Identification of
            <i>Mycobacterium</i>
            Species by
            <i>secA1</i>
            Sequences

Zelazny, Adrian M.; Calhoun, Leslie B.; Li, Li; Shea, Yvonne R.; Fischer, Steven H.

doi:10.1128/jcm.43.3.1051-1058.2005

Cited by 69 publications

(46 citation statements)

References 38 publications

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“…However, in this case, the gene was not shown to be discriminative enough for the identification of Tsukamurella spp., since the differences in the genes are minimal among the different species of the genus (Table 1) (9,10). In contrast, an analysis of a region of the secA1 gene was shown to be suitable for discrimination among four important clinical species of Tsukamurella, as it has been demonstrated for other clinically significant species of aerobic actinomycetes (12,13).…”

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confidence: 96%

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 Bloodstream Infection Identified by secA1 Gene Sequencing

et al. 2015

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“…It has recently been shown that sufficient variability exists in the sequence of the secA1 gene of mycobacteria to allow discrimination of 29 species (13). We describe here a novel method of distinguishing 29 species or taxa of Nocardia, using sequence analysis of both a portion of the secA1 gene and the deduced amino acid sequence.…”

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confidence: 99%

Analysis of secA1 Gene Sequences for Identification of Nocardia Species

2006

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Molecular methodologies, especially 16S rRNA gene sequence analysis, have allowed the recognition of many new species of Nocardia and to date have been the most precise methods for identifying isolates reliably to the species level. We describe here a novel method for identifying Nocardia isolates by using sequence analysis of a portion of the secA1 gene. A region of the secA1 gene of 30 type or reference strains of Nocardia species was amplified using secA1-specific primers. Sequence analysis of 468 bp allowed clear differentiation of all species, with a range of interspecies similarity of 85.0% to 98.7%. Corresponding 16S rRNA gene sequences of a 1,285-bp region for the same isolates showed a range of interspecies similarity of 94.4 to 99.8%. In addition to the type and reference strains, a 468-bp fragment of the secA1 gene was sequenced from 40 clinical isolates of 12 Nocardia species previously identified by 16S rRNA gene sequence analysis. The secA1 gene sequences of most isolates showed >99.0% similarity to the secA1 sequences of the type or reference strain to which their identification corresponded, with a range of 95.3 to 100%. Comparison of the deduced 156 amino acid sequences of the SecA1 proteins of the clinical isolates showed between zero and two amino acid residue differences compared to that of the corresponding type or reference strain. Sequencing of the secA1 gene, and using deduced amino acid sequences of the SecA1 protein, may provide a more discriminative and precise method for the identification of Nocardia isolates than 16S rRNA gene sequencing.

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“…Sequence analyses of the hsp65 gene (6), recA (7), SecA1 (8), DNA gyrase (9), internal transcribed spacer of the 16S-23S rRNA (10), and rpoB (11) have been attempted. Of these, analysis of the rpoB gene has been strongly recommended as a supplementary or alternative method to 16S rRNA gene analysis of mycobacteria (11)(12)(13).…”

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confidence: 99%