177
Views
0
CrossRef citations to date
0
Altmetric
Epidemiological and environmental studies

What can be learned from genotyping of fungi?

, &
Pages S60-S69 | Received 02 Feb 2010, Accepted 08 Apr 2010, Published online: 10 Nov 2010

References

  • van Belkum A, Tassios PT, Dijkshoorn L, . Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Micobiol Infect Dis 2007; 13: 1–46.
  • de Valk HA, Klaassen CHW, Meis JFGM. Molecular typing of Aspergillus species. Mycoses 2008; 51: 463–476.
  • Harun A, Permodo H, Gilgado F, . Genotyping of Scedosporium species: a review of molecular approaches. Med Mycol 2009; 47: 406–414.
  • Nagy E, Kredics L, Antal Z, Papp T. Molecular diagnosis, epidemiology and taxonomy of emerging medically important filamentous fungi. Rev Med Microbiol 2004; 15: 153–162.
  • Birch M, Anderson MJ, Denning DW. Molecular typing of Aspergillus species. J Hosp Infect 1995; 30: 339–351.
  • Varga J. Molecular typing of aspergilli: recent developments and outcomes. Med Mycol 2006; 44: 149–161.
  • Debeaupuis JP, Sarfati J, Chazalet V, Latgé JP. Genetic diversity among clinical and environmental isolates of Aspergillus fumigatus. Infect Immun 1997; 65: 3080–3085.
  • O’Gorman CM, Fuller HT, Dyer PS. Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature 2009; 22: 471–474.
  • Rydholm C, Szakacs G, Lutzoni F. Low genetic variation and no detectable population structure in Aspergillus fumigatus compared to closely related Neosartorya species. Eukaryot Cell 2006; 5: 650–657.
  • Varga J, Tóth B. Genetic variability and reproductive mode of Aspergillus fumigatus. Infect Genet Evol 2003; 3: 3–17.
  • Nagano Y, Elborn S, Millar BC, . Comparison of techniques to examine the diversity of fungi in adult patients with cystic fibrosis. Med Mycol 2010; 48: 166–176.
  • Gil-Lamaignere C, Roilides E, Hacker J, Müller FMC. Molecular typing for fungi – a critical review of the possibilities and limitations of currently and future methods. Clin Microbiol Infect 2003; 9: 172–185.
  • Odds FC, Jacobsen MD. Multilocus sequence typing of pathogenic Candida species. Eukaryot Cell 2008; 7: 1075–1084.
  • Olive DM, Bean P. Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 1999; 37: 1661–1669.
  • Arbeit RD. Laboratory procedures for the epidemiologic analysis of microorganisms. Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH. Manual of Clinical Microbiology, 6th. Washington DC: ASM Press, 1995: 190–208.
  • Vanhee LME, Symoens F, Jacobsen MD, Nelis HJ, Coenye T. Comparison of multiple typing methods for Aspergillus fumigatus. Clin Microbiol Infect 2009; 15: 643–650.
  • Williamson ECM, Leeming JP. Molecular approaches for the diagnosis and epidemiological investigation of Aspergillus infection. Mycoses 1999; 42: 7–10.
  • Brookman JL, Denning DW. Molecular genetics in Aspergillus fumigatus. Curr Opin Microbiol 2000; 3: 468–474.
  • Hinrikson HP, Hurst SF, De Aguirre L, Morrison CJ. Molecular methods for the identification of Aspergillus species. Med Mycol 2005; 43: 129–137.
  • Klaassen CHW, Osherov N. Aspergillus strain typing in the genomics era. Stud Mycol 2007; 59: 47–51.
  • Lin D, Lehmann F, Hamory BH, . Comparison of three typing methods for clinical and environmental isolates of Aspergillus fumigatus. J Clin Microbiol 1995; 33: 1596–1601.
  • Anderson MJ, Gull K, Denning DW. Molecular typing by random amplification of polymorphic DNA and M13 Southern hybridization of related paired isolates of Aspergillus fumigatus. J Clin Microbiol 1996; 34: 87–93.
  • Bertout S, Renaud F, Barton R, . Genetic polymorphism of Aspergillus fumigatus in clinical samples from patients with invasive aspergillosis: investigation using multiple typing methods. J Clin Microbiol 2001; 39: 1731–1737.
  • Bart-Delabesse E, Sarfati J, Debeaupuis JP, . Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplification of polymorphic DNA analyses for fingerprinting Aspergillus fumigatus. J Clin Microbiol 2001; 39: 2683–2686.
  • Lasker BA. Evaluation of performance of four genotypic methods for studying the genetic epidemiology of Aspergillus fumigatus isolates. J Clin Microbiol 2002; 40: 2886–2892.
  • de Valk HA, Meis JFGM, de Pauw BE, Donnelly PJ, Klaassen CHW. Comparison of two highly discriminatory molecular fingerprinting assays for analysis of multiple Aspergillus fumigatus isolates from patients with invasive aspergillosis. J Clin Microbiol 2007; 45: 1415–1419.
  • Klaassen CHW. MLST versus microsatellites for typing Aspergillus fumigatus isolates. Med Mycol 2009; 47: 27–33.
  • Bain JM, Tavanti A, Davidson AD, . Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus. J Clin Microbiol 2007; 45: 1469–1477.
  • de Valk HA, Meis JFGM, Curfs IM, . Use of a novel panel of nine short tandem repeats for exact and high–resolution fingerprinting of Aspergillus fumigatus isolates. J Clin Microbiol 2005; 43: 4112–4120.
  • Araujo R, Pina-Vaz C, Rodrigues AG, Amorim A, Gusmão L. Simple and highly discriminatory microsatellite-based multiplex PCR for Aspergillus fumigatus strain typing. Clin Microbiol Infect 2009; 15: 260–266.
  • Enright MC, Spratt BG. Multilocus sequence typing. Trends Microbiol 1999; 7: 482–487.
  • Urwin R, Maiden MCJ. Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 2003; 11: 479–487.
  • de Valk HA, Meis JFGM, Bretagne S, . Interlaboratory reproducibility of a microsatellite-based typing assay for Aspergillus fumigatus through the use of allelic ladders: proof of concept. Clin Microbiol Infect 2009; 15: 180–187.
  • Coenye T, Vandamme P. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res 2005; 12: 221–233.
  • van Belkum A, Scherer S, van Alphen L, Verbrugh H. Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 1998; 62: 275–293.
  • Symoens F, Viviani MA, Nolard N. Typing by immunoblot of Aspergillus fumigatus from nosocomial infections. Mycoses 1993; 36: 229–237.
  • Girardin H, Sarfati J, Traoré F, . Molecular epidemiology of nosocomial invasive aspergillosis. J Clin Microbiol 1994; 32: 684–690.
  • Leenders A, van Belkum A, Janssen S, . Molecular epidemiology of apparent outbreak of invasive aspergillosis in a hematology ward. J Clin Microbiol 1996; 34: 345–351.
  • Rath PM, Ansorg R. Value of environmental sampling and molecular typing of aspergilli to assess nosocomial sources of aspergillosis. J Hosp Infect 1997; 37: 47–53.
  • Radford SA, Johnson EM, Leeming JP, . Molecular epidemiological study of Aspergillus fumigatus in a bone marrow transplantation unit by PCR amplification of ribosomal intergenic spacer sequences. J Clin Microbiol 1998; 36: 1294–1299.
  • Chazalet V, Debeaupuis JP, Sarfati J, . Molecular typing of environmental and patient isolates of Aspergillus fumigatus from various hospital settings. J Clin Microbiol 1998; 36: 1494–1500.
  • Bart-Delabesse E, Cordonnier C, Bretagne S. Usefulness of genotyping with microsatellite markers to investigate hospital-acquired invasive aspergillosis. J Hosp Infect 1999; 42: 321–327.
  • Leenders ACA, van Belkum A, Behrendt M, Luijendijk A, Verbrugh HA. Density and molecular epidemiology of Aspergillus in air and relationship to outbreaks of Aspergillus infection. J Clin Microbiol 1999; 37: 1752–1757.
  • Thio CL, Smith D, Merz WG, . Refinements of environmental assessment during an outbreak investigation of invasive aspergillosis in a leukemia and bone marrow transplant unit. Infect Control Hosp Epidemiol 2000; 21: 18–23.
  • Mellado E, Diaz-Guerra TM, Cuenca-Estrella M, . Characterization of a possible nosocomial aspergillosis outbreak. Clin Microbiol Infect 2000; 6: 543–548.
  • Pegues DA, Lasker BA, McNeil MM, . Cluster of cases of invasive aspergillosis in a transplant intensive care unit: evidence of person-to-person airborne transmission. Clin Infect Dis 2002; 34: 412–416.
  • Symoens F, Burnod J, Lebeau B, . Hospital-acquired Aspergillus fumigatus infection: can molecular typing methods identify an environmental source? J Hosp Infect 2002; 52: 60–67.
  • Warris A, Klaassen CHW, Meis JFGM, . Molecular epidemiology of Aspergillus fumigatus isolates recovered from water, air, and patients shows two clusters of genetically distinct strains. J Clin Microbiol 2003; 41: 4101–4106.
  • Menotti J, Waller J, Meunier O, . Epidemiological study of invasive pulmonary aspergillosis in a haematology unit by molecular typing of environmental and patient isolates of Aspergillus fumigatus. J Hosp Infect 2005; 60: 61–68.
  • Guarro J, Solé M, Castany R, . Use of random amplified microsatellites to type isolates from an outbreak of nosocomial aspergillosis in a general medical ward. Med Mycol 2005; 43: 365–371.
  • Balajee SA, de Valk HA, Lasker BA, Meis JFGM, Klaassen CHW. Utility of a microsatellite assay for identifying clonally related outbreak isolates of Aspergillus fumigatus. J Microbiol Meth 2008; 73: 252–256.
  • Staab JF, Balajee SA, Marr KA. Aspergillus section Fumigati typing by PCR-RFLP. J Clin Microbiol 2009; 47: 2079–2083.
  • Rodriguez E, De Meeüs T, Mallie M, . Multicentric epidemiological study of Aspergillus fumigatus isolates by multilocus enzyme electrophoresis. J Clin Microbiol 1996; 34: 2559–2568.
  • Mondon P, Brenier MP, Symoens F, . Molecular typing of Aspergillus fumigatus strains by sequence-specific DNA primer (SSDP) analysis. FEMS Immun Med Microbiol 1997; 17: 95–102.
  • Symoens F, Piens MA, Renaud F, Grillot R. A longitudinal study of lung transplant recipients infected with Aspergillus: genetic polymorphism of A. fumigatus. J Heart Lung Transplant 2000; 20: 970–978.
  • Bertout S, Renaud F, Meeüs T, . Multilocus enzyme electrophoresis analysis of Aspergillus fumigatus strains isolated from the first clinical sample from patients with invasive aspergillosis. J Med Microbiol 2000; 49: 375–381.
  • de Ruiter MT, de Valk HA, Meis JFGM, Klaassen CHW. Retrotransposon insertion-site context (RISC) typing: a novel typing method for Aspergillus fumigatus and a convenient PCR alternative to restriction fragment length polymorphism analysis. J Microbiol Meth 2007; 70: 528–534.
  • Vanhee LME, Symoens F, Nelis HJ, Coenye T. Microsatellite typing of Aspergillus fumigatus isolates recovered from deep organ samples of patients with invasive aspergillosis. Diagn Microbiol Infect Dis 2008; 62: 96–98.
  • Alvarez-Perez S, Garcia MA, Bouza E, Pelaez T, Blanca JL. Characterisation of multiple isolates of Aspergillus fumigatus from patients: genotype, mating type and invasiveness. Med Mycol 2009; 47: 601–608.
  • Denning DW, Shankland GS, Stevens DA. DNA fingerprinting of Aspergillus fumigatus isoaltes from patients with aspergilloma. J Med Vet Mycol 1991; 29: 339–342.
  • Loudon KW, Burnie JP, Coke AP, Mattews RC. Application of polymerase chain reaction to fingerprinting Aspergillus fumigatus by random amplification of polymorphic DNA. J Clin Microbiol 1993; 31: 1117–1121.
  • Girardin H, Sarfati J, Kobayashi H, Bouchara JP, Latgé JP. Use of moderately repetitive sequence to type Aspergillus fumigatus isolates from aspergilloma patients. J Infect Dis 1994; 169: 683–685.
  • Chen J, Li H, Li R, Bu D, Wan Z. Mutations in the cyp51A gene and susceptibility to itraconazole in Aspergillus fumigatus serially isolated from a patient with lung aspergilloma. J Antimicrob Chemother 2005; 55: 31–37.
  • Verweij PE, Meis JFGM, Sarfati J, . Genotypic characterization of sequential Aspergillus fumigatus isolates from patients with cystic fibrosis. J Clin Microbiol 1996; 34: 2595–2597.
  • Rath PM, Ratjen F, Ansorg R. Genetic diversity among isolates of Aspergillus fumigatus in patients with cystic fibrosis. Zentralbl Bakteriol 1997; 285: 450–455.
  • Neuvéglise C, Sarfati J, Debeaupuis JP, . Longitudinal study of Aspergillus fumigatus strains isolated from cystic fibrosis patients. Eur J Clin Microbiol Infect Dis 1997; 16: 747–750.
  • Cimon B, Symoens F, Zouhair R, . Molecular epidemiology of airway colonisation by Aspergillus fumigatus in cystic fibrosis patients. J Med Microbiol 2001; 50: 367–374.
  • Vanhee LME, Symoens F, Bouchara JP, Nelis HJ, Coenye T. High-resolution genotyping of Aspergillus fumigatus isolates recovered from chronically colonised patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2008; 27: 1005–1007.
  • de Valk HA, Klaassen CHW, Yntema JB, . Molecular typing and colonisation patterns of Aspergillus fumigatus in patients with cystic fibrosis. J Cyst Fibros 2009; 8: 110–114.
  • Diaz-Guerra T, Mellado E, Cuenca-Estrella M, . Genetic similarity among one Aspergillus flavus strain isolated from a patient who underwent heart surgery and two environmental strains obtained from the operating room. J Clin Microbiol 2000; 38: 2419–2422.
  • Myoken Y, Sugata T, Fuijta Y, . Molecular epidemiology of invasive stomatitis due to Aspergillus flavus in patients with acute leukemia. J Oral Pathol Med 2003; 32: 215–218.
  • Heineman S, Symoens F, Gordts B, Jannes H, Nolard N. Environmental investigations and molecular typing of Aspergillus flavus during an outbreak of postoperative infections. J Hosp Infect 2004; 57: 149–155.
  • Midorikawa GEO, Pinheiro MRR, Vidigal BS, . Characterization of Aspergillus flavus strains from Brazilian Brazil nuts and cashew by RAPD and ribosomal DNA analysis. Lett Appl Microbiol 2008; 47: 12–18.
  • Batista PP, Santos JF, Oliveira NT, . Genetic characterization of Brazilian strains of Aspergillus flavus using DNA markers. Genet Mol Res 2008; 7: 706–717.
  • Moody SF, Tyler BM. Restriction enzyme analysis of mitochondrial DNA of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius. Appl Environ Microbiol 1990; 56: 2441–2452.
  • Moody SF, Tyler BM. Use of nuclear DNA restriction fragment length polymorphisms to analyse the diversity of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius. Appl Environ Microbiol 1990; 56: 2453–2461.
  • James MJ, Lasker BA, McNeil MM, . Use of repetitive DNA probe to type clinical and environmental isolates of Aspergillus flavus from a cluster of cutaneous infections in a neonatal intensive care unit. J Clin Microbiol 2000; 38: 3612–3618.
  • Abed KF. Differentiation of Aspergillus niger by random amplification of polymorphic DNA. J Ind Microbiol Biotechnol 2008; 35: 1027–1032.
  • Esteban A, Leong SLL, Hocking AD, . Utility of microsatellite markers and amplified fragment length polymorphism in the study of potentially ochratoxigenic black aspergilli. Curr Microbiol 2008; 57: 348–355.
  • Rath PM, Kamphoff S, Ansorg R. Value of different methods for the characterisation of Aspergillus terreus strains. J Med Microbiol 1999; 48: 161–166.
  • Birch M, Denning DW. Molecular typing of Aspergillus terreus by random amplification of polymorphic DNA. Eur J Clin Microbiol Infect Dis 1999; 18: 838–841.
  • Symoens F, Bouchara JP, Heinemann S, Nolard N. Molecular typing of Aspergillus terreus isolates by random amplification of polymorphic DNA. J Hosp Infect 2000; 44: 273–280.
  • Cimon B, Zouhair R, Symoens F, . Aspergillus terreus in a cystic fibrosis clinic: environmental distribution and patient colonisation pattern. J Hosp Infect 2003; 53: 81–82.
  • Baddley JW, Pappas PG, Smith AC, Moser SA. Epidemiology of Aspergillus terreus at a university hospital. J Clin Microbiol 2003; 41: 5525–5529.
  • Lass-Flörl C, Grif K, Mayr A, . Epidemiology and outcome of infections due to Aspergillus terreus: 10-year single centre experience. Br J Haematol 2005; 131: 201–207.
  • Lass-Flörl C, Grif K, Kontoyiannis DP. Molecular typing of Aspergillus terreus isolates collected in Houston, Texas, and Innsbruck, Austria: evidence of great genetic diversity. J Clin Microbiol 2007; 45: 2686–2690.
  • Blum G, Perkhofer S, Grif K, . A 1-year Aspergillus terreus surveillance study at the University Hospital of Innsbruck: molecular typing of environmental and clinical isolates. Clin Microbiol Infect 2008; 14: 1146–1151.
  • Sullivan DJ, Coleman DC. Molecular approaches to identification and typing of Candida species. Calderone RA. Candida and Candidiasis, 1st. Washington DC: ASM Press, 2002.
  • Tavanti A, Gow NAR, Senesi S, Maiden MCJ, Odds FC. Optimization and validation of multilocus sequence typing for Candida albicans. J Clin Microbiol 2003; 41: 3765–3776.
  • Bougnoux MA, Morand S, d’Enfert C. Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 2002; 40: 1290–1297.
  • Bougnoux MA, Tavanti A, Bouchier C, . Collaborative consensus for the optimised multilocus sequence typing of Candida albicans. J Clin Microbiol 2003, 41: 5265–5266.
  • Beretta S, Fulgencio JP, Enache-Angoulvant A, . Application of microsatellite typing for the investigation of a cluster of cases of Candida albicans candidaemia. Clin Microbiol Infect 2006; 12: 672–694.
  • Garcia-Hermoso D, Cabaret O, Lecellier G, . Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-based typing of Candida albicans. J Clin Microbiol 2007; 45: 3958–3963.
  • Voss A, Hollis RJ, Pfaller MA, . Investigation of the sequence of colonisation and candidemia in nonneutropenic patients. J Clin Microbiol 1994; 32: 975–980.
  • Noumi E, Snoussi M, Saghrouni F, . Molecular typing of clinical Candida strains using random amplified polymorphic DNA and contour-clamped homogenous electric fields electrophoresis. J Appl Microbiol 2009; 107: 1991–2000.
  • Muthig M, Hebestreit A, Ziegler U, Seidler M, Müller FMC. Persistence of Candida species in the respiratory tract of cystic fibrosis patients. Med Mycol 2009; 31: 1–8.
  • Meersseman W, Lagrou K, Spriet I, . Significance of the isolation of Candida species from airway samples in critically ill patients: a prospective, autopsy study. Intensive Care Med 2009; 35: 1526–1531.
  • Uijthof JMJ, de Hoog GS, de Cock AWAM, Takeo K, Nishimura K. Pathogenicity of strains of the black yeast Exophiala (Wangiella) dermatitidis: an evaluation based on polymerase chain reaction. Mycoses 1994; 37: 235–242.
  • Rath PM, Müller KD, Dermoumi H, Ansorg R. A comparison of methods of phenotypic and genotypic fingerprinting of Exophiala dermatitidis isolated from sputum samples of patients with cystic fibrosis. J Med Mycol 1997; 46: 757–762.
  • Uijthof JMJ, van Belkum A, de Hoog GS, Haase G. Exophiala dermatitidis and Sarcinomyces phaeomuriformis: ITS1-sequencing and nutritional physiology. Med Mycol 1998; 36: 143–151.
  • Matos T, Haase G, Gerrits van den Ende AHG, de Hoog GS. Molecular diversity of oligotropic members of the black yeast genus Exophiala, with accent on E. dermatitidis. Antonie van Leeuwenhoek 2003; 83: 293–303.
  • Nagano Y, Elborn S, Millar BC, . Development of a novel PCR assay for the identification of the black yeast, Exophiala (Wangiella) dermatitidis from adult patients with cystic fibrosis (CF). J Cyst Fibros 2008; 7: 576–580.
  • Zouhair R, Defontaine A, Ollivier C, . Typing of Scedosporium apiospermum by multilocus enzyme electrophoresis and random amplification of polymorphic DNA. J Med Microbiol 2001; 50: 925–932.
  • Williamson ECM, Speers D, Arthur ICH, . Molecular epidemiology of Scedosporium apiospermum infection determined by PCR amplification of ribosomal intergenic spacer sequences in patients with chronic lung disease. J Clin Microbiol 2001; 39: 47–50.
  • Defontaine A, Zouhair R, Cimon B, . Genotyping of Scedosporium apiospermum isolates from patients with cystic fibrosis. J Clin Microbiol 2002; 40: 2108–2114.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.