title: Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
abstract: Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as "LAM-like", 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil; Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho - HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Sidra E G
authors.initials: SE
authors.lastname: Vasconcellos
authors.affiliation: Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Chyntia Carolina
authors.initials: CC
authors.lastname: Acosta
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Lia Lima
authors.initials: LL
authors.lastname: Gomes
authors.affiliation: Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil.
authors.forename: Emilyn Costa
authors.initials: EC
authors.lastname: Conceição
authors.affiliation: Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil.
authors.forename: Karla Valéria
authors.initials: KV
authors.lastname: Lima
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Marcelo Ivens
authors.initials: MI
authors.lastname: de Araujo
authors.affiliation: Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Maria de Lourdes
authors.initials: Mde L
authors.lastname: Leite
authors.affiliation: Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Flávio
authors.initials: F
authors.lastname: Tannure
authors.affiliation: Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Paulo Cesar de Souza
authors.initials: PC
authors.lastname: Caldas
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Harrison M
authors.initials: HM
authors.lastname: Gomes
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Adalberto Rezende
authors.initials: AR
authors.lastname: Santos
authors.affiliation: CNRS-Université Paris-Sud, Institut de Génétique et Microbiologie-Infection Genetics Emerging Pathogens Evolution Team, Orsay, France.
authors.forename: Michel K
authors.initials: MK
authors.lastname: Gomgnimbou
authors.affiliation: CNRS-Université Paris-Sud, Institut de Génétique et Microbiologie-Infection Genetics Emerging Pathogens Evolution Team, Orsay, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Sola
authors.affiliation: Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France.
authors.forename: David
authors.initials: D
authors.lastname: Couvin
authors.affiliation: Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.affiliation: Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho - HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil; Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Neio
authors.initials: N
authors.lastname: Boechat
authors.affiliation: Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Philip Noel
authors.initials: PN
authors.lastname: Suffys
mesh_terms: D000483:Alleles; D001426:Bacterial Proteins / Q000235:genetics; D001938:Brazil; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014376:Tuberculosis / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins