The
            <i>groEL</i>
            Gene Is a Promising Target for Species-Level Identification of Tsukamurella

Teng, Jade L. L.; Tang, Ying; Chiu, Tsz Ho; Cheung, Candy L. W.; Ngan, Antonio H. Y.; Cheung, Nicole W. T.; Wong, Samson S. Y.; Que, Tak Lun; Lau, Susanna K.P.; Woo, Patrick C. Y.

doi:10.1128/jcm.02260-16

Cited by 19 publications

(24 citation statements)

References 5 publications

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“…Teng et al. [53] used 16S rRNA, ssrA (small stable RNA), secA (secretory), rpoB and groEL for differentiation of Tsukamurella species; results indicated that only 16S rRNA and groEL were effective in indicating the exact species. Teng et al.…”

Section: Identification Methodsmentioning

confidence: 99%

“…According to the evidence of Teng et al. [8] , [53] , the 16S rRNA gene was unsuccessful in differentiating T. sinensis from some strains such as T. pulmonis and T. tyrosinosolven; furthermore, secA 1 failed to differentiate between Tsukamurella spumae and Tsukamurella pseudospumae. Two primers used for the hsp65 gene included TB11 (5′-ACCAACGATGGTGTGTCCAT-3′) and TB12 (5′-CTTGTCGAACCGCATACCCT-3′); the results indicated that T. spumae was the cause of an infection in that case report; for 16S rRNA gene sequencing, LPW27807 (5′-TGGCTCAGGACGAACGCT-3′) and LPW27808 (5′-GAGGTGATCCAGCCGCA-3′) were used [50] .…”

Section: Identification Methodsmentioning

confidence: 99%

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Role of Tsukamurella species in human infections: first literature review

Safaei¹,

Bafghi

Pouresmaeil

2018

New Microbes and New Infections

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Tsukamurella is an aerobic, Gram-positive and nonmotile bacterium. It was first isolated in 1941 from the mycetoma and ovaries of the bedbug. The primary strains were named Corynebacterium paurometabolum and Gordona aurantiaca and are different from the Collins et al., 1988 classification of the new Tsukamurella genus. Human infections with Tsukamurella species are rare because the species is a kind of saprophyte bacterium; however, most information regarding this species comes from case reports. Molecular markers for the identification Tsukamurella include sequencing of 16S rRNA, groEL, rpoB, secA1 and ssrA genes. Given the lack of information on the treatment of Tsukamurella infections, a combination of various antibiotic agents is recommended.

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Section: Identification Methodsmentioning

confidence: 99%

Section: Identification Methodsmentioning

confidence: 99%

Role of Tsukamurella species in human infections: first literature review

Safaei¹,

Bafghi

Pouresmaeil

2018

New Microbes and New Infections

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“…6 ), in particularly, the ribosomal proteins that are highly expressed [ 153 ] and enriched by the extraction protocols [ 154 ]. This feature is of phylogenetic importance: in a large-scale study published by researchers at the National Center for Biotechnology Information (NCBI), it was found that horizontal gene transfer (HGT) is rampant among the prokaryotes and even involved some of the traditional phylogenetic marker genes such as groEL [ [155] , [156] , [157] ], whereas no HGT event was found in the study for any of the ribosomal proteins [ 158 ]. If phylogenetic methods, such as maximum parsimony, maximum likelihood [ 159 , 160 ] or Bayesian methods [ 161 ] with appropriate priors can be applied to the analysis of MALDI-TOF ribosomal protein signatures, this widespread clinical method will hold promise to a new generation of low-cost, high-resolution microbial phylogeny – perhaps for the first time in microbiology, initiating not from reference laboratories or research centres, but rather from the network of service laboratories routinely using the MALDI-TOF MS technology and cumulating as novel proposals for bacterial and fungal classification and species discovery.…”

Section: Clinical Mass Spectrometrymentioning

confidence: 99%

Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker’s Guide

Chong

Leung

et al. 2018

Computational and Structural Biotechnology Journal

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Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.

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“…Among the various studied gene targets, the 16S ribosomal RNA (rRNA) gene has been the most widely used for bacterial identification and classification 32 , 33 . However, our previous study showed that this gene target cannot be confidently used for species identification of Tsukamurella as highly similar 16S rRNA gene sequence can be shared by different Tsukamurella species 34 . Sequencing of an alternative gene target, the groEL gene, was shown to be useful and accurate for identification of all existing Tsukamurella species 34 .…”

Section: Introductionmentioning

confidence: 98%

“…However, our previous study showed that this gene target cannot be confidently used for species identification of Tsukamurella as highly similar 16S rRNA gene sequence can be shared by different Tsukamurella species 34 . Sequencing of an alternative gene target, the groEL gene, was shown to be useful and accurate for identification of all existing Tsukamurella species 34 . Nevertheless, PCR sequencing is still considered expensive, time-consuming and technically demanding, and therefore is yet to be incorporated as a routine identification method in clinical microbiology laboratories.…”

Section: Introductionmentioning

confidence: 98%

MALDI-TOF MS for identification of Tsukamurella species: Tsukamurella tyrosinosolvens as the predominant species associated with ocular infections

Teng

Tang

Wong

et al. 2018

Emerging Microbes & Infections

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Although Tsukamurella infections have been increasingly reported in Europe, Asia, America, and Africa, indicating that diseases caused by this group of bacteria are emerging in a global scale, species identification within this genus is difficult in most clinical microbiology laboratories. Recently, we showed that groEL gene sequencing is useful for identification of all existing Tsukamurella species. Nevertheless, PCR sequencing is still considered expensive, time-consuming, and technically demanding, and therefore is yet to be incorporated as a routine identification method in clinical laboratories. Using groEL gene sequencing as the reference method, 60 Tsukamurella isolates were identified as five different Tsukamurella species [T. tyrosinosolvens (n = 31), T. pulmonis (n = 25), T. hongkongensis (n = 2), T. strandjordii (n = 1), and T. sinensis (n = 1)]. The most common source of the patient isolates were the eye (n = 18), sputum (n = 6), and blood (n = 6). None of the 60 isolates were identified correctly to species level by MALDI-TOF MS with the original Bruker database V.6.0.0.0. Using the Bruker database extended with 15 type and reference strains which covered all the currently recognized 11 Tsukamurella species, 59 of the 60 isolates were correctly identified to the species level with score ≥2.0. MALDI-TOF MS should be useful for routine species identification of Tsukamurella in clinical microbiology laboratories after optimization of the database. T. tyrosinosolvens was the most common species observed in patients with Tsukamurella infections and the predominant species associated with ocular infections.

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The groEL Gene Is a Promising Target for Species-Level Identification of Tsukamurella

Cited by 19 publications

References 5 publications

Role of Tsukamurella species in human infections: first literature review

Role of Tsukamurella species in human infections: first literature review

Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker’s Guide

MALDI-TOF MS for identification of Tsukamurella species: Tsukamurella tyrosinosolvens as the predominant species associated with ocular infections

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