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A slow-growing, scotochromogenic mycobacterial strain (24T) was isolated from the sputum of a Chinese male human. Phylogenetic analysis using the 16S rRNA gene assigned strain 24T to the Mycobacterium gordonae complex, which includes Mycobacterium gordonae and Mycobacterium paragordonae . The phenotypic characteristics, unique mycolic acid profile and the results of phylogenetic analysis based on hsp65 and rpoB sequences strongly supported the taxonomic status of strain 24T as a representative of a species distinct from the other members of the M. gordonae complex. The genomic G+C content of strain 24T was 65.40mol%. Genomic comparisons showed that strain 24T and M. gordonae ATCC 14470T had an average nucleotide identity (ANI) value of 81.00 % and a DNA–DNA hybridization (DDH) value of 22.80 %, while the ANI and DDH values between strain 24Tand M. paragordonae 49 061T were 80.98 and 22.80 %, respectively. In terms of phylogenetic, phenotypic and chemotaxonomic features, strain 24T is distinguishable from its closest phylogenetic relatives and represents a novel species of the genus Mycobacterium , therefore the name Mycobacterium vicinigordonae sp. nov. is proposed. The type strain is 24T (=CMCC 93559T=DSM 105979T).

The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘ Mycobacterium avium subsp. hominissuis ’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense , a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.

A previously undescribed, rapidly growing, scotochromogenic species of the genus Mycobacterium (represented by strains PB739T and GK) was isolated from two clinical sources – the sputum of a 76-year-old patient with severe chronic obstructive pulmonary disease, history of tuberculosis exposure and Mycobacterium avium complex isolated years prior; and the blood of a 15-year-old male with B-cell acute lymphoblastic leukaemia status post bone marrow transplant. The isolates grew as dark orange colonies at 25–37 °C after 5 days, sharing features in common with other closely related species. Analysis of the complete 16S rRNA gene sequence (1492 bp) of strain PB739T demonstrated that the isolate shared 98.8 % relatedness with Mycobacterium wolinskyi . Partial 429 bp hsp65 and 744 bp rpoB region V sequence analyses revealed that the sequences of the novel isolate shared 94.8 and 92.1 % similarity with those of Mycobacterium neoaurum and Mycobacterium aurum , respectively. Biochemical profiling, antimicrobial susceptibility testing, HPLC/gas-liquid chromatography analyses and multilocus sequence typing support the taxonomic status of these isolates (PB739T and GK) as representatives of a novel species. Both isolates were susceptible to the Clinical and Laboratory Standards Institute recommended antimicrobials for susceptibility testing of rapidly growing mycobacteria including amikacin, ciprofloxacin, moxifloxacin, doxycycline/minocycline, imipenem, linezolid, clarithromycin and trimethropin/sulfamethoxazole. Both isolates PB739T and GK showed intermediate susceptibility to cefoxitin. We propose the name Mycobacterium grossiae sp. nov. for this novel species and have deposited the type strain in the DSMZ and CIP culture collections. The type strain is PB739T (=DSM 104744T=CIP 111318T).

18 páginas, 1 tabla, 2 figuras, A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing Mycolicibacterium strain, CECT 8783T, recovered from the plant Stellera chamaejasme L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus Mycolicibacterium . The strain was most closely related to Mycolicibacterium moriokaense DSM 44221T with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA–DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of Mycolicibacterium for which the name Mycolicibacterium stellerae sp. nov is proposed; the type strain is I10A-01893T (=CECT 8783T=KCTC 19843T=DSM 45590T)., This project was supported by the School of Natural and Environmental Sciences at Newcastle University

Federal University of Para. Belem, PA, Brazil. University Center of Para. Belem, PA, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. M. paraffinicum, a slow-growing scotochromogenic mycobacterium that uses paraffinic hydrocarbons other than methane, i.e. inorganic carbon sources, was originally isolated from soil samples, but only in 2010 definitely achieved the species status. We have described here the first report of pulmonary disease due to M. paraffinicum in Amazon Region.

Highlights • M. chubuense infection was rare in hand. • This is only the second reported case of a pathogenic M. chubuense infection worldwide but for upper limb especially in the hand, this is the very first case ever presented. • Infection in the right hand of a 53-year-old man who live in the coastal areas of Zhejiang province, China. Culture of lesion were positive for the Mycobacterium chubuense, which was confirmed by PCR and sequencing. • azithromycin combined with levofloxacin can be used as a reference regimen for the treatment of M. chubuense infection., Mycobacterium chubuense is a scotochromogenic rapidly growing mycobacterium (RGM), a nontuberculous mycobacterium (NTM)that was first characterized in 1981. This case report describes a rare case of M. chubuense infection in the right hand of a 53-year-old man who lived in the coastal areas of Zhejiang province, China. To the best of our knowledge, this is only the second reported case of a M. chubuense infection worldwide, the first in a hand. Culture of lesion were positive for Mycobacterium chubuense, which was confirmed by PCR and sequencing. This case report complementsthe literature regarding M. chubuense infection.

A polyphasic study was undertaken to determine the taxonomic status of a rapidly growing, scotochromogenic organism that had been received as Mycobacterium vaccae NCTC 11659T. The organism was found to have chemotaxonomic and cultural properties in accord with its assignment to the genus Mycobacterium and was distinguished from the type strain of Mycobacterium vaccae and from other closely related reference strains on the basis of concatenated sequences of 16S rRNA, gyrB, hsp65, recA and rpoB genes. It was also distinguished from M. vaccae strain DSM 43292T and from the type strain of Mycobacterium obuense , its nearest phylogenetic neighbour, on the basis of chemotaxonomic and phenotypic data and digital DNA –DNA relatedness values of 22.7 and 68.3 %, respectively. These datasets not only indicate that strain NCTC 11659T had been misclassified as M. vaccae but that it merits recognition as representing a novel species of the genus Mycobacterium . It is proposed that the organism be classified as Mycobacteriumkyogaense sp. nov.

Among non-tuberculous mycobacteria (NTM), the Mycobacterium simiae complex is one of the largest groups, consisting of 18 species of slow-growing mycobacteria. In 2009, a case of NTM-associated infectious skin disease was reported in Shiga Prefecture, Japan. The patient presented with scattered nodules on the chest, back and extremities, and an M. simiae-like organism was isolated from skin biopsy specimens obtained from one of these lesions. Based on several assessments, including multiple-gene analyses, biochemical characterization and drug susceptibility testing, we concluded that this isolate represented a novel species of NTM, and proposed the name 'Mycobacterium shigaense'. Since 2009, five more cases of NTM-associated infectious disease in which there was a suspected involvement of 'M. shigaense' have been reported. Interestingly, four of these six cases occurred in Shiga Prefecture. Here we performed multiple-gene phylogenetic analyses, physiological and biochemical characterization tests, drug susceptibility tests, and profiling of proteins, fatty acids and mycolic acids of eight clinical isolates from the six suspected 'M. shigaense' cases. The results confirmed that all of the clinical isolates were 'M. shigaense', a slow-growing, scotochromogenic species. Here M. shigaense is validly proposed as a new member of the M. simiae complex, with the type strain being UN-152T (=JCM 32072T=DSM 46748T).

Mycobacterium shigaense is a slowly growing scotochromogenic species and a member of the Mycobacterium simiae complex group. Here, we report the complete sequence of its genome, comprising a 5.2-Mb chromosome. The sequence will represent the essential data for future phylogenetic and comparative genome studies of the Mycobacterium simiae complex group.

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).

Mycobacterium sp. strain shizuoka-1 is a rapidly growing scotochromogenic mycobacterium and was isolated from well water for a bathing facility in Shizuoka Prefecture in Japan. Here, we report the draft sequence of its genome, comprising a 6.5-Mb chromosome. This mycobacterium has 83.1% identity with Mycobacterium rhodesiae , a human pathogen.

The list of clinically important slow-growing nontuberculous mycobacteria (NTM) continues to expand as new species are identified and older ones are found to be pathogenic. Based on pigment production, the strains may be classified as photochromogenic, scotochromogenic, or unpigmented. Some of these organisms are not newly discovered but have heretofore been considered virtually nonpathogenic. Previously, many were regarded as contaminants when isolated from clinical specimens. Ubiquitous in nature, many NTM have been isolated from groundwater or tap water, soil, house dust, domestic and wild animals, and birds. Most infections result from inhalation or direct inoculation from environmental sources. They are not spread from person to person. The infections may be localized or disseminated. In most cases, the optimal regimen or duration of therapy has not been firmly established. The results of in vitro susceptibility testing may be used to select a therapeutic regimen. Many experts recommend clarithromycin with companion drugs such as rifampin and ethambutol for most, but not all, slowly growing species. Aminoglycosides, clofazimine, fluoroquinolones, linezolid, pyrazinamide, or trimethoprim-sulfamethoxazole also may be effective against some strains. Immunocompetent patients with clinically significant infections with NTM usually should receive 18 to 24 months of therapy. Infected immunocompromised patients, particularly those with disseminated infection, probably should receive therapy as long as their immune systems remain impaired. Some of the species discussed include Mycobacterium alsiense , M. celatum , M. gordonae , M. haemophilum , M. kyorinense , M. malmoense , M. simiae complex, M. szulgai , M. terrae complex, M. ulcerans , and M. xenopi .

Mycobacterium acapulcensis is a rapidly growing scotochromogenic acid-fast bacillus. The draft genome of M. acapulcensis CSURP1424 comprises 5,290,974 bp, exhibiting a 66.67% G+C content, 4,870 protein-coding genes, and 71 predicted RNA genes.

The name ‘Mycobacterium alsiense’, although reported in 2007, has not been validly published. Polyphasic characterization of three available strains of this species led us to the conclusion that they represent a distinct species within the genus Mycobacterium. The proposed novel species grows slowly and presents pale yellow-pigmented colonies. Differentiation from other mycobacteria is not feasible on the basis of biochemical and cultural features alone while genetic analysis, extended to eight housekeeping genes and one spacer region, reveals its clear distinction from all other mycobacteria. Mycobacterium asiaticum is the most closely related species on the basis of 16S rRNA gene sequences (similarity 99.3 %); the average nucleotide identity between the genomes of the two species is 80.72 %, clearly below the suggested cut-off (95–96 %). The name Mycobacterium alsense sp. nov. is proposed here for the novel species and replaces the name ‘M. alsiense’, ex Richter et al. 2007, given at the time of isolation of the first strain. The type strain is TB 1906 T (=DSM 45230 T=CCUG 56586 T).

A novel slow-growing scotochromogenic mycobacterium was isolated from skin biopsies from a patient with a history of Hodgkin’s disease and severe cellular immunodeficiency as an opportunistic pathogen. Clinical characterization of these lesions revealed papules and nodules with pathological granuloma formation. Genotypic analysis using 16S rRNA misidentified this isolate as Mycobacterium simiae. However, multiple gene analysis using the internal transcribed spacer between the 16S and 23S rRNA genes, and the rpoB and hsp65 genes revealed the presence of a novel mycobacterium. The antimicrobial susceptibility of this isolate was completely different from that of M. simiae. On the basis of these findings, we propose naming this new species Mycobacterium shigaense sp. nov., and conclude that multiple gene analysis is required for the appropriate diagnosis and treatment of non-tuberculous mycobacterial infections.

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 acid–alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 °C. However, ‘M. paraffinicum’ strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 °C, 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 12670T =DSM 44181T =NCIMB 10420T, located in collections worldwide, as the type strain.

A previously unidentified, slowly growing, scotochromogenic Mycobacterium species, represented by strain 31118T, was discovered during hsp65 sequence-based reidentification of Korean clinical isolates that had been previously identified as Mycobacterium scrofulaceum by conventional biochemical tests. Although the 16S rRNA gene sequence of strain 31118T was identical to that of the recently described Mycobacterium seoulense, phylogenetic analyses based on three independent alternative targets (rpoB, hsp65 and the 16S–23S internal transcribed spacer) showed that it was closely related to M. seoulense but was a distinct phylogenetic entity. Furthermore, the phenetic characteristics of this strain were more similar to those of M. scrofulaceum than to those of M. seoulense. Taken together, these results support the conclusion that this strain represents a novel mycobacterium species, for which the name Mycobacterium paraseoulense sp. nov. is proposed. The type strain is 31118T (=DSM 45000T =KCTC 19145T).

Contains fulltext : 79803.pdf (Publisher’s version ) (Open Access) Slowly growing, scotochromogenic bacteria of a novel Mycobacterium species were isolated from lymph node samples in two children and pulmonary samples in two elderly patients from different regions in the Netherlands as well as from a surface water sample in Zambia. Its 16S rRNA gene, 16S-23S internal transcribed spacer (ITS), hsp65 and rpoB gene sequences are unique in comparison with other mycobacteria. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that these micro-organisms are most closely related to Mycobacterium scrofulaceum ATCC 19981(T) (8 differences; 0.6 % divergence). The hsp65 sequence shows 96 % similarity to that of Mycobacterium saskatchewanense MB54784 and the rpoB sequence shows 95 % similarity to that of Mycobacterium chimaera CIP 107892(T). The 16S-23S ITS sequence places these micro-organisms within the Mycobacterium avium complex, as a novel ITS sequevar. This is not supported by analysis of the 16S rRNA, hsp65 or rpoB gene sequences. Their scotochromogenicity, combined with mostly positive urease, positive semiquantitative catalase and negative tellurite reduction tests, set these isolates apart from related species. The mycolic acid patterns, obtained by HPLC, are similar to that of Mycobacterium scrofulaceum, though the peak heights and distribution present minor differences. We propose the name Mycobacterium mantenii sp. nov. for this novel species. The type strain, isolated from a lymph node biopsy sample, is strain 04-1474(T) (=NLA000401474(T) =CIP 109863(T) =DSM 45255(T)).

Udgivelsesdato: 2008-Oct A yellow-pigmented, scotochromogenic, slowly growing mycobacterial strain, designated T1921(T), was isolated from the disseminated osteomyelitic lesions of a 7-year-old child with an underlying partial gamma interferon receptor alpha-1 deficiency. Hybridization by the line probe assay indicated the presence of a Mycobacterium species. Sequencing of the 16S rRNA gene, the internally transcribed spacer (ITS) region and the hsp65 and rpoB genes revealed that strain T1921(T) could be differentiated from all recognized species of the genus Mycobacterium. Phylogenetic analysis based on the 16S rRNA gene indicated that strain T1921(T) was related most closely to Mycobacterium intracellulare, whereas analysis based on the ITS and hsp65 and rpoB genes indicated that it was most closely related to Mycobacterium avium. Phenotypic tests were not able to differentiate strain T1921(T) from similar slowly growing mycobacteria. Strain T1921(T) is considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium arosiense sp. nov. is proposed. The type strain is T1921(T) (=DSM 45069(T) =ATCC BAA-1401(T)).

We report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum sample. This is the first draft genome sequence of Mycobacterium obuense , a rapidly growing scotochromogenic mycobacterium.

Four bacterial strains were isolated from independent clinical specimens in different countries and their genotypic and phenotypic characters support their classification in a novel species within the genusMycobacterium. One strain was clearly responsible for a severe, post-traumatic wound infection in a healthy boy. The novel species, for which the nameMycobacterium monacensesp. nov. is proposed, is yellow-pigmented, non-photochromogenic and grows in less than a week on solid medium. Based on phenotypic investigations alone, distinction of these four strains from known scotochromogenic rapidly growing strains is problematic. However, the novel strains differ from any other mycobacterium in each of the molecular species markers investigated: the 16S rRNA gene, the 16S–23S rRNA gene internal transcribed spacer and thehsp65gene. Of the strains investigated, two different sequevars were detected for thehsp65region. Phylogenetic analysis revealed that these four strains were most closely related toMycobacterium doricum. The type strain ofMycobacterium monacensesp. nov. is B9-21-178T(=DSM 44395T=CIP 109237T).

Fourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic approach. Thorough genetic investigation, including whole-genome sequencing, demonstrated that the strains belong to the M. simiae complex, being most closely related to Mycobacterium interjectum . For 14 of the strains, evidence emerged supporting their inclusion in a previously unreported species of the genus Mycobacterium , for which the name Mycobacterium paraense sp. nov. is proposed (type strain, IEC26T = DSM 46749T = CCUG 66121T). The novel species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and a HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions, high sequence microheterogeneity was detected.

The characterization of a novel slowly growing, scotochromogenic Mycobacterium species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus Mycobacterium. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30–35 °C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to Mycobacterium malmoense, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium scrofulaceum. These data support the conclusion that the related five described organisms represent a novel Mycobacterium species, for which the name Mycobacterium nebraskense sp. nov. is proposed, with the type strain UNMC-MY1349T (=ATCC BAA-837T=DSM 44803T).

The isolation and identification of a novel, slow-growing, scotochromogenic, mycobacterial species is reported. A strain, designated MUP 1182T, was isolated from a cervical lymph node of a 3-year-old child. MUP 1182T is alcohol- and acid-fast, with a lipid pattern that is consistent with those of species that belong to the genus Mycobacterium. It grows slowly at 25–37 °C, but does not grow at 42 °C. The isolate was revealed to be biochemically distinct from previously described mycobacterial species: it has urease and Tween hydrolysis activities and lacks nitrate reductase, 3-day arylsulfatase and β-glucosidase activities. Comparative 16S rDNA sequencing showed that isolate MUP 1182T represents a novel, slow-growing species that is related closely to Mycobacterium lentiflavum and Mycobacterium simiae. On the basis of these findings, the name Mycobacterium parmense sp. nov. is proposed, with MUP 1182T (=CIP 107385T=DSM 44553T) as the type strain.

We report a woman in whom a slow-growing scotochromogenic strain of Mycobacterium was cultured from skin lesions. According to its phenotypic and biochemical characteristics we could predict only that it might be M. szulgai, M. scrofulaceum or M. gordonae. Polymerase chain reaction amplification of the hsp65 gene and subsequent restriction fragment length polymorphism analysis on the isolated strain showed that its restriction pattern differed from both M. scrofulaceum and other scotochromogenic species. Ninety-nine per cent similarity was detected between the isolated strain and M. gordonae by sequencing of the hsp65 gene. This result suggests that the isolated strain may be either a slow-growing scotochromogenic Mycobacterium most resembling M. gordonae or a novel mycobacterial species.

A scotochromogenic acid-fast bacillus was isolated from a lymph node of a 2-year-old female. On the basis of conventional testing, the mycobacterium appeared to be Mycobacterium scrofulaceum. Its mycolic acid profile, however, was not identical to that of Mycobacterium scrofulaceum but was similar to that of Mycobacterium interjectum. Direct sequencing of the 16S rRNA gene revealed a unique nucleic acid sequence, suggesting that the isolate represents a previously undescribed pathogenic species.

A new rapidly growing, scotochromogenic mycobacterium was isolated from urine. This strain is thermophilic (it grows at 65 degrees C), tolerates 5% NaCl, and was unable to utilize any of the sugars tested or citrate or to take up iron. The isolate splits benzamide, urea, nicotinamide, and pyrazinamide and is sensitive to streptomycin, ethambutol, cycloserine, ciprofloxacin, and chlarithromycin but resistant to isoniazid, rifampin, and prothionamide. These characteristics clearly place this organism in a new mycobacterial species, which was confirmed by the unique 16S rRNA nucleotide sequence. The high level of similarity between this rapid grower and Mycobacterium xenopi is surprising. For this new rapidly growing scotochromogenic and thermophilic mycobacterium we propose the name Mycobacterium hassiacum sp. nov.

A previously undescribed, slowly growing, scotochromogenic mycobacterial strain (49061T) was isolated from a patient with pulmonary infections during the hsp65-sequence-based identification of Korean clinical isolates. Its 16S rRNA gene sequence was unique and the phylogenetic analysis based on 16S rRNA gene sequence (1393 bp) placed the organism into the slow-growing Mycobacterium group close to Mycobacterium gordonae (99.0 % sequence similarity). Growth characteristics and acid-fastness also supported the placement of this species into the genus Mycobacterium . Phenotypically, this strain was generally similar to Mycobacterium gordonae ; however, of particular interest, the optimal growth temperature of strain 49061T was 25–30 °C, and it was not able to grow at 37 °C on 7H10 agar slants. Unique MALDI-TOF MS profiles of lipids, phylogenetic analysis based on another two gene sequences (hsp65 and rpoB) and a low DNA–DNA relatedness (46.52±0.7) strongly supported the taxonomic status of this strain as a representative of a distinct species from M. gordonae . It was concluded that the strain represents a novel species for which the name Mycobacterium paragordonae is proposed with the type strain 49061T ( = JCM 18565T = KCTC 29126T).

The isolation and characterization of a novel, rapidly growing, scotochromogenic mycobacterial species is reported. Eight independent strains were isolated from clinical specimens from six different countries of the world, two in Iran, two in Italy and one in each of following countries: Greece, the Netherlands, Sweden and the USA. Interestingly, two of the strains were isolated from cerebrospinal fluid. The strains were characterized by rapid growth and presented orange-pigmented scotochromogenic colonies. DNA-based analysis revealed unique sequences in the four regions investigated: the 16S rRNA gene, the rRNA gene internal transcribed spacer 1 and the genes encoding the 65 kDa heat-shock protein and the beta-subunit of RNA polymerase. The phylogenetic analysis placed the strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium gilvum . The genotypic and phenotypic data both strongly supported the inclusion of the strains investigated here as members of a novel species within the genus Mycobacterium; the name Mycobacterium iranicum sp. nov. is proposed to indicate the isolation in Iran of the first recognized strains. The type strain is M05T ( = DSM 45541T = CCUG 62053T = JCM 17461T).

This is the first report of infection caused by “ Mycobacterium lacticola ,” a rapidly growing, scotochromogenic mycobacterium that was isolated from the blood of an immunosuppressed child. The organism was identified by sequence analysis of >1,400 bp of the 16S rRNA gene. The clinical relevance of this isolate, coupled with its unique 16S rRNA gene sequence, should prompt further investigation to establish this organism as a valid mycobacterial species.

Strains of a new type of slowly growing scotochromogenic, rose-pink-pigmented mycobacterium were isolated repeatedly from sphagnum vegetation, true moss, and soil in Ireland. These strains grew at 22, 31, and 37 degrees C but not at 45 degrees C and possessed acid phosphatase and arylsulfatase activities. They reduced nitrate, tolerated 0.1% NaNO2, did not split amides, and were resistant to most of the antituberculous drugs tested, except ethambutol. They did not form acid from glucose and mannose. Their internal phenetic similarity was 97.08% +/- 2.07%. The whole mycolate pattern confirmed the homogeneity of the taxa sharing similar mycolate types with several other mycobacterial species. However, on the basis of the nature of the major pyrolysis esters, the taxon appeared unique. The phylogenetic analysis based on evolutionary distance values revealed that the strains belong to a new species of slowly growing mycobacteria. The DNA-DNA hybridization values confirmed that these strains differ significantly from Mycobacterium nonchromogenicum, M. terrae, M. triviale, and M. thermoresistibile. The strains produced a unique rose-pink pigment and were nonpathogenic for mice, guinea pigs, and rabbits, but they provoked a nonspecific hypersensitivity reaction to bovine tuberculin in guinea pigs and cattle. Hence, they are considered a member of a new species of nonpathogenic slowly growing mycobacteria, for which the name Mycobacterium hiberniae is proposed. Strain Hi 11 is the type strain, a culture of which has been deposited in the American Type Culture Collection as strain ATCC 49874.

Aims: To better understand nontuberculous mycobacteria (NTM) contamination in a hospital setting, six freshwater fish gut homogenates and water in an aquarium fish tank placed on the reception counter of a nursing station were cultured for mycobacteria. Methods and Results: By direct sequencing of 16s rRNA, rpoB and hsp65, scotochromogenic and nonchromogenic Mycobacterium szulgai isolates containing hsp65 type II (GenBank accession nos. FJ384762 and FJ384764, respectively), Mycobacterium gordonae isolates containing rpoB clusters B and E (GenBank accession no. FJ384766), and Mycobacterium kansasii isolates containing hsp65 type VI were collected from the gut homogenates and water from the fish tank. However, no isolates were obtained from the tap water used to refill the fish tank. A randomly amplified polymorphic DNA (RAPD) analysis using a 10-mer primer (5′-TGGTCGCGGC) showed that some NTM from the fish tank water were identical to those obtained from the gut homogenates. Conclusions: Fish and water in the tank were contaminated by the novel NTM. Significance and Impact of the Study: These findings could help to elucidate infection routes and contamination sources of novel NTM from water sources.

A previously unidentified, slowly growing scotochromogenic Mycobacterium was isolated from a Korean patient with symptomatic pulmonary infection. Phenotypically, this strain was generally similar to Mycobacterium terrae complex strains, however it uniquely produced orange pigmentation. Unique mycolic acid profiles and phylogenetic analyses based on three alternative chronometer molecules, 16S rRNA gene, hsp65 and rpoB, confirmed the taxonomic status of this strain as a novel species. These results support that this strain represents a novel Mycobacterium species. The name Mycobacterium paraterrae sp. nov. is proposed. The type strain is 05-2522 (= DSM 45127 = KCTC 19556).

Strains of Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum, Mycobacterium xenopi, and Mycobacterium gordonae were identified by high-performance liquid chromatography (HPLC) analysis of mycolic acids as bromophenacyl esters. HPLC criteria were used to develop a flow chart identification scheme, which was evaluated in our laboratory with a set of 234 strains representing five species and a hitherto undescribed species. Correct identifications of M. gordonae and M. xenopi were easily made. Flow chart differentiation of M. avium, M. intracellulare, and M. scrofulaceum was done with 97.9, 97.5, and 89.2% accuracies, respectively. Independent evaluation of the flow chart at a separate laboratory demonstrated an overall identification accuracy of 97% for M. avium complex. Strains that have been described biochemically as being intermediate between M. avium-M. intracellulare and M. scrofulaceum were identified as one or the other of these known species. Strains which were negative with the species-specific radioactive probe for M. avium complex but which were positive with the nonradioactive SNAP X probe were usually identified as M. intracellulare and M. scrofulaceum but rarely as M. avium.

Introduction: The bone and joint infections sustained by mycobacteria and mainly involving the synovium, tendons and bone stock, may be traumatic, especially in open fractures or iatrogenic post surgical procedures. Methods: The frustules, taken after cleaning the bone, were sent to the Microbiological Laboratory and processed for the presence of Gram-positive and Gram-negative bacterial populations, the mycobacteria Group M. tuberculosis complex and the mycobacteria belonging to the group of NTM (Non Tubercular Mycobacteria). Results: The decontaminated material was sown on liquid culture (MGIT 960 System BD Diagnostics) and on solid growth medium (Löwenstein-Jensen) and kept under observation at 37° C for 60 days. After 15 days on the solid medium there developed a mycobacterium strongly pigmented in orange. By the reverse hybridization method “GenoType® CM; Hain Diagnostika, Nehren, Germany; Arnika”, Mycobacterium szulgai was identified, an organism rarely isolated in our laboratory. On preliminary characterization it resulted scotochromogenic at 37° C and photochromogenic when cultured at 25° C. Conclusions: The isolation of M. szulgai, and the previous isolation of a M. intracellular (paper in press) from a similar material suggest that, in this type of infection, the role of mycobacteria can be clinically relevant and probably underestimated, both because the difficulty of isolating and identifying these organisms and because surgeons almost never request this type of investigation. It would therefore be appropriate to send routinely these materials to dedicated laboratories equipped to search for mycobacteria. Its identification could allow a more realistic picture on the role played by these bacterial infections in osteoarticular infections.

Contains fulltext : 81818.pdf (Publisher’s version ) (Open Access) The Mycobacterium avium complex (MAC) consists of four recognized species, Mycobacterium avium, Mycobacterium colombiense, Mycobacterium intracellulare and Mycobacterium chimaera, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous Mycobacterium species within the M. avium complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99% similar to Mycobacterium colombiense, and the MAC-Q 16S-23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97% similarity to M. avium. The rpoB gene sequence was 98% similar to M. colombiense. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of M. avium and M. colombiense. Together, these findings supported a separate species status within the Mycobacterium avium complex. We propose elevation of scotochromogenic M. avium complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name Mycobacterium vulneris sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).

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 paraffinicum," one cluster that is phenotypically very similar to Mycobacterium avium and Mycobacterium intracellulare but may be a separate genospecies, one cluster that appears to be phenotypically distinct from M. avium 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.

16S rRNA sequences from Mycobacterium tuberculosis, M. avium, M. gastri, M. kansasii, M. marinum, M. chelonae, M. smegmatis, M. terrae, M. gordonae, M. scrofulaceum, M. szulgai, M. intracellulare, M. nonchromogenicum, M. xenopi, M. malmoense, M. simiae, M. flavescens, M. fortuitum, and M. paratuberculosis were determined and compared. The sequence data were used to infer a phylogenetic tree, which provided the basis for a systematic phylogenetic analysis of the genus Mycobacterium. The groups of slow- and fast-growing mycobacteria could be differentiated as distinct entities. We found that M. simiae occupies phylogenetically an intermediate position between these two groups. The phylogenetic relatedness within the slow-growing species did not reflect the Runyon classification of photochromogenic, scotochromogenic, and nonchromogenic mycobacteria. In general, the phylogenetic units identified by using rRNA sequences confirmed the validity of phenotypically defined species; an exception was M. gastri, which was indistinguishable from M. kansasii when this kind of analysis was used.

Strains of a new type of slowly growing scotochromogenic mycobacterium were isolated repeatedly from sphagnum vegetation and surface water of moors in New Zealand. These strains grew at 31 and 22 degrees C but not at 37 degrees C and possessed catalase, acid phosphatase, and arylsulfatase activities. They did not split amides, and most of them were susceptible to antituberculotic drugs. Furthermore, they did not tolerate 0.1% NaOH2 and 0.2% picric acid and did not grow on compounds used as single carbon sources and single nitrogen and carbon sources. The internal similarity of the strains as determined by numerical taxonomy methods was 96.6% +/- 3.09%. The whole-mycolate pattern is unique in that it has not been found previously in 23 species of slowly growing mycobacteria. Evaluation of long-reverse-transcriptase-generated stretches of the primary structure of the 16S rRNA confirmed that these organisms belong to the genus Mycobacterium. The phylogenetic position of these bacteria is unique; they are situated between slowly growing pathogenic and rapidly growing saprophytic species. The strains are not pathogenic for mice, guinea pigs, and rabbits, but they provoke a nonspecific hypersensitivity reaction to bovine tuberculin. Hence, they are considered members of a new species of nonpathogenic, slowly growing mycobacteria, for which the name Mycobacterium cookii is proposed. Strain NZ2 is the type strain; a culture of this strain has been deposited in the American Type Culture Collection as strain ATCC 49103.

A previously undescribed, slowly growing, scotochromogenic mycobacterium was isolated from a patient with symptomatic pulmonary infection during hsp65 sequence-based identification of Korean clinical isolates. Phenetic characteristics of this strain were generally similar to those of Mycobacterium nebraskense and Mycobacterium scrofulaceum. However, some phenetic characteristics differentiated it from these two species. Its 16S rRNA gene sequences were unique and phylogenetic analysis based on 16S rRNA gene sequences placed the organism in the slowly growing Mycobacterium group close to M. nebraskense and M. scrofulaceum. Its unique mycolic acid profiles and the results of phylogenetic analysis based on two independent alternative chronometer molecules, hsp65 and rpoB, confirmed the taxonomic status of this strain as representing a novel species. These data support the conclusion that this strain represents a novel mycobacterial species, for which the name Mycobacterium seoulense sp. nov. is proposed. The type strain is strain 03-19T (=DSM 44998T=KCTC 19146T).

Mycobacterium scrofulaceum is one of the slowly growing scotochromogenic non-tuberculous mycobacterium. In adult, the clinical manifestations of M. scrofulaceum infections include pulmonary disease, hepatitis, osteomyelitis, and cutaneous infection. Herein, we report a rare case of disseminated M. scrofulaceum infection in a patient with lymphoma. The patient had the M. scrofulaceum infections that involved lung and joint, and the clinical condition responded to antimycobacterial agent and surgical debridement well.

This report describes an unusual strain of Mycobacterium avium complex isolated from the sputum of an immunocompromised AIDS patient, which did not react with the MAC probe of the BDProbe Tec system, but was identified as Mycobacterium intracellulare by 16S rRNA gene sequencing. Its PCR restriction-enzyme analysis pattern was compatible with an allelic variant of M. avium. It was scotochromogenic, slow-growing and phenotypically identified as Mycobacterium scrofulaceum. Its clinical significance is not certain.

A 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).

Modern identification techniques at the genomic level have greatly improved the taxonomic knowledge of mycobacteria. In adjunct to nucleic acid sequences, mycobacterial identification has been endorsed by investigation of the lipidic patterns of unique mycolic acids in such organisms. In the present investigation, the routine use of high-performance liquid chromatography (HPLC) of mycolic acids, followed by the sequencing of the 16S rRNA, allowed us to select 72 mycobacterial strains, out of 1,035 screened, that do not belong to any of the officially recognized mycobacterial species. Most strains (i.e., 47) were isolated from humans, 13 were from the environment, 3 were from animals, and 9 were from unknown sources. The majority of human isolates were grown from the respiratory tract and were therefore most likely not clinically significant. Some, however, were isolated from sterile sites (blood, pleural biopsy, central venous catheter, or pus). Many isolates, including several clusters of two or more strains, mostly slow growers and scotochromogenic, presented unique genetic and lipidic features. We hope the data reported here, including the results of major conventional identification tests, the HPLC profiles of strains isolated several times, and the whole sequences of the 16S rRNA hypervariable regions of all 72 mycobacteria, may encourage reporting of new cases. The taxonomy of the genus Mycobacterium is, in our opinion, still far from being fully elucidated, and the reporting of unusual strains provides the best background for the recognition of new species. Our report also shows the usefulness of the integration of novel technology to routine diagnosis, especially in cases involving slow-growing microorganisms such as mycobacteria.

The photochromogenic Mycobacterium vaccae ATCC 15483 was successfully transformed using the recombinant plasmid pC1 which contained a 10.83-kb DNA fragment representing the carotenogenesis operon from the scotochromogenic species Mycobacterium aurum A+. Experiments on the ability of transformed bacteria to synthesize carotenes in the dark or upon photoinduction revealed that transformed organisms were able to synthesize carotenes in the dark. Therefore, it was concluded that the expression of the M. aurum carotenogenesis operon in M. vaccae was not under control by the repressor of the M. vaccae photo-inducible carotenogenesis.

A pathogenic scotochromogenic Mycobacterium xenopi -like organism was isolated from the lung of an immunocompetent young woman. This pathogen caused severe bilateral cavitary lung disease, making two surgical interventions necessary after years of chronic disease. This case prompted us to characterize this mycobacterium by a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers which were typical for the genus Mycobacterium , i.e., the meso isomer of 2,6-diaminopimelic acid, arabinose, and galactose as diagnostic whole-cell sugars, MK-9(H 2 ) as the principal isoprenoid quinone, a mycolic acid pattern of α-mycolates, ketomycolates, and wax ester mycolates, unbranched saturated and unsaturated fatty acids plus a significant amount of tuberculostearic acid, and small amounts of a C 20:0 secondary alcohol. On the basis of its unique 16S rRNA and 16S-23S spacer gene sequences, we propose that the isolate should be assigned to a new species, Mycobacterium heckeshornense . This novel species is phylogenetically closely related to M. xenopi . The type strain of M. heckeshornense is strain S369 (DSM 44428 T ). The GenBank accession number of the 16S rRNA gene of M. heckeshornense is AF174290 .

A previously uncharacterized, slowly growing, scotochromogenic Mycobacterium species was detected by HPLC analysis of the cell-wall-bound mycolic acids. The mycolic acid pattern standard was shown to be a late-eluting, contiguous peak cluster occurring at approximately 8-9 min. The mycolic acid pattern was noted to be most similar in number of peaks and range of elution to that reported previously for Mycobacterium asiaticum. However, the relative distribution of peaks within the elution range demonstrated a pattern with prominent peaks that started to emerge later than the characteristic M. asiaticum pattern. Standard biochemical identification test results were similar to those of the photochromogenic species M. asiaticum. Comparative 16S rRNA gene sequence analysis confirmed the genetic uniqueness of the strains and demonstrated the unclassified mycobacteria to be in a unique, intermediate position between slow and rapid growers in the phylogenetic tree of Mycobacterium. The name Mycobacterium kubicae sp. nov. is proposed for this taxon. The type strain is CDC 941078T (= ATCC 700732T = CIP 106428T).

Three scotochromogenic Mycobacterium xenopi-like organisms were isolated from stream waters in Finland. These strains grew at 36-50 degrees C but not at 30 degrees C. One of the three strains was fully compatible with the M. xenopi type strain according to GLC-MS, biochemical tests, and 16S rDNA and 16S-23S rDNA internal transcribed spacer (ITS) sequencing. Two of the strains closely resembled M. xenopi in lipid analyses and biochemical tests, but analysis by GLC-MS verified the presence of two new marker fatty acids (2,4,6,x-tetramethyl-eicosanoic acid and 2,4,6,x,x-pentamethyl-docosanoic acid). The 16S rDNA and ITS region sequences of these two strains differed from those of M. xenopi and other previously described mycobacterial sequences. Therefore, the strains are regarded as new species of slow-growing mycobacteria, for which the name Mycobacterium botniense sp. nov. is proposed. The chemical, physical and microbiological quality of the water reservoirs of M. xenopi and M. botniense are described. As far as is known, this is the first time that M. xenopi has been isolated from natural waters. The strains of M. botniense sp. nov. (E347T and E43) have been deposited in the ATCC as strains 700701T and 700702, respectively.

A new, slow-growing, scotochromogenic mycobacterium was isolated from sputum of a 53-year-old patient with Down's syndrome suffering from tuberculosis. Growth occurred at temperatures between 25 and 40 degrees C with an optimum at 37 degrees C. This strain had surprisingly few enzymic activities (only positive for 68 degrees C heat-stable catalase and weakly positive for urease) and was sensitive to prothionamide, cycloserine, clarithromycin, gentamicin and amikacin but showed resistance to isoniazid, streptomycin, ethambutol, rifampin and ciprofloxacin. These characteristics assign this organism to a novel mycobacterial species characterized by a unique 16S rDNA nucleotide sequence. The name Mycobacterium bohemicum sp. nov. is proposed for this new, slow-growing, scotochromogenic mycobacterium. The type strain is DSM 44277T.

A slow-growing mycobacterium was isolated from a cervical lymph node of an adolescent male. This isolate produced small, smooth, scotochromogenic colonies after 6 weeks of incubation at 25 degrees C and 30 degrees C (but not at 37 degrees C or 43 degrees C). The results of 16S-rRNA gene sequencing and high-performance liquid chromatography suggest that this isolate belongs to a hitherto unrecognised pathogenic species.