Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12-08

AUTHORS

Simon Thierry, Dongying Wang, Pascal Arné, Manjula Deville, Barbara De Bruin, Adélaïde Nieguitsila, Christine Pourcel, Karine Laroucau, René Chermette, Weiyi Huang, Françoise Botterel, Jacques Guillot

ABSTRACT

BackgroundMultiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus.ResultsWe selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France.ConclusionsMLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts. More... »

PAGES

315

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2180-10-315

DOI

http://dx.doi.org/10.1186/1471-2180-10-315

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1040868566

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21143842


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23 schema:description BackgroundMultiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus.ResultsWe selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France.ConclusionsMLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts.
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31 Aspergillus fumigatus
32 China
33 Chlamydophila psittaci
34 France
35 Guangxi Province
36 MLVA
37 MST analysis
38 Province
39 ResultsWe
40 Simpson index
41 VNTR markers
42 algorithm
43 analysis
44 avian isolates
45 birds
46 chromosomes
47 clear separation
48 clustering
49 clusters
50 database
51 different chromosomes
52 different epidemiological situations
53 different hosts
54 discriminatory power
55 disease outbreaks
56 duck farms
57 environment
58 environmental isolates
59 epidemiological situation
60 excellent discriminatory power
61 farms
62 filamentous fungus Aspergillus fumigatus
63 first cluster
64 fumigatus
65 fungus Aspergillus fumigatus
66 genetic patterns
67 geographic origin
68 good reproducibility
69 hatchery
70 host
71 index
72 individual markers
73 information
74 interesting clustering
75 isolates
76 major clusters
77 markers
78 method
79 microbial isolates
80 minimum spanning tree
81 molecular typing
82 multiple-locus variable-number tandem repeat analysis
83 one
84 origin
85 outbreak
86 panel
87 pathogens
88 pathogens of birds
89 patterns
90 poultry farms
91 power
92 present study
93 psittaci
94 repeat analysis
95 reproducibility
96 respective hosts
97 results
98 second cluster
99 second step
100 separation
101 similar methods
102 situation
103 spanning tree
104 step
105 study
106 subtyping methods
107 tandem repeat analysis
108 third one
109 trees
110 turkey hatchery
111 typing
112 unrelated isolates
113 usefulness
114 variable-number tandem repeat analysis
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