title: A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water.
abstract: BACKGROUND
  Water and High Purity Water (HPW) distribution systems can be contaminated with human pathogenic microorganisms. This biocontamination may pose a risk to human health as HPW is commonly used in the industrial, pharmaceutical and clinical sectors. Currently, routine microbiological testing of HPW is performed using slow and labour intensive traditional microbiological based techniques. There is a need to develop a rapid culture independent methodology to quantitatively detect and identify biocontamination associated with HPW.
  
  
  RESULTS
  A novel internally controlled 5-plex real-time PCR Nucleic Acid Diagnostics assay (NAD), was designed and optimised in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, to rapidly detect, identify and quantify the human pathogenic bacteria Stenotrophomonas maltophilia, Burkholderia species, Pseudomonas aeruginosa and Serratia marcescens which are commonly associated with the biocontamination of water and water distribution systems. The specificity of the 5-plex assay was tested against genomic DNA isolated from a panel of 95 microorganisms with no cross reactivity observed. The analytical sensitivities of the S. maltophilia, B. cepacia, P. aeruginosa and the S. marcescens assays are 8.5, 5.7, 3.2 and 7.4 genome equivalents respectively. Subsequently, an analysis of HPW supplied by a Millipore Elix 35 water purification unit performed using standard microbiological methods revealed high levels of naturally occurring microbiological contamination. Five litre water samples from this HPW delivery system were also filtered and genomic DNA was purified directly from these filters. These DNA samples were then tested using the developed multiplex real-time PCR NAD assay and despite the high background microbiological contamination observed, both S. maltophilia and Burkholderia species were quantitatively detected and identified. At both sampling points the levels of both S. maltophilia and Burkholderia species present was above the threshold of 10 cfu/100 ml recommended by both EU and US guidelines.
  
  
  CONCLUSIONS
  The novel culture independent methodology described in this study allows for rapid (<5 h), quantitative detection and identification of these four human pathogens from biocontaminated water and HPW distribution systems. We propose that the described NAD assay and associated methodology could be applied to routine testing of water and HPW distribution systems to assure microbiological safety and high water quality standards.
authors.affiliation: Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. elizabeth.minogue@nuigalway.ie.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Minogue
authors.affiliation: Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. nina.tuite@nuigalway.ie.
authors.forename: Nina L
authors.initials: NL
authors.lastname: Tuite
authors.affiliation: Marine Microbial Ecology Laboratory, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. cindy.smith@nuigalway.ie.
authors.forename: Cindy J
authors.initials: CJ
authors.lastname: Smith
authors.affiliation: Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. kate.reddington@nuigalway.ie.
authors.forename: Kate
authors.initials: K
authors.lastname: Reddington
authors.affiliation: Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. thomas.barry@nuigalway.ie.
authors.forename: Thomas
authors.initials: T
authors.lastname: Barry
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D015373:Bacterial Typing Techniques / Q000379:methods*; D019117:Burkholderia / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D012706:Serratia marcescens / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D020615:Stenotrophomonas maltophilia / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D014871:Water Microbiology; D018508:Water Purification
chemical_list: D004269:DNA, Bacterial