Research article

Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing

Jean-Louis Koeck¹ , Berthe-Marie Njanpop-Lafourcade² , Sonia Cade¹ , Emmanuelle Varon³ , Lassana Sangare⁴ , Samina Valjevac^5,6 , Gilles Vergnaud^5,6 and Christine Pourcel⁵

¹  Laboratoire de biologie clinique, HIA Robert Picqué, 351, route de Toulouse, 33 140 Villenave d'Ornon, France

²  Association pour l'Aide à la Médecine Préventive, 25-28 rue du Dr Roux, 75 015 Paris, France

³  Centre National de Référence des Pneumocoques, Laboratoire de Microbiologie, Hôpital Européen Georges Pompidou, 20-40 rue Leblanc, 75908 Paris cedex 15, France

⁴  Laboratoire de Virologie-Bactériologie; Centre Hospitalier Universitaire Yalgado Ouédraogo Ouagadougou, Burkina Faso

⁵  Génome, Polymorphisme et Minisatellites (GPMS), Institut de Génétique et Microbiologie, Bat. 400, Université Paris XI, 91405 Orsay cedex, France

⁶  Division of Analytical Microbiology, Centre d'Etude du Bouchet, BP3, 91710 Vert le Petit, France

author email corresponding author email

BMC Microbiology 2005, 5:66doi:10.1186/1471-2180-5-66

Published:	16 November 2005

Abstract

Background

Precise identification of bacterial pathogens at the strain level is essential for epidemiological purposes. In Streptococcus pneumoniae, the existence of 90 different serotypes makes the typing particularly difficult and requires the use of highly informative tools. Available methods are relatively expensive and cannot be used for large-scale or routine typing of any new isolate. We explore here the potential of MLVA (Multiple Loci VNTR Analysis; VNTR, Variable Number of Tandem Repeats), a method of growing importance in the field of molecular epidemiology, for genotyping of Streptococcus pneumoniae.

Results

Available genome sequences were searched for polymorphic tandem repeats. The loci identified were typed across a collection of 56 diverse isolates and including a group of serotype 1 isolates from Africa. Eventually a set of 16 VNTRs was proposed for MLVA-typing of S. pneumoniae. These robust markers were sufficient to discriminate 49 genotypes and to aggregate strains on the basis of the serotype and geographical origin, although some exceptions were found. Such exceptions may reflect serotype switching or horizontal transfer of genetic material.

Conclusion

We describe a simple PCR-based MLVA genotyping scheme for S. pneumoniae which may prove to be a powerful complement to existing tools for epidemiological studies. Using this technique we uncovered a clonal population of strains, responsible for infections in Burkina Faso. We believe that the proposed MLVA typing scheme can become a standard for epidemiological studies of S. pneumoniae.