scholarly journals An Update on the Laboratory Diagnosis of Rickettsia spp. Infection

Pathogens ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1319
Author(s):  
Adam G. Stewart ◽  
Alexandra G. A. Stewart
Keyword(s):  
Laboratory Diagnosis ◽  
Disease Diagnosis ◽  
Turnaround Time ◽  
Epidemiological Surveillance ◽  
Rickettsia Species ◽  
Resource Requirements ◽  
Human Illness ◽  
Diagnostic Modalities ◽  
Species Specific ◽  
Next Generation Sequencing Ngs

Rickettsia species causing human illness are present globally and can cause significant disease. Diagnosis and identification of this intracellular bacteria are challenging with many available diagnostic modalities suffering from several shortcomings. Detection of antibodies directed against Rickettsia spp. via serological methods remains widely used with a broad range of sensitivity and specificity values reported depending on the assay. Molecular methods, including polymerase chain reaction (PCR) testing, enables species-specific identification with a fast turnaround time; however, due to resource requirements, use in some endemic settings is limited. Reports on the use of next-generation sequencing (NGS) and metagenomics to diagnose Rickettsia spp. infection have been increasing. Despite offering several potential advantages in the diagnosis and surveillance of disease, genomic approaches are currently only limited to reference and research laboratories. Continued development of Rickettsia spp. diagnostics is required to improve disease detection and epidemiological surveillance, and to better understand transmission dynamics.

scholarly journals Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay

2021 ◽  
Vol 2 (1) ◽  
pp. 29-41
Author(s):  
Giorgia Acquaviva ◽  
Michela Visani ◽  
Viviana Sanza ◽  
Antonio De Leo ◽  
Thais Maloberti ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Turnaround Time ◽  
Hpv Infection ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hybrid Capture ◽  
Capture Assay ◽  
Anogenital Area ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

(1) Background: Human papillomaviruses (HPVs) are known to be related to the development of about 5% of all human cancers. The clinical relevance of HPV infection has been deeply investigated in carcinomas of the oropharyngeal area, uterine cervix, and anogenital area. To date, several different methods have been used for detecting HPV infection. The aim of the present study was to compare three different methods for the diagnosis of the presence of the HPV genome. (2) Methods: A total of 50 samples were analyzed. Twenty-five of them were tested using both next generation sequencing (NGS) and VisionArray® technology, the other 25 were tested using Hybrid Capture (HC) II assay and VisionArray® technology. (3) Results: A substantial agreement was obtained using NGS and VisionArray® (κ = 0.802), as well as between HC II and VisionArray® (κ = 0.606). In both analyses, the concordance increased if only high risk HPVs I(HR-HPVs) were considered as “positive”. (4) Conclusions: Our data highlighted the importance of technical choice in HPV characterization, which should be guided by the clinical aims, costs, starting material, and turnaround time for results.

scholarly journals Evaluation of a Sample Pooling Strategy for Sars-cov-2 Using Real Time PCR

2021 ◽  
Author(s):  
Annet M Nankya ◽  
Luke Nyakarahuka ◽  
Stephen Balinandi ◽  
John Kayiwa ◽  
Julius Lutwama ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Virus Disease ◽  
Laboratory Diagnosis ◽  
Turnaround Time ◽  
Limited Resources ◽  
Asymptomatic Patients ◽  
Sample Pooling ◽  
Sample Testing ◽  
Pooling Strategy

Abstract Back ground: Corona Virus Disease 2019 (COVID 19) in Uganda was first reported in a male traveler from Dubai on 21st March, 2020 shortly after WHO had announced the condition as a global pandemic. Timely laboratory diagnosis of COVID -19 for all samples from both symptomatic and asymptomatic patients was observed as key in containing the pandemic and breaking the chain of transmission. However, there was a challenge of limited resources required for testing SARS-COV-2 in low and middle income countries. To mitigate this, a study was conducted to evaluate a sample pooling strategy for COVI-19 using real time PCR. The cost implication and the turn around time of pooled sample testing versus individual sample testing were also compared.Methods: In this study, 1260 randomly selected samples submitted to Uganda Virus Research Institute for analysis were batched in pools of 5, 10, and 15. The pools were then extracted using a Qiagen kit. Both individual and pooled RNA were screened for the SARS-COV-2 E gene using a Berlin kit. Results: Out of 1260 samples tested, 21 pools were positive in pools of 5 samples, 16 were positive in pools of 10 and 14 were positive in pools of 15 samples. The study also revealed that the pooling strategy helps to save a lot on resources, time and expands diagnostic capabilities without affecting the sensitivity of the test in areas with low SARS-COV-2 prevalence.Conclusion: This study demonstrated that the pooling strategy for COVID-19 reduced on the turnaround time and there was a substantial increase in the overall testing capacity with limited resources as compared to individual testing.

An Analytical Model for Resource Characterization and Parameter Estimation for DAG-Based Jobs for Homogeneous Systems

2015 ◽  
Vol 6 (1) ◽  
pp. 34-52 ◽  
Author(s):  
Mohammad Sajid ◽  
Zahid Raza
Keyword(s):  
Analytical Model ◽  
High Performance ◽  
Service Providers ◽  
Average Energy ◽  
Electrical Energy ◽  
Turnaround Time ◽  
Service Level ◽  
Resource Requirement ◽  
Service Oriented Architectures ◽  
Resource Requirements

High Performance Computing (HPC) systems demand and consume a significant amount of resources (e.g. server, storage, electrical energy) resulting in high operational costs, reduced reliability, and sometimes leading to waste of scarce natural resources. On one hand, the most important issue for these systems is achieving high performance, while on the other hand, the rapidly increasing resource costs appeal to effectively predict the resource requirements to ensure efficient services in the most optimized manner. The resource requirement prediction for a job thus becomes important for both the service providers as well as the consumers for ensuring resource management and to negotiate Service Level Agreements (SLAs), respectively, in order to help make better job allocation decisions. Moreover, the resource requirement prediction can even lead to improved scheduling performance while reducing the resource waste. This work presents an analytical model estimating the required resources for the modular job execution. The analysis identifies the number of processors required and the maximum and minimum bounds on the turnaround time and energy consumed. Simulation study reveals that the scheduling algorithms integrated with the proposed analytical model helps in improving the average throughput and the average energy consumption of the system. As the work predicts the resource requirements, it can even play an important role in Service-Oriented Architectures (SOA) like Cloud computing or Grid computing.

scholarly journals New Real-Time PCRs to Differentiate Rickettsia spp. and Rickettsia conorii

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4431 ◽  
Author(s):  
Valeria Blanda ◽  
Rosalia D’Agostino ◽  
Elisabetta Giudice ◽  
Kety Randazzo ◽  
Francesco La Russa ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Real Time ◽  
Emerging Infectious Diseases ◽  
Laboratory Diagnosis ◽  
Diagnostic Methods ◽  
Rickettsia Conorii ◽  
Rickettsia Species ◽  
Vector Borne Diseases ◽  
Vector Borne ◽  
Dna Primers

Rickettsia species are an important cause of emerging infectious diseases in people and animals, and rickettsiosis is one of the oldest known vector-borne diseases. Laboratory diagnosis of Rickettsia is complex and time-consuming. This study was aimed at developing two quantitative real-time PCRs targeting ompB and ompA genes for the detection, respectively, of Rickettsia spp. and R. conorii DNA. Primers were designed following an analysis of Rickettsia gene sequences. The assays were optimized using SYBR Green and TaqMan methods and tested for sensitivity and specificity. This study allowed the development of powerful diagnostic methods, able to detect and quantify Rickettsia spp. DNA and differentiate R. conorii species.

scholarly journals EPIDEMIOLOGY, CLINICAL ASPECTES,LABORATORY DIAGNOSIS AND TREATMENT OF RICKESIAL DISEASES IN THE MEDITERRANEAN AREA DURIN COVID-19 PANDEMIC:A REVIEW OF THE LITERATURE

2020 ◽  
Vol 12 (1) ◽  
pp. e2020056
Author(s):  
Andrea De Vito ◽  
Nicholas Geremia ◽  
Maria Sabrina Mameli ◽  
Pier Andrea Serra ◽  
Vito Fiore ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Mediterranean Area ◽  
Laboratory Diagnosis ◽  
Diagnostic Tools ◽  
Nucleotide Sequencing ◽  
Human Pathogens ◽  
Rickettsia Species ◽  
Rickettsial Infections ◽  
The Mediterranean ◽  
Correct Understanding

The purpose of the present review is to give an update regarding the classification, the epidemiology, the clinical manifestation, the diagnoses, and the treatment of the Rickettsiae species present in the Mediterranean area. We performed a comprehensive search, through electronic databases (Pubmed – MEDLINE) and search engines (Google Scholar), of peer-reviewed publications (articles, reviews, and books). The availability of new diagnostic tools, including Polymerase Chain Reaction and nucleotide sequencing has significantly modified the classification of intracellular bacteria, including the order Rickettsiales with more and more new Rickettsia species recognized as human pathogens. Furthermore, emerging Rickettsia species have been found in several countries and are often associated with unique clinical pictures that may challenge the physician in the early detection of the diseases. Rickettsial infections include a wide spectrum of clinical presentations ranging from a benign to a potentially life treating disease that requires prompt recognition and proper management. Recently, due to the spread of SARS-CoV-2 infection, the differential diagnosis with COVID-19 is of crucial importance. The correct understanding of the clinical features, diagnostic tools, and proper treatment can assist clinicians in the management of Rickettsioses in the Mediterranean area.

scholarly journals Development of circulating tumour DNA analysis for gastrointestinal cancers

ESMO Open ◽  
2020 ◽  
Vol 5 (Suppl 1) ◽  
pp. e000600 ◽  
Author(s):  
Yoshiaki Nakamura ◽  
Kohei Shitara
Keyword(s):  
Dna Analysis ◽  
Residual Disease ◽  
Turnaround Time ◽  
Resistance Mechanisms ◽  
Detection Methods ◽  
Comprehensive Genomic Profiling ◽  
Gi Cancers ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Circulating Tumour Dna

Comprehensive genomic profiling using next-generation sequencing (NGS) enables the identification of multiple genomic biomarkers established in advanced gastrointestinal (GI) cancers. However, tissue-based NGS has limitations, such as long turnaround time and failure to detect tumour heterogeneity. Recently, the analysis of circulating tumour DNA (ctDNA) using polymerase chain reaction-based or NGS-based methods has demonstrated the capability to detect genomic alterations with high accuracy compared with tumour tissue analysis with short turnaround time and identify heterogeneous resistance mechanisms. Furthermore, ctDNA analysis can be repeatedly performed on disease progression to clarify resistant clones. Clinical trials that test the outcome of a selected targeted therapy based on a ctDNA result are ongoing to prospectively evaluate the clinical utility of ctDNA analysis. Furthermore, the improvement of ctDNA analysis beyond current technical limits of mutation-based ctDNA detection methods has expanded the potential for detecting the presence of tumours in patients with no clinically evident disease, such as minimal residual disease and early cancer. Although a careful understanding of the advantages and limitations are required and further prospective studies are needed, the ctDNA analysis has the potential to overcome several challenges in the treatment of various types of cancers at all stages, including GI cancers.

The effect of cover and food on space use by wintering Song Sparrows and Field Sparrows

1997 ◽  
Vol 75 (10) ◽  
pp. 1636-1641 ◽  
Author(s):  
Christopher W. Beck ◽  
Bryan D. Watts
Keyword(s):  
Predation Risk ◽  
Positive Response ◽  
Distribution Patterns ◽  
Microhabitat Use ◽  
Vegetative Cover ◽  
Song Sparrows ◽  
Trade Offs ◽  
Resource Requirements ◽  
Woody Cover ◽  
Species Specific

The distribution of birds among microhabitats may reflect species-specific resource requirements. Both food availability and predation risk have been shown to influence patterns of microhabitat use by sparrows during winter. We investigated the influence of vegetative cover and food on microhabitat use using a 2 × 2 factorial design. Both woody cover and food were manipulated at the plot level. The presence of screening cover (weed stems) was manipulated within plots. Sparrows showed a positive response to the presence of both cover and food. Within plots, sparrows selected areas with screening cover. The distribution of birds between areas with and without screening cover was influenced by the presence of woody cover and food. Conversely, the presence of screening cover reduced the influence of woody cover on the distribution of birds within patches. Song Sparrows (Melospiza melodia) and Field Sparrows (Spizella pusilla) differed in their response to treatments both within and across plots, suggesting that trade-offs between foraging and predation risk may be important in the structuring of winter sparrow assemblages. Additionally, screening cover appears to moderate predation risk and therefore to affect distribution patterns.

scholarly journals Molecular Diagnostics for the Sigatoka Disease Complex of Banana

2007 ◽  
Vol 97 (9) ◽  
pp. 1112-1118 ◽  
Author(s):  
Mahdi Arzanlou ◽  
Edwin C. A. Abeln ◽  
Gert H. J. Kema ◽  
Cees Waalwijk ◽  
Jean Carlier ◽  
...  
Keyword(s):  
Management Strategies ◽  
Leaf Tissue ◽  
Pcr Primers ◽  
Disease Diagnosis ◽  
Life Cycles ◽  
Diagnostic Tools ◽  
Disease Epidemiology ◽  
Disease Complex ◽  
Real Time Quantitative Pcr ◽  
Species Specific

The Sigatoka disease complex of banana involves three related ascomycetous fungi, Mycosphaerella fijiensis, M. musicola, and M. eumusae. The exact distribution of these three species and their disease epidemiology remain unclear, because their symptoms and life cycles are rather similar. Disease diagnosis in the Mycosphaerella complex of banana is based on the presence of host symptoms and fungal fruiting structures, which hamper preventive management strategies. In the present study, we have developed rapid and robust species-specific molecular-based diagnostic tools for detection and quantification of M. fijiensis, M. musicola, and M. eumusae. Conventional species-specific polymerase chain reaction (PCR) primers were developed based on the actin gene that detected DNA at as little as 100, 1, and 10 pg/μl from M. fijiensis, M. musicola, and M. eumusae, respectively. Furthermore, TaqMan real-time quantitative PCR assays were developed based on the β-tubulin gene and detected quantities of DNA as low as 1 pg/μl for each Mycosphaerella sp. from pure cultures and DNA at 1.6 pg/μl per milligram of dry leaf tissue for M. fijiensis that was validated using naturally infected banana leaves.

scholarly journals Polymerase Chain Reaction (PCR): A Short Review

2013 ◽  
Vol 4 (1) ◽  
pp. 30-36 ◽  
Author(s):  
Md Tahminur Rahman ◽  
Muhammed Salah Uddin ◽  
Razia Sultana ◽  
Arumina Moue ◽  
Muntahina Setu
Keyword(s):  
Correct Diagnosis ◽  
Medical Science ◽  
Genetic Diagnosis ◽  
High Specificity ◽  
Short Review ◽  
Laboratory Diagnosis ◽  
Molecular Techniques ◽  
Advantages And Disadvantages ◽  
Specificity And Sensitivity ◽  
Diagnostic Modalities

Diagnosis of disease now a days is mostly laboratory dependent. Due to recent advances in medical science and molecular biology, most of the diagnosis of uncommon, complicated, unusual presentation of disease has left the option of molecular diagnosis as the number one diagnostic modalities. Many molecular techniques are now being widely used throughout the  world including PCR, flow cytometry, tissue microarray, different blots, and genetic diagnosis. Among these PCR is the most widely accepted, commonly used diagnostic modalities with very high specificity and sensitivity for correct diagnosis. We have reviewed the principle, application, advantages and disadvantages of PCR in laboratory diagnosis of disease. DOI: http://dx.doi.org/10.3329/akmmcj.v4i1.13682 AKMMC J 2013: 4(1): 30-36    

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