Chapter 48 : Molecular Diagnosis of Gastrointestinal Infections

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Enteric infections cause significant morbidity and mortality and have a significant financial cost worldwide. This chapter discusses the molecular techniques for the clinical identification of the bacteria, viruses, and parasites most commonly responsible for infections of the lower gastrointestinal tract. Numerous studies have reported on the development of PCR assays for the detection of enteric pathogens. Overall, multiplex, real-time PCR assay is favored because of its speed and elimination of postamplification carryover. The chapter summarizes the advancements achieved for the detection of enteric bacterial pathogens by molecular methods and discusses the remaining challenges. It also discusses the special case of hospital-acquired infection and the role of molecular methods in its diagnosis. Except for , which causes disease only in some patients, , , and are intrinsic enteric pathogens in humans. Importantly, the sequence of the viral capsid protein encoded by open reading frame 2 (ORF2) correlates directly with the serotype, making RT-PCR the most common technique for astrovirus detection and typing. The major pathogenic intestinal coccidia include , , , and , with spp. being the most common. The microsporidia are composed of more than 1,000 species of small, spore-forming, obligate intracellular organisms originally classified as protozoa but now considered fungi.

Citation: Pinsky B, Banaei N. 2011. Molecular Diagnosis of Gastrointestinal Infections, p 729-750. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch48

Key Concept Ranking

Infection and Immunity
Lower Gastrointestinal Tract
TaqMan PCR Assay
Molecular Techniques
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1. Abbott, S. L.,, L. S. Seli,, M. Catino, Jr.,, M. A. Hartley, and, J. M. Janda. 1998. Misidentification of unusual Aeromonas species as members of the genus Vibrio: a continuing problem. J. Clin. Microbiol. 36:11031104.
2. Abrahamsen, M. S.,, T. J. Templeton,, S. Enomoto,, J. E. Abrahante,, G. Zhu,, C. A. Lancto,, M. Deng,, C. Liu,, G. Widmer,, S. Tzipori,, G. A. Buck,, P. Xu,, A. T. Bankier,, P. H. Dear,, B. A. Konfortov,, H. F. Spriggs,, L. Iyer,, V. Anantharaman,, L. Aravind, and, V. Kapur. 2004. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304:441445.
3. Abubakar, I.,, S. H. Aliyu,, C. Arumugam,, N. K. Usman, and, P. R. Hunter. 2007. Treatment of cryptosporidiosis in immunocompromised individuals: systematic review and meta-analysis. Br. J. Clin. Pharmacol. 63:387393.
4. Allard, A.,, B. Albinsson, and, G. Wadell. 1992. Detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction. J. Med. Virol. 37:149157.
5. Allard, A.,, B. Albinsson, and, G. Wadell. 2001. Rapid typing of human adenoviruses by a general PCR combined with restriction endonuclease analysis. J. Clin. Microbiol. 39:498505.
6. Allard, A.,, R. Girones,, P. Juto, and, G. Wadell. 1990. Polymerase chain reaction for detection of adenoviruses in stool samples. J. Clin. Microbiol. 28:26592667.
7. Amar, C. F.,, P. H. Dear, and, J. McLauchlin. 2004. Detection and identification by real time PCR/RFLP analyses of Cryptosporidium species from human faeces. Lett. Appl. Microbiol. 38:217222.
8. Ando, T.,, S. S. Monroe,, J. R. Gentsch,, Q. Jin,, D. C. Lewis, and, R. I. Glass. 1995. Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-PCR and Southern hybridization. J. Clin. Microbiol. 33:6471.
9. Anonymous. 1997. WHO/PAHO/UNESCO report. A consultation with experts on amoebiasis, Mexico City, Mexico, 28–29 January, 1997. Epidemiol. Bull. 18:1314.
10. Arista, S.,, E. Vizzi,, C. Alaimo,, D. Palermo, and, A. Cascio. 1999. Identification of human rotavirus strains with the P[14] genotype by PCR. J. Clin. Microbiol. 37:27062708.
11. Avellon, A.,, P. Perez,, J. C. Aguilar,, R. Lejarazu, and, J. E. Echevarria. 2001. Rapid and sensitive diagnosis of human adenovirus infections by a generic polymerase chain reaction. J. Virol. Methods 92:113120.
12. Banerjee, I.,, S. Ramani,, B. Primrose,, M. Iturriza-Gomara,, J. J. Gray,, D. W. Brown, and, G. Kang. 2007. Modification of rotavirus multiplex RT-PCR for the detection of G12 strains based on characterization of emerging G12 rotavirus strains from south India. J. Med. Virol. 79:14131421.
13. Banik, U.,, A. K. Adhikary,, E. Suzuki,, T. Inada, and, N. Okabe. 2005. Multiplex PCR assay for rapid identification of oculopathogenic adenoviruses by amplification of the fiber and hexon genes. J. Clin. Microbiol. 43:10641068.
14. Barbut, F.,, C. Kajzer,, N. Planas, and, J. C. Petit. 1993. Comparison of three enzyme immunoassays, a cytotoxicity assay, and toxigenic culture for diagnosis of Clostridium difficile-associated diarrhea. J. Clin. Microbiol. 31:963967.
15. Bartlett, J. G. 2002. Clinical practice. Antibioticassociated diarrhea. N. Engl. J. Med. 346:334339.
16. Bauer, A.,, and L. M. Rorvik. 2007. A novel multiplex PCR for the identification of Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus. Lett. Appl. Microbiol. 45:371375.
17. Belanger, S. D.,, M. Boissinot,, N. Clairoux,, F. J. Picard, and, M. G. Bergeron. 2003. Rapid detection of Clostridium difficile in feces by real-time PCR. J. Clin. Microbiol. 41:730734.
18. Belanger, S. D.,, M. Boissinot,, C. Menard,, F. J. Picard, and, M. G. Bergeron. 2002. Rapid detection of Shiga toxin-producing bacteria in feces by multiplex PCR with molecular beacons on the Smart Cycler. J. Clin. Microbiol. 40:14361440.
19. Belliot, G.,, H. Laveran, and, S. S. Monroe. 1997. Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region. Arch. Virol. 142:13231334.
20. Besser, R. E.,, P. M. Griffin, and, L. Slutsker. 1999. Escherichia coli O157:H7 gastroenteritis and the hemolytic uremic syndrome: an emerging infectious disease. Annu. Rev. Med. 50:355367.
21. Best, E. L.,, E. J. Powell,, C. Swift,, K. A. Grant, and, J. A. Frost. 2003. Applicability of a rapid duplex realtime PCR assay for speciation of Campylobacter jejuni and Campylobacter coli directly from culture plates. FEMS Microbiol. Lett. 229:237241.
22. Bhattacharya, S.,, I. Som, and, A. Bhattacharya. 1998. The ribosomal DNA plasmids of Entamoeba. Parasitol. Today 14:181185.
23. Bielaszewska, M.,, R. Kock,, A. W. Friedrich,, C. von Eiff,, L. B. Zimmerhackl,, H. Karch, and, A. Mellmann. 2007. Shiga toxin-mediated hemolytic uremic syndrome: time to change the diagnostic paradigm? PLoS ONE 2:e1024.
24. Bines, J. 2006. Intussusception and rotavirus vaccines. Vaccine 24:37723776.
25. Bishop, R. F.,, G. P. Davidson,, I. H. Holmes, and, B. J. Ruck. 1973. Virus particles in epithelial cells of duodenal mucosa from children with acute non-bacterial gastroenteritis. Lancet 2:12811283.
26. Blessmann, J.,, H. Buss,, P. A. Nu,, B. T. Dinh,, Q. T. Ngo,, A. L. Van,, M. D. Alla,, T. F. Jackson,, J. I. Ravdin, and, E. Tannich. 2002. Real-time PCR for detection and differentiation of Entamoeba histolytica and Entamoeba dispar in fecal samples. J. Clin. Microbiol. 40:44134417.
27. Bleves, S.,, and G. R. Cornelis. 2000. How to survive in the host: the Yersinia lesson. Microbes Infect. 2:14511460.
28. Bon, F.,, H. Giraudon,, C. Sancey,, C. Barranger,, M. Joannes,, P. Pothier, and, E. Kohli. 2004. Development and evaluation of a new commercial test allowing the simultaneous detection of noroviruses and sapoviruses by reverse transcription-PCR and microplate hybridization. J. Clin. Microbiol. 42:22182220.
29. Brooks, J. T.,, E. G. Sowers,, J. G. Wells,, K. D. Greene,, P. M. Griffin,, R. M. Hoekstra, and, N. A. Strockbine. 2005. Non-O157 Shiga toxin-producing Escherichia coli infections in the United States, 1983–2002. J. Infect. Dis. 192:14221429.
30. Brown, E.,, G. H. Talbot,, P. Axelrod,, M. Provencher, and, C. Hoegg. 1990. Risk factors for Clostridium difficile toxin-associated diarrhea. Infect. Control Hosp. Epidemiol. 11:283290.
31. Brumpt, E. 1928. Differentiation of the human intestinal amoebae with four-nucleated cysts. Trans. R. Soc. Trop. Med. Hyg. 22:101124.
32. Buesa, J.,, J. Colomina,, J. Raga,, A. Villanueva, and, J. Prat. 1996. Evaluation of reverse transcription and polymerase chain reaction (RT/PCR) for the detection of rotaviruses: applications of the assay. Res. Virol. 147:353361.
33. Burton-MacLeod, J. A.,, E. M. Kane,, R. S. Beard,, L. A. Hadley,, R. I. Glass, and, T. Ando. 2004. Evaluation and comparison of two commercial enzyme-linked immunosorbent assay kits for detection of antigenically diverse human noroviruses in stool samples. J. Clin. Microbiol. 42:25872595.
34. Centers for Disease Control and Prevention. 2004. Salmonella Surveillance: Annual Summary, 2003. U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, GA.
35. Centers for Disease Control and Prevention. 2008. Delayed onset and diminished magnitude of rotavirus activity—United States, November 2007–May 2008. MMWR Morb. Mortal. Wkly. Rep. 57:697700.
36. Chan, M. C.,, J. J. Sung,, R. K. Lam,, P. K. Chan,, R. W. Lai, and, W. K. Leung. 2006. Sapovirus detection by quantitative real-time RT-PCR in clinical stool specimens. J. Virol. Methods 134:146153.
37. Claas, E. C.,, M. W. Schilham,, C. S. de Brouwer,, P. Hubacek,, M. Echavarria,, A. C. Lankester,, M. J. van Tol, and, A. C. Kroes. 2005. Internally controlled realtime PCR monitoring of adenovirus DNA load in serum or plasma of transplant recipients. J. Clin. Microbiol. 43:17381744.
38. Clark, C. G.,, U. C. Alsmark,, M. Tazreiter,, Y. Saito-Nakano,, V. Ali,, S. Marion,, C. Weber,, C. Mukherjee,, I. Bruchhaus,, E. Tannich,, M. Leippe,, T. Sicheritz-Ponten,, P. G. Foster,, J. Samuelson,, C. J. Noel,, R. P. Hirt,, T. M. Embley,, C. A. Gilchrist,, B. J. Mann,, U. Singh,, J. P. Ackers,, S. Bhattacharya,, A. Bhattacharya,, A. Lohia,, N. Guillen,, M. Duchene,, T. Nozaki, and, N. Hall. 2007. Structure and content of the Entamoeba histolytica genome. Adv. Parasitol. 65:51190.
39. Cubitt, W. D.,, D. K. Mitchell,, M. J. Carter,, M. M. Willcocks, and, H. Holzel. 1999. Application of electronmicroscopy, enzyme immunoassay, and RT-PCR to monitor an outbreak of astrovirus type 1 in a paediatric bone marrow transplant unit. J. Med. Virol. 57:313321.
40. Curry, A.,, and H. V. Smith. 1998. Emerging pathogens: Isospora, Cyclospora and microsporidia. Parasitology 117(Suppl.):S143S159.
41. de Bruin, E.,, E. Duizer,, H. Vennema, and, M. P. Koopmans. 2006. Diagnosis of norovirus outbreaks by commercial ELISA or RT-PCR. J. Virol. Methods 137:259264.
42. De Leon, R.,, S. M. Matsui,, R. S. Baric,, J. E. Herrmann,, N. R. Blacklow,, H. B. Greenberg, and, M. D. Sobsey. 1992. Detection of Norwalk virus in stool specimens by reverse transcriptase-polymerase chain reaction and nonradioactive oligoprobes. J. Clin. Microbiol. 30:31513157.
43. Delmee, M. 2001. Laboratory diagnosis of Clostridium difficile disease. Clin. Microbiol. Infect. 7:411416.
44. Dennehy, P. H.,, M. Hartin,, S. M. Nelson, and, S. F. Reising. 1999. Evaluation of the ImmunoCardSTAT! Rotavirus assay for detection of group A rotavirus in fecal specimens. J. Clin. Microbiol. 37:19771979.
45. Dennehy, P. H.,, T. E. Schutzbank, and, G. M. Thorne. 1994. Evaluation of an automated immunodiagnostic assay, VIDAS Rotavirus, for detection of rotavirus in fecal specimens. J. Clin. Microbiol. 32:825827.
46. Desselberger, U.,, and J. Gray. 2003. Viral Gastroenteritis. Elsevier, Amsterdam, The Netherlands.
47. Didier, E. S. 2005. Microsporidiosis: an emerging and opportunistic infection in humans and animals. Acta Trop. 94:6176.
48. Didier, E. S.,, J. A. Maddry,, P. J. Brindley,, M. E. Stovall, and, P. J. Didier. 2005. Therapeutic strategies for human microsporidia infections. Expert Rev. Anti-Infect. Ther. 3:419434.
49. Didier, E. S.,, and L. M. Weiss. 2006. Microsporidiosis: current status. Curr. Opin. Infect. Dis. 19:485492.
50. Dreier, J.,, M. Stormer,, D. Made,, S. Burkhardt, and, K. Kleesiek. 2006. Enhanced reverse transcription-PCR assay for detection of norovirus genogroup I. J. Clin. Microbiol. 44:27142720.
51. Ebner, K.,, M. Suda,, F. Watzinger, and, T. Lion. 2005. Molecular detection and quantitative analysis of the entire spectrum of human adenoviruses by a two-reaction real-time PCR assay. J. Clin. Microbiol. 43:30493053.
52. Elnifro, E. M.,, R. J. Cooper,, P. E. Klapper, and, A. S. Bailey. 2000. PCR and restriction endonuclease analysis for rapid identification of human adenovirus subgenera. J. Clin. Microbiol. 38:20552061.
53. Farkas, T.,, W. M. Zhong,, Y. Jing,, P. W. Huang,, S. M. Espinosa,, N. Martinez,, A. L. Morrow,, G. M. Ruiz-Palacios,, L. K. Pickering, and, X. Jiang. 2004. Genetic diversity among sapoviruses. Arch. Virol. 149:13091323.
54. Fotedar, R.,, D. Stark,, N. Beebe,, D. Marriott,, J. Ellis, and, J. Harkness. 2007. Laboratory diagnostic techniques for Entamoeba species. Clin. Microbiol. Rev. 20:511532.
55. Franzen, C.,, and A. Muller. 1999. Molecular techniques for detection, species differentiation, and phylogenetic analysis of microsporidia. Clin. Microbiol. Rev. 12:243285.
56. Friedman, C. R.,, R. M. Hoekstra,, M. Samuel,, R. Marcus,, J. Bender,, B. Shiferaw,, S. Reddy,, S. D. Ahuja,, D. L. Helfrick,, F. Hardnett,, M. Carter,, B. Anderson, and, R. V. Tauxe for the Emerging Infections Program FoodNet Working Group. 2004. Risk factors for sporadic Campylobacter infection in the United States: a case-control study in FoodNet sites. Clin. Infect. Dis. 38(Suppl. 3):S285S296.
57. Fukuda, S.,, S. Takao,, M. Kuwayama,, Y. Shimazu, and, K. Miyazaki. 2006. Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay. J. Clin. Microbiol. 44:13761381.
58. Fukushima, H.,, Y. Tsunomori, and, R. Seki. 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. J. Clin. Microbiol. 41:51345146.
59. Gannon, V. P.,, M. Rashed,, R. K. King, and, E. J. Thomas. 1993. Detection and characterization of the eae gene of Shiga-like toxin-producing Escherichia coli using polymerase chain reaction. J. Clin. Microbiol. 31:12681274.
60. Garcia, L. S. 2002. Laboratory identification of the microsporidia. J. Clin. Microbiol. 40:18921901.
61. Gaynes, R.,, D. Rimland,, E. Killum,, H. K. Lowery,, T. M. Johnson II,, G. Killgore, and, F. C. Tenover. 2004. Outbreak of Clostridium difficile infection in a long-term care facility: association with gatifloxacin use. Clin. Infect. Dis. 38:640645.
62. Gentsch, J. R.,, R. I. Glass,, P. Woods,, V. Gouvea,, M. Gorziglia,, J. Flores,, B. K. Das, and, M. K. Bhan. 1992. Identification of group A rotavirus gene 4 types by polymerase chain reaction. J. Clin. Microbiol. 30:13651373.
63. Geric, B.,, M. Rupnik,, D. N. Gerding,, M. Grabnar, and, S. Johnson. 2004. Distribution of Clostridium difficile variant toxinotypes and strains with binary toxin genes among clinical isolates in an American hospital. J. Med. Microbiol. 53:887894.
64. Ghosh, S.,, A. Debnath,, A. Sil,, S. De,, D. J. Chattopadhyay, and, P. Das. 2000. PCR detection of Giardia lamblia in stool: targeting intergenic spacer region of multicopy rRNA gene. Mol. Cell. Probes 14:181189.
65. Gilligan, P. H. 2008. Is a two-step glutamate dehyrogenase antigen-cytotoxicity neutralization assay algorithm superior to the Premier toxin A and B enzyme immunoassay for laboratory detection of Clostridium difficile? J. Clin. Microbiol. 46:15231525.
66. Gobet, P.,, J. C. Buisson,, O. Vagner,, M. Naciri,, M. Grappin,, S. Comparot,, G. Harly,, D. Aubert,, I. Varga,, P. Camerlynck, and, A. Bonnin. 1997. Detection of Cryptosporidium parvum DNA in formed human feces by a sensitive PCR-based assay including uracil-N-glycosylase inactivation. J. Clin. Microbiol. 35:254256.
67. Goodgame, R. 2007. Norovirus gastroenteritis. Curr. Infect. Dis. Rep. 9:102109.
68. Goossens, H.,, L. Vlaes,, M. De Boeck,, B. Pot,, K. Kersters,, J. Levy,, P. De Mol,, J. P. Butzler, and, P. Vandamme. 1990. Is “Campylobacter upsaliensis?” an unrecognised cause of human diarrhoea? Lancet 335:584586.
69. Gouvea, V.,, R. I. Glass,, P. Woods,, K. Taniguchi,, H. F. Clark,, B. Forrester, and, Z. Y. Fang. 1990. Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 28:276282.
70. Gray, J. J.,, E. Kohli,, F. M. Ruggeri,, H. Vennema,, A. Sanchez-Fauquier,, E. Schreier,, C. I. Gallimore,, M. Iturriza-Gomara,, H. Giraudon,, P. Pothier,, I. Di Bartolo,, N. Inglese,, E. de Bruin,, B. van der Veer,, S. Moreno,, V. Montero,, M. C. de Llano,, M. Hohne, and, S. M. Diedrich. 2007. European multicenter evaluation of commercial enzyme immunoassays for detecting norovirus antigen in fecal samples. Clin. Vaccine Immunol. 14:13491355.
71. Green, J.,, C. I. Gallimore,, J. P. Norcott,, D. Lewis, and, D. W. Brown. 1995. Broadly reactive reverse transcriptase polymerase chain reaction for the diagnosis of SRSV-associated gastroenteritis. J. Med. Virol. 47:392398.
72. Green, J.,, J. P. Norcott,, D. Lewis,, C. Arnold, and, D. W. Brown. 1993. Norwalk-like viruses: demonstration of genomic diversity by polymerase chain reaction. J. Clin. Microbiol. 31:30073012.
73. Greene, S. R.,, C. L. Moe,, L. A. Jaykus,, M. Cronin,, L. Grosso, and, P. Aarle. 2003. Evaluation of the NucliSens Basic Kit assay for detection of Norwalk virus RNA in stool specimens. J. Virol. Methods 108:123131.
74. Grimm, A. C.,, J. L. Cashdollar,, F. P. Williams, and, G. S. Fout. 2004. Development of an astrovirus RT-PCR detection assay for use with conventional, real-time, and integrated cell culture/RT-PCR. Can. J. Microbiol. 50:269278.
75. Gu, Z.,, S. W. Belzer,, C. S. Gibson,, M. J. Bankowski, and, R. T. Hayden. 2003. Multiplexed, real-time PCR for quantitative detection of human adenovirus. J. Clin. Microbiol. 41:46364641.
76. Guix, S.,, A. Bosch, and, R. M. Pinto. 2005. Human astrovirus diagnosis and typing: current and future prospects. Lett. Appl. Microbiol. 41:103105.
77. Guix, S.,, S. Caballero,, C. Villena,, R. Bartolome,, C. Latorre,, N. Rabella,, M. Simo,, A. Bosch, and, R. M. Pinto. 2002. Molecular epidemiology of astrovirus infection in Barcelona, Spain. J. Clin. Microbiol. 40:133139.
78. Gulke, I.,, G. Pfeifer,, J. Liese,, M. Fritz,, F. Hofmann,, K. Aktories, and, H. Barth. 2001. Characterization of the enzymatic component of the ADP-ribosyltransferase toxin CDTa from Clostridium difficile. Infect. Immun. 69:60046011.
79. Gunson, R. N.,, and W. F. Carman. 2005. Comparison of two real-time PCR methods for diagnosis of norovirus infection in outbreak and community settings. J. Clin. Microbiol. 43:20302031.
80. Gunson, R. N.,, T. C. Collins, and, W. F. Carman. 2006. The real-time detection of sapovirus. J. Clin. Virol. 35:321322.
81. Gunson, R. N.,, J. Miller,, A. Leonard, and, W. F. Carman. 2003. Importance of PCR in the diagnosis and understanding of rotavirus illness in the community. Commun. Dis. Public Health 6:6365.
82. Gutierrez-Aguirre, I.,, A. Steyer,, J. Boben,, K. Gruden,, M. Poljsak-Prijatelj, and, M. Ravnikar. 2008. Sensitive detection of multiple rotavirus genotypes with a single reverse transcription-real-time quantitative PCR assay. J. Clin. Microbiol. 46:25472554.
83. Hansman, G. S.,, R. Guntapong,, Y. Pongsuwanna,, K. Natori,, K. Katayama, and, N. Takeda. 2006. Development of an antigen ELISA to detect sapovirus in clinical stool specimens. Arch. Virol. 151:551561.
84. Hansman, G. S.,, T. Oka,, K. Katayama, and, N. Takeda. 2007. Human sapoviruses: genetic diversity, recombination, and classification. Rev. Med. Virol. 17:133141.
85. Haque, R.,, C. D. Huston,, M. Hughes,, E. Houpt, and, W. A. Petri, Jr. 2003. Amebiasis. N. Engl. J. Med. 348:15651573.
86. Haque, R.,, S. Roy,, A. Siddique,, U. Mondal,, S. M. Rahman,, D. Mondal,, E. Houpt, and, W. A. Petri, Jr. 2007. Multiplex real-time PCR assay for detection of Entamoeba histolytica, Giardia intestinalis, and Cryptosporidium spp. Am. J. Trop. Med. Hyg. 76:713717.
87. Higgins, J. A.,, R. Fayer,, J. M. Trout,, L. Xiao,, A. A. Lal,, S. Kerby, and, M. C. Jenkins. 2001. Real-time PCR for the detection of Cryptosporidium parvum. J. Microbiol. Methods 47:323337.
88. Hoehne, M.,, and E. Schreier. 2006. Detection of norovirus genogroup I and II by multiplex real-time RT-PCR using a 3′-minor groove binder-DNA probe. BMC Infect. Dis. 6:69.
89. Höhne, M.,, and E. Schreier. 2004. Detection and characterization of norovirus outbreaks in Germany: application of a one-tube RT-PCR using a fluorogenic real-time detection system. J. Med. Virol. 72:312319.
90. Honma, S.,, S. Nakata,, K. Kinoshita-Numata,, K. Kogawa, and, S. Chiba. 2000. Evaluation of nine sets of PCR primers in the RNA dependent RNA polymerase region for detection and differentiation of members of the family Caliciviridae, Norwalk virus and Sapporo virus. Microbiol. Immunol. 44:411419.
91. Honma, S.,, S. Nakata,, Y. Sakai,, M. Tatsumi,, K. Numata-Kinoshita, and, S. Chiba. 2001. Sensitive detection and differentiation of Sapporo virus, a member of the family Caliciviridae, by standard and booster nested polymerase chain reaction. J. Med. Virol. 65:413417.
92. Hoorfar, J.,, P. Ahrens, and, P. Radstrom. 2000. Automated 5′ nuclease PCR assay for identification of Salmonella enterica. J. Clin. Microbiol. 38:34293435.
93. Houde, A.,, D. Leblanc,, E. Poitras,, P. Ward,, J. Brassard,, C. Simard, and, Y. L. Trottier. 2006. Comparative evaluation of RT-PCR, nucleic acid sequence-based amplification (NASBA) and real-time RT-PCR for detection of noroviruses in faecal material. J. Virol. Methods 135:163172.
94. Hussain, M. A.,, P. Costello,, D. J. Morris,, A. S. Bailey,, G. Corbitt,, R. J. Cooper, and, A. B. Tullo. 1996. Comparison of primer sets for detection of fecal and ocular adenovirus infection using the polymerase chain reaction. J. Med. Virol. 49:187194.
95. Hymas, W.,, A. Atkinson,, J. Stevenson, and, D. Hillyard. 2007. Use of modified oligonucleotides to compensate for sequence polymorphisms in the real-time detection of norovirus. J. Virol. Methods 142:1014.
96. Iijima, Y.,, N. T. Asako,, M. Aihara, and, K. Hayashi. 2004. Improvement in the detection rate of diarrhoeagenic bacteria in human stool specimens by a rapid realtime PCR assay. J. Med. Microbiol. 53:617622.
97. Ishida, S.,, S. Yoshizumi,, T. Ikeda,, M. Miyoshi,, M. Okano, and, T. Okui. 2008. Sensitive and rapid detection of norovirus using duplex TaqMan reverse transcription-polymerase chain reaction. J. Med. Virol. 80:913920.
98. Ishiguro, T.,, J. Saitoh,, R. Horie,, T. Hayashi,, T. Ishizuka,, S. Tsuchiya,, K. Yasukawa,, T. Kido,, Y. Nakaguchi,, M. Nishibuchi, and, K. Ueda. 2003. Intercalation activating fluorescence DNA probe and its application to homogeneous quantification of a target sequence by isothermal sequence amplification in a closed vessel. Anal. Biochem. 314:7786.
99. Iturriza-Gomara, M.,, J. Green,, D. W. Brown,, U. Desselberger, and, J. J. Gray. 2000. Diversity within the VP4 gene of rotavirus P[8] strains: implications for reverse transcription-PCR genotyping. J. Clin. Microbiol. 38:898901.
100. Iturriza-Gomara, M.,, G. Kang, and, J. Gray. 2004. Rotavirus genotyping: keeping up with an evolving population of human rotaviruses. J. Clin. Virol. 31:259265.
101. Iturriza-Gomara, M.,, J. Xerry,, C. I. Gallimore,, C. Dockery, and, J. Gray. 2008. Evaluation of the Loopamp® (loop-mediated isothermal amplification) kit for detecting norovirus RNA in faecal samples. J. Clin. Virol. 42:389393.
102. Jensen, A. N.,, M. T. Andersen,, A. Dalsgaard,, D. L. Baggesen, and, E. M. Nielsen. 2005. Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples. J. Appl. Microbiol. 99:292300.
103. Jiang, X.,, P. W. Huang,, W. M. Zhong,, T. Farkas,, D. W. Cubitt, and, D. O. Matson. 1999. Design and evaluation of a primer pair that detects both Norwalk- and Sapporolike Caliciviruses by RT-PCR. J. Virol. Methods 83:145154.
104. Jiang, X.,, J. Wang,, D. Y. Graham, and, M. K. Estes. 1992. Detection of Norwalk virus in stool by polymerase chain reaction. J. Clin. Microbiol. 30:25292534.
105. Johnson, S.,, S. A. Kent,, K. J. O’Leary,, M. M. Merrigan,, S. P. Sambol,, L. R. Peterson, and, D. N. Gerding. 2001. Fatal pseudomembranous colitis associated with a variant Clostridium difficile strain not detected by toxin A immunoassay. Ann. Intern. Med. 135:434438.
106. Johnson, S.,, M. H. Samore,, K. A. Farrow,, G. E. Killgore,, F. C. Tenover,, D. Lyras,, J. I. Rood,, P. DeGirolami,, A. L. Baltch,, M. E. Rafferty,, S. M. Pear, and, D. N. Gerding. 1999. Epidemics of diarrhea caused by a clindamycin-resistant strain of Clostridium difficile in four hospitals. N. Engl. J. Med. 341:16451651.
107. Jonassen, T. O.,, C. Monceyron,, T. W. Lee,, J. B. Kurtz, and, B. Grinde. 1995. Detection of all serotypes of human astrovirus by the polymerase chain reaction. J. Virol. Methods 52:327334.
108. Jones, T. F. 2003. From pig to pacifier: chitterlingassociated yersiniosis outbreak among black infants. Emerg. Infect. Dis. 9:10071009.
109. Jothikumar, N.,, T. L. Cromeans,, V. R. Hill,, X. Lu,, M. D. Sobsey, and, D. D. Erdman. 2005. Quantitative real-time PCR assays for detection of human adenoviruses and identification of serotypes 40 and 41. Appl. Environ. Microbiol. 71:31313136.
110. Jothikumar, N.,, A. J. da Silva,, I. Moura,, Y. Qvarnstrom, and, V. R. Hill. 2008. Detection and differentiation of Cryptosporidium hominis and Cryptosporidium parvum by dual TaqMan assays. J. Med. Microbiol. 57:10991105.
111. Jothikumar, N.,, J. A. Lowther,, K. Henshilwood,, D. N. Lees,, V. R. Hill, and, J. Vinje. 2005. Rapid and sensitive detection of noroviruses by using TaqMan-based one-step reverse transcription-PCR assays and application to naturally contaminated shellfish samples. Appl. Environ. Microbiol. 71:18701875.
112. Kageyama, T.,, S. Kojima,, M. Shinohara,, K. Uchida,, S. Fukushi,, F. B. Hoshino,, N. Takeda, and, K. Katayama. 2003. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41:15481557.
113. Kang, G.,, M. Iturriza-Gomara,, J. G. Wheeler,, P. Crystal,, B. Monica,, S. Ramani,, B. Primrose,, P. D. Moses,, C. I. Gallimore,, D. W. Brown, and, J. Gray. 2004. Quantitation of group A rotavirus by real-time reverse-transcription–polymerase chain reaction: correlation with clinical severity in children in South India. J. Med. Virol. 73:118122.
114. Kapikian, A. Z.,, R. G. Wyatt,, R. Dolin,, T. S. Thornhill,, A. R. Kalica, and, R. M. Chanock. 1972. Visualization by immune electron microscopy of a 27-nm particle associated with acute infectious nonbacterial gastroenteritis. J. Virol. 10:10751081.
115. Katinka, M. D.,, S. Duprat,, E. Cornillot,, G. Metenier,, F. Thomarat,, G. Prensier,, V. Barbe,, E. Peyretaillade,, P. Brottier,, P. Wincker,, F. Delbac,, H. El Alaoui,, P. Peyret,, W. Saurin,, M. Gouy,, J. Weissenbach, and, C. P. Vivares. 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450453.
116. Kato, H.,, N. Kato,, K. Watanabe,, N. Iwai,, H. Nakamura,, T. Yamamoto,, K. Suzuki,, S. M. Kim,, Y. Chong, and, E. B. Wasito. 1998. Identification of toxin A-negative, toxin B-positive Clostridium difficile by PCR. J. Clin. Microbiol. 36:21782182.
117. Kelly, C. P.,, and J. T. LaMont. 1998. Clostridium difficile infection. Annu. Rev. Med. 49:375390.
118. Kelly, C. P.,, C. Pothoulakis, and, J. T. LaMont. 1994. Clostridium difficile colitis. N. Engl. J. Med. 330:257262.
119. Khan, A. M.,, A. S. Faruque,, M. S. Hossain,, S. Sattar,, G. J. Fuchs, and, M. A. Salam. 2004. Plesiomonas shigelloides-associated diarrhoea in Bangladeshi children: a hospital-based surveillance study. J. Trop. Pediatr. 50:354356.
120. Kidd, A. H.,, M. Jonsson,, D. Garwicz,, A. E. Kajon,, A. G. Wermenbol,, M. W. Verweij, and, J. C. De Jong. 1996. Rapid subgenus identification of human adenovirus isolates by a general PCR. J. Clin. Microbiol. 34:622627.
121. Knipe, D. M.,, P. M. Howley,, D. E. Griffin,, R. A. Lamb,, M. A. Martin,, B. Roizman, and, S. E. Straus (ed.). 2007. Fields Virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
122. Kojima, S.,, T. Kageyama,, S. Fukushi,, F. B. Hoshino,, M. Shinohara,, K. Uchida,, K. Natori,, N. Takeda, and, K. Katayama. 2002. Genogroup-specific PCR primers for detection of Norwalk-like viruses. J. Virol. Methods 100:107114.
123. Kou, X.,, Q. Wu,, J. Zhang, and, H. Fan. 2006. Rapid detection of noroviruses in fecal samples and shellfish by nucleic acid sequence-based amplification. J. Microbiol. 44:403408.
124. Kyne, L.,, M. B. Hamel,, R. Polavaram, and, C. P. Kelly. 2002. Health care costs and mortality associated with nosocomial diarrhea due to Clostridium difficile. Clin. Infect. Dis. 34:346353.
125. LaGier, M. J.,, L. A. Joseph,, T. V. Passaretti,, K. A. Musser, and, N. M. Cirino. 2004. A real-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli. Mol. Cell. Probes 18:275282.
126. Larson, H. E.,, F. E. Barclay,, P. Honour, and, I. D. Hill. 1982. Epidemiology of Clostridium difficile in infants. J. Infect. Dis. 146:727733.
127. Leclercq, A.,, L. Martin,, M. L. Vergnes,, N. Ounnoughene,, J. F. Laran,, P. Giraud, and, E. Carniel. 2005. Fatal Yersinia enterocolitica biotype 4 serovar O:3 sepsis after red blood cell transfusion. Transfusion 45:814818.
128. Lee, J. A.,, N. H. Kim,, S. J. Kim,, E. H. Choi, and, H. J. Lee. 2005. Rapid identification of human adenovirus types 3 and 7 from respiratory specimens via multiplex type-specific PCR. J. Clin. Microbiol. 43:55095514.
129. Le Guyader, F.,, M. K. Estes,, M. E. Hardy,, F. H. Neill,, J. Green,, D. W. Brown, and, R. L. Atmar. 1996. Evaluation of a degenerate primer for the PCR detection of human caliciviruses. Arch. Virol. 141:22252235.
130. Lenaerts, L.,, E. De Clercq, and, L. Naesens. 2008. Clinical features and treatment of adenovirus infections. Rev. Med. Virol. 18:357374.
131. Li, Q. G.,, A. Henningsson,, P. Juto,, F. Elgh, and, G. Wadell. 1999. Use of restriction fragment analysis and sequencing of a serotype-specific region to type adenovirus isolates. J. Clin. Microbiol. 37:844847.
132. Limor, J. R.,, A. A. Lal, and, L. Xiao. 2002. Detection and differentiation of Cryptosporidium parasites that are pathogenic for humans by real-time PCR. J. Clin. Microbiol. 40:23352338.
133. Linton, D.,, A. J. Lawson,, R. J. Owen, and, J. Stanley. 1997. PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples. J. Clin. Microbiol. 35:25682572.
134. Lipson, S. M.,, L. Svenssen,, L. Goodwin,, D. Porti,, S. Danzi, and, R. Pergolizzi. 2001. Evaluation of two current generation enzyme immunoassays and an improved isolation-based assay for the rapid detection and isolation of rotavirus from stool. J. Clin. Virol. 21:1727.
135. Loftus, B.,, I. Anderson,, R. Davies,, U. C. Alsmark,, J. Samuelson,, P. Amedeo,, P. Roncaglia,, M. Berriman,, R. P. Hirt,, B. J. Mann,, T. Nozaki,, B. Suh,, M. Pop,, M. Duchene,, J. Ackers,, E. Tannich,, M. Leippe,, M. Hofer,, I. Bruchhaus,, U. Willhoeft,, A. Bhattacharya,, T. Chillingworth,, C. Churcher,, Z. Hance,, B. Harris,, D. Harris,, K. Jagels,, S. Moule,, K. Mungall,, D. Ormond,, R. Squares,, S. Whitehead,, M. A. Quail,, E. Rabbinowitsch,, H. Norbertczak,, C. Price,, Z. Wang,, N. Guillen,, C. Gilchrist,, S. E. Stroup,, S. Bhattacharya,, A. Lohia,, P. G. Foster,, T. Sicheritz-Ponten,, C. Weber,, U. Singh,, C. Mukherjee,, N. M. El-Sayed,, W. A. Petri, Jr.,, C. G. Clark,, T. M. Embley,, B. Barrell,, C. M. Fraser, and, N. Hall. 2005. The genome of the protist parasite Entamoeba histolytica. Nature 433:865868.
136. Logan, C.,, J. J. O’Leary, and, N. O’Sullivan. 2006. Real-time reverse transcription-PCR for detection of rotavirus and adenovirus as causative agents of acute viral gastroenteritis in children. J. Clin. Microbiol. 44:31893195.
137. Logan, C.,, J. J. O’Leary, and, N. O’Sullivan. 2007. Real-time reverse transcription PCR detection of norovirus, sapovirus and astrovirus as causative agents of acute viral gastroenteritis. J. Virol. Methods 146:3644.
138. Logan, J. M.,, K. J. Edwards,, N. A. Saunders, and, J. Stanley. 2001. Rapid identification of Campylobacter spp. by melting peak analysis of biprobes in real-time PCR. J. Clin. Microbiol. 39:22272232.
139. Loisy, F.,, R. L. Atmar,, P. Guillon,, P. Le Cann,, M. Pommepuy, and, F. S. Le Guyader. 2005. Real-time RT-PCR for norovirus screening in shellfish. J. Virol. Methods 123:17.
140. Loo, V. G.,, L. Poirier,, M. A. Miller,, M. Oughton,, M. D. Libman,, S. Michaud,, A. M. Bourgault,, T. Nguyen,, C. Frenette,, M. Kelly,, A. Vibien,, P. Brassard,, S. Fenn,, K. Dewar,, T. J. Hudson,, R. Horn,, P. Rene,, Y. Monczak, and, A. Dascal. 2005. A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N. Engl. J. Med. 353:24422449.
141. Louie, M.,, S. Read,, A. E. Simor,, J. Holland,, L. Louie,, K. Ziebell,, J. Brunton, and, J. Hii. 1998. Application of multiplex PCR for detection of non-O157 verocytotoxin-producing Escherichia coli in bloody stools: identification of serogroups O26 and O111. J. Clin. Microbiol. 36:33753377.
142. Luber, P.,, J. Wagner,, H. Hahn, and, E. Bartelt. 2003. Antimicrobial resistance in Campylobacter jejuni and Campylobacter coli strains isolated in 1991 and 2001–2002 from poultry and humans in Berlin, Germany. Antimicrob. Agents Chemother. 47:38253830.
143. Ludert, J. E.,, A. C. Alcala, and, F. Liprandi. 2004. Primer pair p289-p290, designed to detect both noroviruses and sapoviruses by reverse transcription-PCR, also detects rotaviruses by cross-reactivity. J. Clin. Microbiol. 42:835836.
144. Lyerly, D. M.,, H. C. Krivan, and, T. D. Wilkins. 1988. Clostridium difficile: its disease and toxins. Clin. Microbiol. Rev. 1:118.
145. Mackenzie, A. M.,, P. Lebel,, E. Orrbine,, P. C. Rowe,, L. Hyde,, F. Chan,, W. Johnson,, P. N. McLaine, and The SYNSORB Pk Study Investigators. 1998. Sensitivities and specificities of Premier E. coli O157 and Premier EHEC enzyme immunoassays for diagnosis of infection with verotxin (Shiga-like toxin)-producing Escherichia coli. J. Clin. Microbiol. 36:16081611.
146. Madeley, C. R.,, and B. P. Cosgrove. 1975. Letter: 28 nm particles in faeces in infantile gastroenteritis. Lancet ii:451452.
147. Madeley, C. R.,, and B. P. Cosgrove. 1975. Letter: viruses in infantile gastroenteritis. Lancet ii:124.
148. Malorny, B.,, E. Paccassoni,, P. Fach,, C. Bunge,, A. Martin, and, R. Helmuth. 2004. Diagnostic real-time PCR for detection of Salmonella in food. Appl. Environ. Microbiol. 70:70467052.
149. Matsui, M.,, H. Ushijima,, M. Hachiya,, J. Kakizawa,, L. Wen,, M. Oseto,, K. Morooka, and, J. B. Kurtz. 1998. Determination of serotypes of astroviruses by reverse transcription-polymerase chain reaction and homologies of the types by the sequencing of Japanese isolates. Microbiol. Immunol. 42:539547.
150. McDonald, L. C.,, G. E. Killgore,, A. Thompson,, R. C. Owens, Jr.,, S. V. Kazakova,, S. P. Sambol,, S. Johnson, and, D. N. Gerding. 2005. An epidemic, toxin genevariant strain of Clostridium difficile. N. Engl. J. Med. 353:24332441.
151. McFarland, L. V.,, M. E. Mulligan,, R. Y. Kwok, and, W. E. Stamm. 1989. Nosocomial acquisition of Clostridium difficile infection. N. Engl. J. Med. 320:204210.
152. McIver, C. J.,, E. A. Palombo,, J. C. Doultree,, H. Mustafa,, J. A. Marshall, and, W. D. Rawlinson. 2000. Detection of astrovirus gastroenteritis in children. J. Virol. Methods 84:99105.
153. Mead, P. S.,, L. Slutsker,, P. M. Griffin, and, R. V. Tauxe. 1999. Food-related illness and death in the United States—reply to Dr. Hedberg. Emerg. Infect. Dis. 5:841842.
154. Medici, M. C.,, M. Martinelli,, F. M. Ruggeri,, L. A. Abelli,, S. Bosco,, M. C. Arcangeletti,, F. Pinardi,, F. De Conto,, A. Calderaro,, C. Chezzi, and, G. Dettori. 2005. Broadly reactive nested reverse transcription-PCR using an internal RNA standard control for detection of noroviruses in stool samples. J. Clin. Microbiol. 43:37723778.
155. Melliez, H.,, P. Y. Boelle,, S. Baron,, Y. Mouton, and, Y. Yazdanpanah. 2007. Effectiveness of childhood vaccination against rotavirus in sub-Saharan Africa: the case of Nigeria. Vaccine 25:298305.
156. Menotti, J.,, B. Cassinat,, R. Porcher,, C. Sarfati,, F. Derouin, and, J. M. Molina. 2003. Development of a realtime polymerase-chain-reaction assay for quantitative detection of Enterocytozoon bieneusi DNA in stool specimens from immunocompromised patients with intestinal microsporidiosis. J. Infect. Dis. 187:14691474.
157. Menotti, J.,, B. Cassinat,, C. Sarfati,, O. Liguory,, F. Derouin, and, J. M. Molina. 2003. Development of a realtime PCR assay for quantitative detection of Encephalitozoon intestinalis DNA. J. Clin. Microbiol. 41:14101413.
158. Miller, I.,, R. Gunson, and, W. F. Carman. 2002. Norwalk-like virus by Light Cycler PCR. J. Clin. Virol. 25:231232.
159. Min, B. S.,, Y. J. Noh,, J. H. Shin,, S. Y. Baek,, K. I. Min,, S. R. Ryu,, B. G. Kim,, M. K. Park,, S. E. Choi,, E. H. Yang,, S. N. Park,, S. J. Hur, and, B. Y. Ahn. 2006. Assessment of the quantitative real-time polymerase chain reaction using a cDNA standard for human group A rotavirus. J. Virol. Methods 137:280286.
160. Mitchell, D. K.,, S. S. Monroe,, X. Jiang,, D. O. Matson,, R. I. Glass, and, L. K. Pickering. 1995. Virologic features of an astrovirus diarrhea outbreak in a day care center revealed by reverse transcriptase-polymerase chain reaction. J. Infect. Dis. 172:14371444.
161. Moe, C. L.,, J. Gentsch,, T. Ando,, G. Grohmann,, S. S. Monroe,, X. Jiang,, J. Wang,, M. K. Estes,, Y. Seto, and, C. Humphrey. 1994. Application of PCR to detect Norwalk virus in fecal specimens from outbreaks of gastroenteritis. J. Clin. Microbiol. 32:642648.
162. Mohamed, N.,, S. Belak,, K. O. Hedlund, and, J. Blomberg. 2006. Experience from the development of a diagnostic single tube real-time PCR for human caliciviruses, norovirus genogroups I and II. J. Virol. Methods 132:6976.
163. Molina, J. M.,, M. Tourneur,, C. Sarfati,, S. Chevret,, A. de Gouvello,, J. G. Gobert,, S. Balkan,, F. Derouin, and Agence Nationale de Recherches sur le SIDA 090 Study Group. 2002. Fumagillin treatment of intestinal microsporidiosis. N. Engl. J. Med. 346:19631969.
164. Moore, C.,, E. M. Clark,, C. I. Gallimore,, S. A. Corden,, J. J. Gray, and, D. Westmoreland. 2004. Evaluation of a broadly reactive nucleic acid sequence based amplification assay for the detection of noroviruses in faecal material. J. Clin. Virol. 29:290296.
165. Morgan, U. M.,, C. C. Constantine,, D. A. Forbes, and, R. C. Thompson. 1997. Differentiation between human and animal isolates of Cryptosporidium parvum using rDNA sequencing and direct PCR analysis. J. Parasitol. 83:825830.
166. Morgan, U. M.,, L. Pallant,, B. W. Dwyer,, D. A. Forbes,, G. Rich, and, R. C. Thompson. 1998. Comparison of PCR and microscopy for detection of Cryptosporidium parvum in human fecal specimens: clinical trial. J. Clin. Microbiol. 36:995998.
167. Morris, C. A.,, T. H. Flewett,, A. S. Bryden, and, H. Davies. 1975. Epidemic viral enteritis in a long-stay children’s ward. Lancet i:45.
168. Morrison, H. G.,, A. G. McArthur,, F. D. Gillin,, S. B. Aley,, R. D. Adam,, G. J. Olsen,, A. A. Best,, W. Z. Cande,, F. Chen,, M. J. Cipriano,, B. J. Davids,, S. C. Dawson,, H. G. Elmendorf,, A. B. Hehl,, M. E. Holder,, S. M. Huse,, U. U. Kim,, E. Lasek-Nesselquist,, G. Manning,, A. Nigam,, J. E. Nixon,, D. Palm,, N. E. Passamaneck,, A. Prabhu,, C. I. Reich,, D. S. Reiner,, J. Samuelson,, S. G. Svard, and, M. L. Sogin. 2007. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317:19211926.
169. Muller, A.,, R. Bialek,, G. Fatkenheuer,, B. Salzberger,, V. Diehl, and, C. Franzen. 2000. Detection of Isospora belli by polymerase chain reaction using primers based on small-subunit ribosomal RNA sequences. Eur. J. Clin. Microbiol. Infect. Dis. 19:631634.
170. Murray, P. R.,, E. J. Baron,, J. H. Jorgensen,, M. L. Landry, and, M. A. Pfaller (ed.). 2007. Manual of Clinical Microbiology, 9th ed. ASM Press, Washington, DC.
171. Nachamkin, I.,, B. M. Allos, and, T. Ho. 1998. Campylobacter species and Guillain-Barré syndrome. Clin. Microbiol. Rev. 11:555567.
172. Nakata, S.,, K. Kogawa,, K. Numata,, S. Ukae,, N. Adachi,, D. O. Matson,, M. K. Estes, and, S. Chiba. 1996. The epidemiology of human Calicivirus/Sapporo/82/Japan. Arch. Virol. Suppl. 12:263270.
173. Ng, C. T.,, C. A. Gilchrist,, A. Lane,, S. Roy,, R. Haque, and, E. R. Houpt. 2005. Multiplex real-time PCR assay using Scorpion probes and DNA capture for genotype-specific detection of Giardia lamblia on fecal samples. J. Clin. Microbiol. 43:12561260.
174. Nhung, P. H.,, K. Ohkusu,, J. Miyasaka,, X. S. Sun, and, T. Ezaki. 2007. Rapid and specific identification of 5 human pathogenic Vibrio species by multiplex polymerase chain reaction targeted to dnaJ gene. Diagn. Microbiol. Infect. Dis. 59:271275.
175. Noel, J. S.,, R. L. Fankhauser,, T. Ando,, S. S. Monroe, and, R. I. Glass. 1999. Identification of a distinct common strain of “Norwalk-like viruses” having a global distribution. J. Infect. Dis. 179:13341344.
176. Noel, J. S.,, T. W. Lee,, J. B. Kurtz,, R. I. Glass, and, S. S. Monroe. 1995. Typing of human astroviruses from clinical isolates by enzyme immunoassay and nucleotide sequencing. J. Clin. Microbiol. 33:797801.
177. Nordgren, J.,, F. Bucardo,, O. Dienus,, L. Svensson, and, P. E. Lindgren. 2008. Novel light-upon-extension realtime PCR assays for detection and quantification of genogroup I and II noroviruses in clinical specimens. J. Clin. Microbiol. 46:164170.
178. Oka, T.,, K. Katayama,, G. S. Hansman,, T. Kageyama,, S. Ogawa,, F. T. Wu,, P. A. White, and, N. Takeda. 2006. Detection of human sapovirus by real-time reverse transcription-polymerase chain reaction. J. Med. Virol. 78:13471353.
179. Okada, M.,, T. Ogawa,, H. Kubonoya,, H. Yoshizumi, and, K. Shinozaki. 2007. Detection and sequence-based typing of human adenoviruses using sensitive universal primer sets for the hexon gene. Arch. Virol. 152:19.
180. Okada, M.,, K. Shinozaki,, T. Ogawa, and, I. Kaiho. 2002. Molecular epidemiology and phylogenetic analysis of Sapporo-like viruses. Arch. Virol. 147:14451451.
181. O’Neill, H. J.,, C. McCaughey,, P. V. Coyle,, D. E. Wyatt, and, F. Mitchell. 2002. Clinical utility of nested multiplex RT-PCR for group F adenovirus, rotavirus and Norwalk-like viruses in acute viral gastroenteritis in children and adults. J. Clin. Virol. 25:335343.
182. O’Neill, H. J.,, C. McCaughey,, D. E. Wyatt,, F. Mitchell, and, P. V. Coyle. 2001. Gastroenteritis outbreaks associated with Norwalk-like viruses and their investigation by nested RT-PCR. BMC Microbiol. 1:14.
183. Ortega, Y. R.,, and R. D. Adam. 1997. Giardia: overview and update. Clin. Infect. Dis. 25:545549.
184. Pang, X.,, B. Lee,, L. Chui,, J. K. Preiksaitis, and, S. S. Monroe. 2004. Evaluation and validation of real-time reverse transcription-PCR assay using the LightCycler system for detection and quantitation of norovirus. J. Clin. Microbiol. 42:46794685.
185. Pang, X. L.,, J. Joensuu,, Y. Hoshino,, A. Z. Kapikian, and, T. Vesikari. 1999. Rotaviruses detected by reverse transcription polymerase chain reaction in acute gastroenteritis during a trial of rhesus-human reassortant rotavirus tetravalent vaccine: implications for vaccine efficacy analysis. J. Clin. Virol. 13:916.
186. Pang, X. L.,, B. Lee,, N. Boroumand,, B. Leblanc,, J. K. Preiksaitis, and, C. C. Yu Ip. 2004. Increased detection of rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea. J. Med. Virol. 72:496501.
187. Parashar, U. D.,, J. P. Alexander, and, R. I. Glass. 2006. Prevention of rotavirus gastroenteritis among infants and children. Recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recommend. Rep. 55:113.
188. Parashar, U. D.,, E. G. Hummelman,, J. S. Bresee,, M. A. Miller, and, R. I. Glass. 2003. Global illness and deaths caused by rotavirus disease in children. Emerg. Infect. Dis. 9:565572.
189. Parr, J. B.,, J. E. Sevilleja,, A. Samie,, C. Alcantara,, S. E. Stroup,, A. Kohli,, R. Fayer,, A. A. Lima,, E. R. Houpt, and, R. L. Guerrant. 2007. Detection and quantification of Cryptosporidium in HCT-8 cells and human fecal specimens using real-time polymerase chain reaction. Am. J. Trop. Med. Hyg. 76:938942.
190. Patel, M. M.,, M. A. Widdowson,, R. I. Glass,, K. Akazawa,, J. Vinje, and, U. D. Parashar. 2008. Systematic literature review of role of noroviruses in sporadic gastroenteritis. Emerg. Infect. Dis. 14:12241231.
191. Patterson, S. S.,, M. W. Smith,, E. T. Casper,, D. Huffman,, L. Stark,, D. Fries, and, J. H. Paul. 2006. A nucleic acid sequence-based amplification assay for real-time detection of norovirus genogroup II. J. Appl. Microbiol. 101:956963.
192. Peek, R.,, F. R. Reedeker, and, T. van Gool. 2004. Direct amplification and genotyping of Dientamoeba fragilis from human stool specimens. J. Clin. Microbiol. 42:631635.
193. Pehler-Harrington, K.,, M. Khanna,, C. R. Waters, and, K. J. Henrickson. 2004. Rapid detection and identification of human adenovirus species by Adenoplex, a multiplex PCR-enzyme hybridization assay. J. Clin. Microbiol. 42:40724076.
194. Peterson, L. R.,, and P. J. Kelly. 1993. The role of the clinical microbiology laboratory in the management of Clostridium difficile-associated diarrhea. Infect. Dis. Clin. N. Am. 7:277293.
195. Peterson, L. R.,, R. U. Manson,, S. M. Paule,, D. M. Hacek,, A. Robicsek,, R. B. Thomson, Jr., and, K. L. Kaul. 2007. Detection of toxigenic Clostridium difficile in stool samples by real-time polymerase chain reaction for the diagnosis of C. difficile-associated diarrhea. Clin. Infect. Dis. 45:11521160.
196. Prager, R.,, S. Annemuller, and, H. Tschape. 2005. Diversity of virulence patterns among Shiga toxinproducing Escherichia coli from human clinical cases—need for more detailed diagnostics. Int. J. Med. Microbiol. 295:2938.
197. Qvarnstrom, Y.,, C. James,, M. Xayavong,, B. P. Holloway,, G. S. Visvesvara,, R. Sriram, and, A. J. da Silva. 2005. Comparison of real-time PCR protocols for differential laboratory diagnosis of amebiasis. J. Clin. Microbiol. 43:54915497.
198. Rautelin, H.,, J. Jusufovic, and, M. L. Hanninen. 1999. Identification of hippurate-negative thermophilic campylobacters. Diagn. Microbiol. Infect. Dis. 35:912.
199. Reischl, U.,, M. T. Youssef,, J. Kilwinski,, N. Lehn,, W. L. Zhang,, H. Karch, and, N. A. Strockbine. 2002. Real-time fluorescence PCR assays for detection and characterization of Shiga toxin, intimin, and enterohemolysin genes from Shiga toxin-producing Escherichia coli. J. Clin. Microbiol. 40:25552565.
200. Richards, G. P.,, M. A. Watson,, R. L. Fankhauser, and, S. S. Monroe. 2004. Genogroup I and II noroviruses detected in stool samples by real-time reverse transcription-PCR using highly degenerate universal primers. Appl. Environ. Microbiol. 70:71797184.
201. Richards, G. P.,, M. A. Watson, and, D. H. Kingsley. 2004. A SYBR green, real-time RT-PCR method to detect and quantitate Norwalk virus in stools. J. Virol. Methods 116:6370.
202. Rolfe, K. J.,, S. Parmar,, D. Mururi,, T. G. Wreghitt,, H. Jalal,, H. Zhang, and, M. D. Curran. 2007. An internally controlled, one-step, real-time RT-PCR assay for norovirus detection and genogrouping. J. Clin. Virol. 39:318321.
203. Rohayem, J.,, S. Berger,, T. Juretzek,, O. Herchenröder,, M. Mogel,, M. Poppe,, J. Henker, and, A. Rethwilm. 2004. A simple and rapid single-step multiplex RT-PCR to detect norovirus, astrovirus and adenovirus in clinical stool samples. Virol. Methods 118:4959.
204. Rousell, J.,, M. E. Zajdel,, P. D. Howdle, and, G. E. Blair. 1993. Rapid detection of enteric adenoviruses by means of the polymerase chain reaction. J. Infect. 27:271275.
205. Roy, S.,, M. Kabir,, D. Mondal,, I. K. Ali,, W. A. Petri, Jr., and, R. Haque. 2005. Real-time-PCR assay for diagnosis of Entamoeba histolytica infection. J. Clin. Microbiol. 43:21682172.
206. Royuela, E.,, A. Negredo, and, A. Sanchez-Fauquier. 2006. Development of a one-step, real-time RT-PCR method for sensitive detection of human astrovirus. J. Virol. Methods 133:1419.
207. Ruiz-Palacios, G. M.,, I. Perez-Schael,, F. R. Velazquez,, H. Abate,, T. Breuer,, S. C. Clemens,, B. Cheuvart,, F. Espinoza,, P. Gillard,, B. L. Innis,, Y. Cervantes,, A. C. Linhares,, P. Lopez,, M. Macias-Parra,, E. Ortega-Barria,, V. Richardson,, D. M. Rivera-Medina,, L. Rivera,, B. Salinas,, N. Pavia-Ruz,, J. Salmeron,, R. Ruttimann,, J. C. Tinoco,, P. Rubio,, E. Nunez,, M. L. Guerrero,, J. P. Yarzabal,, S. Damaso,, N. Tornieporth,, X. Saez-Llorens,, R. F. Vergara,, T. Vesikari,, A. Bouckenooghe,, R. Clemens,, B. De Vos, and, M. O’Ryan for the Human Rotavirus Vaccine Study Group. 2006. Safety and efficacy of an attenuated vaccine against severe rotavirus gastroenteritis. N. Engl. J. Med. 354:1122.
208. Saito, H.,, S. Saito,, K. Kamada,, S. Harata,, H. Sato,, M. Morita, and, Y. Miyajima. 1998. Application of RT-PCR designed from the sequence of the local SRSV strain to the screening in viral gastroenteritis outbreaks. Microbiol. Immunol. 42:439446.
209. Saito, K.,, H. Ushijima,, O. Nishio,, M. Oseto,, H. Motohiro,, Y. Ueda,, M. Takagi,, S. Nakaya,, T. Ando, and, R. Glass. 1995. Detection of astroviruses from stool samples in Japan using reverse transcription and polymerase chain reaction amplification. Microbiol. Immunol. 39:825828.
210. Sakamoto, T.,, H. Negishi,, Q. H. Wang,, S. Akihara,, B. Kim,, S. Nishimura,, K. Kaneshi,, S. Nakaya,, Y. Ueda,, K. Sugita,, T. Motohiro,, T. Nishimura, and, H. Ushijima. 2000. Molecular epidemiology of astroviruses in Japan from 1995 to 1998 by reverse transcription-polymerase chain reaction with serotype-specific primers (1 to 8). J. Med. Virol. 61:326331.
211. Samuel, M. C.,, D. J. Vugia,, S. Shallow,, R. Marcus,, S. Segler,, T. McGivern,, H. Kassenborg,, K. Reilly,, M. Kennedy,, F. Angulo, and, R. V. Tauxe for the Emerging Infections Program FoodNet Working Group. 2004. Epidemiology of sporadic Camp