Volume 10, Number 10—October 2004
Perspective
Strain Typing Methods and Molecular Epidemiology of Pneumocystis Pneumonia
Table
Gene locus | Primer sequence | Reference | |
---|---|---|---|
β-tubulin | |||
Forward | 5′ TCA TTA GGT GGT GGA ACG GG 3′ | (31) | |
Reverse | 5′ ATC ACC ATA TCC TGG ATC CG 3′ | (31) | |
DHPS (nested) | |||
1st round | DHPS F1 | 5′ CCT GGT ATT AAA CCA GTT TTG CC 3′ | (28) |
DHPS B45 | 5′ CAA TTT AAT AAA TTT CTT TCC AAA TAG CAT C 3′ | (29) | |
2nd round | DHPS AHUM | 5′ GCG CCT ACA CAT ATT ATG GCC ATT TTA AAT C 3′ | (29) |
DHPS BN | 5′ GGA ACT TTC AAC TTG GCA ACC AC 3′ | (29) | |
ITS (nested) | |||
1st round | 1724F | 5′ AAG TTG ATC AAA TTT GGT C 3′ | (22) |
ITS2R | 5′ CTC GGA CGA GGA TCC TCG CC 3′ | (22) | |
2nd round | ITS1F | 5′ CGT AGG TGA ACC TGC GGA AAG GAT C 3′ | (22) |
ITS2R1 | 5′ GTT CAG CGG GTG ATC CTG CCT G 3′ | (22) | |
ITS (nested) | |||
1st round | N18SF | 5′GGT CTT CGG ACT GGC AGC 3′ | (26) |
N26SRX | 5′ TTA CTA AGG GAA TCC TTG TTA 3′ | (26) | |
2nd round | ITSF3 | 5′ CTG CGG AAG GAT CAT TAG AAA 3′ | (24) |
ITS2R3 | 5′ GAT TTG AGA TTA AAA TTC TTG 3′ | (24) | |
MSG | |||
Forward | GK242 | 5′ TAT TTC TTG TAT CTA TGC GCT 3′ | (33) |
Reverse | GK244 | 5′ TCC GCG CAA AAA TAA GCA CT 3′ | (33) |
mt LSU rRNA (nested) | |||
1st Round | pAZ102-H | 5′ GTG TAC GTT GCA AAG TAC TC 3′ | (28) |
pAZ102-E | 5′ GAT GGC TGT TTC CAA GCC CA 3′ | (28) | |
2nd Round | pAZ102-X | 5′ GTG AAA TAC AAA TCG GAC TAG G 3′ | (25) |
pAZ102-Y | 5′ TCA CTT AAT ATT AAT TGG GGA GC 3′ | (25) | |
Nuclear 26S rRNA | |||
Forward | 5′ GAA GAA ATT CAA CCA AGC 3′ | (31) | |
Reverse | 5′ ATT TGG CTA CCT TAA GAG 3′ | (31) |
aDHPS, dihydropteroate synthase; ITS, internal transcribed spacer; MSG, major surface glycoprotein; mt LSU, mitochondrial large subunit.
References
- Vaneck J, Jirovec O, Lukes J. Interstitial plasma cell pneumonia in infants. Ann Pediatr (Paris). 1953;180:1–20.
- Edman JC, Kovacs JA, Masur H, Santi DV, Elwood HJ, Sogin ML. Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the Fungi. Nature. 1988;334:519–22. DOIPubMedGoogle Scholar
- Stringer SL, Stringer JL, Blase MA, Walzer PD, Cushion MT. Pneumocystis carinii: sequence from ribosomal RNA implies a close relationship with Fungi. Exp Parasitol. 1989;68:450–61. DOIPubMedGoogle Scholar
- Stringer JR, Beard CB, Miller RF, Wakefield AE. A new name (Pneumocystis jirovecii) for pneumocystis from humans. Emerg Infect Dis. 2002;8:891–6.PubMedGoogle Scholar
- Erikson OE. Pneumocystis carinii, a parasite in lungs of mammals, referred to a new family and order (Pneumocystidaceae, Pneumocystidales, Ascomycota). Systema Ascomycetum. 1994;13:165–80.
- Latouche S, Ortona E, Mazars E, Margutti P, Tamburrini E, Siracusano A, Biodiversity of Pneumocystis carinii hominis: typing with different DNA regions. J Clin Microbiol. 1997;35:383–7.PubMedGoogle Scholar
- Wakefield AE. DNA sequences indentical to Pneumocystis carinii f. sp. carinii and Pneumocystis carinii f. sp. hominis in samples of air spora. J Clin Microbiol. 1996;34:1754–9.PubMedGoogle Scholar
- Beard CB, Carter JL, Keely SP, Huang L, Pienazek NJ, Bens MS, Genetic variation in Pneumocystis carinii isolates from different geographic regions: implications for transmission. Emerg Infect Dis. 2000;6:265–72. DOIPubMedGoogle Scholar
- Helweg-Larsen J, Tsolaki AG, Miller RF, Lundgren B, Wakefield AE. Clusters of Pneumocystis carinii pneumonia: analysis of person-to-person transmission by genotyping. QJM. 1998;91:813–20. DOIPubMedGoogle Scholar
- Miller RF, Ambrose HE, Novelli V, Wakefield AE. Probable mother-to-infant transmission of Pneumocystis carinii f. sp. hominis infection. J Clin Microbiol. 2002;40:1555–7. DOIPubMedGoogle Scholar
- Keely SP, Stringer JR, Baughman RP, Linke MJ, Walzer PD, Smulian AG. Genetic variation among Pneumocystis carinii hominis isolates in recurrent pneumocystosis. J Infect Dis. 1995;172:595–8. DOIPubMedGoogle Scholar
- Totet A, Pautard JC, Raccurt C, Roux R, Nevez G. Genotypes at the internal transcribed spacers of the nuclear rRNA operon of Pneumocystis jirovecii in non-immunosuppressed infants without severe pneumonia. J Clin Microbiol. 2003;41:1173–80. DOIPubMedGoogle Scholar
- Nevez G, Totet A, Jounieaux V, Schmit JL, Dei-Cas E, Raccurt C. Pneumocystis jirovecii 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;41:181–6. DOIPubMedGoogle Scholar
- Wakefield AE, Lindley AR, Ambrose HE, Denis C-M, Miller RF. Limited asymptomatic carriage of Pneumocystis jirovecii in human immunodeficiency virus–infected patients. J Infect Dis. 2003;187:901–8. DOIPubMedGoogle Scholar
- Miller RF, Wakefield AE. Pneumocystis carinii genotypes and severity of pneumonia. Lancet. 1999;353:2039–40. DOIPubMedGoogle Scholar
- Helweg-Larsen J, Benfield TL, Eugen-Olsen J, Lundgren JD, Lundgren B. Effects of mutations in Pneumocystis carinii dihydropteroate synthase gene on outcome of AIDS-associated P. carinii pneumonia. Lancet. 1999;354:1347–51. DOIPubMedGoogle Scholar
- Kazanjian P, Armstrong W, Hossler PA, Burman W, Richardson J, Lee CH, Pneumocystis carinii mutations are associated with duration of sulfa or sulfone prophylaxis exposure in AIDS patients. J Infect Dis. 2000;182:551–7. DOIPubMedGoogle Scholar
- Huang L, Beard CB, Creasman J, Levy D, Duchin JS, Lee S, Sulfa or sulfone prophylaxis and geographic region predict mutations in the Pneumocystis carinii dihydropteroate synthase gene. J Infect Dis. 2000;182:1192–8. DOIPubMedGoogle Scholar
- Mei Q, Gurunathan S, Masur H, Kovacs JA. Failure of co-trimoxazole in Pneumocystis carinii infection and mutations in dihydropteroate synthase gene. Lancet. 1998;351:1631–2. DOIPubMedGoogle Scholar
- Denis CM, Mazars E, Guyot K, Odberg-Ferragut C, Viscogliosi E, Dei-Cas E, Genetic divergence at the SODA locus of six different formae speciales of Pneumocystis carinii. Med Mycol. 2000;38:289–300.PubMedGoogle Scholar
- Banerji S, Lugli EB, Miller RF, Wakefield AE. Analysis of genetic diversity at the arom locus in isolates of Pneumocystis carinii. J Eukaryot Microbiol. 1995;42:675–9. DOIPubMedGoogle Scholar
- Lu J-J, Bartlett MS, Shaw MM, Queener SF, Smith JW, Oritiz-Rivera M, Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes. J Clin Microbiol. 1994;32:2904–12.PubMedGoogle Scholar
- Lee CH, Helweg-Larsen J, Tang X, Jin S, Li B, Bartlett MS, Update of Pneumocystis carinii f. sp. hominis typing based on nucleotide sequence variation in internal transcribed spacer regions of rRNA genes. J Clin Microbiol. 1998;36:734–41.PubMedGoogle Scholar
- 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;174:141–56. DOIPubMedGoogle Scholar
- Tsolaki AG, Beckers P, Wakefield AI. Pre-AIDS era isolates of Pneumocystis carinii f. sp. hominis: high genotype similarity with contemporary isolates. J Clin Microbiol. 1998;36:90–3.PubMedGoogle Scholar
- 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. DOIPubMedGoogle Scholar
- Nimri LF, Moura NS, Huang L, del Rio C, Rimland D, Duchin JS, Genetic diversity of Pneumocystis carinii f. sp. hominis based on variations in nucleotide sequences of the internal transcribed spacers of rRNA genes. J Clin Microbiol. 2002;40:1146–51. DOIPubMedGoogle Scholar
- Wakefield AE, Pixley FJ, Banerji S, Sinclair K, Miller RF, Moxon EF, Detection of Pneumocystis carinii with DNA amplification. Lancet. 1990;336:451–3. DOIPubMedGoogle Scholar
- Lane BR, Ast JC, Hossler PA, Mindell DP, Bartlett MS, Smith JW, Dihydropteroate synthase polymorphisms in Pneumocystis carinii. J Infect Dis. 1997;175:482–5. DOIPubMedGoogle Scholar
- Armstrong W, Meshnick S, Kazanjian P. Pneumocystis carinii mutations associated with sulfa and sulfone prophylaxis failures in immunocompromised patients. Microbes Infect. 2000;2:61–7. DOIPubMedGoogle Scholar
- Nahimana A, Blanc DS, Francioli P, Bille J, Hauser PM. Typing of Pneumocystis carinii f. sp. hominis by PCR-SSCP to indicate high frequency of co-infections. J Med Microbiol. 2000;49:753–8.PubMedGoogle Scholar
- Hauser PM, Blanc DS, Sudre P, Manoloff ES, Nahimana A, Bille J, Genetic diversity of Pneumocystis carinii in HIV-positive and -negative patients as revealed by PCR-SSCP typing. AIDS. 2001;15:461–6. DOIPubMedGoogle Scholar
- Ma L, Kutty G, Jia Q, Imamichi H, Huang L, Atzori C, Analysis of variation in tandem repeats in the intron of the major surface glycoprotein expression site of the human form of Pneumocystis carinii. J Infect Dis. 2002;186:1647–54. DOIPubMedGoogle Scholar
- Edman JC, Hatton TW, Nam M, Turner R, Mei Q, Angus CW, A single expression site with a conserved leader sequence regulates variation of expression of the Pneumocystis carinii family of major surface glycoprotein genes. DNA Cell Biol. 1996;15:989–99. DOIPubMedGoogle Scholar
- Kutty G, Ma L, Kovacs JA. Characterization of the expression site of the major surface glycoprotein of human-derived Pneumocystis carinii. Mol Microbiol. 2001;42:183–93. DOIPubMedGoogle Scholar
- Helweg-Larsen J, Lee C-H, Jin S, Hsueh JY, Benfield TL, Hansen J, Clinical correlation of variations in the internal transcribed spacer regions of rRNA genes in Pneumocystis carinii f. sp. hominis. AIDS. 2001;15:451–9. DOIPubMedGoogle Scholar
- Huang SN, Fisher SH, O’Shaughnessy E, Gill VJ, Masur H, Kovacs JA. Development of a PCR assay for diagnosis of Pneumocystis carinii pneumonia based on amplification of the multicopy major surface glycoprotein gene family. Diagn Microbiol Infect Dis. 1999;35:27–32. DOIPubMedGoogle Scholar
- Larsen HH, Masur H, Kovacs JA, Gill VJ, Silcott VA, Kogulan P, Development and evaluation of a quantitative, touch-down, real-time PCR assay for diagnosing Pneumocystis carinii pneumonia. J Clin Microbiol. 2002;40:490–4. DOIPubMedGoogle Scholar
- Maher NH, Vermund SH, Welsh DA, Dillon HK, Awooda A, Unnasch TR. Development and characterization of a molecular viability assay for Pneumocystis carinii f. sp. hominis. J Infect Dis. 2001;183:1825–7. DOIPubMedGoogle Scholar
- Latouche S, Totet A, Lacube P, Bolognini J, Nevez G, Roux P. Development of an RT-PCR on the heatshock protein 70 gene for viability detection of Pneumocystis carinii f. sp. hominis in patients with pneumocystosis and in air sample. J Eukaryot Microbiol. 2001;48(Suppl):176–7S. DOIGoogle Scholar
Page created: March 30, 2011
Page updated: March 30, 2011
Page reviewed: March 30, 2011
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.