Evaluation of molecular community analysis methods for discerning fecal sources and human waste

Molecular microbial community analyses provide information on thousands of microorganisms simultaneously, and integrate biotic and abiotic perturbations caused by fecal contamination entering water bodies. A few studies have explored community methods as emerging approaches for microbial source tracking (MST), however, an evaluation of the current state of this approach is lacking. Here, we utilized three types of community-based methods with 64 blind, single- or dual-source, challenge samples generated from 12 sources, including: humans (feces), sewage, septage, dogs, pigs, deer, horses, cows, chickens, gulls, pigeons, and geese. Each source was a composite from multiple donors from four representative geographical regions in California. Methods evaluated included terminal restriction fragment polymorphism (TRFLP), phylogenetic microarray (PhyloChip), and next generation (Illumina) sequencing. These methods correctly identified dominant (or sole) sources in over 90% of the challenge samples, and exhibited excellent specificity regardless of source, rarely detecting a source that was not present in the challenge sample. Sensitivity, however, varied with source and community analysis method. All three methods distinguished septage from human feces and sewage, and identified deer and horse with 100% sensitivity and 100% specificity. Method performance improved if the composition of blind dual-source reference samples were defined by DNA contribution of each single source within the mixture, instead of by Enterococcus colony forming units. Data analysis approach also influenced method performance, indicating the need to standardize data interpretation. Overall, results of this study indicate that community analysis methods hold great promise as they may be used to identify any source, and they are particularly useful for sources that currently do not have, and may never have, a source-specific single marker gene.

Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study

The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 41 MST methodologies by analyzing data generated in 27 laboratories. MST methodologies that targeted human, cow, ruminant, dog, gull, pig, horse, and sheep were tested against sewage, septage, human, cow, dog, deer, pig, chicken, pigeon, gull, horse, and goose fecal samples. Each laboratory received 64 blind samples containing a single source (singletons) or two sources (doubletons), as well as diluted singleton samples to assess method sensitivity. Laboratories utilized their own protocols when performing the methods and data were deposited in a central database before samples were unblinded. Between one and seven laboratories tested each method. The most sensitive and specific assays, based on an analysis of presence/absence of each marker in target and non-target fecal samples, were HF183 endpoint and HF183SYBR (human), CF193 and Rum2Bac (ruminant), CowM2 and CowM3 (cow), BacCan (dog), Gull2SYBR and LeeSeaGull (gull), PF163 and pigmtDNA (pig), HoF597 (horse), PhyloChip (pig, horse, chicken, deer), Universal 16S TRFLP (deer), and Bacteroidales 16S TRFLP (pig, horse, chicken, deer); all had sensitivity and specificity higher than 80% in all or the majority of laboratories. When the abundance of MST markers in target and non-target fecal samples was examined, some assays that performed well in the binary analysis were found to not be sensitive enough as median concentrations fell below a minimum abundance criterion (set at 50 copies per colony forming units of enterococci) in target fecal samples. Similarly, some assays that cross-reacted with non-target fecal sources in the binary analysis were found to perform well in a quantitative analysis because the cross-reaction occurred at very low levels. Based on a quantitative analysis, the best performing methods were HF183Taqman and BacH (human), Rum2Bac and BacR (ruminant), LeeSeaGull (gull), and Pig2Bac (pig); no cow or dog-specific assay met the quantitative specificity and sensitivity criteria. Some of the best performing assays in the study were run by just one laboratory so further testing of assay portability is needed. While this study evaluated the marker performance in defined samples, further field testing as well as development of frameworks for fecal source allocation and risk assessment are needed.

Genomics in marine monitoring: new opportunities for assessing marine health status

This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.

SLE disease per se contributes to deterioration in bone mineral density, microstructure and bone strength

OBJECTIVE

The objective of this report is to assess the effect of systemic lupus erythematosus (SLE) disease itself on deterioration of bone mineral density (BMD), microstructure and bone strength.

METHOD

Thirty age-matched SLE patients on long-term glucocorticoids (GC) (SLE/GC), 30 SLE patients without GC (SLE/non-GC) and 60 healthy controls were examined. Areal BMD (aBMD) was measured by dual-energy X-ray absorptiometry. Bone geometry, volumetric BMD (vBMD), and architectural parameters at the nondominant distal radius were assessed by high-resolution peripheral quantitative computed tomography (HR-pQCT). Bone strength was estimated by HR-pQCT-based micro-finite element analysis.

RESULTS

Adjusted for menopausal status and adjusted calcium level, when compared with controls, SLE/non-GC patients had significantly lower aBMD at femoral neck and total hip, and diminished radial total vBMD, cortical area, vBMD and thickness, respectively, by 8.3%, 8%, 2.7% and 9.2%, as well as significant compromised bone strength (stiffness, failure load and apparent modulus) by 8.3%, 9.1% and 9.5%, respectively. Similar alterations were also found in SLE/GC patients when compared to controls. In the premenopausal subgroup analysis, when compared with controls, total hip aBMD and radial cortical area were significantly lower in SLE/non-GC patients, and cortical area and thickness were significantly deficit in SLE/GC patients. However, no significant difference in any bone variables was present between SLE/GC and SLE/non-GC patients in the entire cohort or in the premenopausal subgroup.

CONCLUSION

SLE disease per se contributes to the deterioration in bone density, cortical microstructure and bone strength. This might help to explain the considerably higher fracture risk seen in SLE patients.

Alterations of bone geometry, density, microarchitecture, and biomechanical properties in systemic lupus erythematosus on long-term glucocorticoid: a case-control study using HR-pQCT

Compared to controls, HR-pQCT at distal radius of SLE patients on chronic glucocorticoid (SLE/GC) revealed reduced bone area, vBMD, deteriorated microarchitecture, and unevenly distributed stresses limited to cortical bone. Despite similar trabecular quality, whole bone strength decreased in patients. These alterations may partly explain high fracture rates in SLE/GC.

INTRODUCTION

To assess bone geometric, densitometric, microarchitectural, and biomechanical properties in patients with systemic lupus erythematosus (SLE) on long-term glucocorticoid (GC) (SLE/GC) as compared with healthy controls.

METHODS

A total of 180 female SLE patients and 180 healthy controls were in this cross-sectional study to assess areal bone mineral density (aBMD) by dual-energy X-ray absorptiometry. High-resolution peripheral quantitative computed tomography (HR-pQCT) and microfinite element analysis (μFEA) was performed at distal radius.

RESULTS

In addition to significantly lower aBMD at femoral neck, total hip and lumbar spine, cortical area, average volumetric BMD (vBMD) and cortical vBMD also significantly reduced by 5.3, 5.7, to 1.9 % in SLE patients, respectively. Deteriorations of cortical microarchitecture were pronounced in patients, with 6.3 % reduction in cortical thickness and 13.6 % higher in cortical porosity. Local stresses were more unevenly distributed through cortical bone in patients. SLE/GC patients had decreased whole bone stiffness, estimated failure load, and apparent modulus. Parameters related to trabecular bone density and microarchitecture were comparable between patients and controls.

CONCLUSION

In SLE/GC patients, despite a reduction in bone area, vBMD and deteriorated microarchitecture and unevenly distributed stresses limited to the cortical compartment, whole bone strength decreased. HR-pQCT and μFEA were promising in elucidating the potential underlying pathophysiology of bone loss and propensity to fracture in SLE/GC and provide us additional information about alterations of bone quality which might better predict fracture risk beyond aBMD in SLE/GC.

Prevalence and risk factors of radiographic vertebral fractures in elderly Chinese men and women: results of Mr. OS (Hong Kong) and Ms. OS (Hong Kong) studies

This study investigated the prevalence of radiographic vertebral fractures using Genant's semiquantitative (SQ) scoring system in elderly Chinese men (n = 2,000; mean age, 72.4 years) and women (n = 2,000; mean age, 72.6 years). Vertebral deformities had similar prevalence in elderly men (14.9 %) and women (16.5 %). Majority of the deformities in men were mild (9.9 %, grade = 1). The prevalence of vertebral fractures (grade ≥ 2) was 5.0 % among men and 12.1 % among women.

INTRODUCTION

Vertebral fracture is a serious consequence of osteoporosis and is often under-diagnosed. Researches on different ethnicities and territories to estimate the prevalence of vertebral fractures and to identify the risk factors are necessary.

METHODS

Mr. OS (Hong Kong) and Ms. OS (Hong Kong) represent the first large-scale cohort studies ever conducted on bone health in elderly Chinese men (n = 2,000) and women (n = 2,000). The current study investigated the prevalence of radiographic vertebral fractures in these subjects using Genant's SQ scoring system and identified risk factors for vertebral fractures.

RESULTS

The radiographs of all men (mean age, 72.4 years) and women (mean age, 72.6 years) were obtained. Six hundred twenty-seven subjects (15.7 %) had at least one vertebral deformity (SQ grade ≥ 1), including 297 men (14.9 %) and 330 women (16.5 %, p = 0.151). Three hundred forty-two participants (8.6 %) were defined as having at least one vertebra fracture (SQ grade ≥ 2), consisted of 100 men (5.0 %) and 242 women (12.1 %, p < 0.001). Older age, lower bone mineral density, lower physical activity, lower grip strength, fracture history, and low back pain were significantly associated with higher vertebral fracture rate for both men and women.

CONCLUSION

Vertebral deformity had similar prevalence in older men and women, while vertebral fracture was more common in women. Majority of deformities in men was mild. The vertebral deformity prevalence of women from this study is similar to previous reports of other East Asian women and Latin American women.

Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods

Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an option for recreational water quality testing in the United States (USEPA, 2011. EPA-OW-2011-0466, FRL-9609-3, Notice of Availability of Draft Recreational Water Quality Criteria and Request for Scientific Views). However, transition of qPCR from a research tool to routine water quality testing requires information on how various method variations affect target enumeration. Here we compared qPCR performance and enumeration of enterococci in spiked and environmental water samples using three qPCR platforms (Applied Biosystem StepOnePlus™, the BioRad iQ™5 and the Cepheid SmartCycler(®) II), two reference materials (lyophilized cells and frozen cells on filters) and two comparative CT quantification models (ΔCT and ΔΔCT). Reference materials exerted the biggest influence, consistently affecting results by approximately 0.5 log(10) unit. Platform had the smallest effect, generally exerting <0.1 log(10) unit difference in final results. Quantification model led to small differences (0.04-0.2 log(10) unit) in this study with relatively uninhibited samples, but has the potential to cause as much as 8-fold (0.9 log(10) unit) difference in potentially inhibitory samples. Our findings indicate the need for a certified and centralized source of reference materials and additional studies to assess applicability of the quantification models in analyses of PCR inhibitory samples.

A multi-beach study of Staphylococcus aureus, MRSA, and enterococci in seawater and beach sand

Incidences of Staphylococcus aureus and methicillin resistant S. aureus (MRSA) have risen worldwide prompting a need to better understand routes of human exposure and whether standard bacterial water quality monitoring practices adequately account for this potential threat. Beach water and sand samples were analyzed during summer months for S. aureus, enterococci, and MRSA at three southern California beaches (Avalon, Doheny, Malibu Surfrider). S. aureus frequently was detected in samples of seawater (59%, n = 328) and beach sand (53%, n = 358). MRSA sometimes was detected in seawater (1.6%, n = 366) and sand (2.7%, n = 366) at relatively low concentrations. Site specific differences were observed, with Avalon Beach presenting the highest concentrations of S. aureus and Malibu Surfrider the lowest in both seawater and sand. S. aureus concentrations in seawater and sand were correlated to each other and to a variety of other parameters. Multiple linear regression on the combined beach data indicated that significant explanatory variables for S. aureus in seawater were S. aureus in sand, water temperature, enterococci in seawater, and the number of swimmers. In sand, S. aureus concentrations were related to S. aureus in seawater, water temperature, enterococci in seawater, and inversely to surf height classification. Only the correlation to water temperature held for individually analyzed beaches and for S. aureus concentrations in both seawater and sand. To provide context for these results, the prevalence of S. aureus in sand was compared to published fomite studies, and results suggested that beach prevalence was similar to that in homes.

Vertebral body corner oedema vs gadolinium enhancement as biomarkers of active spinal inflammation in ankylosing spondylitis

OBJECTIVE

To investigate the relative performance of T(2) weighted short tau inversion-recovery (STIR) and fat-suppressed T(1) weighted gadolinium contrast-enhanced sequences in depicting active inflammatory lesions in ankylosing spondylitis (AS).

METHODS

Whole-spine MRI was performed on 32 patients with AS, who participated in a clinical trial of infliximab treatment, by STIR and contrast-enhanced sequences at baseline and after 30 weeks. The AS spine MRI-activity (ASspiMRI-a) scoring method was used. The images from these two imaging techniques were evaluated separately by two independent readers.

RESULTS

For the pre-treatment lesion status, the intraclass correlation coefficients comparing STIR readings and contrast-enhanced readings were 0.69±0.23 for Reader 1 and 0.65±0.21 for Reader 2. At baseline, the mean ASspiMRI-a score was 15.4% and 17.7% higher for contrast-enhanced images than for STIR images for Reader 1 and Reader 2, respectively. After infliximab treatment, Reader 1 rated an ASspiMRI-a score reduction of 50.8±33.6% and 25.3±35.3% for STIR images and contrast-enhanced images, respectively, whereas Reader 2 rated an ASspiMRI-a score reduction of 42.4±50.4% and 32.9±35.6% for STIR images and contrast-enhanced images, respectively.

CONCLUSION

While both contrast-enhanced and STIR sequences showed sensitivity to change over a short period of time after infliximab treatment, these two sequences may reflect different disease mechanisms.

Effectiveness of qPCR permutations, internal controls and dilution as means for minimizing the impact of inhibition while measuring Enterococcus in environmental waters

AIMS

  Draft criteria for the optional use of qPCR for recreational water quality monitoring have been published in the United States. One concern is that inhibition of the qPCR assay can lead to false-negative results and potentially inadequate public health protection. We evaluate the effectiveness of strategies for minimizing the impact of inhibition.

METHODS AND RESULTS

  Five qPCR method permutations for measuring Enterococcus were challenged with 133 potentially inhibitory fresh and marine water samples. Serial dilutions were conducted to assess Enterococcus target assay inhibition, to which inhibition identified using four internal controls (IC) was compared. The frequency and magnitude of inhibition varied considerably among qPCR methods, with the permutation using an environmental master mix performing substantially better. Fivefold dilution was also effective at reducing inhibition in most samples (>78%). ICs were variable and somewhat ineffective, with 54-85% agreement between ICs and serial dilution.

CONCLUSIONS

  The current IC methods appear to not accurately predict Enterococcus inhibition and should be used with caution; fivefold dilution and the use of reagents designed for environmental sample analysis (i.e. more robust qPCR chemistry) may be preferable.

SIGNIFICANCE AND IMPACT OF THE STUDY

  Suitable approaches for defining, detecting and reducing inhibition will improve implementation of qPCR for water monitoring.

Using rapid indicators for Enterococcus to assess the risk of illness after exposure to urban runoff contaminated marine water

BACKGROUND

Traditional fecal indicator bacteria (FIB) measurement is too slow (>18 h) for timely swimmer warnings.

OBJECTIVES

Assess relationship of rapid indicator methods (qPCR) to illness at a marine beach impacted by urban runoff.

METHODS

We measured baseline and two-week health in 9525 individuals visiting Doheny Beach 2007-08. Illness rates were compared (swimmers vs. non-swimmers). FIB measured by traditional (Enterococcus spp. by EPA Method 1600 or Enterolert™, fecal coliforms, total coliforms) and three rapid qPCR assays for Enterococcus spp. (Taqman, Scorpion-1, Scorpion-2) were compared to health. Primary bacterial source was a creek flowing untreated into ocean; the creek did not reach the ocean when a sand berm formed. This provided a natural experiment for examining FIB-health relationships under varying conditions.

RESULTS

We observed significant increases in diarrhea (OR 1.90, 95% CI 1.29-2.80 for swallowing water) and other outcomes in swimmers compared to non-swimmers. Exposure (body immersion, head immersion, swallowed water) was associated with increasing risk of gastrointestinal illness (GI). Daily GI incidence patterns were different: swimmers (2-day peak) and non-swimmers (no peak). With berm-open, we observed associations between GI and traditional and rapid methods for Enterococcus; fewer associations occurred when berm status was not considered.

CONCLUSIONS

We found increased risk of GI at this urban runoff beach. When FIB source flowed freely (berm-open), several traditional and rapid indicators were related to illness. When FIB source was weak (berm-closed) fewer illness associations were seen. These different relationships under different conditions at a single beach demonstrate the difficulties using these indicators to predict health risk.

Application of phylogenetic microarray analysis to discriminate sources of fecal pollution

Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suite of bacteria that define major sources of fecal contamination in coastal California. Fecal wastes were collected from 42 different populations of humans, birds, cows, horses, elk, and pinnipeds. We characterized bacterial community composition using a DNA microarray that probes for 16S rRNA genes of 59,316 different bacterial taxa. Cluster analysis revealed strong differences in community composition among fecal wastes from human, birds, pinnipeds, and grazers. Actinobacteria, Bacilli, and many Gammaproteobacteria taxa discriminated birds from mammalian sources. Diverse families within the Clostridia and Bacteroidetes taxa discriminated human wastes, grazers, and pinnipeds from each other. We found 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These OTUs can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.

Compromised perfusion in femoral head in normal rats: distinctive perfusion MRI evidence of contrast washout delay

OBJECTIVES

The femoral head is prone to osteonecrosis. This study investigated dynamic contrast-enhanced (DCE) MRI contrast washout features of the femoral head and compared the data with data from other bony compartments in normal rats.

METHODS

7-month-old Wistar rats were used. DCE MRI of the right hip (n=18), right knee (n=12) and lumbar spine (n=10) was performed after an intravenous bolus injection of Gd-DOTA (0.3 mmol kg(-1)). Temporal resolution was 0.6 s for hip and spine, and 0.3 s for knee. The total scan duration was 8 min for hip and spine, and 4.5 min for knee. The regions of interest for enhancement measurement included femoral head, proximal femoral diaphysis, distal femoral diaphysis and epiphysis, proximal tibial epiphysis and diaphysis, and lumbar vertebrae L1-5.

RESULTS

Femoral head showed no enhancement signal decay during the DCE MRI period, while all other bony compartments showed a contrast washin phase followed by a contrast washout phase. In the knee joint, the contrast washout of the proximal tibia diaphysis was slower that of other bony compartments of the knee.

CONCLUSION

Based on the evidence of delayed contrast washout, this study showed that blood perfusion in the femoral head could be compromised in normal rats.

TENOSYNOVIAL OSTEOCHONDROMATOSIS OF BOTH FLEXOR AND EXTENSOR TENDONS

An unusual case of a 52-year-old woman with tenosynovial osteochondromatosis involving both of the wrist flexor and extensor tendons is reported.

ULTRASOUND FOR THE DETECTION OF VEGETATIVE FOREIGN BODY IN HAND — A CASE REPORT

Foreign bodies in soft tissues are commonly encountered in daily orthopaedic practice. While most of the metals and glass foreign bodies can be detected by plain radiograph, organic substances such as wood and vegetative materials are radiolucent. Unfortunately, these radiolucent foreign bodies are usually more prone to cause an inflammatory reaction and infection. The detection can be even more difficult in cases of multiple foreign bodies and in penetrating injuries with small innocuous skin wounds. Ultrasonography is a sensitive and reliable investigation for detection of foreign bodies in soft tissue. We present a case of penetration injury to thumb with residual radiolucent foreign bodies and demonstrate the proper role of ultrasonography in the management of foreign bodies in soft tissues.

A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution

AIMS

To develop a quantitative, real-time PCR assay to detect the nifH gene of Methanobrevibacter smithii. Methanobrevibacter smithii is a methanogenic archaea found in the intestinal tract of humans that may be a useful indicator of sewage pollution in water.

METHODS AND RESULTS

Quantification standards were prepared from Meth. smithii genomic DNA dilutions, and a standard curve was used to quantify the target gene and calculate estimated genome equivalency units. A competitive internal positive control was designed and incorporated into the assay to assess inhibition in environmental extracts. Testing the assay against a panel of 23 closely related methanogen species demonstrated specificity of the assay for Meth. smithii. A set of 36 blind water samples was then used as a field test of the assay. The internal control identified varying levels of inhibition in 29 of 36 (81%) samples, and the Meth. smithii target was detected in all water samples with known sewage input.

CONCLUSIONS

The quantitative PCR assay developed in this study is a sensitive and rapid method for the detection of the Meth. smithii nifH gene that includes an internal control to assess inhibition. Further research is required both to better evaluate host specificity of this assay and the correlation with human health risks.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research is the first description of the development of a rapid and sensitive quantitative assay for a methanogenic archaeal indicator of sewage pollution.

Relationship between gender, bone mineral density, and disc degeneration in the lumbar spine: a study in elderly subjects using an eight-level MRI-based disc degeneration grading system

The study cohort comprised 196 females and 163 males. Lumbar spine bone mineral density (BMD) and magnetic resonance imaging (MRI) were acquired. Females had more severe disc degeneration than males. Lumbar spine lower BMD was associated with less severe disc degeneration. Lumbar disc spaces were more likely to be narrower when vertebral BMD was higher.

INTRODUCTION

The purpose of this paper is to study the relationship between gender, BMD, and disc degeneration in the lumbar spine.

METHODS

The study cohort comprised 196 females and 163 males (age range 67-89 years) with no age difference between the two groups. Lumbar spine BMD was measured with dual X-ray densitometry, and MRI was acquired at 1.5 T. A subgroup of 48 males had additional lumbar vertebral quantitative computerized tomography densitometry. Lumbar disc degeneration was assessed using a MRI-based eight-level grading system.

RESULTS

Female subjects had more severe disc degeneration than male subjects. After removing age effect, a positive trend was observed between T-score and severity of lumbar disc degeneration. This was significant in female subjects while not significant in male subjects. Lumbar disc spaces were more likely to be narrowed when vertebral BMD was higher. These observations were more significant in the midlumbar region (L3/4 and L4/5) and less so at the thoracolumbar junction.

CONCLUSION

Female subjects tended to have slightly more severe lumbar disc degeneration than male subjects. Lower lumbar spine BMD was associated with less severe disc degeneration.

Large scale analysis of virulence genes in Escherichia coli strains isolated from Avalon Bay, CA

Contamination of recreational waters with Escherichia coli and Enterococcus sp. is a widespread problem resulting in beach closures and loss of recreational activity. While E. coli is frequently used as an indicator of fecal contamination, and has been extensively measured in waterways, few studies have examined the presence of potentially pathogenic E. coli strains in beach waters. In this study, a combination of high-throughput, robot-assisted colony hybridization and PCR-based analyses were used to determine the genomic composition and frequency of virulence genes present in E. coli isolated from beach water in Avalon Bay, Santa Catalina Island, CA. A total of 24,493 E. coli isolates were collected from two sites at a popular swimming beach between August through September 2007 and from July through August 2008. All isolates were examined for the presence of shiga-like toxins (stx1/stx2), intimin (eaeA), and enterotoxins (ST/LT). Of the 24,493 isolates examined, 3.6% contained the eaeA gene, indicating that these isolates were potential EPEC strains. On five dates, however, greater than 10% of the strains were potential EPEC, suggesting that incidence of virulence genes at this beach has a strong temporal component. No STEC or ETEC isolates were detected, and only eight (<1.0%) of the potential EPEC isolates were found to carry the EAF plasmid. The potential EPEC isolates mainly belonged to E. coli phylogenetic groups B1 or B2, and carried the β intimin subtype. DNA fingerprint analyses of the potential EPEC strains indicated that the isolates belonged to several genetically diverse groups, although clonal isolates were frequently detected. While the presence of virulence genes alone cannot be used to determine the pathogenicity of strains, results from this study show that potential EPEC strains can be found in marine beach water and their presence needs to be considered as one of the factors used in decisions concerning beach closures.

Use of an exogenous plasmid standard and quantitative PCR to monitor spatial and temporal distribution of Enterococcus spp. in beach sands

Studies using culture dependent methods have indicated that enterococci, the fecal indicator used to monitor marine waters for the potential of enteric disease risk to swimmers, can be abundant in beach sands and may contribute to water column indicator exceedances. A quantitative PCR (qPCR) method for the Enterococcus genus was tested and applied to more rapidly determine the amount of enterococci in beach sands and study their distribution over space and time. The qPCR method amplified a 23S rDNA sequence specific to Enterococcus (Ludwig and Schliefer, 2000), and was used to examine subsamples and composite samples of wet and dry beach sand from Avalon Bay, CA. The differences in efficiency of DNA recovery and inhibition in qPCR reactions were accounted for by spiking pairs of duplicate subsamples with a known amount of pGEM plasmid before or after extraction, respectively (Coyne et al. 2005). This study revealed levels of environmental inhibition that were similar in wet and dry sands, and efficiency of DNA recovery that was observably lower for wet beach sands and varied between years. Using the correction factors generated by this method to estimate the abundance of Enterococcus, we show that wet and dry beach sands both have Enterococcus spp. populations that can vary dramatically from day to day, and often are potentially higher than the equivalent health standards mandated for recreational waters.

Microbiological water quality at non-human influenced reference beaches in southern California during wet weather

Although urban wet weather discharges may have elevated concentrations of fecal indicator bacteria impacting water quality at swimming beaches, not all of these bacteria may arise from human sources. In this study, the contribution of non-human fecal indicator bacteria was quantified by sampling coastal reference beaches in southern California. Samples were collected at beaches near stormwater discharges from undeveloped watersheds and analyzed for total coliform, Escherichia coli, and enterococci. Surfzone samples exceeded water quality thresholds >10 times more frequently during wet weather than dry weather. Exceedences were greatest <24h following rainfall, then steadily declined on successive days. Early season storms exceeded thresholds more frequently, and by greater magnitude, compared to late season storms. Large storms exceeded thresholds more frequently than smaller-sized storms, partly due to the breaching of sand berms. When discharges did reach the surf zone, bacterial concentrations in the wave wash were correlated with watershed bacterial flux.

Covalently linked immunomagnetic separation/adenosine triphosphate technique (Cov-IMS/ATP) enables rapid, in-field detection and quantification of Escherichia coli and Enterococcus spp. in freshwater and marine environments

AIMS

Developing a rapid method for detection of faecal pollution is among the critical goals set forth by the Environmental Protection Agency in its revision of water quality criteria. The purpose of this study is to devise and test covalently linked antibody-bead complexes for faecal indicator bacteria (FIB), specifically Escherichia coli or Enterococcus spp., in measuring water quality in freshwater and marine systems.

METHODS AND RESULTS

Covalently linked complexes were 58-89% more robust than antibody-bead complexes used in previous studies. Freshwater and marine water samples analysed using covalently linked immunomagnetic separation/adenosine triphosphate quantification technique (Cov-IMS/ATP) and culture-based methods yielded good correlations for E. coli (R = 0·87) and Enterococcus spp. (R = 0·94), with method detection limits below EPA recreational water quality health standards for single standard exceedances (E. coli- 38 cells per 100 ml; Enterococcus spp. - 25 cells per 100 ml). Cov-IMS/ATP correctly classified 87% of E. coli and 94% of Enterococcus spp. samples based on these water quality standards. Cov-IMS/ATP was also used as a field method to rapidly distinguish differential loading of E. coli between two stream channels to their confluence.

CONCLUSIONS

Cov-IMS/ATP is a robust, in-field detection method for determining water quality of both fresh and marine water systems as well as differential loading of FIB from two converging channels.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first work to present a viable rapid, in-field assay for measuring FIB concentrations in marine water environments. Cov-IMS/ATP is a potential alternative detection method, particularly in areas with limited laboratory support and resources, because of its increased economy and portability.

Evaluation of rapid methods and novel indicators for assessing microbiological beach water quality

A broad suite of new measurement methods and indicators based on molecular measurement technology have been developed to assess beach water quality, but they have generally been subjected to limited testing outside of the laboratory in which they were developed. Here we evaluated 29 assays targeting a variety of bacterial, viral, and chemical analytes by providing the method developers with twelve blind samples consisting of samples spiked with known concentration of sewage or gull guano and negative controls. Each method was evaluated with respect to its ability to detect the target organism, absence of signal in the negative controls and repeatability among replicates. Only six of the 30 methods detected their targets in at least 75% of the samples while consistently determining the absence of the target in the negative controls. Among quantitative methods, QPCR for Bacteroides thetaiotamicron and Enterococcus detected by Luminex reliably identified all but one sample containing human fecal material and produced no false positive results. Among non-quantitative methods, the Enterococcus esp gene, the Bacteroidales human specific marker and culture-based coliphage were the most reliable for identifying human fecal material. We also found that investigator-specific variations of methods targeting the same organism often produced different results.

Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters

Concentrations of fecal indicator bacteria (FIB; e.g. Escherichia coli, and Enterococcus sp.) can only be used in limited ways for determining the source of fecal contamination in recreational waters because they cannot distinguish human from non-human fecal contamination. Several Bacteroides spp. have been suggested as potential alternative indicators. We have developed a rapid, culture-independent method for quantifying fecal Bacteroides spp. using quantitative PCR (QPCR) targeting the 16S rRNA gene. The assay specifically targets and quantifies the most common human Bacteroides spp. The details of the method are presented, including analyses of a wide range of fecal samples from different organisms. Specificity and performance of the QPCR assay were also tested via a laboratory experiment where human sewage and gull guano were inoculated into a range of environmental water samples. Concentrations of fecal Bacteroides spp., total Enterococcus sp., Enterococcus faecium, Enterococcus faecalis, and Enterococcus casseliflavus were measured using QPCR, and total Enterococcus sp. and E. coli were quantified by membrane filtration (MF). Samples spiked with gull guano were highly concentrated with total Enterococcus sp., E. coli, E. faecalis, and E. casseliflavus, demonstrating that these indicators are prominent in animal feces. On the other hand, fecal Bacteroides spp. concentrations were high in samples containing sewage and were relatively low in samples spiked with gull guano. Sensitivity and specificity results suggest that the rapid fecal Bacteroides spp. QPCR assay may be a useful tool to effectively predict the presence and concentration of human-specific fecal pollution.

Evaluation of optical brightener photodecay characteristics for detection of human fecal contamination

Detection of optical brighteners by fluorometry combined with ultraviolet light (UV) exposure has been proposed as an inexpensive method for detection of human fecal contamination, but has received limited testing. This study evaluated the approach in southern California by applying it to a variety of detergents, sewage and septage samples from the region, as well as to natural stream water as a negative control. The concept of using UV exposure to differentiate fluorescence from natural organic matter proved valid, as the method produced no false positives. However, the method failed to detect half of the detergents tested in natural stream water at 5 microL/L, due to its conservative thresholds. This study identified a method modification that provides greater sensitivity by taking advantage of differences in the shape of photodecay curves between optical brighteners and natural organic matter. This method modification resulted in detection of all detergents, sewage at 1:10 dilution and septage at 1:100 dilution. Several caveats for its use remain, including our observation that the optical brightener signal degraded rapidly in strong sunlight. Additionally, there was low sensitivity for some environmentally friendly detergents, which does not present a problem on a community basis where a mix of detergents are used, but could be of concern for assessing septic inputs from individual homes. Still, the method is simple to employ in the field, yields rapid results and is useful as a low-cost initial screening tool.

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources

AIM

Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills.

METHODS AND RESULTS

Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0.23 and -1.02 per day, and for enterococci between -0.5 and -1.0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall.

CONCLUSIONS

Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels.

SIGNIFICANCE AND IMPACT OF THE STUDY

Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent.