Evaluation of practical chromatographic procedures for identification of clinical isolates of mycobacteria

19 Schiff bases as antimycobacterial agents: synthesis, molecular docking and a plausible mechanism of action

Aim: To discover novel anti-Mycobacterium tuberculosis (Mtb) drugs, 19 compounds were synthesized; their anti-Mtb effects were evaluated and mechanisms of action were preliminarily explored. Materials & methods: The compounds were synthesized and their anti-Mtb activity was elucidated using resazurin microtiter assays. The plausible target of the potential compound was investigated by microimaging techniques, gas chromatography-mass spectrometry analysis and molecular docking. Results: 19 compounds inhibited Mtb growth with minimum inhibitory concentrations ranging from 1 to 32 μg/ml. Compounds 1-17 showed inhibition of Mtb KatG enzyme. Compound 19, the most potent, might be an inhibitor of Pks13 polyketide synthase. Conclusion: This study suggests that 2-((6-fluoropyridin-3-yl)methylene) hydrazine-1-carbothioamide (19) is a potential anti-Mtb lead compound with a novel mechanism of action.

Characterization of Mycobacterium tuberculosis Mycolic Acids by Multiple-Stage Linear Ion-Trap Mass Spectrometry

Mycobacterium tuberculosis (Mtb) cells are known to synthesize very long chain (C60-90) structurally complex mycolic acids with various functional groups. In this study, we applied linear ion-trap (LIT) multiple-stage mass spectrometry (MSn), combined with high-resolution mass spectrometry to study the mechanisms underlying the fragmentation processes of mycolic acid standards desorbed as lithiated adduct ions by ESI. This is followed by structural characterization of a Mtb mycolic acid family (Bovine strain). Using the insight fragmentation processes gained from the study, we are able to achieve a near complete characterization of the whole mycolic acid family, revealing the identity of the α-alkyl chain, the location of the functional groups including methyl, methoxy, and keto groups along the meroaldehyde chain in each lipid species. This study showcased the power of LIT MSn toward structural determination of complex lipids in a mixture, which would be otherwise very difficult to define using other analytical techniques.

A re-investigation of the mycolic acids of Mycobacterium avium

Mycolic acid methyl esters were extracted from Mycobacterium avium by a mild saponification protocol, designed to preserve labile components. The resulting mixture of α-, keto- and wax ester mycolates was accompanied by some degraded ω-carboxymycolic acid dimethyl esters, whose overall structures were found to support previous studies. Chromatography of the mono-carboxylic mycolates gave an inseparable mixture of keto- and wax ester mycolates and separate α-mycolates. Reduction of the ketomycolate components allowed isolation and characterisation of intact wax ester mycolates for the first time. Minor α- and ω-carboxymycolates were detected in which methyl branches were located on either the proximal or distal sides of trans-alkene groups.

Mycobacterium avium subsp. paratuberculosis (Map) Fatty Acids Profile Is Strain-Dependent and Changes Upon Host Macrophages Infection

Johne's disease is a chronic granulomatous enteritis of ruminants caused by the intracellular bacterium Mycobacterium avium subsp. paratuberculosis (Map). We previously demonstrated that Map isolates from sheep persisted within host macrophages in lower CFUs than cattle isolates after 7 days of infection. In the current study, we hypothesize that these phenotypic differences between Map isolates may be driven be the fatty acids (FAs) present on the phosphadidyl-1-myo-inositol mannosides of the Map cell wall that mediate recognition by the mannose receptors of host macrophages. FAs modifications may influence Map's envelope fluidity ultimately affecting pathogenicity. To test this hypothesis, we investigated the responses of two Map isolates from cattle (K10 isolate) and sheep (2349/06-1) to the bovine and ovine macrophage environment by measuring the FAs content of extracellular and intracellular bacteria. For this purpose, macrophages cell lines of bovine (BOMAC) and ovine (MOCL-4) origin were infected with the two isolates of Map for 4 days at 37°C. The relative FAs composition of the two isolates recovered from infected BOMAC and MOCL-4 cells was determined by gas chromatography and compared with that of extracellular bacteria and that of bacteria grown in Middlebrook 7H9 medium. Using this approach, we demonstrated that the FAs composition of extracellular and 7H9-grown bacteria was highly conserved within each Map isolate, and statistically different from that of intracellular bacteria. Analysis of FAs composition from extracellular bacteria enabled the distinction of the two Map strains based on the presence of the tuberculostearic acid (18:0 10Me) exclusively in the K10 strain of Map. In addition, significant differences in the content of Palmitic acid and cis-7 Palmitoleic acid between both isolates harvested from the extracellular environment were observed. Once the infection established itself in BOMAC and MOCL-4 cells, the FAs profiles of both Map isolates appeared conserved. Our results suggest that the FAs composition of Map might influence its recognition by macrophages and influence the survival of the bacillus within host macrophages.

[Infections due to Mycobacterium simiae]

Mycobacterium simiae is a slow-growing photochromogenic environmental mycobacterium, first described in 1965. Rarely associated with human infections, possibly due to its limited pathogenicity, it mainly produces lung infection in immunocompetent elderly patients with underlying lung disease, and in disseminated infections in immunosuppressed young patients with AIDS. A microbiological culture is needed to confirm the clinical suspicion, and genetic sequencing techniques are essential to correctly identify the species. Treating M. simiae infections is complicated, owing to the multiple resistance to tuberculous drugs and the lack of correlation between in vitro susceptibility data and in vivo response. Proper treatment is yet to be defined, but must include clarithromycin combined with other antimicrobials such as moxifloxacin and cotrimoxazole. It is possible that M. simiae infections are undiagnosed.

Current Perspectives on Mycobacterium farcinogenes and Mycobacterium senegalense, the Causal Agents of Bovine Farcy

Mycobacterium farcinogenes and M. senegalense are the causal agents of bovine farcy, a chronic, progressive disease of the skin and lymphatics of zebu cattle. The disease, which is prevalent mainly in sub-Saharan Africa, was in earlier times thought to be caused by Nocardia farcinica and can be described as one of the neglected diseases in cattle. Some aspects of the disease have been investigated during the last five decades but the major development had been in the bacteriological, chemotaxonomic, and phylogenetic aspects. Molecular analyses confirmed that M. farcinogenes and M. senegalense fall in a subclade together with M. houstonense and M. fortuitum. This subclade is closely related to the one accommodating M. peregrinum, M. porcinum, M. septicum, M. neworleansense, and M. alvei. DNA probes were designed from 16S-23S rRNA internal transcribed spacer and could be used for the rapid diagnosis of bovine farcy. An ELISA assay has been evaluated for the serodiagnosis of the disease. The zoonotic potentials of M. farcinogenes and M. senegalense are unknown; few studies reported the isolation of M. senegalense and M. farcinogenes from human clinical sources but not from environmental sources or from other domestic or wild animals.

Rapid determination of growth inhibition of Mycobacterium tuberculosis by GC-MS/MS quantitation of tuberculostearic acid

Classical determination of growth inhibition of Mycobacterium tuberculosis in macrophages and mice by new candidate anti-TB drugs utilizes the determination of colony forming units (CFUs) from lung homogenates, a labor-intensive process requiring 2-3 weeks incubation. Qualitative analysis of tuberculostearic acid (TBSA), a cell wall associated biomarker found in M. tuberculosis, has been investigated for clinical diagnosis of tuberculosis (TB) but few reports exist of attempts to quantitate TBSA. Gas chromatography-mass spectroscopy (GC-MS/MS) was used in quantitating the derivatized methyl ester of TBSA during growth of M. tuberculosis in axenic medium, macrophage cultures and in the lungs of gamma interferon knockout (GKO) mice with and without exposure to anti-TB agents. The quantity of TBSA methyl ester (TBSAME) in the absence of and following exposure to anti-TB drugs was positively correlated with CFU in all three models. The stability of TBSA precludes its use as a surrogate for bactericidal activity but its exceptional thermal stability enables lung homogenates to be autoclaved prior to analysis. GC-MS/MS determination of TBSA is a rapid, sensitive and accurate means of detecting growth inhibition of any strain of M. tuberculosis in cell culture and in vivo.

Identification of potential biomarkers to distinguish Mycobacterium colombiense from other mycobacterial species

Mycobacterium avium complex (MAC) consists of 9 species of slow-growing mycobacteria with differing degrees of pathogenicity, host preference and environmental distribution. Mycobacterium colombiense is a novel member of MAC that is responsible for disseminated infections in HIV-infected patients in Colombia and lymphadenopathy cases in Europe. At present, methods to easily differentiate novel members of MAC are lacking. In this study, we identified possible biomarkers that are potentially useful for the detection of M. colombiense by PCR or chromatography. The Randomly Amplified Polymorphic DNA (RAPD) technique was used to amplify genomic fragments of M. colombiense CECT 3035 that were subsequently used in the development of a direct colony-specific PCR assay using specific primers. The designed primers amplified a 634-bp fragment of DNA from M. colombiense, which included a 450-bp genomic region that encodes a hypothetical protein of 149 amino acids that is exclusive to M. colombiense. Bioinformatic analyses revealed that this hypothetical protein had no signal peptide, active sites or functional domains to aid its identification or classification. In addition, using thin-layer chromatography, we identified a different profile of mycolates for M. colombiense strains. The test developed in this study has potential applications in the routine identification of M. colombiense and in molecular assays designed for the surveillance of MAC strains.

A metabolomics approach to characterise and identify various Mycobacterium species

We investigated the potential use of gas chromatography mass spectrometry (GC-MS), in combination with multivariate statistical data processing, to build a model for the classification of various tuberculosis (TB) causing, and non-TB Mycobacterium species, on the basis of their characteristic metabolite profiles. A modified Bligh-Dyer extraction procedure was used to extract lipid components from Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium bovis, and Mycobacterium kansasii cultures. Principle component analyses (PCA) of the GC-MS generated data showed a clear differentiation between all the Mycobacterium species tested. Subsequently, the 12 compounds best describing the variation between the sample groups were identified as potential metabolite markers, using PCA and partial least-squares discriminant analysis (PLS-DA). These metabolite markers were then used to build a discriminant classification model based on Bayes' theorem, in conjunction with multivariate kernel density estimation. This model subsequently correctly classified 2 "unknown" samples for each of the Mycobacterium species analysed, with probabilities ranging from 72 to 100%. Furthermore, Mycobacterium species classification could be achieved in less than 16 h, and the detection limit for this approach was 1×10(3)bacteriamL(-1). This study proves the capacity of a GC-MS, metabolomics pattern recognition approach for its possible use in TB diagnostics and disease characterisation.

Mycobacterium alsiense, a novel, slowly growing species isolated from two patients with pulmonary disease

A previously undescribed, slowly growing Mycobacterium species was isolated from pulmonary specimens of two patients, one from Denmark and one from Italy. The isolates showed unique 16S rRNA internal transcribed spacers and hsp65 sequences: the 16S rRNA was most closely related to Mycobacterium szulgai and Mycobacterium malmoense.

Utility of gas chromatography for rapid identification of mycobacterial species frequently encountered in clinical laboratory

Over the last years, the clinical importance of mycobacteria has been raised. In this regard, it is important their identification in order to establish either the clinical significance or the appropriate therapy of the disease. Biochemical tests are usually time consuming until the report of results, that is why more rapid techniques are needed. As an alternative identification method, we have used a commercially available system for microbial identification based on whole cellular fatty acids analysis using gas-chromatography (GC). Sixty-eight strains of Mycobacterium tuberculosis, Mycobacterium gordonae, Mycobacterium xenopi, Mycobacterium kansasii, Mycobacterium fortuitum, and Mycobacterium avium-intracellulare were clearly identified by their unique fatty acid profile using the Sherlock Microbial Identification System (MIS). The results were in agreement with those obtained with traditional methods. This method is highly automated, rapid, easy to perform with a sample preparation for lipid analysis which is neither time consuming nor requiring a particular expertise. On this basis the MIS-GC method for the identification of some clinically important mycobacteria appears to be suitable for routine clinical use.

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 production of a new extracellular putative long-chain saturated polyester by smooth variants of Mycobacterium vaccae interferes with Th1-cytokine production

Mycobacterium vaccae is of major pharmaceutical interest as an immunotherapeutic agent. Although M. vaccae 15483 ATCC(T) strain displays smooth and rough colonial morphologies on solid culture media, it is not known in which conditions M. vaccae switches from one colonial morphotype to the other or whether there are biological differences, especially immunological, between them. We have found that the change from a smooth to rough stable variant occurs spontaneously at 30 degrees C. The analysis of the composition of the cell wall in both variants showed that the smooth morphotype presents an extracellular material that has never previously been described and was identified as a long-chain saturated polyester that, interestingly, is not produced by the rough morphotype. Our results also indicate that this compound could be implicated in the spreading ability of smooth colonies. Proliferation, IFN-gamma and IL-12(p40) production by splenocyte cultures was significantly higher in mice immunised with the rough variant compared with those immunised with the smooth one. This latter finding suggests that the different colonial morphology of M. vaccae may affect the immunomodulatory effects induced from M. vaccae preparations.

Comparison of the sodium hydroxide specimen processing method with the C18-carboxypropylbetaine specimen processing method using independent specimens with auramine smear, the MB/BacT liquid culture system, and the COBAS AMPLICOR MTB test

A study was performed to diagnose tuberculosis by smear, culture, and nucleic acid amplification. The study was comprised of two independent arms. Each arm used a different specimen processing method; in one arm, all specimens were processed with N-acetyl-l-cysteine-sodium hydroxide, and in the other arm, all specimens were processed with C(18)-carboxypropylbetaine and lytic enzymes. In each arm, all processed sediments were split for analysis by auramine smear, by culture using the MB/BacT liquid culture system and solid media, and by nucleic acid amplification using the COBAS AMPLICOR MTB test. In the N-acetyl-l-cysteine-sodium hydroxide arm, 1,468 specimens were analyzed: 65 were smear positive; 88 and 42 were culture positive for Mycobacterium tuberculosis and nontuberculous mycobacteria, respectively; and 103 were PCR positive. Relative to cultures positive for M. tuberculosis, the sensitivity and specificity of the smear were 68.2% and 99.6%, respectively, and those of PCR were 75.0% and 97.3%, respectively. In the C(18)-carboxypropylbetaine study arm, 1,423 specimens were analyzed: 44 were smear positive; 82 and 31 were culture positive for M. tuberculosis and nontuberculous mycobacteria, respectively; and 91 were PCR positive. The sensitivity and specificity of the smear were 48.8% and 99.7%, respectively, and those of PCR were 78.0% and 98.0%, respectively. When the two arms were compared, C(18)-carboxypropylbetaine specimen processing significantly increased the number of smear-negative and culture-positive specimens and significantly increased the PCR sensitivity among this same group of specimens while at the same time significantly reducing the inhibition rate.

A comparison of mycolic acid analysis for nontuberculous mycobacteria identification by thin-layer chromatography and molecular methods

The development of fast, inexpensive, and reliable tests to identify nontuberculous mycobacteria (NTM) is needed. Studies have indicated that the conventional identification procedures, including biochemical assays, are imprecise. This study evaluated a proposed alternative identification method in which 83 NTM isolates, previously identified by conventional biochemical testing and in-house M. avium IS1245-PCR amplification, were submitted to the following tests: thin-layer chromatography (TLC) of mycolic acids and PCR-restriction enzyme analysis of hsp65(PRA). High-performance liquid chromatography (HPLC) analysis of mycolic acids and Southern blot analysis for M. avium IS1245 were performed on the strains that evidenced discrepancies on either of the above tests. Sixty-eight out of 83 (82%) isolates were concordantly identified by the presence of IS1245 and PRA and by TLC mycolic acid analysis. Discrepant results were found between the phenotypic and molecular tests in 12/83 (14.4%) isolates. Most of these strains were isolated from non-sterile body sites and were most probably colonizing in the host tissue. While TLC patterns suggested the presence of polymycobacterial infection in 3/83 (3.6%) cultures, this was the case in only one HPLC-tested culture and in none of those tested by PRA. The results of this study indicated that, as a phenotypic identification procedure, TLC mycolic acid determination could be considered a relatively simple and cost-effective method for routine screening of NTM isolates in mycobacteriology laboratory practice with a potential for use in developing countries. Further positive evidence was that this method demonstrated general agreement on MAC and M. simiae identification, including in the mixed cultures that predominated in the isolates of the disseminated infections in the AIDS patients under study. In view of the fact that the same treatment regimen is recommended for infections caused by these two species, TLC mycolic acid analysis may be a useful identification tool wherever molecular methods are unaffordable.

Requirement of the mymA operon for appropriate cell wall ultrastructure and persistence of Mycobacterium tuberculosis in the spleens of guinea pigs

We had recently reported that the mymA operon (Rv3083 to Rv3089) of Mycobacterium tuberculosis is regulated by AraC/XylS transcriptional regulator VirS (Rv3082c) and is important for the cell envelope of M. tuberculosis. In this study, we further show that a virS mutant (MtbdeltavirS) and a mymA mutant (Mtbmym::hyg) of M. tuberculosis exhibit reduced contents and altered composition of mycolic acids along with the accumulation of saturated C24 and C26 fatty acids compared to the parental strain. These mutants were markedly more susceptible to major antitubercular drugs at acidic pH and also showed increased sensitivity to detergent (sodium dodecyl sulfate) and to acidic stress than the parental strain. We show that disruption of virS and mymA genes impairs the ability of M. tuberculosis to survive in activated macrophages, but not in resting macrophages, suggesting the importance of the mymA operon in protecting the bacterium against harsher conditions. Infection of guinea pigs with MtbdeltavirS, Mtbmym::hyg, and the parental strain resulted in an approximately 800-fold-reduced bacillary load of the mutant strains compared with the parental strain in spleens, but not in the lungs, of animals at 20 weeks postinfection. Phenotypic traits were fully complemented upon reintroduction of the virS gene into MtbdeltavirS. These observations show the important role of the mymA operon in the pathogenesis of M. tuberculosis at later stages of the disease.

Mycobacterium fluoranthenivorans sp. nov., a fluoranthene and aflatoxin B1 degrading bacterium from contaminated soil of a former coal gas plant

Mycobacterium strain FA4T was isolated with fluoranthene as the single carbon source from soil of a former coal gas plant, polluted with polycyclic aromatic hydrocarbons. The physiological properties, fatty acid pattern, and the 16S ribosomal RNA gene sequence indicated membership to the genus Mycobacterium, but were different from all type strains of Mycobacterium species. Based on comparative 16S rRNA gene sequence analyses strain FA4T could be assigned to the Mycobacterium neoaurum taxon showing 98% sequence similarity to M. diernhoferi as its closest neighbour. The occurrence of epoxymycolate in the cell wall differentiates FA4 from all members of this taxon which synthesize wax-ester mycolates in addition to alpha-mycolates. Strain FA4T is able to degrade aflatoxin B1. This biological attribute might be useful in biological detoxification processes of foods and feeds. From the investigated characteristics it is concluded that strain FA4T represents a new species, for which we propose the name Mycobacterium fluoranthenivorans sp. nov. The type strain of Mycobacterium fluoranthenivorans is FA4T (DSM 44556T = CIP 108203T).

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).

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).

Comparative evaluation of the new version of the INNO-LiPA Mycobacteria and genotype Mycobacterium assays for identification of Mycobacterium species from MB/BacT liquid cultures artificially inoculated with Mycobacterial strains

The performance of two DNA line probe assays, a new version of INNO-LiPA Mycobacteria (Innogenetics, Ghent, Belgium) and the GenoType Mycobacterium (Hain Diagnostika, Nehren, Germany), were evaluated for identification of mycobacterial species isolated from liquid cultures. Both tests are based on a PCR technique and designed for simultaneous identification of different mycobacterial species by reverse hybridization and line probe technology. The INNO-LiPA Mycobacteria v2 targeting the 16S-23S rRNA gene spacer region was developed for the simultaneous identification of 16 different mycobacterial species. The GenoType Mycobacterium, which targets the 23S rRNA gene, allows simultaneous identification of 13 mycobacterial species. Both tests were evaluated on 110 mycobacterial strains belonging to 22 different mycobacterial species (20 reference strains, 83 clinical strains, and 4 Mycobacterium kansasii strains isolated from tap water) that were previously inoculated into MB/BacT bottles. The sensitivity of both methods, defined as the number of positive results obtained with the Mycobacterium genus probe together with an interpretable result on the number of samples tested was 110 of 110 (100%) for INNO-LiPA and 102 of 110 (92.7%) for GenoType. For samples with interpretable results, INNO-LiPA was able to correctly identify 109 of 110 samples (99.1%), whereas the GenoType correctly identified 100 of 102 samples (98.0%). Both tests were easy to perform, rapid, and reliable when applied to mycobacterial identification directly from MB/BacT bottles.

Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov

The possibility that the strains included within the Mycobacterium avium complex (MAC), but not belonging either to M. avium or to Mycobacterium intracellulare, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S–23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species M. intracellulare on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name Mycobacterium chimaera sp. nov.; this increases the number of species included in the M. avium complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).

Novel mass spectrometry-based tool for genotypic identification of mycobacteria

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for the identification of mycobacteria. Full-length 16S rDNA reference sequences of 12 type strains of Mycobacterium spp. frequently isolated from clinical specimens were determined by PCR, cloning, and sequencing. For MALDI-TOF MS-based comparative sequence analysis, mycobacterial 16S rDNA signature sequences ( approximately 500 bp) of the 12 type strains and 24 clinical isolates were PCR amplified using RNA promoter-tagged forward primers. T7 RNA polymerase-mediated transcription of forward strands in the presence of 5-methyl ribo-CTP maximized mass differences of fragments generated by base-specific cleavage. In vitro transcripts were subsequently treated with RNase T1, resulting in G-specific cleavage. Sample analysis by MALDI-TOF MS showed a specific mass signal pattern for each of the 12 type strains, allowing unambiguous identification. All 24 clinical isolates were identified unequivocally by comparing their detected mass signal pattern to the reference sequence-derived in silico pattern of the type strains and to the in silico mass patterns of published 16S rDNA sequences. A 16S rDNA microheterogeneity of the Mycobacterium xenopi type strain (DSM 43995) was detected by MALDI-TOF MS and later confirmed by Sanger dideoxy sequencing. In conclusion, analysis of 16S rDNA amplicons by MS after base-specific cleavage of RNA transcripts allowed fast and reliable identification of the Mycobacterium tuberculosis complex and ubiquitous mycobacteria (mycobacteria other than tuberculosis). The technology delivers an open platform for high-throughput microbial identification on the basis of any specific genotypic marker region.

RIDOM: comprehensive and public sequence database for identification of Mycobacterium species

Background

Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases.

Methods

In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined.

Results

Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum / M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD ± 0.57) were present.

Conclusions

The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project ), for similarity searches.

Comparison of a multiplex-PCR assay with mycolic acids analysis and conventional methods for the identification of mycobacteria

A fast, sensitive and cost-effective multiplex-PCR assay for Mycobacterium tuberculosis complex (MTC) and Mycobacterium avium (M. avium) identification for routine diagnosis was evaluated. A total of 158 isolates of mycobacteria from 448 clinical specimens from patients with symptoms of mycobacterial disease were analyzed. By conventional biochemical methods 151 isolates were identified as M. tuberculosis, five as M. avium and two as Mycobacterium chelonae (M. chelonae). Mycolic acid patterns confirmed these results. Multiplex-PCR detected only IS6110 in isolates identified as MTC, and IS1245 was found only in the M. avium isolates. The method applied to isolates from two patients, identified by conventional methods and mycolic acid analysis, one as M. avium and other as M. chelonae, resulted positive for IS6110, suggesting co-infection with M. tuberculosis. These patients were successfully submitted to tuberculosis treatment. The multiplex-PCR method may offer expeditious identification of MTC and M. avium, which may minimize risks for active transmission of these organisms and provide useful treatment information.

Evaluation of two different cell lysis methods for releasing mycobacterial nucleic acids in the INNO-LiPA mycobacteria test

The INNO-LiPA Mycobacteria Test (Innogenetics, N.V., Belgium) is a PCR-based reverse hybridization assay for the simultaneous identification of several mycobacterial species. We evaluated two simplified lysis methods for mycobacterial DNA release for application in the INNO-LiPA Mycobacteria Test. The two methods were based on either (i) heat treatment or (ii) sonication. Both methods were performed directly on 45 positive liquid cultures (MB-BacT, BioMérieux, Marcy l'Etoile, France) containing 17 different mycobacterial species. These two simple lysis procedures demonstrated similar effectiveness (100%) to that recommended by the manufacturer. They also significantly shortened the time required for mycobacterial DNA release.

Gas-chromatographic lipid profiles in identification of currently known slowly growing environmental mycobacteria

Cellular fatty acid analysis by GLC is widely used in the species identification of mycobacteria. Combining mycolic acid cleavage products with shorter cellular fatty acids increases the informative value of the analysis. A key has been created to aid in the identification of all currently known slowly growing environmental species. In this scheme, the species are classified into six categories, each characterized by a combination of fatty markers shared by those species. Within each category, individual species may be distinguished by the presence or absence of specific marker substances, such as methyl-branched fatty acids or secondary alcohols. This study also describes earlier unpublished GLC profiles of 14 rare, slowly growing, environmental mycobacteria, Mycobacterium asiaticum, Mycobacterium botniense, Mycobacterium branderi, Mycobacterium conspicuum, Mycobacterium cookii, Mycobacterium doricum, Mycobacterium heckeshornense, Mycobacterium heidelbergense, Mycobacterium hiberniae, Mycobacterium kubicae, Mycobacterium lentiflavum, Mycobacterium scrofulaceum, Mycobacterium triplex and Mycobacterium tusciae. Though no single identification technique alone, even sequencing of an entire single gene such as 16S rRNA, can identify all mycobacterial species accurately, GLC has proven to be both reliable and reproducible in the identification of slowly growing mycobacteria. In cases of earlier unknown species, it generates useful information that allows their further classification and may lead to the description of novel species.

Identification of three strains of Mycobacterium species isolated from clinical samples using fatty acid methyl ester profiling

The cellular fatty acid profiles of 67 strains belonging to three different species of the genus Mycobacterium were determined by gas chromatography of the fatty acid methyl esters, using the MIDI Sherlock Microbial Identification System (MIS). The species M. tuberculosis, M. xenopi and M. avium complex were clearly distinguishable and could be identified based on the presence and concentrations of 12 fatty acids: 14:0, 15:0, 16:1 omega 7c, 16:1 omega 6c, 16:0, 17:0, 18:2 omega 6.9c, 18:1 omega 9c, 18:0, 10Me-18:0 tuberculostearic acid, alcohol and cyclopropane. Fatty acid analysis showed that there is great homogeneity within and heterogeneity between Mycobacterium species. Thus the MIS is an accurate, efficient and relatively rapid method for the identification of mycobacteria.

Comparison of the sodium dodecyl sulfate-sodium hydroxide specimen processing method with the C18-carboxypropylbetaine specimen processing method using the MB/BacT liquid culture system

The ability of physicians to diagnose tuberculosis is impacted by the use of smear and culture techniques combined with specimen processing methods. The objective of this study was to evaluate the effects of specimen processing on smear and culture sensitivity by comparing the specimen processing method that uses C(18)-carboxypropylbetaine with the method that combines sodium dodecyl sulfate and sodium hydroxide. A total of 1,201 specimens were entered into this study. Specimens were split approximately equally such that one-half of each specimen was processed with sodium dodecyl sulfate-sodium hydroxide, while the other half was processed with C(18)-carboxypropylbetaine. All sediments were subjected to acid-fast staining and then analyzed using the MB/BacT liquid culture system (bioMérieux, France) and solid media. The sensitivity of smear following processing with sodium dodecyl sulfate-sodium hydroxide and C(18)-carboxypropylbetaine was 61.2% and 58.6% (P>0.05), respectively, while the specificities were identical (99.7%). The sensitivity of culture was 84.2% and 96.1% (P<0.05), respectively. The time to detection in the MB/BacT liquid culture system was 13.2+/-5.6 and 15.0+/-8.8 days (P>0.05), respectively, and 20.0+/-7.6 and 15.7+/-8.9 days (P<0.05), respectively, on solid media. The contamination rates in the MB/BacT system were 0.8% and 8.7%, respectively, whereas the contamination rates on solid media were 2.6% and 4.3%, respectively. C(18)-carboxypropylbetaine specimen processing was less labor-intensive than sodium dodecyl sulfate-sodium hydroxide processing and improved the ability of laboratory staff to detect the presence of mycobacteria by culture.

The HPLC-double-cluster pattern of some Mycobacterium gordonae strains is due to their dicarboxy-mycolate content

The mycolic acids of several strains of Mycobacterium gordonae were examined by chromatographic and spectroscopic techniques. Both HPLC and TLC revealed two patterns of mycolates among the M. gordonae strains studied. As determined by TLC, one pattern was composed of alpha-, methoxy- and keto-mycolates; the other was composed of these mycolates plus an additional component, which was identified as dicarboxy-mycolates. The dicarboxy-mycolates were only found in those M. gordonae strains that displayed a so-called HPLC-double-cluster pattern. Detailed structural analyses of the dicarboxy-mycolates indicated that these compounds contained predominantly 61-65 carbon atoms (C(63) was the major component) and a trans-1,2-disubstituted cyclopropane ring. Thus, the dicarboxy-mycolate content of strains of M. gordonae determines their HPLC pattern. In spite of the differences in their HPLC patterns, and although they belonged to different PCR-restriction length polymorphism clusters, all of the M. gordonae strains examined in this study were closely related on the basis of the structural features of their alpha-, keto- and methoxy-mycolates; the predominant alpha-mycolates contained two cis-1,2-disubstituted cyclopropane rings, the major keto-mycolates contained a trans-1,2-disubstituted cyclopropane ring and the methoxy-mycolates contained one cis- or one trans-1,2-disubstituted cyclopropane ring. It is noteworthy that the strains containing dicarboxy-mycolates also displayed significant amounts of alpha-mycolates that contained one cis-1,2-disubstituted cyclopropane ring and one cis double bond. The results obtained in this study demonstrate heterogeneity among M. gordonae strains.

Lack of usefulness of carbon utilization tests for identification of Mycobacterium mucogenicum

Carbon utilization tests have proven to be useful for the identification of some species of rapidly growing mycobacteria and have been described as one of the few tests useful for the differentiation of Mycobacterium mucogenicum from other rapid growers. We have found the carbon utilization tests to be unreliable for the identification of patient isolates of this species. In this study, using 28 isolates of rapidly growing mycobacteria, we examined several variables which might have an effect on results of citrate, inositol, and mannitol utilization: inoculum concentration, incubation temperature, and medium manufacturer. None of these variables affected results obtained for most species of rapid growers or for ATCC strains of M. mucogenicum. Results for patient isolates of M. mucogenicum were found to be inconsistent regardless of the methodology employed and resulted in an ambiguous identification of these isolates or an incorrect identification as Mycobacterium chelonae. Molecular or cell wall analysis may be the best technique to employ for accurate identification of M. mucogenicum.

Characterization of Mycobacterium bohemicum isolated from human, veterinary, and environmental sources

Chemotaxonomic and genetic properties were determined for 14 mycobacterial isolates identified as members of a newly described species Mycobacterium bohemicum. The isolates recovered from clinical, veterinary, and environmental sources were compared for lipid composition, biochemical test results, and sequencing of the 16S ribosomal DNA (rDNA) and the 16S-23S rDNA internal transcribed spacer (ITS) regions. The isolates had a lipid composition that was different from those of other known species. Though the isolates formed a distinct entity, some variations were detected in the features analyzed. Combined results of the phenotypic and genotypic analyses were used to group the isolates into three clusters. The major cluster (cluster A), very homogenous in all respects, comprised the M. bohemicum type strain, nine clinical and veterinary isolates, and two of the five environmental isolates. Three other environmental isolates displayed an insertion of 14 nucleotides in the ITS region; they also differed from cluster A in fatty alcohol composition and produced a positive result in the Tween 80 hydrolysis test. Among these three, two isolates were identical (cluster B), but one isolate (cluster C) had a unique high-performance liquid chromatography profile, and its gas liquid chromatography profile lacked 2-octadecanol, which was present in all other isolates analyzed. Thus, sequence variation in the 16S-23S ITS region was associated with interesting variations in lipid composition. Two of the isolates analyzed were regarded as potential inducers of human or veterinary infections. Each of the environmental isolates, all of which were unrelated to the cases presented, was cultured from the water of a different stream. Hence, natural waters are potential reservoirs of M. bohemicum.

Mycobacterium heckeshornense sp. nov., A new pathogenic slowly growing Mycobacterium sp. Causing cavitary lung disease in an immunocompetent patient

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 alpha-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.

Use of nucleic acid probes for identification of Mycobacterium tuberculosis directly from MB/BacT bottles

The feasibility of using nucleic acid probes directly from positive MB/BacT broth to identify mycobacteria was determined in this study. A total number of 2,727 specimens were cultured into the MB/BacT (Organon Teknika) automated system and on conventional Loweinstein-Jensen (LJ) slants. The Gen-Probe AccuProbe culture identification tests (DNA probes) were used on samples from bottles which were identified as positive for mycobacteria by MB/BacT. Samples of positive MB/BacT broth (0.1 ml) were used directly in the broth culture method for the DNA probes as published by Gen-Probe. Centrifugation of the contents of the bottle was not done prior to probe testing. The number of mycobacteria detected by MB/BacT and LJ was 253 (221 isolates of M. tuberculosis and 32 isolates of mycobacteria other than M. tuberculosis [MOTT]). A total of 96.4% (213 of 221) of the bottles growing M. tuberculosis produced a positive direct DNA probe result for M. tuberculosis complex. One hundred percent (16 of 16) of the bottles growing M. gordonae produced a positive direct DNA probe result for M. gordonae. A total of 3.6% (8 of 221) of the bottles growing M. tuberculosis did not yield a positive direct DNA probe result for M. tuberculosis complex. The testing of subcultures made onto solid media from the positive bottles by AccuProbe identified six of these eight M. tuberculosis isolates. Two (0.9%) M. tuberculosis isolates gave a negative result for the M. tuberculosis probe test applied on the MB/BacT broth and its subculture. The rest of the positive MB/BacT bottles growing MOTT (16 of 32) were negative for M. gordonae, M. avium, M. intracellulare, and M. kansasii probes. The sensitivity and specificity of AccuProbe for the identification of M. tuberculosis and M. gordonae directly from MB/BacT broth were 96.4 and 100% for M. tuberculosis and 100 and 100% for M. gordonae, respectively. The direct testing of positive MB/BacT broth by AccuProbe, without prior centrifugation, allows for the accurate and rapid identification of M. tuberculosis and M. gordonae.

Mycobacterium malmoense-specific nested PCR based on a conserved sequence detected in random amplified polymorphic DNA fingerprints

Mycobacterium malmoense is an opportunistic human pathogen of increasing clinical importance. Since it is difficult to detect and identify the organism by conventional techniques, it was decided to seek a nucleic acid amplification method specific for M. malmoense. The method was based on detection of a conserved band in random amplified polymorphic DNA (RAPD) fingerprints of 45 M. malmoense strains. This band was a 1,046-bp product which was proven to be M. malmoense specific in dot blot hybridization analysis with a panel of mycobacterial strains belonging to 39 other species. The fragment was sequenced, and oligonucleotide primers were synthesized to evaluate the specificity of the PCR. Two primer pairs were found to be specific and sensitive in the nested PCR that was developed. All 49 M. malmoense strains analyzed produced a PCR product of the expected size. In contrast, no strains belonging to the other mycobacterial species tested produced amplicons with these primers under specified reaction conditions. The results of the electrophoresis were confirmed by the hybridization with the M. malmoense-specific oligonucleotide probe. This method could be applied to the analysis of clinical or environmental samples, permitting the rapid detection of M. malmoense.

LCx: a diagnostic alternative for the early detection of Mycobacterium tuberculosis complex

This study aims to evaluate the performance of a new diagnostic method (LCx Tuberculosis Assay, Abbott Laboratories) based on Ligase Chain Reaction (LCR) technology, for the detection of Mycobacterium tuberculosis in respiratory and non-respiratory specimens and compare it with standard microbiological data and the clinical diagnosis of tuberculosis. Nine hundred specimens were collected from patients with a high suspicion of tuberculosis (740 respiratory samples and 160 non-respiratory specimens). The study was divided into two separate groups: samples washed and distilled water (207 samples) and unwashed samples that were directly resuspended in phosphate buffer (693 samples). The overall sensitivity, specificity, positive and negative predictive values of samples washed with distilled water after decontamination with SDS-NaOH were: 54%, 100%, 100%, and 94%, respectively. If these results were divided according to origin of specimens, the sensitivity, specificity, positive and negative predictive values in respiratory and non-respiratory samples were 54.5%, 100%, 100%, 94% and 50 100%, 100%, 93%, respectively. In contrast, for the non-washed samples, values were 85%, 95%, 80% and 98%, respectively. Respiratory and non-respiratory samples gave values of 84%, 96%, 77%, and 97.5% versus 89%, 99%, 94%, and 98%. The LCx M. tuberculosis assay is a novel, semi-automated assay and a rapid and highly specific technique for screening all forms of tuberculosis, including non-respiratory forms.

Identification of mycobacteria by thin layer chromatographic analysis of mycolic acids and conventional biochemical method: four years of experience

Mycolic acids analysis by thin-layer chromatography (TLC) has been employed by several laboratories worldwide as a method for fast identification of mycobacteria. This method was introduced in Brazil by our laboratory in 1992 as a routine identification technique. Up to the present, 861 strains isolated were identified by mycolic acids TLC and by standard biochemical tests; 61% out of these strains came as clinical samples, 4% isolated from frogs and 35% as environmental samples. Mycobacterium tuberculosis strains identified by classical methods were confirmed by their mycolic acids contents (I, III and IV). The method allowed earlier differentiation of M. avium complex-MAC (mycolic acids I, IV and VI) from M. simiae (acids I, II and IV), both with similar biochemical properties. The method also permitted to distinguish M. fortuitum (acids I and V) from M. chelonae (acids I and II), and to detect mixed mycobacterial infections cases as M. tuberculosis with MAC and M. fortuitum with MAC. Concluding, four years experience shows that mycolic acids TLC is an easy, reliable, fast and inexpensive method, an important tool to put together conventional mycobacteria identification methods.

Improved identification of mycobacteria by using the microbial identification system in combination with additional trimethylsulfonium hydroxide pyrolysis

The MIDI automated Microbial Identification System (MIS) uses gas chromatography (GC) analysis of whole-cell fatty acid methyl esters (FAMEs) between 9 and 20 carbons in length to characterize a wide range of bacterial genera and species, including mycobacteria. Mycolic acid cleavage products (MACPs) with chain lengths of C22 to C26 are not released by MIDI sample preparation of mycobacteria. Therefore, the MIS library search report often matches several mycobacterial species without any significant difference in the similarity indices. The problem is solved by adding trimethylsulfonium hydroxide (TMSH) instead of sodium sulfate in the last step of sample preparation, thus allowing the identification of MACPs in addition to FAMEs. Only one GC run parameter has to be changed: the temperature program must be extended from 260 to 310 degrees C. The MIS library search report for the identification of bacteria is not disturbed by TMSH. The combination of conventional library search report with the information of typical MACP patterns yields significantly better discrimination of mycobacterial species than the MIDI method allows.

Use of microscopic morphology in smears prepared from radiometric cultures for presumptive identification of Mycobacterium tuberculosis complex, Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium xenopi

The aim of this study was to assess the feasibility of a method for presumptive identification of mycobacteria, based on the morphology in smears prepared from radiometric Bactec-positive cultures (Becton Dickinson, USA) and to select the appropriate DNA probe (AccuProbe; Gen Probe, USA). The smear morphology of acid-fast bacilli was evaluated in 468 positive cultures from clinical samples: 313 Mycobacterium tuberculosis complex, 67 Mycobacterium avium complex, 32 Mycobacterium kansasii, 49 Mycobacterium xenopi, and seven Mycobacterium gordonae. The sensitivity and specificity for various morphological patterns were as follows: cord formation for Mycobacterium tuberculosis complex 90% and 100%, respectively; striped bacilli for Mycobacterium kansasii, 66% and 99%; sea urchin for Mycobacterium xenopi, 96% and 99%; short bacilli for Mycobacterium avium complex, 61% and 99%; fine-striped bacilli associated with Mycobacterium avium complex from blood samples, 33% and 98%. This criterion was applied in the selection of a suitable DNA probe for the identification of 178 cultures. The correct probe was selected in 98%, 97%, and 72% of cultures, respectively, for Mycobacterium tuberculosis complex, Mycobacterium avium complex, and Mycobacterium kansasii. The observation of acid-fast bacilli morphology in radiometric cultures is a rapid and cost-efficient method for presumptive identification of common clinical isolates of mycobacteria.

Rapid diagnosis of extrapulmonary tuberculosis by ligase chain reaction amplification

A rapid amplification-based test for the diagnosis of extrapulmonary tuberculosis, the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, was evaluated. Results from the LCx M. tuberculosis Assay were compared with those from culture and the final clinical diagnosis for each patient. A total of 526 nonrespiratory specimens from 492 patients were tested. The specimens included urine; feces; lymph node exudates; pleural, cerebrospinal, articular, and ascitic fluids; tissue biopsies; gastric aspirates; purulent exudates; blood; and bone marrow aspirates. After combination of the culture results and the patient's clinical data, a total of 135 specimens were collected from 122 patients with a diagnosis of extrapulmonary tuberculosis. The sensitivity, specificity, and positive and negative predictive values for the LCx M. tuberculosis Assay were 77.7, 98.7, 95.2, and 93.1%, respectively; these values rose in resolved cases of TB to 78.5, 100, 100, and 93.1%, respectively. For 37 (27.4%) specimens from patients smear positive for the disease and 98 (72.6%) specimens from patients smear negative for the disease, the sensitivities of the LCx M. tuberculosis Assay were 100 and 71.1%, respectively. Statistically significant differences (P < 0.01) in sensitivities were found between culture and the LCx M. tuberculosis Assay. These differences were even greater among smear-negative specimens. The results demonstrate that the LCx M. tuberculosis Assay will provide rapid and valuable information for the diagnosis of extrapulmonary tuberculosis.

Analysis of lipids reveals differences between 'Mycobacterium habana' and Mycobacterium simiae

Fatty and mycolic acids and the pattern of glycolipids were studied in a collection of 34 strains of 'Mycobacterium habana' and in two strains of Mycobacterium simiae. Major glycolipids of these micro-organisms were assigned to the glycopeptidolipid (GPL) structural type, but both mycobacteria differed in the patterns obtained by TLC. The strains of 'M. habana' were separated into four groups (A-D), taking into account the presence or absence of several polar GPLs: group A contained GPL-I, GPL-II and GPL-III; group B contained GPL-I, GPL-II', GPL-II and GPL-III; group C contained GPL-II', GPL-II and GPL-III; group D did not contain any of these compounds. Fatty acids of both bacteria were similar, and ranged from 14 to 26 carbon atoms, hexadecanoic, octadecenoic and tuberculostearic acids being predominant. Mycolic acids were also similar by TLC and HPLC, and consisted of alpha-, alpha'- and ketomycolates. Partial structural analysis by MS carried out in strains 'M. habana' TMC 5135 and M. simiae ATCC 25275T revealed that alpha- and ketomycolates ranged, in general, from 79 to 87 carbon atoms, and alpha'-mycolates from 58 to 67 carbon atoms. The alpha- and ketomycolates belonged to several structural series, and minor variations were found between the two strain examined. The data obtained justified the synonymy between 'M. habana' and M. simiae but indicated, in turn, that the former can be distinguished on the basis of GPL analysis. Most strains of 'M. habana' can be defined by the presence of GPL-II and GPL-III, a finding that could be useful in the quality control of potential vaccine strains.

Differentiation of Mycobacterium ulcerans, M. marinum, and M. haemophilum: mapping of their relationships to M. tuberculosis by fatty acid profile analysis, DNA-DNA hybridization, and 16S rRNA gene sequence analysis

Although Mycobacterium ulcerans, M. marinum, and M. haemophilum are closely related, their exact taxonomic placements have not been determined. We performed gas chromatography of fatty acids and alcohols, as well as DNA-DNA hybridization and 16S rRNA gene sequence analysis, to clarify their relationships to each other and to M. tuberculosis. M. ulcerans and M. marinum were most closely related to one another, and each displayed very strong genetic affinities to M. tuberculosis; they are actually the two mycobacterial species outside the M. tuberculosis complex most closely related to M. tuberculosis. M. haemophilum was more distinct from M. ulcerans and M. marinum, and it appeared to be as related to these two species as to M. tuberculosis. These results are important with regard to the development of diagnostic and epidemiological tools such as species-specific DNA probes and PCR assays for M. ulcerans, M. marinum, and M. haemophilum. In addition, the finding that M. ulcerans and M. marinum are more closely related to M. tuberculosis than are other pathogenic mycobacterial species suggests that they may be evaluated as useful models for studying the pathogenesis of M. tuberculosis. M. marinum may be particularly useful in this regard since strains of this species grow much more rapidly than M. tuberculosis and yet can cause systemic disease in immunocompromised hosts.

Comparative evaluation of initial and new versions of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for direct detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens

We evaluated the initial version of the Amplified Mycobacterium Tuberculosis Direct Test (Gen-Probe) (AMTDT 1) and the new version of AMTDT (AMTDT 2) for the detection of Mycobacterium tuberculosis directly from respiratory and nonrespiratory samples and compared the results with those of culture and staining methods. The assays were applied to 410 respiratory and 272 nonrespiratory samples collected from 515 patients. The combination of the culture results and clinical diagnosis was considered to be the "gold standard." Ninety-five respiratory specimens were collected from 67 patients with a diagnosis of pulmonary tuberculosis (TB) and 68 nonrespiratory specimens were collected from 61 patients with a diagnosis of extrapulmonary TB. With respiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 96%, respectively, for AMTDT 1 and 94.7, 100, 100, and 98.4%, respectively, for AMTDT 2. With nonrespiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 94%, respectively, for AMTDT 1 and 86.8, 100, 100, and 98.4%, respectively, for AMTDT 2. The overall results of AMTDT 1 and AMTDT 2 were concordant for 97% (661 of 682) of the samples. Statistically significant differences in sensitivities were found between AMTDT 1 and AMTDT 2 with respiratory specimens. It was concluded that although both nucleic acid amplification methods are rapid, sensitive, and specific for the detection of M. tuberculosis complex in all types of clinical samples, AMTDT 2 appeared to be more sensitive than AMTDT 1 when applied to smear-negative specimens. In contrast AMTDT 2 is more susceptible than AMTDT 1 to inhibitory substances in the amplification reaction. The turnaround time of AMTDT 2 is shorter (3.5 h) than that for AMTDT 1 (5 h).

Comparative evaluation of two commercial assays for direct detection of Mycobacterium tuberculosis in respiratory specimens

Two commercial systems for the amplification and detection of Mycobacterium tuberculosis directly from respiratory samples were compared. The Roche Cobas Amplicor MTB Test and the Roche manual Amplicor MTB Test (Roche Diagnostic Systems, USA) were applied to 755 decontaminated respiratory specimens collected from 470 patients. Results were compared with those of acid-fast staining and culture. A total of 251 specimens were collected from 156 patients diagnosed with pulmonary tuberculosis, including 28 specimens corresponding to 13 patients that were receiving antituberculous treatment. Given the overall positivity rate of 33.2% (251/755), the sensitivity, specificity, and positive and negative predictive values were 92.4, 100, 100, and 96.5%, respectively, for the Cobas Amplicor MTB Test and 90.8, 100, 100, and 95.8%, respectively, for the Amplicor MTB Test. For 204 (81.3%) smear positive specimens and 47 (19.7%) smear negative specimens, the sensitivity values were 100 and 59.6%, respectively, for the Cobas Amplicor MTB Test and 100 and 51%, respectively, for the Amplicor MTB Test. There were no statistically significant differences in sensitivity or specificity between the two assays and culture (p>0.05). The overall results of both assays were concordant for 99.5% of the samples. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of Mycobacterium tuberculosis complex in respiratory specimens, the Cobas Amplicor MTB Test appears to be slightly more sensitive than the Amplicor MTB Test when smear negative specimens are investigated.

Use of gas chromatographic fatty acid and mycolic acid cleavage product determination to differentiate among Mycobacterium genavense, Mycobacterium fortuitum, Mycobacterium simiae, and Mycobacterium tuberculosis

Three Mycobacterium genavense strains and three American Type Culture Collection reference strains each of Mycobacterium fortuitum, Mycobacterium simiae, and Mycobacterium tuberculosis were subcultured onto Mycobacteria 7H11 agar (Difco Laboratories, Detroit, Mich.) supplemented with mycobactin J (Allied Laboratories, Fayette, Mo.). After 4 weeks of incubation at 37 degrees C in 10% CO2, the cultures were analyzed by gas-liquid chromatography (GLC) for their fatty acids and mycolic acid cleavage products. M. fortuitum was clearly differentiated from M. genavense by the presence of the specific marker 2-methyloctadecenoic acid in M. fortuitum and by the ratio of tetracosanoic acid to hexacosanoic acid. This ratio was <1 for M. genavense and >3 for M. fortuitum. M. fortuitum also contained docosanoic acid, which was not detected in M. genavense. M. genavense, M. simiae, and M. tuberculosis, which have similar GLC profiles, were also differentiated from each other by the presence of either cis-10-hexadecenoic acid or cis-11-hexadecenoic acid and by tetradecanoic acid content.