Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for
 hsp65
 Gene-Based Identification of
 Nocardia
 Species

Rodríguez-Nava, Verónica; Couble, A.; Devulder, Grégory; Flandrois, Jean-Pierre; Boiron, P.; Laurent, François

doi:10.1128/jcm.44.2.536-546.2006

Cited by 148 publications

(128 citation statements)

References 34 publications

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“…Thus, the use of PRA can lead to erroneous species identification of both clinical and environmental Nocardia isolates [19]. In our study, the pattern obtained by PCR-RFLP were confirmed by nucleotide sequence analysis of this fragment, which showed 100% homology with sequences of Nocardia asteroides retrieved from GenBank (ATCC no.…”

Section: Resultssupporting

confidence: 76%

PCR-RFLP Methodology to Identify Nocardia Isolates in Cuba

Armas¹,

Fernández²,

Dı́az³

et al. 2015

AiM

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Nocardiosis diagnosis is a major challenge. The clinical features and radiological findings are nonspecific. Traditionally, Nocardia identification is based on colonial and microscopical morphology and biochemical tests. However, molecular biology techniques allow a better characterization of species and biotypes. PCR-RFLP of the 65-kDa heat shock protein (HSP) gene provides a rapid, sensitive, and time and labor-efficient method for this proposal. Using this technique, six of eight isolates tested were identified as Nocardia asteroides type VI. PCR-RFLP of the 65-kDa HSP gene could be very useful for determining the incidence of this pathogen in different population groups and its association with susceptibility/resistance profiles to the drugs of choice for treatment. This work is the first molecular detection of Nocardia species in Cuba.

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Section: Resultssupporting

confidence: 76%

PCR-RFLP Methodology to Identify Nocardia Isolates in Cuba

Armas¹,

Fernández²,

Dı́az³

et al. 2015

AiM

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“…Currently, 16S rRNA gene sequencing is considered a better method for identification of Nocardia to the species level (Borriello et al, 2007), although certain isolates that have been found to have a high sequence similarity (99.8 %) from 16S rRNA sequences are recorded as distinct species by DNA-DNA hybridization (Conville et al, 2004;Rodríguez-Nava et al, 2006). McTaggart et al (2010) applied multilocus sequence analysis to 190 clinical isolates of Nocardia spp.…”

Section: Discussionmentioning

confidence: 99%

“…As the hsp65 gene has more microheterogeneity regions compared with the 16S rRNA gene and is three to four times more discriminatory, this gene sequence has been targeted for Nocardia spp. identification (Rodríguez-Nava et al, 2006;Schlaberg et al, 2008;Yin et al, 2007). However, very few sequences of the hsp65 gene of Nocardia spp.…”

Section: Introductionmentioning

confidence: 99%

Molecular identification of clinical Nocardia isolates from India

Rudramurthy

Honnavar

Kaur

et al. 2015

Journal of Medical Microbiology

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The epidemiology of nocardiosis is evolving with increasing number of Nocardia spp. causing human infection. In recent years, molecular techniques have been used to identify Nocardia spp. There are limited data available on the spectrum of Nocardia spp. isolated from clinical samples in India. Here, a molecular study was carried on 30 clinical isolates maintained in our National Culture Collection to evaluate the techniques used for identifying the agents. The isolates were identified by sequencing two promising genes: the 16S rRNA gene and hsp65. Both hsp65 and the 16S rRNA gene could reliably identify 90 % of Nocardia isolates, i.e. N. farcinica, N. cyriacigeorgica, N. brasiliensis, N. otitidiscaviarum, N. amamiensis and N. pneumoniae. The mean percentage dissimilarity of sequence identification was higher using the hsp65 gene (4 %, range 0-7.9 %) compared with the 16S rRNA gene (2.3 %, range 0-8.9 %). Two isolates that showed ambiguous results in both the short segment of the 16S rRNA gene and hsp65 sequences could be resolved by sequencing a larger fragment (,1000 bp) of the 16S rRNA gene. Both of these isolates were identified as N. beijingensis with similarities of 99.8 and 100 % compared with the standard strain. Genotyping of N. cyriacigeorgica strains was performed using hsp65 gene sequences and compared with previously described genotypes. Our N. cyriacigeorgica isolates belonged to genotype 1 (n54) and genotype 2 (n52). The present study highlights a wide spectrum of Nocardia spp. in India and emphasizes the need for molecular techniques for identification to the species level.

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“…Restriction endonuclease analysis using portions of the 16S rRNA gene and the 65-kDa heat shock protein gene has been used in the past for the identification of commonly isolated Nocardia species (4,10). However, the usefulness of this procedure is becoming limited (8) due to the need to determine restriction fragment length polymorphisms (RFLPs) for the expanding number of described pathogenic species and the increasing number of restriction endonucleases required to make the species distinctions among these species. Therefore, sequence analysis of an alternative gene appears to be a viable adjunct to, or even a substitute for, 16S rRNA gene sequencing for the precise identification of Nocardia species.…”

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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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Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species

Cited by 148 publications

References 34 publications

PCR-RFLP Methodology to Identify <i>Nocardia</i> Isolates in Cuba

PCR-RFLP Methodology to Identify <i>Nocardia</i> Isolates in Cuba

Molecular identification of clinical Nocardia isolates from India

Analysis of secA1 Gene Sequences for Identification of Nocardia Species

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Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species

Cited by 148 publications

References 34 publications

PCR-RFLP Methodology to Identify &lt;i&gt;Nocardia&lt;/i&gt; Isolates in Cuba

PCR-RFLP Methodology to Identify &lt;i&gt;Nocardia&lt;/i&gt; Isolates in Cuba

Molecular identification of clinical Nocardia isolates from India

Analysis of secA1 Gene Sequences for Identification of Nocardia Species

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PCR-RFLP Methodology to Identify <i>Nocardia</i> Isolates in Cuba

PCR-RFLP Methodology to Identify <i>Nocardia</i> Isolates in Cuba