title: Mycobacterium saopaulense sp. nov., a rapidly growing mycobacterium closely related to members of the Mycobacterium chelonae--Mycobacterium abscessus group.
abstract: Five isolates of non-pigmented, rapidly growing mycobacteria were isolated from three patients and,in an earlier study, from zebrafish. Phenotypic and molecular tests confirmed that these isolates belong to the Mycobacterium chelonae-Mycobacterium abscessus group, but they could not be confidently assigned to any known species of this group. Phenotypic analysis and biochemical tests were not helpful for distinguishing these isolates from other members of the M. chelonae–M.abscessus group. The isolates presented higher drug resistance in comparison with other members of the group, showing susceptibility only to clarithromycin. The five isolates showed a unique PCR restriction analysis pattern of the hsp65 gene, 100 % similarity in 16S rRNA gene and hsp65 sequences and 1-2 nt differences in rpoB and internal transcribed spacer (ITS) sequences.Phylogenetic analysis of a concatenated dataset including 16S rRNA gene, hsp65, and rpoB sequences from type strains of more closely related species placed the five isolates together, as a distinct lineage from previously described species, suggesting a sister relationship to a group consisting of M. chelonae, Mycobacterium salmoniphilum, Mycobacterium franklinii and Mycobacterium immunogenum. DNA–DNA hybridization values .70 % confirmed that the five isolates belong to the same species, while values ,70 % between one of the isolates and the type strains of M. chelonae and M. abscessus confirmed that the isolates belong to a distinct species. The polyphasic characterization of these isolates, supported by DNA–DNA hybridization results,demonstrated that they share characteristics with M. chelonae–M. abscessus members, butconstitute a different species, for which the name Mycobacterium saopaulense sp. nov. is proposed. The type strain is EPM10906T (5CCUG 66554T5LMG 28586T5INCQS 0733T).
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
authors.forename: Christiane Lourenço
authors.initials: CL
authors.lastname: Nogueira
authors.affiliation: SUNY-ESF, State University of New York College of Environmental Science and Forestry, Environmental and Forest Biology, 1 Forestry Drive, Syracuse, NY, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Whipps
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
authors.forename: Cristianne Kayoko
authors.initials: CK
authors.lastname: Matsumoto
authors.affiliation: Núcleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz, São Paulo, SP, Brazil.
authors.forename: Erica
authors.initials: E
authors.lastname: Chimara
authors.affiliation: Division of Bacteriology, University of Bern, Switzerland.
authors.forename: Sara
authors.initials: S
authors.lastname: Droz
authors.affiliation: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Tortoli
authors.affiliation: Departamento de Oftalmologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
authors.forename: Denise
authors.initials: D
authors.lastname: de Freitas
authors.affiliation: Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Margo
authors.initials: M
authors.lastname: Cnockaert
authors.affiliation: Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Palomino
authors.affiliation: Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Anandi
authors.initials: A
authors.lastname: Martin
authors.affiliation: Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
authors.forename: Sylvia Cardoso
authors.initials: SC
authors.lastname: Leão
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D001482:Base Composition; D001938:Brazil; D003315:Cornea / Q000382:microbiology; D004269:DNA, Bacterial / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005227:Fatty Acids / Q000737:chemistry; D005798:Genes, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D009164:Mycobacterium Infections / Q000382:microbiology; D016926:Mycobacterium chelonae; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D015027:Zebrafish / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer; D005227:Fatty Acids; D012336:RNA, Ribosomal, 16S