scholarly journals Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness

2015 ◽  
Vol 53 (12) ◽  
pp. 3723-3728 ◽  
Author(s):  
Matthew J. Binnicker
Keyword(s):  
Cost Effectiveness ◽  
Test Performance ◽  
Diarrheal Disease ◽  
Gastrointestinal Disease ◽  
Microbial Pathogens ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Performance Result ◽  
Detection And Identification ◽  
Result Interpretation

Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.

scholarly journals Rose Rosette Disease: Recent Advances on Molecular Diagnostic Tools

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 596-600 ◽  
Author(s):  
Binoy Babu ◽  
Gary Knox ◽  
Mathews L. Paret ◽  
Francisco M. Ochoa-Corona
Keyword(s):  
The United States ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Department Of Agriculture ◽  
Specialty Crop ◽  
Detection And Identification ◽  
Research Initiative ◽  
Highly Sensitive ◽  
Rose Rosette ◽  
Rose Rosette Disease

Rose rosette emaravirus (RRV, genus Emaravirus), the causal agent of rose rosette disease, is the topmost pathogen of concern for the rose industry in the United States. The only strategy available for disease management is early identification and eradication of the infected plants. Highly reliable, specific, and sensitive detection assays are thus required to test and confirm the presence of RRV in suspected plant samples. RRV is only a recently characterized virus and hence limits the diagnostic tools available for its early detection. With a U.S. Department of Agriculture (USDA) Specialty Crop Research Initiative (SCRI) project sponsorship, several diagnostic tools including end-point reverse transcription-polymerase chain reaction (RT-PCR) and RT-qPCR assays targeting single and multiple genes targets were developed for routine diagnostics. This review introduces an overall view of the different diagnostic tools developed, which are reliable, highly sensitive, and can be easily implemented for detection and identification in laboratories providing diagnostic services and confirmation of RRV-infected samples.

Molecular studies on pig cryptosporidiosis in Poland

2014 ◽  
Vol 17 (4) ◽  
pp. 577-582 ◽  
Author(s):  
A. Rzeżutka ◽  
A. Kaupke ◽  
I. Kozyra ◽  
Z. Pejsak
Keyword(s):  
Intestinal Parasites ◽  
Cryptosporidium Species ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Nucleotide Sequence Analysis ◽  
Fecal Samples ◽  
Detection And Identification ◽  
Pcr Rflp ◽  
Pig Farms ◽  
Asymptomatic Infections

AbstractCryptosporidium intestinal parasites have been detected in farmed pigs worldwide. Infections are usually asymptomatic with a low number of oocysts shed in pig feces. This makes the recognition of infection difficult or unsuccessful when microscopic methods are used. The aim of this study was molecular identification of Cryptosporidium species in pig herds raised in Poland with regard to the occurrence of zoonotic species. In total, 166 pig fecal samples were tested. The examined pigs were aged 1 to 20 weeks. Overall, 39 pig farms were monitored for parasite presence. The detection and identification of Cryptosporidium DNA was performed on the basis of PCR-RFLP and nucleotide sequence analysis of the amplified 18 SSU rRNA and COWP gene fragments. Infected animals were housed in 21 (53.8%) of the pig farms monitored. The presence of Cryptosporidum was confirmed in 46 (27.7%) samples of pig feces. Among positive fecal samples, 34 (29.3%) were collected from healthy animals, and 12 (24%) from diarrheic pigs. Most infected animals (42.1%) were 2 to 3 months old. The following parasite species were detected: C. scrofarum, C. suis and C. parvum. Indeed, asymptomatic infections caused by C. scrofarum were observed in the majority of the herds. Mixed infections caused by C. suis and C. scrofarum were not common; however, they were observed in 8.6% of the positive animals. C. parvum DNA was found only in one sample collected from a diarrheic pig. The application of molecular diagnostic tools allowed for detection and identification of Cryptosporidium species in pigs. The sporadic findings of C. parvum are subsequent evidence for the contribution of pigs in the transmission of cryptosporidiosis from animals to humans.

scholarly journals A Fully Integrated Real-Time Detection, Diagnosis, and Control of Community Diarrheal Disease Clusters and Outbreaks (the INTEGRATE Project): Protocol for an Enhanced Surveillance System

10.2196/13941 ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. e13941 ◽  
Author(s):  
Kirsty Marie McIntyre ◽  
Frederick J Bolton ◽  
Rob M Christley ◽  
Paul Cleary ◽  
Elizabeth Deja ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Real Time ◽  
Surveillance System ◽  
Diarrheal Disease ◽  
Gastrointestinal Disease ◽  
Diagnostic Methods ◽  
Surveillance Systems ◽  
National Implementation ◽  
The Cost ◽  
And Control

Background Diarrheal disease, which affects 1 in 4 people in the United Kingdom annually, is the most common cause of outbreaks in community and health care settings. Traditional surveillance methods tend to detect point-source outbreaks of diarrhea and vomiting; they are less effective at identifying low-level and intermittent food supply contamination. Furthermore, it can take up to 9 weeks for infections to be confirmed, reducing slow-burn outbreak recognition, potentially impacting hundreds or thousands of people over wide geographical areas. There is a need to address fundamental problems in traditional diarrheal disease surveillance because of underreporting and subsequent unconfirmed infection by patients and general practitioners (GPs); varying submission practices and selective testing of samples in laboratories; limitations in traditional microbiological diagnostics, meaning that the timeliness of sample testing and etiology of most cases remains unknown; and poorly integrated human and animal surveillance systems, meaning that identification of zoonoses is delayed or missed. Objective This study aims to detect anomalous patterns in the incidence of gastrointestinal disease in the (human) community; to target sampling; to test traditional diagnostic methods against rapid, modern, and sensitive molecular and genomic microbiology methods that identify and characterize responsible pathogens rapidly and more completely; and to determine the cost-effectiveness of rapid, modern, sensitive molecular and genomic microbiology methods. Methods Syndromic surveillance will be used to aid identification of anomalous patterns in microbiological events based on temporal associations, demographic similarities among patients and animals, and changes in trends in acute gastroenteritis cases using a point process statistical model. Stool samples will be obtained from patients’ consulting GPs, to improve the timeliness of cluster detection and characterize the pathogens responsible, allowing health protection professionals to investigate and control outbreaks quickly, limiting their size and impact. The cost-effectiveness of the proposed system will be examined using formal cost-utility analysis to inform decisions on national implementation. Results The project commenced on April 1, 2013. Favorable approval was obtained from the Research Ethics Committee on June 15, 2015, and the first patient was recruited on October 13, 2015, with 1407 patients recruited and samples processed using traditional laboratory techniques as of March 2017. Conclusions The overall aim of this study is to create a new One Health paradigm for detecting and investigating diarrhea and vomiting in the community in near-real time, shifting from passive human surveillance and management of laboratory-confirmed infection toward an integrated, interdisciplinary enhanced surveillance system including management of people with symptoms. International Registered Report Identifier (IRRID) DERR1-10.2196/13941

scholarly journals A Fully Integrated Real-Time Detection, Diagnosis, and Control of Community Diarrheal Disease Clusters and Outbreaks (the INTEGRATE Project): Protocol for an Enhanced Surveillance System (Preprint)

2019 ◽  
Author(s):  
Kirsty Marie McIntyre ◽  
Frederick J Bolton ◽  
Rob M Christley ◽  
Paul Cleary ◽  
Elizabeth Deja ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Real Time ◽  
Surveillance System ◽  
Diarrheal Disease ◽  
Gastrointestinal Disease ◽  
Diagnostic Methods ◽  
Surveillance Systems ◽  
National Implementation ◽  
The Cost ◽  
And Control

BACKGROUND Diarrheal disease, which affects 1 in 4 people in the United Kingdom annually, is the most common cause of outbreaks in community and health care settings. Traditional surveillance methods tend to detect point-source outbreaks of diarrhea and vomiting; they are less effective at identifying low-level and intermittent food supply contamination. Furthermore, it can take up to 9 weeks for infections to be confirmed, reducing slow-burn outbreak recognition, potentially impacting hundreds or thousands of people over wide geographical areas. There is a need to address fundamental problems in traditional diarrheal disease surveillance because of underreporting and subsequent unconfirmed infection by patients and general practitioners (GPs); varying submission practices and selective testing of samples in laboratories; limitations in traditional microbiological diagnostics, meaning that the timeliness of sample testing and etiology of most cases remains unknown; and poorly integrated human and animal surveillance systems, meaning that identification of zoonoses is delayed or missed. OBJECTIVE This study aims to detect anomalous patterns in the incidence of gastrointestinal disease in the (human) community; to target sampling; to test traditional diagnostic methods against rapid, modern, and sensitive molecular and genomic microbiology methods that identify and characterize responsible pathogens rapidly and more completely; and to determine the cost-effectiveness of rapid, modern, sensitive molecular and genomic microbiology methods. METHODS Syndromic surveillance will be used to aid identification of anomalous patterns in microbiological events based on temporal associations, demographic similarities among patients and animals, and changes in trends in acute gastroenteritis cases using a point process statistical model. Stool samples will be obtained from patients’ consulting GPs, to improve the timeliness of cluster detection and characterize the pathogens responsible, allowing health protection professionals to investigate and control outbreaks quickly, limiting their size and impact. The cost-effectiveness of the proposed system will be examined using formal cost-utility analysis to inform decisions on national implementation. RESULTS The project commenced on April 1, 2013. Favorable approval was obtained from the Research Ethics Committee on June 15, 2015, and the first patient was recruited on October 13, 2015, with 1407 patients recruited and samples processed using traditional laboratory techniques as of March 2017. CONCLUSIONS The overall aim of this study is to create a new One Health paradigm for detecting and investigating diarrhea and vomiting in the community in near-real time, shifting from passive human surveillance and management of laboratory-confirmed infection toward an integrated, interdisciplinary enhanced surveillance system including management of people with symptoms. INTERNATIONAL REGISTERED REPORT DERR1-10.2196/13941

scholarly journals Development of a loop-mediated isothermal amplification (LAMP) assay for the identification of the invasive wood borer Aromia bungii (Coleoptera: Cerambycidae) from frass

3 Biotech ◽  
2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Domenico Rizzo ◽  
Nicola Luchi ◽  
Daniele Da Lio ◽  
Linda Bartolini ◽  
Francesco Nugnes ◽  
...  
Keyword(s):  
Lamp Assay ◽  
Isothermal Amplification ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Loop Mediated Isothermal Amplification ◽  
Larval Stages ◽  
Longhorn Beetle ◽  
Rapid Monitoring ◽  
Major Pest ◽  
Wood Borer

AbstractThe red-necked longhorn beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) is native to east Asia, where it is a major pest of cultivated and ornamental species of the genus Prunus. Morphological or molecular discrimination of adults or larval specimens is required to identify this invasive wood borer. However, recovering larval stages of the pest from trunks and branches causes extensive damage to plants and is timewasting. An alternative approach consists in applying non-invasive molecular diagnostic tools to biological traces (i.e., fecal pellets, frass). In this way, infestations in host plants can be detected without destructive methods. This paper presents a protocol based on both real-time and visual loop-mediated isothermal amplification (LAMP), using DNA of A. bungii extracted from fecal particles in larval frass. Laboratory validations demonstrated the robustness of the protocols adopted and their reliability was confirmed performing an inter-lab blind panel. The LAMP assay and the qPCR SYBR Green method using the F3/B3 LAMP external primers were equally sensitive, and both were more sensitive than the conventional PCR (sensitivity > 103 to the same starting matrix). The visual LAMP protocol, due to the relatively easy performance of the method, could be a useful tool to apply in rapid monitoring of A. bungii and in the management of its outbreaks.

scholarly journals The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
James M. Hodge ◽  
Andrey A. Yurchenko ◽  
Dmitriy A. Karagodin ◽  
Reem A. Masri ◽  
Ryan C. Smith ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Internal Transcribed Spacer ◽  
Single Species ◽  
Its2 Sequence ◽  
Pathogen Transmission ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequence Length ◽  
Phylogenetic Position ◽  
Internal Transcribed Spacer 2

Abstract Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

scholarly journals Impact of Patient Adherence and Test Performance on the Cost-Effectiveness of Cervical Cancer Screening in Developing Countries

2010 ◽  
Vol 20 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Rebecca B. Perkins ◽  
Sarah M. Langrish ◽  
Linda J. Stern ◽  
James F. Burgess ◽  
Carol J. Simon
Keyword(s):  
Cervical Cancer ◽  
Developing Countries ◽  
Cost Effectiveness ◽  
Cancer Screening ◽  
Cervical Cancer Screening ◽  
Test Performance ◽  
Patient Adherence ◽  
The Cost

scholarly journals Laboratory diagnosis of pneumonia in the molecular age

2016 ◽  
Vol 48 (6) ◽  
pp. 1764-1778 ◽  
Author(s):  
Antoni Torres ◽  
Nelson Lee ◽  
Catia Cilloniz ◽  
Jordi Vila ◽  
Menno Van der Eerden
Keyword(s):  
Laboratory Diagnosis ◽  
High Rate ◽  
Microbial Pathogens ◽  
Molecular Diagnostic ◽  
Respiratory Pathogens ◽  
Major Advance ◽  
Lung Microbiome ◽  
Microbiological Methods ◽  
New Knowledge ◽  
Diagnostic Technology

Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.

scholarly journals Clinical Application of Next-Generation Sequencing of Plasma Cell-Free DNA for Genotyping Untreated Advanced Non-Small Cell Lung Cancer

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2707
Author(s):  
Maria Gabriela O. Fernandes ◽  
Natália Cruz-Martins ◽  
Conceição Souto Moura ◽  
Susana Guimarães ◽  
Joana Pereira Reis ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Clinical Outcomes ◽  
Test Performance ◽  
Molecular Diagnostic ◽  
Test Accuracy ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Clinical Value ◽  
Generation Sequencing

Background: Analysis of circulating tumor DNA (ctDNA) has remarkable potential as a non-invasive lung cancer molecular diagnostic method. This prospective study addressed the clinical value of a targeted-gene amplicon-based plasma next-generation sequencing (NGS) assay to detect actionable mutations in ctDNA in patients with newly diagnosed advanced lung adenocarcinoma. Methods: ctDNA test performance and concordance with tissue NGS were determined, and the correlation between ctDNA findings, clinical features, and clinical outcomes was evaluated in 115 patients with paired plasma and tissue samples. Results: Targeted-gene NGS-based ctDNA and NGS-based tissue analysis detected 54 and 63 genomic alterations, respectively; 11 patients presented co-mutations, totalizing 66 hotspot mutations detected, 51 on both tissue and plasma, 12 exclusively on tissue, and 3 exclusively on plasma. NGS-based ctDNA revealed a diagnostic performance with 81.0% sensitivity, 95.3% specificity, 94.4% PPV, 83.6% NPV, test accuracy of 88.2%, and Cohen’s Kappa 0.764. PFS and OS assessed by both assays did not significantly differ. Detection of ctDNA alterations was statistically associated with metastatic disease (p = 0.013), extra-thoracic metastasis (p = 0.004) and the number of organs involved (p = 0.010). Conclusions: This study highlights the potential use of ctDNA for mutation detection in newly diagnosed NSCLC patients due to its high accuracy and correlation with clinical outcomes.

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