Detection of diarrhoeal pathogens in human faeces using an automated, robotic platform

Molecular and Cellular Probes

Volumn 26, Issue 1, 2012, Pages 11-15

  Jex, Aaron R ^a   Stanley, Keith K ^b   Lo, William ^b   Littman, Rachael ^a   Verweij, Jaco J ^c   Campbell, Bronwyn E ^a   Nolan, Matthew J ^a   Pangasa, Aradhana ^a   Stevens, Melita A ^d   Haydon, Shane ^d   Gasser, Robin B ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b AusDiagnostics Pty Ltd   (Australia)

^c LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^d MELBOURNE WATER CORPORATION   (Australia)

Author keywords

Diarrhoeal disease; Pathogens; PCR

Indexed keywords

GENOMIC DNA;

ADENOVIRUS; ARTICLE; BACTERIUM DETECTION; CAMPYLOBACTER; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; CRYPTOSPORIDIOSIS; CRYPTOSPORIDIUM; DNA SEQUENCE; FECES ANALYSIS; GIARDIA; HUMAN; INFECTIOUS DIARRHEA; MICROORGANISM DETECTION; MULTIPLEX POLYMERASE CHAIN REACTION; MULTIPLEXED TANDEM POLYMERASE CHAIN REACTION; NONHUMAN; NOROVIRUS; PARASITE IDENTIFICATION; PRIORITY JOURNAL; SALMONELLA; SENSITIVITY ANALYSIS; SHIGELLA; SINGLE STRAND CONFORMATION POLYMORPHISM; VIRUS DETECTION;

ADENOVIRIDAE; CLOSTRIDIUM DIFFICILE; CRYPTOSPORIDIUM; DIARRHEA; FECES; GIARDIA; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; ROBOTICS; SENSITIVITY AND SPECIFICITY; SHIGELLA;

ADENOVIRIDAE; CAMPYLOBACTER; CLOSTRIDIUM DIFFICILE; CRYPTOSPORIDIUM; GIARDIA; NOROVIRUS; PROTISTA; SALMONELLA; SHIGELLA;

EID: 84855963244     PISSN: 08908508     EISSN: 10961194     Source Type: Journal    
DOI: 10.1016/j.mcp.2011.10.004     Document Type: Article

References (51)

1. Anon World health report 2004: changing history 2004, World Health Organization, Geneva.
2. Ashbolt N.J. Microbial contamination of drinking water and disease outcomes in developing regions. Toxicology 2004, 198:229-238.
3. Savioli L., Smith H., Thompson A. Giardia and Cryptosporidium join the 'Neglected Diseases Initiative'. Trends Parasitol 2006, 22:203-208.
4. Jex A.R., Smith H.V., Monis P.T., Campbell B.E., Gasser R.B. Cryptosporidium - biotechnological advances in the detection, diagnosis and analysis of genetic variation. Biotechnol Adv 2008, 26:304-317.
5. Fall A., Thompson R.C., Hobbs R.P., Morgan-Ryan U. Morphology is not a reliable tool for delineating species within Cryptosporidium. JParasitol 2003, 89:399-402.
6. Glass R.I., Parashar U.D., Estes M.K. Norovirus gastroenteritis. NEngl J Med 2009, 361:1776-1785.
7. Okhuysen P.C., Chappell C.L., Crabb J.H., Sterling C.R., DuPont H.L. Virulence of three distinct Cryptosporidium parvum isolates for healthy adults. JInfect Dis 1999, 180:1275-1281.
8. On S.L. Identification methods for campylobacters, helicobacters, and related organisms. Clin Microbiol Rev 1996, 9:405-422.
9. Quílez J., Sánchez-Acedo C., Clavel A., del Cacho E., López-Bernad F. Comparison of an acid-fast stain and a monoclonal antibody-based immunofluorescence reagent for the detection of Cryptosporidium oocysts in faecal specimens from cattle and pigs. Vet Parasitol 1996, 67:75-81.
10. Gasser R. Molecular tools - advances, opportunities and prospects. Vet Parasitol 2006, 136:69-89.
11. Stamper P.D., Babiker W., Alcabasa R., Aird D., Wehrlin J., Ikpeama I., et al. Evaluation of a new commercial TaqMan PCR assay for direct detection of the Clostridium difficile toxin B gene in clinical stool specimens. JClin Microbiol 2009, 47:3846-3850.
12. Pangasa A., Jex A.R., Campbell B.E., Bott N.J., Whipp M., Hogg G., et al. High resolution melting-curve (HRM) analysis for the diagnosis of cryptosporidiosis in humans. Mol Cell Probes 2009, 20:10-15.
13. Jex A.R., Ryan U.M., Ng J., Campbell B.E., Xiao L., Stevens M., et al. Specific and genotypic identification of Cryptosporidium from a broad range of host species by nonisotopic SSCP analysis of nuclear ribosomal DNA. Electrophoresis 2007, 28:2818-2825.
14. Elnifro E.M., Ashshi A.M., Cooper R.J., Klapper P.E. Multiplex PCR: optimization and application in diagnostic virology. Clin Microbiol Rev 2000, 13:559-570.
15. Verweij J.J., Blange R.A., Templeton K., Schinkel J., Brienen E.A., van Rooyen M.A., et al. Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR. JClin Microbiol 2004, 42:1220-1223.
16. Yan H., Yagyu F., Okitsu S., Nishio O., Ushijima H. Detection of norovirus (GI, GII), Sapovirus and astrovirus in fecal samples using reverse transcription single-round multiplex PCR. JVirol Methods 2003, 114:37-44.
17. Stals A., Baert L., Botteldoorn N., Werbrouck H., Herman L., Uyttendaele M., et al. Multiplex real-time RT-PCR for simultaneous detection of GI/GII noroviruses and murine norovirus 1. JVirol Methods 2009, 161:247-253.
18. LaGier M.J., Joseph L.A., Passaretti T.V., Musser K.A., Cirino N.M. Areal-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli. Mol Cell Probes 2004, 18:275-282.
19. Amar C.F., Dear P.H., McLauchlin J. Detection and genotyping by real-time PCR/RFLP analyses of Giardia duodenalis from human faeces. JMed Microbiol 2003, 52:681-683.
20. Tajiri-Utagawa E., Hara M., Takahashi K., Watanabe M., Wakita T. Development of a rapid high-throughput method for high-resolution melting analysis for routine detection and genotyping of noroviruses. JClin Microbiol 2009, 47:435-440.
21. Stanley K.K., Szewczuk E. Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection. Nucleic Acids Res 2005, 33:e180.
22. Lau A., Sorrell T.C., Lee O., Stanley K., Halliday C. Colony multiplex-tandem PCR for rapid, accurate identification of fungal cultures. JClin Microbiol 2008, 46:4058-4060.
23. Lau A., Sorrell T.C., Chen S., Stanley K., Iredell J., Halliday C. Multiplex tandem PCR: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens. JClin Microbiol 2008, 46:3021-3027.
24. Gasser R.B., Abs EL-Osta Y.G., Chalmers R.M. Electrophoretic analysis of genetic variability within Cryptosporidium parvum from imported and autochthonous cases of human cryptosporidiosis in the United Kingdom. Appl Environ Microbiol 2003, 69:2719-2730.
25. Jex A.R., Gasser R.B. Analysis of the genetic diversity within Cryptosporidium hominis and Cryptosporidium parvum from imported and autochtonous cases of human cryptosporidiosis by mutation scanning. Electrophoresis 2008, 29:4119-4129.
26. Toogood C.I., Hay R.T. DNA sequence of the adenovirus type 41 hexon geneandpredicted structure of the protein. JGen Virol 1988, 69(Pt 9):2291-2301.
27. Pearson B.M., Gaskin D.J., Segers R.P., Wells J.M., Nuijten P.J., van Vliet A.H. The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). JBacteriol 2007, 189:8402-8403.
28. Barroso L.A., Wang S.Z., Phelps C.J., Johnson J.L., Wilkins T.D. Nucleotide sequence of Clostridium difficile toxin B gene. Nucleic Acids Res 1990, 18:4004.
29. Xiao L., Escalante L., Yang C., Sulaiman I., Escalante A.A., Montali R.J., et al. Phylogenetic analysis of Cryptosporidium parasites based on the small-subunit rRNA gene locus. Appl Environ Microbiol 1999, 65:1578-1583.
30. Sogin M.L., Gunderson J.H., Elwood H.J., Alonso R.A., Peattie D.A. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 1989, 243:75-77.
31. Ando T., Monroe S.S., Noel J.S., Glass R.I. Aone-tube method of reverse transcription-PCR to efficiently amplify a 3-kilobase region from the RNA polymerase gene to the poly(A) tail of small round-structured viruses (Norwalk-like viruses). JClin Microbiol 1997, 35:570-577.
32. Bajaj V., Hwang C., Lee C.A. hilA is a novel ompR/toxR family member that activates the expression of Salmonella typhimurium invasion genes. Mol Microbiol 1995, 18:715-727.
33. Venkatesan M.M., Buysse J.M., Hartman A.B. Sequence variation in two ipaH genes of Shigella flexneri 5 and homology to the LRG-like family of proteins. Mol Microbiol 1991, 5:2435-2445.
34. Stark D., Al-Qassab S.E., Barratt J.L., Stanley K., Roberts T., Marriott D., et al. Evaluation of multiplex tandem real-time PCR for detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in clinical stool samples. JClin Microbiol 2011, 49:257-262.
35. Gasser R.B., Hu M., Chilton N.B., Campbell B.E., Jex A.R., Otranto D., et al. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. Nat Protoc 2006, 1:3121-3128.
36. Ronaghi M., Uhlen M., Nyren P. Asequencing method based on real-time pyrophosphate. Science 1998, 281(363):365.
37. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 24:4876-4882.
38. Papin J.F., Vahson W., Dittmer D.P. SYBR green-based real-time quantitative PCR assay for detection of West Nile virus circumvents false-negative results due to strain variability. JClin Microbiol 2004, 42:4.
39. Jiang S., Dezfulian H., Chiu W. Real-time quantitative PCR for enteric adenovirus serotype 40 in environmental waters. Can J Microbiol 2005, 51:393-398.
40. Thompson E.W., Warton K., Blick T., Wafai R., Hill P., Stanley K. Multiplexed tandem polymerase chain reaction identifies strong expression of oestrogen receptor and Her-2 from single, formalin-fixed paraffin-embedded breast cancer sections. Pathology 2010, 42:1-13.
41. Checkley W., Gilman R.H., Epstein L.D., Suarez M., Diaz J.F., Cabrera L., et al. Asymptomatic and symptomatic cryptosporidiosis: their acute effect on weight gain in Peruvian children. Am J Epidemiol 1997, 145:156-163.
42. Hellard M.E., Sinclair M.I., Hogg G.G., Fairley C.K. Prevalence of enteric pathogens among community based asymptomatic individuals. JGastroenterol Hepatol 2000, 15:290-293.
43. Chen X.M., Keithly J.S., Paya C.V., LaRusso N.F. Cryptosporidiosis. NEngl J Med 2002, 346:1723-1731.
44. Toze S. PCR and the detection of microbial pathogens in water and wastewater. Water Res 1999, 33:3545-3556.
45. Loge F.J., Thompson D.E., Call D.R. PCR detection of specific pathogens in water: a risk-based analysis. Environ Sci Technol 2002, 36:2754-2759.
46. Spigaglia P., Barbanti F., Mastrantonio P. Detection of a genetic linkage between genes coding for resistance to tetracycline and erythromycin in Clostridium difficile. Microb Drug Resist 2007, 13:90-95.
47. Spigaglia P., Carattoli A., Barbanti F., Mastrantonio P. Detection of gyrA and gyrB mutations in Clostridium difficile isolates by real-time PCR. Mol Cell Probes 2009.
48. Gasser R.B., Cantacessi C., Campbell B.E. Improved molecular diagnostic tools for human hookworms. Expert Rev Mol Diagn 2009, 9:17-21.
49. Gasser R.B., Cantacessi C., Loukas A. DNA technological progress toward advanced diagnostic tools to support human hookworm control. Biotechnol Adv 2008, 26:35-45.
50. Gasser R.B., Bott N.J., Chilton N.B., Hunt P., Beveridge I. Toward practical, DNA-based diagnostic methods for parasitic nematodes of livestock-bionomic and biotechnological implications. Biotechnol Adv 2008, 26:325-334.
51. Bott N.J., Campbell B.E., Beveridge I., Chilton N.B., Rees D., Hunt P.W., et al. Acombined microscopic-molecular method for the diagnosis of strongylid infections in sheep. Int J Parasitol 2009, 39:1277-1287.