Molecular phylogenetics of Candida albicans

Frank Odds, Marie-Elisabeth Bougnoux, D.J. Shaw, Judith Margaret Bain, Amanda D. Davidson, D. Diogo, Mette Jacobsen, M. Lecomte, S Y Li, Arianna Tavanti, Martin Maiden, Neil Andrew Robert Gow, Christophe d'Enfert

Research output: Contribution to journalArticle

207 Citations (Scopus)

Abstract

We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.

Original languageEnglish
Pages (from-to)1041-1052
Number of pages12
JournalEukaryotic Cell
Volume6
Issue number6
DOIs
Publication statusPublished - Jun 2007

Keywords

  • mating-type
  • population-structure
  • human pathogen
  • European committee
  • locus homozygosis
  • chromosome loss
  • sexual cycle
  • opaque cells
  • MTL locus
  • sequence

Cite this

Odds, F., Bougnoux, M-E., Shaw, D. J., Bain, J. M., Davidson, A. D., Diogo, D., ... d'Enfert, C. (2007). Molecular phylogenetics of Candida albicans. Eukaryotic Cell, 6(6), 1041-1052. https://doi.org/10.1128/EC.00041-07

Molecular phylogenetics of Candida albicans. / Odds, Frank; Bougnoux, Marie-Elisabeth; Shaw, D.J.; Bain, Judith Margaret; Davidson, Amanda D.; Diogo, D.; Jacobsen, Mette; Lecomte, M.; Li, S Y ; Tavanti, Arianna; Maiden, Martin; Gow, Neil Andrew Robert; d'Enfert, Christophe.

In: Eukaryotic Cell, Vol. 6, No. 6, 06.2007, p. 1041-1052.

Research output: Contribution to journalArticle

Odds, F, Bougnoux, M-E, Shaw, DJ, Bain, JM, Davidson, AD, Diogo, D, Jacobsen, M, Lecomte, M, Li, SY, Tavanti, A, Maiden, M, Gow, NAR & d'Enfert, C 2007, 'Molecular phylogenetics of Candida albicans', Eukaryotic Cell, vol. 6, no. 6, pp. 1041-1052. https://doi.org/10.1128/EC.00041-07
Odds F, Bougnoux M-E, Shaw DJ, Bain JM, Davidson AD, Diogo D et al. Molecular phylogenetics of Candida albicans. Eukaryotic Cell. 2007 Jun;6(6):1041-1052. https://doi.org/10.1128/EC.00041-07
Odds, Frank ; Bougnoux, Marie-Elisabeth ; Shaw, D.J. ; Bain, Judith Margaret ; Davidson, Amanda D. ; Diogo, D. ; Jacobsen, Mette ; Lecomte, M. ; Li, S Y ; Tavanti, Arianna ; Maiden, Martin ; Gow, Neil Andrew Robert ; d'Enfert, Christophe. / Molecular phylogenetics of Candida albicans. In: Eukaryotic Cell. 2007 ; Vol. 6, No. 6. pp. 1041-1052.
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abstract = "We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7{\%}) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.",
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author = "Frank Odds and Marie-Elisabeth Bougnoux and D.J. Shaw and Bain, {Judith Margaret} and Davidson, {Amanda D.} and D. Diogo and Mette Jacobsen and M. Lecomte and Li, {S Y} and Arianna Tavanti and Martin Maiden and Gow, {Neil Andrew Robert} and Christophe d'Enfert",
note = "ACKNOWLEDGMENTS This work is based on data generated from several projects that were supported by the Wellcome Trust (grants 069615 and 074898), the Ministe`re de la Recherche et de la Technologie (Programme de Recherche Fondamentale en Microbiologie, Maladies Infectieuses et Parasitaires-Re´seau Infections Fongiques), Pasteur Genopole-Ile-deFrance, Merck, Sharp & Dohme, Pfizer UK, the Center for Disease Control, Department of Health, Taiwan (grant DOH94-DC-2011), the National Science Council, Taiwan (grant 94-0324-19-F-00-00-00-35), and the European Commission (Euresfun; grant LSHM-CT-2005- 518199). We are grateful to the many individuals who have supplied us with the C. albicans isolates, past and present, that formed the experimental material for this study, including J. B. Anderson, G. Chaves, M. Cuenca-Estrella, D. H. Ellis, J.-M. Gomez, G. Haase, M. Hanson, R. Hollis, E. M. Johnson, B. Jones, G. Just, C. C. Kibbler, N. Nolard, M. A. Pfaller, J.-L. Rodriguez-Tudela, J. Schmid, D. R. Soll, D. A. Stevens, F. Symoens, S. Takakura, and K. Y. Yuen. We gratefully acknowledge the skilled technical assistance of Christiane Bouchier, Diana Sharafi, and Julie Whyte. Keith Jolley (University of Oxford) provided valuable guidance in carrying out congruence analysis.",
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AU - Jacobsen, Mette

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AB - We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.

KW - mating-type

KW - population-structure

KW - human pathogen

KW - European committee

KW - locus homozygosis

KW - chromosome loss

KW - sexual cycle

KW - opaque cells

KW - MTL locus

KW - sequence

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JO - Eukaryotic Cell

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