Low-cost Real-time PCR Research Articles

Development of a passive quenching SiPM-based detection system for quantification of real time PCR products based on fluorescence lifetime

This paper presents a technique for development of a high-performance and low cost real time PCR detection system based on fluorescence lifetime of fluorescent dyes by using silicon photomultipliers. A high gain passive quenching silicon photomultiplier is used as a detector in a relatively high photon rate condition along with a devised low cost discrete electronic circuitry to implement a detection system in which both time- and frequency-resolved measurements are performed. The requirements and restrictions to implement and test the system for quantification of the amplified dsDNA PCR products are discussed. The SYBR Green I as an intercalating double-stranded DNA fluoresenct-dye has been used to stain PCR products. It is demonstrated that the quantification of PCR products based on fluorescence lifetime by passive quenching silicon photomultiplier, without using any optical filter, is an efficient and cost effective method in real time PCR instrumentation.

Leishmania-FAST15: A rapid, sensitive and low-cost real-time PCR assay for the detection of Leishmania infantum and Leishmania braziliensis kinetoplast DNA in canine blood samples

We describe an improved real-time PCR assay (designated as “Leishmania-FAST15”) for the detection and quantification of Leishmania infantum and Leishmania braziliensis kinetoplast DNA minicircles in canine blood samples. The analytical sensitivity of this technique is 0.1 fg of DNA, which is equivalent to 0.002 parasite per reaction. This assay uses a small reaction volume (15 μl) and is rapid to perform, with the results being available in less than 34 min. This improved assay might also be suitable for detecting and quantifying L. infantum and L. braziliensis DNA in other tissues, such as bone marrow and lymph nodes.

PCR em tempo real para detecção do vírus da doença de Aujeszky

O objetivo deste trabalho foi desenvolver uma PCR em tempo real (qPCR) para o diagnóstico rápido e sensível da doença de Aujeszky. Os iniciadores amplificaram um fragmento de 123 pares de base do gene codificante da glicoproteína D. A qPCR foi testada em 25 amostras de cérebro de suíno positivas e 85 amostras negativas para DA no isolamento viral e na soroneutralização. A sensibilidade analítica foi calculada com acréscimo de um isolado brasileiro do SuHV-1 titulado em amostras de cérebro de suíno negativas na soroneutralização e na PCR. A técnica apresentou sensibilidade analítica de 10-0,5 TCID50/50µL. A qPCR foi capaz de distinguir reações inespecíficas devido a dímero de oligonucleotídeos iniciadores ou amplificações, além do alvo designado (evitando, assim, os falso-positivos), e de obter resultados rápidos.

A rapid low-cost real-time PCR for the detection of klebsiella pneumonia carbapenemase genes

BackgroundKlebsiella pneumonia carbapenemases (KPCs) are able to hydrolyze the carbapenems, which cause many bacteria resistance to multiple classes of antibiotics, so the rapid dissemination of KPCs is worrisome. Laboratory identification of KPCs-harboring clinical isolates would be a key to limit the spread of the bacteria. This study would evaluate a rapid low-cost real-time PCR assay to detect KPCs.MethodsReal-time PCR assay based on SYBR GreenIwas designed to amplify a 106bp product of the blaKPC gene from the159 clinical Gram-negative isolates resistant to several classes of -lactam antibiotics through antimicrobial susceptibility testing. We confirmed the results of real-time PCR assay by the conventional PCR-sequencing. At the same time, KPCs of these clinical isolates were detected by the modified Hodge test (MHT). Then we compared the results of real-time PCR assay with those of MHT from the sensitivity and specificity. Moreover, we evaluated the sensitivity of the real-time PCR assay.ResultsThe sensitivity and specificity of the results of the real-time PCR assay compared with those of MHT was 29/29(100%) and 130/130(100%), respectively. The results of the real-time PCR and the MHT were strongly consistent (Exact Sig. (2-tailed) =1. 000; McNemar test). The real-time PCR detection limit was about 0.8cfu using clinical isolates.ConclusionThe real-time PCR assay could rapidly and accurately detect KPCs -harboring strains with high analytical sensitivity and specificity.

Development of a simple and low-cost real-time PCR method for the identification of commonly encountered mycobacteria in a high throughput laboratory

To facilitate efficient identification of commonly encountered mycobacteria species (Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium fortuitum complex, Mycobacterium chelonae/abscessus, Mycobacterium kansasii, Mycobacterium gordonae) in high throughput laboratories, a 16s rDNA sequence based real-time PCR assay was developed and evaluated. Oligonucleotide primers and hybridization probes were designed based on sequence differences of the mycobacterial 16S rDNA gene. This assay was evaluated with 1649 suspected non-tuberculosis mycobacterial isolates. Apart from 3 out of 40 M. avium isolates that showed false signal with M. intracellulare specific probe, 100% specificity was obtained for all tested probes. Assay sensitivity varied from 88.9 to 100% depending on species. Average cost for obtaining a definite identification was only USD 1.1 with an average turn around time of less than 3 days. A rapid, simple and inexpensive real-time PCR assay was developed for the identification of common encountered mycobacteria in a high throughput laboratory setting. With this assay, more than 80% of the clinically isolated nontuberculous mycobacteria could be identified in a highly cost effective manner. This helped to save resources for other laboratory activities especially in high throughput mycobacterial laboratories.