Evaluation of genotyping methods for tracking the spread of Sporothrix during epidemics and outbreaks

Jamile Ambrosio de Carvalho; Ferry  Hagen; Alexander Bonifaz; Rui Kano; Zoilo Pires de Camargo; Anderson Messias Rodriguesb

doi:10.1016/j.funbio.2025.101566

Evaluation of genotyping methods for tracking the spread of Sporothrix during epidemics and outbreaks

Jamile Ambrosio de Carvalho, Ferry Hagen, Alexander Bonifaz, Rui Kano, Zoilo Pires de Camargo, Anderson Messias Rodriguesb

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

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Sporotrichosis, a neglected mycosis caused by Sporothrix species, has shown notable increases in prevalence and geographic spread, driven largely by the rise of cat-transmitted cases. Robust molecular tools are crucial for tracking this emergence. This study compared the performance of four genotyping methods—calmodulin (CAL) sequencing, amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and T3B-random amplified polymorphic DNA (T3B-RAPD)—in differentiating Sporothrix, determining intraspecific diversity, and recognizing genotypes, using a collection of 53 isolates. CAL sequencing, with 108 variable sites and 17 haplotypes, was highly effective for species identification (bootstrap values: 92–100) but offered limited insight into intraspecific diversity (H = 0.351–0.897). AFLP analysis, particularly with primer combination #5 (Rp = 40.6415; H = 0.3306), showed greater resolving power and identified intraspecific subgroups. A panel of 15 SSRs demonstrated superior strain differentiation (MI = 0.9153; PIC = 0.9094; D = 0.7424). T3B-RAPD showed moderate diversity (H = 0.3837; PIC = 0.3101), aligning with CAL for species differentiation but exhibiting limitations in detailed genetic analysis (Rp = 7.1320). The AFLP markers showed high congruence with each other (up to r = 88.4 %) and with the SSRs (up to r = 79.41 %), whereas they were poorly concordant with CAL and T3B (r = 47.05–69.87 %). A strategy using AFLP or SSR is recommended to dissect both deep- and fine-scale genetic structures, whereas CAL and T3B are suitable for species identification, particularly in resource-limited settings. This approach enhances molecular epidemiology and surveillance efforts, supporting the effective tracking of Sporothrix outbreaks and guiding public health interventions.

Originele taal-2	Engels
Pagina's (van-tot)	101566
Tijdschrift	Fungal Biology
Volume	129
DOI's	https://doi.org/10.1016/j.funbio.2025.101566
Status	Gepubliceerd - 23 mrt. 2025

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10.1016/j.funbio.2025.101566

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@article{57a5b4496a96427b94b56f09afcc2a1b,

title = "Evaluation of genotyping methods for tracking the spread of Sporothrix during epidemics and outbreaks",

abstract = "Sporotrichosis, a neglected mycosis caused by Sporothrix species, has shown notable increases in prevalence and geographic spread, driven largely by the rise of cat-transmitted cases. Robust molecular tools are crucial for tracking this emergence. This study compared the performance of four genotyping methods—calmodulin (CAL) sequencing, amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and T3B-random amplified polymorphic DNA (T3B-RAPD)—in differentiating Sporothrix, determining intraspecific diversity, and recognizing genotypes, using a collection of 53 isolates. CAL sequencing, with 108 variable sites and 17 haplotypes, was highly effective for species identification (bootstrap values: 92–100) but offered limited insight into intraspecific diversity (H = 0.351–0.897). AFLP analysis, particularly with primer combination #5 (Rp = 40.6415; H = 0.3306), showed greater resolving power and identified intraspecific subgroups. A panel of 15 SSRs demonstrated superior strain differentiation (MI = 0.9153; PIC = 0.9094; D = 0.7424). T3B-RAPD showed moderate diversity (H = 0.3837; PIC = 0.3101), aligning with CAL for species differentiation but exhibiting limitations in detailed genetic analysis (Rp = 7.1320). The AFLP markers showed high congruence with each other (up to r = 88.4 %) and with the SSRs (up to r = 79.41 %), whereas they were poorly concordant with CAL and T3B (r = 47.05–69.87 %). A strategy using AFLP or SSR is recommended to dissect both deep- and fine-scale genetic structures, whereas CAL and T3B are suitable for species identification, particularly in resource-limited settings. This approach enhances molecular epidemiology and surveillance efforts, supporting the effective tracking of Sporothrix outbreaks and guiding public health interventions.",

author = "{de Carvalho}, {Jamile Ambrosio} and Ferry Hagen and Alexander Bonifaz and Rui Kano and {de Camargo}, {Zoilo Pires} and Rodriguesb, {Anderson Messias}",

year = "2025",

month = mar,

day = "23",

doi = "10.1016/j.funbio.2025.101566",

language = "English",

volume = "129",

pages = "101566",

journal = "Fungal Biology",

issn = "1878-6146",

publisher = "Elsevier B.V.",

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TY - JOUR

T1 - Evaluation of genotyping methods for tracking the spread of Sporothrix during epidemics and outbreaks

AU - de Carvalho, Jamile Ambrosio

AU - Hagen, Ferry

AU - Bonifaz, Alexander

AU - Kano, Rui

AU - de Camargo, Zoilo Pires

AU - Rodriguesb, Anderson Messias

PY - 2025/3/23

Y1 - 2025/3/23

N2 - Sporotrichosis, a neglected mycosis caused by Sporothrix species, has shown notable increases in prevalence and geographic spread, driven largely by the rise of cat-transmitted cases. Robust molecular tools are crucial for tracking this emergence. This study compared the performance of four genotyping methods—calmodulin (CAL) sequencing, amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and T3B-random amplified polymorphic DNA (T3B-RAPD)—in differentiating Sporothrix, determining intraspecific diversity, and recognizing genotypes, using a collection of 53 isolates. CAL sequencing, with 108 variable sites and 17 haplotypes, was highly effective for species identification (bootstrap values: 92–100) but offered limited insight into intraspecific diversity (H = 0.351–0.897). AFLP analysis, particularly with primer combination #5 (Rp = 40.6415; H = 0.3306), showed greater resolving power and identified intraspecific subgroups. A panel of 15 SSRs demonstrated superior strain differentiation (MI = 0.9153; PIC = 0.9094; D = 0.7424). T3B-RAPD showed moderate diversity (H = 0.3837; PIC = 0.3101), aligning with CAL for species differentiation but exhibiting limitations in detailed genetic analysis (Rp = 7.1320). The AFLP markers showed high congruence with each other (up to r = 88.4 %) and with the SSRs (up to r = 79.41 %), whereas they were poorly concordant with CAL and T3B (r = 47.05–69.87 %). A strategy using AFLP or SSR is recommended to dissect both deep- and fine-scale genetic structures, whereas CAL and T3B are suitable for species identification, particularly in resource-limited settings. This approach enhances molecular epidemiology and surveillance efforts, supporting the effective tracking of Sporothrix outbreaks and guiding public health interventions.

AB - Sporotrichosis, a neglected mycosis caused by Sporothrix species, has shown notable increases in prevalence and geographic spread, driven largely by the rise of cat-transmitted cases. Robust molecular tools are crucial for tracking this emergence. This study compared the performance of four genotyping methods—calmodulin (CAL) sequencing, amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and T3B-random amplified polymorphic DNA (T3B-RAPD)—in differentiating Sporothrix, determining intraspecific diversity, and recognizing genotypes, using a collection of 53 isolates. CAL sequencing, with 108 variable sites and 17 haplotypes, was highly effective for species identification (bootstrap values: 92–100) but offered limited insight into intraspecific diversity (H = 0.351–0.897). AFLP analysis, particularly with primer combination #5 (Rp = 40.6415; H = 0.3306), showed greater resolving power and identified intraspecific subgroups. A panel of 15 SSRs demonstrated superior strain differentiation (MI = 0.9153; PIC = 0.9094; D = 0.7424). T3B-RAPD showed moderate diversity (H = 0.3837; PIC = 0.3101), aligning with CAL for species differentiation but exhibiting limitations in detailed genetic analysis (Rp = 7.1320). The AFLP markers showed high congruence with each other (up to r = 88.4 %) and with the SSRs (up to r = 79.41 %), whereas they were poorly concordant with CAL and T3B (r = 47.05–69.87 %). A strategy using AFLP or SSR is recommended to dissect both deep- and fine-scale genetic structures, whereas CAL and T3B are suitable for species identification, particularly in resource-limited settings. This approach enhances molecular epidemiology and surveillance efforts, supporting the effective tracking of Sporothrix outbreaks and guiding public health interventions.

U2 - 10.1016/j.funbio.2025.101566

DO - 10.1016/j.funbio.2025.101566

M3 - Article

SN - 1878-6146

VL - 129

SP - 101566

JO - Fungal Biology

JF - Fungal Biology

ER -