Use of a genetically-engineered Escherichia coli strain as a sample process control for quantification of the host-specific bacterial genetic markers

Applied Microbiology and Biotechnology

Volumn 97, Issue 20, 2013, Pages 9165-9173

  Kobayashi, Ayano ^a   Sano, Daisuke ^a   Taniuchi, Asami ^a   Ishii, Satoshi ^a   Okabe, Satoshi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Bacteroides Prevotella 16S rRNA genetic markers; Fecal contamination; Microbial source tracking; Propidium monoazide; Quantitative PCR assay; Sample process control

Indexed keywords

FECAL CONTAMINATION; GENETIC MARKERS; MICROBIAL SOURCE TRACKING; PROPIDIUM; QUANTITATIVE PCR;

ASSAYS; CONTAMINATION; DNA; EFFICIENCY; ESCHERICHIA COLI; MEASUREMENT ERRORS; POLYMERASE CHAIN REACTION; PROCESS CONTROL; RNA;

EXTRACTION;

BACTERIAL DNA; BACTERIAL RNA; RNA 16S;

AMPLIFICATION; BACTERIUM; BIOASSAY; BIOMARKER; DNA; EXTRACTION; POLYMERASE CHAIN REACTION; RECOVERY; STRAIN;

ARTICLE; BACTERIAL STRAIN; BACTEROIDES FRAGILIS; CONTROLLED STUDY; DNA EXTRACTION; ESCHERICHIA COLI K 12; GENETIC MARKER; NONHUMAN; POLYMERASE CHAIN REACTION; PREVOTELLA; PROCESS CONTROL; QUANTITATIVE ANALYSIS; RELIABILITY; TRANSGENIC ORGANISM; WASTE WATER MANAGEMENT; WATER CONTAMINATION; WATER SAMPLING;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES FRAGILIS; ESCHERICHIA COLI; PREVOTELLA;

ANIMALS; BACTEROIDES; CATTLE; CHICKENS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FECES; FRESH WATER; GENETIC ENGINEERING; GENETIC MARKERS; HOST SPECIFICITY; HUMANS; POLYMERASE CHAIN REACTION; PREVOTELLA; QUALITY CONTROL; SPECIES SPECIFICITY; SWINE; WASTE WATER;

EID: 84885390935     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5188-z     Document Type: Article

References (39)

1. APHA, AWWA, WEF (2005) Standard method for the examination of water and wastewater, 21st edn. American Public Health Association, Washington D.C
2. Bae S, Wuertz S (2009) Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide. Appl Environ Microbiol 75:2940-2944
3. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462
4. Cho J-C, Kim S-J (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66:956-965
5. D'Agostino M, Cook N, Rodriguez-Lazaro D, Rutjes S (2011) Nucleic acid amplification-based methods for detection of enteric viruses: definition of controls and interpretation of results. Food Environ Virol 2:55-60
6. Diez-Valcarce M, Cook N, Hernandez M, Rodriguez-Lazaro D (2011) Analytical application of a sample process control in detection of foodborne viruses. Food Anal Methods 4:614-618
7. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640-6645
8. Field KG, Bernhard AE, Brodeur TJ (2003) Molecular approaches to microbiological monitoring: fecal source detection. Environ Monit Assess 81:313-326
9. Field KG, Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:3517-3538
10. Fremaux B, Boa T, Yost CK (2010) Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water sources. Appl Environ Microbiol 76:4886-4889
11. Green HC, Field KG (2012) Sensitive detection of sample interference in environmental qPCR. Water Res 46:3251-3260
12. Harwood VJ, Brownell M, Wang S, Lepo J, Ellender RD, Ajidahun A, Hellein KN, Kennedy E, Ye X, Flood C (2009) Validation and field testing of library-dependent microbial source tracking methods in the Gulf of Mexico. Water Res 43(19):4812-4819
13. Haugland RA, Varma M, Sivaganesan M, Kelty C, Peed L, Shanks OC (2010) Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales sp. and human fecal waste by qPCR. Syst Appl Microbiol 33(6):348-357
14. Ishii S, Segawa T, Okabe S (2013) Simultaneous quantification of multiple food and waterborne pathogens by use of microfluidic quantitative PCR. Appl Environ Microbiol 79:2891-2898
15. Kassa H, Harrington B, Bisesi MS (2001) Risk of occupational exposure to Cryptosporidium, Giardia, and Campylobacter associated with the feces of giant Canada geese. Appl Occup Environ Hyg 16(9):905-909
16. Kildare BJ, Leutenegger CM, McSwain BS, Bambic DG, Rajal VB, Wuertz S (2007) 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales, a Bayesian approach. Water Res 41:3701-3715
17. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2000) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181-184
18. Kobashi Y, Hasebe A, Nishio M (2005) Antibiotic-resistant bacteria from feces of livestock, farmyard manure, and farmland in Japan - Case report. Microbes Environ 20(1):53-60
19. Kobayashi A, Sano D, Hatori J, Ishii S, Okabe S (2013) Chicken- and duck-associated Bacteroides-Prevotella genetic markers for detecting fecal contamination in environmental water. Appl Microbiol Biotechnol 97:7427-7437
20. Meays CL, Broersma K, Nordin R, Mazumder A (2004) Source tracking fecal bacteria in water: a critical review of current method. J Environ Manag 73:71-79
21. Mieszkin S, Furet JP, Corthier G, Gourmelon M (2009a) Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. Appl Environ Microbiol 75:3045-3054
22. Mieszkin S, Yala J-F, Joubrel R, Gourmelon M (2009b) Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant fecal pollution by real-time PCR. J Appl Microbiol 108:974-984
23. Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosafety Res 6(1-2):37-53
24. Nocker A, Cheung CY, Camper AK (2006) Comparison of propidium monoazide with ethidium monoazide for differentiation of live versus dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods 67(2):310-320
25. Okabe S, Okayama N, Savichtcheva O, Ito T (2007) Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74:890-901
26. Okabe S, Shimazu Y (2007) Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl Microbiol Biotechnol 76:935-944
27. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory. Manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor
28. Savichtcheva O, Okabe S (2006) Alternative indicators of fecal pollution: relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring, and future application perspectives. Water Res 40:2463-2476
29. Savichtcheva O, Okayama N, Okabe S (2007) Relationships between Bacteroides 16S rRNA genetic markers and presence of bacterial enteric pathogens and conventional fecal indicators. Water Res 41:3615-3628
30. Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68:5796-5803
31. Seurinck S, Defoirdt T, Verstraete W, Siciliano SD (2005) Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human fecal pollution in freshwater. Environ Microbiol 7:249-259
32. 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
33. Simpson JM, Santo Domingo JW, Reaspner DJ (2002) Microbial source tracking: state of the science. Environ Sci Technol 24:5279-5288
34. Smalla K, van Overbeek LS, Pukall R, van Elsas JD (1993) Prevalence of nptII and Tn5 in kanamycin-resistant bacteria from different environments. FEMS Microbiol Ecol 13:47-58
35. Stewart JR, Ellender RD, Gooch JA, Jiang S, Myoda SP, Weisberg SB (2003) Recommendations for microbial source tracking: lessons from a methods comparison study. J Water Health 1(4):225-231
36. Stoeckel DM, Stelzer EA, Dick LK (2009) Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res 43:4820-4827
37. Taskin B, Gozen AG, Duran M (2011) Selective quantification of viable Escherichia coli in biosolids by quantitative PCR with propidium monoazide. Appl Environ Microbiol 77:4329-4335
38. Varma M, Field R, Stinson M, Rukovets B, Wymer L, Haugland R (2009) Quantitative real-time PCR analysis of total and propidium monoazide-resistant fecal indicator bacteria in wastewater. Water Res 43:4790-4801
39. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119