Multiple loci VNTR analysis

Multiple loci VNTR analysis (MLVA) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. A "VNTR" is a "variable-number tandem repeat". This method is well known in forensic science since it is the basis of DNA fingerprinting in humans. When applied to bacteria, it contributes to forensic microbiology through which the source of a particular strain might eventually be traced back, making it a useful technique for outbreak surveillance.

In a typical MLVA, a number of well-selected and characterised (in terms of mutation rate and diversity) loci are amplified by polymerase chain reaction (PCR), so that the size of each locus can be measured, usually by electrophoresis of the amplification products together with reference DNA fragments (a so-called DNA size marker). Different electrophoresis equipment can be used depending on the required size estimate accuracy, and the local laboratory set-up, from basic agarose gel electrophoresis up to the more sophisticated and high-throughput capillary electrophoresis devices.^[1] From this size estimate, the number of repeat units at each locus can be deduced. The resulting information is a code which can be easily compared to reference databases once the assay has been harmonised and standardised.^[2]^[3]

MLVA has become a major first line typing tool in a number of pathogens where such an harmonisation could be achieved, including Mycobacterium tuberculosis,^[4] Bacillus anthracis,^[5] Brucella.^[6]^[7]

Some MLVA-associated web sites

Software for analysis of MLVA data

GeneMapper A commercial software for normalisation and size calling of peaks from a certain brand of capillary electrophoresis machines.
BioNumerics A commercial bioinformatics solution to store and analyze a large panel of biological data, including MLVA, and more generally character datasets. Normalisation, size calling, size correction, assignment of number of repeats and cluster analysis on MLVA data can be performed.

References

^ Vergnaud G, Pourcel C (2009). "Multiple locus variable number of tandem repeats analysis". Molecular Epidemiology of Microorganisms. Methods Mol. Biol. Vol. 551. pp. 141–58. doi:10.1007/978-1-60327-999-4_12. ISBN 978-1-60327-998-7. PMID 19521873.
^ Grissa I, Bouchon P, Pourcel C, Vergnaud G (2008). "On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing". Biochimie. 90 (4): 660–8. doi:10.1016/j.biochi.2007.07.014. PMID 17822824.
^ Nadon CA, Trees E, Ng LK, Møller Nielsen E, Reimer A, Maxwell N, Kubota KA, Gerner-Smidt P, the MLVA Harmonization Working Group (2013). "Development and application of MLVA methods as a tool for inter-laboratory surveillance". Euro Surveill. 18 (35): 20565. doi:10.2807/1560-7917.es2013.18.35.20565. PMC 5667538. PMID 24008231.
^ Blouin Y, Hauck Y, Soler C, Fabre M, Vong R, Dehan C, Cazajous G, Massoure PL, Kraemer P, Jenkins A, Garnotel E, Pourcel C, Vergnaud G (2012). "Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade". PLOS ONE. 7 (12): e52841. doi:10.1371/journal.pone.0052841. PMC 3531362. PMID 23300794.
^ Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N (2014). "Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database". PLOS ONE. 9 (6): e95131. doi:10.1371/journal.pone.0095131. PMC 4046976. PMID 24901417.
^ Scholz HC, Vergnaud G (2013). "Molecular characterisation of Brucella species". Rev. Sci. Tech. 32 (1): 149–62. doi:10.20506/rst.32.1.2189. PMID 23837373.
^ Lindstedt BA, Torpdahl M, Vergnaud G, Le Hello S, Weill FX, Tietze E, Malorny B, Prendergast DM, Ní Ghallchoir E, Lista RF, Schouls LM, Söderlund R, Börjesson S, Åkerström S (2013). "Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012". Euro Surveill. 18 (4): 20385. doi:10.2807/ese.18.04.20385-en. hdl:11250/219465. PMID 23369388.

[1] Vergnaud G, Pourcel C (2009). "Multiple locus variable number of tandem repeats analysis". Molecular Epidemiology of Microorganisms. Methods Mol. Biol. Vol. 551. pp. 141–58. doi:10.1007/978-1-60327-999-4_12. ISBN 978-1-60327-998-7. PMID 19521873.

[2] Grissa I, Bouchon P, Pourcel C, Vergnaud G (2008). "On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing". Biochimie. 90 (4): 660–8. doi:10.1016/j.biochi.2007.07.014. PMID 17822824.

[3] Nadon CA, Trees E, Ng LK, Møller Nielsen E, Reimer A, Maxwell N, Kubota KA, Gerner-Smidt P, the MLVA Harmonization Working Group (2013). "Development and application of MLVA methods as a tool for inter-laboratory surveillance". Euro Surveill. 18 (35): 20565. doi:10.2807/1560-7917.es2013.18.35.20565. PMC 5667538. PMID 24008231.

[4] Blouin Y, Hauck Y, Soler C, Fabre M, Vong R, Dehan C, Cazajous G, Massoure PL, Kraemer P, Jenkins A, Garnotel E, Pourcel C, Vergnaud G (2012). "Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade". PLOS ONE. 7 (12): e52841. doi:10.1371/journal.pone.0052841. PMC 3531362. PMID 23300794.

[5] Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N (2014). "Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database". PLOS ONE. 9 (6): e95131. doi:10.1371/journal.pone.0095131. PMC 4046976. PMID 24901417.

[6] Scholz HC, Vergnaud G (2013). "Molecular characterisation of Brucella species". Rev. Sci. Tech. 32 (1): 149–62. doi:10.20506/rst.32.1.2189. PMID 23837373.

[7] Lindstedt BA, Torpdahl M, Vergnaud G, Le Hello S, Weill FX, Tietze E, Malorny B, Prendergast DM, Ní Ghallchoir E, Lista RF, Schouls LM, Söderlund R, Börjesson S, Åkerström S (2013). "Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012". Euro Surveill. 18 (4): 20385. doi:10.2807/ese.18.04.20385-en. hdl:11250/219465. PMID 23369388.

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