The Most Common Molecular Diagnostic Method in Microbiology: Polymerase Chain Reaction

Year 2023, , 118 - 125, 22.06.2023

Oğuz Kağan Türedi , Esra Şeker

https://doi.org/10.31196/huvfd.1246738

Cited By: 1

Abstract

This review briefly explains Polymerase Chain Reaction (PCR) types commonly used in diagnostic microbiology. PCR, first discovered by Kary Banks Mullis in 1985 for DNA search, is an in vitro method involving the enzymatic amplification of a specific DNA segment by primers, creating many copies. Today, interest in PCR and PCR-based diagnostic methods is increasing, and PCR remains up-to-date as the most widely used molecular diagnostic method in the diagnosis of infectious diseases of humans and animals and epidemiological studies. When molecular diagnostic procedures are constantly updated, new techniques are added, and become more affordable, accessible, and applicable in routine diagnosis, the frequency and equality of use of these techniques in diagnostic microbiology will increase at the same rate.

Keywords

Diagnostic microbiology, molecular diagnosis, PCR, PCR types

Mikrobiyolojide En Yaygın Moleküler Tanı Yöntemi: Polimeraz Zincir Reaksiyonu

Abstract

Sunulan bu derlemenin amacı diagnostik mikrobiyoloji alanında yaygın olarak kullanılan Polimeraz Zincir Reaksiyonu (PZR) tipleri hakkında kısa bilgi verilmesidir. İlk olarak 1985 yılında Kary Banks Mullis tarafından DNA araştırması için keşfedilen PZR, belirli bir DNA segmentinin primerler aracılığıyla enzimatik amplifikasyonunu sağlayarak çok sayıda kopyasını oluşturan in vitro bir yöntemdir. Günümüzde PZR ve PZR tabanlı tanı yöntemlerine ilgi giderek artmakta ve PZR, insan ve hayvanların infeksiyöz hastalıklarının tanısında ve epidemiyolojik araştırmalarda en yaygın kullanılan moleküler tanı yöntemi olarak güncelliğini korumaktadır. Sürekli güncellenen ve yeni teknikler eklenen moleküler tanı yöntemleri rutin tanıda daha ekonomik, ulaşılabilir ve uygulanabilir hale geldiğinde tanısal mikrobiyoloji alanında bu tekniklerin kullanım sıklığı ve çeşitliliği aynı oranda artacaktır.

Keywords

Diagnostik mikrobiyoloji, moleküler tanı, PZR, PZR tipleri

References

• Bagasra O, 2007: Protocols for the in situ PCR-amplification and detection of mRNA and DNA sequences. Nat Protoc, 2 (11), 2782-2795.
• Bhatia D, Wing RA, Singh K, 2013: Genotyping by sequencing, its implications and benefits. Crop Improv, 40 (6), 101–111.
• Buckingham L, Flaws ML, 2007: Molecular Diagnostics Fundamentals, Methods, & Clinical Applications. FA Davis Company., Philadelphia, USA.
• Cao H, Shockey JM, 2012: Comparison of TaqMan and SYBR green qPCR methods for quantitative gene expression in tung tree tissues. J Agric Food Chem, 60 (50), 12296-12303.
• Carr J, Williams DG, Hayden RT 2010: Molecular detection of multiple respiratory viruses. In: Molecular Diagnostics: Techniques and Applications for the Clinical Laboratory (First Ed), Wayne WG (Ed), 289-300, Academic Press, Elsevier Inc, USA.
• Çadırcı BH, Bebek O, Çam D, 2017: Thermococcus gorgonius DNA polimerazının rekombinant olarak üretimi. Selçuk Üniv Fen Fak Fen Derg 43 (1), 1-9.
• Darcan C, Türkyılmaz O, 2018: Yeni Nesil Dizileme Teknolojisine Genel Bakış. Bilecik Şeyh Edebali Univ Fen Bilim Derg, 5 (1), 41-49.
• Deschamps S, Llaca V, May GD, 2012: Genotyping by Sequencing in Plants. Biology, 1 (3), 460-483.
• Drabik A, Bodzon-Kulakowska A, Silberring J, 2016: Gel Electrophoresis. Brenner’s Encyclopedia of Genetics, (Second Edition), 165–167, Academic Press, Elsevier Inc, USA.
• Erali M, Voelkerding KV, Wittwer CT, 2008: High resolution melting applications for clinical laboratory medicine. Exp Mol Pathol, 85 (1), 50–58.
• Garibyan L, Avashia N, 2013: Research techniques made simple: Polymerase chain reaction. J Invest Dermatol, 133 (3), 1–4.
• Green MR, Sambrook J, 2018: Touchdown polymerase chain reaction (PCR). Cold Spring Harbor Protoc, 2018 (5), 350–353.
• Green MR, Sambrook J, 2019a: Polymerase chain reaction. Cold Spring Harb Protoc, 436-456.
• Green MR, Sambrook J, 2019b: Inverse polymerase chain reaction (PCR). Cold Spring Harb Protoc, 2019 (2).
• Gürsoy NC, Otlu B, 2017: Mikrobiyota çalışmalarında moleküler tanı yöntemleri. J Biotechnol and Strategic Health Res, 1 (Special issue), 56–67.
• Heather JM, Chain B. 2016: The sequence of sequencers: The history of sequencing DNA. Genomics, 107 (1), 1-8.
• Hirschhorn JW, Schandl CA, Nolte FS, 2022: Polymerase chain reaction and other nucleic acid amplification technology. In: Henry's Clinical Diagnosis and Management by Laboratory Methods, McPherson RA, Pincus MR (Ed), 1387-1400, Elsevier Inc, USA.
• Kahya S, Buyukcangaz E, Carlı KT, 2013: Polimeraz Zincir Reaksiyonu (PCR) Optimizasyonu. Uludag Univ J Fac Vet Med, 32 (1), 31-38.
• Kavsaoğlu AR, Mersinkaya İ, 2019: Python ile Mini Jel Elektroforez Kontrol Yazılımı ve Sistem Tasarımı. GU J Sci Part C, 7 (4), 969-984.
• Kekeç I, Sipahi N, İkiz S, 2022: New generation genome sequencing methods. J Surg Med, 6 (4), 503-506. Kengen SWM, 2017: Pyrococcus furiosus, 30 years on. Microb Biotechnol, 10 (6), 1441-4.
• Kralik P, Ricchi M, 2017: A basic guide to Real Time PCR in microbial diagnostics: definitions, parameters, and everything. Front Microbiol, 8, 108.
• Li J, Makrigiorgos GM, 2009: COLD-PCR: A new platform for highly improved mutation detection in cancer and genetic testing. Biochem Soc Trans, 37 (Pt 2): 427-32.
• Lorenz TC, 2012: Polymerase chain reaction: Basic protocol plus troubleshooting and optimization strategies. J Vis Exp, (63): 1–15.
• Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. 2012: Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One, 7 (2), 7 (3), e30087.
• Mao X, Liu C, Tong H, Chen Y, Liu K, 2019: Principles of digital PCR and its applications in current obstetrical and gynecological diseases. Am J Transl Res, 11 (12), 7209-7222.
• Mo Y, Wan R, Zhang Q, 2012: Application of reverse transcription-PCR and real-time PCR in nanotoxicity research. Methods Mol Biol, 926, 99-112.
• Mohammed S, Birhan G, Admassu B, Shite A, Yeneneh H, 2015: Review on polymerase chain reaction and its diagnostic merit over conventional techniques in animal disease. Int J Basic Appl Sci, 7 (5), 262-281.
• Mullis KB, 1990: The unusual origin of the polymerase chain reaction. Sci Am, 262 (4), 56-65.
• Nehdi A, Samman N, Aguilar-Sánchez V, Farah A, Yurdusev E, Boudjelal M, Perreault J, 2020: Novel strategies to optimize the amplification of single-stranded DNA. Front Bioeng Biotechnol, 8, 401.
• Öz Aydın S, 2004: RAPD (Rastgele Arttırılmış Polimofik DNA) belirleyicileri ve bitki sistematiği. Journal of Scientific Reports-A, 6, 113-130.
• Patrinos GP, Danielson PB, Ansorge WJ, 2016: Molecular Diagnostics: Past, Present, and Future. In Molecular Diagnostics: Third Edition. Elsevier Ltd. Amsterdam, NL.
• Pavšič J, Žel J, Milavec M, 2016: Assessment of the real-time PCR and different digital PCR platforms for DNA quantification. Anal Bioanal Chem, 408, 107–121.
• Perkel J, 2015: Guiding our PCR experiments. BioTechniques, 58 (5), 217.
• Pierce KE, Wangh LJ, 2007: Linear-after-the-exponential polymerase chain reaction and allied technologies. Real-time detection strategies for rapid, reliable diagnosis from single cells. Methods Mol Med, 132, 65–85.
• Price CW, Leslie DC, Landers JP, 2009: Nucleic acid extraction techniques and application to the microchip. Lab Chip, 9, 2484-2494.
• Porta AR, Enners E, 2012: Determining annealing temperatures for polymerase chain reaction. Am Biol Teach, 74 (4), 256–260.
• Phung TTB, Chu SV, Vu ST, Pham HT, Nguyen HM, Nguyen HD, Le NT, Nguyen DV, Truong PT, Vu VTT, Nguyen ATV, 2020: COLD-PCR method for early detection of antiviral drug-resistance mutations in treatment-naive children with chronic Hepatitis B. Diagnostics, 10 (7), 491.
• Ryazantsev DY, Voronina DV, Zavriev SK, 2016: Immuno-PCR: achievements and perspectives. Biochem (Mosc), 81 (13), 1754-1770.
• Sanger F, Nicklen S, ve Coulson AR, 1977: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA, 74 (12), 5463–5467.
• Sanchez JA, Pierce KE, Rice JE, Wangh LJ, 2004: Linear-After-The-Exponential (LATE)–PCR: An advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci, 101 (7), 1933-1938.
• Seker E, Kus FS, 2019: Prevalence, virulence factors and antibiotic resistance of Escherichia coli O157 on feces of adult ruminants slaughtered in three provinces of Turkey. Vet Arhiv, 89 (1), 107-121.
• Seker E, Ozenc E, Turedi OK, Yilmaz M, 2022: Prevalence of mecA and pvl genes in coagulase negative staphylococci isolated from bovine mastitis in smallholder dairy farms in Turkey. Anim Biotechnol, DOI: 10.1080/10495398.2022.2094802
• Seok Y, Byun JY, Mun H, Kim MG, 2014: Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme. Microchim Acta, 181, 1965-1971.
• Sevindik E, 2013: Nested PCR and applications area. Türk Bilimsel Derlemeler Dergisi, 6 (2), 22-26.
• Simsek M, Demir C, Seker E, 2021: Investigation of New Delhi metallo-beta-lactamase-1 (blaNDM-1) gene in carbapenem-resistant Enterobacterales strains isolated from a university hospital in Turkey. Med Sci, 10 (2), 571-576.
• Şeker E, Özenç E, Baki Acar D, Yilmaz M, 2019: Prevalence of methicillin resistance and Panton-Valentine leukocidin genes in Staphylococci isolated from Pirlak Sheep with subclinical mastitis in Turkey. Kocatepe Vet J, 12 (4), 424-429.
• Tekin K, Aygar İS, Hoşbul T, 2020: Basic Principles of Polymerase Chain Reaction Technology. J Mol Virol Immunol, 1 (1): 57-66.
• Ugozzoli L, Wallace RB, 1991: Allele-specific polymerase chain reaction. Methods, 2 (1), 42-48.
• Wang X, Lim HJ, Son A, 2014: Characterization of denaturation and renaturation of DNA for DNA hybridization. J Toxicol Environ, 29 (1), e2014007.
• Wang Y, Zhao Y, Bollas A, Wang Y, Au KF, 2021: Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol, 39 (11), 1348-1365.
• Watson JD, Crick FH, 1953: Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171 (4356), 737-738.
• Witter CD, Herrmann MG, Moss AA, Rasmussen RP, 1997: Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques, 22, 130-138.
• Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J, Pao W, Engelman JA, Iafrate AJ, Leet LP, 2014: Anchored multiplex PCR for targeted next-generation sequencing. Nat Med, 20, 1479-1484.
• Zhu H, Zhang H, Xu Y, Laššáková S, Korabečná M, Neužil P, 2020: PCR past, present and future. BioTechniques, 69 (4), 317-325.