Circulating genotypes of Pneumocystis jirovecii and its clinical correlation in patients from a single tertiary center in India

  • Y. Singh
  • B. R. Mirdha
  • R. Guleria
  • S. Khalil
  • A. Panda
  • R. Chaudhry
  • A. Mohan
  • S. K. Kabra
  • L. Kumar
  • S. K. Agarwal
Original Article
First Online:
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Accepted:

Abstract

The present study was carried out with the objectives of genotyping Pneumocystis jirovecii at three distinct loci, to identify the single nucleotide polymorphisms (SNPs), and to study its clinical implications in patients with Pneumocystis pneumonia (PCP). Analysis of genetic diversity in P. jirovecii from immunocompromised patients was carried out by genotyping at three distinct loci encoding mitochondrial large subunit rRNA (mtLSU rRNA), cytochrome b (CYB), and superoxide dismutase (SOD) using polymerase chain reaction (PCR) assays followed by direct DNA sequencing. Of the 300 patients enrolled in the present study, 31 (10.33%) were positive for PCP by a specific mtLSU rRNA nested PCR assay, whereas only 15 P. jirovecii could be amplified at the other two loci (SOD and CYB). These positives were further subjected to sequence typing. Important genotypic combinations between four SNPs (mt85, SOD110, SOD215, and CYB838) and clinical outcomes could be observed in the present study, and mt85A, mt85T, and SOD110C/SOD215T were frequently associated with “negative follow-up”. These SNPs were also noted to be relatively more prevalent amongst circulating genotypes in our study population. The present study is the first of its kind from the Indian subcontinent and demonstrated that potential SNPs of P. jirovecii may possibly be attributed to the clinical outcome of PCP episodes in terms of severity or fatality in different susceptible populations likely to develop PCP during their course of illness.

Keywords

Polymerase Chain Reaction Assay Polymerase Chain Reaction Condition Human Immunodeficiency Virus Status Atovaquone Pneumocystis Jirovecii 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Notes

Acknowledgments

The authors sincerely thank the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Government of India, New Delhi, for providing the necessary financial support to carry out this work.

Compliance with ethical standards

Funding

Provided by the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), New Delhi, Government of India (DST grant number: SB/SO/HS-0046/2013).

Conflict of interest

The authors declare no conflict of interest.

Ethical approval

The study was approved by the institutional ethical committee (IESC/T-77).

Informed consent

Written Informed consent was obtained from all the patients who participated in this study.

References

  1. 1.
    Centers for Disease Control and Prevention (CDC) (1991) HIV/AIDS surveillance report 1990Google Scholar
  2. 2.
    Kaplan JE, Hanson D, Dworkin MS et al (2000) Epidemiology of human immunodeficiency virus-associated opportunistic infections in the United States in the era of highly active antiretroviral therapy. Clin Infect Dis 30(Suppl 1):S5–S14. doi: 10.1086/313843 CrossRefPubMedGoogle Scholar
  3. 3.
    Morris A, Sciurba FC, Lebedeva IP et al (2004) Association of chronic obstructive pulmonary disease severity and Pneumocystis colonization. Am J Respir Crit Care Med 170:408–413. doi: 10.1164/rccm.200401-094OC CrossRefPubMedGoogle Scholar
  4. 4.
    Morris A, Sciurba FC, Norris KA (2008) Pneumocystis: a novel pathogen in chronic obstructive pulmonary disease? COPD 5:43–51. doi: 10.1080/15412550701817656 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Chabé M, Dei-Cas E, Creusy C et al (2004) Immunocompetent hosts as a reservoir of Pneumocystis organisms: histological and rt-PCR data demonstrate active replication. Eur J Clin Microbiol Infect Dis 23:89–97. doi: 10.1007/s10096-003-1092-2 CrossRefPubMedGoogle Scholar
  6. 6.
    Monnet X, Vidal-Petiot E, Osman D et al (2008) Critical care management and outcome of severe Pneumocystis pneumonia in patients with and without HIV infection. Crit Care 12:R28. doi: 10.1186/cc6806 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Matos O, Esteves F (2010) Epidemiology and clinical relevance of Pneumocystis jirovecii Frenkel, 1976 dihydropteroate synthase gene mutations. Parasite 17:219–232. doi: 10.1051/parasite/2010173219 CrossRefPubMedGoogle Scholar
  8. 8.
    Schmoldt S, Schuhegger R, Wendler T et al (2008) Molecular evidence of nosocomial Pneumocystis jirovecii transmission among 16 patients after kidney transplantation. J Clin Microbiol 46:966–971. doi: 10.1128/JCM.02016-07 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Huang L, Cattamanchi A, Lucian Davis J et al (2011) HIV-associated Pneumocystis pneumonia. Proc Am Thorac Soc 8(3):294–300. doi: 10.1513/pats.201009-062WR CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Curran T, McCaughey C, Coyle PV (2013) Pneumocystis jirovecii multilocus genotyping profiles in Northern Ireland. J Med Microbiol 62:1170–1174. doi: 10.1099/jmm.0.057794-0 CrossRefPubMedGoogle Scholar
  11. 11.
    Miller RF, Lindley AR, Malin AS et al (2005) Isolates of Pneumocystis jirovecii from Harare show high genotypic similarity to isolates from London at the superoxide dismutase locus. Trans R Soc Trop Med Hyg 99:202–206. doi: 10.1016/j.trstmh.2004.09.005 CrossRefPubMedGoogle Scholar
  12. 12.
    Miller RF, Lindley AR, Copas A et al (2005) Genotypic variation in Pneumocystis jirovecii isolates in Britain. Thorax 60:679–682. doi: 10.1136/thx.2004.039818 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Esteves F, Gaspar J, Marques T et al (2010) Identification of relevant single-nucleotide polymorphisms in Pneumocystis jirovecii: relationship with clinical data. Clin Microbiol Infect 16:878–884. doi: 10.1111/j.1469-0691.2009.03030.x CrossRefPubMedGoogle Scholar
  14. 14.
    Esteves F, Gaspar J, Tavares A et al (2010) Population structure of Pneumocystis jirovecii isolated from immunodeficiency virus-positive patients. Infect Genet Evol 10:192–199. doi: 10.1016/j.meegid.2009.12.007 CrossRefPubMedGoogle Scholar
  15. 15.
    Matos O, Esteves F (2010) Pneumocystis jirovecii multilocus gene sequencing: findings and implications. Future Microbiol 5:1257–1267. doi: 10.2217/fmb.10.75 CrossRefPubMedGoogle Scholar
  16. 16.
    Beard CB, Carter JL, Keely SP et al (2000) Genetic variation in Pneumocystis carinii isolates from different geographic regions: implications for transmission. Emerg Infect Dis 6:265–272. doi: 10.3201/eid0603.000306 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Esteves F, Montes-Cano MA, de la Horra C et al (2008) Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain. Clin Microbiol Infect 14:356–362. doi: 10.1111/j.1469-0691.2007.01944.x CrossRefPubMedGoogle Scholar
  18. 18.
    Wakefield AE, Pixley FJ, Banerji S et al (1990) Amplification of mitochondrial ribosomal RNA sequences from Pneumocystis carinii DNA of rat and human origin. Mol Biochem Parasitol 43:69–76. doi: 10.1016/0166-6851(90)90131-5 CrossRefPubMedGoogle Scholar
  19. 19.
    Esteves F, Gaspar J, de Sousa B et al (2012) Pneumocystis jirovecii multilocus genotyping in pooled DNA samples: a new approach for clinical and epidemiological studies. Clin Microbiol Infect 18:E177–E184. doi: 10.1111/j.1469-0691.2012.03828.x CrossRefPubMedGoogle Scholar
  20. 20.
    Barry SM, Johnson MA (2001) Pneumocystis carinii pneumonia: a review of current issues in diagnosis and management. HIV Med 2:123–132. doi: 10.1046/j.1468-1293.2001.00062.x CrossRefPubMedGoogle Scholar
  21. 21.
    Walzer PD, Evans HE, Copas AJ et al (2008) Early predictors of mortality from Pneumocystis jirovecii pneumonia in HIV-infected patients: 1985–2006. Clin Infect Dis 46:625–633. doi: 10.1086/526778 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Wakefield AE (1996) DNA sequences identical to Pneumocystis carinii f. sp. carinii and Pneumocystis carinii f. sp. hominis in samples of air spora. J Clin Microbiol 34:1754–1759PubMedPubMedCentralGoogle Scholar
  23. 23.
    Kazanjian P, Armstrong W, Hossler PA et al (2001) Pneumocystis carinii cytochrome b mutations are associated with atovaquone exposure in patients with AIDS. J Infect Dis 183:819–822. doi: 10.1086/318835 CrossRefPubMedGoogle Scholar
  24. 24.
    Walker DJ, Wakefield AE, Dohn MN et al (1998) Sequence polymorphisms in the Pneumocystis carinii cytochrome b gene and their association with atovaquone prophylaxis failure. J Infect Dis 178:1767–1775CrossRefPubMedGoogle Scholar
  25. 25.
    Helweg-Larsen J, Benfield TL, Eugen-Olsen J et al (1999) Effects of mutations in Pneumocystis carinii dihydropteroate synthase gene on outcome of AIDS-associated P. carinii pneumonia. Lancet 354:1347–1351. doi: 10.1016/S0140-6736(99)03320-6 CrossRefPubMedGoogle Scholar
  26. 26.
    Hauser PM, Sudre P, Nahimana A et al (2001) Prophylaxis failure is associated with a specific Pneumocystis carinii genotype. Clin Infect Dis 33:1080–1082. doi: 10.1086/322659 CrossRefPubMedGoogle Scholar
  27. 27.
    Crothers K, Beard CB, Turner J et al (2005) Severity and outcome of HIV-associated Pneumocystis pneumonia containing Pneumocystis jirovecii dihydropteroate synthase gene mutations. AIDS 19:801–805. doi: 10.1097/01.aids.0000168974.67090.70 CrossRefPubMedGoogle Scholar
  28. 28.
    Gupta R, Mirdha BR, Guleria R et al (2011) Genotypic variation of Pneumocystis jirovecii isolates in India based on sequence diversity at mitochondrial large subunit rRNA. Int J Med Microbiol 301(3):267–272. doi: 10.1016/j.ijmm .2010.05.001 CrossRefPubMedGoogle Scholar
  29. 29.
    Montes Cano MA, de la Horra C, Martín-Juan J et al (2004) Pneumocystis jiroveci genotypes in the Spanish population. Clin Infect Dis 39(1):123–128. doi: 10.1086/421778 CrossRefPubMedGoogle Scholar
  30. 30.
    Respaldiza N, Montes-Cano MA, Dapena FJ et al (2005) Prevalence of colonisation and genotypic characterisation of Pneumocystis jirovecii among cystic fibrosis patients in Spain. Clin Microbiol Infect 11:1012–1015. doi: 10.1111/j.1469-0691.2005.01276.x CrossRefPubMedGoogle Scholar
  31. 31.
    van Hal SJ, Gilgado F, Doyle T et al (2009) Clinical significance and phylogenetic relationship of novel Australian Pneumocystis jirovecii genotypes. J Clin Microbiol 47:1818–1823. doi: 10.1128/JCM.02102-08 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Kim T, Lee S-O, Hong H-L et al (2015) Clinical characteristics of hospital-onset Pneumocystis pneumonia and genotypes of Pneumocystis jirovecii in a single tertiary centre in Korea. BMC Infect Dis 15:102. doi: 10.1186/s12879-015-0847-6 CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Höcker B, Wendt C, Nahimana A et al (2005) Molecular evidence of Pneumocystis transmission in pediatric transplant unit. Emerg Infect Dis 11(2):330–332. doi: 10.3201/eid1102.040820 CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Denis CM, Guyot K, Wakefield AE et al (1998) Molecular cloning and characterization of a superoxide dismutase (SOD) gene in Pneumocystis carinii. J Eukaryot Microbiol 45:475–483. doi: 10.1111/j.1550-7408.1998.tb05103.x CrossRefPubMedGoogle Scholar
  35. 35.
    Denis CM, Mazars E, Guyot K et al (2000) Genetic divergence at the SODA locus of six different formae speciales of Pneumocystis carinii. Med Mycol 38:289–300. doi: 10.1080/mmy.38.4.289.300 CrossRefPubMedGoogle Scholar
  36. 36.
    Wakefield AE, Lindley AR, Ambrose HE et al (2003) Limited asymptomatic carriage of Pneumocystis jiroveci in human immunodeficiency virus-infected patients. J Infect Dis 187:901–908. doi: 10.1086/368165 CrossRefPubMedGoogle Scholar
  37. 37.
    Lane BR, Ast JC, Hossler PA et al (1997) Dihydropteroate synthase polymorphisms in Pneumocystis carinii. J Infect Dis 175:482–485. doi: 10.1093/infdis/175.2.482 CrossRefPubMedGoogle Scholar
  38. 38.
    Monroy-Vaca EX, de Armas Y, Illnait-Zaragozí MT et al (2014) Genetic diversity of Pneumocystis jirovecii in colonized Cuban infants and toddlers. Infect Genet Evol 22:60–66. doi: 10.1016/j.meegid.2013.12.024 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Y. Singh
    • 1
  • B. R. Mirdha
    • 1
  • R. Guleria
    • 2
  • S. Khalil
    • 1
  • A. Panda
    • 1
  • R. Chaudhry
    • 1
  • A. Mohan
    • 2
  • S. K. Kabra
    • 3
  • L. Kumar
    • 4
  • S. K. Agarwal
    • 5
  1. 1.Department of MicrobiologyAll India Institute of Medical SciencesNew DelhiIndia
  2. 2.Department of Pulmonary Medicine and Sleep DisordersAll India Institute of Medical SciencesNew DelhiIndia
  3. 3.Department of PediatricsAll India Institute of Medical SciencesNew DelhiIndia
  4. 4.Department of Medical OncologyAll India Institute of Medical SciencesNew DelhiIndia
  5. 5.Department of NephrologyAll India Institute of Medical SciencesNew DelhiIndia

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