Cryptosporidium, Giardia, Cryptococcus, Pneumocystis Genetic Variability: Cryptic Biological Species or Clonal Near-Clades?

PLoS Pathogens

Volumn 10, Issue 4, 2014, Pages

  Tibayrenc, Michel ^a   Ayala, Francisco J ^b  

^a UNIV MONTPELLIER   (France)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLONAL EVOLUTION; CRYPTOCOCCUS; CRYPTOSPORIDIUM; DISEASE TRANSMISSION; GENETIC VARIABILITY; GENOTYPE; GIARDIA; MOLECULAR EPIDEMIOLOGY; MULTILOCUS ENZYME ELECTROPHORESIS; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PARTHENOGENESIS; PLASMODIUM FALCIPARUM; PNEUMOCYSTIS; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TAXONOMY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; PATHOGENICITY;

CRYPTOSPORIDIUM; GENETIC VARIATION; GIARDIA; LINKAGE DISEQUILIBRIUM; PNEUMOCYSTIS;

EID: 84901333443     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1003908     Document Type: Article

References (70)

1. Tibayrenc M, Kjellberg F, Ayala FJ, (1990) A clonal theory of parasitic protozoa: the population structure of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas and Trypanosoma, and its medical and taxonomical consequences. Proc Nat Acad Sci U S A 87: 2414-2418.
2. Tibayrenc M, Kjellberg F, Arnaud J, Oury B, Brenière SF, et al. (1991) Are eukaryotic microorganisms clonal or sexual? A population genetics vantage. Proc Natl Acad Sci U S A 88: 5129-5133.
3. Tibayrenc M, Ayala FJ, (2012) Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Nat Acad Sci U S A 109: E3305-E3313 doi:10.1073/pnas.1212452109.
4. Andersson JO, (2012) Double peaks reveal rare diplomonad sex. Trends Parasitol 28: 46-52.
5. Bovers M, Hagen F, Kuramae EE, Boekhout T, (2008) Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genet Biol 45: 400-421.
6. Cooper MA, Adam RD, Worobey M, Sterling CR, (2007) Population Genetics Provides Evidence for Recombination in Giardia. Curr Biol 17: 1984-1988.
7. Gatei W, Das P, Dutta P, Sen A, Cama V, et al. (2007) Multilocus sequence typing and genetic structure of Cryptosporidium hominis from children in Kolkata, India. Infect Genet Evol 7: 197-205.
8. Lin X, Heitman J, (2006) The Biology of the Cryptococcus neoformans Species Complex. Ann Rev Microbiol 60: 69-105.
9. Morrison LJ, Mallon ME, Smith HV, MacLeod A, Xiao L, et al. (2008) The population structure of the Cryptosporidium parvum population in Scotland: A complex picture. Infect Genet Evol 8: 121-129.
10. Tibayrenc M, Ayala FJ, (2013) How clonal are Trypanosoma and Leishmania? Trends Parasitol 29: 264-269.
11. Tibayrenc M, Ayala FJ, (2014) New insights into Clonality and Panmixia in Plasmodium and Toxoplasma. Adv Parasitol 84: 253-268.
12. Calo S, Billmyre BB, Heitman J, (2013) Generators of Phenotypic Diversity in the Evolution of Pathogenic Microorganisms. PLoS Pathog 9: e1003181 doi:10.1371/journal.ppat.1003181.
13. Ortega-Pierres G, Smith HV, Caccio SM, Thompson RC, (2009) New tools provide further insights into Giardia and Cryptosporidium biology. Trends Parasitol 25: 410-416.
14. Ramírez JD, Tapia-Calle G, Guhl F, (2013) Genetic structure of Trypanosoma cruzi in Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach. BMC Genet 14: 96.
15. Tibayrenc M, Ayala FJ, (2013) Unisexual reproduction is a particular case of clonality. Comment on: Feretzaki F, Heitman J. (2013) Unisexual Reproduction Drives Evolution of Eukaryotic Microbial Pathogens. PLoS Pathog 9: e1003674 doi:10.1371/journal.ppat.1003674.
16. Birky CW Jr, (2009) Giardia Sex? Yes, but how and how much? Trends Parasitol 26: 70-74.
17. Heitman J, (2006) Sexual reproduction and the evolution of microbial pathogens. Curr Biol 16: R711-R725.
18. Ni M, Feretzaki M, Li W, Floyd-Averette A, Mieczkowski P, et al. (2013) Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans. PLoS Biol 11: e1001653 doi:10.1371/journal.pbio.1001653.
19. Xu J, (2006) Fundamentals of Fungal Molecular Population Genetic Analyses. Curr Issues Mol Biol 8: 75-80.
20. Lehtonen J, Schmidt DJ, Heubel K, Kokko H, (2013) Evolutionary and ecological implications of sexual parasitism. Trends Ecol Evol 28: 297-306.
21. Feretzaki F, Heitman J, (2013) Unisexual Reproduction Drives Evolution of Eukaryotic Microbial Pathogens. PLoS Pathog 9: e1003674 doi:10.1371/journal.ppat.1003674.
22. Rougeron V, De Meeûs T, Kako Ouraga S, Hide M, Bañuls AL, (2010) "Everything You Always Wanted to Know about Sex (but Were Afraid to Ask)" in Leishmania after Two Decades of Laboratory and Field Analyses. PLoS Pathog 6: e1001004 doi:10.1371/journal.ppat.1001004.
23. Messenger LA, Llewellyn MS, Bhattacharyya T, Franzén O, Lewis MD, et al. (2012) Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing. PLoS Negl Trop Dis 6: e1584 doi:10.1371/journal.pntd.0001584.
24. Cacciò SM, Ryan U, (2008) Molecular epidemiology of giardiasis. Molec Biochem Parasitol 160: 75-80.
25. Esteves F, Gaspar J, Tavares A, Moser I, Antunes F, et al. (2010) Population structure of Pneumocystis jirovecii isolated from immunodeficiency virus-positive patients. Infect Genet Evol 10: 192-199.
26. Khayhan K, Hagen F, Pan W, Simwami S, Fisher MC, et al. (2013) Geographically Structured Populations of Cryptococcus neoformans Variety grubii in Asia Correlate with HIV Status and Show a Clonal Population Structure. PLoS ONE 8: e72222 doi:10.1371/journal.pone.0072222.
27. Maynard Smith J, Smith NH, O'Rourke M, Spratt BG, (1993) How clonal are bacteria? Proc Natl Acad Sci U S A 90: 4384-4388.
28. Schurko AM, Neiman M, Logsdon JM Jr, (2008) Signs of sex: what we know and how we know it. Trends Ecol Evol 2: 208-217.
29. Avise JC (2004) Molecular markers, Natural History and Evolution. 2nd ed. New York, London: Chapman & Hall.
30. Ngamskulrungroj P, Gilgado F, Faganello J, Litvintseva AP, Leal AL, et al. (2009) Genetic Diversity of the Cryptococcus Species Complex Suggests that Cryptococcus gattii Deserves to Have Varieties. PLoS ONE 4: e5862 doi:10.1371/journal.pone.0005862.
31. Voelz K, Ma H, Phadke S, Byrnes EJ, Zhu P, et al. (2013) Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii. PLoS Genet 9: e1003771 doi:10.1371/journal.pgen.1003771.
32. Campbell LT, Currie BJ, Krockenberger M, Malik R, Meyer W, et al. (2005) Clonality and Recombination in Genetically Differentiated Subgroups of Cryptococcus gattii. Eukaryotic Cell 4: 1403-1409.
33. Anderson TJ, Haubold B, Williams JT, Estrada-Franco JG, Richardson L, et al. (2000) Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol Biol Evol 17: 1467-1482.
34. Agrawal AF, (2006) Evolution of Sex: Why Do Organisms Shuffle Their Genotypes? Curr Biol 16: R696-R704.
35. Birky CW, (2005) Sex: is Giardia doing it in the dark? Curr Biol 15: R56-R58.
36. Monis PT, Caccio SM, Thompson RCA, (2009) Variation in Giardia: towards a taxonomic revision of the genus. Trends Parasitol 25: 93-100.
37. Takumi K, Swart A, Mank T, Lasek-Nesselquist E, Lebbad M, et al. (2012) Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure. Parasit Vectors 5: 168.
38. Campbell LT, Carter DE, (2006) Looking for sex in the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Res 6: 588-598.
39. Carriconde F, Gilgado F, Arthur I, Ellis D, Malik R, et al. (2011) Clonality and α-a Recombination in the Australian Cryptococcus gattii VGII Population- An Emerging Outbreak in Australia. PLoS ONE 6: e16936 doi:10.1371/journal.pone.0016936.
40. Chowdhary A, Hiremath SS, Sun S, Kowshik T, Randhawa HS, et al. (2011) Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India. Environm Microbiol 13: 1875-1888.
41. Li W, Averette AF, Desnos-Ollivier M, Ni M, Dromer F, et al. (2012) Genetic Diversity and Genomic Plasticity of Cryptococcus neoformans AD Hybrid Strains. G3 (Bethesda) 2: 83-97.
42. Chaturvedi V, Chaturvedi S, (2011) Cryptococcus gattii: a resurgent fungal pathogen. Trends Microbiol 19: 564-571.
43. Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Wright JR, et al. (2005) Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 437: 1360-1364.
44. Litvintseva AP, Mitchell TG, (2012) Population Genetic Analyses Reveal the African Origin and Strain Variation of Cryptococcus neoformans var. grubii. PLoS Pathog 8: e1002495 doi:10.1371/journal.ppat.1002495.
45. Matos O, Esteves F, (2010) Pneumocystis jirovecii multilocus gene sequencing: findings and implications. Future Microbiol 5: 1257-1267.
46. Cacciò SM, Sprong H, (2010) Giardia duodenalis: Genetic recombination and its implications for taxonomy and molecular epidemiology. Exp Parasitol 124: 107-112.
47. Feng Y, Xiao L, (2011) Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis. Clin Microbiol Rev 24: 110 doi:10.1128/CMR.00033-10.
48. Ryan A, Cacciò SM, (2013) Zoonotic potential of Giardia. Int J Parasitol 43: 943-956.
49. Mazars E, Guyot K, Durand I, Dei-Cas E, Boucher S, et al. (1997) Isoenzyme Diversity in Pneumocystis carinii from Rats, Mice, and Rabbits. J Infect Dis 175: 655-660.
50. Aliouat-Denis CM, Chabé M, Demanche C, Aliouat EM, Viscogliosi E, et al. (2008) Pneumocystis species, co-evolution and pathogenic power. Infect Genet Evol 8: 708-726.
51. Plutzer J, Ongerth J, Karanis P, (2010) Giardia taxonomy, phylogeny and epidemiology: Facts and open questions. Int J Hyg Environm Health 213: 321-333.
52. Wielinga CM, Thompson RCA, (2007) Comparative evaluation of Giardia duodenalis sequence data. Parasitol 134: 1795-1821.
53. Widmer G, Sullivan S, (2012) Genomics and population biology of Cryptosporidium species. Parasite Immunol 34: 61-71.
54. De Waele V, Van den Broeck F, Huyse T, McGrath G, Higgins I, et al. (2013) Panmictic Structure of the Cryptosporidium parvum Population in Irish Calves: Influence of Prevalence and Host Movement. Appl Environ Microbiol 79: 2534-2541.
55. Herges GR, Widmer G, Clark ME, Khan E, Giddings CW, et al. (2012) Evidence that Cryptosporidium parvum Populations Are Panmictic and Unstructured in the Upper Midwest of the United States. Appl Environ Microbiol 78: 8096-8101.
56. Su C, Khan A, Zhou P, Majumdara D, Ajzenberg D, et al. (2012) Globally diverse Toxoplasmagondii isolates comprise six major clades originating from a small number of distinct ancestral lineages. Proc Nat Acad Sci U S A 109: 5844-5849.
57. Xu J, (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molec Ecol 15: 1713-1731.
58. Zingales B, Miles MA, Campbell D, Tibayrenc M, Macedo AM, et al. (2012) The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications. Infect Genet Evol 12: 240-253.
59. Tanri{dotless}verdi S, Grinberg A, Chalmers RM, Hunter PR, Petrovic Z, et al. (2008) Inferences about the Global Population Structures of Cryptosporidium parvum and Cryptosporidium hominis. Appl Env Microbiol 74: 7227-7234.
60. Feng Y, Yang W, Ryan U Zhang L, Kvác M, et al. (2011) Development of a Multilocus Sequence Tool for Typing Cryptosporidium muris and Cryptosporidium andersoni. J Clin Microbiol 49: 34-41.
61. Wang R, Jian F, Zhang L, Ning C, Liu A, et al. (2012) Multilocus Sequence Subtyping and Genetic Structure of Cryptosporidium muris and Cryptosporidium andersoni. PLoS ONE 7: e43782 doi:10.1371/journal.pone.0043782.
62. Ngouanesavanh T, Guyot K, Certad G, Le Fichoux Y, Chartier C, et al. (2006) Cryptosporidium Population Genetics: Evidence of Clonality in Isolates from France and Haiti. J Euk Microbiol 53: S33-S36.
63. Xiao L, (2010) Molecular epidemiology of cryptosporidiosis: An update. Exp Parasitol 124: 80-89.
64. Widmer G, Lee Y, (2010) Comparison of Single- and Multilocus Genetic Diversity in the Protozoan Parasites Cryptosporidium parvum and C. hominis. Appl Environm Microbiol 76: 6639-6644.
65. Tibayrenc M, (1993) Entameba, Giardia and Toxoplasma: clones or cryptic species? Parasitol Today 9: 102-105.
66. Dobzhansky T (1937) Genetics and the origin of species. New York: Columbia University Press.
67. Cracraft J (1983) Species concept and speciation analysis. In: Johnson RF, editor. Current ornithology. New York: Plenum Press. pp. 159-187.
68. Fayer R, (2010) Taxonomy and species delimitation in Cryptosporidium. Exp Parasitol 124: 90-97.
69. Lasek-Nesselquist E, Welch DM, Thompston RCA, Steuart RF, Sogin ML, (2009) Genetic Exchange Within and Between Assemblages of Giardia duodenalis. J Euk Microbiol 56: 504-518.
70. Xu F, Jerlström-Hultqvist J, Andersson JO, (2012) Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species. Mol Biol Evol 29: 2895-2898.