Genomic diversity and molecular epidemiology of Mycobacterium tuberculosis strains of Beijing genotype isolated in Tuscany, Italy

Introduction: The Beijing genotype of Mycobacterium tuberculosis (MTB) is cause of global concern as it is rapidly spreading worldwide, is considered hypervirulent, and is most often associated to MDR/XDR tuberculosis, although these properties have not been confirmed for all strains and in all geographic settings. In this study we report the molecular characterization of a collection of Beijing strains isolated in Tuscany, Italy, a region where the ethnic diversity of patients provides an opportunity to study a global sample of Beijing strains and gain new insights into the heterogeneity and phylogeny of the Beijing genotype. Materials and Methods: A total of 80 MTB Beijing strains isolated in the years 2002-2010 from 18 Italian- and 62 foreign-born patients were studied. Spoligotype patterns, deletions of large genomic sequences RD105, RD181, RD150 and RD142, missense mutations in putative DNA repair genes mutT4 and mutT2, and MIRU-VNTR profiles, based on 11 discriminative loci, were determined according to standard procedures. Results: Molecular analysis of MTB Beijing isolates revealed 56 MIRU-VNTR profiles, 6 spoligotype patterns, 3 deletions of large genomic sequences and polymorphic codons in mutT genes. Based on these polymorphisms, a phylogenetic reconstruction of the Beijing lineage was drawn. A minimun spanning tree (MST), constructed by the MIRU-VNTR profiles, showed that strains with deletions RD105 and RD181 and mutated mutT4/mutT2 genes form a large clonal complex of strains linked together, representing the prevalent expanding strain population and that RD105/RD181-deleted strains with mutated mutT4 and wild-type mutT2 form two star-like clonal complexes typical of expanding strain populations. Moreover, MIRU-VNTR analysis revealed 47 unique profiles and 9 clusters including 33 (41%) isolates; active transmission rate of Beijing strains (30.0%) was two-fold higher than non-Beijing strains previously reported in our setting. Conclusions: Our study shows a considerable genomic heterogeneity of MTB Beijing isolates, yielding both ancient and recent phylogenetic sublineages, and confirms the high transmissibility of Beijing strains also in our setting. Notably, as the prevalent Beijing sublineages harbour missense mutations in one or both putative DNA repair mutT genes, it can be speculated that a defective DNA repair system may confer selective advantages and contribute to the successful spreading of the Beijing family.