Draft Genome Sequences of Two Sporothrix schenckii Clinical Isolates Associated with Human Sporotrichosis in Colombia

Gómez, Oscar Mauricio Hernández; Alvarez, Laura C.; Muñoz, José F.; Misas, Elizabeth; Gallo, Juan Esteban; Jiménez, María del Pilar; Arango, Myrtha; McEwen, Juan G.; Hernández, Orville; Clay, Oliver

doi:10.1128/genomea.00495-18

Cited by 10 publications

(8 citation statements)

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“…Disadvantages include the dominance of alleles, and the possible non-homology of comigrating fragments belonging to different loci, leading to suboptimal reproducibility, particularly across different platforms. However, we took advantage of the growing number of full genome sequences available for Sporothrix [58][59][60][61][62][63] to generate 2,304 virtual fingerprints of Sporothrix DNA, reducing time and costs related to extensive trials, minimizing possible reproducibility errors.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species

et al. 2020

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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 (H avp = 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 PLOS NEGLECTED TROPICAL DISEASES

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Section: Discussionmentioning

confidence: 99%

Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species

et al. 2020

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“…We used three additional sets of Illumina paired-end reads from S. schenckii isolates from Colombia (EM7 and MS1 - [ 28 ]) and Puerto Rico (ATCC 58251 - [ 29 ]). To root phylogenetic trees (see below), we retrieved additional genomic assemblies from other Sporothrix species from the NCBI genome browser (Supplementary Table 1).…”

Section: Methodsmentioning

confidence: 99%

A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic

Filho

Santos

Reis

et al. 2020

Emerging Microbes & Infections

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A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic Sporotrichosis is a subcutaneous infection caused by fungi from the genus Sporothrix. It is transmitted by inoculation of infective particles found in plant-contaminated material or diseased animals, characterizing the classic sapronotic and emerging zoonotic transmission, respectively. Since 1998, southeastern Brazil has experienced a zoonotic sporotrichosis epidemic caused by S. brasiliensis, centered in the state of Rio de Janeiro. Our observation of feline sporotrichosis cases in Brasília (Midwestern Brazil), around 900 km away from Rio de Janeiro, led us to question whether the epidemic caused by S. brasiliensis has spread from the epicenter in Rio de Janeiro, emerged independently in the two locations, or if the disease has been present and unrecognized in Midwestern Brazil. A retrospective analysis of 91 human and 4 animal cases from Brasília, ranging from 1993 to 2018, suggests the occurrence of both sapronotic and zoonotic transmission. Molecular typing of the calmodulin locus identified S. schenckii as the agent in two animals and all seven human patients from which we were able to recover clinical isolates. In two other animals, the disease was caused by S. brasiliensis. Whole-genome sequence typing of seven Sporothrix spp. strains from Brasília and Rio de Janeiro suggests that S. brasiliensis isolates from Brasília are genetically distinct from those obtained at the epicenter of the outbreak in Rio de Janeiro, both in phylogenomic and population genomic analyses. The two S. brasiliensis populations seem to have separated between 2.2 and 3.1 million years ago, indicating independent outbreaks or that the zoonotic S. brasiliensis outbreak might have started earlier and be more widespread in South America than previously recognized.

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“…Sporothrix phasma has the smallest genome size when compared to other Sporothrix species for which genome sequences are available. Sprorothrix pallida has the largest genome size (37.8 Mb), followed by S. globosa (33.5 Mb), S. brasiliensis (33.2 Mb) and S. schenckii (32.3 Mb) (D' Alessandro et al 2016;Huang et al 2016;Gomez et al 2018).…”

Section: Resultsmentioning

confidence: 99%

Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa

et al. 2019

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Draft genome sequences of five Calonectria species [including Calonectria aciculata, C. crousiana, C. fujianensis, C. honghensis and C. pseudoturangicola], Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa are presented. Species of Calonectria are the causal agents of Eucalyptus leaf blight disease, threatening the growth and sustainability of Eucalyptus plantations in China. Celoporthe dispersa is the causal agent of stem canker in native Syzygium cordatum and exotic Tibouchina granulosa in South Africa. Sporothrix phasma was first discovered in the infructescences of Protea laurifolia and Protea neriifolia in South Africa. Alectoria sarmentosa is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi.

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Draft Genome Sequences of Two Sporothrix schenckii Clinical Isolates Associated with Human Sporotrichosis in Colombia

Abstract: Sporothrix schenckii is a thermodimorphic fungal pathogen with a high genetic diversity. In this work, we present the assembly and similarity analysis of the whole-genome sequences of two clinical isolates from Colombia of S. schenckii sensu stricto.

Cited by 10 publications

References 9 publications

Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species

Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species

A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic

Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa

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