Biomedical subjects

Rachel T Noble

Publications and source records attributed to Rachel T Noble.

8 recordsLinked to original sources

PubMed2006

Bacteriological water quality along the Tijuana-Ensenada, Baja California, México shoreline.

This survey was part of a Binational Program (Mexico-United States) in microbiological water quality, with a goal to assess the shoreline bacteriological water quality from Tijuana to Ensenada, Mexico. Samples were collected at 29 sites (19 beaches and 10 outfalls), from the United States border to Punta Banda, Baja California, during summer (1998) and winter (1999). Total coliforms, fecal coliforms and enterococci were used as bacterial indicators. Standard methods were used for total and fecal coliforms, while the Enterolert quick method (IDEXX) was used for the enterococci. Compared with outfalls, the beaches exceeded water quality standards by a small percent, 25.3% in summer and 17% in winter. For outfalls, the percentage of shoreline that exceeded bacterial indicator thresholds had a minor value in summer (32.7%) than in winter (50%). Sites near wastewater discharges had the lowest quality and did not meet the microbiological water quality criteria for recreational use.

Bathing Beaches↗

PubMed2006

Rapid one-step quantitative reverse transcriptase PCR assay with competitive internal positive control for detection of enteroviruses in environmental samples.

Human enteroviruses can serve as a more accurate indicator of human fecal contamination than conventional bacteriological fecal indicators. We describe here a quantitative reverse transcriptase PCR (qRT-PCR) assay specifically tailored to detect these viruses in environmental waters. The assay included a competitive internal positive control (CIPC) that allowed the inhibition of qRT-PCRs to be quantitatively assessed. Coamplification of the CIPC with enteroviral genetic material did not affect the sensitivity, specificity, or reproducibility of the enteroviral qRT-PCR assay. The assay is rapid (less than 5 h from sample to result), has a wide dynamic range (>3 logs), and is capable of detecting as few as 25 enteroviral genomes with an average amplification efficiency of 0.91. In samples with low or moderate inhibition, the delay in CIPC amplification was used to adjust enterovirus qRT-PCR concentrations to account for losses due to inhibition. Samples exhibiting significant inhibition were not corrected but instead diluted twofold and immediately assayed again. Using significantly inhibited samples, it was found that dilution relieved inhibition in 93% (25 of 27) of the samples. In addition, 15% (4 of 27) of these previously negative samples contained enteroviral genomes. The high-throughput format of the assay compared to conventional culture-based methods offers a fast, reliable, and specific method for detecting enteroviruses in environmental water samples. The ability of the assay to identify false negatives and provide improved quantitative assessments of enterovirus concentrations will facilitate the tracking of human fecal contamination and the assessment of potential public health risk due to enteroviruses in recreational and shellfish harvesting waters.

Base Sequence↗

PubMed2006

Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California.

The ubiquity of fecal indicator bacteria such as Escherichia coli and Enterococcus spp. in urban environments makes tracking of fecal contamination extremely challenging. A multitiered approach was used to assess sources of fecal pollution in Ballona Creek, an urban watershed that drains to the Santa Monica Bay (SMB) near Los Angeles, Calif. A mass-based design at six main-stem sites and four major tributaries over a 6-h period was used (i) to assess the flux of Enterococcus spp. and E. coli by using culture-based methods (tier 1); (ii) to assess levels of Enterococcus spp. by using quantitative PCR and to detect and/or quantify additional markers of human fecal contamination, including a human-specific Bacteroides sp. marker and enterovirus, using quantitative reverse transcriptase PCR (tier 2); and (iii) to assess the specific types of enterovirus genomes found via sequence analysis (tier 3). Sources of fecal indicator bacteria were ubiquitous, and concentrations were high, throughout Ballona Creek, with no single tributary dominating fecal inputs. The flux of Enterococcus spp. and E. coli averaged 10(9) to 10(10) cells h(-1) and was as high at the head of the watershed as at the mouth prior to discharge into the SMB. In addition, a signal for the human-specific Bacteroides marker was consistently detected: 86% of the samples taken over the extent during the study period tested positive. Enteroviruses were quantifiable in 14 of 36 samples (39%), with the highest concentrations at the site furthest upstream (Cochran). These results indicated the power of using multiple approaches to assess and quantify fecal contamination in freshwater conduits to high-use, high-priority recreational swimming areas.

Bacteroides↗

PubMed2005

Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR.

Despite viral contamination of recreational waters, only bacterial, not viral, indicators are monitored routinely, due to a lack of rapid and cost-effective assays. We used negatively charged filters to capture enteroviruses from seawater and freshwater. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (qRT-PCR). Poliovirus (6.6 to 330,000 virus particles/ml) was added to samples from watersheds in Los Angeles, California, and analysis showed that with 50-ml samples, a cellulose acetate/nitrate (HA) filter yielded final recovery of 51% (r2= 0.99) in fresh water and 23% (r2= 0.90) in seawater. However, for additions of low levels of virus (more likely to represent field samples; <10(4) enterovirus particles/ml), the recovery was lower and more variable, with HA being best in freshwater (17%, r2= 0.97) and the type GF/F glass filter having higher average recovery in seawater (GF/F, 17%; r2= 0.93; HA 12%, r2= 0.87). The optimized method was used with 1-liter field samples from two very different freshwater "creeks" that drain into Santa Monica Bay, California: Topanga Creek (TC), a relatively pristine mountain creek, and Ballona Creek (BC), a concrete-lined urban storm drain. One TC site out of 10 and 2 BC sites out of 7 tested significantly positive for enteroviruses, with higher enterovirus concentrations in BC than in TC (ca. 10 to 25 versus 1 equivalent enterovirus particle/ml). The presented filtration-qRT-PCR approach is fast (<8 h from sampling to results), sensitive, and cost efficient and is promising for monitoring viral contamination in environmental water samples.

Cellulose↗

PubMed2005

A review of technologies for rapid detection of bacteria in recreational waters.

Monitoring of recreational beaches for fecal indicator bacteria is currently performed using culture-based technology that can require more than a day for laboratory analysis, during which time swimmers are at risk. Here we review new methods that have the potential to reduce the measurement period to less than an hour. These methods generally involve two steps. The first is target capture, in which the microbial group of interest (or some molecular/chemical/or biochemical signature of the group) is removed, tagged or amplified to differentiate it from the remaining material in the sample. We discuss three classes of capture methods: 1) Surface and whole-cell recognition methods, including immunoassay techniques and molecule-specific probes; 2) Nucleic acid methods, including polymerase chain reaction (PCR), quantitative PCR (Q-PCR), nucleic acid sequence based amplification (NASBA) and microarrays; and 3) Enzyme/substrate methods utilizing chromogenic or fluorogenic substrates. The second step is detection, in which optical, electrochemical or piezoelectric technologies are used to quantify the captured, tagged or amplified material. The biggest technological hurdle for all of these methods is sensitivity, as EPA's recommended bathing water standard is less than one cell per ml and most detection technologies measure sample volumes less than 1 ml. This challenge is being overcome through addition of preconcentration or enrichment steps, which have the potential to boost sensitivity without the need to develop new detector technology. The second hurdle is demonstrating a relationship to health risk, since most new methods are based on measuring cell structure without assessing viability and may not relate to current water quality standards that were developed in epidemiology studies using culture-based methods. Enzyme/substrate methods may be the first rapid methods adopted because they are based on the same capture technology as currently-approved EPA methods and their relationship to health risk can be established by demonstrating equivalency to existing procedures. Demonstration of equivalency may also be possible for some surface and whole-cell recognition methods that capture bacteria in a potentially viable state. Nucleic acid technologies are the most versatile, but measure nonviable structure and will require inclusion in epidemiological studies to link their measurement with health risk.

Bacteria↗

PubMed2003

Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study.

Assays for the detection and typing of adenoviruses, enteroviruses and F+ specific coliphages were performed on samples created as part of a national microbial source tracking methods comparison study. The samples were created blind to the researchers, and were inoculated with a variety of types of fecal contamination source (human, sewage, dog, seagull and cow) and mixtures of sources. Viral tracer and pathogen assays demonstrated a general ability to discriminate human from non-human fecal contamination. For example, samples inoculated with sewage were correctly identified as containing human fecal contamination because they contained human adenovirus or human enterovirus. In samples containing fecal material from individual humans, human pathogen analysis yielded negative results probably because the stool samples were taken from healthy individuals. False positive rates for the virus-based methods (0-8%) were among the lowest observed during the methods comparison study. It is suggested that virus-based source tracking methods are useful for identification of sewage contamination, and that these methods may also be useful as an indication of the public health risk associated with viral pathogens. Overall, virus-based source tracking methods are an important approach to include in the microbial source tracking 'toolbox'.

Adenoviridae↗

PubMed2003

Storm effects on regional beach water quality along the southern California shoreline.

Two regional studies conducted during dry weather demonstrated that the Southern California Bight (SCB) shoreline has good water quality, except near areas that drain land-based runoff. Here, we repeat those regional studies 36 h after a rainstorm to assess the influence of runoff under high flow conditions. Two hundred and fifty-four shoreline sites between Santa Barbara, California and Ensenada, Mexico were sampled using a stratified-random sampling design with four strata: sandy beaches, rocky shoreline, shoreline adjacent to urban runoff outlets that flow intermittently, and shoreline adjacent to outlets that flow year-round. Each site was sampled for total coliforms, fecal coliforms (or E. coli), and enterococci. Sixty percent of the shoreline failed water quality standards after the storm compared to only 6% during dry weather. Failure of water quality standards increased to more than 90% for shoreline areas adjacent to urban runoff outlets. During dry weather, most water quality failures occurred for only one of the three bacterial indicators and concentrations were barely above State of California standards; following the storm, most failures were for multiple indicators and exceeded State of California standards by a large margin. The condition of the shoreline in Mexico and the United States was similar following rainfall, which was not the case during dry weather.

Bathing Beaches↗

PubMedDate not supplied

Comparison of beach bacterial water quality indicator measurement methods.

Three methods (membrane filtration, multiple tube fermentation, and chromogenic substrate technology kits manufactured by IDEXX Laboratories, Inc.) are routinely used to measure indicator bacteria for beach water quality. To assess comparability of these methods, quantify within-laboratory variability for each method, and place that variability into context of variability among laboratories using the same method, 22 southern California laboratories participated in a series of intercalibration exercises. Each laboratory processed three to five replicates from thirteen samples, with total coliforms, fecal coliforms or enterococci measured depending on the sample. Results were generally comparable among methods, though membrane filtration appeared to underestimate the other two methods for fecal coliforms, possibly due to clumping. Variability was greatest for the multiple tube fermentation method. For all three methods, within laboratory variability was greater than among laboratories variability.

Calibration↗