title: Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region.
abstract: METHODS
  A retrospective study in an urban setting with a high tuberculosis incidence.
  
  
  OBJECTIVE
  To study the molecular epidemiology and disease dynamics of a prevalent Mycobacterium tuberculosis strain family, F29, a subset of the Beijing strains.
  
  
  METHODS
  Multi-locus DNA fingerprinting and genomic analysis was used to characterise F29 isolates. Demographic and molecular epidemiologic data were correlated with those of other isolates from the setting. The geographic locations of five F29 strain clusters were plotted using a geographic information system (GIS) and an index for geographic distribution was calculated. Their cumulative temporal occurrence was also plotted.
  
  
  RESULTS
  The genomic similarity of F29 to the Beijing-strains was confirmed. A high degree of clustering predicted high disease transmission. Spatial distribution was mostly widespread except for one cluster. Smaller foci of transmission were observed. The temporal spread showed ongoing transmission.
  
  
  CONCLUSIONS
  F29 belongs to the Beijing strain group. The prevalence and high degree of strain clustering, with limited geographic clustering, indicates that F29 strains are endemic in the study community. However, recent epidemiologic events also contributed to the disease spread. The combination of molecular epidemiologic, spatial and temporal data has enhanced our understanding of the disease dynamics of Beijing strains in our study community.
authors.affiliation: Medical Research Council Centre for Molecular and Cellular Biology, Department of Biochemistry, University of Stellenbosch, Tygerberg, South Africa. mr6@sun.ac.za
authors.forename: M
authors.initials: M
authors.lastname: Richardson
authors.forename: S W P
authors.initials: SW
authors.lastname: van Lill
authors.forename: G D
authors.initials: GD
authors.lastname: van der Spuy
authors.forename: Z
authors.initials: Z
authors.lastname: Munch
authors.forename: C N
authors.initials: CN
authors.lastname: Booysen
authors.forename: N
authors.initials: N
authors.lastname: Beyers
authors.forename: P D
authors.initials: PD
authors.lastname: van Helden
authors.forename: R M
authors.initials: RM
authors.lastname: Warren
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000032:analysis*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction; D015995:Prevalence; D012189:Retrospective Studies; D013019:South Africa / Q000453:epidemiology; D013183:Sputum / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology* / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial