Mycobacterium doricum sp. nov

A novel mycobacterial species is described in this study. The strain was isolated from the cerebrospinal fluid of a severely immunocompromised AIDS patient. It was scotochromogenic and slow-growing. Characteristic features for its differentiation from other mycobacteria are its lipid pattern and the unique gene sequences within the hypervariable regions of the 16S rDNA. The strain shows susceptibility to current antimycobacterial drugs. The pathogenicity of the novel mycobacterium and its clinical significance are not certain, as the neurological symptoms of the patient could also be due to concomitant infection with Cryptococcus neoformans. The name Mycobacterium doricum sp. nov. is proposed for the novel mycobacterium; the type strain is strain FI-13295T (= DSM 44339T = CIP 106867T).

Burden of unidentifiable mycobacteria in a reference laboratory

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.

Multicenter evaluation of a pathogenic mycobacterium screening probe

The introduction of nucleic acid amplification assays into the clinical laboratory has reduced the time needed to diagnose diseases caused by members of the Mycobacterium tuberculosis complex (MTBC). However, several mycobacterial species other than those of the MTBC are known to cause disease, especially in immunocompromised individuals. A screening assay has been developed for the detection of the major pathogenic mycobacterial species. The assay utilizes pan-genus primers to amplify mycobacterial DNA and a screening probe (KY493) that detects all major pathogenic mycobacteria. A multicenter European study was conducted to assess the performance of the screening probe in the clinical laboratory. The screening probe was evaluated against individual probes specific for M. tuberculosis, M. avium, and M. intracellulare, a genus-specific probe with broader species coverage, and culture. The screening probe had a sensitivity equivalent to that of the species-specific probes; all specimens positive with any of the species-specific probes were also positive with the screening probes. Compared to culture, the sensitivity of the screening probe was 89% (154 of 173) for all culture-positive specimens tested. This value was 89.6% for the genus-specific probe. The screening probe was more specific than the genus-specific probe. Specificity was 93.9% (661 of 704) compared to culture results alone. The comparable specificity value for the genus-specific probe was 84.8%. When clinical data were taken into consideration, the sensitivity of the screening assay was similar to that of culture (81% versus 76.2%) but the positive predictive value of the test was lower (76.2% versus 100% for culture). However, the screening probe was more sensitive than smear and may be a useful tool in the rapid diagnosis of mycobacterial disease.

Phylogenetic analysis of Pasteurella multocida subspecies and molecular identification of feline P. multocida subsp. septica by 16S rRNA gene sequencing

Pasteurella multocida is commonly found in the oral cavity of cats and dogs. In humans it is known as an opportunistic pathogen after bites from these animals. Phenotypic identification of P. multocida based on biochemical reactions is often limited and usually only done on a species level, even though 3 subspecies are described. For molecular taxonomy and diagnostic purposes a phylogenetic analysis of the three subspecies of P. multocida based on their 16S rRNA (rrs) gene sequence was therefore carried out. We found P. multocida subsp. septica on a distinguished branch on the phylogenetic tree of Pasteurellaceae, due to a 1.5% divergence of its rrs gene compared to the two other, more closely related subspecies multocida and gallicida. This phylogenetic divergence can be used for the identification of P. multocida subsp. septica by rrs gene determination since they form a phylogenetically well isolated and defined group as shown with a set of feline isolates. Comparison to routine phenotypic identification shows the advantage of the sequence-based identification over conventional methods. It is therefore helpful for future unambiguous identification and molecular taxonomy of P. multocida as well as for epidemiological investigations.

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.

Bloodstream infections caused by small-colony variants of coagulase-negative staphylococci following pacemaker implantation

Small-colony variants (SCVs) of Staphylococcus aureus cause persistent and relapsing infections. Relatively little is known regarding infections caused by SCVs of coagulase-negative staphylococci. We report two cases of pacemaker electrode infections due to SCVs of Staphylococcus epidermidis and Staphylococcus capitis. Sequence analysis of a portion of the 16S rRNA gene (16S rDNA) confirmed the identity of the staphylococcal species as S. capitis and S. epidermidis. Isolates from cultures of blood obtained over at least a 2-week interval were compared by pulsed-field gel electrophoresis and found to be clonal even though the colony morphology was very different. Analysis for auxotrophism revealed hemin dependencies for all isolated SCVs. The two cases have several clinical and laboratory characteristics (which are also seen with S. aureus SCV infections) and strongly suggest that SCVs of coagulase-negative staphylococci must be actively sought, because they grow very slowly and can be easily missed.

Mycobacterium tusciae sp. nov

A new, slow-growing, scotochromogenic mycobacterium was isolated from a lymph node of an immunocompromised child and subsequently from tap water and from a respiratory specimen of a patient with chronic fibrosis. Alcohol-acid-fastness, lipid patterns and the G + C content clearly support the placement of this organism in the genus Mycobacterium. The isolates grew very slowly at temperatures ranging from 25 to 32 degrees C and showed activities of nitrate reductase, catalase, urease, arylsulfatase and Tween 80 hydrolysis. The organism was susceptible to all antimycobacterial drugs tested. The 16S rDNA sequence was unique and phylogenetic analysis placed the organism close to fast-growing species such as Mycobacterium farcinogenes, Mycobacterium komossense and Mycobacterium aichiense. These data support the conclusion that the isolates represent a new mycobacterial species, for which the name Mycobacterium tusciae sp. nov. is proposed. The type strain is strain FI-25796T; a culture of this strain has been deposited in the DSMZ as strain DSM 44338T.

Mycobacterium bohemicum sp. nov., a new slow-growing scotochromogenic mycobacterium

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.

16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene

Direct sequencing of the 16S rRNA gene (16S rDNA) of Mycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

Pulmonary infection due to Mycobacterium szulgai, case report and review of the literature

We describe the case of a patient with a chronic pulmonary infection due to a mycobacterium tentatively identified as Mycobacterium flavescens, but finally shown to be Mycobacterium szulgai; this is the first M. szulgai infection reported in Italy. The patient responded to treatment with multiple antituberculosis drugs only after two cycles of 10 and 6 months, respectively. The literature concerning previous case reports in which M. szulgai is involved is revised and the difficulty concerning the identification of this rare mycobacterium, along with its in vitro and in vivo susceptibility, are discussed.

Characterization of an isolate belonging to the newly described species Mycobacterium hassiacum

The isolation, from a urine sample, of a rapidly growing acid-fast mycobacterium assigned to the thermophilic species Mycobacterium hassiacum led to further insight into present knowledge of this newly described organism. Already known phenotypic traits of M. hassiacum were extended and its susceptibility to additional antimicrobials was investigated. The high-performance liquid chromatography pattern of mycolic acids is, for the first time, presented. So far, no clinical relevance was proved for our isolate; likewise for the one which led to the species' original description.

Evaluation of the MB/BacT system and comparison to the BACTEC 460 system and solid media for isolation of mycobacteria from clinical specimens

The MB/BacT automated system is designed for the isolation of mycobacteria from clinical specimens. It utilizes a colorimetric sensor and reflected light to continuously monitor the CO2 concentration in the culture medium. We compared its performance to that of the BACTEC 12B media for the radiometric BACTEC 460 instrument and that of solid culture media. Respiratory specimens and urine samples were decontaminated with 4% NaOH. The vials of the two instruments were inoculated with 500 microl of sample and two solid egg-based media at 200 microl each. All vials were incubated at 37 degrees C for 6 weeks. A total of 1,078 specimens (633 respiratory specimens, 78 cerebrospinal fluid specimens, 177 other body fluid specimens, 87 urine specimens, and 103 other types of specimens) were cultured in parallel. Mycobacteria could be identified from 73 (6.8%) specimens: 67 M. tuberculosis, 3 M. kansasii, 1 M. xenopi, 1 M. terrae, and 1 mixed M. avium with M. scrofulaceum. Of these, 63 (86.3%) specimens were positive with the MB/BacT system, 67 (91.8%) were positive with the BACTEC 460 instrument, and 58 (79.5%) were positive with the two egg-based media. MB/BacT cultures were positive on average after 17.5 (+/-6.4) days, BACTEC cultures with a growth index of >20 (mean, 200) were positive after 14.3 (+/-8.2) days, and egg-based media were positive after 24.2 (+/-7.5) days. Microorganisms other than mycobacteria contaminated 46 (4.3%) MB/BacT cultures and 31 (2.9%) BACTEC cultures, which had to be discarded. The MB/BacT system is a well-automated system for the detection of M. tuberculosis in clinical specimens without using radioactive reagents. Further trials are required to determine whether it is suitable for the culture of nontuberculous mycobacteria.

Two different 16S rRNA genes in a mycobacterial strain

Sequencing of the gene coding for 16S rRNA (16S rDNA) is a well-established method used to identify bacteria, particularly mycobacteria. Unique sequences allow identification of a particular genus and species. If more than one 16S rDNA is present on one mycobacterial genome, their sequences are assumed to be strictly or almost identical. We have isolated a slowly growing Mycobacterium strain, "X", identified by conventional biochemical tests as Mycobacterium terrae. Identification by amplification and direct sequencing of 16S rDNA yielded ambiguous results in two variable regions, suggesting the presence of different copies of the sequenced gene. Total DNA was digested by restriction enzymes and hybridized after Southern blotting to a probe representing about two-thirds of the 16S rDNA. Two copies of 16S rDNA were identified and cloned. By sequencing, the clones were of two different types, A and B, differing in 18 positions. Oligonucleotides specific to each copy of the 16S rDNA were used to distinguish the positions of the two genes observed in the Southern blot. We conclude that Mycobacterium strain "X" has two different copies of 16S rDNA. Variations in the sequence between two copies of 16S rDNA gene have been described in archaeobacteria, but not in mycobacteria. When placed in a phylogenetic tree together with other slowly growing mycobacteria gene A shows a common root with M. terrae, whereas gene B is placed separately.

[Disseminated infection with Mycobacterium celatum]

A 29-year-old patient with AIDS was hospitalized with weight loss, fever and cough. Mycobacterial cultures from sputum, blood and bronchoalveolar lavage became positive after 3 weeks' incubation. When using a DNA probe for identification of Mycobacterium tuberculosis complex, a weakly positive signal was obtained. Tuberculosis was suspected and treatment was started with isoniazid, ethambutol and ciprofloxacin. Sequencing of the gene of the 16S rRNA, however, identified the isolates as belonging to a new, slow-growing atypical mycobacterial species, Mycobacterium celatum (M. celatum). Treatment was modified to take into account the previously described primary resistance of M. celatum to antituberculous drugs, whereupon the patient improved.

Isolation and characterization of a unique group of slowly growing mycobacteria: description of Mycobacterium lentiflavum sp. nov

A distinct group of slowly growing mycobacteria was identified on the basis of growth characteristics, biochemical and lipid profiles, and nucleic acid analyses. The isolates showed growth at 22 to 37 degrees C, yellow pigmentation, and negative tests for Tween 80 hydrolysis, nicotinic acid, nitrate reductase, and urease; tests for arylsulfatase, pyrazinamidase, and heat-stable catalase were variable. Analysis of cellular fatty acids by gas-liquid chromatography and mycolic acids by thin-layer chromatography and high-performance liquid chromatography indicated a distinctive pattern which was unlike those of other species. Determination of the 16S rRNA gene sequence showed a unique sequence closely related to Mycobacterium simiae and M. genavense. On the basis of DNA homology studies, we suggest that these organisms are representatives of a novel species, for which the name M. lentiflavum sp. nov. is proposed.

Growth-deficient mycobacteria in patients with AIDS: diagnosis by analysis of DNA amplified from blood or tissue

Amplification and sequencing of mycobacterial ribosomal RNA genes (16S rDNA) may permit the detection of growth-deficient species (i.e., those exhibiting no growth or those whose growth is delayed for more than 12 weeks). Of blood samples from 26 patients with AIDS and a liver sample from one additional AIDS patient, three samples (two of blood and the one of liver) were positive by polymerase chain reaction only; cultures of these three samples remained negative for more than 12 weeks. Analysis of amplified 16S rDNA from blood revealed a sequence characteristic of Mycobacterium genavense in the first case, in which one of many previous blood cultures had also been positive for M. genavense. The sequences found in the second and third cases were characteristic of Mycobacterium avium. The sample from the second patient was a liver biopsy specimen in which acid-fast bacilli were visualized; the culture of this specimen yielded M. avium after 7 months. The third sample was a blood sample from a patient in whom a relapse of treated M. avium infection was suspected. These results indicate that amplification and sequencing of mycobacterial 16S rDNA may permit early diagnosis and provide a rationale for treatment of infections due to growth-deficient mycobacteria.

Chronic destructive lung disease associated with a novel mycobacterium

A woman born in 1920 has suffered from a chronic destructive lung disease since 1972, with development of a severe combined restrictive and obstructive ventilatory defect. Large quantities of acid-fast microorganisms have been repeatedly observed in her sputum. Multiple courses of antimycobacterial treatment did not stop the progression of the disease. The mycobacterium involved was first identified as Mycobacterium gordonae, and later as Mycobacterium scrofulaceum. Analysis of part of the amplified gene of the 16S rRNA, however, revealed that its sequence differed from that of any established mycobacterial species, although it was observed once before in a German lymph node isolate, for which the name "Mycobacterium interjectum" has been proposed. Retrospective analysis confirmed the presence of this sequence in frozen samples which had been provided by the patient in 1983, 1985, 1989, 1990, and 1993. Our case confirms the value of amplification and sequencing of mycobacterial 16S rRNA for classifying mycobacteria, and suggests that "Mycobacterium interjectum" may be involved in cases of chronic destructive lung disease.

Disseminated Mycobacterium genavense infection in two patients with AIDS

Mycobacterium genavense is a recently defined fastidious organism that has been identified as a cause of disseminated infection in patients with AIDS. We report the cases of two patients who had advanced AIDS and a clinical syndrome of fever, anorexia, abdominal pain, diarrhea, and weight loss. In addition, splenomegaly and lymphadenopathy were prominent in both cases, and in one patient's case radiographic findings were suggestive of splenic abscesses. Mycobacteria isolated from specimens of blood and bone marrow grew in liquid media but not on solid media. The results of DNA probe tests for Mycobacterium tuberculosis and Mycobacterium avium complex were false-positive for both patients. After treatment of the broth cultures to lyse red blood cells, the results of DNA probe tests were negative for these pathogens. Amplification and sequencing of 16S rRNA with use of the polymerase chain reaction indicated that the mycobacterial isolates from both patients had sequences identical to those previously reported for M. genavense. One patient survived 5 months after diagnosis, the other 2 months after diagnosis; only one patient responded (transiently) to antimycobacterial chemotherapy.

Infection of human fibroblasts and osteoblast-like cells with HIV-1

Primary human skin- and lung-derived fibroblast cell cultures and continuous human osteoblast-like and fibroblast-like cell lines were infected with different strains of HIV-1. Infection was measured at the single-cell level using the immunoperoxidase staining method to detect viral proteins. No cytopathic effects were observed in HIV-1-infected cell cultures. One continuous cell line (LC5), derived from embryonic lung, was readily infectable with HIV-1 and showed continuous production of infectious virus. Infection of LC5 cells could be blocked with anti-CD4 monoclonal antibodies. These findings indicate that fibroblasts of skin and lung, and osteogenic cells may be considered as potential target cells for HIV-1, thereby possibly contributing to the establishment of local HIV reservoirs.