Tsukamurella pulmonis sp. nov.

Yassin, A. F.; Rainey, Fred A.; Brzezinka, H.; Burghardt, Jutta; Rifa’i, Muhaimin; Seifert, Paul S.; Feldmann, Knut; Schaal, K. P.

doi:10.1099/00207713-46-2-429

Cited by 66 publications

(60 citation statements)

References 14 publications

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“…It has been demonstrated previously that high levels of 16S rRNA gene sequence similarity between strains belonging to the same genus do not necessarily indicate membership of the same species (Yassin et al, 1995(Yassin et al, , 1996. Here again, it is clear that high 16S rRNA gene sequence similarities can be found between strains that have low DNA-DNA reassociation values, since strain IMMIB R-1434 T shares 98n6 % gene sequence similarity but only 19n8 % reassociation with Nocardia salmonicida.…”

Section: Utilization As Sole Sources Of Carbon and Nitrogen Ofsupporting

confidence: 48%

“…DNA-DNA hybridization studies were carried out by using the thermal renaturation method (Yassin et al, 1993b). Genomic DNA extraction, PCR-mediated amplification of the 16S rDNA and purification of PCR products were carried out using procedures described previously (Rainey et al, 1996). Purified PCR products were sequenced using a Taq DyeDeoxy Terminator cycle sequencing kit (Applied Biosystems) as described in the manufacturer's protocol.…”

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confidence: 99%

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Nocardia ignorata sp. nov.

Yassin¹,

Rainey²,

Steiner³

2001

International Journal of Systematic and Evolutionary Microbiology

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An isolate that was received during a mycobacterial quality control test and which was thought to be a Mycobacterium species was subjected to a polyphasic taxonomic study after mycolic acid analysis showed that it possessed mycolates characteristic of the nocardiae. Further chemotaxonomic and 16S rRNA gene sequence analyses of this isolate demonstrated that it belongs to the genus Nocardia. 16S rRNA gene sequence data, DNA-DNA hybridization studies and the biochemical characteristics of the isolate indicate that it belongs to a novel species that differs from previously described members of the genus Nocardia. The name Nocardia ignorata sp. nov. is proposed for this isolate with the type strain IMMIB R-1434 T (l DSM 44496 T l NRRL B-24141 T ).Keywords : Nocardia salmonicida, mycobacterial quality control tests, chemotaxonomy, DNA-DNA hybridization, 16S rRNA gene sequence Data quality is a central requirement of scientific research and external monitoring is essential in multicentric clinical trials. Performance of quality control in the clinical microbiological laboratory includes a wide variety of specimens that are issued. These include specimens for general bacteriology, including isolation, sensitivity testing and serology ; mycobacterial bacteriology ; virus isolation ; general viral serology ; rubella serology, hepatitis B antigen detection ; electron microscopy ; mycology ; parasitology ; and public health specimens including milk and water. During a mycobacterial quality control test, the Microbiological Quality Control Laboratory (MQCL) dispatched, among other specimens, one that was evaluated at the MQCL as a species of Mycobacterium. However, after subjecting this specimen, labelled by us as strain IMMIB R-1434 T , to chemotaxonomic as well as molecular taxonomic methods in our laboratory, it became clear that it belongs to the genus Nocardia. This case raises questions about the authenticity of some of the test specimens that are used in quality control assurance programmes. It also underlines the requirement of the MQCL for reference strains that should be identified directly by reliable taxonomic methods at the MQCL before being dispatched to participants. Chemotaxonomic and molecular systematic data promoted a radical reappraisal of the genus Nocardia (Goodfellow, 1997 ;Goodfellow et al., 1999 ;Lechevalier, 1976). The improved classification provides a sound framework for the recognition of additional species. The genus now encompasses more than 27 validly described species that form a distinct phylogenetic line within the evolutionary radiation occupied by the mycolic acid-containing actinomycetes (Chun & Goodfellow, 1995 ;Rainey et al., 1995 ;Ruimy et al., 1994). On the basis of phylogenetic and phenotypic evidence, it is proposed that strain IMMIB R-1434 T be classified as Nocardia ignorata sp. nov.Strain IMMIB R-1434 T was cultured on brain-heart infusion agar to determine its morphological properties. The strain was characterized biochemically by using tests to determine hydrolysis of complex...

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Section: Utilization As Sole Sources Of Carbon and Nitrogen Ofsupporting

confidence: 48%

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confidence: 99%

Nocardia ignorata sp. nov.

Yassin¹,

Rainey²,

Steiner³

2001

International Journal of Systematic and Evolutionary Microbiology

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“…However, within the chosen 10 MRM pairs (Table 1) the lowest number of carbon atoms in the analyzed mycolic acid moiety is 78. The only one environmental isolate without any clinical significance, described as T. carboxydivorans poses a similar range of the total carbon atoms ), but overlapped range of the total carbon atoms do not have to lead to the cross-signal as Tsukamurella genus is also characterized by highly unsaturated (up to 8 double bonds) meromycolic chain without any functional groups (Yassin et al 1996). In the case of Mycobacterium there are three potential locations where double bonds could appear in alpha mycolic acids and also three places where functional groups could appear in keto-or metoxymycolic acids.…”

Section: Discussionmentioning

confidence: 99%

Rapid method for Mycobacterium tuberculosis identification using electrospray ionization tandem mass spectrometry analysis of mycolic acids

Szewczyk

Kowalski

Janiszewska-Drobińska³

et al. 2013

Diagnostic Microbiology and Infectious Disease

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Mycolic acids, which play a crucial role in the architecture of mycobacterial cell walls, were analyzed using electrospray ionization tandem mass spectrometry (ESI-MS/MS). A targeted analysis based on the 10 most abundant and characteristic multiple reaction monitoring (MRM) pairs was used to profile the crude fatty acid mixtures from Mtb and several nontuberculous mycobacterial strains. Comparative analysis yielded unique profiles for mycolic acids, enabling the reliable identification of mycobacterial species. In a case-control study of TB and non-TB Polish patients, we demonstrated the potential diagnostic utility of our approach for the rapid diagnosis of active TB with sensitivity and specificity surpassing those of existing methods. This robust method allows the identification of TB-positive patients after 2 h of sample preparation in the case of direct sputum analysis or 10 days of culturing, both of which are followed by one minute of LC-MS/MS analysis.

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“…Yassin et al isolated and described the species of interest, T. pulmonis, in 1996 from the sputum of a 92-year-old woman with a history of lung tuberculosis (2).…”

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confidence: 99%

Tsukamurella pulmonis Bloodstream Infection Identified by secA1 Gene Sequencing

et al. 2015

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CASE REPORTA 3-year-old female was diagnosed with acute lymphoblastic leukemia (ALL), with intermediate risk (immunophenotype pre-B), when she was 23 months old. In order to start her chemotherapy, a central venous access device (subcutaneous port [SP]) was implanted in September 2009. The patient was treated with SHOP-05 (Spanish Pediatric Hematology Society-2005) protocols for high-risk ALL, and she was in complete remission after the induction phase and completed four consolidation and reinduction phases, as was mandatory. Near the end of the second year of maintenance, when she was receiving only oral mercaptopurine (50 mg/m 2 /daily) and intramuscular methotrexate (20 mg/m 2 / weekly), the patient had a fever peak 5 h after a blood collection from the SP. The patient was treated empirically with oral cefixime (8 mg/kg of body weight/daily) when the fever started because she had had a prior isolation documented as Klebsiella pneumoniae that was sensitive to cephalosporins, and since she was not neutropenic and had no other signs or symptoms of interest, outpatient management was tried first. We obtained one pediatric blood culture, which grew long, slightly curved, thin, nonbranching Gram-positive rods. Culture of blood samples after 48 h of incubation at 35°C Ϯ 2°C in 5% CO 2 on chocolate and blood agar showed small, rough, whitish colonies which did not produce aerial mycelium. The biochemical profile of the isolate obtained with the API Coryne identification system (bioMérieux, Marcy l'Etoile, France) after 48 h of incubation (2150004) corresponded to Rhodococcus spp. at a confidence level of 82.9%. By sequencing the 16S rRNA gene with the universal primers PA (5=-AGAGTTTGATCC TGGCTCAG-3=) and PLO6R (5=-GCGCTCGTTGCGGGACTTA ACC-3=) and the internal primer UP1R (5=-TTACCGCGGCTGC TGGCAC-3=), we obtained a sequence of 1,025 nucleotides that revealed maximal identity with Tsukamurella pulmonis (GenBank accession number AB564289). However, the 16S rRNA gene sequences of different Tsukamurella spp. were shown to be quite similar (99%).Two weeks later, due to the persistence of intermittent fever in spite of cefixime therapy and two subsequent blood culture sets again positive for the same bacterium (T. pulmonis), the patient was admitted to the hospital. Antibiotic susceptibility was determined after 48 to 72 h of incubation at 35°C Ϯ 2°C in ambient air by gradient diffusion (Etest; bioMérieux, Marcy l'Etoile, France) using Mueller-Hinton agar plates. Interpretations were based on CLSI breakpoints for mycobacteria, nocardiae, and other aerobic actinomycetes but not breakpoints for meropenem (MIC Ͼ 32 g/ml) and vancomycin (MIC, 2 g/ml) because they were not assessed in this document. The isolate was susceptible to amikacin (MIC, 1 g/ml), tobramycin (MIC, 4 g/ml), ciprofloxacin (MIC, 0.25 g/ml), clarithromycin (MIC, 0.125 g/ml), and linezolid (MIC, 1 g/ml) and resistant to amoxicillin-clavulanic acid (MIC Ͼ 256 g/ml) and ceftriaxone (MIC Ͼ 32 g/ml).For 3 days, she received ertapenem intravenously (15 mg/kg/12 h), ...

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Tsukamurella pulmonis sp. nov.

Cited by 66 publications

References 14 publications

Nocardia ignorata sp. nov.

Nocardia ignorata sp. nov.

Rapid method for Mycobacterium tuberculosis identification using electrospray ionization tandem mass spectrometry analysis of mycolic acids

Tsukamurella pulmonis Bloodstream Infection Identified by secA1 Gene Sequencing

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