- Volume 54, Issue 5, 2004
Volume 54, Issue 5, 2004
- New Taxa
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- Gram-Positive Bacteria
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Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine
An acid-fast, rapidly growing, psychrotolerant short rod was isolated from pond water near a uranium mine. Phylogenetic analysis of the 16S rRNA gene sequence grouped this strain with the rapidly growing mycobacteria. The 16S rRNA gene sequence of isolate WA101T showed highest similarity to that of Mycobacterium sphagni DSM 44076T; however, DNA–DNA relatedness between the two strains was less than 30 %. Chemotaxonomic analyses, which included fatty acid and mycolic acid patterns, confirmed the classification of strain WA101T in the genus Mycobacterium. Physiological data, including antibiotic resistance, NaCl tolerance, carbon sources, temperature growth range and enzyme activities, were also determined. Based on the genotypic and phenotypic results it is proposed that isolate WA101T represents a novel Mycobacterium species. The name Mycobacterium psychrotolerans sp. nov. is proposed, with type strain WA101T (=DSM 44697T=LMG 21953T).
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Clostridium jejuense sp. nov., isolated from soil
More LessA strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 °C, pH 7·0 and 0–0·5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G+C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96·65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (=IMSNU 40003T=KCTC 5026T=DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.
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Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov.
More LessTwo thermophilic bacilli were isolated from mud and water samples of the Ayder and Kestanbol hot springs in the provinces of Rize and Canakkale, respectively, in Turkey. Strains AB04T and K4T were sporulating, Gram-positive, rod-shaped bacteria. These isolates were moderately thermophilic (with an optimum temperature for growth of 50–55 °C), facultative anaerobes able to grow on a wide range of carbon sources including d-glucose, d-raffinose, d-sucrose, d-xylose, d-fructose, l-arabinose, maltose, d-mannose and d-mannitol. Analysis of the 16S rRNA gene sequences showed that these isolates resembled Anoxybacillus flavithermus DSM 2641T and Anoxybacillus gonensis NCIMB 13933T. DNA–DNA hybridization data revealed that thermophilic isolate AB04T has only 51·2 % relatedness to A. flavithermus, 45·1 % relatedness to Anoxybacillus pushchinoensis and 68·6 % relatedness to A. gonensis. Thermophilic isolate K4T showed only 60·4 % relatedness to A. flavithermus, 42·9 % relatedness to A. pushchinoensis and 38·5 % relatedness to A. gonensis. On the basis of the DNA–DNA hybridization data, isolates AB04T and K4T are not related to A. flavithermus DSM 2641T, A. pushchinoensis DSM 12423T or A. gonensis NCIMB 13933T at the species level, but show relatedness to one another of 40·5 %. On the basis of the data presented, it is proposed that strains AB04T (=NCIMB 13972T=NCCB 100050T) and K4T (=NCIMB 13971T=NCCB 100051T) be designated as the type strains of Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov., respectively.
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Vagococcus carniphilus sp. nov., isolated from ground beef
Nine enterococcus-like strains were referred to the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) for further identification from the National Antimicrobial Resistance Monitoring System Laboratory at the CDC. The cultures were isolated from ground beef purchased from retail in Oregon in 2000. Conventional biochemical testing and analysis of whole-cell protein electrophoretic profiles distinguished these strains from known species of enterococci and vagococci. Comparative 16S rRNA gene sequencing studies revealed that these strains were most closely related to the species Vagococcus fluvialis. DNA–DNA reassociation studies confirmed that these nine strains represented a new taxon. The relative binding ratio was 87 % or greater at the optimal temperature, and the divergence was less than 1 % for strains hybridized against the isolate designated the type strain. DNA–DNA relatedness was 25 % to V. fluvialis and 9 % or less to the other three species of Vagococcus. DNA–DNA relatedness was 33 % or less to the 25 currently described species of Enterococcus. On the basis of this evidence, it is proposed that these strains be classified as Vagococcus carniphilus sp. nov. The type strain of V. carniphilus is 1843-02T (=ATCC BAA-640T=CCUG 46823T). The clinical significance (if any) of these strains is yet to be determined.
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Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment
More LessAn endospore-forming strain, 20CMT, was isolated from Antarctic sediment and identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The organism stained Gram-variable and was facultatively anaerobic. Strain 20CMT was psychrotolerant, growing optimally at 10–15 °C. Like other Paenibacillus species, it contained anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C content was 40·7 mol%. 16S rRNA gene sequence analysis placed strain 20CMT within the Paenibacillus cluster, with a similarity value of 99·5 % to Paenibacillus macquariensis DSM 2T. DNA–DNA hybridization experiments between the Antarctic isolate and P. macquariensis DSM 2T revealed a reassociation value of 47 %, indicating that strain 20CMT and P. macquariensis DSM 2T belong to different species. Based on evaluation of morphological, physiological, chemotaxonomic and phylogenetic analyses, a novel species, Paenibacillus antarcticus sp. nov., is proposed; the type strain is 20CMT (=LMG 22078T=CECT 5836T).
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Streptomyces africanus sp. nov., a novel streptomycete with blue aerial mycelium
An actinomycete with blue aerial mycelium and yellow substrate mycelium was isolated from a suburban soil sample collected in Cape Town, South Africa and named strain CPJVR-HT. The colour of the substrate mycelium was not sensitive to changes in pH. The organism produced spiny spores in Spirales spore chains. Chemical taxonomy indicated that it is a member of the genus Streptomyces. Strain CPJVR-HT grew at 45 °C and did not produce melanin or any diffusible pigments. It exhibited weak antibacterial activity against a clinical isolate of Enterococcus faecium, but no antibacterial activity against Escherichia coli ATCC 25922 or Pseudomonas aeruginosa ATCC 27853. Analysis of its 16S rRNA gene sequence, DNA–DNA hybridization studies and the results of physiological tests showed that this strain represents a novel species of Streptomyces, for which the name Streptomyces africanus sp. nov. is proposed. The type strain is CPJVR-HT (=NRRL B-24143T=DSM 41829T).
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Brevibacterium picturae sp. nov., isolated from a damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria)
More LessThree strains showing highly similar (GTG)5-PCR patterns were isolated from a heavily damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria). On the basis of 16S rRNA gene sequence similarity, the strains were attributed to Brevibacterium, with Brevibacterium casei (96·7 %), Brevibacterium iodinum (96·7 %) and Brevibacterium linens (96·6 %) as the closest related species. Chemotaxonomic data [peptidoglycan contains meso-diaminopimelic acid; mycolic acids absent; MK-8(H2) as the major menaquinone; polar lipids phosphatidylglycerol and diphosphatidylglycerol present; anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids] supported the affiliation of the strains to the genus Brevibacterium. Additional physiological and biochemical tests confirmed the taxonomic position of the strains and allowed phenotypic differentiation from Brevibacterium species with validly published names. The isolates from the mural painting, therefore, represent a novel species, for which the name Brevibacterium picturae sp. nov. is proposed, with LMG 22061T (=DSM 16132T) as the type strain.
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Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae
More LessA group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).
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Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus
The taxonomic position of Agromyces fucosus subsp. hippuratus is revised on the basis of molecular and phenotypic data. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA relatedness values and differences from other species in phenotypic traits revealed in this and earlier studies suggested reclassification of A. fucosus subsp. hippuratus as a separate species, Agromyces hippuratus sp. nov., comb. nov. The type strain is VKM Ac-1352T (=JCM 9087T). An emended description of Agromyces fucosus is given.
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Helcococcus sueciensis sp. nov., isolated from a human wound
More LessA previously undescribed, Gram-positive, catalase-negative, coccus-shaped organism that originated from a human wound was subjected to taxonomic study. On the basis of its cellular morphology and the results of biochemical testing, the unknown organism was identified tentatively as a member of the genus Helcococcus, but it did not correspond to either of the two recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium was associated phylogenetically with the genus Helcococcus, with the unidentified organism forming a hitherto unknown subline within the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism that was recovered from a human wound should be classified as a novel species of the genus Helcococcus, namely Helcococcus sueciensis sp. nov. The type strain is CCUG 47334T (=CIP 108183T).
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Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan
More LessA Gram-positive bacterial strain containing l-ornithine as the diagnostic diamino acid was isolated from a sea-water-sample from the East Sea, Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JC1078T represents a phyletic line within the suborder Micrococcineae of the order Actinomycetales, adjacent to the genus Ornithinimicrobium. The highest sequence similarity values to the isolate were observed against Ornithinimicrobium humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). The strain was strictly aerobic and moderately halophilic with optimal growth at 2–3 % (w/v) NaCl. Cells were non-motile, non-sporulating and coccoid-shaped. The cell wall contains l-ornithine, glutamic acid, alanine, glycine and serine. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were of the iso- and anteiso-methyl-branched types. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown glycolipid. The acyl type of the glycan chain of peptidoglycan is acetyl. The DNA G+C content was 72 mol%. The combination of physiological, biochemical and chemotaxonomical data clearly separated the marine isolate from other members of the suborder Micrococcineae. On the basis of polyphasic evidence, it is proposed to classify strain JC1078T in a novel genus and species, for which the name Serinicoccus marinus gen. nov., sp. nov. is proposed. The type strain is JC1078T (=IMSNU 14026T=KCTC 9980T=DSM 15273T).
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Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)
More LessA hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (=CIP 107991T=CCUG 48084T).
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Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment
An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T=KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.
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Lactobacillus curvatus subsp. melibiosus is a later synonym of Lactobacillus sakei subsp. carnosus
More LessOn the basis of phenotypic and DNA–DNA reassociation studies, strain CCUG 34545T has been considered to represent a distinct Lactobacillus curvatus subspecies, Lactobacillus curvatus subsp. melibiosus. However, in several independent studies dealing with Lactobacillus sakei and L. curvatus strains, the subspecies division of L. curvatus has been found to be controversial. The original study distinguishing the two subspecies within both L. curvatus and L. sakei also lacked 16S rRNA gene sequence analyses. Therefore, the taxonomic position of L. curvatus subsp. melibiosus CCUG 34545T was re-evaluated in a polyphasic taxonomy study that included 16S rRNA gene sequence analysis, DNA–DNA reassociation, DNA G+C content determination, numerical analysis of ribotypes and whole-cell protein patterns and the examination of some fundamental phenotypic properties. The results obtained indicate that strain CCUG 34545T and its duplicate, CCUG 41580T, are Lactobacillus sakei subsp. carnosus strains and that L. curvatus subsp. melibiosus is a later synonym of L. sakei subsp. carnosus.
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Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates
The Mycobacterium fortuitum third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of M. fortuitum third biovariant complex sorbitol-negative (n=21), M. fortuitum third biovariant complex sorbitol-positive (n=3), M. fortuitum (n=3), Mycobacterium peregrinum (pipemidic acid-susceptible) (n=1), Mycobacterium porcinum (n=1), Mycobacterium senegalense (n=2) and Mycobacterium septicum (n=1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G+C content and DNA–DNA relatedness analyses. The results of these studies indicated that the strains comprised M. porcinum (n=13), M. septicum (n=1) and four novel closely related genetic groups within the M. fortuitum third biovariant complex: Mycobacterium boenickei sp. nov. (n=6), Mycobacterium houstonense sp. nov. (n=2), Mycobacterium neworleansense sp. nov. (n=1) and Mycobacterium brisbanense sp. nov. (n=1), with type strains ATCC 49935T (=W5998T=DSM 44677T), ATCC 49403T (=W5198T=DSM 44676T) ATCC 49404T (=W6705T=DSM 44679T) and ATCC 49938T (=W6743T=DSM 44680T), respectively.
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Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae
More LessSeven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).
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Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate
More LessA polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97·2 and 97·5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (=AS 4.1808T=JCM 11884T).
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Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA
More LessA thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35–65 °C (optimum 55 °C) and at pH 2·0–6·0 (optimum 4·0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97·8 % identity) and Alicyclobacillus sendaiensis (96·9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96·1–96·5 %) and Alicyclobacillus genomic species FR-6 (96·3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of ω-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA–DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T=DSM 16176T).
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Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov.
More LessThe taxonomic positions of seven atypical Enterococcus strains, isolated from artisanal Italian cheeses, were investigated in a polyphasic study. By using 16S rRNA gene sequencing, DNA–DNA hybridization and intergenic transcribed spacer analysis, as well as by examining the phenotypic properties, the novel isolates were shown to constitute a novel enterococcal species. Their closest relatives are Enterococcus sulfureus and Enterococcus saccharolyticus, having a 16S rRNA gene sequence similarity of 96·7 %. This group of strains can be easily differentiated from the other Enterococcus species by DNA–DNA hybridization and by their phenotypic characteristics: the strains do not grow in 6·5 % NaCl, and they do not produce acid from l-arabinose, melezitose, melibiose, raffinose or ribose. The name Enterococcus italicus sp. nov. is proposed for this species, with strain DSM 15952T (=LMG 22039T) as the type strain.
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Mycobacterium canariasense sp. nov.
A novel rapidly growing, non-pigmented mycobacterium was isolated from blood samples obtained from 17 patients with febrile syndrome. Bacterial growth occurred at 30 and 37 °C on Löwenstein–Jensen medium and also on MacConkey agar without crystal violet. Strains contained α- and α′-mycolates in their cell wall. Sequence analysis of the hsp65 and 16S rRNA genes identified the isolates as rapidly growing mycobacteria. Sequences of both genes were unique within the mycobacteria. DNA–DNA hybridization showed that the isolates had less than 15 % reassociation with 13 other recognized rapidly growing mycobacteria. The name Mycobacterium canariasense sp. nov. is proposed for this novel opportunistic pathogen, which is most closely related to Mycobacterium diernhoferi. The type strain is 502329T (=CIP 107998T=CCUG 47953T).
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Volumes and issues
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Volume 74 (2024)
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