applications.
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Affiliation(s)
- Timothy W Janzen
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Matthew C Thomas
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Noriko Goji
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Michael J Shields
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kristen R Hahn
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4
| | - Kingsley K Amoako
- Canadian Food Inspection Agency, National Centers for Animal Disease, Lethbridge Laboratory, P.O. Box 640, Township Road 9-1, Lethbridge, Alberta, Canada T1J 3Z4.
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168
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El-Sharoud WM. Developing a time and effort-effective, highly sensitive TaqMan probe-based real-time polymerase chain reaction protocol for the detection of Salmonella in milk, yoghurt, and cheese. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2014.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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169
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Sting R, Molz K, Hoferer M. Creating standards for absolute quantification of Coxiella burnetii in real-time PCR--a comparative study based on transmission electron microscopy. Biologicals 2014; 43:18-22. [PMID: 25465354 DOI: 10.1016/j.biologicals.2014.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/02/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022] Open
Abstract
Quantitative standards are a prerequisite for quality control and quantification of pathogens. In this study the creation of quantitative standards for use in qPCR is described using the pathogen Coxiella burnetii. Quantification of Coxiella burnetii particles by transmission electron microscopy (TEM) was used as primary standard and compared with data obtained by light microscopy as well as genome equivalents (GE) and plasmid units (recombinant plasmid). Based on pathogen quantification using TEM and light microscopy, pathogen detection limits of 6 and 2 C. burnetii particles could be determined per com1 qPCR reaction, respectively. In comparison, the detection limits were 17 and 13 pathogen units using GE and plasmid units, respectively. The standard generated by TEM can be used as gold standard for universal application due to high accuracy, quantitative control of the producing process and supplying intact pathogen particles.
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Affiliation(s)
- Reinhard Sting
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany.
| | - Kerstin Molz
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
| | - Marc Hoferer
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
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170
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Di Marco E. Real-time PCR detection of Mycoplasma pneumoniae in the diagnosis of community-acquired pneumonia. Methods Mol Biol 2014; 1160:99-105. [PMID: 24740224 DOI: 10.1007/978-1-4939-0733-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction is a useful technique in microbial diagnostics to detect and quantify DNA or RNA of low abundance. Bacterial and viral nucleic acid can be amplified by PCR upon clinical sample extraction using specific primers for classical qualitative PCR and primers and probes for real-time PCR. Here we describe the Scorpion-probe real-time PCR-based assay that offers thermodynamic advantages due to its kinetic reaction and provides faster performances compared to a classical double-labeled probe-based assays.
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Affiliation(s)
- Eddi Di Marco
- Department of Translational Medicine, Istituto Giannina Gaslini, Largo G. Gaslini 5, Genova, 16147, Italy,
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171
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Correlates of illness severity in infectious mononucleosis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 25:277-80. [PMID: 25371691 PMCID: PMC4211352 DOI: 10.1155/2014/514164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Infectious mononucleosis is caused by Epstein-Barr virus and can lead to complications, including hepatitis and hematological abnormalities, in a subset of patients. The authors of this article assessed measures of illness severity as well as viral load at presentation and six weeks later among a cohort of individuals <25 years of age for the purpose of informing the management of patients with infectious mononucleosis. INTRODUCTION: Understanding the spectrum and frequencies of Epstein-Barr virus (EBV) complications and markers of illness severity in immunocompetent patients with primary EBV infection will inform management of patients with EBV-related illnesses. OBJECTIVES: To determine the clinical and laboratory correlates of illness severity among infants, children and youth with infectious mononucleosis (IM). METHODS: Study subjects with confirmed IM were prospectively enrolled. Illness severity was assessed at baseline and at six weeks using a scoring tool. Peripheral blood viral loads served as a measure of viral burden. RESULTS: Among 32 children and young adults with IM, the median age was 16 years (range two to 24 years). The predominant clinical findings were lymphadenopathy (23 of 32 [72%]), pharyngitis (16 of 32 [50%]), fever (nine of 32 [28%]) and splenomegaly (six of 32 [19%]). With respect to symptoms or signs that persisted to at least six weeks after illness onset, the predominant complaint was lymphadenopathy in 35% of subjects available for reassessment. Deranged liver function tests were present at presentation in up to 44% of subjects. Patients with the highest viral loads at presentation had significantly higher illness severity scores associated with fatigue (P=0.02). Other than the scores associated with fatigue, viral load values were not significantly correlated with the illness severity scores at baseline and at six weeks. CONCLUSION: In IM, viral loads are not necessarily correlated with illness severity, with the exception of fatigue. EBV-related hepatitis is common in IM, confirming the status of this virus as a relatively common cause of transient hepatitis in children and youth. This entity is not necessarily a marker of disease severity.
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172
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Comparison of conventional RT-PCR, reverse-transcription loop-mediated isothermal amplification, and SYBR green I-based real-time RT-PCR in the rapid detection of bovine viral diarrhea virus nucleotide in contaminated commercial bovine sera batches. J Virol Methods 2014; 207:204-9. [DOI: 10.1016/j.jviromet.2014.05.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 12/22/2022]
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173
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Kolosovas-Machuca ES, Vera-Reveles G, Rodríguez-Aranda MC, Ortiz-Dosal LC, Segura-Cardenas E, Gonzalez FJ. Resistance-Based Biosensor of Multi-Walled Carbon Nanotubes. J Immunoassay Immunochem 2014; 36:142-8. [DOI: 10.1080/15321819.2014.908129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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174
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Wernike K, Beer M, Freuling CM, Klupp B, Mettenleiter TC, Müller T, Hoffmann B. Molecular double-check strategy for the identification and characterization of Suid herpesvirus 1. J Virol Methods 2014; 209:110-5. [PMID: 25200377 DOI: 10.1016/j.jviromet.2014.08.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/20/2014] [Accepted: 08/28/2014] [Indexed: 11/16/2022]
Abstract
Large scale vaccination with glycoprotein E (gE)-deleted marker vaccines and the rapid and reliable differentiation of wild-type and marker vaccine strains are important aspects in eradication programs for Suid herpesvirus 1 [SuHV-1, syn. Aujeszky's disease virus (ADV) or pseudorabies virus (PrV)]. Therefore, two multiplex real-time PCR (qPCR) assays for the genetic differentiation of wild-type and gE-deleted vaccine SuHV-1 strains have been developed. In the first multiplex qPCR SuHV-1 gB-gene specific detection was combined with a gE-gene specific assay and an internal control based on heterologous DNA. In the second system, a SuHV-1 UL19 (major capsid protein gene) assay, a different gE-gene specific assay and an internal control based on the beta-actin gene were combined. The gB-gene, UL19 as well as both gE-gene specific assays had an analytical sensitivity of less than 10 genome copies per reaction in the respective multiplex approaches. A series of reference strains including field isolates obtained from domestic and wild animals, and gE-deleted SuHV-1 were reliably detected, while genetically related non-SuHV-1 herpesviruses tested negative. Both newly developed triplex SuHV-1-specific qPCR assays are specific and sensitive methods for the rapid genetic differentiation of wild-type viruses and gE-deleted vaccine strains in a single reaction.
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Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Barbara Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany.
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
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175
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Mo F, Zhao J, Liu N, Cao LH, Jiang SX. Validation of reference genes for RT-qPCR analysis of CYP4T expression in crucian carp. Genet Mol Biol 2014; 37:500-7. [PMID: 25249772 PMCID: PMC4171773 DOI: 10.1590/s1415-47572014000400005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/24/2014] [Indexed: 12/19/2022] Open
Abstract
Reference genes are commonly used for normalization of target gene expression during RT-qPCR analysis. However, no housekeeping genes or reference genes have been identified to be stable across different tissue types or under different experimental conditions. To identify the most suitable reference genes for RT-qPCR analysis of target gene expression in the hepatopancreas of crucian carp (Carassius auratus) under various conditions (sex, age, water temperature, and drug treatments), seven reference genes, including beta actin (ACTB), beta-2 microglobulin (B2M), embryonic elongation factor-1 alpha (EEF1A), glyceraldehyde phosphate dehydrogenase (GAPDH), alpha tubulin (TUBA), ribosomal protein l8 (RPL8) and glucose-6-phosphate dehydrogenase (G6PDH), were evaluated in this study. The stability and ranking of gene expression were analyzed using three different statistical programs: GeNorm, Normfinder and Bestkeeper. The expression errors associated with selection of the genes were assessed by the relative quantity of CYP4T. The results indicated that all the seven genes exhibited variability under the experimental conditions of this research, and the combination of ACTB/TUBA/EEF1A or of ACTB/EEF1A was the best candidate that raised the accuracy of quantitative analysis of gene expression. The findings highlighted the importance of validation of housekeeping genes for research on gene expression under different conditions of experiment and species.
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Affiliation(s)
- Fei Mo
- Nanjing Agricultural University, China
| | - Jie Zhao
- Nanjing Agricultural University, China
| | - Na Liu
- Nanjing Agricultural University, China
| | - Li-hua Cao
- Nanjing Agricultural University, China; Guangdong Agribusiness Group Corporation, China
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176
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Hawash Y. DNA extraction from protozoan oocysts/cysts in feces for diagnostic PCR. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:263-71. [PMID: 25031466 PMCID: PMC4096637 DOI: 10.3347/kjp.2014.52.3.263] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 12/02/2022]
Abstract
PCR detection of intestinal protozoa is often restrained by a poor DNA recovery or by inhibitors present in feces. The need for an extraction protocol that can overcome these obstacles is therefore clear. QIAamp® DNA Stool Mini Kit (Qiagen) was evaluated for its ability to recover DNA from oocysts/cysts directly from feces. Twenty-five Giardia-positive, 15 Cryptosporidium-positive, 15 Entamoeba histolytica-positive, and 45 protozoa-free samples were processed as control by microscopy and immunoassay tests. DNA extracts were amplified using 3 sets of published primers. Following the manufacturer's protocol, the kit showed sensitivity and specificity of 100% towards Giardia and Entamoeba. However, for Cryptosporidium, the sensitivity and specificity were 60% (9/15) and 100%, respectively. A series of optimization experiments involving various steps of the kit's protocol were conducted using Cryptosporidium-positive samples. The best DNA recoveries were gained by raising the lysis temperature to the boiling point for 10 min and the incubation time of the InhibitEX tablet to 5 min. Also, using a pre-cooled ethanol for nucleic acid precipitation and small elution volume (50-100 µl) were valuable. The sensitivity of the amended protocol to Cryptosporidium was raised to 100%. Cryptosporidium DNA was successfully amplified by either the first or the second primer set. When applied on parasite-free feces spiked with variable oocysts/cysts counts, ≈ 2 oocysts/cysts were theoretically enough for detection by PCR. To conclude, the Qiagen kit with the amended protocol was proved to be suitable for protozoan DNA extraction directly from feces and support PCR diagnosis.
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Affiliation(s)
- Yousry Hawash
- Department of Medical Parasitology, NLI, Menoufia University, Shebin El-Koom, Menoufia, Egypt. ; Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Al-Taif University, Al-Taif, Saudi Arabia
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177
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Fusco V, Quero GM. Culture-Dependent and Culture-Independent Nucleic-Acid-Based Methods Used in the Microbial Safety Assessment of Milk and Dairy Products. Compr Rev Food Sci Food Saf 2014; 13:493-537. [DOI: 10.1111/1541-4337.12074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Vincenzina Fusco
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| | - Grazia Marina Quero
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
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178
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The effect of fibre source on the numbers of some fibre-degrading bacteria of Arabian camel's (Camelus dromedarius) foregut origin. Trop Anim Health Prod 2014; 46:1161-6. [PMID: 24898095 DOI: 10.1007/s11250-014-0621-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
The total bacterial community of Fibrobacter succinogenes and Ruminococcus flavefaciens in fibre-enriched culture of the foregut contents of 12 adult feral camels (Camelus dromedaries) fed on native vegetation in Australia was investigated using quantitative PCR. Foregut contents were collected postmortem, pooled and filtered before divided into two fractions. One fraction was used for extraction of DNA, while the other fraction was inoculated straight away into BM 10 contained filter paper (FP), cotton thread (CT) or neutral detergent fibre (NDF) as the sole carbohydrate sources in Hungate tubes. The tubes were incubated anaerobically at 39 °C for 1 week. After a near complete degradation of the FP and CT and extensive turbidity in the NDF, media subculturing was carried out into fresh media tubes. This was repeated twice before genomic DNA was extracted and used for quantification of bacteria. Using an absolute quantification method, the numbers of cells in 1 ml of each sample ranged from 4.07 × 10(6) to 2.73 × 10(9) for total bacteria, 1.34 × 10(3) to 2.17 × 10(5) for F. succinogenes and 5.78 × 10(1) to 3.53 × 10(4) for R. flavefaciens. The mean cell number of F. succinogenes was highest in the FP enrichment medium at approximately 107-fold, whereas for the R. flavefaciens targeted primer, the NDF enrichment media had the highest mean cell number at approximately 4-fold when compared to the rumen content. The data presented here provide evidence of fibre type preference by the two main fibre-degrading bacteria and would help us understand the interaction between fibre type and fibre-degrading microorganisms, which has ramification on camel nutrition at different seasons and environments.
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Development and application of quantitative detection method for viral hemorrhagic septicemia virus (VHSV) genogroup IVa. Viruses 2014; 6:2204-13. [PMID: 24859343 PMCID: PMC4036551 DOI: 10.3390/v6052204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 01/18/2023] Open
Abstract
Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis.
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180
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Strepparava N, Wahli T, Segner H, Petrini O. Detection and quantification of Flavobacterium psychrophilum in water and fish tissue samples by quantitative real time PCR. BMC Microbiol 2014; 14:105. [PMID: 24767577 PMCID: PMC4005812 DOI: 10.1186/1471-2180-14-105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 04/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Flavobacterium psychrophilum is the agent of Bacterial Cold Water Disease and Rainbow Trout Fry Syndrome, two diseases leading to high mortality. Pathogen detection is mainly carried out using cultures and more rapid and sensitive methods are needed. Results We describe a qPCR technique based on the single copy gene β’ DNA-dependent RNA polymerase (rpoC). Its detection limit was 20 gene copies and the quantification limit 103 gene copies per reaction. Tests on spiked spleens with known concentrations of F. psychrophilum (106 to 101 cells per reaction) showed no cross-reactions between the spleen tissue and the primers and probe. Screening of water samples and spleens from symptomless and infected fishes indicated that the pathogen was already present before the outbreaks, but F. psychrophilum was only quantifiable in spleens from diseased fishes. Conclusions This qPCR can be used as a highly sensitive and specific method to detect F. psychrophilum in different sample types without the need for culturing. qPCR allows a reliable detection and quantification of F. psychrophilum in samples with low pathogen densities. Quantitative data on F. psychrophilum abundance could be useful to investigate risk factors linked to infections and also as early warning system prior to potential devastating outbreak.
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Affiliation(s)
- Nicole Strepparava
- Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6500 Bellinzona, Switzerland.
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181
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Becker CE, Kretzmann NA, Mattos AAD, Veiga ABGD. Melting curve analysis for the screening of hepatitis B virus genotypes A, D and F in patients from a general hospital in southern Brazil. ARQUIVOS DE GASTROENTEROLOGIA 2014; 50:219-25. [PMID: 24322195 DOI: 10.1590/s0004-28032013000200039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 06/18/2013] [Indexed: 01/04/2023]
Abstract
CONTEXT Hepatitis B virus (HBV) can cause fulminant hepatitis, cirrhosis and hepatocellular carcinoma, and is one of the most common causes of acute and chronic liver failure. The genetic variants of HBV can be decisive for the evolution of these diseases as well as for the election of therapy. OBJECTIVES The aim of this study was to evaluate and standardize an in house methodology based on the analysis of the melting curve polymerase chain reaction (PCR) of real-time (qPCR) to screen for genotypes A, D and F of HBV in patients from a hospital in Rio Grande do Sul, Brazil. METHODS We evaluated 104 patients presumably with HBV chronic infection. Viral DNA was extracted from plasma and viral genotypes and different mutations were determined using PCR-based protocols. RESULTS A PCR-based methodology was standardized for the analysis of genotypes A, D and F of HBV. The technique was based in a nested PCR with the final step consisting of a multiplex real-time PCR, using the melting curve as a tool for the differentiation of fragments. A higher frequency of genotype D (44.4%), followed by genotype A (22.2%) and genotype F (3.7%) was observed. CONCLUSION The standardized assay, a nested PCR-multiplex qPCR using specific primers, provides a rapid and accurate method for the differentiation of HBV genotypes that are more frequent in Southern Brazil - A, D and F. This method can be applied in the clinical practice.
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Affiliation(s)
- Carlos Eduardo Becker
- Universidade Federal de Ciências da Saúde de Porto Alegre, Programa de Pós-Graduação em Medicina: Hepatologia
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182
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Tajadini M, Panjehpour M, Javanmard SH. Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes. Adv Biomed Res 2014; 3:85. [PMID: 24761393 PMCID: PMC3988599 DOI: 10.4103/2277-9175.127998] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/22/2013] [Indexed: 12/14/2022] Open
Abstract
Background: Real-time polymerase chain reaction (PCR) is based on the revolutionary method of PCR. This technique is the result of PCR enormous sensitivity and real-time monitoring combination. In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled oligonucleotide and exonuclease activity of Taq polymerase enzyme. Specificity is the most important concern with the usage of any non-specific dsDNA-binding Dyes such as SYBR Green whiles more specificity showed by labeled oligonucleotide method such as TaqMan. In this study, we compared two common RT PCR methods, TaqMan and SYBR Green in measurement gene expression profile of adenosine receptors. Materials and Methods: Gene expression profiles of A1, A2A, A2B and A3 Adenosine receptors were analyzed by optimized TaqMan and SYBR Green quantitative RT PCR in breast cancer tissues. Primary expression data was normalizing by B. actin reference gene. Results: Efficiencies were calculated more than 95% for TaqMan and SYBR Green methods in all genes. The correlations between means of normalized data of each gene in two methods were positive and significant (P < 0.05). Conclusion: Data analysis showed that with the use of high performance primer and by use proper protocols and material we can make precise data by SYBR Green as TaqMan method. In other word by optimization of SYBR Green method, its performance and quality could be comparable to TaqMan method.
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Affiliation(s)
- Mohamadhasan Tajadini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran ; Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojtaba Panjehpour
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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183
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Gizzi ABDR, Oliveira ST, Leutenegger CM, Estrada M, Kozemjakin DA, Stedile R, Marcondes M, Biondo AW. Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel. BMC Vet Res 2014; 10:23. [PMID: 24433321 PMCID: PMC3896730 DOI: 10.1186/1746-6148-10-23] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 01/15/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Infectious diarrhea can be caused by bacteria, viruses, or protozoan organisms, or a combination of these. The identification of co-infections in dogs is important to determine the prognosis and to plan strategies for their treatment and prophylaxis. Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. The objective of this study was to use a real-time PCR diarrhea panel to survey the frequencies of pathogens and co-infections in owned dogs attended in a veterinary hospital with and without diarrhea, as well the frequency in different countries. Feces samples were tested for canine distemper virus, canine coronavirus, canine parvovirus type 2 (CPV-2), Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., Giardia spp., and Salmonella spp. using molecular techniques. RESULTS In total, 104 diarrheic and 43 control dogs that were presented consecutively at a major private veterinary hospital were included in the study. Overall, 71/104 (68.3%) dogs with diarrhea were positive for at least one pathogen: a single infection in 39/71 dogs (54.9%) and co-infections in 32/71 dogs (45.1%), including 21/32 dogs (65.6%) with dual, 5/32 (15.6%) with triple, and 6/32 (18.8%) with quadruple infections. In the control group, 13/43 (30.2%) dogs were positive, all with single infections only. The most prevalent pathogens in the diarrheic dogs were CPA (40/104 dogs, 38.5%), CPV-2 (36/104 dogs, 34.6%), and Giardia spp. (14/104 dogs, 13.5%). CPV-2 was the most prevalent pathogen in the dual co-infections, associated with CPA, Cryptosporidium spp., or Giardia spp. No statistical difference (P = 0.8374) was observed in the duration of diarrhea or the number of deaths (P = 0.5722) in the presence or absence of single or co-infections. CONCLUSIONS Diarrheic dogs showed a higher prevalence of pathogen infections than the controls. Whereas the healthy dogs had only single infections, about half the diarrheic dogs had co-infections. Therefore, multiple pathogens should be investigated in dogs presenting with diarrhea. The effects of multiple pathogens on the disease outcomes remain unclear because the rate of death and the duration of diarrhea did not seem to be affected by these factors.
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Affiliation(s)
- Aline Baumann da Rocha Gizzi
- Department of Veterinary Medicine, Federal University of Parana, 1540 R dos Funcionários, Curitiba, PR 80035-050, Brazil
| | - Simone Tostes Oliveira
- Department of Veterinary Medicine, Federal University of Parana, 1540 R dos Funcionários, Curitiba, PR 80035-050, Brazil
| | | | - Marko Estrada
- IDEXX Laboratories Inc., 2825 Kovr Drive, West Sacramento, CA 95605, USA
| | | | - Rafael Stedile
- Department of Animal Medicine, Federal University of Rio Grande do Sul, 9090 Avenue Bento Gonçalves, Porto Alegre, RS 91540-000, Brazil
| | - Mary Marcondes
- Department of Clinics, Surgery and Animal Reproduction, College of Veterinary Medicine, São Paulo State University, 793 R Clovis Pestana, Araçatuba, SP 16050-680, Brazil
| | - Alexander Welker Biondo
- Department of Veterinary Medicine, Federal University of Parana, 1540 R dos Funcionários, Curitiba, PR 80035-050, Brazil
- Department of Veterinary Pathobiology, University of Illinois, 2001 S Lincoln Avenue, Urbana, IL 61802, USA
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Bissonnette L, Bergeron MG. Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine. Expert Rev Mol Diagn 2014; 6:433-50. [PMID: 16706745 DOI: 10.1586/14737159.6.3.433] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.
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Affiliation(s)
- Luc Bissonnette
- Département de Biologie Médicale (Microbiologie), Faculté de Médecine, Université Laval, Québec City, Canada.
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185
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GRAY J, COUPLAND LJ. The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections. Epidemiol Infect 2014; 142:1-11. [PMID: 24093495 PMCID: PMC9152551 DOI: 10.1017/s0950268813002367] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 02/04/2023] Open
Abstract
On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.
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Affiliation(s)
- J. GRAY
- Norwich Medical School, University of East Anglia, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
| | - L. J. COUPLAND
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
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186
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Takei F, Tani H, Matsuura Y, Nakatani K. Detection of hepatitis C virus by single-step hairpin primer RT-PCR. Bioorg Med Chem Lett 2014; 24:394-6. [DOI: 10.1016/j.bmcl.2013.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
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187
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de Abreu MM, Roselino A, Enokihara M, Nonogaki S, Prestes-Carneiro L, Weckx L, Alchorne M. Mycobacterium leprae is identified in the oral mucosa from paucibacillary and multibacillary leprosy patients. Clin Microbiol Infect 2014; 20:59-64. [DOI: 10.1111/1469-0691.12190] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 02/03/2013] [Accepted: 02/07/2013] [Indexed: 11/29/2022]
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188
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Patterson AS, Hsieh K, Soh HT, Plaxco KW. Electrochemical real-time nucleic acid amplification: towards point-of-care quantification of pathogens. Trends Biotechnol 2013; 31:704-12. [DOI: 10.1016/j.tibtech.2013.09.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 09/18/2013] [Accepted: 09/25/2013] [Indexed: 01/03/2023]
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189
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El-Sharoud WM, Darwish MS, Batt CA. A real-time PCR-based microfluidics platform for the detection of Cronobacter sakazakii in reconstituted milks. Int Dairy J 2013. [DOI: 10.1016/j.idairyj.2013.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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190
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Wernike K, Beer M, Hoffmann B. Rapid detection of foot-and-mouth disease virus, influenza A virus and classical swine fever virus by high-speed real-time RT-PCR. J Virol Methods 2013; 193:50-4. [DOI: 10.1016/j.jviromet.2013.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/07/2013] [Accepted: 05/13/2013] [Indexed: 01/24/2023]
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191
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Development of a one-step SYBR Green I real-time RT-PCR assay for the detection and quantitation of Araraquara and Rio Mamore hantavirus. Viruses 2013; 5:2272-81. [PMID: 24056673 PMCID: PMC3798901 DOI: 10.3390/v5092272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023] Open
Abstract
Hantaviruses are members of the family Bunyaviridae and are an emerging cause of disease worldwide with high lethality in the Americas. In Brazil, the diagnosis for hantaviruses is based on immunologic techniques associated with conventional RT-PCR. A novel one-step SYBR Green real-time RT-PCR was developed for the detection and quantitation of Araraquara hantavirus (ARAV) and Rio Mamore hantavirus (RIOMV). The detection limit of assay was 10copies/µL of RNA in vitro transcribed of segment S. The specificity of assay was evaluated by melting curve analysis, which showed that the Araraquara virus amplified product generated a melt peak at 80.83 ± 0.89 °C without generating primer-dimers or non-specific products. The assay was more sensitive than conventional RT-PCR and we detected two samples undetected by conventional RT-PCR. The one-step SYBR Green real-time quantitative RT-PCR is specific, sensible and reproducible, which makes it a powerful tool in both diagnostic applications and general research of ARAV and RIOMV and possibly other Brazilian hantaviruses.
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192
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Kao PM, Tung MC, Hsu BM, Chiu YC, She CY, Shen SM, Huang YL, Huang WC. Identification and quantitative detection of Legionella spp. in various aquatic environments by real-time PCR assay. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6128-6137. [PMID: 23536272 DOI: 10.1007/s11356-013-1534-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 06/02/2023]
Abstract
In this study, a SYBR green quantitative real-time PCR was developed to quantify and detect the Legionella spp. in various environmental water samples. The water samples were taken from watershed, water treatment plant, and thermal spring area in Taiwan. Legionella was detected in 13.6 % (24/176), and the detection rate for river water, raw drinking water, and thermal spring water was 10, 21.4, and 16.6 %, respectively. Using real-time PCR, concentration of Legionella spp. in detected samples ranged between 9.75 × 10(4) and 3.47 × 10(5) cells/L in river water, 6.92 × 10(4) and 4.29 × 10(5) cells/L in raw drinking water, and 5.71 × 10(4) and 2.12 × 10(6) cells/L for thermal spring water samples. The identified species included Legionella pneumophila (20.8 %), Legionella jordanis (4.2 %), Legionella nautarum (4.2 %), Legionella sp. (4.2 %), and uncultured Legionella sp. (66.6 %). The presence of L. pneumophila in aquatic environments suggested a potential public health threat that must be further examined.
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Affiliation(s)
- Po-Min Kao
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan, Republic of China
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193
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Cnops L, Soentjens P, Clerinx J, Van Esbroeck M. A Schistosoma haematobium-specific real-time PCR for diagnosis of urogenital schistosomiasis in serum samples of international travelers and migrants. PLoS Negl Trop Dis 2013; 7:e2413. [PMID: 24009791 PMCID: PMC3757062 DOI: 10.1371/journal.pntd.0002413] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 07/27/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Diagnosis of urogenital schistosomiasis by microscopy and serological tests may be elusive in travelers due to low egg load and the absence of seroconversion upon arrival. There is need for a more sensitive diagnostic test. Therefore, we developed a real-time PCR targeting the Schistosoma haematobium-specific Dra1 sequence. METHODOLOGY/PRINCIPAL FINDINGS The PCR was evaluated on urine (n = 111), stool (n = 84) and serum samples (n = 135), and one biopsy from travelers and migrants with confirmed or suspected schistosomiasis. PCR revealed a positive result in 7/7 urine samples, 11/11 stool samples and 1/1 biopsy containing S. haematobium eggs as demonstrated by microscopy and in 22/23 serum samples from patients with a parasitological confirmed S. haematobium infection. S. haematobium DNA was additionally detected by PCR in 7 urine, 3 stool and 5 serum samples of patients suspected of having schistosomiasis without egg excretion in urine and feces. None of these suspected patients demonstrated other parasitic infections except one with Blastocystis hominis and Entamoeba cyst in a fecal sample. The PCR was negative in all stool samples containing S. mansoni eggs (n = 21) and in all serum samples of patients with a microscopically confirmed S. mansoni (n = 22), Ascaris lumbricoides (n = 1), Ancylostomidae (n = 1), Strongyloides stercoralis (n = 1) or Trichuris trichuria infection (n = 1). The PCR demonstrated a high specificity, reproducibility and analytical sensitivity (0.5 eggs per gram of feces). CONCLUSION/SIGNIFICANCE The real-time PCR targeting the Dra1 sequence for S. haematobium-specific detection in urine, feces, and particularly serum, is a promising tool to confirm the diagnosis, also during the acute phase of urogenital schistosomiasis.
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Affiliation(s)
- Lieselotte Cnops
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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194
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Faltin B, Zengerle R, von Stetten F. Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem 2013; 59:1567-82. [PMID: 23938456 DOI: 10.1373/clinchem.2013.205211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.
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195
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Chalkia AK, Spandidos DA, Detorakis ET. Viral involvement in the pathogenesis and clinical features of ophthalmic pterygium (Review). Int J Mol Med 2013; 32:539-43. [PMID: 23856952 PMCID: PMC3782552 DOI: 10.3892/ijmm.2013.1438] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/12/2013] [Indexed: 11/06/2022] Open
Abstract
Pterygium is a potentially vision-threatening fibrovascular lesion originating from the conjunctiva that often extends on the corneal surface. Although it has been extensively studied, its pathogenesis has yet to be fully elucidated. Recent evidence on molecular genetic abnormalities in pterygium suggested neoplastic changes of limbal stem cells potentially associated with exposure to ultraviolet (UV) light. Human papillomavirus (HPV) is an oncogenic virus, associated with squamo-proliferative lesions of the anogenital region, skin and oropharynx. Several studies have shown HPV involvement in the pathogenesis of conjunctival neoplastic lesions, including papilloma and squamous cell carcinoma. The involvement of HPV as a co-factor in the pathogenesis of pterygium, although suggested by several studies using PCR and immunohistochemical techniques, remains controversial. Moreover, a marked variation in the prevalence of HPV in ophthalmic pterygium has been reported by different studies. Ethnic susceptibility and methodological differences in the detection of HPV may account for this variation. Surgical excision, often using sophisticated techniques, is the standard current method of therapy for pterygium. However, recurrences are frequent and recurrent lesions tend to be more aggressive. If indeed HPV is involved in pterygium pathogenesis or recurrence, anti-viral medications or vaccination may be new options in pterygium therapy.
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Affiliation(s)
- Aikaterini K Chalkia
- Department of Ophthalmology, University Hospital of Heraklion, 71110 Heraklion, Crete, Greece
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196
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Achilleos C, Berthier F. Quantitative PCR for the specific quantification of Lactococcus lactis and Lactobacillus paracasei and its interest for Lactococcus lactis in cheese samples. Food Microbiol 2013; 36:286-95. [PMID: 24010609 DOI: 10.1016/j.fm.2013.06.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/01/2013] [Accepted: 06/29/2013] [Indexed: 02/04/2023]
Abstract
The first objective of this work was to develop real-time quantitative PCR (qPCR) assays to quantify two species of mesophilic lactic acid bacteria technologically active in food fermentation, including cheese making: Lactococcus lactis and Lactobacillus paracasei. The second objective was to compare qPCR and plate counts of these two species in cheese samples. Newly designed primers efficiently amplified a region of the tuf gene from the target species. Sixty-three DNA samples from twenty different bacterial species, phylogenetically related or commonly found in raw milk and dairy products, were selected as positive and negative controls. Target DNA was successfully amplified showing a single peak on the amplicon melting curve; non-target DNA was not amplified. Quantification was linear over 5 log units (R(2) > 0.990), down to 22 gene copies/μL per well for Lc. lactis and 73 gene copies/μL per well for Lb. paracasei. qPCR efficiency ranged from 82.9% to 93.7% for Lc. lactis and from 81.1% to 99.5% for Lb. paracasei. At two stages of growth, Lc. lactis was quantified in 12 soft cheeses and Lb. paracasei in 24 hard cooked cheeses. qPCR proved to be useful for quantifying Lc. lactis, but not Lb. paracasei.
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Affiliation(s)
- Christine Achilleos
- INRA, UR342 Technologie et Analyses Laitières, BP 20089, F-39800 Poligny, France.
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Kent RJ. Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies. Mol Ecol Resour 2013; 9:4-18. [PMID: 21564560 DOI: 10.1111/j.1755-0998.2008.02469.x] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-based methods have greatly enhanced the sensitivity and specificity of hematophagous arthropod bloodmeal identification. A variety of methods have been applied to study the blood-feeding behaviour of mosquitoes, ticks, black flies and other blood-feeding arthropods as it relates to host-parasite interactions and pathogen transmission. Overviews of the molecular techniques used for bloodmeal identification, their advantages, disadvantages and applications are presented for DNA sequencing, group-specific polymerase chain reaction primers, restriction fragment length polymorphism, real-time polymerase chain reaction, heteroduplex analysis, reverse line-blot hybridization and DNA profiling. Technical challenges to bloodmeal identification including digestion and analysis of mixed bloodmeals are discussed. Analysis of bloodmeal identification results remains a challenge to the field, particularly with regard to incorporation of vertebrate census and ecology data. Future research directions for molecular analysis of arthropod bloodmeals are proposed.
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Affiliation(s)
- Rebekah J Kent
- Arbovirus Diseases Branch, Division of Vector-borne and Infectious Diseases, Centers for Disease Control and Prevention, 3150 Rampart Road, Fort Collins, CO 80521, USA
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198
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Propidium monoazide combined with real-time quantitative PCR to quantify viable Alternaria spp. contamination in tomato products. Int J Food Microbiol 2013; 165:214-20. [PMID: 23796654 DOI: 10.1016/j.ijfoodmicro.2013.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/13/2013] [Accepted: 05/17/2013] [Indexed: 11/22/2022]
Abstract
Alternaria is a common contaminating genus of fungi in fruits, grains, and vegetables that causes severe economic losses to farmers and the food industry. Furthermore, it is claimed that Alternaria spp. are able to produce phytotoxic metabolites, and mycotoxins that are unsafe for human and animal health. DNA amplification techniques are being increasingly applied to detect, identify, and quantify mycotoxigenic fungi in foodstuffs, but the inability of these methods to distinguish between viable and nonviable cells might lead to an overestimation of mycotoxin-producing living cells. A promising technique to overcome this problem is the pre-treatment of samples with nucleic acid intercalating dyes, such as propidium monoazide (PMA), prior to quantitative PCR (qPCR). PMA selectively penetrates cells with a damaged membrane inhibiting DNA amplification during qPCRs. In our study, a primer pair (Alt4-Alt5) to specifically amplify and quantify Alternaria spp. by qPCR was designed. Quantification data of qPCR achieved a detection limit of 10(2)conidia/g of tomato. Here, we have optimized for the first time a DNA amplification-based PMA sample pre-treatment protocol for detecting viable Alternaria spp. cells. Artificially inoculated tomato samples treated with 65μM of PMA, showed a reduction in the signal by almost 7cycles in qPCR between live and heat-killed Alternaria spp. conidia. The tomato matrix had a protective effect on the cells against PMA toxicity, reducing the efficiency to distinguish between viable and nonviable cells. The results reported here indicate that the PMA-qPCR method is a suitable tool for quantifying viable Alternaria cells, which could be useful for estimating potential risks of mycotoxin contamination.
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199
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Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: Comparative study between CARD-FISH and Real Time PCR. J Microbiol Methods 2013; 93:127-33. [DOI: 10.1016/j.mimet.2013.02.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/22/2022]
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200
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Thomas KM, McCann MS, Collery MM, Moschonas G, Whyte P, McDowell DA, Duffy G. Transfer of verocytotoxigenic Escherichia coli O157, O26, O111, O103 and O145 from fleece to carcass during sheep slaughter in an Irish export abattoir. Food Microbiol 2013; 34:38-45. [DOI: 10.1016/j.fm.2012.11.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 11/23/2012] [Indexed: 01/26/2023]
Affiliation(s)
- K M Thomas
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
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