Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms

• Authors: Beata Krawczyk , Józef Kur , Karolina Stojowska-Swędrzyńska , Marta Śpibida
• Languages of publication: EN

Abstracts

EN

A significant number of DNA-based techniques has been introduced into the field of microorganisms' characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before DNA amplification by PCR, known as Ligation-Mediated PCR methods (LM PCR), have been successfully applied for the typing of microorganisms below the species level. These molecular methods include: Amplified Fragment Length Polymorphism (AFLP), Amplification of DNA fragments Surrounding Rare Restriction Sites (ADSRRS), PCR Melting Profiles (PCR MP), Ligation Mediated PCR/Shifter (LM PCR/Shifter), Infrequent-Restriction-Site Amplification (IRS PCR), double digestion Ligation Mediated Suppression PCR (ddLMS PCR). These techniques are now applied more and more often because they involve less time, are comparably inexpensive, and require only standard lab equipment. Here, we present a general review of this group of methods showing their possibilities and limitations. We also identify questions and propose solutions which may be helpful in choosing a particular LM PCR method for the achievement of the required goal.

Keywords

EN

rapid methods; molecular epidemiology; genotyping; microbial phylogenetics; PCR (polymerase chain reaction)

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2016
• Volume: 63
• Issue: 1
• Pages: 39-52

Dates

published

2016

received

2015-09-23

revised

2015-11-25

accepted

2015-12-18

(unknown)

2016-02-17

Contributors

author

Beata Krawczyk

• Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland

author

Józef Kur

• Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland

author

Karolina Stojowska-Swędrzyńska

• Department of Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland

author

Marta Śpibida

• Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland

References

• Antonishyn NA, McDonald RR, Chan EL, Horsman G, Woodmansee C E, Falk PS, Mayhall CG (2000) Evaluation of fluorescence-based amplified fragment length polymorphism analysis for molecular typing in hospital epidemiology: comparison with pulsed-field gel electrophoresis for typing strains of vancomycin-resistant Enterococcus faecium. J Clin Microbiol 38: 4058-4065.
• Arricau-Bouvery N, Hauck Y, Bejaoui A, Frangoulidis D, Bodier CC, Souriau A, Meyer H, Neubauer H, Rodolakis A, Vergnaud G (2006) Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing. BMC Microbiol 6: 38.
• Bachem CW, van der Hoeven RS, de Bruijn SM, Vreugdenhi D, Zabeau M, Visser RG (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9: 745-753.
• Bachem CW, Oomen RJFJ, Visser RGF (1998) Transcript imaging with cDNA-AFLP: A step-by-step protocol. Plant Mol Biol Rep 16: 157-173.
• Ball LM, Bes MA, Theelen B, Boekhout T, Egeler RM, Kuijper EJ (2004) Significance of amplified fragment length polymorphism in identification and epidemiological examination of Candida species colonization in children undergoing allogeneic stem cell transplantation. J Clin Microbiol 42: 1673-1679.
• Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14: 2899-2914.
• Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13: 3261-3273.
• Borst A, Theelen B, Reinders E, Boekhout T, Fluit AC, Savelkoul PH (2003) Use of amplified fragment length polymorphism analysis to identify medically important Candida spp., including C. dubliniensis. J Clin Microbiol 41: 1357-1362.
• Crawford LA, Koscinski D, Keyghobadi N (2012) A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research. Mol Ecol 21: 5911-5917.
• Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93: 6025-6030.
• Dijkshoorn L, Aucken H, Gerner-Smidt P, Janssen P, Kaufmann ME, Garaizar J, Ursing J, Pitt TL (1996) Comparison of outbreak and nonoutbreak Acinetobacter baumannii strains by genotypic and phenotypic methods. J Clin Microbiol 34: 1519-1525.
• Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54: 1839-1854.
• Fry NK, Afshar B, Visca P, Jonas D, Duncan J, Nebuloso E, Underwood A, Harrison T G (2005) Assessment of fluorescent amplified fragment length polymorphism analysis for epidemiological genotyping of Legionella pneumophila serogroup 1. Clin Microbiol Infect 11: 704-712.
• Gibson JR, Slater E, Xerry J, Tompkins DS, Owen RJ (1998) Use of an amplified-fragment length polymorphism technique to fingerprint and differentiate isolates of Helicobacter pylori. J Clin Microbiol 36: 2580-2585.
• Grech K, Martinelli A, Pathirana S, Walliker D, Hunt P, Carter R (2002) Numerous, robust genetic markers for Plasmodium chabaudi by the method of amplified fragment length polymorphism. Mol Biochem Parasitol 123: 95-104.
• Hartl L, Seefelder S (1998) Diversity of selected hop cultivars detected by fluorescent AFLPs. Theor Appl Genet 96: 112-116.
• Huang J, Sun M (1999) A modified AFLP with fluorescence-labelled primers and automated DNA sequencer detection for efficient fingerprinting analysis in plants. Biotechnol Tech 13: 277-278.
• Huang YC, Lee CY, Su LH, Chang LY, Lin TY (2005) Methicillin-resistant Staphylococcus aureus bacteremia in neonatal intensive care units: genotyping analysis and case-control study. Acta Paediatr Taiwan 46: 156-160.
• Janssen P, Coopman R, Huys G (1996) Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142: 1881-1893.
• Janssen P, Maquelin K, Coopman R, Tjernberg I, Bouvet P, Kersters K, Dijkshoorn L (1997) Discrimination of Acinetobacter genomic species by AFLP fingerprinting. Int J Syst Bacteriol 47: 1179-1187.
• Koeleman JG, Stoof J, Biesmans DJ, Savelkoul PH, Vandenbroucke-Grauls CM (1998) Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J Clin Microbiol 36: 2522-2529.
• Krauss SL (1999) Complete exclusion of nonsires in an analysis of paternity in a natural plant population using amplified fragment length polymorphism (AFLP). Mol Ecol 8: 217-226.
• Krawczyk B, Lewandowski K, Bronk M, Samet A, Myjak P, Kur J (2003a) Evaluation of a novel method based on amplification of DNA fragments surrounding rare restriction sites (ADSRRS fingerprinting) for typing strains of vancomycin-resistant Enterococcus faecium. J Microbiol Methods 52: 341-351.
• Krawczyk B, Naumiuk L, Lewandowski K, Baraniak A, Gniadkowski M, Samet A, Kur J (2003b) Evaluation and comparison of random amplification of polymorphic DNA, pulsed-field gel electrophoresis and ADSRRS-fingerprinting for typing Serratia marcescens outbreaks. FEMS Immunol Med Microbiol 38: 241-248.
• Krawczyk B, Samet A, Czarniak E, Szczapa J, Kur J (2005) Extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in a neonatal unit:1 control of an outbreak using a new ADSRRS technique. Pol J Microbiol 54: 105-110.
• Krawczyk B, Samet A, Leibner J, Śledzińska A, Kur J (2006) Evaluation of a PCR Melting Profile technique for bacterial strain differentiation. J Clin Microbiol 44: 2327-2332.
• Krawczyk B, Leibner J, Barańska-Rybak W, Samet A, Nowicki R, Kur J (2007a) ADSRRS-fingerprinting and PCR MP techniques for studies of intraspecies genetic relatedness in Staphylococcus aureus. J Microbiol Methods 71: 114-122.
• Krawczyk B, Leibner J, Stojowska K, Bronk M, Samet A, Kur J (2007b) PCR melting profile method for genotyping analysis of vancomycin-resistant Enterococcus faecium isolates from Hematological Unit patients. Pol J Microbiol 56: 65-70.
• Krawczyk B, Leibner-Ciszak J, Mielech A, Nowak M, Kur J (2009) PCR melting profile (PCR MP) - a new tool for differentiation of Candida albicans strains. BMC Infect Dis 9: 177.
• Krawczyk B, Leibner-Ciszak J, Stojowska K, Kur J (2011) The new LM-PCR/shifter method for the genotyping of microorganisms based on the use of class IIS restriction enzyme and ligation mediated PCR. J Microbiol Biotechnol 21: 1336-1344.
• Krutkiewicz A, Klimuszko D (2010) Genotyping and PCR detection of potential virulence genes in Campylobacter jejuni and Campylobacter coli isolates from different sources in Poland. Folia Microbiol (Praha) 55: 167.
• Kumar A, Misra P, Dube A (2013) Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites. Parasitol Res 112: 457.
• Leibner-Ciszak J, Dobrowolska A, Krawczyk B, Kaszuba A, Stączek P (2010) Evaluation of a PCR melting profile method for intraspecies differentiation of Trichophyton rubrum and Trichophyton interdigitale. J Med Microbiol 59: 185-192.
• Martinelli A, Hunt P, Fawcett R, Cravo PV, Walliker D, Carter R (2005) An AFLP-based genetic linkage map of Plasmodium chabaudi chabaudi. Malar J 4: 11.
• Masny A, Plucienniczak A (2001) Fingerprinting of bacterial genomes by amplifcation of DNA fragments surrounding rare restriction sites. BioTechniques 31: 930-936.
• Masny A, Płucienniczak A (2003) Ligation mediated PCR performed at low denaturation temperatures-PCR melting profiles. Nucleic Acids Res 31: e114.
• Mazurek GH, Reddy V, Marston BJ, Haas WH, Crawford JT (1996) DNA fingerprinting by infrequent-restriction-site amplification. J Clin Microbiol 34: 2386-2390.
• Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14: 389-394.
• Palittapongarnpim P, Chomyc S, Fanning A, Kunimoto D (1993) DNA fingerprinting of Mycobacterium tuberculosis isolates by ligation-mediated polymerase chain reaction. Nucleic Acids Res 21: 761-762.
• Prod'hom G, Guilhot C, Gutierrez MC, Varnerot A, Gicquel B, Vincent V (1997) Rapid discrimination of Mycobacterium tuberculosis complex strains by ligation-mediated PCR fingerprint analysis. J Clin Microbiol 35: 3331-3334.
• Reisig F, Kremer K, Amthor B, van Soolingen D, Haas WH (2005) Fast ligation-mediated PCR, a fast and reliable method for IS6110-based typing of Mycobacterium tuberculosis complex. J Clin Microbiol 43: 5622-5627.
• Riffard S, Lo Presti F, Vandenesch F, Forey F, Reyrolle M, Etienne J (1998) Comparative analysis of infrequent-restriction-site PCR and pulsed-field gel electrophoresis for epidemiological typing of Legionella pneumophila serogroup 1 strains. J Clin Microbiol 36: 161-167.
• Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14: 1163-1175.
• Stefańska I, Rzewuska M, Binek M (2008) Evaluation of three methods for DNA fingerprinting of Corynebacterium pseudotuberculosis strains isolated from goats in Poland. Pol. J. Microbiol 57: 105-12.
• Stojowska K, Krawczyk B, Kałużewski S, Kur J (2009a) Retrospective analysis of the genetic diversity of Klebsiella oxytoca isolated in Poland over a 50-year period. Eur J Clin Microbiol Infect Dis 28: 1263.
• Stojowska K, Kałużewski S, Krawczyk B (2009b) Usefulness of PCR melting profile method for genotyping analysis of Klebsiella oxytoca isolates from patients of a single hospital unit. Pol J Microbiol 58: 247-253.
• Stojowska K, Krawczyk B (2014) A new double digestion ligation mediated suppression PCR method for simultaneous bacteria DNA-typing and confirmation of species: an Acinetobacter sp. model. PLoS One 9: e115181.
• Su LH, Leu HS, Chiu YP, Chia JH, Kuo AJ, Sun CF, Lin TY, Wu TL (2000) Molecular investigation of two clusters of hospital-acquired bacteraemia caused by multi-resistant Klebsiella pneumoniae using pulsed-field gel electrophoresis and in frequent restriction site PCR. Infection Control Group. J Hosp Infect 46: 110-117.
• Sunnucks P (2000) Efficient genetic markers for population biology. Trends Ecol Evol 15: 199-203.
• Tavanti A, Hensgens LA, Ghelardi E, Campa M, Senesi S (2007) Genotyping of Candida orthopsilosis clinical isolates by amplification fragment length polymorphism reveals genetic diversity among independent isolates and strain maintenance within patients. J Clin Microbiol 45: 1455-1462.
• Xu M, Li X, Korban SS (2004) DNA-methylation alterations and exchanges during in vitro cellular differentiation in rose (Rosa hybrida L.). Theor Appl Genet 109: 899-910.
• Yoo JH, Choi JH, Shin WS, Huh DH, Cho YK, Kim KM, Kim MY, Kang MW (1999) Application of infrequent-restriction-site PCR to clinical isolates of Acinetobacter baumannii and Serratia marcescens. J Clin Microbiol 37: 3108-3112.
• Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11: 139-151.
• Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
• Woksepp H, Jernberg C, Tärnberg M, Ryberg A, Brolund A, Nordvall M, Olsson-Liljequist B, Wisell KT, Monstein HJ, Nilsson LE, Schön T (2011) High-Resolution melting-curve analysis of Ligation-Mediated Real-Time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-Beta-lactamase-producing Escherichia coli. J Clin Microbiol 49: 4032-4039.
• van der Wurff AW, Chan YL, van Straalen NM, Schouten J (2000) TE-AFLP: combining rapidity and robustness in DNA fingerprinting. Nucleic Acids Res 28: E105.
• Zaczek A, Brzostek A, Górna A, Sajduda A, Wojtasik A, Dziadek J (2013) Application of FLiP method for differentiation of Mycobacterium tuberculosis strains in comparison to commonly used methods, spoligotyping and MIRU-VNTR typing. Pol J Microbiol 62: 73-76.
• Zaczek A, Brzostek A, Kuroń A, Wojtasik A, Sajduda A, Dziadek J (2014) Development of a new ligation-mediated PCR method for the differentiation of Mycobacterium tuberculosis strains. Int J Tuberc Lung Dis 18: 302-309.
• Zaczek A, Wojtasik A, Izdebski R, Gorecka E, Wojcik EA, Nowak T, Kwiecinski P, Dziadek J (2015) PCR melting profile as a tool for outbreak studies of Salmonella enterica in chickens. BMC Vet Res. 11: 137.
• Zasada AA, Forminska K, Wołkowicz T, Badell E, Guiso N (2014) The utility of the PCR melting profile technique for typing Corynebacterium diphtheriae isolates. Lett Appl Microbiol 59: 292.

Identifiers

DOI

10.18388/abp.2015_1192