MLVA

MLVA stands for multi-locus variable-number tandem-repeat analysis. It is a molecular typing method used to differentiate bacterial strains by exploiting variation in the number of tandem repeats at multiple genomic loci.

In an MLVA assay, DNA is extracted and a predefined set of VNTR loci is amplified by PCR. For each locus, the size of the PCR product reflects the number of repeat units, yielding a numeric value for that locus. The result across all loci forms an MLVA profile, often expressed as a string of numbers. Fragment sizes are typically determined by capillary electrophoresis; some protocols use sequencing to confirm repeat counts. Profiles are compared within established schemes or databases to assess relatedness.

MLVA offers high discriminatory power, rapid turnaround, and relatively low cost, and the numeric profiles can be shared and compared across laboratories if standardized. The method is scalable and suitable for high-throughput typing and for creating outbreak-associated fingerprints that can be tracked over time.

It has been widely applied to outbreak investigation and surveillance of several pathogens, notably Salmonella enterica and Campylobacter, as well as Bordetella pertussis and various Bacillus species, among others. The choice of loci and the interpretation framework are species-specific and standardized schemes are often maintained by reference laboratories or consortia.

Limitations include homoplasy, where unrelated strains converge on the same VNTR profile, and variable mutation rates among loci, which can affect interpretation. MLVA requires quality DNA and standardized panels with reference data; results are most informative when used alongside other typing methods, and increasing use of whole-genome sequencing provides higher-resolution alternatives.