Abstract
Bacterial genotyping methods have been used in several areas of microbiology and have facilitated the identification of bacterial strains, as well as the study of virulence and resistance factors, epidemiological surveillance, among others. Constituting, in this way, as complementary or alternative to phenotypic methods. This chapter reviews some of the methods of bacterial genotyping used nowadays, explains briefly how they are performed, and highlights some limitations and advantages they have.
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Tang YW, Ellis NM, Hopkins MK et al (1998) Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 36:3674–3679
Li W, Raoult D, Fournier PE (2009) Bacterial strain typing in the genomic era. FEMS Microbiol Rev 33:892–916
Fernández-Olmos A, García de la Fuente C, Saéz-Nieto J, Valdezate-Ramos S (2010) In: Cercenado E, Cantón R (eds) Métodos de identificación bacteriana en el laboratorio de microbiología. Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Spain
Taha MK, Olcen P (2004) Molecular genetic methods in diagnosis and direct characterization of acute bacterial central nervous system infections. APMIS 112:753–770
Bergeron MG, Ouellette M (1998) Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory. J Clin Microbiol 36:2169–2172
Botstein DWR, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Human Genet 32:314–331
Damasceno LS, Leitão TM, Taylor ML et al (2016) The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review. Eur J Clin Microbiol Infect Dis 35:19–27
Castro-Escarpulli G, Alonso-Aguilar NM, Rivera-Sánchez G et al (2015) Identification and typing methods for the study of bacterial infections: a brief review and mycobacterial as case of study. Arch Clin Microbiol 7:3
Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75
Cardozo-Bernal AM, Ramón LF, Poutou-Piñales RA et al (2013) Electroforesis en Gel de Campo Pulsado (PFGE) para la diferenciación molecular de Listeria monocytogenes. Univ Sci 18:203–222
Virtanen S, Laukkanen-Ninios R, Ortiz Martinez P et al (2013) Multiple-locus variable-number tandem-repeat analysis in genotyping Yersinia enterocolitica strains from human and porcine origins. J Clin Microbiol 51:2154–2159
Fukiya S, Mizoguchi H, Tobe T, Mori H (2004) Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J Bacteriol 186:3911–3921
Taboada EN, Acedillo RR, Luebbert CC et al (2005) A new approach for the analysis of bacterial microarray-based comparative genomic hybridization: insights from an empirical study. BMC Genomics 6:78
Dorrell N, Mangan JA, Laing KG et al (2001) Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res 11:1706–1715
Pearson BM, Pin C, Wright J et al (2003) Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett 554:224–230
Roetzer A, Diel R, Kohl TA et al (2013) Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10:e1001387
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Ochoa-Díaz, M.M., Daza-Giovannetty, S., Gómez-Camargo, D. (2018). Bacterial Genotyping Methods: From the Basics to Modern. In: Medina, C., López-Baena, F. (eds) Host-Pathogen Interactions. Methods in Molecular Biology, vol 1734. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7604-1_2
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DOI: https://doi.org/10.1007/978-1-4939-7604-1_2
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