title: Genetic diversity of medically important and emerging Candida species causing invasive infection.
abstract: BACKGROUND
  Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.
  
  
  METHODS
  We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.
  
  
  RESULTS
  Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.
  
  
  CONCLUSIONS
  Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.
authors.affiliation: Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil. ka.belli@yahoo.com.br.
authors.forename: Karina Bellinghausen
authors.initials: KB
authors.lastname: Merseguel
authors.affiliation: Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil. angelanishikaku@yahoo.com.
authors.forename: Angela Satie
authors.initials: AS
authors.lastname: Nishikaku
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo, São Paulo, Brazil. amrodrigues.amr@gmail.com.
authors.forename: Anderson Messias
authors.initials: AM
authors.lastname: Rodrigues
authors.affiliation: Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil. carolina.padovan@unifesp.br.|Departamento de Microbiologia e Imunologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG, Brazil. carolina.padovan@unifesp.br.
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Padovan
authors.affiliation: Laboratório de Genômica Evolutiva e Biocomplexidade, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil. renata.carmona@unifesp.br.
authors.forename: Renata Carmona
authors.initials: RC
authors.lastname: e Ferreira
authors.affiliation: Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil. analy.salles@unifesp.br.
authors.forename: Analy Salles
authors.initials: AS
authors.lastname: de Azevedo Melo
authors.affiliation: Laboratório de Genômica Evolutiva e Biocomplexidade, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil. marcelo.briones@unifesp.br.
authors.forename: Marcelo Ribeiro da Silva
authors.initials: MR
authors.lastname: Briones
authors.affiliation: Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil. arnaldolcolombo@gmail.com.
authors.forename: Arnaldo Lopes
authors.initials: AL
authors.lastname: Colombo
mesh_terms: D002175:Candida / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D058365:Candidiasis, Invasive / Q000235:genetics / Q000382:microbiology*; D021821:Communicable Diseases, Emerging / Q000235:genetics / Q000382:microbiology*; D003428:Cross Infection / Q000235:genetics / Q000382:microbiology*; D004252:DNA Mutational Analysis; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D010802:Phylogeny; D011110:Polymorphism, Genetic
chemical_list: D021903:DNA, Ribosomal Spacer