Large-scale comparative studies of DNA fingerprints prefer automated chip capillary electrophoresis over conventional gel planar electrophoresis due to the higher precision of the digitalization process. However, the determination of band sizes is still limited by the device resolution and sizing accuracy. Band matching, therefore, remains the key step in DNA fingerprint analysis. Most current methods evaluate only the pairwise similarity of the samples, using heuristically determined constant thresholds to evaluate the maximum allowed band size deviation; unfortunately, that approach significantly reduces the ability to distinguish between closely related samples. This study presents a new approach based on global multiple alignments of bands of all samples, with an adaptive threshold derived from the detailed migration analysis of a large number of real samples. The proposed approach allows the accurate automated analysis of DNA fingerprint similarities for extensive epidemiological studies of bacterial strains, thereby helping to prevent the spread of dangerous microbial infections.

Department of Biomedical Engineering Brno University of Technology Technicka 12 616 00 Brno Czech Republic

Department of Internal Medicine Hematology and Oncology Masaryk University and University Hospital Brno Cernopolni 212 9 662 63 Brno Czech Republic

Zobrazit více v PubMed

Serrano I., De Vos D., Santos J.P., Bilocq F., Leitão A., Tavares L. Antimicrobial resistance and genomic rep-PCR fingerprints of Pseudomonas aeruginosa strains from animals on the background of the global population structure. BMC Vet Res. 2017;13(1):58. PubMed PMC

Hirzel C., Donà V., Guilarte Y.N., Furrer H., Marschall J., Endimiani A. Clonal analysis of Aerococcus urinae isolates by using the repetitive extragenic palindromic PCR (rep-PCR) J Infect. 2016;72(2):262–265. PubMed

Viau R.A., Kiedrowski L.M., Kreiswirth B.N., Adams M., Perez F., Marchaim D. A comparison of molecular typing methods applied to enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST. Pathog Immun. 2017;2(1):23–33. PubMed PMC

Momeni S.S., Whiddon J., Cheon K., Ghazal T., Moser S.A., Childers N.K. Genetic diversity and evidence for transmission of Streptococcus mutans by DiversiLab rep-PCR. J Microbiol Methods. 2016;128(Supplement C):108–117. PubMed PMC

Pavel A.B., Vasile C.I. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinf. 2012;13:9. PubMed PMC

Khakabimamaghani S., Najafi A., Ranjbar R., Raam M. GelClust: A software tool for gel electrophoresis images analysis and dendrogram generation. Comput Methods Programs Biomed. 2013;111(2):512–518. PubMed

Heras J., Domínguez C., Mata E., Pascual V., Lozano C., Torres C. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinf. 2015;16(1):270. PubMed PMC

Fuhrmann D.R., Krzywinski M.I., Chiu R., Saeedi P., Schein J.E., Bosdet I.E. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003;13(5):940–953. PubMed PMC

Heras J., Domínguez C., Mata E., Pascual V., Lozano C., Torres C. A survey of tools for analysing DNA fingerprints. Brief Bioinform. 2016;17(6):903–911. PubMed

Intarapanich A., Kaewkamnerd S., Shaw P.J., Ukosakit K., Tragoonrung S., Tongsima S. Automatic DNA diagnosis for 1D gel electrophoresis images using bio-image processing technique. BMC Genom. 2015;16(Suppl 12):S15. PubMed PMC

Skutkova H., Vitek M., Krizkova S., Kizek R., Provaznik I. Preprocessing and classification of electrophoresis gel images using dynamic time warping. Int J Electrochem Scopy. 2013;8(2):1609–1622.

Edgar R.C., Batzoglou S. Multiple sequence alignment. Curr Opin Struct Biol. 2006;16(3):368–373. PubMed

Chatzou M., Magis C., Chang J.-M., Kemena C., Bussotti G., Erb I. Multiple sequence alignment modeling: methods and applications. Brief Bioinform. 2016;17(6):1009–1023. PubMed

Skutkova H., Vitek M., Sedlar K., Provaznik I. Progressive alignment of genomic signals by multiple dynamic time warping. J Theor Biol. 2015;385:20–30. PubMed

Rosenberg M.S. Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinf. 2005;6:278. PubMed PMC

Phillips A., Janies D., Wheeler W. Multiple sequence alignment in phylogenetic analysis. Mol Phylogenet Evol. 2000;16(3):317–330. PubMed

Feng D.-F., Doolittle R.F. Progressive sequence alignment as a prerequisitetto correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. PubMed

Versalovic J., Koeuth T., Lupski J.R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991;19(24):6823–6831. PubMed PMC

Schmidt M., Kutzner A., Heese K. A novel specialized single-linkage clustering algorithm for taxonomically ordered data. J Theor Biol. 2017;427:1–7. PubMed

Nurhayati Priyambada I.D., Radjasa O.K., Widada J. Repetitive element palindromic PCR (Rep-PCR) as a genetic tool to study diversity in amylolytic bacteria. Adv Sci Lett. 2017;23(7):6458–6461.

Ishii S., Sadowsky M.J. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol. 2009;11(4):733–740. PubMed

Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

Word Entropy-Based Approach to Detect Highly Variable Genetic Markers for Bacterial Genotyping

Zobrazit více v PubMed

figshare
10.6084/m9.figshare.7464452.v2