Analysis of
            <i>secA1</i>
            Gene Sequences for Identification of
            <i>Nocardia</i>
            Species

Conville, Patricia S.; Zelazny, Adrian M.; Witebsky, Frank G.

doi:10.1128/jcm.00155-06

Cited by 90 publications

(80 citation statements)

References 12 publications

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“…Our results further support the general notion of the use of more than one genetic locus for species determination (5,12,24). Indeed, the incorporation of probes targeted at the 16S-23S rRNA gene spacer region into the RLB assay as an additional, although smaller, set of probes allowed the 14 test Nocardia species to be identified with an increased sensitivity (99.2%) and high specificity (99%).…”

Section: Discussionsupporting

confidence: 84%

“…Sequence polymorphisms within the Nocardia 65-kDa heat shock protein (hsp65) and essential secretary protein A (SecA1) gene (secA1) targets were also reported to enable the identification of isolates to the species level (12,24,28). The introduction of these identification methods has predictably led to substantial species reassignment and the reporting of new species within the genus, especially among "Nocardia asteroides" isolates: over 80 species have now been described, ϳ33 of which have been implicated in human disease (http://www.ncbi.nlm.nih.gov).…”

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confidence: 99%

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Identification of Pathogenic Nocardia Species by Reverse Line Blot Hybridization Targeting the 16S rRNA and 16S-23S rRNA Gene Spacer Regions

et al. 2010

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Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 speciesspecific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n ‫؍‬ 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacerdirected probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.

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Section: Discussionsupporting

confidence: 84%

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confidence: 99%

Identification of Pathogenic Nocardia Species by Reverse Line Blot Hybridization Targeting the 16S rRNA and 16S-23S rRNA Gene Spacer Regions

et al. 2010

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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: 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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“…Comparison of a 465-bp region of the secA1 gene showed the two organisms to have 99.1% sequence similarity (four base differences); a similarity of Ͼ99.0% with this gene has been shown to indicate species identity (10). The deduced amino acid sequence of the SecA1 protein of N. asteroides drug pattern type VI was identical to that of N. cyriacigeorgica.…”

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confidence: 88%

“…DNA was extracted for amplification and gene sequencing, as previously described (8). Sequencing of the 16S rRNA gene, the HSP gene, and the secA1 gene was performed as previously described (7,8,10). The deduced amino acid sequences of the HSP and secA1 genes for both isolates were determined with Megalign software (DNA Star, Inc., Madison, WI).…”

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confidence: 99%