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Taxonomy Citation ID Reference
13535 Adékambi  T, Reynaud-Gaubert  M, Greub  G, Gevaudan  MJ, La Scola  B, Raoult  D, Drancourt  M,     ( 2004 )

Amoebal coculture of "Mycobacterium massiliense" sp. nov. from the sputum of a patient with hemoptoic pneumonia.

Journal of clinical microbiology 42 (12)
PMID : 15583272 DOI  :   10.1128/JCM.42.12.5493-5501.2004     PMC  :   PMC535245    
Abstract >>
A nonphotochromogenic, rapidly growing Mycobacterium strain was isolated in pure culture from the sputum and the bronchoalveolar fluid of a patient with hemoptoic pneumonia by using axenic media and an amoebal coculture system. Both isolates grew in less than 7 days at 24 to 37 degrees C with an optimal growth temperature of 30 degrees C. The isolates exhibited biochemical and antimicrobial susceptibility profiles overlapping those of Mycobacterium abscessus, Mycobacterium chelonae, and Mycobacterium immunogenum, indicating that they belonged to M. chelonae-M. abscessus group. They differed from M. abscessus in beta-galactosidase, beta-N-acetyl-beta-glucosaminidase, and beta-glucuronidase activities and by the lack of nitrate reductase and indole production activities, as well as in their in vitro susceptibilities to minocycline and doxycycline. These isolates and M. abscessus differed from M. chelonae and M. immunogenum by exhibiting gelatinase and tryptophane desaminase activities. Their 16S rRNA genes had complete sequence identity with that of M. abscessus and >99.6% similarity with those of M. chelonae and M. immunogenum. Further molecular investigations showed that partial hsp65 and sodA gene sequences differed from that of M. abscessus by five and three positions over 441 bp, respectively. Partial rpoB and recA gene sequence analyses showed 96 and 98% similarities with M. abscessus, respectively. Similarly, 16S-23S rRNA internal transcribed spacer sequence of the isolates differed from that of M. abscessus by a A-->G substitution at position 60 and a C insertion at position 102. Phenotypic and genotypic features of these two isolates indicated that they were representative of a new mycobacterial species within the M. chelonae-M. abscessus group. Phylogenetic analysis suggested that these isolates were perhaps recently derived from M. abscessus. We propose the name of "Mycobacterium massiliense" for this new species. The type strain has been deposited in the Collection Institut Pasteur as CIP 108297(T) and in Culture Collection of the University of Goteborg, Goteborg, Sweden, as CCUG 48898(T).
KeywordMeSH Terms
53725 Gupta  RS, Lo  B, Son  J,     ( 2018 )

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.

Frontiers in microbiology 9 (N/A)
PMID : 29497402 DOI  :   10.3389/fmicb.2018.00067     PMC  :   PMC5819568    
Abstract >>
The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.
KeywordMeSH Terms
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
Mycobacterium classification
abscessus-chelonae clade
conserved signature indels and signature proteins
fortuitum-vaccae clade
phylogenomic analysis
slow-growing and fast-growing mycobacteria
terrae clade
triviale clade
46975 Tortoli  E, Kohl  TA, Brown-Elliott  BA, Trovato  A, Leão  SC, Garcia  MJ, Vasireddy  S, Turenne  CY, Griffith  DE, Philley  JV, Baldan  R, Campana  S, Cariani  L, Colombo  C, Taccetti  G, Teri  A, Niemann  S, Wallace  RJ, Cirillo  DM,     ( 2016 )

Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacteriumabscessus subsp. bolletii and designation of Mycobacteriumabscessus subsp. massiliense comb. nov.

International journal of systematic and evolutionary microbiology 66 (11)
PMID : 27499141 DOI  :   10.1099/ijsem.0.001376    
Abstract >>
The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).
KeywordMeSH Terms
Phylogeny
25347 Leao  SC, Tortoli  E, Viana-Niero  C, Ueki  SY, Lima  KV, Lopes  ML, Yubero  J, Menendez  MC, Garcia  MJ,     ( 2009 )

Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae-M. abscessus group is needed.

Journal of clinical microbiology 47 (9)
PMID : 19571015 DOI  :   10.1128/JCM.00808-09     PMC  :   PMC2738059    
Abstract >>
An outbreak of postsurgical infections caused by rapidly growing mycobacteria has been ongoing in Brazil since 2004. The degrees of similarity of the rpoB and hsp65 sequences from the clinical isolates and the corresponding sequences from both the Mycobacterium massiliense and the M. bolletii type strains were above the accepted limit for interspecies variability, leading to conflicting identification results. Therefore, an extensive characterization of members of the M. chelonae-M. abscessus group was carried out. The M. abscessus, M. chelonae, M. immunogenum, M. massiliense, and M. bolletii type strains and a subset of clinical isolates were analyzed by biochemical tests, high-performance liquid chromatography, drug susceptibility testing, PCR-restriction enzyme analysis of hsp65 (PRA-hsp65), rpoB, and hsp65 gene sequencing and analysis of phylogenetic trees, DNA-DNA hybridization (DDH), and restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene (RFLP-16S rRNA). The clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains could not be separated by phenotypic tests and were grouped in the phylogenetic trees obtained. The results of DDH also confirmed the >70% relatedness of the clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains; and indistinguishable RFLP-16S rRNA patterns were obtained. On the contrary, the separation of clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains from M. chelonae and M. immunogenum was supported by the results of PRA-hsp65, DDH, and RFLP-16S rRNA and by the rpoB and hsp65 phylogenetic trees. Taken together, these results led to the proposition that M. abscessus, M. massiliense, and M. bolletii represent a single species, that of M. abscessus. Two subspecies are also proposed, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, and these two subspecies can be distinguished by two different PRA-hsp65 patterns, which differ by a single HaeIII band, and by differences in their rpoB (3.4%) and hsp65 (1.3%) sequences.
KeywordMeSH Terms
Disease Outbreaks
52656 Tortoli  E, Kohl  TA, Brown-Elliott  BA, Trovato  A, Cardoso-Leão  S, Garcia  MJ, Vasireddy  S, Turenne  CY, Griffith  DE, Philley  JV, Niemann  S, Wallace  RJ, Cirillo  DM,     ( 2018 )

Mycobacterium abscessus, a taxonomic puzzle.

International journal of systematic and evolutionary microbiology 68 (1)
PMID : 29139343 DOI  :   10.1099/ijsem.0.002457    
Abstract >>
N/A
KeywordMeSH Terms
Mycobacterium abscessus
abscessus
bolletii
massiliense
subspecies
Mycobacterium abscessus
abscessus
bolletii
massiliense
subspecies
Mycobacterium abscessus
abscessus
bolletii
massiliense
subspecies
Mycobacterium abscessus
abscessus
bolletii
massiliense
subspecies
Bacterial Typing Techniques
Mycobacterium abscessus
51398 Adekambi  T, Sassi  M, van Ingen  J, Drancourt  M,     ( 2017 )

Reinstating Mycobacterium massiliense and Mycobacterium bolletii as species of the Mycobacterium abscessus complex.

International journal of systematic and evolutionary microbiology 67 (8)
PMID : 28820087 DOI  :   10.1099/ijsem.0.002011    
Abstract >>
TheMycobacterium abscessus complex is a group of rapidly growing, multiresistant mycobacteria previously divided into three species. Proposal for the union of Mycobacterium bolletii and Mycobacterium massiliense into one subspecies, so-called M. abscessus subsp. massiliense, created much confusion about the routine identification and reporting of M. abscessus clinical isolates for clinicians. Results derived from multigene sequencing unambiguously supported the reinstatement of M. massiliense and M. bolletii as species, culminating in the presence of erm(41)-encoded macrolide resistance in M. bolletii. Present genome-based analysis unambiguously supports the reinstatement of M. massiliense and M. bolletii as species after the average nucleotide identity values of 96.7 % for M. abscessus versus M. bolletii, and 96.4 % for M. abscessus versus M. massiliense, and the 96.6 % identity between M. bolletii and M. massiliense was put into the perspective of a larger, 28-species analysis. Accordingly, DNA-DNA hybridization values predicted by the complete rpoB gene sequencing analysis were between 68.7 and 72.3 % in this complex. These genomic data as well as the phenotypic characteristics prompted us to propose to reinstate the previously known M. massiliense and M. bolletii into two distinct species among the M. abscessus complex.
KeywordMeSH Terms
Phylogeny
54778 Validation List No. 181: "List of new names and new combinations previously effectively, but not validly, published." Int. J. Syst. Evol. Microbiol. (2018) 68:1411-1417.

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