Comparison of Different DNA-Based Methods for Molecular Typing of Histoplasma capsulatum

Histoplasma capsulatum is very prevalent in the environment and is one of the most common causes of mycoses in humans and diverse animals in Brazil. Multiple typing methods have been developed to study H. capsulatum epidemiology; however, there is limited information concerning comparisons of results obtained with different methods using the same set of isolates. To explore the diversity of H. capsulatum in Brazil and to determine correlations between the results of three different molecular typing techniques, we examined 51 environmental, animal, and human isolates by M13 PCR fingerprinting, PCR-restriction fragment length polymorphism (RFLP) analysis of the internal transcribed region 1 (ITS1)-5.8S-ITS2 region of the rDNA locus, and DNA sequencing and phylogenetic analysis of parts of four protein-encoding genes, the Arf (ADP ribosylation factor), H-anti (H antigen precursor), Ole (delta-9 fatty acid desaturase), and Tub1 (alpha-tubulin) genes. Each method identified three major genetic clusters, and there was a high level of concordance between the results of the typing techniques. The M13 PCR fingerprinting and PCR-RFLP analyses produced very similar results and separated the H. capsulatum isolates included in this study into three major groups. An additional approach used was comparison of our Brazilian ITS1-5.8S-ITS2 sequences with the sequences deposited previously in NCBI data banks. Our analyses suggest that H. capsulatum can be divided into different molecular types that are dispersed around the world. Our results indicate that the three methods used in this study are reliable and reproducible and that they have similar sensitivities. However, M13 PCR fingerprinting has some advantages over the other two methods as it is faster, cheaper, and more user friendly, which especially increases its utility for molecular typing of Histoplasma in situations where laboratory facilities are relatively limited.Histoplasmosis is a serious community-acquired infection in the United States (28) and in certain countries of Latin America, where it is an especially significant problem in patients with AIDS (14). This disease is one of the most common systemic mycoses in Brazil, where epidemiological surveys carried out using the histoplasmin skin test have indicated that it is endemic in all areas surveyed (15). Data suggest that the numbers of cases of histoplasmosis in Brazil may be underestimated and that the areas where it is endemic are more widespread than previously thought.Histoplasma capsulatum is a dimorphic fungus that grows as a mold and produces aerial hyphae at 25 to 30°C, but it undergoes morphogenesis to a yeast phase at 37°C. The filamentous phase of this organism is usually found in soil enriched with several compounds, such as nitrogen and phosphate compounds. When conidial or hyphal fragments are inhaled by humans or animals, H. capsulatum changes to the yeast form and continues to replicate as a yeast. Although H. capsulatum has been recognized as an important fungal pathogen in immunocompromised hosts, particularly AIDS patients (27), there are significant gaps in our knowledge of this species'' epidemiology and pathogenesis. For instance, systemic histoplasmosis has been found in patients with AIDS who do not reside in regions where it is endemic (29), leading to the suggestion that the disease can result from reactivation of a previously acquired H. capsulatum infection. The clinical manifestations of histoplasmosis range from asymptomatic infections, mild flu-like symptoms, or pneumonia to a systemic disease involving the skin, brain, intestine, adrenal glands, and/or bone marrow (6). Importantly, diverse strains of H. capsulatum have been identified worldwide, and the strains vary in virulence. In addition to classical biochemical assays, distinctions between strains may be based on colony morphology or polymorphism of the genome (19).Multiple typing methods have been developed to study the epidemiology of H. capsulatum. These methods are based on phenotypic characteristics, such as antigenic profiles (13) and multilocus enzyme electrophoresis results (2), or on DNA-based analysis. Most recently, typing has been accomplished by analysis of fatty acid profiles of H. capsulatum (34). Molecular typing methods are generally considered to have advantages over phenotypic methods in terms of the stability of genomic markers and greater levels of typeability. Several genotype-based methods, such as hybridization of target genes (probes), chromosomal DNA typing, restriction fragment length polymorphism (RFLP) analysis, random amplified polymorphic DNA (RAPD) analysis, and sequencing, have been described for H. capsulatum (4, 5, 7, 8, 11, 17, 19). Despite the abundance of previously developed molecular techniques, there is limited information concerning comparisons of the results obtained with different methods using the same set of isolates. In H. capsulatum, no single approach based on DNA assays has been the dominant method.The current study was done to explore the diversity of H. capsulatum in Brazil and to determine the correlation between the results of three different molecular typing techniques. For this analysis, we used M13 PCR fingerprinting, PCR-RFLP analysis of the internal transcribed spacer 1 (ITS1)-5.8S-ITS2 region of the rDNA gene, and analysis of the nucleotide sequence polymorphism of four partial genes. M13 PCR fingerprinting (25) is based on generation of multiple PCR products with different electrophoretic mobilities. PCR fingerprinting primers are typically designed using repetitive DNA sequences (31), and the products facilitate detection of two types of genetic variations: (i) differences in the length of DNA and (ii) alterations in the sequence of the priming regions. PCR-RFLP analysis of the ITS1-5.8S-ITS2 region of the rDNA gene (9) involves use of a gene-specific PCR in combination with restriction digestion in order to generate highly stable and reproducible markers. Analysis of the nucleotide sequence polymorphism is based on the sequences of four partial protein-encoding genes (Arf, the H-anti gene, Ole, Tub1) (4). Additionally, to assess the utility of an assay to study the global epidemiology of the fungus, we performed a DNA sequencing analysis of the ITS1-5.8S-ITS2 region to compare the Brazilian H. capsulatum ITS1-5.8S-ITS2 sequences with sequences obtained for H. capsulatum strains isolated in other countries.