title: Use of cluster-graphs from spoligotyping data to study genotype similarities and a comparison of three indices to quantify recent tuberculosis transmission among culture positive cases in French Guiana during a eight year period.
abstract: BACKGROUND
  French Guiana has the highest tuberculosis (TB) burden among all French departments, with a strong increase in the TB incidence over the last few years. It is now uncertain how best to explain this incidence. The objective of this study was to compare three different methods evaluating the extent of recent TB transmission in French Guiana.
  
  
  METHODS
  We conducted a population-based molecular epidemiology study of tuberculosis in French Guiana based on culture-positive TB strains (1996 to 2003, n = 344) to define molecular relatedness between isolates, i.e. potential transmission events. Phylogenetic relationships were inferred by comparing two methods: a "cluster-graph" method based on spoligotyping results, and a minimum spanning tree method based on both spoligotyping and variable number of tandem DNA repeats (VNTR). Furthermore, three indices attempting to reflect the extent of recent TB transmission (RTIn, RTIn-1 and TMI) were compared.
  
  
  RESULTS
  Molecular analyses showed a total amount of 120 different spoligotyping patterns and 273 clinical isolates (79.4%) that were grouped in 49 clusters. The comparison of spoligotypes from French Guiana with an international spoligotype database (SpolDB4) showed that the majority of isolates belonged to major clades of M. tuberculosis (Haarlem, 22.6%; Latin American-Mediterranean, 23.3%; and T, 32.6%). Indices designed to quantify transmission of tuberculosis gave the following values: RTIn = 0.794, RTIn-1 = 0.651, and TMI = 0.146.
  
  
  CONCLUSIONS
  Our data showed a high number of Mycobacterium tuberculosis clusters, suggesting a high level of recent TB transmission, nonetheless an estimation of transmission rate taking into account cluster size and mutation rate of genetic markers showed a low ongoing transmission rate (14.6%). Our results indicate an endemic mode of TB transmission in French Guiana, with both resurgence of old spatially restricted genotypes, and a significant importation of new TB genotypes by migration of TB infected persons from neighgouring high-incidence countries.
authors.affiliation: UMR 2724 IRD-CNRS, Génétique et Evolution des Maladies Infectieuses, Equipe Dynamique des Systèmes & Maladies Infectieuses, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 05, France. vanina.guernier@u707.jussieu.fr
authors.forename: Vanina
authors.initials: V
authors.lastname: Guernier
authors.forename: Christophe
authors.initials: C
authors.lastname: Sola
authors.forename: Karine
authors.initials: K
authors.lastname: Brudey
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Guégan
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
mesh_terms: D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics; D005616:French Guiana / Q000453:epidemiology; D005838:Genotype; D006801:Humans; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission*
chemical_list: D004269:DNA, Bacterial