Large-Restriction-Fragment Polymorphism Analysis of Mycobacterium chelonae and Mycobacterium terrae Isolates

Mycobacterium chelonae and Mycobacterium terrae were reported to be frequently present in the environment of the Mycobacterium bovis BCG trial area in south India. Six isolates of M. chelonae and four isolates of M. terrae obtained from different sources in this area were analyzed by pulsed-field gel electrophoresis (PFGE) to examine large-restriction-fragment (LRF) polymorphism using the chromosomal DNA digested with DraI and XbaI restriction enzymes. With the exception of one isolate of M. terrae, DNA from all other isolates could be digested with DraI and XbaI and resulted in separable fragments. Visual comparison of the LRFs showed a unique pattern for each of the isolates tested. A computer-assisted dendrogram of the percent similarity demonstrated a high degree of genetic diversity in this group of isolates. This study demonstrates that species of nontuberculous mycobacteria, particularly M. chelonae and M. terrae, can be successfully typed by their LRF pattern using PFGE, which does not require species-specific DNA probes.     

Large-restriction-fragment polymorphism analysis of Mycobacterium chelonae and Mycobacterium terrae isolates

Mycobacterium chelonae and Mycobacterium terrae were reported to be frequently present in the environment of the Mycobacterium bovis BCG trial area in south India. Six isolates of M. chelonae and four isolates of M. terrae obtained from different sources in this area were analyzed by pulsed-field gel electrophoresis (PFGE) to examine large-restriction-fragment (LRF) polymorphism using the chromosomal DNA digested with DraI and XbaI restriction enzymes. With the exception of one isolate of M. terrae, DNA from all other isolates could be digested with DraI and XbaI and resulted in separable fragments. Visual comparison of the LRFs showed a unique pattern for each of the isolates tested. A computer-assisted dendrogram of the percent similarity demonstrated a high degree of genetic diversity in this group of isolates. This study demonstrates that species of nontuberculous mycobacteria, particularly M. chelonae and M. terrae, can be successfully typed by their LRF pattern using PFGE, which does not require species-specific DNA probes.     

Comparison of proteins from Mycobacterium fortuitum, Mycobacterium nonchromogenicum and Mycobacterium terrae using flat bed electrophoresis.

Polyacrylamide gel electrophoresis of bacterial lysates in a flat bed gives a linear relationship between 1n mol. wt of the proteins and the square root of their migration distances, thereby allowing standardization of different electrophoresis runs and precise comparison between homologous bands. The results obtained with Mycobacterium fortuitum, M. terrae and M. nonchromogenicum strains were used in numerical analysis. Mycobacterium fortuitum and M. nonchromogenicum showed a greater internal similarity than M. terrae, while two strains of the latter clustered with M. nonchromogenicum. The method described allows the comparison of mycobacteria with different generation times and provides a large number of good characters for numerical taxonomy.     

Assessment of DNA damage and repair in Mycobacterium terrae after exposure to UV irradiation

AIM: Ultraviolet (UV) irradiation for drinking water treatment was examined for inactivation and subsequent dark and photo-repair of Mycobacterium terrae. METHODS AND RESULTS: UV sources tested were low pressure (monochromatic, 254 nm) and medium pressure (polychromatic UV output) Hg lamps. UV exposure resulted in inactivation, and was followed by dark or photo-repair experiments. Inactivation and repair were quantified utilizing a molecular-based endonuclease sensitive site (ESS) assay and conventional colony forming unit (CFU) viability assay. Mycobacterium terrae was more resistant to UV disinfection compared to many other bacteria, with approximately 2-log reduction at a UV fluence of 10 mJ cm(-2) ; similar to UV inactivation of M. tuberculosis. There was no difference in inactivation between monochromatic or polychromatic UV lamps. Mycobacterium terrae did not undergo detectable dark repair. Photo-repair resulted in recovery from inactivation by approximately 0.5-log in less than 30 min for both UV lamp systems. CONCLUSIONS: Mycobacterium terrae is able to photo-repair DNA damage within a short timeframe. The number of pyrimidine dimers induced by UV light were similar for Escherichia coli and M. terrae, however, this similarity did not hold true for viability results. SIGNIFICANCE AND IMPACT OF THE STUDY: There is no practical difference between UV sources for disinfection or prevention of DNA repair for M. terrae. The capability of M. terrae to photo-repair UV damage fairly quickly is important for wastewater treatment applications where disinfected effluent is exposed to sunlight. Finally, molecular based assay results should be evaluated with respect to differences in the nucleic acid content of the test micro-organism.     

一株毒死蜱降解新菌株Sphingopyxis terrae R17的分离鉴定及降解特性

从农药厂排污沟污泥中分离到一株能降解毒死蜱的新菌株,命名为R17,经生理生化和16S rDNA序列同源性分析,鉴定为Sphingopyxis terrae.R17可以利用毒死蜱作为唯一碳源生长,该菌株的最适生长温度为35℃、最适pH为7～8,在此条件下培养28 h后,菌落浓度达9.18×108cfu/mL.研究了该菌在...     

Production of Multivalent Fluorescent Antisera for Identification of Organisms in the Mycobacterium avium-Mycobacterium intracellulare Complex

Antisera to ten strains of mycobacteria in the Mycobacterium avium-Mycobacterium intracellulare group were obtained by injecting rabbits with ultraviolet light-killed cells. The antisera were conjugated with fluorescein isothiocyanate and used in the direct fluorescent antibody test. Individual antisera reacted specifically with the mycobacterial serotype used to produce them. The antisera were then combined in two multivalent pools. Each multivalent pool reacted specifically with its corresponding antigens. The multivalent antisera were thus found to provide a rapid identification method for the mycobacteria studied.     

Relationship between Mycobacterium nonchromogenicum,Mycobacterium terrae,Mycobacterium novum and Subgroup “V” (Mycobacterium trivial)

Comparison was made among Mycobacterium nonchromogenicum, M. terrae, M. novum and subgroup “V” (M. trivial) These organisms together are differentiated from other mycobacteria of group II and group III by the following characters: (1) Sensitiveness to ethambutol; (2) Tolerance to nitrite; (3) Tolerance to Tween 80; (4) Inability to utilize glucose and succinate in the presence of glutamate. To exclude the influence of growth rate, rough colony mutants (R-type mutants) were isolated from M. nonchromogenicum, M. terrae and M. novum and compared with each other and subgroup “V” that was originally of R-type. The R-type mutants of M. nonchromogenicum were similar to those of M. terrae, with the exception of the intensity of nicotinamidase and pyrazinamidase activities. These two have been suggested to belong to the same taxon, appropriate name of which is M. nonchromogenicum. The R-type mutants of M. novum were similar to the subgroup “V”, with the exception of the intensity of arylsulfatase activity. It has been considered that subgroup “V” is an R-type mutant of M. novum. Although M. nonchromogenicum and M. novum could be differentiated from each other by the intensity of the arylsulfatase, nicotinamidase and pyrazinamidase activities and requirement of nitrogen compounds, these two organisms are differentiated from other mycobacteria by the same characteristics and are therefore considered to be closely related organisms.     

Two Types of Slowly Growing,Nonphotochromogenic Mycobacteria Obtained from Soil by the Mouse Passage Method: Mycobacterium terrae and Mycobacterium novum

Two types of slowly growing, nonphotochromogenic mycobacteria, Mycobacterium terrae and Mycobacterium novum, were isolated from soil by mouse body passage method. The former was presented previously by the present author as a new species. Its characteristics are better clarified in this paper based on the data of 93 strains. Mycobacterium novum is a slowly growing nonphotochromogen. It grows at 10 to 14 days on egg media and does not grow on Sauton agar. It grows on Ogawa egg medium containing either 0.2% (w/v) sodium p-aminosalicylate, 0.1% (w/v) sodium salicylate or 0.25 mg/ml NH₂OH·HCl. It is differentiated from M. tuberculosis, M. bovis and M. microti by these characters. It grows at 28 C and 37 C, but does not grow at 45 C. Other characteristics are: nitrate not reduced; negative two week arylsulphatase; negative niacin test; and no amidase clemonstrated. None of the carbohydrates and nitrogen compounds tested could be utilized as the sole source of carbon or of nitrogen in synthetic agar medium. It survived in mouse organs for three to four weeks. It was noticed that these mycobacteria occur very commonly in soil.     

Influence of storage on monodispersed cells of Mycobacterium terrae used for quantitative carrier test prEN 14563

The degree of cell clumping increased with time of storage (1% cell clumps immediately after homogenization and 3 and 6.5% after 48 and 96 h of storage, respectively), and the number of living single cells decreased. Quantitative carrier tests were carried out with these cells using ortho-phthaldialdehyde (OPA) and coco fatty aminoxethylate as biocides. In contrast to OPA, with coco fatty aminoxethylate the reductions obtained with freshly homogenized mycobacteria were significantly higher (P = 0.02) than those obtained with mycobacteria kept in the refrigerator for 4 days. Therefore, it is advisable to prepare the test suspension freshly for each test.     

Influence of Storage on Monodispersed Cells of Mycobacterium terrae Used for Quantitative Carrier Test prEN 14563

The degree of cell clumping increased with time of storage (1% cell clumps immediately after homogenization and 3 and 6.5% after 48 and 96 h of storage, respectively), and the number of living single cells decreased. Quantitative carrier tests were carried out with these cells using ortho-phthaldialdehyde (OPA) and coco fatty aminoxethylate as biocides. In contrast to OPA, with coco fatty aminoxethylate the reductions obtained with freshly homogenized mycobacteria were significantly higher (P = 0.02) than those obtained with mycobacteria kept in the refrigerator for 4 days. Therefore, it is advisable to prepare the test suspension freshly for each test.     

Identification of a New Steroid-Transforming Strain of Mycobacteria as Mycobacterium neoaurum

The ability to utilize sterols as a sole source of carbon was studied in 80 strains and consortia of hydrocarbon-oxidizing bacteria. One of the strains, which efficiently transformed both individual sterols and their mixtures, was identified as Mycobacterium neoaurum based on the analysis of the sequence of the 16S rRNA gene.     

Differential Identification of Mycobacterium kansasii and Mycobacterium marinum

This report deals with the differential diagnosis between Mycobacterium marinum and M. kansasii. We found that the two species could be differentiated by using six main tests, namely, the nitrate reduction test, the arylsulfatase test, the ability to grow in the presence of 10.0 mug of amithiazone per ml, the ability to grow in the presence of 5.0 mug of kanamycin per ml, the temperature-ratio test, and the rate of growth on solid medium. In contrast to M. kansasii, considerable variation was observed among strains of M. marinum. However, the evidence obtained was not considered sufficient to justify the conclusion that more than one species was represented among the strains identified as M. marinum.     

Mycobacterium paraterrae sp. nov. recovered from a clinical specimen: novel chromogenic slow growing mycobacteria related to Mycobacterium terrae complex

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).     

Two New Rapid SNP-Typing Methods for Classifying Mycobacterium tuberculosis Complex into the Main Phylogenetic Lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the "Beijing" sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.     

Mycobacterium kumamotonense Sp. Nov. recovered from clinical specimen and the first isolation report of Mycobacterium arupense in Japan: Novel slowly growing, nonchromogenic clinical isolates related to Mycobacterium terrae complex

Three mycobacterium strains isolated from clinical specimens in Japan were provisionally assigned to the genus Mycobacterium based on their phenotypical characteristics. These isolates were further investigated to determine their specific taxonomic statuses. Mycolic acid analysis and 16S rRNA gene, rpoB, and hsp65 sequence data for the isolates showed that they are most similar to M. terrae complex. DNA-DNA hybridization studies indicated that the three strains were of two species and were distinguishable from M. terrae, M. nonchromogenicum, and M. hiberniae. Therefore, these strains represent two novel species within the genus Mycobacterium. However, one potential new species should have been considered as M. arupense with the 16S rRNA gene and hsp65 sequences similarities of 99.8% and 100% respectively; it was isolated from human specimens in the United States and was proposed in June 2006 as a new species. This report describes the first isolation of M. arupense in Japan, suggesting that the organism is clinically relevant. In addition, we propose the novel species designation Mycobacterium kumamotonense sp. nov. The type strain is CST 7247(T) (=GTC 2729(T), =JCM 13453(T), =CCUG 51961(T)).     

The genomic heterogeneity among Mycobacterium terrae complex displayed by sequencing of 16S rRNA and hsp 65 genes

The species identification within Mycobacterium terrae complex has been known to be very difficult. In this study, the genomic diversity of M. terrae complex with eighteen clinical isolates, which were initially identified as M. terrae complex by phenotypic method, was investigated, including that of three type strains (M. terrae, M. nonchromogenicum, and M. triviale ). 16S rRNA and 65-kDa heat shock protein (hsp 65) gene sequences of mycobacteria were determined and aligned with eleven other references for the comparison using similarity search against the GenBank and Ribosomal Database Project II (RDP) databases. 16S rRNA and hsp 65 genes of M. terrae complex showed genomic heterogeneity. Amongst the eighteen clinical isolates, nine were identified as M. nonchromogenicum, eight as M. terrae, one as M. mucogenicum with the molecular characteristic of rapid growth. M. nonchromogenicum could be subdivided into three subgroups, while M. terrae could be subdivided into two subgroups using a 5 bp criterion (>1% difference). Seven isolates in two subgroups of M. nonchromogenicum were Mycobacterium sp. strain MCRO 6, which was closely related to M. nonchromogenicum. The hsp 65 gene could not differentiate one M. nonchromogenicum from M. avium or one M. terrae from M. intracellulare. The nucleotide sequence analysis of 16S rRNA and hsp 65 genes was shown to be useful in identifying the M. terrae complex, but hsp 65 was less discriminating than 16S rRNA.