MLVA-NET – a standardised web database for bacterial genotyping and surveillance

Abstract

Strain typing is an important aid to surveillance networks and outbreak investigations of infectious diseases [1]. MLVA (Multilocus VNTR Analysis, with VNTR standing for Variable Number of Tandem Repeats) has emerged as a highly discriminatory and widely applicable genotyping method that is now being applied for strain tracking in a growing number of bacterial pathogens [2,3]. The genomic loci containing tandem repeats are often maintained among strains of a bacterial species, while individual strains harbour different copy numbers that can be determined simply by PCR amplification. Similar to sequence-based methods such as Multilocus Sequence Typing (MLST), the MLVA method indexes genetic variation at well defined genomic loci and produces reproducible allelic profiles that can be coded in a simple digital format. Hence, they represent an attractive alternative to banding profile-based methods such as pulsed-field gel electrophoresis (PFGE), which requires dedicated efforts (e.g. http://www.cdc.gov/pulsenet) in order to produce fingerprinting data that are comparable across laboratories. Indeed, to be useful to surveillance networks and for global epidemiology, a genotyping method has to be technically accessible, reproducible and to yield easily portable data. In addition, electronic databases that are made accessible through the Internet can render exchange and comparison of data among laboratories very effective for local, national, and international surveillance. Existing databases of MLST data accessible through web portals (http://www.pubmlst.org,http://www.mlst.net, http://www.pasteur.fr/mlst) represent a common language for strain typing that has proven extremely useful for collaborative research and global epidemiology of bacterial and fungal pathogens [4]. However, given the much faster evolutionary rate of tandem repeats compared to nucleotide sequences, MLVA markers provide much improved resolution compared to MLST, thus representing a subtyping tool that is especially useful for strain discrimination in genetically homogeneous pathogens, such as M. tuberculosis [5], Bacillus anthracis [6] or Salmonella enterica serotype Typhimurium [7]. Web-accessible MLVA databases are not yet widely used for international collaboration [8], but the development in this area is very active (http://mlva.u-psud.fr/, http://www.mlva.eu/, http://www.miru-vntrplus.org).