Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-02-09

AUTHORS

Philippe Le Flèche, Isabelle Jacques, Maggy Grayon, Sascha Al Dahouk, Patrick Bouchon, France Denoeud, Karsten Nöckler, Heinrich Neubauer, Laurence A Guilloteau, Gilles Vergnaud

ABSTRACT

BACKGROUND: The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification. RESULTS: Eighty tandem repeat loci predicted to be polymorphic by genome sequence analysis of three available Brucella genome sequences were tested for polymorphism by genotyping 21 Brucella strains (18 reference strains representing the six 'classical' species and all biovars as well as 3 marine mammal strains currently recognized as members of two new species). The MLVA data efficiently cluster the strains as expected according to their species and biovar. For practical use, a subset of 15 loci preserving this clustering was selected and applied to the typing of 236 isolates. Using this MLVA-15 assay, the clusters generated correspond to the classical biotyping scheme of Brucella spp. The 15 markers have been divided into two groups, one comprising 8 user-friendly minisatellite markers with a good species identification capability (panel 1) and another complementary group of 7 microsatellite markers with higher discriminatory power (panel 2). CONCLUSION: The MLVA-15 assay can be applied to large collections of Brucella strains with automated or manual procedures, and can be proposed as a complement, or even a substitute, of classical biotyping methods. This is facilitated by the fact that MLVA is based on non-infectious material (DNA) whereas the biotyping procedure itself requires the manipulation of the living agent. The data produced can be queried on a dedicated MLVA web service site. More... »

PAGES

9-9

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2180-6-9

DOI

http://dx.doi.org/10.1186/1471-2180-6-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1009949728

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16469109


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32 Brucella MLVA
33 Brucella genome sequences
34 Brucella spp
35 DNA-based methods
36 MLVA data
37 MLVA web service site
38 MLVA-15 assay
39 absence
40 absence of standardization
41 addition
42 agents
43 analysis
44 assays
45 available Brucella genome sequences
46 biotyping
47 biotyping methods
48 biotyping procedure
49 biotyping scheme
50 biovars
51 capability
52 characteristics
53 classical biotyping methods
54 classical biotyping scheme
55 classification
56 classification of Brucella
57 clustering
58 clusters
59 collection
60 complement
61 complementary groups
62 data
63 dedicated MLVA web service site
64 difficulties
65 discriminatory power
66 efficient DNA-based methods
67 evaluation
68 fact
69 genome sequence
70 genome sequence analysis
71 good species identification capability
72 group
73 high discriminatory power
74 identification
75 identification capability
76 interpretation
77 isolates
78 large collection
79 loci
80 locus variable number tandem repeat analysis
81 manipulation
82 manual procedure
83 markers
84 materials
85 method
86 microsatellite markers
87 minisatellite markers
88 multiple-locus variable-number tandem repeat analysis
89 non-infectious materials
90 number tandem repeat analysis
91 phenotypic characteristics
92 polymorphism
93 power
94 practical use
95 procedure
96 reagents
97 relies
98 repeat analysis
99 repeat loci
100 resolution
101 results
102 scheme
103 selection
104 sequence
105 sequence analysis
106 service sites
107 sites
108 species
109 species identification
110 species identification capability
111 spp
112 standardization
113 strains
114 subset
115 substitute
116 suitability
117 tandem repeat analysis
118 tandem repeat loci
119 typing
120 typing reagents
121 use
122 user-friendly minisatellite markers
123 variable-number tandem repeat analysis
124 web service site
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