Simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative PCR

Applied and Environmental Microbiology

Volumn 79, Issue 9, 2013, Pages 2891-2898

  Ishii, Satoshi ^a   Segawa, Takahiro ^b   Okabe, Satoshi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF POLAR RESEARCH   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENTERIC PATHOGENS; ENVIRONMENTAL WATER SAMPLES; FECAL CONTAMINATION; FECAL INDICATOR BACTERIA; QUANTITATIVE PCR; ROUTINE MONITORING; SIMULTANEOUS DETECTION; WATER-BORNE PATHOGENS;

ESCHERICHIA COLI; FOOD MICROBIOLOGY; MICROFLUIDICS; PATHOGENS; RISK ASSESSMENT;

POLYMERASE CHAIN REACTION;

BACTERIUM; BIOINDICATOR; DETECTION METHOD; ENVIRONMENTAL MONITORING; FECES; PATHOGEN; POLYMERASE CHAIN REACTION; PUBLIC HEALTH; QUANTITATIVE ANALYSIS; RISK ASSESSMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

BACTERIAL DNA; PRIMER DNA;

BACTERIA; DNA MICROARRAY; ENVIRONMENTAL MONITORING; ESCHERICHIA COLI; FECES; FOOD CONTROL; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLUIDICS; PLASMID; POLYMERASE CHAIN REACTION; PROCEDURES; SENSITIVITY AND SPECIFICITY;

BACTERIA; DNA PRIMERS; DNA, BACTERIAL; ENVIRONMENTAL MONITORING; ESCHERICHIA COLI; FECES; FOOD MICROBIOLOGY; MICROFLUIDICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; WATER MICROBIOLOGY;

EID: 84876329785     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00205-13     Document Type: Article

References (49)

1. Aw TG, Rose JB. 2012. Detection of pathogens in water: from phylochips to qPCR to pyrosequencing. Curr. Opin. Biotechnol. 23:422-430.
2. Hass CN, Rose JB, Gerba CP. 1999. In Quantitative microbial risk assessment. John Wiley & Sons, New York, NY.
3. Byappanahalli MN, Nevers MB, Korajkic A, Staley ZR, Harwood VJ. 2012. Enterococci in the environment. Microbiol. Mol. Biol. Rev. 76: 685-706.
4. Ishii S, Sadowsky MJ. 2008. Escherichia coli in the environment: implications for water quality and human health. Microbes Environ. 23:101-108.
5. Cunningham SA, Sloan LM, Nyre LM, Vetter EA, Mandrekar J, Patel R. 2010. Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture. J. Clin. Microbiol. 48:2929-2933.
6. de Boer RF, Ott A, Kesztyüs B, Kooistra-Smid AMD. 2010. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. J. Clin. Microbiol. 48:4140-4146.
7. Fukushima H, Tsunomori Y, Seki R. 2003. Duplex real-time SYBR Green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. J. Clin. Microbiol. 41:5134-5146.
8. Guion CE, Ochoa TJ, Walker CM, Barletta F, Cleary TG. 2008. Detection of diarrheagenic Escherichia coli by use of melting-curve analysis and real-time multiplex PCR. J. Clin. Microbiol. 46:1752-1757.
9. LaGier MJ, Joseph LA, Passaretti TV, Musser KA, Cirino NM. 2004. A real-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli. Mol. Cell. Probes 18:275-282.
10. Ramalingam N, Rui Z, Liu H-B, Dai C-C, Kaushik R, Ratnaharika B, Gong H-Q. 2010. Real-time PCR-based microfluidic array chip for simultaneous detection of multiple waterborne pathogens. Sensors Actuat. B Chem. 145:543-552.
11. Lee D-Y, Shannon K, Beaudette LA. 2006. Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. J. Microbiol. Methods 65:453-467.
12. Kostić T, Weilharter A, Rubino S, Delogu G, Uzzau S, Rudi K, Sessitsch A, Bodrossy L. 2007. A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens. Anal. Biochem. 360:244-254.
13. Donhauser SC, Niessner R, Seidel M. 2011. Sensitive quantification of Escherichia coli O157:H7, Salmonella enterica, and Campylobacter jejuni by combining stopped polymerase chain reaction with chemiluminescence flow-through DNA microarray analysis. Anal. Chem. 83:3153-3160.
14. Sergeev N, Distler M, Courtney S, Al-Khaldi SF, Volokhov D, Chizhikov V, Rasooly A. 2004. Multipathogen oligonucleotide microarray for environmental and biodefense applications. Biosens. Bioelectron. 20: 684-698.
15. Straub TM, Dockendorff BP, Quiñonez-Díaz MD, Valdez CO, Shutthanandan JI, Tarasevich BJ, Grate JW, Bruckner-Lea CJ. 2005. Automated methods for multiplexed pathogen detection. J. Microbiol. Methods 62: 303-316.
16. Li Y, Cu YTH, Luo D. 2005. Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes. Nat. Biotechnol. 23: 885-889.
17. Liu J, Kibiki G, Maro V, Maro A, Kumburu H, Swai N, Taniuchi M, Gratz J, Toney D, Kang G, Houpt E. 2011. Multiplex reverse transcription PCR Luminex assay for detection and quantitation of viral agents of gastroenteritis. J. Clin. Virol. 50: 308-313.
18. Liu J, Gratz J, Maro A, Kumburu H, Kibiki G, Taniuchi M, Howlader AM, Sobuz SU, Haque R, Talukder KA, Qureshi S, Zaidi A, Haverstick DM, Houpt ER. 2012. Simultaneous detection of six diarrhea-causing bacterial pathogens with an in-house PCR-Luminex assay. J. Clin. Microbiol. 50:98-103.
19. O'Leary J, Corcoran D, Lucey B. 2009. Comparison of the EntericBio multiplex PCR system with routine culture for detection of bacterial enteric pathogens. J. Clin. Microbiol. 47:3449-3453.
20. Taniuchi M, Verweij JJ, Noor Z, Sobuz SU, van Lieshout L, Petri WA, Jr, Haque R, Houpt ER. 2011. High throughput multiplex PCR and probe-based detection with Luminex beads for seven intestinal parasites. Am. J. Trop. Med. Hyg. 84:332-337.
21. Akhras MS, Thiyagarajan S, Villablanca AC, Davis RW, Nyrén P, Pourmand N. 2007. PathogenMip assay: a multiplex pathogen detection assay. PLoS One 2:e223. doi:10.1371/journal.pone.0000223.
22. Ye L, Zhang T. 2011. Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ. Sci. Technol. 45:7173-7179.
23. Ibekwe AM, Watt PM, Grieve CM, Sharma VK, Lyons SR. 2002. Multiplex fluorogenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands. Appl. Environ. Microbiol. 68: 4853-4862.
24. Malorny B, Paccassoni E, Fach P, Bunge C, Martin A, Helmuth R. 2004. Diagnostic real-time PCR for detection of Salmonella in food. Appl. Environ. Microbiol. 70:7046-7052.
25. Moltzahn F, Olshen AB, Baehner L, Peek AS, Fong L, Stoppler HJ, Simko J, Hilton JF, Carroll PR, Blelloch R. 2011. Microfluidic based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in sera of prostate cancer patients. Cancer Res. 71:550-560.
26. Spurgeon SL, Jones RC, Ramakrishnan R. 2008. High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One 3:e1662. doi:10.1371/journal.pone.0001662.
27. Yoo AS, Sun AX, Li L, Shcheglovitov A, Portmann T, Li Y, Lee-Messer C, Dolmetsch RE, Tsien RW, Crabtree GR. 2011. MicroRNA-mediated conversion of human fibroblasts to neurons. Nature 476:228-231.
28. Gruzdev N, McClelland M, Porwollik S, Ofaim S, Pinto R, Saldinger-Sela S. 2012. Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium. Appl. Environ. Microbiol. 78:7866-7875.
29. Bugarel M, Beutin L, Scheutz F, Loukiadis E, Fach P. 2011. Identification of genetic markers for differentiation of Shiga toxin-producing, enteropathogenic, and avirulent strains of Escherichia coli O26. Appl. Environ. Microbiol. 77:2275-2281.
30. Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K. 2011. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields. Microbes Environ. 26:30-35.
31. Hamilton MJ, Hadi AZ, Griffith JF, Ishii S, Sadowsky MJ. 2010. Large scale analysis of virulence genes in Escherichia coli strains isolated from Avalon Bay, CA. Water Res. 44:5463-5473.
32. Kobayashi A, Sano D, Hatori J, Ishii S, Okabe S. 2012. Chicken- and duck-associated Bacteroides-Prevotella genetic markers for detecting fecal contamination in environmental water. Appl. Microbiol. Biotechnol. doi: 10.1007/s00253-012-4469-2.
33. Ishii S, Tago K, Nishizawa T, Oshima K, Hattori M, Senoo K. 2011. Complete genome sequence of the denitrifying and N2O-reducing bacterium Pseudogulbenkiania sp. strain NH8B. J. Bacteriol. 193:6395-6396.
34. Mouritzen P, Noerholm M, Nielsen PS, Jacobsen N, Lomholt C, Pfundheller HM, Tolstrup N. 2005. ProbeLibrary: a new method for faster design and execution of quantitative real-time PCR. Nat. Methods 2:313-316.
35. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
36. Blackstone GM, Nordstrom JL, Bowen MD, Meyer RF, Imbro P, DePaola A. 2007. Use of a real time PCR assay for detection of the ctxA gene of Vibrio cholerae in an environmental survey of Mobile Bay. J. Microbiol. Methods 68:254-259.
37. Blackstone GM, Nordstrom JL, Vickery MCL, Bowen MD, Meyer RF, DePaola A. 2003. Detection of pathogenic Vibrio parahaemolyticus in oyster enrichments by real time PCR. J. Microbiol. Methods 53:149-155.
38. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. 2009. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55:611-622.
39. Altekruse SF, Stern NJ, Fields PI, Swerdlow DL. 1999. Campylobacter jejuni-an emerging foodborne pathogen. Emerg. Infect. Dis. 5:28-35.
40. Escobar-Páramo P, Giudicelli C, Parsot C, Denamur E. 2003. The evolutionary history of Shigella and enteroinvasive Escherichia coli revised. J. Mol. Evol. 57:140-148.
41. Miyamoto K, Li J, McClane BA. 2012. Enterotoxigenic Clostridium perfringens: detection and identification. Microbes Environ. 27:343-349.
42. Segawa T, Takeuchi N, Rivera A, Yamada A, Yoshimura Y, Barcaza G, Shinbori K, Motoyama H, Kohshima S, Ushida K. 2013. Distribution of antibiotic resistance genes in glacier environments. Environ. Microbiol. Rep. 5:127-134.
43. Ushida K, Segawa T, Kohshima S, Takeuchi N, Fukui K, Li Z, Kanda H. 2010. Application of real-time PCR array to the multiple detection of antibiotic resistant genes in glacier ice samples. J. Gen. Appl. Microbiol. 56:43-52.
44. Stedtfeld RD, Baushke SW, Tourlousse DM, Miller SM, Stedtfeld TM, Gulari E, Tiedje JM, Hashsham SA. 2008. Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl. Environ. Microbiol. 74:3831-3838.
45. Farber JM, Peterkin PI. 1991. Listeria monocytogenes, a food-borne pathogen. Microbiol. Rev. 55:476-511.
46. Craven SE, Stern NJ, Line E, Bailey JS, Cox NA, Fedorka-Cray P. 2000. Determination of the incidence of Salmonella spp., Campylobacter jejuni, and Clostridium perfringens in wild birds near broiler chicken houses by sampling intestinal droppings. Avian Dis. 44:715-720.
47. Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA. 2009. Quantitative PCR for genetic markers of human fecal pollution. Appl. Environ. Microbiol. 75:5507-5513.
48. Stoeckel DM, Stelzer EA, Dick LK. 2009. Evaluation of two spike-andrecovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res. 43:4820-4827.
49. van Doorn R, Klerks MM, van Gent-Pelzer MPE, Speksnijder AGCL, Kowalchuk GA, Schoen CD. 2009. Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using Biotrove OpenArrays. Appl. Environ. Microbiol. 75:7253-7260.