Second Report of the Cooperative, Open-Ended Study of Slowly Growing Mycobacteria by the International Working Group on Mycobacterial Taxonomy

Wayne, Lawrence G.; Good, Robert C.; Krichevsky, Micah I.; BEAM, R. E.; Blacklock, Zeta M.; David, H.L.; Dawson, David J.; Gross, W.; Hawkins, Jean E.; Jenkins, P. A.; Juhlin, I; Käppler, W; Kleeberg, H. H.; Krasnow, Irving; Lefford, M J; Mankiewicz, E.; McDURMONT, C.; Nel, Elmarie; Portaels, F; Richards, PA; RUSCH, S.; SCHRODER, K. H.; Silcox, Vella A.; Szabó, István; Tsukamura, M; BREEN, L. VANDEN; Vergmann, B

doi:10.1099/00207713-33-2-265

Cited by 25 publications

(30 citation statements)

References 7 publications

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“…Many different features requiring complex and specialized tests are necessary to identify mycobacteria at the species level (Wayne & Kubica, 1986;Goodfellow & Cross, 1983). Numerous investigations have been undertaken to define reliable features and test assays' for differentiating between species (Wayne et al, 1974(Wayne et al, , 1976(Wayne et al, , 1983(Wayne et al, , 1989. Attempts to subdivide mycobacterial species on the basis of immunological methods, DNA homology and related analyses (Baess, 1979(Baess, , 1983 McFadden et al, 1987 ; Gross & Wayne, 1970 ;Imaeda et al, 1988;Wayne & Kubica, 1986) have proved useful in Abbreuiation : PCR, polymerase chain reaction.…”

Section: Introductionmentioning

confidence: 99%

Differentiation of Mycobacterium species by direct sequencing of amplified DNA

Rogall¹,

Flohr

Böttger

1990

Journal of General Microbiology

271

214

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Nucleotide sequences specific for a range of Myco6acterium species were defined by computer-assisted sequence comparisons of small subunit ribosomal RNA. A polymerase chain reaction-based sequencing strategy was used to demonstrate that the 16s rRNA sequence can be used for the rapid identification of mycobacterial isolates. Identification at the species level can be obtained within 2 d, requiring < loo00 bacteria. This procedure reliably differentiates Myco6acterium spp. which are difficult to identify by classical methods, such as M. malmoense, M. szulgai and M. flavescens.

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Section: Introductionmentioning

confidence: 99%

Differentiation of Mycobacterium species by direct sequencing of amplified DNA

Rogall¹,

Flohr

Böttger

1990

Journal of General Microbiology

271

214

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“…However, the IWGMT continued to include 'M. paraffinicum' in subsequent numerical taxonomic studies, but noted that it was premature to revive the name as the status of the species was unclear because it could not be distinguished with confidence from M. scrofulaceum (Wayne et al, 1983(Wayne et al, , 1989 et al, 1991). However, the species was phenotypically dissimilar to Mycobacterium avium-Mycobacterium intracellulare (MAC) species, and it was recommended that the strains be referred to by an informal vernacular term, 'the paraffinicum group ' (Wayne et al, 1991).…”

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confidence: 99%

“…However, the IWGMT continued to include 'M. paraffinicum' in subsequent numerical taxonomic studies, but noted that it was premature to revive the name as the status of the species was unclear because it could not be distinguished with confidence from M. scrofulaceum (Wayne et al, 1983(Wayne et al, , 1989. The IWGMT recommended semantide-based comparative studies to determine whether the name 'M.…”

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confidence: 99%

Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

Toney

Adékambi

Toney

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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The omission of the name 'Mycobacterium paraffinicum' from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, 'M. paraffinicum' strains grew slowly in .7 days, stained acidalcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 6C. However, 'M. paraffinicum' strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 6C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered 'M. paraffinicum' with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of 'M. paraffinicum', ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of 'M. paraffinicum' with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670 T 5DSM 44181 T 5NCIMB 10420 T , located in collections worldwide, as the type strain.In 1956, multiple strains of a soil bacterium were isolated below the level of grass roots in oily pools. They were characterized as Gram-positive, acid-alcohol-fast, nonmotile, rod-shaped bacilli, with white colonies that became yellow with age and were waxy and wrinkled on selective isolation medium of mineral salts agar in a gaseous atmosphere of 40 % ethane in air. Subsequently, the bacteria were grown on ethanol-and acetate-containing medium and the name 'Mycobacterium paraffinicum' was suggested to represent a paraffinic, gaseous hydrocarbonutilizing, non-tuberculous mycobacterium (NTM). The proposed name was 'meant to connote the general utilization of gaseous and liquid paraffinic hydrocarbons' (Davis et al., 1956). Furthermore, these mycobacteria were abundant in soil samples of petroliferous emanation, principally oilfields, and demonstrated specificity for ethane and higher paraffinic hydrocarbons (Davis et al., 1959). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, hsp65 and rpoB gene sequences of isolates 90683, 90750, 30760, 70769 and 80776 and 'M. paraffinicum' ATCC 12670 are respectively GQ153265-GQ153270 (16S rRNA gene), GQ153283-GQ153288 (hsp65) and GQ153299-GQ153304 (rpoB).A comparison of mycolic acid patterns, a dendrogram based on ETs and neighbour-joining tree...

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“…Subsequently, a cooperative open-ended study was initiated in which new strains of slowly growing mycobacteria were introduced on a continuing basis, and the data were analyzed at intervals (32)(33)(34). The purpose of this study of an expanding set of cultures was to characterize slowly growing mycobacterial strains that represented uncommonly encountered species that had not been represented in the first six studies, as well as to recognize clusters of previously unknown taxa.…”

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confidence: 99%

“…asiaticum OES 90126 (from TMC 803 [ Editing and analysis of data. The criteria and editing programs for suppression of irrelevant, redundant, and incomplete data that were used in generating the NT matrices have been described previously (25,(32)(33)(34). Features were coded according to the RKC scheme of Rogosa et al (15).…”

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confidence: 99%

Fourth Report of the Cooperative, Open-Ended Study of Slowly Growing Mycobacteria by the International Working Group on Mycobacterial Taxonomy

Wayne

Good²,

Krichevsky³

et al. 1991

International Journal of Systematic Bacteriology

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The open-ended study of the International Working Group on Mycobacterial Taxonomy is an ongoing project to characterize slowly growing strains of mycobacteria that do not belong to well-established or thoroughly characterized species. In this fourth report we describe two numerical taxonomic clusters that represent subspecies or biovars of Mycobacterium simiae, one cluster that encompasses the erstwhile type strain of the presently invalid species "Mycobacterium parafinicum," one cluster that is phenotypically very similar to Mycobacterium avium and Mycobacterium intraceltulare but may be a separate genospecies, one cluster that appears to be phenotypically distinct from M . aviurn but reacts with a nucleic acid probe specific for M . avium, and three tentatively defined clusters in proximity to a cluster that encompasses the type strain of Mycobacterium malmoense. Of special practical interest is the fact that one of the latter three clusters is composed of clinically significant scotochromogenic bacteria that can be misidentified as the nonpathogenic organism Mycobacterium gordonae if insufficient biochemical tests are performed.In their first cooperative studies, the members of the International Working Group on Mycobacterial Taxonomy (IWGMT) applied numerical taxonomic (NT) analysis methods to discrete and limited sets of mycobacteria to provide broad-based characterizations of clusters that corresponded to previously established species (5,10,12,16,26,31). Subsequently, a cooperative open-ended study was initiated in which new strains of slowly growing mycobacteria were introduced on a continuing basis, and the data were analyzed at intervals (32-34). The purpose of this study of an expanding set of cultures was to characterize slowly growing mycobacterial strains that represented uncommonly encountered species that had not been represented in the first six studies, as well as to recognize clusters of previously unknown taxa.A total of 38 new strains have been added to the openended study since the most recent report (341, and most of these fell into groups that exhibited phenotypic affinities to clusters that encompass the type strains of Mycohacterium simiae, M . intracellulare, M . avium, M . scrofulaceum, M . malmoense, and the presently invalid species " M . parafinicum." As noted in the previous report (34), these clusters are phenotypically less clearly resolved from one another than clusters that represent other species of slowly growing mycobacteria, and in this study we analyzed the expanded data base for these organisms. MATERIALS AND METHODS Selection of strains.The criteria for introducing new cultures into this study have been described previously (32,34 Editing and analysis of data. The criteria and editing programs for suppression of irrelevant, redundant, and incomplete data that were used in generating the NT matrices have been described previously (25,(32)(33)(34). Features were coded according to the RKC scheme of Rogosa et al. (15).NT analyses were based on simple matching coefficients,...

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Second Report of the Cooperative, Open-Ended Study of Slowly Growing Mycobacteria by the International Working Group on Mycobacterial Taxonomy

Cited by 25 publications

References 7 publications

Differentiation of Mycobacterium species by direct sequencing of amplified DNA

Differentiation of Mycobacterium species by direct sequencing of amplified DNA

Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

Fourth Report of the Cooperative, Open-Ended Study of Slowly Growing Mycobacteria by the International Working Group on Mycobacterial Taxonomy

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