2. changing species names - amazon s3 · cbs - knaw fungal biodiversity centre - clinical and...
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CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
2. Changing species names
Sporotrichosis by Sporothrix
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Lymphocutaneous Disseminated
Fixed Anderson Rodrigues
Yu Zhang
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Sporotrichosis epidemics in Brazil
0
500
1000
1500
2000
2500
1996 1998 2000 2002 2004 2006 2008 2010
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Sporothrix brasiliensis: zoonotic transmission by fighting stray cats
LIZ600 EcoRI-AC + MseI-A
100908070605040302010
LIZ600 EcoRI-AC + MseI-A
CBS 125438
CBS 129719
CBS 132923
CBS 129718
CBS 129720
CBS 130116
CBS 129724
CBS 129721
CBS 129723
CBS 132925
CBS 129722
CBS 292.55
CBS 130117
CBS 120340
CBS 130105
CBS 132922
CBS 130115
CBS 130104
CBS 340.35
CBS 125601
CBS 129717
CBS 937.72
CBS 132966
CBS 132977
CBS 132975
CBS 132981
CBS 132979
CBS 132980
CBS 132961
CBS 132982
CBS 132968
CBS 132973
CBS 132964
CBS 132983
CBS 130097
CBS 130100
CBS 132969
CBS 130111
CBS 132926
CBS 130099
CBS 132976
CBS 130098
CBS 132962
CBS 132963
CBS 356.29
CBS 132974
CBS 132970
CBS 132971
CBS 132972
CBS 444.67
CBS 117842
CBS 117440
CBS 119145
CBS 130103
CBS 133002
CBS 133003
CBS 133001
CBS 133000
CBS 132999
CBS 132997
CBS 130114
CBS 130113
CBS 130101
CBS 130102
CBS 130112
CBS 133012
CBS 133010
CBS 133016
CBS 133017
CBS 120339
CBS 133013
CBS 133015
CBS 133014
CBS 130108
CBS 133005
CBS 130106
CBS 133008
CBS 133018
CBS 133007
CBS 133011
CBS 133006
CBS 133009
CBS 133022
CBS 130110
CBS 132990
CBS 132989
CBS 132995
CBS 132998
CBS 133019
CBS 132991
CBS 132996
CBS 132992
CBS 132993
CBS 130109
CBS 132994
CBS 133021
CBS 132988
CBS 132987
CBS 130107
CBS 132986
CBS 133020
CBS 129725
CBS 133004
CBS 132985
CBS 938.72
CBS 211.61
CBS 359.36
CBS 472.48
CBS 132984
CBS 345.53
CBS 132928
CBS 132927
CBS 132924
CBS 133192
CBS 120342
CBS 120341
CBS 115870
CBS 120256
CBS 118129
CBS 201.53
CBS 101428
Colombia
China
Brazil
China
China
Spain
China
China
China
Brazil
China
UK
Japan
Spain
Spain
Brazil
Spain
Spain
Japan
Colombia
China
South Africa
Brazil
Mexico
Brazil
Brazil
Peru
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Bolivia
Argentina
Brazil
Colombia
Brazil
Peru
Japan
Peru
Brazil
Brazil
Unknown
Brazil
Brazil
Brazil
Brazil
Mozambique
South Africa
South Africa
South Africa
Argentina
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Peru
Peru
Peru
Peru
Peru
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
China
Brazil
Brazil
France
South Africa
Unknown
Unknown
USA
Netherlands
Brazil
Brazil
Brazil
Italy
Mexico
Mexico
South Africa
South Africa
South Africa
South Africa
USA, Maryland
Sporothrix globosa
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. luriei
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix mexicana
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix mexicana
Sporothrix mexicana
Sporothrix globosa
Sporothrix brasiliensis
Sporothrix mexicana
Sporothrix mexicana
Sporothrix schenckii
Sporothrix humicola
Sporothrix humicola
Sporothrix schenckii var. schenckii
Sporothrix schenckii
S. globosa global
S. luriei
S. brasiliensis-A Brazil
S. schenckii-C Peru
S. brasiliensis-B Brazil
S. brasiliensis-C Brazil -1
S. schenckii-E global S. schenckii-D global
S. mexicana-A Brazil
S. schenckii-A South America -1
S. schenckii-B Africa -1
S. mexicana-B global
T
T
T
T
LIZ600 EcoRI-AC + MseI-A
100908070605040302010
LIZ600 EcoRI-AC + MseI-A
CBS 125438
CBS 129719
CBS 132923
CBS 129718
CBS 129720
CBS 130116
CBS 129724
CBS 129721
CBS 129723
CBS 132925
CBS 129722
CBS 292.55
CBS 130117
CBS 120340
CBS 130105
CBS 132922
CBS 130115
CBS 130104
CBS 340.35
CBS 125601
CBS 129717
CBS 937.72
CBS 132966
CBS 132977
CBS 132975
CBS 132981
CBS 132979
CBS 132980
CBS 132961
CBS 132982
CBS 132968
CBS 132973
CBS 132964
CBS 132983
CBS 130097
CBS 130100
CBS 132969
CBS 130111
CBS 132926
CBS 130099
CBS 132976
CBS 130098
CBS 132962
CBS 132963
CBS 356.29
CBS 132974
CBS 132970
CBS 132971
CBS 132972
CBS 444.67
CBS 117842
CBS 117440
CBS 119145
CBS 130103
CBS 133002
CBS 133003
CBS 133001
CBS 133000
CBS 132999
CBS 132997
CBS 130114
CBS 130113
CBS 130101
CBS 130102
CBS 130112
CBS 133012
CBS 133010
CBS 133016
CBS 133017
CBS 120339
CBS 133013
CBS 133015
CBS 133014
CBS 130108
CBS 133005
CBS 130106
CBS 133008
CBS 133018
CBS 133007
CBS 133011
CBS 133006
CBS 133009
CBS 133022
CBS 130110
CBS 132990
CBS 132989
CBS 132995
CBS 132998
CBS 133019
CBS 132991
CBS 132996
CBS 132992
CBS 132993
CBS 130109
CBS 132994
CBS 133021
CBS 132988
CBS 132987
CBS 130107
CBS 132986
CBS 133020
CBS 129725
CBS 133004
CBS 132985
CBS 938.72
CBS 211.61
CBS 359.36
CBS 472.48
CBS 132984
CBS 345.53
CBS 132928
CBS 132927
CBS 132924
CBS 133192
CBS 120342
CBS 120341
CBS 115870
CBS 120256
CBS 118129
CBS 201.53
CBS 101428
Colombia
China
Brazil
China
China
Spain
China
China
China
Brazil
China
UK
Japan
Spain
Spain
Brazil
Spain
Spain
Japan
Colombia
China
South Africa
Brazil
Mexico
Brazil
Brazil
Peru
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Bolivia
Argentina
Brazil
Colombia
Brazil
Peru
Japan
Peru
Brazil
Brazil
Unknown
Brazil
Brazil
Brazil
Brazil
Mozambique
South Africa
South Africa
South Africa
Argentina
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Peru
Peru
Peru
Peru
Peru
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
Brazil
China
Brazil
Brazil
France
South Africa
Unknown
Unknown
USA
Netherlands
Brazil
Brazil
Brazil
Italy
Mexico
Mexico
South Africa
South Africa
South Africa
South Africa
USA, Maryland
Sporothrix globosa
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix globosa
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix globosa
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. luriei
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix mexicana
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii
Sporothrix brasiliensis
Sporothrix brasiliensis
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii var. schenckii
Sporothrix schenckii
Sporothrix schenckii var. schenckii
Sporothrix mexicana
Sporothrix mexicana
Sporothrix globosa
Sporothrix brasiliensis
Sporothrix mexicana
Sporothrix mexicana
Sporothrix schenckii
Sporothrix humicola
Sporothrix humicola
Sporothrix schenckii var. schenckii
Sporothrix schenckii
S. globosa global
S. luriei
S. brasiliensis-A Brazil
S. schenckii-C Peru
S. brasiliensis-B Brazil
S. brasiliensis-C Brazil -1
S. schenckii-E global S. schenckii-D global
S. mexicana-A Brazil
S. schenckii-A South America -1
S. schenckii-B Africa -1
S. mexicana-B global
T
T
T
T
10090807060504030
Sporothrix globosa: global distribution of AFLP types
CBS 125438
CBS 129719
CBS 132923
CBS 129718
CBS 129720
CBS 130116
CBS 129724
CBS 129721
CBS 129723
CBS 132925
CBS 129722
CBS 292.55
CBS 130117
CBS 120340
CBS 130105
CBS 132922
CBS 130115
CBS 130104
CBS 340.35
CBS 125601
CBS 129717
Colombia
China
Brazil
China
China
Spain
China
China
China
Brazil
China
UK
Japan
Spain
Spain
Brazil
Spain
Spain
Japan
Colombia
China
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Colombia
Peru
Bolivia
Argentina
Mexico
South Africa
UK France
Netherlands
Italy Germany
Mozambique
Japan
Venezuela Guatemala
USA
Brazil 312
3 5 33
Spain n=15
S.schenckii
S.brasiliensis
S.globosa
S.mexicana
S.luriei
India 12
China 121
1 6
6 1
15
3
13
1
2 2
20 3
2 1
1
1
1 1 2
1
1
1 1
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Traditional corn harvest in Jilin Province, China
Jianxin Xia et al. – Chin. J. Mycol. 2009
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Frequent occurrence of fixed facial sporotrichosis in Jilin Province, China
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Conclusion: molecular systematics provide detailed insight in diversity.
Usefulness depends on the question: - Research - Routine
Morphology, ITS: broad concept matches with classical species A
B
C
D
E
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Clinical parameters identical
Multi-gene phylogeny: five species.
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
ITS sequence data of Cladosporium, Ubiquitous contaminants in the clinical laboratory
former Cladosporium herbarum
former Cladosporium cladosporioides
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
ITS Cladosporium
Cladosporium herbarum complex
Cladosporium cladosporioides complex
Cladosporium pseudoiridis
Cladosporium subtilissimum
Cladosporium ossifragi
Cladosporium echinulatum
Cladosporium …. (n)
Cladosporium herbarum complex
Sporothrix brasiliensis
Sporothrix globosa
Sporothrix globosa
Sporothrix mexicana
Sporothrix luriei
No species complex in Sporothrix
ITS2: Joseph et al. – Nucleic Acids Res 1999
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
Barcode identifiers selected from highly conserved stems with compensatory mutations versus highly variable loops Heinrichs et al JCM 2013
Species Strain Accession Number
Barcode identifier Position Habitat
Cladophialophora arxii 1
CBS 306.94T
EU103986.1 TTGG ACGGTTTGGTGGAAGGGTGACACCCTTCCGCCCGT CCTAA 400-443 man
Cladophialophora arxii 2
CBS 409.96 EU103987.1 TTGG ACGGTTCGGTGGGGAAGGGGTACACCCTTCCACCCGT CCTAA 399-444 man
Cladophialophora bantiana
CBS 173.52T
EU103989.1 TTGG ACGGTCTGGCGGAAGTGTCGTGCACCCCGCCCCT CCTAA 392-444 man
Cladophialophora carrionii 1
CBS 160.54LT
AF050262.1 TTGG ACGGTTTTGGTCGAGTGTTCTCGACCCCT CCTAA 391-428 man
Cladophialophora carrionii 2
CBS 163.54 EU137304.1 TTGG ACGGTCTTGGTCGAGTGTTCTCGACCCCT CCTAA 389-426 man
Cladophialophora carrionii 3
CBS 260.83 EU137292.1 TTGG ACGGTTTTGGTCGAGTGTTCTCGACCCCT CCTAA 389-426 man, skin lesion
Cladophialophora carrionii 4
FMC.248 AF397181.1 TTGG ACGGTCTTGGTCGAGTGTTCTCGACCCCC CCTAA 411-448 man
Cladophialophora devriesii 1
CBS 147.84T
EU103985.1 TTGG ACGGCTTGGTAGAGTCCCTACCCCT CCTAA 394-427 man
Cladophialophora devriesii 2
IFM 51369 AB091212.1 TTGG ACGGCTTGGTAAATTCCCTACCCCT CCTAA 416-449 -
Cladophialophora aff. devriesii crab
CBS 119710T
FJ385275.1 (CBS118720)
TTGG ACGGCTTGGTAGAGAGTCTCTACCCCT CCTAA 394-429 crab
Cladophialophora emmonsii 1
CBS 979.96T
EU103996.1 TTGG ACGGCCTGGCGGAGTGCACGACACTCTGCCCCT CCTAA 389-430 man, subcutaneous lesion right forearm
Cladophialophora emmonsii 2
CBS 640.96 EU103995.1 TTGG ACGGCCTGGCGGAGTGCACGACACCCTGCCCCT CCTAA 349-390 cat, subcutaneous lesion
Cladophialophora immunda 1
CBS 834.96T
EU137318.1 TTGG ACGGTTTGGTAGGGCGCCTACCCCT CCTAA 396-429 man
Cladophialophora immunda 2
CBS 102227
EU137319.1 TTGG ACGGTTTGGTAGAGTGCCTACCCCT CCTAA 399-432 Syagrum romanzoffianum, stem
Cladophialophora modesta
CBS 985.96T
GU225939.1 TTGG AATCTCAGTTGAGTGATCAACTGGTT CCCAA 383-416 man
Cladophialophora mycetomatis 1
CBS 122637T
FJ385276.1 TTGG ACGGTTTGGTCGACGACACCCGACCCCT CCCAA 380-416 man
Cladophialophora mycetomatis 2
CBS 454.82 EU137293.1 TTGG ACGGTTTGGTCGACGACATCCGACCCCT CCCAA 399-435 culture contaminant
Cladophialophora psammophila
CBS 110553T
AY857517.1 TTGG ACGGTCTGGCGGAAGTGTCGTGCACGCCGCCCCT CCTAA 398-440 gasolin-polluted soil
Cladophialophora samoensis
CBS 259.83T
EU137291.1 TTGG AGGGTCCCTGGTCGAGGCTCTACCTCGACCT CCTAA 393-432 man, skin lesion
Cladophialophora saturnica
CBS 118724T
EU103984.1 TTGG ACGGCTTGGTAGAGTTCCCTCTACCCT CCTAA 398-433 interdigital, tinea nigra-like skin lesion of 4-year old HIV positive child
Cladophialophora subtilis
CBS 122642T
FJ385273.1 TTGG ACGGCCTTGGTCGCGCACGCGCCGACCCCT CCTAA 387-425 ice tea
Cladophialophora yegresii
CBS 114405T
EU137322.1 TTGG ACGGTTTTGGTCGAGTGTCCCTCGACCCCT CCTAA 394-432 Stenocereus griseus CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi
CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi CBS - KNAW Fungal Biodiversity Centre - Clinical and Extremophilic Fungi