Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies

Bogiel, Tomasz; Mikucka, Agnieszka; Kanarek, Piotr

doi:10.3390/gels8120760

Cited by 2 publications

(2 citation statements)

References 28 publications

(31 reference statements)

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“…Additionally, this technique does not always allow for the differentiation of closely related strains. Currently, the RAPD method is used for the preliminary diagnosis of bacterial infections or as an auxiliary method confirming results obtained by other bacterial strain typing methods [ 65 , 66 ]. PCR-based approaches are fast and effective methods for quantifying the number of genes and/or transcripts in the samples examined.…”

Section: Genotyping Of Strains From Wound Infectionsmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

Gieroń,

Żarnowiec,

Zegadło

et al. 2023

IJMS

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The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.

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Section: Genotyping Of Strains From Wound Infectionsmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

Gieroń,

Żarnowiec,

Zegadło

et al. 2023

IJMS

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“…However, the analysis that meets these three main criteria requires optimization of the method used. The lack of standardization in research procedures is the most frequent reason, making the repeatability of results impossible, which causes erroneous interpretation and limits the wider use of genetic methods in microorganism diagnostics [ 2 , 16 , 18 , 19 , 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

Improved RAPD Method for Candida parapsilosis Fingerprinting

Wojciechowska‐Koszko

Mnichowska-Polanowska

Roszkowska

et al. 2023

Genes

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Recently, methods based on the analysis of arbitrarily amplified target sites of genome microorganisms have been extensively applied in microbiological studies, and especially in epidemiological studies. The range of their application is limited by problems with discrimination and reproducibility resulting from a lack of standardized and reliable methods of optimization. The aim of this study was to obtain optimal parameters of the Random Amplified Polymorphic DNA (RAPD) reaction by using an orthogonal array as per the Taguchi and Wu protocol, modified by Cobb and Clark for Candida parapsilosis isolates. High Simpson’s index values and low Dice coefficients obtained in this study indicated a high level of interspecies DNA polymorphism between C. parapsilosis strains, and the optimized RAPD method proved useful in the microbiological and epidemiological study.

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Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies

Cited by 2 publications

References 28 publications

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

Improved RAPD Method for Candida parapsilosis Fingerprinting

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