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Chapter 12.3 : Molecular Methods for Identification of Cultured Microorganisms

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Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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References

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1. Greene WC. 1991. The molecular biology of human immunodeficiency virus type 1 infection. N Engl J Med 324:308317.
2. Mellors JW, Kingsley LA, Rinaldo CR, Todd JA, Hoo BS, Kokka RP, Gupta P. 1995. Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann Intern Med 122:573579.
3. Mellors JW, Rinaldo CR, Gupta P, White RM, Todd JA, Kingsley LA. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272:11671170.
4. Mellors JW, Munoz A, Giorgi J, Margolick JB, Tassoni CJ, Gupta P, Kingsley LA, Todd JA, Saah AJ, Detels R, Phair JP, Rinaldo CR. 1997. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Ann Intern Med 126:946954.
5. O’Brien TR, Blattner WA, Waters D, Eyster E, Hilgartner MW, Cohen AR, Luban N, Hatzakis A, Aledort LM, Rosenberg PS, Miley WJ, Kroner BL, Goedert JJ. 1996. Serum HIV-1 RNA levels and time to development of AIDS in the Multicenter Hemophilia Cohort Study. JAMA 276:105110.
6. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents. Department of Health and Human Services. http://aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf. Accessed 10 October 2013.
7. O’Brien WA, Hartigan PM, Martin D, Esinhart J, Hill A, Benoit S, Rubin M, Simberkoff MS, Hamilton JD. 1996. Changes in plasma HIV-1 RNA and CD4+ lymphocyte counts and the risk of progression to AIDS. Veterans Affairs Cooperative Study Group on AIDS. N Engl J Med 334:426431.
8. Raboud JM, Montaner JS, Conway B, Rae S, Reiss P, Vella S, Cooper D, Lange J, Harris M, Wainberg MA, Robinson P, Myers M, Hall D. 1998. Suppression of plasma viral load below 20 copies/ml is required to achieve a long-term response to therapy. AIDS 12:16191624.
9. Branson BM, Handsfield HH, Lampe MA, Janssen RS, Taylor AW, Lyss SB, Clark JE. 2006. Revised recommendations for HIV testing of adults, adolescents, and pregnant women in health-care settings. MMWR Recomm Rep 55:117.
10. Hecht FM, Busch MP, Rawal B, Webb M, Rosenberg E, Swanson M, Chesney M, Anderson J, Levy J, Kahn JO. 2002. Use of laboratory tests and clinical symptoms for identification of primary HIV infection. AIDS 16:11191129.
11. Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, Peddada L, Heldebrant C, Smith R, Conrad A, Kleinman SH, Busch MP. 2003. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17:18711879.
12. CLSI. 2011. Criteria for Laboratory Testing and Diagnosis of Human Immunodeficiency Virus Infection; Approved Guideline. CLSI document M53-A. CLSI, Wayne, PA.
13. Read JS, Committee on Pediatric AIDS, Americna Academy of Pediatrics. 2007. Diagnosis of HIV-1 infection in children younger than 18 months in the United States. Pediatrics 120:e1547e1562.
14. Schneider E, Whitmore S, Glynn MK, Dominguez K, Mitsch A, McKenna MT. 2008. Revised surveillance case definitions for HIV infection among adults, adolescents, and children aged <18 months and for HIV infection and AIDS among children aged 18 months to <13 years – United States, 2008. MMWR Recomm Rep 57:18.
15. Anonymous. 2013. Detection of acute HIV infection in two evaluations of a new HIV diagnostic testing algorithm – United States, 2011-2013. MMWR Morb Mortal Wkly Rep 62:489494.
16. Miller JM, Astles R, Baszler T, Chapin K, Carey R, Garcia L, Gray L, Larone D, Pentella M, Pollock A, Shapiro DS, Weirich E, Wiedbrauk D, Biosafety Blue Ribbon Panel;, Centers for Disease Control and Prevention (CDC). 2012. Guidelines for safe work practices in human and animal medical diagnostic laboratories. Recommendations of a CDC-convened, Biosafety Blue Ribbon Panel. MMWR Surveill Summ 61(Suppl):1102.
17. Ethridge SF, Wesolowski LG, Nasrullah M, Kennedy MS, Delaney KP, Candal D, Owen SM. 2011. Comparative evaluation of Aptima HIV-1 Qualitative RNA assay performance using plasma and serum specimens from persons with established HIV-1 infection. J Clin Virol 52:S63S66.
18. Griffith BP, Rigsby MO, Garner RB, Gordon MM, Chacko TM. 1997. Comparison of the Amplicor HIV-1 monitor test and the nucleic acid sequence-based amplification assay for quantitation of human immunodeficiency virus RNA in plasma, serum, and plasma subjected to freeze-thaw cycles. J Clin Microbiol 35:32883291.
19. Ginocchio CC, Wang XP, Kaplan MH, Mulligan G, Witt D, Romano JW, Cronin M, Carroll R. 1997. Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma. J Clin Microbiol 35:28862893.
20. Lew J, Reichelderfer P, Fowler M, Bremer J, Carrol R, Cassol S, Chernoff D, Coombs R, Cronin M, Dickover R, Fiscus S, Herman S, Jackson B, Kornegay J, Kovacs A, Mc-Intosh K, Meyer W, Michael N, Mofenson L, Moye J, Quinn T, Robb M, Vahey M, Weiser B, Yeghiazarian T. 1998. Determinations of levels of human immunodeficiency virus type 1 RNA in plasma: reassessment of parameters affecting assay outcome. TUBE Meeting Workshop Attendees. Technology Utilization for HIV-1 Blood Evaluation and Standardization in Pediatrics. J Clin Microbiol 36:14711479.
21. Peluso MJ, Ferretti F, Peterson J, Lee E, Fuchs D, Boschini A, Gisslén M, Angoff N, Price RW, Cinque P, Spudich S. 2012. Cerebrospinal fluid HIV escape associated with progressive neurologic dysfunction in patients on antiretroviral therapy with well controlled plasma viral load. AIDS 26:17651774.
22. Rottinghaus EK, Ugbena R, Diallo K, Bassey O, Azeez A, Devos J, Zhang G, Aberle-Grasse J, Nkengasong J, Yang C. 2012. Dried blood spot specimens are a suitable alternative sample type for HIV-1 viral load measurement and drug resistance genotyping in patients receiving first-line antiretroviral therapy. Clin Infect Dis 54:11871195.
23. Sebire K, McGavin K, Land S, Middleton T, Birch C. 1998. Stability of human immunodeficiency virus RNA in blood specimens as measured by a commercial PCR-based assay. J Clin Microbiol 36:493498.
24. Donovan RM, Bush CE, Markowitz NP, Baxa DM, Saravolatz LD. 1996. Changes in virus load markers during AIDS-associated opportunistic diseases in human immunodeficiency virus-infected persons. J Infect Dis 174:401403.
25. CDC. State HIV Testing Laws: Consent And Counseling Requirements. www.cdc.gov/hiv/policies/law/states/testing.html. Accessed 10 October 2013.
26. CDC. State HIV Laws. http://www.cdc.gov/hiv/policies/law/states/index.html. Accessed 10 October 2013.
27. Davis C, Berry N, Heath A, Holmes H. 2008. An international collaborative study to establish a replacement World Health Organization International Standard for human immunodeficiency virus 1 RNA nucleic acid assays. Vox Sang 95:218225.
28. Glaubitz J, Sizmann D, Simon CO, Hoffmann KS, Drogan D, Hesse M, Lang G, Kroeh M, Simmler P, Dewald M, Haberhausen G, Lindauer A, Beyser K, Reber A, Baumeister A, Wolf E, Jaeger H, Babiel R. 2011. Accuracy to 2nd International HIV-1 RNA WHO Standard: assessment of three generations of quantitative HIV-1 RNA nucleic acid amplification tests. J Clin Virol 50:119124.
29. Braun P, Ehret R, Wiesmann F, Zabbai F, Knickmann M, Kühn R, Thamm S, Warnat G, Knechten H. 2007. Comparison of four commercial quantitative HIV-1 assays for viral load monitoring in clinical daily routine. Clin Chem Lab Med 45:9399.
30. Panel on Antiretroviral Therapy and Medical Management of HIV-Infected Children. Guidelines for the Use of Antiretroviral Agents in Pediatric HIV Infection. Department of Health and Human Services. http://aidsinfo.nih.gov/contentfiles/lvguidelines/pediatricguidelines.pdf. Accessed 10 October 2013.
31. Palmer S, Wiegand AP, Maldarelli F, Bazmi H, Mican JM, Polis M, Dewar RL, Planta A, Liu S, Metcalf JA, Mellors JW, Coffin JM. 2003. New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 41:45314536.
32. Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM. 2008. The challenge of HIV-1 subtype diversity. N Engl J Med 358:15901602.
33. Plantier JC, Leoz M, Dickerson JE, De Oliveira F, Cordonnier F, Lemee V, Damond F, Robertson DL, Simon F. 2009. A new human immunodeficiency virus derived from gorillas. Nat Med 15:871872.
34. Baxter JD, Mayers DL, Wentworth DN, Neaton JD, Hoover ML, Winters MA, Mannheimer SB, Thompson MA, Abrams DI, Brizz BJ, Ioannidis JP, Merigan TC. 2000. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy; CPCRA 046 study team for the Terry Beirn community programs for clinical research on AIDS. AIDS 14:F83F93.
35. Cohen CJ, Hunt S, Sension M, Farthing C, Conant M, Jacobson S, Nadler J, Verbiest W, Hertogs K, Ames M, Rinehart AR, Graham NM, VIRA3001 Study Group. 2002. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS 16:579588.
36. DeGruttola V, Dix L, D’Aquila R, Holder D, Phillips A, Ait-Khaled M, Baxter J, Clevenbergh P, Hammer S, Harrigan R, Katzenstein D, Lanier R, Miller M, Para M, Yerly S, Zolopa A, Murray J, Patick A, Miller V, Castillo S, Pedneault L, Mellors J. 2000. The relation between HIV drug resistance and response to anti-retroviral therapy: re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antivir Ther 5:4148.
37. Durant J, Clevenbergh P, Halfon P, Delgiudice P, Porsin S, Simonet P, Montagne N, Boucher CA, Schapiro JM, Dellamonica P. 1999. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet 353:21952199.
38. Hammer SM Pedneault L. 2000. Antiretroviral resistance testing comes of age. Antivir Ther 5:2326.
39. Hirsch M, Brun-Vezinet F, Clotet B, Conway B, Kuritzkes DR, D’Aquila RT, Demeter LM, Hammer SM, Johnson VA, Loveday C, Mellors JW, Jacobsen DM, Richman DD. 2003. Anti-retroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society—USA Panel. Clin Infect Dis 37:113128.
40. Little SJ, Holte S, Routy JP, Daar ES, Markowitz M, Collier AC, Koup RA, Mellors JW, Connick E, Conway B, Kilby M, Wang L, Whitcomb JM, Hellmann NS, Richman DD. 2002. Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 347:385394.
41. Melnick D, Rosenthal J, Cameron M. 2002. Impact of Phenotypic Antiretroviral Drug Resistance Testing on the Response to Salvage Antiretroviral Therapy (ART) in Heavily Experienced Patients, 7th Conference on Retroviruses and Opportunistic Infections, San Francisco, CA, 30 January to 2 February 2000.
42. Meynard JL, Vray M, Morand-Joubert L. 2000. Impact of treatment guided by phenotypic or genotypic resistance tests on the response to antiviral therapy (ART): a randomised trial (NARVAL; ANRS 088), 40th ICAAC Abstracts, Toronto, Ontario, Canada, 17–20 September 2000.
43. Richman DD. 2000. Principles of HIV resistance testing and overview of assay performance characteristics. Antivir Ther 5:2731.
44. Tulal C, Ruiz L, Holtzer C, Schapiro J, Viciana P, González J, Domingo P, Boucher C, Rey-Joly C, Clotet B; Havana Study Group. 2002. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS 16:209218.
1. Lok ASF, McMahon BJ. 2009. Chronic hepatitis B: Update 2009. Hepatology 50:661662.
2.European Association for the Study of the Liver. 2012. EASL clinical practice guidelines: management of chronic hepatitis B virus infection. J. Hepatol. 57:167185.
3.European Association for the Study of the Liver. 2012. EASL clinical practice guidelines: management of chronic hepatitis B virus infection. J Hepatol 57:167185. (Erratum: 58:201, 2013)
4. Flink HJ, van Zonneveld M, Hansen BE, de Man RA, Schalm SW, Janssen HL. 2006. Treatment with Peg-Interferon α-2b for HBeAg-positive chronic hepatitis B: HBsAg loss is associated with HBV genotype. Am J Gastroenterol 101:297303.
5. Yuen M-F, Tanaka Y, Shinkai N, Poon RT, But DY-K, Fong DY-T, Fung J, Wong DKH, Yuen JC-H, Mizokami M, Lai C-L. 2008. Risk for hepatocellular carcinoma with respect to hepatitis B virus genotypes B/C, specific mutations of enhancer II/core promoter/precore regions and HBV DNA levels. Gut 57:98102.
6. Yin J, Xie J, Liu S, Zhang H, Han L, Lu W, Shen Q, Xu G, Dong H, Shen J, Zhang J, Han J, Wang L, Liu Y, Wang F, Zhao J, Zhang Q, Ni W, Wang H, Cao G. 2011. Association between the various mutations in viral core promoter region to different stages of hepatitis B, ranging of asymptomatic carrier state to hepatocellular carcinoma. Am J Gastroenterol 106:8192.
7. Martin CM, Welge JA, Shire NJ, Rouster SD, Shata MT, Sherman KE, Blackard JT. 2010. Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals. J Viral Hepat 17:588597.
8. Purdy MA. 2007. Hepatitis B virus S gene escape mutants. Asian J Transfus Sci 1:6270.
9. Tabor E. 2006. Infections by hepatitis B surface antigen gene mutants in Europe and North America. J Med Virol 78:S43S47.
10. Weber B. 2005. Genetic variability of the S gene of hepatitis B virus: clinical and diagnostic impact. J. Clin. Virol. 32:102112.
11. Basaras M, Arrese E, Blanco S, Arroyo LS, Ruiz P, Cisterna R. 2013. Comparison of INNO-LIPA and TRUGENE assays for genotyping and drug-resistance mutations in chronic hepatitis B virus infection. Intervirology 56:190194.
12. Bouchardeau F, Cantaloube JF, Chevaliez S, Portal C, Razer A, Lefrere J-J, Pawlotsky JM, De Micco P, Laperche S. 2007. Improvement of hepatitis c virus (HCV) geno-type determination with the new version of the INNO-LiPA HCV assay. J Clin Microbiol 45:11401145.
13. Hussain M, Chu C-J, Sablon E, Lok ASF. 2003. Rapid and sensitive assays for determination of hepatitis B virus (HBV) genotypes and detection of HBV precore and core promoter variants. J Clin Microbiol 41:36993705.
14. Mercier M, Laperche S, Girault A, Sureau C, Servant-Delmas A. 2011. Overestimation of incidence of hepatitis B virus mixed-genotype infections by use of the new line probe INNO-LiPA genotyping assay. J Clin Microbiol 49:11541156.
15. Germer JJ, Abraham P, Mandrekar JN, Yao JDC. 2013. Evaluation of the Abbott HBV ruo sequencing assay combined with laboratory-modified interpretive software. J Clin Microbiol 51:95100.
60. Guirgis BSS, Abbas RO, Azzazy HME. 2010. Hepatitis B virus genotyping: current methods and clinical implications. Int J Infect Dis 14:e941e953.
1. Quigley D, Unger E. 2011. Molecular detection of human papillomaviruses, p 593–604. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington DC.
2. Liu YQ, He X, Xu SS, Qu JX, Wang Y, Diao XL, Liu J, Wang SZ. 2015. Epidemiology and genotype distribution of high-risk human papillomavirus in population of hospital opportunistic screening. Int J Clin Exp Med 8:1600716014.
3. CDC. 2015. Cervical Cancer Screening Guidelines for Average Risk Women. http://www.cdc.gov/cancer/cervical/pdf/guidelines.pdf. Accessed 13 January 2016.
4. Wright TCJr, Stoler MH, Behrens CM, Apple R, Derion T, Wright TL. 2012. The ATHENA human papillomavirus study: design, methods, and baseline results. Am J Obstet Gynecol 206:46.e146.e11.
5. Meijer CJ, Berkhof J, Castle PE, Hesselink AT, Franco EL, Ronco G, Arbyn M, Bosch FX, Cuzick J, Dillner J, Heideman DA, Snijders PJ. 2009. Guidelines for human papillomavirus DNA test requirements for primary cervical cancer screening in women 30 years and older. Int J Cancer 124:516520.
6. Saslow D, Solomon D, Lawson HW, Killackey M, Kulasingam SL, Cain J, Garcia FA, Moriarty AT, Waxman AG, Wilbur DC, Wentzensen N, Downs LSJr, Spitzer M, Moscicki AB, Franco EL, Stoler MH, Schiffman M, Castle PE, Myers ER; American Cancer Society; American Society of Colposcopy and Cervical Pathology; American Society for Clinical Pathology. 2012. American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology screening guidelines for the prevention and early detection of cervical cancer. Am J Clin Pathol 137:516542.
7. Saslow D, Solomon D, Lawson HW, Killackey M, Kulasingam SL, Cain J, Garcia FA, Moriarty AT, Waxman AG, Wilbur DC, Wentzensen N, Downs LSJr, Spitzer M, Moscicki AB, Franco EL, Stoler MH, Schiffman M, Castle PE, Myers ER; ACSASCCP-ASCP Cervical Cancer Guideline Committee. 2012. American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology screening guidelines for the prevention and early detection of cervical cancer. CA Cancer J Clin 62:147172.
8. Saslow D, Solomon D, Lawson HW, Killackey M, Kulasingam SL, Cain J, Garcia FA, Moriarty AT, Waxman AG, Wilbur DC, Wentzensen N, Downs LSJr, Spitzer M, Moscicki AB, Franco EL, Stoler MH, Schiffman M, Castle PE, Myers ER, Chelmow D, Herzig A, Kim JJ, Kinney W, Herschel WL, Waldman J. 2012. American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology screening guidelines for the prevention and early detection of cervical cancer. J Low Genit Tract Dis 16:175204.
9. USPSTF. 2012. Screening for Cervical Cancer. http://www.uspreventiveservicestaskforce.org/uspstf11/cervcancer/cervcancerrs.htm. Accessed 13 January 2016.
10. Committee on Practice Bulletins-Gynecology. 2012. ACOG Practice Bulletin Number 131: Screening for cervical cancer. Obstet Gynecol 120:12221238.
11. Huh WK, Ault KA, Chelmow D, Davey DD, Goulart RA, Garcia FA, Kinney WK, Massad LS, Mayeaux EJ, Saslow D, Schiffman M, Wentzensen N, Lawson HW, Einstein MH. 2015. Use of primary high-risk human papillomavirus testing for cervical cancer screening: interim clinical guidance. Gynecol Oncol 125:330337.
1. Fatahzadeh M, Schwartz RA. 2007. Human herpes simplex virus infections: Epidemiology, pathogenesis, symptomatology, diagnosis, and management. J Am Acad Dermatol 57:737763.
2. Mueller NH, Gilden DH, Cohrs RJ, Mahalingam R, Nagel MA. 2008. Varicella zoster virus infection: clinical features, molecular pathogenesis of disease, and latency. Neurol Clin 26:675697.
3. Shiley K, Blumberg E. 2011. Herpesviruses in transplant recipients: HSV, VZV, human perpes viruses, and EBV. Hematol Oncol Clin North Am 25:171191.
4. Whitley RJ, Alford CA, Hirsch MS, Schooley RT, Luby JP, Aoki FY, Hanley D, Nahmias AJ, Soong SJ. 1986. Vidarabine versus acyclovir therapy in herpes simplex encephalitis. N Engl J Med 314:144149.
5. Nahass GT, Goldstein BA, Zhu WY, Serfling U, Penneys NS, Leonardi CL. 1992. Comparison of Tzanck smear, viral culture, and DNA diagnostic methods in detection of herpes simplex and varicella–zoster infection. JAMA 268:25412544.
6. Chan EL, Brandt K, Horsman GB. 2001. Comparison of Chemicon SimulFluor direct fluorescent antibody staining with cell culture and shell vial direct immunoperoxidase staining for detection of herpes simplex virus and with cytospin direct immunofluorescence staining for detection of varicella zoster virus. Clin Diagn Lab Immunol 8:909912.
7. Fan F, Day S, Lu X, Tang YW. 2014. Laboratory diagnosis of HSV and varicella zoster virus infections. Future Virol 9:721731.
8. Tang YW, Mitchell PS, Espy MJ, Smith TF, Persing DH. 1999. Molecular diagnosis of herpes simplex virus infections in the central nervous system. J Clin Microbiol 37:21272136.
9. Selvaraju SB, Wurst M, Horvat RT, Selvaranga R. 2009. Evaluation of three analytespecific reagents for detection and typing of herpes simplex virus in cerebrospinal fluid. Diagn Microbiol Infect Dis 63:286291.
10. Buelow DR, Bankowski MJ, Fofana D, Gu Z, Pounds S, Hayden RT. 2013. Comparison of two multiplexed PCR assays for the detection of HSV-1, HSV-2, and VZV with extracted and unextracted cutaneous and mucosal specimens. J Clin Virol 58:8488.
82. CLSI. 2004. Evaluation of Precision Performance of Quantitative Measurement Methods; Approved Guideline. 2nd ed. CLSI/NCCLS document EP05-A2. CLSI, Wayne, PA.
83. CLSI. 2004. Protocols for Determination of Limits of Detection and Limits of Quantitation; Approved Guideline. CLSI/NCCLS document EP17-A. CLSI, Wayne, PA.
84. CLSI. 2006. User Verification of Performance for Precision and Trueness; Approved Guideline. 2nd ed. CLSI document EP15-A2. CLSI, Wayne, PA.
85. CLSI. 2010. Method Comparison and Bias Estimation Using Patient Samples; Approved Guideline. 2nd ed. (Interim Revision). CLSI document EP09-A2-IR. CLSI, Wayne, PA.
1. Kotton CN, Kumar D, Caliendo AM, As berg A, Chou S, Danziger-Isakov L, Humar A. 2013. Updated international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation 96:333360.
2. Ljungman P, de la Camara R, Cordonnier C, Einsele H, Engelhard D, Reusser P, Styczynski J, Ward K. 2008. Management of CMV, HHV-6, HHV-7 and Kaposi-sarcoma herpesvirus (HHV-8) infections in patients with hematological malignancies and after SCT. Bone Marrow Transplant 42:227240.
3. Ljungman P, Griffiths P, Paya C. 2002. Definitions of cytomegalovirus infection and disease in transplant recipients. Clin Infect Dis 34:10941097.
4. Emery VC, Sabin CA, Cope AV, Gor D, Hassan-Walker AF, Griffiths PD. 2000. Application of viral-load kinetics to identify patients who develop cytomegalovirus disease after transplantation. Lancet 355:20322036.
5. Meyers JD, Ljungman P, Fisher LD. 1990. Cytomegalovirus excretion as a predictor of cytomegalovirus disease after marrow transplantation: importance of cytomegalovirus viremia. J Infect Dis 162:373380.
6. Einsele H, Ehninger G, Hebart H, Witt-kowski KM, Schuler U, Jahn G, Mackes P, Herter M, Klingebiel T, Loffler J, Wagner S, Muller CA. 1995. Polymerase chain reaction monitoring reduces the incidence of cytomegalovirus disease and the duration and side effects of antiviral therapy after bone marrow transplantation. Blood 86:28152820.
7. Waggoner J, Ho DY, Libiran P, Pinsky BA. 2012. Clinical significance of low cytomegalovirus DNA levels in human plasma. J Clin Microbiol 50:23782383.
8. Razonable RR, Asberg A, Rollag H, Duncan J, Boisvert D, Yao JD, Caliendo AM, Humar A, Do TD. 2013. Virologic suppression measured by a cytomegalovirus (CMV) DNA test calibrated to the world health organization international standard is predictive of CMV disease resolution in transplant recipients. Clin Infect Dis 56:15461553.
9. Caliendo AM, Shahbazian MD, Schaper C, Ingersoll J, Abdul-Ali D, Boonyaratanakornkit J, Pang XL, Fox J, Preiksaitis J, Schonbrunner ER. 2009. A commutable cytomegalovirus calibrator is required to improve the agreement of viral load values between laboratories. Clin Chem 55:17011710.
10. Hayden RT, Yan X, Wick MT, Rodriguez AB, Xiong X, Ginocchio CC, Mitchell MJ, Caliendo AM. 2012. Factors contributing to variability of quantitative viral PCR results in proficiency testing samples: a multivariate analysis. J Clin Microbiol 50:337345.
11. Roche Molecular Systems. 2012. COBAS AmpliPrep/COBAS TaqMan CMV Test package insert. Roche Molecular Systems, Branch-burg, NJ.
12. Hirsch HH, Lautenschlager I, Pinsky BA, Cardenoso L, Aslam S, Cobb B, Vilchez RA, Valsamakis A. 2013. An international multicenter performance analysis of cytomegalovirus load tests. Clin Infect Dis 56:367373.
1. Lurain NS, Chou S. 2010. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev 23:689712.
2. Kotton CN, Kumar D, Caliendo AM, Asberg A, Chou S, Danziger-Isakov L, Humar A, on behalf of The Transplantation Society International CMV Consensus Group. 2013. Updated international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplant 96:333360.
3. Zürcher S, Mooser C, Lüthi AU, Mühle-mann K, Barbani MT, Mohacsi P, Garzoni C, Gorgievski-Hrisoho M, Schaller A, Flatz L. 2012. Sensitive and rapid detection of ganciclovir resistance by PCR based MALDI-TOF analysis. J Clin Virol 54:359363.
4. Sahoo MK, Lefterova MI, Yamamoto F, Waggoner JJ, Chou S, Holmes SP, Anderson MW, Pinsky BA. 2013. Detection of cytomegalovirus drug resistance mutations by next-generation sequencing. J Clin Microbiol 51:37003710.
5. Castor J, Cook L, Corey L, Jerome KR. 2007. Rapid detection directly from patient serum samples of human cytomegalovirus ul97 mutations conferring ganciclovir resistance. J Clin Microbiol 45:26812683.
6. Chou S, Guentzel S, Michels KR, Miner RC, Drew WL. 1995. Frequency of UL97 phosphotransferase mutations related to ganciclovir resistance in clinical cytomegalovirus isolates. J Infect Dis 172:239242.
7. Chou S, Lurain NS, Weinberg A, Cai G-Y, Sharma PL, Crumpacker CS. 1999. Interstrain variation in the human cytomegalovirus DNA polymerase sequence and its effect on genotypic diagnosis of antiviral drug resistance. Antimicrob Agents Chemother 43:15001502.
8. Daikoku T, Saito K, Aihara T, Ikeda M, Takahashi Y, Hosoi H, Nishida T, Takemoto M, Shiraki K. 2013. Rapid detection of human cytomegalovirus UL97 and UL54 mutations for antiviral resistance in clinical specimens: sensitive resistance genotyping of HCMV. Microbiol Immunol 57:396399.
9. Fillet A-M, Auray L, Alain S, Gourlain K, Imbert BM, Najioullah F, Champier G, Gouarin S, Carquin J, Houhou N, Garrigue I, Ducancelle A, Thouvenot D, Mazeron MC. 2004. Natural polymorphism of cytomegalovirus DNA polymerase lies in two nonconserved regions located between domains delta-C and II and between domains III and I. Antimicrob Agents Chemother 48:18651868.
10. Jabs DA, Martin BK, Forman MS, Dunn JP, Davis JL, Weinberg DV, Biron KK, Baldanti F. 2001. Mutations conferring ganciclovir resistance in a cohort of patients with acquired immunodeficiency syndrome and cytomegalovirus retinitis. J Infect Dis 183:333337.
11. Marfori JE, Exner MM, Marousek GI, Chou S, Drew WL. 2007. Development of new cytomegalovirus UL97 and DNA polymerase mutations conferring drug resistance after valganciclovir therapy in allogeneic stem cell recipients. J Clin Virol 38:120125.
12. Sedlak RH, Castor J, Butler-Wu SM, Chan E, Cook L, Limaye AP, Jerome KR. 2013. Rapid detection of human cytomegalovirus UL97 and UL54 mutations directly from patient samples. J Clin Microbiol 51:23542359.
13. Kotton CN, Kumar D, Caliendo AM, Asberg A, Chou S, Snydman DR, Allen U, Humar A, on behalf of The Transplantation Society International CMV Consensus Group 9. 2010. International consensus guidelines on the management of cytomegalovirus in solid organ transplantation. Transplant. 89:779795.
14. Chevillotte M, von Einem J, Meier BM, Lin F-M, Kestler HA, Mertens T. 2010. A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes. Antiviral Res 85:318327.
112. Chou S. 2010. Recombinant phenotyping of cytomegalovirus UL97 kinase sequence variants for ganciclovir resistance. Antimicrob Agents Chemother 54:23712378.
113. Chou S. 2011. Phenotypic diversity of cytomegalovirus DNA polymerase gene variants observed after antiviral therapy. J Clin Virol 50:287291.
114. Chou S, Boivin G, Ives J, Elston R. 2014. Phenotypic evaluation of previously uncharacterized cytomegalovirus DNA polymerase sequence variants detected in a Valganciclovir Treatment Trial. J Infect Dis 209:12191226.
115. Hantz S, Cotin S, Borst E, Couvreux A, Salmier A, Garrigue I, Merville P, Mengelle C, Attal M, Messerle M, Alain S. 2013. Novel DNA polymerase mutations conferring cytomegalovirus resistance: Input of BAC-recombinant phenotyping and 3D model. Antiviral Res 98:130134.
116. Lurain NS Chou S. 2010. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev 23:689712.
117. Martin M, Goyette N, Ives J, Boivin G. 2010. Incidence and characterization of cytomegalovirus resistance mutations among pediatric solid organ transplant patients who received valganciclovir prophylaxis. J Clin Virol 47:321324.
1. Johannsen EC, Schooley RT, Kaye KM. 2004. Epstein-Barr virus (infectious mononucleosis), p 18011820. In Mandel GL, Bennet JE, Dolin R (ed), Principles and Practices of Infectious Diseases, 6th ed. Elsevier, Churchill, Livingstone, Philadelphia, PA.
2. Henle G, Henle W, Clifford P, Diehl V, Kafuko GW, Kirya BG, Klein G, Morrow RH, Munube GM, Pike P, Tukei PM, Ziegler JL. 1969. Antibodies to Epstein-Barr virus in Burkitt’s lymphoma and control groups. J Natl Cancer Inst 43:11471154.
3. Pereira MS, Blake JM, Macrae AD. 1969. EB virus antibody at different ages. Br Med J 4:526527.
4. Babcock Gj, Decker LL, Volk M, Thorley-Lawson DA. 1998. EBV persistence in memory B cells in vivo. Immunity 9:395404.
5. Wagner HJ, Bein G, Bitch A, Kirchner H. 1992. Detection and quantification of latently infected B lymphocytes in Epstein-Barr virus-seropositive, healthy individuals by polymerase chain reaction. J Clin Microbiol 30:28262829.
6. Gottschalk S, Rooney CM, Heslop H. 2005. Post-transplant lymphoproliferative disorders. Annu Rev Med 56:29-44.
7. Scheuermann RH, Domiati-Saad R, Rogers BB. 2004. DNA virus detection, p 429440. In Persing DH, Tenover FC, Versalovic J, Tang YW, Unger ER, Relman DA, White TJ (ed), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
8. Bai X, Hosler G, Rogers BB, Dawson DB, Scheuermann RH. 1997. Quantitative polymerase chain reaction for human herpesvirus diagnosis and measurement of Epstein-Barr virus burden in post-transplant lymphoproliferative disease. Clin Chem 43:18431849.
9. MacMahon EM, Glass JD, Hayward SD, Mann RB, Becker PS, Charache P, Mc-Arthur JC, Ambinder RF. 1991. Epstein-Barr virus in AIDS-related primary central nervous system lymphoma. Lancet 338:969973.
10. Kim SC, Jang HJ, Han DJ. 1998. Acute disseminated encephalomyelitis after renal transplantation in patients with Epstein-Barr virus antibody. Transplant Proc 30:3139. doi: 10.1016/S0041-1345(98)00967-1.
11. MacGinley R, Bartley PB, Sloots T, Johnson DW. 2001. Epstein-Barr virus encephalitis in a renal allograft recipient diagnosed by polymerase chain reaction on cerebrospinal fluid and successfully treated with ganciclovir. Nephrol Dial Transplant 6:197198.
12. Behr J, Schaefer M, Littman E, Klingebiel R, Heinz A. 2006. Psychiatric symptoms and cognitive dysfunction caused by Epstein-Barr virus-induced encephalitis. Eur Psychiatry 21:521522.
13. Stevens SJC, Pronk I, Middeldorp JM. 2001. Toward standardization of Epstein-Barr Virus DNA load monitoring: unfractionated whole blood as preferred clinical specimen. J Clin Microbiol 39:12111216.
14. Bakker NA, Verschuuren EA, Veeger NJ, van der Bij W, van Imhoff GW, Kallenberg CG, Hepkema BG. 2008. Quantification of Epstein-Barr virus-DNA load in lung transplant recipients: a comparison of plasma versus whole blood. J Heart Lung Transplant 27:710.
15. Hakim H, Gibson C, Pan J, Srivastava K, Gu Z, Bankowski MJ, Hayden RT. 2007. Comparison of various blood compartments and reporting units for the detection and quantification of Epstein-Barr virus in peripheral blood. J Clin Microbiol 45:21512155.
16. Wagner HJ, Wessel M, Jabs W, Smets F, Fischer L, Offner G, Bucsky P. 2001. Patients at risk for development of posttransplant lymphoproliferative disorder: plasma versus peripheral blood mononuclear cells as material for quantification of Epstein-Barr viral load by using real-time quantitative polymerase chain reaction. Transplantation 72:10121019.
17. Hayden RT, Hokanson KM, Pounds SB, Bankowski MJ, Belzer SW, Carr J, Diorio D, Forman MS, Joshi Y, Hillyard D, Hodinka RL, Nikiforova MN, Romain CA, Stevenson J. Valsamakis A, Balfour HH, U.S. EBV Working Group. 2008. Multicenter comparison of different real-time PCR assay for quantitative detection of Epstein-Barr virus. J Clin Microbiol 46:157163.
1. Knowles WA. 2006. Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV) Adv Exp Med Biol 577:1945.
2. Weber T, Trebst C, Frye S, Cinque P, Vago L, Sindic CJ, Schulz-Schaeffer WJ, Kretzschmar HA, Enzensberger W, Hunsmann G, Lüke W. 1997. Analysis of the systemic and intrathecal humoral immune response in progressive multifocal leukoencephalopathy. J Infect Dis 176:250254.
3. Padgett BL, Walker DL, ZuRhein GM, Eckroade RJ, Dessel BH. 1971. Cultivation of papova-like virus from human brain with progressive multifocal leucoencephalopathy. Lancet 1:12571260.
4. Gardner SD, Field AM, Coleman DV, Hulme B. 1971. New human papovavirus (B.K.) isolated from urine after renal transplantation. Lancet 1:12531257.
5. Demeter LM. JC, BK, and other polyomaviruses; progressive multifocal leukoencephalopathy, p 18561863. In Mandel GL, Bennett JE, Dolin R (ed), Principles and Practices of Infectious Diseases, 6th ed. Elsevier, Churchill, Livingstone, Philadelphia, PA.
6. Mantyjarvi RA, Meurman OH, Vihma L, Berglund B. 1973. A human papovavirus (B.K.), biological properties and seroepidemiology. Ann Clin Res 5:283287.
7. Doerries K. 2006. Human polyomavirus JC and BK persistent infection. Adv Exp Med Biol 577:102116.
8. Kitamura T, Aso Y, Kuniyoshi N. 1990. High incidence of urinary JC virus excretion in nonimmunosuppressed older patients. J Infect Dis 161:11281133.
9. Hirsch HH, Brennan DC, Drachenberg CB, Ginevri F, Gordon J, Limaye AP, Mihatsch MJ, Nickeleit V, Ramos E, Randhawa P, Shapiro R, Steiger J, Suthanthiran M, Trofe J. 2005. Polyomavirus-associated nephropathy in renal transplantation: interdisciplinary analyses and recommendations. Transplantation 79:12771286.
10. Imperiale MJ, Major EO. Polyomaviruses. p 22652298 In Knipe DM, Howley PM (ed), Fields Virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
11. Hirsch HH, Brennan DC, Drachenberg CB, Ginervi F, Gordon J, Limaye AP, Mihatsch MJ, Nickeleit V, Ramos E, Randhawa P, Shapiro R, Steiger J, Suthanthiran M, Trofe J. 2005. Polyomavirus-associated nephropathy in renal transplantation: interdisciplinary analyses and recommendations. Transplantation 79:12771286.
1. Binnicker MJ. 26 August 2015. Multiplex molecular panels for the diagnosis of gastrointestinal infection: performance, result interpretation and cost-effectiveness. J Clin Microbiol doi:10.1128/JCM.02103-15.
2. Buchan BW, Olson WJ, Pezewski M, Marcon MJ, Novicki T, Uphoff TS, Chandramohan L, Revell P, Ledeboer NA. 2013. Clinical evaluation of a real-time PCR assay for identification of Salmonella, Shigella, Campylobacter (Campylobacter jejuni and C. coli), and shiga toxin-producing Escherichia coli isolates in stool specimens. J Clin Microbiol 51:40014007.
3. Biswas JS, Al-Ali A, Rajput P, Smith D, Goldenberg SD. 2014. A parallel diagnostic accuracy study of three molecular panels for the detection of bacterial gastroenteritis. Eur J Clin Microbiol Infect Dis 33:20752081.
4. Coupland LJ, McElarney I, Meader E, Cowley K, Alcock L, Naunton J, Gray J. 2013. Simultaneous detection of viral and bacterial enteric pathogens using the Seeplex(R) Diarrhea ACE detection system. Epidemiol Infect 141:21112121.
5. Onori M, Coltella L, Mancinelli L, Argentieri M, Menichella D, Villani A, Grandin A, Valentini D, Raponi M, Russo C. 2014. Evaluation of a multiplex PCR assay for simultaneous detection of bacterial and viral enteropathogens in stool samples of paediatric patients. Diagn Microbiol Infect Dis 79:149154.
6. McHardy IH, Wu M, Shimizu-Cohen R, Couturier MR, Humphries RM. 2014. Detection of intestinal protozoa in the clinical laboratory. J Clin Microbiol 52:712720.
7. Ramos F, Zurabian R, Moran P, Ramiro M, Gomez A, Clark CG, Melendro EI, Garcia G, Ximenez C. 1999. The effect of formalin fixation on the polymerase chain reaction characterization of Entamoeba histolytica. Trans R Soc Trop Med Hyg 93:335336.
8. Hurd S, Patrick M, Hatch J, Clogher P, Wymore K, Cronquist AB, Segler S, Robinson T, Hanna S, Smith G, Fitzgerald C. 2012. Clinical laboratory practices for the isolation and identification of Campylobacter in Foodborne Diseases Active Surveillance Network (FoodNet) sites: baseline information for understanding changes in surveillance data. Clin Infect Dis 54(Suppl 5):S440445.
9. Lewis SJ, Heaton KW. 1997. Stool form scale as a useful guide to intestinal transit time. Scand J Gastroenterol 32:920924.
10. Wessels E, Rusman LG, van Bussel MJ, Claas EC. 2014. Added value of multiplex Luminex Gastrointestinal Pathogen Panel (xTAG((R)) GPP) testing in the diagnosis of infectious gastroenteritis. Clin Microbiol Infect 20:O182O187.
11. Halligan E, Edgeworth J, Bisnauthsing K, Bible J, Cliff P, Aarons E, Klein J, Patel A, Goldenberg S. 10 January 2014. Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study. Clin Microbiol Infect doi: 10.1111/1469-0691.12476.
12. Mengelle C, Mansuy JM, Prere MF, Grouteau E, Claudet I, Kamar N, Huynh A, Plat G, Benard M, Marty N, Valentin A, Berry A, Izopet J. 2013. Simultaneous detection of gastrointestinal pathogens with a multiplex Luminex-based molecular assay in stool samples from diarrhoeic patients. Clin Microbiol Infect 19:E458E465.
13. Navidad JF, Griswold DJ, Gradus MS, Bhattacharyya S. 2013. Evaluation of Luminex xTAG gastrointestinal pathogen analyte-specific reagents for high-throughput, simultaneous detection of bacteria, viruses, and parasites of clinical and public health importance. J Clin Microbiol 51:30183024.
159. 1 Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS, Hoen AG, Sankoh O, Myers MF, George DB, Jaenisch T, Wint GR, Simmons CP, Scott TW, Farrar JJ, Hay SI. 2013. The global distribution and burden of dengue. Nature 496:504507.
160. 2World Health Organization. 2009. Dengue: Guidelines for Diagnosis, Treatment, Prevention and Control. WHO Press, France.
161. 3 Chien L, Liao T, Shu P, Huang J, Gubler DJ, Chang GJ. 2006. Development of real-time reverse transcriptase PCR assays to detect and serotype dengue viruses. J Clin Micobiol 44:12951304.
162. 4 Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vorndam V. 1992. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Micobiol 30:545551.
163. 5 Hue KDT, Tuan TV, Thi HTN, Bich CTN, Anh HHL, Wills BA, Simmons CP. 2011. Validation of an internally controlled one-step real-time multiplex RT-PCR assay for the detection and quantitation of dengue virus RNA in plasma. J Virol Meth 177:168173.
164. 6 Johnson BW, Russell BJ, Lanciotti RS. 2005. Serotype-specific detection of dengue viruses in a fourplex real-time reverse transcriptase PCR assay. J Clin Micobiol 43:49774983.
165. 7 Lai Y, Chung Y, Tan H, Yap H, Yap G, Ooi E, Ng L. 2007. Cost-effective real-time reverse trancriptase PCR (RT-PCR) to screen for Dengue virus followed by rapid single-tube multiplex RT-PCR for serotyping of the virus. J Clin Micobiol 45:935941.
166. 8 Leparc-Goffart I, Baragatti M, Temmam S, Tuiskunen A, Moureau G, Charrel R, de Lamballerie X. 2009. Development and validation of real-time one-step reverse transcription-PCR for the detection and typing of dengue viruses. J Clin Virol 45:6166.
167. 9 Munoz-Jordan J, Collins CS, Vergne E, Santiago GA, Peterson L, Sun W, Linnen JM. 2009. Highly sensitive detection of dengue virus nucleic acid in samples from clinically ill patients. J Clin Micobiol 47:927931.
168. 10 Santiago GA, Vergne E, Quiles Y, Cosme J, Vazquez J, Medina JF, Medina F, Colon C, Margolis H, Munoz-Jordan JL. 2013. Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus. PLoS Negl Trop Dis 7:e2311. doi: 10.1371/journal.pntd.0002311.
169. 11 Waggoner J, Abeynayake J, Sahoo MK, Gresh L, Tellez Y, Gonzalez K, Ballesteros G, Pierro AM, Gaibani P, Guo FP, Sambri V, Balmaseda A, Karunarante K, Harris E, Pinsky BA. 2013. Single-reaction, multiplex, real-time RT-PCR for the detection, quantitation, and serotyping of dengue viruses. PLoS Negl Trop Dis 7:e2116. doi: 10.1371/journal.pntd.0002116.
170. 12 Waggoner JJ, Abeynayake J, Sahoo MK, Gresh L, Tellez Y, Gonzalez K, Ballesteros G, Balmaseda A, Karunaratne K, Harris E, Pinsky BA. 2013. Development of an internally controlled real-time reverse transcriptase PCR assay for pan-dengue virus detection and comparison of four molecular dengue virus detection assays. J Clin Microbiol 51:21722181.
171. 13 Vaughn DW, Green S, Kalayanarooj S, Innis BL, Nimmannitya S, Suntayakorn S, Endy TP, Raengsakulrach B, Rothman AL, Ennis FA, Nisalak A. 2000. Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity. J Infect Dis 181:29.
172. 14 Dumoulin A, Marti H, Panning M, Hatz C, Hirsch HH. 2008. Pan-Dengue virus detection by PCR for travelers returning from the tropics. J Clin Micobiol 46:31043106.
173. 15 Waggoner JJ, Abeynayake J, Sahoo MK, Gresh L, Tellez Y, Gonzalez K, Ballesteros G, Guo FP, Balmaseda A, Karunaratne K, Harris E, Pinsky BA. 2013. Comparison of the FDA-approved CDC DENV-1-4 Real-Time RT-PCR with a laboratory-developed assay for dengue virus detection and serotyping. J Clin Microbiol 51:34183420.
174. 16 Lorono-Pino MA, Cropp CB, Farfan JA, Vorndam AV, Rodriguez-Angulo EM, Rosado-Paredes EP, Flores-Flores LF, Beaty BJ, Gubler DJ. 1999. Common occurrence of concurrent infections by multiple dengue virus serotypes. Am J Trop Med Hyg 61:725730.
175. 17 Hertz JT, Munishi OM, Ooi EE, Howe S, Lim WY, Chow A, Morrissey AB, Bartlett JA, Onyango JJ, Maro VP, Kinabo GD, Saganda W, Gubler DJ, Crump JA. 2012. Chikungunya and dengue fever among hospitalized febrile patients in northern Tanzania. Am J Trop Med Hyg 86:171177.
1. Satterwhite CL, Torrone E, Meites E, Dunne EF, Mahajan R, Ocfemia MC, Su J, Xu F, Weinstock H. 2013. Sexually transmitted infections among US women and men: prevalence and incidence estimates, 2008. Sex Transm Dis 40:187193.
2. National Center for HIV/AIDS VH, STD and TB Prevention, Centers for Disease Control and Prevention. 2014. 2013 Sexually Transmitted Diseases Surveillance. CDC, Atlanta, GA.
3. Weinstock H, Berman S, Cates WJr. 2004. Sexually transmitted diseases among American youth: incidence and prevalence estimates, 2000. Perspect Sex Reprod Health 36:610.
4. Datta SD, Torrone E, Kruszon-Moran D, Berman S, Johnson R, Satterwhite CL, Papp J, Weinstock H. 2012. Chlamydia trachomatis trends in the United States among persons 14 to 39 years of age, 1999-2008. Sex Transm Dis 39:9296.
5. Miller WC, Ford CA, Morris M, Handcock MS, Schmitz JL, Hobbs MM, Cohen MS, Harris KM, Udry JR. 2004. Prevalence of chlamydial and gonococcal infections among young adults in the United States. JAMA 291:22292236.
6. Dicker LW, Mosure DJ, Berman SM, Levine WC. 2003. Gonorrhea prevalence and coinfection with chlamydia in women in the United States, 2000. Sex Transm Dis 30:472476.
7. Kahn RH, Mosure DJ, Blank S, Kent CK, Chow JM, Boudov MR, Brock J, Tulloch S, Jail STD Prevalence Monitoring Project. 2005. Chlamydia trachomatis and Neisseria gonorrhoeae prevalence and coinfection in adolescents entering selected US juvenile detention centers, 1997-2002. Sex Transm Dis 32:255259.
8. LeFevre ML, Force USPST. 2014. Screening for Chlamydia and gonorrhea: U.S. Preventive Services Task Force recommendation statement. Ann Intern Med 161:902910.
9. Barry PM, Kent CK, Philip SS, Klausner JD. 2010. Results of a program to test women for rectal chlamydia and gonorrhea. Obstet Gynecol 115:753759.
10. Javanbakht M, Gorbach P, Stirland A, Chien M, Kerndt P, Guerry S. 2012. Prevalence and correlates of rectal Chlamydia and gonorrhea among female clients at sexually transmitted disease clinics. Sex Transm Dis 39:917922.
11. Papp JR, Schachter J, Gaydos CA, Van Der Pol B. 2014. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae—2014. MMWR Recomm Rep 63:119.
12. Schachter J, Chernesky MA, Willis DE, Fine PM, Martin DH, Fuller D, Jordan JA, Janda W, Hook EWIII. 2005. Vaginal swabs are the specimens of choice when screening for Chlamydia trachomatis and Neisseria gonorrhoeae: results from a multicenter evaluation of the APTIMA assays for both infections. Sex Transm Dis 32:725728.
13. Chernesky M, Jang D, Gilchrist J, Hatchette T, Poirier A, Flandin JF, Smieja M, Ratnam S. 2014. Head-to-head comparison of second-generation nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae on urine samples from female subjects and self-collected vaginal swabs. J Clin Microbiol 52:23052310.
14. Van Der Pol B, Taylor SN, Liesenfeld O, Williams JA, Hook EWIII. 2013. Vaginal swabs are the optimal specimen for detection of genital Chlamydia trachomatis or Neisseria gonorrhoeae using the Cobas 4800 CT/NG test. Sex Transm Dis 40:247250.
15. Chernesky MA, Hook EWIII, Martin DH, Lane J, Johnson R, Jordan JA, Fuller D, Willis DE, Fine PM, Janda WM, Schachter J. 2005. Women find it easy and prefer to collect their own vaginal swabs to diagnose Chlamydia trachomatis or Neisseria gonorrhoeae infections. Sex Transm Dis 32:729733.
16. Van Der Pol B, Liesenfeld O, Williams JA, Taylor SN, Lillis RA, Body BA, Nye M, Eisenhut C, Hook EWIII. 2012. Performance of the cobas CT/NG test compared to the Aptima AC2 and Viper CTQ/GCQ assays for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 50:2244;–2249;.
17. Schachter J, Moncada J, Liska S, Shayevich C, Klausner JD. 2008. Nucleic acid amplification tests in the diagnosis of chlamydial and gonococcal infections of the oropharynx and rectum in men who have sex with men. Sex Transm Dis 35:637642.
18. Bachmann LH, Johnson RE, Cheng H, Markowitz L, Papp JR, Palella FJJr, Hook EWIII. 2010. Nucleic acid amplification tests for diagnosis of Neisseria gonorrhoeae and Chlamydia trachomatis rectal infections. J Clin Microbiol 48:18271832.
19. Alexander S, Ison C, Parry J, Llewellyn C, Wayal S, Richardson D, Phillips A, Smith H, Fisher M, Brighton Home Sampling Kits Steering G. 2008. Self-taken pharyngeal and rectal swabs are appropriate for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in asymptomatic men who have sex with men. Sex Transm Infect 84:488492.
20. Patton ME, Kidd S, Llata E, Stenger M, Braxton J, Asbel L, Bernstein K, Gratzer B, Jespersen M, Kerani R, Mettenbrink C, Mohamed M, Pathela P, Schumacher C, Stirland A, Stover J, Tabidze I, Kirkcaldy RD, Weinstock H. 2014. Extragenital gonorrhea and chlamydia testing and infection among men who have sex with men--STD Surveillance Network, United States, 2010-2012. Clin Infect Dis 58:15641570.
21. Bachmann LH, Johnson RE, Cheng H, Markowitz LE, Papp JR, Hook EWIII. 2009. Nucleic acid amplification tests for diagnosis of Neisseria gonorrhoeae oropharyngeal infections. J Clin Microbiol 47:902907.
22. Tabrizi SN, Unemo M, Limnios AE, Hogan TR, Hjelmevoll SO, Garland SM, Tapsall J. 2011. Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species. J Clin Microbiol 49:36103615.
23. Upton A, Bromhead C, Whiley DM. 2013. Neisseria gonorrhoeae false-positive result obtained from a pharyngeal swab by using the Roche cobas 4800 CT/NG assay in New Zealand in 2012. J Clin Microbiol 51:16091610.
24. Dize L, West S, Williams JA, Van Der Pol B, Quinn TC, Gaydos CA. 2013. Comparison of the Abbott m2000 RealTime CT assay and the Cepheid GeneXpert CT/NG assay to the Roche Amplicor CT assay for detection of Chlamydia trachomatis in ocular samples from Tanzania. J Clin Microbiol 51:16111613.
25. Kowalski RP, Karenchak LM, Raju LV, Ismail N. 14 October 2014. The verification of nucleic acid amplification testing (Gen-Probe Aptima Assay) for Chlamydia trachomatis from ocular samples. Ophthalmology doi:10.1016/j.ophtha.2014.08.038.
26. Gaydos CA, Van Der Pol B, Jett-Goheen M, Barnes M, Quinn N, Clark C, Daniel GE, Dixon PB, Hook EWIII, Group CNS. 2013. Performance of the Cepheid CT/NG Xpert Rapid PCR test for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 51:16661672.
27. Unemo M, Clarke IN. 2011. The Swedish new variant of Chlamydia trachomatis. Curr Opin Infect Dis 24:6269.
28. Hadgu A, Dendukuri N, Wang L. 2012. Evaluation of screening tests for detecting Chlamydia trachomatis: bias associated with the patient-infected-status algorithm. Epidemiology 23:7282.
29. Ratnam S, Jang D, Gilchrist J, Smieja M, Poirier A, Hatchette T, Flandin JF, Chernesky M. 2014. Workflow and maintenance characteristics of five automated laboratory instruments for the diagnosis of sexually transmitted infections. J Clin Microbiol 52:22992304.
30. Williams JA, Eddleman L, Pantone A, Martinez R, Young S, Van Der Pol B. 2013. Time-motion analysis of four automated systems for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification testing. J Lab Autom 19:423426.
31. Hammerschlag MR, Gaydos CA. 2012. Guidelines for the use of molecular biological methods to detect sexually transmitted pathogens in cases of suspected sexual abuse in children. Methods Mol Biol 903:307317.
1. Sobel JD. 1990. Vaginal infections in adult women. Med Clin N Am 74:15731602.
2. Becton Dickinson and Co. 2009. BD Affirm VPIII Microbial Identification Test package insert, 670160JAA. Becton Dickinson and Co., Sparks, MD.
3. Kent HL. 1991. Epidemiology of vaginitis. Am J Obstet Gynecol 165:11681176.
210. Andrea SB, Chapin KC. 2011. Comparison of Aptima Trichomonas vaginalis transcription-mediated amplification assay and BD affirm VPIII for detection of T. vaginalis in symptomatic women: performance parameters and epidemiological implications. J Clin Microbiol 49:866869.
211. Briselden AM, Hillier SL. 1994. Evaluation of Affirm VP microbial identification. J Med Microbiol 32:148152.
212. Brown HL, Fuller DD, Jasper LT, Davis TE, Wright JD. 2004. Clinical evaluation of Affirm VPIII in the detection and identification of Trichomonas vaginalis, Gardnerella vaginalis, and Candida species in vaginitisvaginosis. Infect Dis Gynecol 12:1217.
213. Cartright CP, Lembke BD, Ramachandran K, Body BA, Ny MB, Rivers CA, Schwebke JR. 2013. Comparison of nucleic acid amplification assays with the BD Affirm VPIII for the diagnosis of vaginitis in symptomatic women. J Clin Microbiol 51:36943699.
214. Levi AM, Harigopal M, Hui P, Schofield K, Chhieng DC. 2011. Comparison of Affirm VPIII and Papanicolaou tests in the detection of infectious vaginitis. Am J Clin Pathol 135:442447.
215. Mulhem E, Boyanton BLJr, Robinson-Dunn B, Ebert C, Dzebo R. 2014. Performance of the Affirm VP-III using residual vaginal discharge collected from speculum to characterize vaginitis in symptomatic women. J Low Genit Tract Dis 18:344346.
216. Pappas S, Makrilakis K, Anyfantis I, Mitroussia-Ziouva A, Hadjisoteriou M, Petrikkos G. 2008. Clinical evaluation of affirm VP III in the detection and identification of bacterial vaginosis. J Chemother 20:764-765.
217. Petrikkos G, Makrilakis K, Pappas S. 2007. Affirm VP III in the detection and identification of Candida species in vaginitis. Int J Gynaecol Obstet 96:3940.
218. Rivers CA, Lee JY, Sharples N, Ledoeboer NA, Schwebke JR. 2014. ESwab as an optional collection device for use with the Affirm VPIII microbial test system. J Clin Microbiol 52:16981705.
219. Schwiertz A, Taras D, Rusch K, Rusch V. 2006. Throwing the dice for diagnosis of vaginal complaints? Ann Clin Microbiol Antimicrob 5:4. doi: 10.11861476-0711-5-4.
220. Witt A, Petricevic L, Kaufmann U, Gregor H, Kiss H. 2002. DNA hybridization test: rapid diagnostic tool for excluding bacterial vaginosis in pregnant women with symptoms suggestive of infection. J Clin Microbiol 40:30573059.

Tables

Generic image for table
Table 12.3.1–1

Comparison of FDA-approved HIV-1 RNA tests: preanalytical considerations

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
Generic image for table
Table 123.1–2

Comparison of FDA-approved HIV-1 RNA tests: analytical considerations

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
Generic image for table
Table 123.1–3

Comparison of CE-marked HIV-1 RNA tests: preanalytical considerations

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
Generic image for table
Table 123.1–4

Comparison of CE-marked HIV-1 RNA tests: analytical considerations

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
Generic image for table
Available tests

Available tests

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.3–1

Comparison of commercially available HBV genotyping tests

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.3–2

Summary of equipment and instruments required for HBV genotyping assays

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.3–3

Comparison of advantages and limitations of HBV genotyping methods

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.4–1

Summary of cervical cancer screening guidelines

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.4–2

Summary of characteristics of the 4 FDA-cleared HR HPV tests

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.5–1

Commercially available FDA-cleared or -approved assays

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Untitled

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.7–1

Selected CMV resistance assays using Sanger sequencing

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 123.8–1

Commercially available EBV PCR kits or reagents

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.9–1

Commercially available BK PCR kits or reagents

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.10–1

Commercially available multiplex gastrointestinal pathogen panel assays and platform/panel specifications

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.10–2

Stool submission conditions and common fixatives and preservatives used in clinical microbiology with intended use

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.11–1

Selected molecular tests for DENV detection

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.11–2

Primer sequences for the DENV multiplex assay

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.11–3

Molecular beacon sequences for the DENV multiplex assay

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.11–4

DENV multiplex RT-PCR master mix

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.11–5

Molecular beacon signals for each DENV serotype

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.12–1

Preanalytical considerations for FDA-cleared tests

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3
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Table 12.3.12–2

Analytic considerations for FDA-cleared tests

Citation: Leber A. 2016. Molecular Methods for Identification of Cultured Microorganisms, p 12.3.1.1-12.3.13.6. In Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch12.3

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