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Chapter 22 : Future Trends in Diagnosis of Infections in the Immunocompromised Population

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Future Trends in Diagnosis of Infections in the Immunocompromised Population, Page 1 of 2

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Abstract:

The focused and unique health care management of the immunocompromised patient has grown significantly over the last several decades. Biomarkers of the immune response, such as procalcitonin (PCT), are evolving in clinical utility for the diagnosis of severe bacterial infections such as sepsis, for prediction of sepsis complications, and for therapeutic follow-up. Microbial and fungal infections are among the most common causes of high morbidity and mortality in critically ill patients in the United States; mortality rates can exceed 80%. Several molecular platforms are slated to play a role in advancing the diagnostic capabilities of clinical laboratories. Only time, cost-benefit studies, and practical evidence-based reviews can reveal the ultimate utility of these methods for diagnosis of infections in the immunocompromised population. Rapid testing for genetic resistance markers is an emerging clinical practice that can not only identify the potential for drug resistance but also help distinguish ambiguous breakpoints associated with susceptibility testing. Biomarkers of the immune response, such as PCT, are useful for the diagnosis of severe bacterial infections such as sepsis, for prediction of sepsis complications, and for therapeutic follow-up. Immunocompromised patients are a unique population, for which extreme measures may be required to make relevant diagnoses, prevent infection, or prevent overuse of health care resources.

Citation: Marlowe E, Wolk D. 2009. Future Trends in Diagnosis of Infections in the Immunocompromised Population, p 443-462. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch22

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References

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1. Reference deleted.
2. Reference deleted.
3. Reference deleted.
4. Aarestrup, F. M.,, P. Ahrens,, M. Madsen,, L. V. Pallesen,, R. L. Poulsen, and, H. Westh. 1996. Glycopeptide susceptibility among Danish Enterococcus faecium and Enterococcus faecalis isolates of animal and human origin and PCR identification of genes within the VanA cluster. Antimicrob. Agents Chemother. 40:19381940.
5. Abbott, W.,, E. Gane,, I. Winship,, S. Munn, and, C. Tukuitonga. 2007. Polymorphism in intron 1 of the interferon-gamma gene influences both serum immunoglobulin E levels and the risk for chronic hepatitis B virus infection in Polynesians. Immunogenetics 59:187195.
6. Adelson, M. E.,, M. Feola,, J. Trama,, R. C. Tilton, and, E. Mordechai. 2005. Simultaneous detection of herpes simplex virus types 1 and 2 by real-time PCR and pyrosequencing. J. Clin. Virol. 33:2534.
7. Alexander, B. D.,, E. D. Ashley,, L. B. Reller, and, S. D. Reed. 2006. Cost savings with implementation of PNA FISH testing for identification of Candida albicans in blood cultures. Diagn. Microbiol. Infect. Dis. 54:277282.
8. al-Nawas, B.,, and P. M. Shah. 1996. Procalcitonin in patients with and without immunosuppression and sepsis. Infection 24:434436.
9. Reference deleted.
10. Reference deleted.
11. Reference deleted.
12. Athanasopoulos, A.,, P. Devogel,, C. Beken,, C. Pille,, I. Bernier, and, P. Gavage. 2007. Comparison of three selective chromogenic media for methicillin-resistant Staphylococcus aureus detection. Pathol. Biol. (Paris) 55:366369.
13. Beck, R. C.,, D. J. Kohn,, M. J. Tuohy,, R. A. Prayson,, B. Yen-Lieberman, and, G. W. Procop. 2004. Detection of polyoma virus in brain tissue of patients with progressive multifocal leukoencephalopathy by real-time PCR and pyrosequencing. Diagn. Mol. Pathol. 13:1521.
14. Becker, K.,, D. Harmsen,, A. Mellmann,, C. Meier,, P. Schumann,, G. Peters, and, C. von Eiff. 2004. Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J. Clin. Microbiol. 42:49884995.
15. Benson, D.,, D. J. Lipman, and, J. Ostell. 1993. GenBank. Nucleic Acids Res. 21:29632965.
16. Blackwood, K. S.,, C. Y. Turenne,, D. Harmsen, and, A. M. Kabani. 2004. Reassessment of sequence-based targets for identification of Bacillus species. J. Clin. Microbiol. 42:16261630.
17. Bochud, P. Y.,, A. S. Magaret,, D. M. Koelle,, A. Aderem, and, A. Wald. 2007. Polymorphisms in TLR2 are associated with increased viral shedding and lesional rate in patients with genital herpes simplex virus type 2 infection. J. Infect. Dis. 196:505509.
18. Bogut, A.,, M. Koziol-Montewka,, I. Baranowicz,, L. Jozwiak,, A. Ksiazek,, Z. Al-Doori,, D. Morrison,, D. Kaczor, and, J. Paluch-Oles. 2007. Characterisation of Staphylococcus aureus nasal and skin carriage among patients undergoing haemodialysis treatment. New Microbiol. 30:149154.
19. Brouqui, P.,, and D. Raoult. 2001. Endocarditis due to rare and fastidious bacteria. Clin. Microbiol. Rev. 14:177207.
20. Brunstein, J.,, and E. Thomas. 2006. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco respiratory panels 1 and 2. Diagn. Mol. Pathol. 15:169173.
21. Brunstein, J. D.,, C. L. Cline,, S. McKinney, and, E. Thomas. 2008. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections. J. Clin. Microbiol. 46:97102.
22. Caliendo, A. M.,, and D. Yen-Lieberman. 2004. Viral genotyping, p. 489–499. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
23. Carretto, E.,, D. Barbarini,, C. Farina,, A. Grosini,, P. Nicoletti, and, E. Manso. 2008. Use of the DiversiLab(R) semiautomated repetitive-sequence-based polymerase chain reaction for epidemiologic analysis on Acinetobacter baumannii isolates in different Italian hospitals. Diagn. Microbiol. Infect. Dis. 60:17.
24. Chapman, S. J.,, C. C. Khor,, F. O. Vannberg,, A. Frodsham,, A. Walley,, N. A. Maskell,, C. W. Davies,, S. Segal,, C. E. Moore,, S. H. Gillespie,, P. Denny,, N. P. Day,, D. W. Crook,, R. J. Davies, and, A. V. Hill. 2007. IkappaB genetic polymorphisms and invasive pneumococcal disease. Am. J. Respir. Crit. Care Med. 176:181187.
25. Chawes, B. L.,, C. Rechnitzer,, K. Schmiegelow, and, M. Tvede. 2007. Procalcitonin for early diagnosis of bacteraemia in children with cancer. Ugeskr. Laeger 169:138142.
26. Cherkaoui, A.,, G. Renzi,, P. Francois, and, J. Schrenzel. 2007. Comparison of four chromogenic media for culture-based screening of methicillin-resistant Staphylococcus aureus. J. Med. Microbiol. 56:500503.
27. Chun, J. Y.,, K. J. Kim,, I. T. Hwang,, Y. J. Kim,, D. H. Lee,, I. K. Lee, and, J. K. Kim. 2007. Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene. Nucleic Acids Res. 35:e40.
28. Ciok-Pater, E.,, P. Zalas, and, E. Gospodarek. 2006. Evaluation of Agar Candida ID2 (bioMerieux) a chromogenic medium for yeasts differentiation. Med. Dosw. Mikrobiol. 58:247251.
29. Clark, N. C.,, R. C. Cooksey,, B. C. Hill,, J. M. Swenson, and, F. C. Tenover. 1993. Characterization of glycopeptide-resistant enterococci from U.S. hospitals. Antimicrob. Agents Chemother. 37:23112317.
30. Clarke, S. C. 2005. Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications. Expert Rev. Mol. Diagn. 5:947953.
31. Del Vecchio, V. G.,, J. M. Petroziello,, M. J. Gress,, F. K. McCleskey,, G. P. Melcher,, H. K. Crouch, and, J. R. Lupski. 1995. Molecular genotyping of methicillin-resistant Staphylococcus aureus via fluorophore-enhanced repetitive-sequence PCR. J. Clin. Microbiol. 33:21412144.
32. Deplano, A.,, A. Schuermans,, J. Van Eldere,, W. Witte,, H. Meugnier,, J. Etienne,, H. Grundmann,, D. Jonas,, G. T. Noordhoek,, J. Dijkstra,, A. van Belkum,, W. van Leeuwen,, P. T. Tassios,, N. J. Legakis,, Z. A. van der,, A. Bergmans,, D. S. Blanc,, F. C. Tenover,, B. C. Cookson,, G. O’Neil,, M. J. Struelens, et al. 2000. Multicenter evaluation of epidemiological typing of methicillin-resistant Staphylococcus aureus strains by repetitive-element PCR analysis. J. Clin. Microbiol. 38:35273533.
33. Descamps, D.,, V. Calvez,, G. Collin,, A. Cecille,, C. Apetrei,, F. Damond,, C. Katlama,, S. Matheron,, J. M. Huraux, and, F. Brun-Vezinet. 1998. Line probe assay for detection of human immunodeficiency virus type 1 mutations conferring resistance to nucleoside inhibitors of reverse transcriptase: comparison with sequence analysis. J. Clin. Microbiol. 36:21432145.
34. DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents—a Working Group of the Office of AIDS Research Advisory Council (OARAC). 2007. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Office of AIDS Research Advisory Council, Bethesda, MD.
35. Diederen, B.,, I. van Duijn,, A. van Belkum,, P. Willemse,, P. van Keulen, and, J. Kluytmans. 2005. Performance of CHROMagar MRSA medium for detection of methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 43:19251927.
36. Diekema, D. J.,, K. J. Dodgson,, B. Sigurdardottir, and, M. A. Pfaller. 2004. Rapid detection of antimicrobial-resistant organism carriage: an unmet clinical need. J. Clin. Microbiol. 42:28792883.
37. Reference deleted.
38. Diekema, D. J.,, and M. A. Pfaller. 2003. Infection control epidemiology and clinical microbiology, p. 129–138. In P. M. Murray,, E. J. Baron,, J. H. Jorgenson,, M. A. Pfaller, and, R. H. Yolken (ed.), Manual of Clinical Microbiology. ASM Press, Washinton, DC.
39. Douglas, J. F. 2004. Elucidations of diagnostic and vaccine candidates by mass spectroscopy and proteomics, p. 307–319. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
40. Dunbar, S. A.,, C. A. Vander Zee,, K. G. Oliver,, K. L. Karem, and, J. W. Jacobson. 2003. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J. Microbiol. Methods 53:245252.
41. Ecker, D. J.,, R. Sampath,, L. B. Blyn,, M. W. Eshoo,, C. Ivy,, J. A. Ecker,, B. Libby,, V. Samant,, K. A. Sannes-Lowery,, R. E. Melton,, K. Russell,, N. Freed,, C. Barrozo,, J. Wu,, K. Rudnick,, A. Desai,, E. Moradi,, D. J. Knize,, D. W. Robbins,, J. C. Hannis,, P. M. Harrell,, C. Massire,, T. A. Hall,, Y. Jiang,, R. Ranken,, J. J. Drader,, N. White,, J. A. McNeil,, S. T. Crooke, and, S. A. Hofstadler. 2005. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc. Natl. Acad. Sci. USA 102:80128017.
42. Edlind, T. D. 2004. Molecular detection of antifungal resistance, p. 569–575. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
43. Erali, M.,, S. Page,, L. G. Reimer, and, D. R. Hillyard. 2001. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J. Clin. Microbiol. 39:21572165.
44. Eraso, E.,, M. D. Moragues,, M. Villar-Vidal,, I. H. Sahand,, N. Gonzalez-Gomez,, J. Ponton, and, G. Quindos. 2006. Evaluation of the new chromogenic medium Candida ID 2 for isolation and identification of Candida albicans and other medically important Candida species. J. Clin. Microbiol. 44:33403345.
45. Fitch, J. P., et al. 2002. Rapid development of nucleic acid diagnostics, p. 1708–1720. In Proc. IEEE. IEEE, Los Alamitos, CA.
46. Flayhart, D.,, J. F. Hindler,, D. A. Bruckner,, G. Hall,, R. K. Shrestha,, S. A. Vogel,, S. S. Richter,, W. Howard,, R. Walther, and, K. C. Carroll. 2005. Multicenter evaluation of BBL CHROMagar MRSA medium for direct detection of methicillin-resistant Staphylococcus aureus from surveillance cultures of the anterior nares. J. Clin. Microbiol. 43:55365540.
47. Fluit, A. C.,, M. R. Visser, and, F. J. Schmitz. 2001. Molecular detection of antimicrobial resistance. Clin. Microbiol. Rev. 14:836871.
48. Fofanov, Y.,, Y. Luo,, C. Katili,, J. Wang,, Y. Belosludtsev,, T. Powdrill,, C. Belapurkar,, V. Fofanov,, T. B. Li,, S. Chumakov, and, B. M. Pettitt. 2004. How independent are the appearances of n-mers in different genomes? Bioinformatics 20:24212428.
49. Fofanov, Y.,, and B. M. Pettitt. 2002. Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: local invariants approach. J. Biomed. Inform. 35:343351.
50. Forrest, G. N.,, K. Mankes,, M. A. Jabra-Rizk,, E. Weekes,, J. K. Johnson,, D. P. Lincalis, and, R. A. Venezia. 2006. Peptide nucleic acid fluorescence in situ hybridization-based identification of Candida albicans and its impact on mortality and antifungal therapy costs. J. Clin. Microbiol. 44:33813383.
51. Forrest, G. N.,, S. Mehta,, E. Weekes,, D. P. Lincalis,, J. K. Johnson, and, R. A. Venezia. 2006. Impact of rapid in situ hybridization testing on coagulase-negative staphylococci positive blood cultures. J. Antimicrob. Chemother. 58:154158.
52. Francois, P.,, D. Pittet,, M. Bento,, B. Pepey,, P. Vaudaux,, D. Lew, and, J. Schrenzel. 2003. Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay. J. Clin. Microbiol. 41:254260.
53. Francois, P.,, G. Renzi,, D. Pittet,, M. Bento,, D. Lew,, S. Harbarth,, P. Vaudaux, and, J. Schrenzel. 2004. A novel multiplex real-time PCR assay for rapid typing of major staphylococcal cassette chromosome mec elements. J. Clin. Microbiol. 42:33093312.
54. Freymuth, F.,, A. Vabret,, D. Cuvillon-Nimal,, S. Simon,, J. Dina,, L. Legrand,, S. Gouarin,, J. Petitjean,, P. Eckart, and, J. Brouard. 2006. Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness. J. Med. Virol. 78:14981504.
55. Galor, A.,, G. S. Hall,, G. W. Procop,, M. Tuohy,, M. E. Millstein, and, B. H. Jeng. 2007. Rapid species determination of nocardia keratitis using pyrosequencing technology. Am. J. Ophthalmol. 143:182183.
56. Reference deleted.
57. Gavino, M.,, and E. Wang. 2007. A comparison of a new rapid real-time polymerase chain reaction system to traditional culture in determining group B streptococcus colonization. Am. J. Obstet. Gynecol. 197:388.e1388.e4.
58. Gegia, M.,, N. Mdivani,, R. E. Mendes,, H. Li,, M. Akhalaia,, J. Han,, G. Khechinashvili, and, Y. W. Tang. 2008. Prevalence of and molecular basis for tuberculosis drug resistance in the Republic of Georgia: validation of a QIAplex system for the detection of drug resistance-related mutations. Antimicrob. Agents Chemother. 52:725729.
59. Gharizadeh, B.,, E. Norberg,, J. Loffler,, S. Jalal,, J. Tollemar,, H. Einsele,, L. Klingspor, and, P. Nyren. 2004. Identification of medically important fungi by the pyrosequencing technology. Mycoses 47:2933.
60. Giamarellos-Bourboulis, E. J.,, A. Mega,, P. Grecka,, N. Scarpa,, G. Koratzanis,, G. Thomopoulos, and, H. Giamarellou. 2002. Procalcitonin: a marker to clearly differentiate systemic inflammatory response syndrome and sepsis in the critically ill patient? Intensive Care Med. 28:13511356.
61. Goering, R. V. 2000. Molecular strain typing for the clinical laboratory. Clin. Microbiol. Newsl. 22:169173.
62. Gonzalez, V.,, E. Padilla,, M. Gimenez,, C. Vilaplana,, A. Perez,, G. Fernandez,, M. D. Quesada,, M. A. Pallares, and, V. Ausina. 2004. Rapid diagnosis of Staphylococcus aureus bacteremia using S. aureus PNA FISH. Eur. J. Clin. Microbiol. Infect. Dis. 23:396398.
63. Gordts, B.,, H. Van Landuyt,, M. Ieven,, P. Vandamme, and, H. Goossens. 1995. Vancomycin-resistant enterococci colonizing the intestinal tracts of hospitalized patients. J. Clin. Microbiol. 33:28422846.
64. Granell, M.,, A. Urbano-Ispizua,, J. I. Arostegui,, F. Fernandez-Aviles,, C. Martinez,, M. Rovira,, J. Rius,, S. Plaza,, A. Gaya,, A. Navarro,, C. Talarn,, E. Carreras,, M. Monzo,, E. Montserrat, and, J. Yague. 2006. Effect of NOD2/CARD15 variants in T-cell depleted allogeneic stem cell transplantation. Haematologica 91:13721376.
65. Grant, R. M.,, D. R. Kuritzkes,, V. A. Johnson,, J. W. Mellors,, J. L. Sullivan,, R. Swanstrom,, R. T. D’Aquila,, M. Van Gorder,, M. Holodniy,, J. R. Lloyd, Jr.,, C. Reid,, G. F. Morgan, and, D. L. Winslow. 2003. Accuracy of the TRUGENE HIV-1 genotyping kit. J. Clin. Microbiol. 41:15861593.
66. Gravett, M. G.,, M. J. Novy,, R. G. Rosenfeld,, A. P. Reddy,, T. Jacob,, M. Turner,, A. McCormack,, J. A. Lapidus,, J. Hitti,, D. A. Eschenbach,, C. T. Roberts, Jr., and, S. R. Nagalla. 2004. Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers. JAMA 292:462469.
67. Grisold, A. J.,, E. Leitner,, G. Muhlbauer,, E. Marth, and, H. H. Kessler. 2002. Detection of methicillin-resistant Staphylococcus aureus and simultaneous confirmation by automated nucleic acid extraction and real-time PCR. J. Clin. Microbiol. 40:23922397.
68. Han, J.,, D. C. Swan,, S. J. Smith,, S. H. Lum,, S. E. Sefers,, E. R. Unger, and, Y. W. Tang. 2006. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology. J. Clin. Microbiol. 44:41574162.
69. Han, Z.,, E. Lautenbach,, N. Fishman, and, I. Nachamkin. 2007. Evaluation of mannitol salt agar, CHROMagar Staph aureus and CHROMagar MRSA for detection of methicillin-resistant Staphylococcus aureus from nasal swab specimens. J. Med. Microbiol. 56:4346.
70. Hanage, W. P.,, E. J. Feh,, A. B. Breuggmann, and, B. G. Spratt. 2004. Multilocus sequence typing: strain characterization, population biology, and patterns of evolutionary descent, p. 235–243. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
71. Hanna, G. J.,, and R. T. D’Aquila. 2001. Clinical use of genotypic and phenotypic drug resistance testing to monitor antiretroviral chemotherapy. Clin. Infect. Dis. 32:774782.
72. Harmsen, D.,, H. Claus,, W. Witte,, J. Rothganger,, H. Claus,, D. Turnwald, and, U. Vogel. 2003. Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J. Clin. Microbiol. 41:54425448.
73. Harmsen, D.,, S. Dostal,, A. Roth,, S. Niemann,, J. Rothganger,, M. Sammeth,, J. Albert,, M. Frosch, and, E. Richter. 2003. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC Infect. Dis. 3:26.
74. Harmsen, D.,, J. Rothganger,, M. Frosch, and, J. Albert. 2002. RIDOM: Ribosomal Differentiation of Medical Micro-Organisms Database. Nucleic Acids Res. 30:416417.
75. Harmsen, D.,, C. Singer,, J. Rothganger,, T. Tonjum,, G. S. de Hoog,, H. Shah,, J. Albert, and, M. Frosch. 2001. Diagnostics of Neisseriaceae and Moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms. J. Clin. Microbiol. 39:936942.
76. Harriau, P.,, F. Ruffel, and, J. B. Lardy. 2006. Use of BioRad plating agar MRSASelect for the daily detection of methicillin resistant staphylococci isolated from samples taken from blood culture bottles. Pathol. Biol. (Paris) 54:506509.
77. Hartmann, H.,, H. Stender,, A. Schafer,, I. B. Autenrieth, and, V. A. Kempf. 2005. Rapid identification of Staphylococcus aureus in blood cultures by a combination of fluorescence in situ hybridization using peptide nucleic acid probes and flow cytometry. J. Clin. Microbiol. 43:48554857.
78. Hedin, G.,, and H. Fang. 2005. Evaluation of two new chromogenic media, CHROMagar MRSA and S. aureus ID, for identifying Staphylococcus aureus and screening methicillin-resistant S. aureus. J. Clin. Microbiol. 43:42424244.
79. Heller, A. 1 February 2007, accession date. On the front lines of biodefense. http://www.eurekalert.org/features/doe/2004-04/dlnl-otf041204.php.
80. Hohl, M.,, S. Kurtz, and, E. Ohlebusch. 2002. Efficient multiple genome alignment. Bioinformatics 18(Suppl. 1):S312S320.
81. Huletsky, A.,, R. Giroux,, V. Rossbach,, M. Gagnon,, M. Vail-lancourt,, M. Bernier,, F. Gagnon,, K. Truchon,, M. Bastien,, F. J. Picard,, A. van Belkum,, M. Ouellette,, P. H. Roy, and, M. G. Bergeron. 2004. New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J. Clin. Microbiol. 42:18751884.
82. Hussain, Z.,, L. Stoakes,, V. Massey,, D. Diagre,, V. Fitzgerald,, S. El Sayed, and, R. Lannigan. 2000. Correlation of oxacillin MIC with mecA gene carriage in coagulase-negative staphylococci. J. Clin. Microbiol. 38:752754.
83. Inderleid, C. B.,, and G. E. Pfyffer. 2003. Susceptibility test methods: mycobacteria, p. 1149–1177. In P. M. Murray,, E. J. Baron,, J. H. Jorgenson,, M. A. Pfaller, and, R. H. Yolken (ed.), Manual of Clinical Microbiology. ASM Press, Washington, DC.
84. Isola, D.,, M. Pardini,, F. Varaine,, S. Niemann,, S. Rusch-Gerdes,, L. Fattorini,, G. Orefici,, F. Meacci,, C. Trappetti,, O. M. Rinaldo, and, G. Orru. 2005. A pyrosequencing assay for rapid recognition of SNPs in Mycobacterium tuberculosis embB306 region. J. Microbiol. Methods 62:113120.
85. Iyampillai, T.,, J. S. Michael,, E. Mathai, and, M. S. Mathews. 2004. Use of CHROMagar medium in the differentiation of Candida species: is it cost-effective in developing countries? Ann. Trop. Med. Parasitol. 98:279282.
86. Jonas, D.,, M. Speck,, F. D. Daschner, and, H. Grundmann. 2002. Rapid PCR-based identification of methicillin-resistant Staphylococcus aureus from screening swabs. J. Clin. Microbiol. 40:18211823.
87. Jonasson, J.,, M. Olofsson, and, H. J. Monstein. 2002. Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110:263272.
88. Jones, L. P.,, H. Q. Zheng,, R. A. Karron,, T. C. Peret,, C. Tsou, and, L. J. Anderson. 2002. Multiplex assay for detection of strain-specific antibodies against the two variable regions of the G protein of respiratory syncytial virus. Clin. Diagn. Lab. Immunol. 9:633638.
89. Jureen, P.,, L. Engstrand,, S. Eriksson,, A. Alderborn,, M. Krabbe, and, S. E. Hoffner. 2006. Rapid detection of rifampin resistance in Mycobacterium tuberculosis by pyrosequencing technology. J. Clin. Microbiol. 44:19251929.
90. Kaye, M.,, S. Skidmore,, H. Osman,, M. Weinbren, and, R. Warren. 2006. Surveillance of respiratory virus infections in adult hospital admissions using rapid methods. Epidemiol. Infect. 134:792798.
91. Khudaier, B. Y.,, R. Tewari,, S. Shafiani,, M. Sharma,, R. Emmanuel,, M. Sharma, and, N. Taneja. 2007. Epidemiology and molecular characterization of vancomycin resistant enterococci isolates in India. Scand. J. Infect. Dis. 39:662670.
92. Kobayashi, N.,, T. W. Bauer,, M. J. Tuohy,, I. H. Lieberman,, V. Krebs,, D. Togawa,, T. Fujishiro, and, G. W. Procop. 2006. The comparison of pyrosequencing molecular Gram stain, culture, and conventional Gram stain for diagnosing orthopaedic infections. J. Orthop. Res. 24:16411649.
93. Kola, A.,, I. F. Chaberny,, F. Mattner,, U. Reischl,, R. P. Vonberg,, K. Weist,, C. Wendt,, W. Witte,, S. Ziesing,, S. Suerbaum, and, P. Gastmeier. 2006. Control of methicillin-resistant S. aureus by active surveillance. Results of a workshop held by the Deutsche Gesellschaft fur Hygiene und Mikrobiologie. Anaesthesist 55:778783.
94. Kost, C. B.,, B. Rogers,, M. S. Oberste,, C. Robinson,, B. L. Eaves,, K. Leos,, S. Danielson,, M. Satya,, F. Weir, and, F. S. Nolte. 2007. Multicenter beta trial of the GeneXpert enterovirus assay. J. Clin. Microbiol. 45:10811086.
95. Larsen, N.,, G. J. Olsen,, B. L. Maidak,, M. J. McCaughey,, R. Overbeek,, T. J. Macke,, T. L. Marsh, and, C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21:30213023.
96. Ledeboer, N. A.,, K. Das,, M. Eveland,, C. Roger-Dalbert,, S. Mailler,, S. Chatellier, and, W. M. Dunne. 2007. Evaluation of a novel chromogenic agar medium for isolation and differentiation of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis isolates. J. Clin. Microbiol. 45:15561560.
97. Lee, W. M.,, K. Grindle,, T. Pappas,, D. J. Marshall,, M. J. Moser,, E. L. Beaty,, P. A. Shult,, J. R. Prudent, and, J. E. Gern. 2007. High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses. J. Clin. Microbiol. 45:26262634.
98. Lee, W. M.,, K. Grindle,, T. Pappas,, D. J. Marshall,, M. J. Moser,, E. L. Beaty,, P. A. Shult,, J. R. Prudent, and, J. E. Gern. 2007. High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses. J. Clin. Microbiol. 45:26262634.
99. Reference deleted.
100. Lee, W. M.,, C. Kiesner,, T. Pappas,, I. Lee,, K. Grindle,, T. Jartti,, B. Jakiela,, R. F. Lemanske,, P. A. Shult, and, J. E. Gern. 2007. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS ONE 2:e966.
101. Lenhof, H. P.,, B. Morgenstern, and, K. Reinert. 1999. An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics 15:203210.
102. Li, H.,, M. A. McCormac,, R. W. Estes,, S. E. Sefers,, R. K. Dare,, J. D. Chappell,, D. D. Erdman,, P. F. Wright, and, Y. W. Tang. 2007. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections. J. Clin. Microbiol. 45:21052109.
103. Li, P.,, K. C. Kupfer,, C. J. Davies,, D. Burbee,, G. A. Evans, and, H. R. Garner. 1997. PRIMO: a primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476485.
104. Louie, L.,, J. Goodfellow,, P. Mathieu,, A. Glatt,, M. Louie, and, A. E. Simor. 2002. Rapid detection of methicillin-resistant staphylococci from blood culture bottles by using a multiplex PCR assay. J. Clin. Microbiol. 40:27862790.
105. Louie, L.,, A. E. Simor,, S. Chong,, K. Luinstra,, A. Petrich,, J. Mahony,, M. Smieja,, G. Johnson,, F. Gharabaghi,, R. Tellier,, B. M. Willey,, S. Poutanen,, T. Mazzulli,, G. Broukhanski,, F. Jamieson,, M. Louie, and, S. Richardson. 2006. Detection of severe acute respiratory syndrome coronavirus in stool specimens by commercially available real-time reverse transcriptase PCR assays. J. Clin. Microbiol. 44:41934196.
106. Maes, N.,, J. Magdalena,, S. Rottiers,, G. Y. De, and, M. J. Struelens. 2002. Evaluation of a triplex PCR assay to discriminate Staphylococcus aureus from coagulase-negative staphylococci and determine methicillin resistance from blood cultures. J. Clin. Microbiol. 40:15141517.
107. Mahony, J.,, S. Chong,, F. Merante,, S. Yaghoubian,, T. Sinha,, C. Lisle, and, R. Janeczko. 2007. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay. J. Clin. Microbiol. 45:29652970.
108. Reference deleted.
109. Maidak, B. L.,, J. R. Cole,, T. G. Lilburn,, C. T. Parker, Jr.,, P. R. Saxman,, R. J. Farris,, G. M. Garrity,, G. J. Olsen,, T. M. Schmidt, and, J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173174.
110. Maidak, B. L.,, J. R. Cole,, T. G. Lilburn,, C. T. Parker, Jr.,, P. R. Saxman,, J. M. Stredwick,, G. M. Garrity,, B. Li,, G. J. Olsen,, S. Pramanik,, T. M. Schmidt, and, J. M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:173174.
111. Maidak, B. L.,, N. Larsen,, M. J. McCaughey,, R. Overbeek,, G. J. Olsen,, K. Fogel,, J. Blandy, and, C. R. Woese. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22:34853487.
112. Marra, A. R.,, K. Bar,, G. M. Bearman,, R. P. Wenzel, and, M. B. Edmond. 2006. Systemic inflammatory response syndrome in adult patients with nosocomial bloodstream infection due to Pseudomonas aeruginosa. J. Infect. 53:3035.
113. Marra, A. R.,, M. B. Edmond,, B. A. Forbes,, R. P. Wenzel, and, G. M. Bearman. 2006. Time to blood culture positivity as a predictor of clinical outcome of Staphylococcus aureus bloodstream infection. J. Clin. Microbiol. 44:13421346.
114. Marshall, D. J.,, E. Reisdorf,, G. Harms,, E. Beaty,, M. J. Moser,, W. M. Lee,, J. E. Gern,, F. S. Nolte,, P. Shult, and, J. R. Prudent. 2007. Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting. J. Clin. Microbiol. 45:38753882.
115. Martins, T. B. 2002. Development of internal controls for the Luminex instrument as part of a multiplex seven-analyte viral respiratory antibody profile. Clin. Diagn. Lab. Immunol. 9:4145.
116. Mascini, E. M.,, A. C. Gigengack-Baars,, R. J. Hene,, T. E. Kamp-Hopmans,, A. J. Weersink, and, M. J. Bonten. 2000. Epidemiologic increase of various genotypes of vancomycin-resistant Enterococcus faecium in a university hospital. Ned. Tijdschr. Geneeskd. 144:25722576.
117. Mathema, B.,, and B. N. Kreiswirth. 2004. Genotyping bacteria by using variable-number tandem repeats, p. 223–234. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
118. McLeod, H. L. 2005. Pharmacogenetic analysis of clinically relevant genetic polymorphisms. Clin. Infect. Dis. 41(Suppl. 7):S449S452.
119. Mellmann, A.,, J. L. Cloud,, S. Andrees,, K. Blackwood,, K. C. Carroll,, A. Kabani,, A. Roth, and, D. Harmsen. 2003. Evaluation of RIDOM, MicroSeq, and GenBank services in the molecular identification of Nocardia species. Int. J. Med. Microbiol. 293:359370.
120. Mellmann, A.,, A. W. Friedrich,, F. Kipp,, F. Hinder,, U. Keckevoet, and, D. Harmsen. 2005. Evidence-based infection control methods using spa genotyping for MRSA spread in hospitals. Dtsch. Med. Wochenschr. 130:13641368.
121. Mellmann, A.,, A. W. Friedrich,, N. Rosenkotter,, J. Rothganger,, H. Karch,, R. Reintjes, and, D. Harmsen. 2006. Automated DNA sequence-based early warning system for the detection of methicillin-resistant Staphylococcus aureus outbreaks. PLoS Med. 3:e33.
122. Molenkamp, R.,, A. van der Ham,, J. Schinkel, and, M. Beld. 2007. Simultaneous detection of five different DNA targets by real-time Taqman PCR using the Roche LightCycler480: application in viral molecular diagnostics. J. Virol. Methods 141:205211.
123. Murray, C. K.,, M. L. Beckius,, J. A. Green, and, D. R. Hospenthal. 2005. Use of chromogenic medium in the isolation of yeasts from clinical specimens. J. Med. Microbiol. 54:981985.
124. Naas, T.,, L. Poirel, and, P. Nordmann. 2006. Pyrosequencing for rapid identification of carbapenem-hydrolysing OXA-type beta-lactamases in Acinetobacter baumannii. Clin. Microbiol. Infect. 12:12361240.
125. Nahimana, I.,, P. Francioli, and, D. S. Blanc. 2006. Evaluation of three chromogenic media (MRSA-ID, MRSA-Select and CHROMagar MRSA) and ORSAB for surveillance cultures of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect. 12:11681174.
126. Nguyen, H. B.,, E. P. Rivers,, B. P. Knoblich,, G. Jacobsen,, A. Muzzin,, J. A. Ressler, and, M. C. Tomlanovich. 2004. Early lactate clearance is associated with improved outcome in severe sepsis and septic shock. Crit. Care Med. 32:16371642.
127. Nguyen Van, J. C.,, M. D. Kitzis,, A. Ly,, A. Chalfine,, J. Carlet,, A. A. Ben, and, F. Goldstein. 2006. Detection of nasal colonization methicillin-resistant Staphylococcus aureus: a prospective study comparing real-time genic amplification assay vs selective chromogenic media. Pathol. Biol. (Paris) 54:285292.
128. Reference deleted.
129. Nilsson, I.,, I. Shabo,, J. Svanvik, and, H. J. Monstein. 2005. Multiple displacement amplification of isolated DNA from human gallstones: molecular identification of Helicobacter DNA by means of 16S rDNA-based pyrosequencing analysis. Helicobacter 10:592600.
130. Nolte, F. S.,, D. J. Marshall,, C. Rasberry,, S. Schievelbein,, G. G. Banks,, G. A. Storch,, M. Q. Arens,, R. S. Buller, and, J. R. Prudent. 2007. MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses. J. Clin. Microbiol. 45:27792786.
131. Reference deleted.
132. Olive, D. M.,, and P. Bean. 1999. Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37:16611669.
133. Oliveira, K.,, S. M. Brecher,, A. Durbin,, D. S. Shapiro,, D. R. Schwartz,, P. C. De Girolami,, J. Dakos,, G. W. Procop,, D. Wilson,, C. S. Hanna,, G. Haase,, H. Peltroche-Llacsahuanga,, K. C. Chapin,, M. C. Musgnug,, M. H. Levi,, C. Shoemaker, and, H. Stender. 2003. Direct identification of Staphylococcus aureus from positive blood culture bottles. J. Clin. Microbiol. 41:889891.
134. Oliveira, K.,, G. Haase,, C. Kurtzman,, J. J. Hyldig-Nielsen, and, H. Stender. 2001. Differentiation of Candida albicans and Candida dubliniensis by fluorescent in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 39:41384141.
135. Reference deleted.
136. Oliveira, K.,, G. W. Procop,, D. Wilson,, J. Coull, and, H. Stender. 2002. Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 40:247251.
137. Ornskov, D.,, B. Kolmos,, H. P. Bendix,, N. J. Nederby,, I. Brandslund, and, P. Schouenborg. 2008. Screening for methicillin-resistant Staphylococcus aureus in clinical swabs using a high-throughput real-time PCR-based method. Clin. Microbiol. Infect. 14:2228.
138. Padiglione, A. A.,, E. A. Grabsch,, D. Olden,, M. Hellard,, M. I. Sinclair,, C. K. Fairley, and, M. L. Grayson. 2000. Fecal colonization with vancomycin-resistant enterococci in Australia. Emerg. Infect. Dis. 6:534536.
139. Palenzuela, L.,, N. M. Hahn,, R. P. Nelson, Jr.,, J. N. Arno,, C. Schobert,, R. Bethel,, L. A. Ostrowski,, M. R. Sharma,, P. P. Datta,, R. K. Agrawal,, J. E. Schwartz, and, M. Hirano. 2005. Does linezolid cause lactic acidosis by inhibiting mitochondrial protein synthesis? Clin. Infect. Dis. 40:e113e116.
140. Pape, J.,, J. Wadlin, and, I. Nachamkin. 2006. Use of BBL CHROMagar MRSA medium for identification of methicillin-resistant Staphylococcus aureus directly from blood cultures. J. Clin. Microbiol. 44:25752576.
141. Pappas, P. G.,, J. H. Rex,, J. D. Sobel,, S. G. Filler,, W. E. Dismukes,, T. J. Walsh, and, J. E. Edwards. 2004. Guidelines for treatment of candidiasis. Clin. Infect. Dis. 38:161189.
142. Paule, S. M.,, D. M. Hacek,, B. Kufner,, K. Truchon,, R. B. Thomson, Jr.,, K. L. Kaul,, A. Robicsek, and, L. R. Peterson. 2007. Performance of the BD GeneOhm methicillin-resistant Staphylococcus aureus test before and during high-volume clinical use. J. Clin. Microbiol. 45:29932998.
143. Pearman, J. W. 2006. 2004 Lowbury Lecture: the Western Australian experience with vancomycin-resistant enterococci—from disaster to ongoing control. J. Hosp. Infect. 63:1426.
144. Perry, J. D.,, A. Davies,, L. A. Butterworth,, A. L. Hopley,, A. Nicholson, and, F. K. Gould. 2004. Development and evaluation of a chromogenic agar medium for methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 42:45194523.
145. Pfaller, M. A.,, and R. J. Hollis. 2004. Automated ribotyping, p. 245–258. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
146. Pitarch, A.,, J. Abian,, M. Carrascal,, M. Sanchez,, C. Nom-bela, and, C. Gil. 2004. Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies. Proteomics 4:30843106.
147. Plouzeau, C.,, M. Paccalin,, A. Beby-Defaux,, G. Giraudeau,, C. Godet, and, G. Agius. 2007. Diagnosis and epidemiological surveillance of influenza and respiratory syncytial virus infections: interest of multiplex PCR. Med. Mal. Infect. 37:728733.
148. Poirel, L.,, T. Naas, and, P. Nordmann. 2006. Pyrosequencing as a rapid tool for identification of GES-type extended-spectrum beta-lactamases. J. Clin. Microbiol. 44:30083011.
149. Pounder, J. I.,, D. Hansen, and, G. L. Woods. 2006. Identification of Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species by repetitive-sequence-based PCR. J. Clin. Microbiol. 44:29772982.
150. Pounder, J. I.,, S. Williams,, D. Hansen,, M. Healy,, K. Reece, and, G. L. Woods. 2005. Repetitive-sequence-PCR-based DNA fingerprinting using the Diversilab system for identification of commonly encountered dermatophytes. J. Clin. Microbiol. 43:21412147.
151. Proutski, V.,, and E. C. Holmes. 1996. Primer Master: a new program for the design and analysis of PCR primers. Comput. Appl. Biosci. 12:253255.
152. Putonti, C.,, S. Chumakov,, R. Mitra,, G. E. Fox,, R. C. Willson, and, Y. Fofanov. 2006. Human-blind probes and primers for dengue virus identification. FEBS J. 273:398408.
153. Putonti, C.,, Y. Luo,, C. Katili,, S. Chumakov,, G. E. Fox,, D. Graur, and, Y. Fofanov. 2006. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol. Biol. Evol. 23:18631868.
154. Rademaker, J. L.,, and P. Savelkoul. 2004. PCR amplification-based microbial typing, p. 197–221. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
155. Rasheed, J. K.,, and F. C. Tenover. 2003. Detection and characterization of antimicrobial resistance genes in bacteria, p. 1196–1213. In P. R. Murray,, E. J. Murray,, E. J. Baron,, M. A. Pfaller,, F. C. Tenover, and, R. H. Yolken (ed.), Manual Of Clinical Microbiology. ASM Press, Washington, DC.
156. Reingardene, D. 2004. Procalcitonin as a marker of the systemic inflammatory response to infection. Medicina 40:696701.
157. Rigby, S.,, G. W. Procop,, G. Haase,, D. Wilson,, G. Hall,, C. Kurtzman,, K. Oliveira,, S. Von Oy,, J. J. Hyldig-Nielsen,, J. Coull, and, H. Stender. 2002. Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J. Clin. Microbiol. 40:21822186.
158. Rivers, E.,, B. Nguyen,, S. Havstad,, J. Ressler,, A. Muzzin,, B. Knoblich,, E. Peterson, and, M. Tomlanovich. 2001. Early goal-directed therapy in the treatment of severe sepsis and septic shock. N. Engl. J. Med. 345:13681377.
159. Reference deleted.
160. Rodriguez, E.,, F. Symoens,, P. Mondon,, M. Mallie,, M. A. Piens,, B. Lebeau,, A. M. Tortorano,, F. Chaib,, A. Carlotti,, J. Villard,, M. A. Viviani,, F. Chapuis,, N. Nolard,, R. Grillot,, J. M. Bastide, et al. 1999. Combination of three typing methods for the molecular epidemiology of Aspergillus fumigatus infections. J. Med. Microbiol. 48:181194.
161. Rose, T. M.,, E. R. Schultz,, J. G. Henikoff,, S. Pietrokovski,, C. M. McCallum, and, S. Henikoff. 1998. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26:16281635.
162. Ross, T. L.,, W. G. Merz,, M. Farkosh, and, K. C. Carroll. 2005. Comparison of an automated repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for analysis of outbreaks of methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 43:56425647.
163. Rossney, A. S.,, C. M. Herra,, M. M. Fitzgibbon,, P. M. Morgan,, M. J. Lawrence, and, B. O’Connell. 2007. Evaluation of the IDI-MRSA assay on the SmartCycler real-time PCR platform for rapid detection of MRSA from screening specimens. Eur. J. Clin. Microbiol. Infect. Dis. 26:459466.
164. Rothganger, J.,, M. Weniger,, T. Weniger,, A. Mellmann, and, D. Harmsen. 2006. Ridom TraceEdit: a DNA trace editor and viewer. Bioinformatics 22:493494.
165. Sampath, R.,, S. A. Hofstadler,, L. B. Blyn,, M. W. Eshoo,, T. A. Hall,, C. Massire,, H. M. Levene,, J. C. Hannis,, P. M. Harrell,, B. Neuman,, M. J. Buchmeier,, Y. Jiang,, R. Ranken,, J. J. Drader,, V. Samant,, R. H. Griffey,, J. A. McNeil,, S. T. Crooke, and, D. J. Ecker. 2005. Rapid identification of emerging pathogens: coronavirus. Emerg. Infect. Dis. 11:373379.
166. Satake, S.,, N. Clark,, D. Rimland,, F. S. Nolte, and, F. C. Tenover. 1997. Detection of vancomycin-resistant enterococci in fecal samples by PCR. J. Clin. Microbiol. 35:23252330.
167. Sauer, M.,, K. Tiede,, R. Volland,, D. Fuchs, and, F. Zintl. 2000. Procalcitonin in comparison to C-reactive protein as markers of the course of sepsis in severely immunocompromised children after bone marrow transplantation. Klin. Padiatr. 212:1015.
168. Saunte, D. M.,, L. Klingspor,, S. Jalal,, J. Arnau, and, M. C. Arendrup. 2005. Four cases of Candida albicans infections with isolates developing pink colonies on CHROMagar Candida plates. Mycoses 48:378381.
169. Schmit, J. C.,, L. Ruiz,, L. Stuyver,, K. Van Laethem,, I. Vanderlinden,, T. Puig,, R. Rossau,, J. Desmyter,, E. De Clercq,, B. Clotet, and, A. M. Vandamme. 1998. Comparison of the LiPA HIV-1 RT test, selective PCR and direct solid phase sequencing for the detection of HIV-1 drug resistance mutations. J. Virol. Methods 73:7782.
170. Schneider, H. G.,, and Q. T. Lam. 2007. Procalcitonin for the clinical laboratory: a review. Pathology 39:383390.
171. Sendid, B.,, N. Francois,, A. Standaert,, E. Dehecq,, F. Zerimech,, D. Camus, and, D. Poulain. 2007. Prospective evaluation of the new chromogenic medium CandiSelect 4 for differentiation and presumptive identification of the major pathogenic Candida species. J. Med. Microbiol. 56:495499.
172. Sesti, F.,, G. W. Abbott,, J. Wei,, K. T. Murray,, S. Saksena,, P. J. Schwartz,, S. G. Priori,, D. M. Roden,, A. L. George, Jr., and, S. A. Goldstein. 2000. A common polymorphism associated with antibiotic-induced cardiac arrhythmia. Proc. Natl. Acad. Sci. USA 97:1061310618.
173. Shafer, R. W.,, and S. Chou. 2003. Mechanisms of resistance to antiviral agents, p. 1625–1635. In P. R. Murray,, E. J. Murray,, E. J. Baron,, M. A. Pfaller,, F. C. Tenover, and, R. H. Yolken (ed.), Manual of Clinical Microbiology. ASM Press, Washington, DC.
174. Shevchenko, A.,, M. Wilm,, O. Vorm, and, M. Mann. 1996. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68:850858.
175. Shopsin, B.,, and B. N. Kreiswirth. 2001. Molecular epidemiology of methicillin-resistant Staphylococcus aureus. Emerg. Infect. Dis. 7:323326.
176. Slezak, T.,, T. Kuczmarski,, L. Ott,, C. Torres,, D. Medeiros,, J. Smith,, B. Truitt,, N. Mulakken,, M. Lam,, E. Vitalis,, A. Zemla,, C. E. Zhou, and, S. Gardner. 2003. Comparative genomics tools applied to bioterrorism defence. Brief. Bioinform. 4:133149.
177. Sloan, L. M.,, J. R. Uhl,, E. A. Vetter,, C. D. Schleck,, W. S. Harmsen,, J. Manahan,, R. L. Thompson,, J. E. Rosenblatt, and, F. R. Cockerill III. 2004. Comparison of the Roche LightCycler vanA/vanB detection assay and culture for detection of vancomycin-resistant enterococci from perianal swabs. J. Clin. Microbiol. 42:26362643.
178. Reference deleted.
179. Sogaard, M.,, H. Stender, and, H. C. Schonheyder. 2005. Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes. J. Clin. Microbiol. 43:19471949.
180. Soll, D. R.,, S. R. Lockhart, and, C. Pujol. 2003. Laboratory procedures for the epidemiological analysis of microorganisms, p. 139–161. In P. M. Murray,, E. J. Baron,, J. H. Jorgenson,, M. A. Pfaller, and, R. H. Yolken (ed.), Manual of Clinical Microbiology. ASM Press, Washington, DC.
181. Stamper, P. D.,, M. Cai,, C. Lema,, K. Eskey, and, K. C. Carroll. 2007. Comparison of the BD GeneOhm VanR assay to culture for identification of vancomycin-resistant enterococci in rectal and stool specimens. J. Clin. Microbiol. 45:33603365.
182. Stender, H. 2003. PNA FISH: an intelligent stain for rapid diagnosis of infectious diseases. Expert Rev. Mol. Diagn. 3:649655.
183. Stoakes, L.,, R. Reyes,, J. Daniel,, G. Lennox,, M. A. John,, R. Lannigan, and, Z. Hussain. 2006. Prospective comparison of a new chromogenic medium, MRSASelect, to CHROMagar MRSA and mannitol-salt medium supplemented with oxacillin or cefoxitin for detection of methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 44:637639.
184. Stover, A.,, E. Jeffery,, J. Xu, and, D. H. Persing. 2004. Hybridization array technology, p. 619–639. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
185. Stranden, A.,, R. Frei, and, A. F. Widmer. 2003. Molecular typing of methicillin-resistant Staphylococcus aureus: can PCR replace pulsed-field gel electrophoresis? J. Clin. Microbiol. 41:31813186.
186. Strommenger, B.,, C. Kettlitz,, T. Weniger,, D. Harmsen,, A. W. Friedrich, and, W. Witte. 2006. Assignment of Staphylococcus isolates to groups by spa typing, SmaI macrorestriction analysis, and multilocus sequence typing. J. Clin. Microbiol. 44:25332540.
187. Strommenger, B.,, C. Kettlitz,, G. Werner, and, W. Witte. 2003. Multiplex PCR assay for simultaneous detection of nine clinically relevant antibiotic resistance genes in Staphylococcus aureus. J. Clin. Microbiol. 41:40894094.
188. Symoens, F.,, S. Bertout,, M. A. Piens,, J. Burnod,, F. Renaud,, N. Nolard,, F. Chapuis, and, R. Grillot. 2001. A longitudinal study of lung transplant recipients infected with Aspergillus: genetic polymorphism of A fumigatus. J. Heart Lung Transplant. 20:970978.
189. Tenover, F. C.,, R. D. Arbeit,, R. V. Goering, et al. 1997. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Infect. Control Hosp. Epidemiol. 18:426439.
190. Tenover, F. C.,, R. D. Arbeit,, R. V. Goering,, P. A. Mickelsen,, B. E. Murray,, D. H. Persing, and, B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:22332239.
191. Tenover, F. C.,, and J. K. Rasheed. 2004. Detection of antimicrobial resistance genes and mutations associated with antimicrobial resistance in microorganisms, p. 391–406. In D. H. Persing,, F. C. Tenover,, J. Versalovic,, Y. Tang,, E. R. Unger,, D. A. Relman, and, T. J. White (ed.), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
192. Thompson, J. D.,, D. G. Higgins, and, T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:46734680.
193. Thompson, J. D.,, D. G. Higgins, and, T. J. Gibson. 1994. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 10:1929.
194. Toombs, L.,, E. Weeks,, G. N. Forrest,, D. Licalis,, J. K. Johnson, and, R. A. Venezia. 2007. Impact of peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH) for enterococcal blood stream infections, abstr. 131. Abstr. IDSA 2006 Annu. Meet. Infectious Disease Society of America, Arlington, VA.
195. Trama, J. P.,, E. Mordechai, and, M. E. Adelson. 2005. Detection of Aspergillus fumigatus and a mutation that confers reduced susceptibility to itraconazole and posaconazole by real-time PCR and pyrosequencing. J. Clin. Microbiol. 43:906908.
196. Troesch, A.,, H. Nguyen,, C. G. Miyada,, S. Desvarenne,, T. R. Gingeras,, P. M. Kaplan,, P. Cros, and, C. Mabilat. 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37:4955.
197. Tuohy, M. J.,, G. S. Hall,, M. Sholtis, and, G. W. Procop. 2005. Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp. Diagn. Microbiol. Infect. Dis. 51:245250.
198. Ueta, M.,, C. Sotozono,, T. Inatomi,, K. Kojima,, K. Tashiro,, J. Hamuro, and, S. Kinoshita. 2007. Toll-like receptor 3 gene polymorphisms in Japanese patients with Stevens-Johnson syndrome. Br. J. Ophthalmol. 91:962965.
199. van der Steen, L. F.,, M. J. Bonten,, E. van Kregten,, J. J. Harssema-Poot,, R. Willems, and, C. A. Gaillard. 2000. Vancomycin-resistant Enterococcus faecium outbreak in a nephrology ward. Ned. Tijdschr. Geneeskd. 144:25682572.
200. van der Zee, A.,, H. Verbakel,, J. C. van Zon,, I. Frenay,, A. van Belkum,, M. Peeters,, A. Buiting, and, A. Bergmans. 1999. Molecular genotyping of Staphylococcus aureus strains: comparison of repetitive element sequence-based PCR with various typing methods and isolation of a novel epidemicity marker. J. Clin. Microbiol. 37:342349.
201. Van Ert, M. N.,, S. A. Hofstadler,, Y. Jiang,, J. D. Busch,, D. M. Wagner,, J. J. Drader,, D. J. Ecker,, J. C. Hannis,, L. Y. Huynh,, J. M. Schupp,, T. S. Simonson, and, P. Keim. 2004. Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 37:642648.
202. van Loo, I. H.,, S. van Dijk,, I. Verbakel-Schelle, and, A. G. Buiting. 2007. Evaluation of a chromogenic agar (MRSASelect) for the detection of methicillin-resistant Staphylococcus aureus with clinical samples in The Netherlands. J. Med. Microbiol. 56:491494.
203. Versalovic, J.,, T. Koeuth, and, J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:68236831.
204. Vinh, D. C.,, K. A. Nichol,, F. Rand, and, J. A. Karlowsky. 2006. Not so pretty in pink: Staphylococcus cohnii masquerading as methicillin-resistant Staphylococcus aureus on chromogenic media. J. Clin. Microbiol. 44:46234624.
205. Vuilleumier, N.,, M. F. Rossier,, A. Chiappe,, F. Degoumois,, P. Dayer,, B. Mermillod,, L. Nicod,, J. Desmeules, and, D. Hochstrasser. 2006. CYP2E1 genotype and isoniazid-induced hepatotoxicity in patients treated for latent tuberculosis. Eur. J. Clin. Pharmacol. 62:423429.
206. Warren, D. K.,, R. S. Liao,, L. R. Merz,, M. Eveland, and, W. M. Dunne, Jr. 2004. Detection of methicillin-resistant Staphylococcus aureus directly from nasal swab specimens by a real-time PCR assay. J. Clin. Microbiol. 42:55785581.
207. Weller, T. M. 2000. Methicillin-resistant Staphylococcus aureus typing methods: which should be the international standard? J. Hosp. Infect. 44:160172.
208. Westin, L.,, C. Miller,, D. Vollmer,, D. Canter,, R. Radtkey,, M. Nerenberg, and, J. P. O’Connell. 2001. Antimicrobial resistance and bacterial identification utilizing a microelectronic chip array. J. Clin. Microbiol. 39:10971104.
209. Wheeler, D. L.,, T. Barrett,, D. A. Benson,, S. H. Bryant,, K. Canese,, V. Chetvernin,, D. M. Church,, M. Dicuccio,, R. Edgar,, S. Federhen,, M. Feolo,, L. Y. Geer,, W. Helmberg,, Y. Kapustin,, O. Khovayko,, D. Landsman,, D. J. Lipman,, T. L. Madden,, D. R. Maglott,, V. Miller,, J. Ostell,, K. D. Pruitt,, G. D. Schuler,, M. Shumway,, E. Sequeira,, S. T. Sherry,, K. Sirotkin,, A. Souvorov,, G. Starchenko,, R. L. Tatusov,, T. A. Tatusova,, L. Wagner, and, E. Yaschenko. 2007. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35:D5D12.
210. Wilson, D. A.,, M. J. Joyce,, L. S. Hall,, L. B. Reller,, G. D. Roberts,, G. S. Hall,, B. D. Alexander, and, G. W. Procop. 2005. Multicenter evaluation of a Candida albicans peptide nucleic acid fluorescent in situ hybridization probe for characterization of yeast isolates from blood cultures. J. Clin. Microbiol. 43:29092912.
211. Reference deleted.
212. Wilson, J. W.,, P. Bean,, T. Robins,, F. Graziano, and, D. H. Persing. 2000. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J. Clin. Microbiol. 38:30223028.
213. Wise, M. G.,, M. Healy,, K. Reece,, R. Smith,, D. Walton,, W. Dutch,, A. Renwick,, J. Huong,, S. Young,, J. Tarrand, and, D. P. Kontoyiannis. 2007. Species identification and strain differentiation of clinical Candida isolates using the Diversi-Lab system of automated repetitive sequence-based PCR. J. Med. Microbiol. 56:778787.
214. Reference deleted.
215. Wittwer, C. T.,, M. G. Herrmann,, C. N. Gundry, and, K. S. Elenitoba-Johnson. 2001. Real-time multiplex PCR assays. Methods 25:430442.
216. Wolk, D. M. 2006. PCR mass-spectrometry characterization of community-acquired oxacillin-resistant Staphylococcus aureus isolates, abstr. K-1187. Abstr. 46th Intersci. Conf. Antimicrob. Agents Chemother. American Society for Microbiology, Washington, DC.
217. Woods, C. R.,, J. Versalovic,, T. Koeuth, and, J. R. Lupski. 1993. Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J. Clin. Microbiol. 31:19271931.
218. Yang, Z. J.,, M. Z. Tu,, J. Liu,, X. L. Wang, and, H. Z. Jin. 2006. Comparison of amplicon-sequencing, pyrosequencing and real-time PCR for detection of YMDD mutants in patients with chronic hepatitis B. World J. Gastroenterol. 12:71927196.
219. Zhao, J. R.,, Y. J. Bai,, Y. Wang,, Q. H. Zhang,, M. Luo, and, X. J. Yan. 2005. Rapid detection of rifampin resistance of Mycobacterium tuberculosis using high-throughput pyrosequencing technique. Zhonghua Jie He He Hu Xi Za Zhi 28:297300.
220. Zhao, J. R.,, Y. J. Bai,, Q. H. Zhang,, Y. Wang,, M. Luo, and, X. J. Yan. 2005. Pyrosequencing-based approach for rapid detection of rifampin-resistant Mycobacterium tuberculosis. Diagn. Microbiol. Infect. Dis. 51:135137.
221. Zheng, S.,, E. Ross,, M. A. Legg, and, M. J. Wirth. 2006. High-speed electroseparations inside of silica colloidal crystals. J. Am. Chem. Soc. 128:90169017.