Phylogenetic Studies of Gordonia Species Based on gyrB and secA1 Gene Analyses

Kang, Yingqian; Takeda, Kenjiro; Yazawa, Kazunaga; Mikami, Yuzuru

doi:10.1007/s11046-008-9151-y

Cited by 33 publications

(30 citation statements)

References 22 publications

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“…and Streptococcus pneumoniae (6) for evaluation. Bacterial DNA extraction, PCR amplification, and DNA sequencing of the 16S rRNA and secA1 genes were performed according to our previous publication (7), except for the primer pairs used (G268F/G1096R [8] for the 16S rRNA gene and SecA1-f/SecA1-r [9] for the secA1 gene). Comparative sequence identity analysis and phylogenetic analysis using the maximum likelihood method were performed according to our previous publication (10), except that MEGA 6.06 (11) was used instead.…”

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confidence: 99%

Gordonia Species as Emerging Causes of Continuous-Ambulatory-Peritoneal-Dialysis-Related Peritonitis Identified by 16S rRNA and secA1 Gene Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

Lam

Leung³

et al. 2015

J Clin Microbiol

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We report here four cases of continuous ambulatory peritoneal dialysis-related peritonitis caused by three different species of Gordonia. The portal of entry was likely through Tenckhoff catheters. 16S rRNA and secA1 gene sequencing are so far the most reliable methods for the accurate identification of Gordonia species. Gordonia species are Gram-positive weakly acid-fast coryneform bacteria. Although Gordonia species have been implicated in a variety of infections, only seven cases of continuous ambulatory peritoneal dialysis (CAPD)-related peritonitis caused by Gordonia species have been described (1-4). Furthermore, the methods used for identifying these seven Gordonia isolates were not mentioned in five cases (2, 4), and the accuracy of the identifications could not be ascertained. In this article, we described four cases of CAPD-related peritonitis caused by three different species of Gordonia confirmed by 16S rRNA and secA1 gene sequencing.Clinical specimens were collected and handled according to standard protocols, and the clinical data were collected by analyzing the patients' hospital records. Phenotypic identification was performed using standard conventional biochemical methods and the API Coryne system (bioMérieux, France). All tests were performed in triplicate. The MICs were determined using Etests (bioMérieux), according to the standards of the Clinical and Laboratory Standards Institute (CLSI) (5), with Escherichia coli strain ATCC 25922 and Pseudomonas aeruginosa strain ATCC 27853 as controls; the results were compared with the CLSI MIC interpretive standards for Staphylococcus spp. and Streptococcus pneumoniae (6) for evaluation. Bacterial DNA extraction, PCR amplification, and DNA sequencing of the 16S rRNA and secA1 genes were performed according to our previous publication (7), except for the primer pairs used (G268F/G1096R [8] for the 16S rRNA gene and SecA1-f/SecA1-r [9] for the secA1 gene). Comparative sequence identity analysis and phylogenetic analysis using the maximum likelihood method were performed according to our previous publication (10), except that MEGA 6.06 (11) was used instead. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was performed according to our previous publication (12), and the protein profiles obtained were processed and analyzed using MALDI Biotyper 3.1 (Bruker Daltonics, Germany) for the generation of the hierarchical cluster analysis (HCA) dendrogram and for identification. Case 1. A 65-year-old Chinese man was admitted for cloudy dialysis effluent for 1 day. He had end-stage renal failure (ESRF) of unknown etiology and had been undergoing CAPD for 7 years. He was afebrile but had turbid dialysis effluent. The total leukocyte count of the dialysis fluid was 930/mm 3 , with neutrophil predominance. A Gram smear of the dialysis effluent after centrifugation revealed numerous leukocytes without any organisms. Empirical intraperitoneal (i.p.) cefazolin and gentamicin therapies were started. As the clinical condition of...

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confidence: 99%

Gordonia Species as Emerging Causes of Continuous-Ambulatory-Peritoneal-Dialysis-Related Peritonitis Identified by 16S rRNA and secA1 Gene Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

Lam

Leung³

et al. 2015

J Clin Microbiol

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“…Due to acid-fast nature of the organism, infections caused by this genus can lead to easy confusion with Mycobacterium spp., without 16S rRNA gene sequencing to differentiate them. Sequencing of gyrB and secA1 genes can be of additional help to discriminate between the species because the rate of molecular evolution of these genes is reportedly greater than that of 16S rRNA [1,6].…”

Section: Discussionmentioning

confidence: 99%

“…The isolate was positive for AFB stain and negative for MPT64 antigen. Additionally, the isolate was identified as To resolve the discrepancy between the results of the above-mentioned assays targeting ITS and 16S rRNA genes, the isolate was analyzed by additional sequencing of gyrB and secA1 genes according to a previous study with modifications [1]. PCR amplification of gyrB was performed with degenerate Phylogenetic trees for 16S rRNA, gyrB and secA1 genes ( Fig.…”

Section: Case Reportmentioning

confidence: 99%

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A Case of ChronicGordonia otitidisLung Infection Initially Regarded as Nontuberculous Mycobacterial Lung Disease

Kim

et al. 2017

Ann Clin Microbiol

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The genus Gordonia is one of the mycolic acid-containing aerobic actinomycetes. This genus has 38 named species that are widespread in the natural environment; however, Gordonia species rarely cause human infections. A 76-year-old woman presented with cough and sputum for over 1 year and was suspected of having nontuberculous mycobacterial (NTM) lung disease. An NTM isolate from the sputum was initially identified as Mycobacterium lentiflavum or Mycobacterium genavense by genotypic identification targeting internal transcribed spacer (ITS). However, the isolate was finally confirmed as Gordonia otitidis by sequencing of 16S rRNA, gyrB and secA1 genes.In patients with suspected NTM lung disease, the etiologic agent might be an organism other than NTM such as G. otitidis but still be identified as NTM without sequencing of 16S rRNA or other genes. Especially in case that a possible NTM isolate is identified as M. lentiflavum or M. genavense by the genotypic method targeting ITS, additional genotypic tests such as sequencing of 16S rRNA and other genes would be necessary for more reliable identification. (Ann Clin Microbiol 2017;20:13-16)

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“…Gene polymorphisms within alternate molecular targets, including gyrB and the 16S-23S rRNA ITS region (13,(22)(23)(24), have also been reported to improve species identification, yet the selection of the gene target as an adjunct to, or even a substitute for, 16S rRNA gene sequencing for the identification of Nocardia spp. requires careful consideration.…”

Section: Discussionmentioning

confidence: 99%

secA1 Gene Sequence Polymorphisms for Species Identification of Nocardia Species and Recognition of Intraspecies Genetic Diversity

et al. 2010

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Sequence analysis of the Nocardia essential secretory protein SecA1 gene (secA1) for species identification of 120 American Type Culture Collection (ATCC) and clinical isolates of Nocardia (16 species) was studied in comparison with 5-end 606-bp 16S rRNA gene sequencing. Species determination by both methods was concordant for all 10 ATCC strains. secA1 gene sequencing provided the same species identification as 16S rRNA gene analysis for 94/110 (85.5%) clinical isolates. However, 40 (42.6%) isolates had sequences with <99.0% similarity to archived secA1 sequences for the species, including 29 Nocardia cyriacigeorgica (96.6 to 98.9% similarity) and 4 Nocardia veterana (91.5 to 98.9% similarity) strains. Discrepant species identification was obtained for 16 (14.5%) clinical isolates, including 13/23 Nocardia nova strains (identified as various Nocardia species by secA1 sequencing) and 1 isolate each of Nocardia abscessus (identified as Nocardia asiatica), Nocardia elegans (Nocardia africana), and Nocardia transvalensis (Nocardia blacklockiae); both secA1 gene sequence analysis and deduced amino acid sequence analysis determined the species to be different from those assigned by 16S rRNA gene sequencing. The secA1 locus showed high sequence diversity (66 sequence or genetic types versus 40 16S rRNA gene sequence types), which was highest for N. nova (14 secA1 sequence types), followed by Nocardia farcinica and N. veterana (n ‫؍‬ 7 each); there was only a single sequence type among eight Nocardia paucivorans strains. The secA1 locus has potential for species identification as an adjunct to 16S rRNA gene sequencing but requires additional deduced amino acid sequence analysis. It may be a suitable marker for phylogenetic/subtyping studies.Nocardia spp. are Gram-positive saprophytic bacteria capable of causing suppurative infections, including pulmonary, cutaneous, central nervous system, and disseminated diseases. To date, approximately 90 species have been described (NCBI taxonomy for Nocardia [http://www.ncbi.nlm.nih.gov/Taxonomy /

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Phylogenetic Studies of Gordonia Species Based on gyrB and secA1 Gene Analyses

Cited by 33 publications

References 22 publications

Gordonia Species as Emerging Causes of Continuous-Ambulatory-Peritoneal-Dialysis-Related Peritonitis Identified by 16S rRNA and secA1 Gene Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

Gordonia Species as Emerging Causes of Continuous-Ambulatory-Peritoneal-Dialysis-Related Peritonitis Identified by 16S rRNA and secA1 Gene Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

A Case of ChronicGordonia otitidisLung Infection Initially Regarded as Nontuberculous Mycobacterial Lung Disease

secA1 Gene Sequence Polymorphisms for Species Identification of Nocardia Species and Recognition of Intraspecies Genetic Diversity

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