Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species.
Journal
PLoS neglected tropical diseases
ISSN: 1935-2735
Titre abrégé: PLoS Negl Trop Dis
Pays: United States
ID NLM: 101291488
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
22
12
2019
accepted:
27
04
2020
entrez:
2
7
2020
pubmed:
2
7
2020
medline:
19
8
2020
Statut:
epublish
Résumé
Sporotrichosis is a chronic subcutaneous mycosis caused by Sporothrix species, of which the main aetiological agents are S. brasiliensis, S. schenckii, and S. globosa. Infection occurs after a traumatic inoculation of Sporothrix propagules in mammals' skin and can follow either a classic route through traumatic inoculation by plant debris (e.g., S. schenckii and S. globosa) or an alternative route through zoonotic transmission from animals (e.g., S. brasiliensis). Epizootics followed by a zoonotic route occur in Brazil, with Rio de Janeiro as the epicenter of a recent cat-transmitted epidemic. DNA-based markers are needed to explore the epidemiology of these Sporothrix expansions using molecular methods. This paper reports the use of amplified-fragment-length polymorphisms (AFLP) to assess the degree of intraspecific variability among Sporothrix species. We used whole-genome sequences from Sporothrix species to generate 2,304 virtual AFLP fingerprints. In silico screening highlighted 6 primer pair combinations to be tested in vitro. The protocol was used to genotype 27 medically relevant Sporothrix. Based on the overall scored AFLP markers (97-137 fragments), the values of polymorphism information content (PIC = 0.2552-0.3113), marker index (MI = 0.002-0.0039), effective multiplex ratio (E = 17.8519-35.2222), resolving power (Rp = 33.6296-63.1852), discriminating power (D = 0.9291-0.9662), expected heterozygosity (H = 0.3003-0.3857), and mean heterozygosity (Havp = 0.0001) demonstrated the utility of these primer combinations for discriminating Sporothrix. AFLP markers revealed cryptic diversity in species previously thought to be the most prevalent clonal type, such as S. brasiliensis, responsible for cat-transmitted sporotrichosis, and S. globosa responsible for large sapronosis outbreaks in Asia. Three combinations (#3 EcoRI-FAM-GA/MseI-TT, #5 EcoRI-FAM-GA/MseI-AG, and #6 EcoRI-FAM-TA/MseI-AA) provide the best diversity indices and lowest error rates. These methods make it easier to track routes of disease transmission during epizooties and zoonosis, and our DNA fingerprint assay can be further transferred between laboratories to give insights into the ecology and evolution of pathogenic Sporothrix species and to inform management and mitigation strategies to tackle the advance of sporotrichosis.
Identifiants
pubmed: 32609739
doi: 10.1371/journal.pntd.0008330
pii: PNTD-D-19-02101
pmc: PMC7329091
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0008330Subventions
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Mem Inst Oswaldo Cruz. 2001 Aug;96(6):777-9
pubmed: 11562701
J Clin Microbiol. 2007 Oct;45(10):3198-206
pubmed: 17687013
Med Mycol. 2008 Sep;46(6):621-5
pubmed: 19180753
Genome Announc. 2014 May 22;2(3):
pubmed: 24855299
Mycopathologia. 2020 Feb 12;:
pubmed: 32052359
Evolution. 1985 Jul;39(4):783-791
pubmed: 28561359
J Clin Microbiol. 2012 Jun;50(6):2159-62
pubmed: 22403427
Virulence. 2013 Apr 1;4(3):241-9
pubmed: 23324498
J Fungi (Basel). 2017 Oct 18;3(4):
pubmed: 29371573
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
J Mol Evol. 1980 Dec;16(2):111-20
pubmed: 7463489
PLoS Pathog. 2016 Jul 14;12(7):e1005638
pubmed: 27415796
Nat Rev Genet. 2005 Nov;6(11):847-59
pubmed: 16304600
Med Mycol. 2013 May;51(4):405-12
pubmed: 22989196
Nucleic Acids Res. 1995 Nov 11;23(21):4407-14
pubmed: 7501463
Mol Biol Evol. 1999 Jan;16(1):37-48
pubmed: 10331250
Am J Hum Genet. 1980 May;32(3):314-31
pubmed: 6247908
J Clin Microbiol. 2003 Sep;41(9):4101-6
pubmed: 12958232
Med Mycol. 2010 Sep;48(6):800-6
pubmed: 20302550
Genome Announc. 2018 Jun 14;6(24):
pubmed: 29903814
PLoS Negl Trop Dis. 2014 Sep 18;8(9):e3094
pubmed: 25233227
J Clin Microbiol. 2005 Mar;43(3):1348-52
pubmed: 15750106
Bioinformatics. 2007 Dec 1;23(23):3119-24
pubmed: 17933852
Clin Infect Dis. 2004 Feb 15;38(4):529-35
pubmed: 14765346
An Bras Dermatol. 2017 Sep-Oct;92(5):606-620
pubmed: 29166494
BMC Genomics. 2014 Oct 29;15:943
pubmed: 25351875
Fungal Biol. 2016 Feb;120(2):246-64
pubmed: 26781380
PLoS Negl Trop Dis. 2013 Jun 20;7(6):e2281
pubmed: 23818999
PLoS Negl Trop Dis. 2015 Dec 01;9(12):e0004190
pubmed: 26623643
Mol Ecol. 2004 Nov;13(11):3261-73
pubmed: 15487987
An Bras Derm Sifilogr. 1955 Mar;30(1):9-12
pubmed: 13238814
Genome Announc. 2016 Mar 31;4(2):
pubmed: 27034494
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):5107-10
pubmed: 10220426
Stud Mycol. 2016;83:165-91
pubmed: 27616802
J Clin Microbiol. 2006 Sep;44(9):3251-6
pubmed: 16954256
Syst Biol. 2010 May;59(3):288-97
pubmed: 20525636
Rev Iberoam Micol. 2009 Sep 30;26(3):218-22
pubmed: 19635441
Mol Ecol. 1994 Apr;3(2):91-9
pubmed: 8019690
Emerg Microbes Infect. 2017 Oct 11;6(10):e88
pubmed: 29018254
Genome Biol Evol. 2016 May 12;8(5):1374-87
pubmed: 27071652
Persoonia. 2015 Dec;35:1-20
pubmed: 26823625
Skinmed. 2007 May-Jun;6(3):139-41
pubmed: 17483658
Br J Dermatol. 2015 Apr;172(4):1116-9
pubmed: 25155197
Bioinformatics. 2003 Apr 12;19(6):776-7
pubmed: 12691992
Nucleic Acids Res. 2016 Jul 8;44(W1):W147-53
pubmed: 27190236
Front Microbiol. 2015 Dec 08;6:1385
pubmed: 26696992
J Clin Microbiol. 1999 Oct;37(10):3083-91
pubmed: 10488158
J Evol Biol. 2011 Nov;24(11):2346-56
pubmed: 21848979
Lancet Infect Dis. 2017 Nov;17(11):e367-e377
pubmed: 28774696
PLoS Negl Trop Dis. 2015 Sep 25;9(9):e0004096
pubmed: 26407300
J Am Vet Med Assoc. 2004 May 15;224(10):1623-9
pubmed: 15154732
PLoS One. 2014 Jan 23;9(1):e86819
pubmed: 24466257
PLoS Pathog. 2017 Jan 19;13(1):e1006077
pubmed: 28103311
BMC Genomics. 2010 May 07;11:287
pubmed: 20459671
PLoS One. 2013 Apr 16;8(4):e61704
pubmed: 23613908
Med Mycol. 2018 Apr 1;56(suppl_1):126-143
pubmed: 29538731
J Clin Microbiol. 2003 Apr;41(4):1357-62
pubmed: 12682114
Microbiology. 2001 Apr;147(Pt 4):891-907
pubmed: 11283285
Med Mycol. 2018 Apr 1;56(suppl_1):165-187
pubmed: 29538732
PLoS Negl Trop Dis. 2017 Aug 30;11(8):e0005903
pubmed: 28854184
Eukaryot Cell. 2015 Feb;14(2):158-69
pubmed: 25480940
BMC Vet Res. 2018 Jan 18;14(1):19
pubmed: 29347940
Emerg Microbes Infect. 2014 May;3(5):e32
pubmed: 26038739
BMC Infect Dis. 2014 Apr 23;14:219
pubmed: 24755107
Eur J Clin Microbiol Infect Dis. 2016 Nov;35(11):1803-1810
pubmed: 27477855
Fungal Biol. 2010 Sep;114(9):746-52
pubmed: 20943184
J Small Anim Pract. 2003 Sep;44(9):395-8
pubmed: 14510328
Trends Ecol Evol. 1999 Oct;14(10):389-394
pubmed: 10481200
Nat Protoc. 2007;2(6):1387-98
pubmed: 17545976
Methods Enzymol. 2005;395:145-61
pubmed: 15865966
Biopreserv Biobank. 2015 Apr;13(2):131-4
pubmed: 25880473
J Eur Acad Dermatol Venereol. 2013 Mar;27(3):313-8
pubmed: 22176524
Genome Biol Evol. 2016 Dec 14;8(11):3292-3296
pubmed: 27635048
Diagn Microbiol Infect Dis. 2014 Apr;78(4):383-7
pubmed: 24525143
J Fungi (Basel). 2018 Aug 12;4(3):
pubmed: 30103554
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
Mycoses. 2015 Nov;58(11):652-8
pubmed: 26404561
BMC Vet Res. 2014 Nov 19;10:269
pubmed: 25407096