Search

Current microbial source tracking techniques that rely on grab samples analyzed by individual endpoint assays are inadequate to explain microbial sources across space and time. Modeling and predicting host sources of microbial contamination could add a useful tool for watershed management. In this study, we tested and evaluated machine learning models to predict the major sources of microbial contamination in a watershed. We examined the relationship between microbial sources, land cover, weather, and hydrologic variables in a watershed in Northern California, United States. Six models, including K-nearest neighbors (KNN), Naïve Bayes, Support vector machine (SVM), simple neural network (NN), Random Forest, and XGBoost, were built to predict major microbial sources using land cover, weather and hydrologic variables. The results showed that these models successfully predicted microbial sources classified into two categories (human and non-human), with the average accuracy ranging from 69% (Naïve Bayes) to 88% (XGBoost). The area under curve (AUC) of the receiver operating characteristic (ROC) illustrated XGBoost had the best performance (average AUC = 0.88), followed by Random Forest (average AUC = 0.84), and KNN (average AUC = 0.74). The importance index obtained from Random Forest indicated that precipitation and temperature were the two most important factors to predict the dominant microbial source. These results suggest that machine learning models, particularly XGBoost, can predict the dominant sources of microbial contamination based on the relationship of microbial contaminants with daily weather and land cover, providing a powerful tool to understand microbial sources in water. [ABSTRACT FROM AUTHOR]

Some birds are viewed as pests and vectors of foodborne pathogens in farmlands, yet birds also benefit growers by consuming pests. While many growers seek to prevent birds from accessing their farms, few studies have attempted to quantify the net effects of bird services and disservices, let alone how net effects shift across farm management strategies. We quantified the net effect of birds on crop production across 20 California strawberry (Fragaria × ananassa) farms that varied in local management practices and landscape context. We surveyed farms for berry damage and bird droppings (as potential sources of pathogens) and implemented a large‐scale exclusion experiment to quantify the impact of birds on production. We found that birds had only a slightly negative overall impact on strawberry production, reducing economic value by 3.6%. Direct bird damage and intraguild predation contributed equally to this net effect, underscoring the importance of indirect trophic interactions that may be less apparent to growers. In simple landscapes (e.g., low proportions of surrounding seminatural habitat), birds provided pest control in the interiors of farm fields, and costs from bird damage to crops peaked at field edges. In complex landscapes (e.g., high proportions of seminatural habitat), birds were more likely to disrupt pest control by feeding as intraguild predators. Nonetheless, seminatural habitat dampened bird services and disservices, and our models predicted that removing habitat around farm fields would increase costs from bird damage to crops by up to 76%. Fecal contamination of crops was extremely rare (0.01%). However, both fecal contamination and bird damage did increase on farms with higher densities of fencing and wires, where birds often perch. Our results demonstrate that maintaining seminatural habitat around farms may enhance bird diversity and mitigate bird damage without increasing food safety risks. We also show that the net effects of birds depend on farming context and vary in complex ways in relation to locations within a farm, local farm attributes, and the surrounding landscape. This context‐specific variation must be considered in order to optimize the management of wild birds in agroecosystems. [ABSTRACT FROM AUTHOR]

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (-4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments. [ABSTRACT FROM AUTHOR]

Field trials were conducted in July-August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 x 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (~5-log reduction) to >3.45 x 1012 MPN/head (~5-log growth). Relative to C0, on day 10 (Ct=12 ) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7. [ABSTRACT FROM AUTHOR]

Due to increased concerns regarding fecal pollution at marine recreational beaches, daily relative dog abundance and fecal density were estimated on an intensively managed (Beach 1) and a minimally managed (Beach 2) dog beach in Monterey County, California. Fecal loading and factors predictive of fecal deposition also were assessed. After standardizing for beach area, daily beach use and fecal densities did not differ between beaches and yearly fecal loading estimates revealed that unrecovered dog feces likely contributes significantly to fecal contamination (1.4 and 0.2 metric tonnes/beach). Detection of feces was significantly associated with beach management type, transect position relative to mean low tideline, presence of beach wrack, distance to the nearest beach entrance, and season. Methodologies outlined in this study can augment monitoring programs at coastal beaches to optimize management, assess visitor compliance, and improve coastal water quality. [ABSTRACT FROM AUTHOR]

• Beach water samples were assayed for male-specific and somatic coliphage using the new EPA Method 1642. • The relationships observed between enterococci and coliphage were site-dependent and correlated at 7 out of 11 beach sites. • Fewer public health warnings would have been issued using coliphage compared to Enterococcus. • Coliphage provides complementary site prioritization information to FIB at certain locations. Coliphage have been suggested as an alternative to fecal indicator bacteria for assessing recreational beach water quality, but it is unclear how frequently and at what types of beaches coliphage produces a different management outcome. Here we conducted side-by-side sampling of male-specific and somatic coliphage by the new EPA dead-end hollow fiber ultrafiltration (D-HFUF-SAL) method and Enterococcus at southern California beaches over two years. When samples were combined for all beach sites, somatic and male-specific coliphage both correlated with Enterococcus. When examined categorically, Enterococcus would have resulted in approximately two times the number of health advisories as somatic coliphage and four times that of male-specific coliphage,using recently proposed thresholds of 60 PFU/100 mL for somatic and 30 PFU/100 mL for male-specific coliphage. Overall, only 12% of total exceedances would have been for coliphage alone. Somatic coliphage exceedances that occurred in the absence of an Enterococcus exceedance were limited to a single site during south swell events, when this beach is known to be affected by nearby minimally treated sewage. Thus, somatic coliphage provided additional valuable health protection information, but may be more appropriate as a supplement to FIB measurements rather than as replacement because: (a) EPA-approved PCR methods for Enterococcus allow a more rapid response, (b) coliphage is more challenging owing to its greater sampling volume and laboratory time requirements, and (c) Enterococcus ' long data history has yielded predictive management models that would need to be recreated for coliphage. [ABSTRACT FROM AUTHOR]

Objective: Variations in processes for different clinics and health systems can dramatically change the way preventive interventions are implemented. We present a method for documenting these variations using workflow diagrams and demonstrate how understanding workflow aided an electronic health record (EHR) embedded colorectal cancer screening intervention. Materials and Methods: We mapped variation in processes for ordering and documenting fecal testing, current colonoscopy, prior colonoscopies, and pathology results. This work was part of a multi-site cluster-randomized pragmatic trial to test a mailed approach to offering fecal testing at 26 safety net clinics (in eight organizations) in Oregon and Northern California. We created clinic-specific workflow diagrams and then distilled them into consolidated diagrams that captured the variations. Results: Clinics had varied practices for storing and using information about colorectal cancer screening. Developing workflow diagrams of key processes enabled clinics to find optimal ways to send fecal test kits to patients due for screening. The workflows informed the rollout of new EHR tools and identified best practices for data capture. Discussion: Diagramming workflows can have great utility when implementing and refining EHR tools for clinical practice, especially when doing so across multiple clinical sites. The process of developing the workflows uncovered successful practice recommendations and revealed limitations and potential effects of a research intervention. Conclusion: Our method of documenting clinical process variation might inform other EHR-powered, multi-site research and can improve data feedback from EHR systems to clinical caregivers. [ABSTRACT FROM AUTHOR]

• Fecal and wastewater bacterial communities were at low proportions in surf zones. • Recycled water bacterial communities were absent in surf zone waters. • HF183 copies in surf zones were mainly from human feces and treated WWTP effluent. • Bather shedding contributed low levels of human fecal contamination in surf zones. • Sequencing based fecal source proportions appeared uncorrelated to qPCR results. Fecal sources to recreational surf zone waters should be identified to protect public health. While watershed origins of human and other fecal sources are often discoverable by quantitative polymerase chain reaction (qPCR) of fecal markers using spatially stratified samples, similarly assessing wastewater treatment plant (WWTP) outfall and other offshore contributions to surf zones is challenged by individual marker fate and transport. Here, bacterial communities were assessed for relatedness between all hypothesized fecal sources and surf zone waters for two urban California recreational beaches, by sequencing genes encoding 16S rRNA and analyzing data using SourceTracker and FEAST. Ambient marine bacterial communities dominated the surf zone, while fecal (human, dog, or gull) or wastewater (sewage or treated WWTP effluent) bacterial communities were present at low proportions and those from recycled water were absent. Based on the relative abundances of bacterial genera specifically associated with human feces, the abundances of HF183 in bacterial community sequences, and FEAST and SourceTracker results when benchmarked to HF183, the major sources of HF183 to surf zone waters were human feces and treated WWTP effluent. While surf zone sequence proportions from human sources (feces, sewage and treated WWTP effluent) appeared uncorrelated to previously obtained qPCR HF183 results, the proportions of human fecal and potential human pathogen sequences in surf zone waters were elevated when there were more swimmers (i.e. during weekday afternoons, holidays and busy weekends, and race events), thus confirming previously-published qPCR-based conclusions that bather shedding contributed low levels of human fecal contamination. Here, bacterial community sequencing also showed evidence that treated WWTP effluent from an offshore outfall was entering the surf zone, thereby resolving a prior uncertainty. Thus, bacterial community sequencing not only confirms qPCR HF183-based human marker detections, but further allows for confirming fecal sources for which individual marker quantification results can be equivocal. [Display omitted] [ABSTRACT FROM AUTHOR]

Traditional beach management that uses concentrations of cultivatable fecal indicator bacteria (FIB) may lead to delayed notification of unsafe swimming conditions. Predictive, nowcast models of beach water quality may help reduce beach management errors and enhance protection of public health. This study compares performances of five different types of statistical, data-driven predictive models: multiple linear regression model, binary logistic regression model, partial least-squares regression model, artificial neural network, and classification tree, in predicting advisories due to FIB contamination at 25 beaches along the California coastline. Classification tree and the binary logistic regression model with threshold tuning are consistently the best performing model types for California beaches. Beaches with good performing models usually have a rainfall/flow related dominating factor affecting beach water quality, while beaches having a deteriorating water quality trend or low FIB exceedance rates are less likely to have a good performing model. This study identifies circumstances when predictive models are the most effective, and suggests that using predictive models for public notification of unsafe swimming conditions may improve public health protection at California beaches relative to current practices. [ABSTRACT FROM AUTHOR]

Elevated levels of fecal indicator bacteria (FIB), including Escherichia coli and enterococd, trigger coastal beach advisories and signal public health risks. Solving FIB pollution in suburban coastal watersheds is challenging, as there are many potential sources. The Arroyo Burro watershed in Santa Barbara, CA is an example, with its popular, but chronically FIB-contaminated beach. To address, a microbial source tracking study was performed. Surface waters were sampled over 2 years, FIB were quantified, and DNA was analyzed for host-associated fecal markers. Surf zone FIB were only elevated when the coastal lagoon was discharging. Among the fecal sources into the lagoon, including upstream human sources and coastal birds, canines were the most important. Canine sources included input via upstream creek water, which decreased after creek-side residences were educated about proper pet waste disposal, and direct inputs to the lagoon and surf zone, where dog waste could have been tidally exchanged with the lagoon. Based on this study, canine waste can be an influential, yet controllable, fecal source to suburban coastal beaches. [ABSTRACT FROM AUTHOR]

Abstract: The State of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusion of cow-associated methods a logical choice. Because the performance of these methods has been shown to change based on geography and/or local animal feeding practices, laboratory comparisons are needed to determine which assays are best suited for implementation. We describe the performance characterization of two end-point PCR assays (CF128 and CF193) and five real-time quantitative PCR (qPCR) assays (Rum2Bac, BacR, BacCow, CowM2, and CowM3) reported to be associated with either ruminant or cattle feces. Each assay was tested against a blinded set of 38 reference challenge filters (19 duplicate samples) containing fecal pollution from 12 different sources suspected to impact water quality. The abundance of each host-associated genetic marker was measured for qPCR-based assays in both target and non-target animals and compared to quantities of total DNA mass, wet mass of fecal material, as well as Bacteroidales, and enterococci determined by 16S rRNA qPCR and culture-based approaches (enterococci only). Ruminant- and cow-associated genetic markers were detected in all filters containing a cattle fecal source. However, some assays cross-reacted with non-target pollution sources. A large amount of variability was evident across laboratories when protocols were not fixed suggesting that protocol standardization will be necessary for widespread implementation. Finally, performance metrics indicate that the cattle-associated CowM2 qPCR method combined with either the BacR or Rum2Bac ruminant-associated methods are most suitable for implementation. [Copyright &y& Elsevier]

Abstract: A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study. [Copyright &y& Elsevier]

Fecal coliform and Escherichia coli associated with suspended solids (SS) and water in five northern California estuaries were studied to document process influences and water quality monitoring biases affecting indicator bacteria concentrations. We collected and analyzed 2371 samples during 10 sampling events for the five studied estuaries. Concentrations during wet‐season stormflow conditions were greater than during wet‐season base flow and dry‐season base flow conditions. Results also document concentration gradients across the length of the studied estuaries and with depth of sample collection. Highest concentrations were associated with shallow samples collected furthest inland. Corresponding decreases occurred the deeper and closer to the estuary mouth a sample was collected. Results also identify direct relationships of wind speed and discharge velocity and indirect relationship of tide stage to indicator bacteria concentrations. Bacteria associated with suspended solids (SS), after conversion to the same units of measurement (mass), were three orders of magnitude greater than in the water fraction. However, the mean proportion contributed by SS to composite water sample concentrations was 8% (SE 0.3) for fecal coliform and 7% (SE 0.3) for E. coli. Bacteria from the SS proportion is related to seasonality, tide stage, and discharge velocity that are consistent with mechanisms for entrainment, transport of SS, and reduced particle settling. These results are important for both managing and monitoring these systems by improving sample spatial and temporal context and corresponding bacteria concentration values across the freshwater–saltwater interface. [ABSTRACT FROM AUTHOR]

Several studies have examined how fecal indicator bacteria (FIB) measurements compare between quantitative PCR (qPCR) and the culture methods it is intended to replace. Here, we extend those studies by examining the stability of that relationship within a beach, as affected by time of day and seasonal variations in source. Enterococcus spp. were quantified at three southern California beaches in the morning and afternoon using two qPCR assays, membrane filtration, and defined-substrate testing. While qPCR and culture-based measurements were consistently and significantly correlated, strength of the correlation varied both among and within beaches. Correlations were higher in the morning (0.45 < p < 0.74 [P < 0.002]) than in the afternoon (0.18 < p < 0.45 [P < 0.021]) and higher when the fecal contamination was concentrated (0.38 < p < 0.83 [P < 0.001]) than when it was diffuse (0.19

Escherichia coli are widely used as indicators of fecal contamination, and in some cases to identify host sources of fecal contamination in surface water. Prevalence, genetic diversity and antimicrobial susceptibility were determined for 600 generic E. coli isolates obtained from surface water and sediment from creeks and channels along the middle Santa Ana River (MSAR) watershed of southern California, USA, after a 12 month study. Evaluation of E. coli populations along the creeks and channels showed that E. coli were more prevalent in sediment compared to surface water. E. coli populations were not significantly different (P = 0.05) between urban runoff sources and agricultural sources, however, E. coli genotypes determined by pulsed-field gel electrophoresis (PFGE) were less diverse in the agricultural sources than in urban runoff sources. PFGE also showed that E. coli populations in surface water were more diverse than in the sediment, suggesting isolates in sediment may be dominated by clonal populations.Twenty four percent (144 isolates) of the 600 isolates exhibited resistance to more than one antimicrobial agent. Most multiple resistances were associated with inputs from urban runoff and involved the antimicrobials rifampicin, tetracycline, and erythromycin. The occurrence of a greater number of E. coli with multiple antibiotic resistances from urban runoff sources than agricultural sources in this watershed provides useful evidence in planning strategies for water quality management and public health protection. [ABSTRACT FROM AUTHOR]

Abstract: 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. [ABSTRACT FROM AUTHOR]

In this paper we present a quantitative sanitary survey of the Middle Santa Ana River, in southern California, utilizing a variety of source tracking tools, including traditional culture-dependent fecal markers (Enterococcus and Escherichia coli by IDEXX), speciation of enterococci isolates, culture-independent fecal markers (human-specific HF183 Bacteroides and Enterococcus by quantitative polymerase chain reaction, qPCR), and chemical markers of sewage and wastewater (nutrients, enantiomeric fraction (EF) of propranolol and ethylenediaminetetraacetic acid). To facilitate comparison of these different methods, data are interpreted in a loading (i.e., mass per time) framework that enables a quantitative apportionment of fecal markers and nutrients to specific source waters in the Middle Santa Ana River. Multiple lines of evidence support the hypothesis that Enterococcus in the Middle Santa Ana River originates primarily from in situ growth in streambed sediments, not from significant and persistent sources of untreated human waste. The EF of propranolol of tertiary treated wastewater effluent is in the range (0.42 to 0.71) previously reported for raw sewage, making EF of propranolol an unsuitable marker for fecal pollution, at least at this site. The human fecal marker HF183 Bacteroides was detected at a few sites, although not in a source of disinfected and tertiary treated wastewater effluent Based on the results presented here and prior experience at other sites in southern California, HF183 Bacteroides would appear to be a candidate marker of fecal contamination for inland waters, although more qPCR measurements in disinfected wastewater effluent are needed to account for variations due to treatment plant performance and other factors. More generally, our results support the notion that regrowth of fecal indicator bacteria (FIB) in river sediments may lead to a decoupling between FIB and pathogen concentrations in the water column and thus limit the utility of FIB as an indicator of recreational waterborne illness in inland waters. [ABSTRACT FROM AUTHOR]

The value of Bacteroidales genetic markers and fecal indicator bacteria (FIB) to predict the occurrence of waterborne pathogens was evaluated in ambient waters along the central California coast. Bacteroidales host-specific quantitative PCR (qPCR) was used to quantify fecal bacteria in water and provide insights into contributing host fecal sources. Over 140 surface water samples from 10 major rivers and estuaries within the Monterey Bay region were tested over 14 months with four Bacteroidales-specific assays (universal, human, dog, and cow), three FIB (total coliforms, fecal coliforms, and enterococci), two protozoal pathogens (Cryptosporidium and Giardia spp.), and four bacterial pathogens (Campylobacter spp., Escherichia coli O157:H7, Salmonella spp., and Vibrio spp.). Indicator and pathogen distribution was widespread, and detection was not highly seasonal. Vibrio cholerae was detected most frequently, followed by Giardia, Cryptosporidium, Salmonella, and Campylobacter spp. Bayesian conditional probability analysis was used to characterize the Bacteroidales performance assays, and the ratios of concentrations determined using host-specific and universal assays were used to show that fecal contamination from human sources was more common than livestock or dog sources in coastal study sites. Correlations were seen between some, but not all, indicator-pathogen combinations. The ability to predict pathogen occurrence in relation to indicator threshold cutoff levels was evaluated using a weighted measure that showed the universal Bacteroidales genetic marker to have a comparable or higher mean predictive potential than standard FIB. This predictive ability, in addition to the Bacteroidales assays providing information on contributing host fecal sources, supports using Bacteroidales assays in water quality monitoring programs. [ABSTRACT FROM AUTHOR]

Near-infrared spectroscopy (NIRS) of fecal samples has been used to predict the crude protein and digestible organic matter of forages consumed by grazing animals. However, for NIRS predictions to be accurate, the equation used must be based on samples from the target population. The Texas A&M Grazinglands Animal Nutrition Laboratory has developed a NIRS program based on forages in Texas, the Midwest and Canada's lower prairie provinces. California producers have been using these equations even though they had never been evaluated for California conditions. We conducted beef-cattle digestibility trials on two California rangeland summer forages to produce forage-fecal pairs for testing the existing NIRS ones and developing new equations as necessary. The predictions from the original equations were significantly different from the true values determined in the digestibility trials. The addition of data from this research has improved the predictive capability for both crude protein and digestible organic matter in California. [ABSTRACT FROM AUTHOR]

The study used existing indicator bacterial data and a number of physicochemical parameters that can be measured instantaneously to determine if a decision tree approach, especially classification and regression tree, could be used to predict bacterial concentrations in timely manner for beach closure management. Each indicator bacteria showed different tree structures and each had its own significant variables; Dissolved oxygen played an important role for both total coliform and fecal coliform and turbidity was the most important factor to predict concentrations of enterococci for decision tree approaches. Root mean squared error stayed between 5 and 6.5% of the average values of observations; RMSEs from each simulation, 0.25 for total coliform, 0.31 for fecal coliform, and 0.29 for enterococci. Estimations from tree structures would be regarded as a good representation of the actual data. In addition to results of the objective function, RMSE, 77.5% of actual value fell into the 95% of confidence interval of estimations for total coliform concentrations, 60% for fecal coliform concentrations, and 62.5% for enterococci concentrations. The approach showed reliable estimations for the majority of the data processed, although the method did not portray low concentrations of bacteria as well. [ABSTRACT FROM AUTHOR]

Fecal indicator bacteria (FIB) have long been used as a marker of fecal pollution in surface waters subject to point source and non-point source discharges of treated or untreated human waste. In this paper, we set out to determine the source(s) of elevated FIB concentrations in Cucamonga Creek, a concrete-lined urban stream in southern California. Flow in the creek consists primarily of treated and disinfected wastewater effluent, mixed with relatively smaller but variable flow of runoff from the surrounding urban landscape. Dry and wet weather runoff contributes nearly 100% of FIB loading to Cucamonga Creek, while treated wastewater contributes significant loading of nutrients, including dissolved organic carbon (DOC), phosphorus, nitrate, and ammonium. FIB concentrations are strongly positively correlated with DOC concentration in runoff (Spearman's ρ ≥ 0.66, P ≤ 0.037), and microcosm studies reveal that the survival of Escherichia coli and enterococci bacteria in runoff is strongly dependent on the concentration of both DOC and phosphorus. Below threshold concentrations of 7 and 0.07 mg/L, respectively, FIB die off exponentially (die-off rate 0.09 h-1). Above these thresholds, FIB either grow exponentially (growth rate 0.3 h-1) or exhibit a periodic steady-state in which bacterial concentrations fluctuate around some mean value. The periodic steady-state pattern is consistent with a Lotka—Volterra predator—prey oscillation model, and the clearance rate (20 μL predator-1 h-1) obtained by fitting the model to our data is consistent with the hypothesis that predacious protozoa regulate FIB concentrations in runoff at high DOC concentrations. Collectively, these results indicate that FIB impairment of Cucamonga Creek is best viewed as an ecological phenomenon characterized by both bottom-up and top-down control. [ABSTRACT FROM AUTHOR]

Fecal contamination of coastal waters has led local public health agencies to issue tens of thousands of beach advisories annually and to advise against ocean swimming and surfing for 72 hours following a rain. The responsiveness of recreationists to beach advisories and the "72 hour rule" is estimated by merging four years of multi-daily surfer and beachgoer counts at one beach in Southern California with hourly data on beach advisories, recent precipitation, meteorological conditions, and the UCSB academic calendar. Both surfing and beach-going decreased significantly following rainfall in response to the 72 hour rule, showing that recreationists are willing to engage in health risk-reducing avoiding behavior. However, neither surfing nor beach-going decreased significantly during beach advisories. Surfers were significantly more responsive to beach advisories during dry periods than during wet periods, consistent with the hypothesis that recreationists are most likely to respond to a risk warning that they believe provides accurate and additional health risk information beyond what they can observe personally. Additional studies of beach advisories elsewhere could clarify whether responsiveness to beach advisories varies by recreationist demographic, recreational activity, frequency of advisories, or frequency of repeat visitation. Increasing the accuracy and additional information provided by beach advisories, as proposed by numerous authors, could lead to increased responsiveness. [ABSTRACT FROM AUTHOR]

Using a unique sterile design intended to eliminate outside seed contamination of horse feces, we investigated whether weed seeds germinate after digestion by horses. Feces were collected from selected National Parks and other locations in central and northern California. All potted fecal samples were irrigated and grown in an enclosed sterile nursery environment. Thirty-two plant species emerged from these fecal samples, 24 of which were not native to California. None of these were identified on the California Department of Agriculture's Noxious Weed List, which is used as a basis to certify equine feed as weed free. However, seven of the non-native species are identified as moderately invasive on the California Invasive Plant Council's (Cal-IPC) list. These species are: Hirschfeldia incana, Hordeum marinum, Lolium multiflorum, Mentha pulegium, Rumex acetosella, Trifolium hirtum, and Vulpia myuros. In addition, the following four non-native plants are listed at the limited invasiveness level on the Cal-IPC list: Hypochaeris glabra, Lythrum hyssopifolium, Medicago polymorpha, and Poa pratensis. Because we did not survey invasive plant cover in locations from which we sampled, we cannot guarantee that species identified in our samples would have also germinated in the field. Our results add to a growing body of literature documenting germination of seeds after passing through the digestive system of horses and suggest that conscientious horse owners should select feed sources that are free of weeds. We also find that the current list of noxious weeds used to certify weed-free feed for equines should be comprehensive. [ABSTRACT FROM AUTHOR]

We report the design and validation of new TaqMan® assays for microbial source tracking based on the amplification of fecal 16S rRNA marker sequences from uncultured cells of the order Bacteroidales. The assays were developed for the detection and enumeration of non-point source input of fecal pollution to watersheds. The quantitative “universal”Bacteroidales assay BacUni-UCD detected all tested stool samples from human volunteers (18 out of 18), cat (7 out of 7), dog (8 out of 8), seagull (10/10), cow (8/8), horse (8/8), and wastewater effluent (14/14). The human assay BacHum-UCD discriminated fully between human and cow stool samples but did not detect all stool samples from human volunteers (12/18). In addition, there was 12.5% detection of dog stool (1/8), but no cross-reactivity with cat, horse, or seagull fecal samples. In contrast, all wastewater samples were positive for the BacHum-UCD marker, supporting its designation as 100% sensitive for mixed-human source identification. The cow-specific assay BacCow-UCD fully discriminated between cow and human stool samples. There was 38% detection of horse stool (3/8), but no cross-specificity with any of the other animal stool samples tested. The dog assay BacCan-UCD discriminated fully between dog and cow stool or seagull guano samples and detected 62.5% stool samples from dogs (5/8). There was some cross-reactivity with 22.2% detection of human stool (4/18), 14.3% detection of cat stool (1/7), and 28.6% detection of wastewater samples (4/14). After validation using stool samples, single-blind tests were used to further demonstrate the efficacy of the developed markers; all assays were sensitive, reproducible, and accurate in the quantification of mixed fecal sources present in aqueous samples. Finally, the new assays were compared with previously published sequences, which showed the new methodologies to be more specific and sensitive. Using Bayes’ Theorem, we calculated the conditional probability that the four assays would correctly identify general and host-specific fecal pollution in a specific watershed in California for which 73 water samples had been analyzed. Such an approach allows for a direct comparison of the efficacy of different MST methods, including those based on library-dependent methodologies. For the universal marker BacUni-UCD, the probability that fecal pollution is present when the marker is detected was 1.00; the probability that host-specific pollution is present was 0.98, 0.84, and 0.89 for the human assay HF160F, the cow assay BacCow-UCD, and the dog assay BacCan-UCD, respectively. The application of these markers should provide meaningful information to assist with efforts to identify and control sources of fecal pollution to impaired watersheds. [Copyright &y& Elsevier]

The contribution of freshwater discharge to fecal indicator bacteria (FIB) impairment of an estuarine environment can be approximated from simple, two end-member mixing models using salinity as a tracer. We conducted a yearlong time series investigation of Newport Bay, a regionally important estuarine embayment in southern California, assessing the concentrations of FIB, specifically Escherichia coli and enterococci bacteria, and salinity. In total, eight within-bay stations and one offshore control site were sampled nearly once per week and the three tributaries draining into Newport Bay were sampled approximately daily. Using salinity as a conservative tracer for water mass mixing and determining the end-member values of FIB in both the creek sites and the offshore site, we created a linear, two end-member mixing model of FIB within Newport Bay. Deviations from the mixing model suggest either an additional source of FIB to the bay (e.g. bird feces, storm drain discharge) or regrowth and/or die-off of FIB within the bay. Our results indicate that salinity mixing models can be useful in predicting changes in FIB concentrations in the estuarine environments and can help narrow the search for sources of FIB to the bay and enhance our understanding of the fate of FIB within the bay. [Copyright &y& Elsevier]

Fecal coliform recurrence has been observed at the City of Los Angeles Hyperion Treatment Plant during pilot-scale experiments with a designated thermophilic battery of six anaerobic digesters, while other digesters were still at a mesophilic temperature. Several lab and full-scale experiments indicated the following possible causes of the growth/reactivation of fecal coliforms in post-digestion: a) contamination of thermophilically digested biosolids with mesophilically digested biosolids; b) a large drop in the biosolids temperature between the centrifuges and silos, which could have allowed the reactivation and/or growth of fecal coliforms. These were resolved by the full plant conversion to thermophilic anaerobic digestion and design modifications of the post-digestion train. [ABSTRACT FROM AUTHOR]

The United States (U.S.) Clean Water Act triggered over $1 trillion in investments in water pollution abatement. However, treated sewage discharge and untreated runoff water that are contaminated by fecal matter are discharged into California beach waters daily. Warnings are posted to thwart the public from contacting polluted coastal water, according to the California Code of Regulations (CCR). This paper evaluated the current policy by empirically examining the productivity loss, in the form of sick leave, which is caused by fecal-contaminated water along the California coast under the CCR. The findings of this study showed that Californians suffer productivity losses in the amount of 3.56 million sick leave days per year due to recreational beach water pollution. This paper also empirically examined the pollution-to-sickness graph that Cabelli's classic study theoretically proposed. The results of the research assure that the existing water quality thresholds are still reasonably safe and appropriate, despite the thresholds being based on studies from the 1950s. The weakness of the CCR lies in its poor enforcement or compliance. Better compliance, in terms of posting pollution advisories and increasing public awareness regarding beach pollution effects on health, would lead to a significant decrease in sick leaves and a corresponding increase in productivity. Therefore, this study advocates for stronger enforcement by displaying pollution advisories and better public awareness of beach pollution effects on health.