Pneumocystis jirovecii haplotypes at the internal transcribed spacers of the rRNA operon in French HIV-negative patients with diverse clinical presentations of Pneumocystis infections

Medical Mycology

Volumn 51, Issue 8, 2013, Pages 851-862

  Le Gal, Solene ^a,b   Rouille, Amelie ^b   Gueguen, Paul ^b,c   Virmaux, Michele ^a   Berthou, Christian ^b,d   Guillerm, Gaëlle ^b,d   Couturaud, Francis ^b,c   Le Meur, Yann ^b,d   Damiani, Celine ^e,f   Totet, Anne ^e,f   Nevez, Gilles ^a,b  

^a SERVICE DE RHUMATOLOGIE   (France)

^b BREST UNIVERSITY HOSPITAL   (France)

^c UNIVERSITÉ DE BRETAGNE OCCIDENTALE   (France)

^d Universite de Brest   (France)

^e AMIENS UNIVERSITY HOSPITAL   (France)

^f UNIVERSITÉ DE PICARDIE JULES VERNE   (France)

Author keywords

Colonization; HIV negative; Internal transcribed spacers; Pneumocystis jirovecii; Pneumocystis pneumonia

Indexed keywords

INTERNAL TRANSCRIBED SPACER 1; INTERNAL TRANSCRIBED SPACER 2; RIBOSOME RNA;

ADOLESCENT; ADULT; ARTICLE; CHILD; CONTROLLED STUDY; EUROPE; FEMALE; FRANCE; FUNGAL COLONIZATION; FUNGAL DETECTION; FUNGAL EXAMINATION; FUNGUS ISOLATION; GENE AMPLIFICATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS NEGATIVE PATIENT; IN VITRO STUDY; MAJOR CLINICAL STUDY; MALE; MIXED INFECTION; NUCLEOTIDE SEQUENCE; OPERON; PATIENT; PNEUMOCYSTIS JIROVECI; PNEUMOCYSTIS PNEUMONIA; PNEUMOCYSTOSIS; PRESCHOOL CHILD; RETROSPECTIVE STUDY; SCHOOL CHILD; UNITED STATES;

FUNGI; PNEUMOCYSTIS; PNEUMOCYSTIS JIROVECII;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; CHILD; CHILD, PRESCHOOL; DNA, RIBOSOMAL SPACER; FEMALE; FRANCE; GENETIC VARIATION; HAPLOTYPES; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PNEUMOCYSTIS INFECTIONS; PNEUMOCYSTIS JIROVECII; YOUNG ADULT;

EID: 84885904373     PISSN: 13693786     EISSN: 14602709     Source Type: Journal    
DOI: 10.3109/13693786.2013.824123     Document Type: Article

References (49)

1. Walzer PD, Cushion MT (eds) . P neumocystis Pneumonia . New York: Marcel Dekke r; 2005
2. Stringer JR, Beard CB, Miller RF, Wakefield AE . A new name (P neumocystis jiroveci) for Pneumocystis from humans . Emerg Infect Dis 2002 ; 8: 891-896
3. Le Gal S, Damiani C, Rouille A, et al . A cluster of Pneumocystis infections among renal transplant recipients: Molecular evidence of colonized patients as potential infectious sources of Pneumocystis jirovecii . Clin Infect Dis 2012 ; 54: E62-71
4. Redhead SA, Cushion MT, Frenkel JK, Stringer JR . P neumocystis and Trypanosoma cruzi: Nomenclature and typifications . J Eukaryot Microbiol 2006 ; 53: 2-11
5. Tasaka S, Tokuda H . P neumocystis jirovecii pneumonia in non-HIVinfected patients in the era of novel immunosuppressive therapies. J Infect Chemother 2012 ; 18: 793-806
6. Morris A, Norris KA . Colonization by P neumocystis jirovecii and its role in disease . Clin Microbiol Rev 2012 ; 25: 297-317
7. Nevez G, Raccurt C, Jounieaux V, Dei-Cas E, Mazars E . Pneumocystosis versus pulmonary Pneumocystis carinii colonization in HIVnegative and HIV-positive patients . AIDS 1999 ; 13: 535-536
8. Hauser PM, Burdet FX, Cisse OH, et al . Comparative genomics suggests that the fungal pathogen Pneumocystis is an obligate parasite scavenging amino acids from its host ' s lungs . PLoS One 2010; 5: E15152
9. Lu JJ, Bartlett MS, Shaw MM, et al . Typing of P neumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes . J Clin Microbiol 1994 ; 32: 2904-2912
10. Lee CH, Helweg-Larsen J, Tang X, et al . Update on Pneumocystis carinii f. sp. hominis typing based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes . J Clin Microbiol 1998 ; 36: 734-741
11. Tsolaki AG, Miller RF, Underwood AP, Banerji S, Wakefield AE. Genetic diversity at the internal transcribed spacer regions of the rRNA operon among isolates of Pneumocystis carinii from AIDS patients with recurrent pneumonia . J Infect Dis 1996 ; 174: 141-156
12. Tsolaki AG, Miller RF, Wakefield AE . Oropharyngeal samples for genotyping and monitoring response to treatment in AIDS patients with Pneumocystis carinii pneumonia . J Med Microbiol 1999 ; 48: 897-905
13. Miller RF, Wakefield AE . Pneumocystis carinii genotypes and severity of pneumonia . Lancet 1999 ; 353: 2039-2040
14. Tsolaki AG, Beckers P, Wakefield AE . Pre-AIDS era isolates of Pneumocystis carinii f. sp. hominis: High genotype similarity with contemporary isolates . J Clin Microbiol 1998 ; 36: 90-93
15. Helweg-Larsen J, Lee CH, Jin S, et al . Clinical correlation of variations in the internal transcribed spacer regions of rRNA genes in Pneumocystis carinii f. sp. hominis . AIDS 2001 ; 15: 451-459
16. Matos O, Lee CH, Jin S, et al . Pneumocystis jiroveci in Portuguese immunocompromised patients: Association of specifi c ITS genotypes with treatment failure, bad clinical outcome and childhood . Infect Genet Evol 2003 ; 3: 281-285
17. Esteves F, Montes-Cano MA, de la Horra C, et al . Pneumocystis jirovecii multilocus genotyping profi les in patients from Portugal and Spain . Clin Microbiol Infect 2008 ; 14: 356-362
18. Valerio A, Tronconi E, Mazza F, et al . Genotyping of Pneumocystis jiroveci pneumonia in Italian AIDS patients. Clinical outcome is infl uenced by dihydropteroate synthase and not by internal transcribed spacer genotype . J Acquir Immune Defi c Syndr 2007 ; 45: 521-528
19. Beser J, Botero-Kleiven S, Lebbad M, Hagblom P, Fernandez V. A limited number of ITS haplotypes defi nes the diversity of Pneumocystis jirovecii strains in Sweden . Infect Genet Evol 2011 ; 11: 948-954
20. Nimri LF, Moura IN, Huang L, et al . Genetic diversity of P neumocystis carinii f. sp. hominis based on variations in nucleotide sequences of internal transcribed spacers of rRNA genes . J Clin Microbiol 2002 ; 40: 1146-1151
21. Robberts FJ, Liebowitz LD, Chalkley LJ . Genotyping and coalescent phylogenetic analysis of Pneumocystis jiroveci from South Africa. J Clin Microbiol 2004 ; 42: 1505-1510
22. van Hal SJ, Gilgado F, Doyle T, et al . Clinical signifi cance and phylogenetic relationship of novel Australian Pneumocystis jirovecii genotypes . J Clin Microbiol 2009 ; 47: 1818-1823
23. Hosoya N, Takahashi T, Wada M, et al . Genotyping of P neumocystis carinii f. sp. hominis isolates in Japan based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes. Microbiol Immunol 2000 ; 44: 591-596
24. Matsumura Y, Shindo Y, Iinuma Y, et al . Clinical characteristics of Pneumocystis pneumonia in non-HIV patients and prognostic factors including microbiological genotypes . BMC Infect Dis 2011; 11: 76
25. Siripattanapipong S, Worapong J, Mungthin M, Leelayoova S, Tanariya P . Genotypic study of Pneumocystis jirovecii in human immunodefi ciency virus-positive patients in Thailand . J Clin Microbiol 2005 ; 43: 2104-2110
26. Gupta R, Mirdha BR, Guleria R, et al . Genotyping and phylogenetic analysis of Pneumocystis jirovecii isolates from India . Infect Genet Evol 2010 ; 10: 712-719
27. Li K, He A, Cai WP, et al . Genotyping of Pneumocystis jirovecii isolates from Chinese HIV-infected patients based on nucleotide sequence variations in the internal transcribed spacer regions of rRNA genes . Med Mycol 2013 ; 51: 108-112
28. Nevez G, Totet A, Jounieaux V, et al . Pneumocystis jiroveci internal transcribed spacer types in patients colonized by the fungus and in patients with pneumocystosis from the same French geographic region. J Clin Microbiol 2003 ; 41: 181-186
29. Latouche S, Poirot JL, Bernard C, Roux P . Study of internal transcribed spacer and mitochondrial large-subunit genes of Pneumocystis carinii hominis isolated by repeated bronchoalveolar lavage from human immunodefi ciency virus-infected patients during one or several episodes of pneumonia . J Clin Microbiol 1997 ; 35: 1687-1690
30. Totet A, Pautard JC, Raccurt C, Roux P, Nevez G . Genotypes at the internal transcribed spacers of the nuclear rRNA operon of Pneumocystis jiroveci in nonimmunosuppressed infants without severe pneumonia . J Clin Microbiol 2003 ; 41: 1173-1180
31. Meliani L, Develoux M, Marteau-Miltgen M, et al . Real time quantitative PCR assay for Pneumocystis jirovecii detection . J Eukaryot Microbiol 2003; 50 (Suppl.): 651
32. Totet A, Meliani L, Lacube P, et al . Immunocompetent infants as a human reservoir for Pneumocystis jirovecii: Rapid screening by noninvasive sampling and real-time PCR at the mitochondrial large subunit rRNA gene . J Eukaryot Microbiol 2003 ; 50 (Suppl.): 668-669
33. Beser J, Hagblom P, Fernandez V . Frequent in vitro recombination in internal transcribed spacers 1 and 2 during genotyping of Pneumocystis jirovecii . J Clin Microbiol 2007 ; 45: 881-886
34. Helweg-Larsen J . P neumocystis jiroveci . Applied molecular microbiology, epidemiology and diagnosis. Dan Med Bull 2004 ; 51: 251-273
35. Struelens MJ . Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems . Clin Microbiol Infect 1996 ; 2: 2-11
36. Hunter PR . Reproducibility and indices of discriminatory power of microbial typing methods . J Clin Microbiol 1990 ; 28: 1903-1905
37. Choukri F, Menotti J, Sarfati C, et al . Quantification and spread of Pneumocystis jirovecii in the surrounding air of patients with Pneumocystis pneumonia . Clin Infect Dis 2010 ; 51: 259-265
38. Tang X, Bartlett MS, Smith JW, Lu JJ, Lee CH . Determination of copy number of rRNA genes in Pneumocystis carinii f. sp. hominis . J Clin Microbiol 1998 ; 36: 2491-2494
39. Cisse OH, Pagni M, Hauser PM . D e Novo assembly of the P neumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient . MBio 2012 ; 4: E00428-12
40. Meyerhans A, Vartanian JP, Wain-Hobson S . DNA recombination during PCR . Nucleic Acids Res 1990 ; 18: 1687-1691
41. Tanabe K, Sakihama N, Farnert A, et al . In vitro recombination during PCR of Plasmodium falciparum DNA: A potential pitfall in molecular population genetic analysis . Mol Biochem Parasitol 2002 ; 122: 211-216
42. Lundberg KS, Shoemaker DD, Adams MW, et al . High-fi delity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus . Gene 1991 ; 108: 1-6
43. Hauser PM, Blanc DS, Sudre P, et al . Genetic diversity of Pneumocystis carinii in HIV-positive and -negative patients as revealed by PCR-SSCP typing . AIDS 2001 ; 15: 461-466
44. Beard CB, Roux P, Nevez G, et al . S train typing methods and molecular epidemiology of Pneumocystis pneumonia . Emerg Infect Dis 2004 ; 10: 1729-1735
45. Matos O, Esteves F . Pneumocystis jirovecii multilocus gene sequencing: Fi ndings and implications . Future Microbiol 2010 ; 5: 1257-1267
46. Kasuga T, White TJ, Taylor JW . Estimation of nucleotide substitution rates in Eurotiomycete fungi . Mol Biol Evol 2002 ; 19: 2318-2324
47. Institut de Veille Sanitaire . Infection à VIH et Sida, Base de Donn é es Sida [database on the Internet] . Saint-Maurice: Institut de Veille Sanitaire (France) [cited 2013 Feb 28]. Available at: Http:// www.invs.sante.fr/surveillance/vih-sida/bdd-sida/index.htm
48. Le Gal S, Damiani C, Perrot M, et al . Circulation of P neumocystis dihydropteroate synthase mutants in France . Diagn Microbiol Infect Dis 2012 ; 74: 119-124
49. Damiani C, Choukri F, Le Gal S, et al . Possible nosocomial transmission of Pneumocystis jirovecii . Emerg Infect Dis 2012 ; 18: 877-878