Decay of bacterial pathogens, fecal indicators, and real-time quantitative PCR genetic markers in manure-amended soils

Black soldier fly-based bioconversion of biosolids: Microbial community dynamics and fate of antibiotic resistance genes

Biosolids as by-products of wastewater treatment can contain a large spectrum of pathogens and antibiotic resistance genes (ARGs). Insect-based bioconversion using black soldier fly larvae (BSFL) is an emerging technology that has shown to reduce significant amounts of biosolids quickly and produce larvae biomass containing low heavy metal concentrations. However, to the best of our knowledge, this is the first study investigating the transfer of pathogens and ARGs from biosolids into the process' end-products, BSFL and frass. We hypothesized that BSF-based bioconversion can decrease the abundance of pathogenic bacteria and ARGs in biosolids. In this study, we performed BSFL feeding trials with biosolids blended or not blended with wheat bran, and wheat bran alone as a low bioburden diet (control). We conducted 16S rRNA amplicon sequencing to monitor changes of the BSFL-associated microbial community and the fate of biosolids-associated pathogens. A diverse set of ARGs (ermB, intl1, sul1, tetA, tetQ, tetW, and blaCTX-M-32) were quantified by qPCR and were linked to changes in substrate- and BSFL-associated microbiomes. BSF-based bioconversion of biosolids-containing substrates led to a significant reduction of the microbial diversity, the abundance of several pathogenic bacteria and the investigated ARGs (< 99 %). Feeding with a high bioburden biosolid diet resulted in a higher microbial diversity, and the accumulation of pathogenic bacteria and ARGs in the BSFL. Results of this study demonstrated that BSF-based bioconversion can be a suitable waste management technology to (1) reduce significant amounts of biosolids and (2) reduce the presence of pathogens and ARGs. However, the resulting larvae biomass would need to undergo further post-treatment to reduce the pathogenic load to allow them as animal feed.

Enhancing hydro-epidemiological modelling of nearshore coastal waters with source-receptor connectivity study

Faecal Indicator Organism (FIO) concentrations in nearshore coastal waters may lead to significant public health concerns and economic loss. A three-dimensional numerical source-receptor connectivity study was conducted to improve the modelling of FIO transport and decay processes and identify major FIO sources impacting sensitive receptors (source apportionment). The study site was Swansea Bay, UK and the effects of wind, density, and tracer microbe (surrogate FIO) decay models were investigated by comparing the model simulations to microbial tracer field studies. The relevance of connectivity tests to source apportionment was demonstrated by hindcasting FIO concentration in Swansea Bay with the identified FIO source and the Impulse Response Function (IRF) in Control System theory. This is the first time the IRF approach has been applied for FIO modelling in bathing waters. Results show the importance of density, widely ignored in fully mixed water bodies, and the potential for biphasic decay models to improve prediction accuracy. The microbe-carrying riverine freshwater, having a smaller hydrostatic pressure, could not intrude on the heavier seawater and remained in the nearshore areas. The freshwater and the associated tracer microbes then travelled along the shoreline and reached bathing water sites. This effect cannot be faithfully modelled without the inclusion of the density effect. Biphasic decay models improved the agreement between measured and modelled microbe concentrations. The IRF hindcasted and measured FIO concentrations for Swansea Bay agreed reasonably, demonstrating the importance of connectivity tests in identifying key FIO sources. The findings of this study, namely enhancing hydro-epidemiological modelling and highlighting the effectiveness of connectivity studies in identifying key FIO sources, directly benefit hydraulics and water quality modellers, regulatory authorities, water resource managers and policy.

Shifting terrains: Understanding residential contaminants after flood disasters

Flood disasters can induce the mass transport of soils and sediments. This has the potential to distribute contaminants and present novel combinations to new locations - including residential neighborhoods. Even when soil contaminants cannot be directly attributed to the disaster, data on bacterial and heavy metal(loids) can facilitate an environmentally just recovery by enabling reconstruction decisions that fill data gaps to minimize future exposure. These data-gathering interventions may be especially useful in poor, rural, and racially diverse communities where there is a high probability of exposure to multiple hazards and a potential dependency on the financial resources of disaster aid as a means of reducing chronic exposures to other environmental pollutants. At the same time, entering these post-disasters spaces is ethically complex. To acknowledge this complexity, we pilot a framework for work that gathers social-ecological hazard information while retaining a fair-minded approach to transdisciplinary work. Assembled a transdisciplinary team to recruit participants from 90 households subjected to flooding in the southeastern US. Participating households agreed to interviews to elicit flood experience and environmental health concerns, soil sampling for fecal bacteria (E. coli) and soil sampling for selected heavy metals and metalloids (Pb, As, Cd) at their flooded residence. Soil sampling found a wide range of E. coli concentrations in soil (0.4-1115.7 CFU/ dry gram). Heavy metal(loid)s were detected at most residences (As 97.9 %; Ca 25.5 %; Pb 100 %). Individually, heavy metal(loid) concentrations did not exceed regulatory thresholds. Hazard, risk, and mitigation concerns expressed during interviews reveal that integrated human-nature concepts complicate common understandings of how hazard perceptibility (smell, sight, touch, and information) affects research-action spaces. Qualitative analysis of interviews and field notes revealed that soil-related hazards addressed by our biophysical protocols were less salient than changes with direct causal associations with flooding. We conclude by discussing the potential for the social-ecological hazard information that is fair-minded and transdisciplinary (SHIFT) framework to advance environmentally just approaches to research-action spaces after disasters.

Effects of conservation buffer systems on adsorption of fluorescent-labeled Escherichia coli

The magnitude of bacterial transport through runoff into surface water or infiltration into groundwater is influenced by the adsorption processes in soil. The objective of this study was to evaluate fluorescent-labeled Escherichia coli (E. coli) adsorption by soil under agroforestry buffer (AB), grass buffer (GB), and row crop (RC) management. Adsorption experiments were conducted by inoculating three masses (0.5, 1, and 10 g) of each treatment (AB, GB, and RC) with E. coli O157:H7-GFP with concentration ranges of 10⁵ -10⁸ colony-forming units (cfu) ml^-1 . Adsorption data were evaluated using Langmuir, Freundlich, and Temkin adsorption isotherm models. The Freundlich isotherm model described the observed data well for all treatments using the 10-g soil mass, with the R² values closer to unity in all treatments. The Freundlich K_f parameter, an indicator of adsorption capacity, was higher for the AB treatment (9.93 cfu ml^-1 ) compared with the GB and RC treatments (2.32 and 1.27 cfu ml^-1 , respectively). The multiple pairwise comparisons test (Tukey test) of the Freundlich 1/n_f parameter demonstrated a significant difference (p < .05) between the AB treatment and the RC and GB treatments. Similarly, the K_f values were significantly (p = .05) higher for the 10-g mass under the same test conditions, but no significant differences were observed in the 0.5- and 1-g masses. This study demonstrated that AB has a higher E. coli adsorption capacity and the potential for mitigating the effects of E. coli O157:H7 transport to surface or groundwater through the soil ecosystem.

Mobilization of Escherichia coli and fecal source markers from decomposing cowpats

In rural environments, the sources of fecal contamination in freshwater environments are often diffuse and a mix of fresh and aged fecal sources. It is important for water monitoring purposes, therefore, to understand the impacts of weathering on detection of the fecal source markers available for mobilization from livestock sources. This study targets the impacts of rainfall events on the mobilization of fecal source tracking (FST) markers from simulated cowpats decomposing in situ for five-and-a-half-months. The FST markers analysed were Escherichia coli, microbial source tracking (MST) markers, fecal steroids and a fecal ageing ratio based on the ratio between counts of river microflora and total coliforms. There was a substantial concentration of E. coli (10⁴/100 mL) released from the ageing cowpats suggesting a long-term reservoir of E. coli in the cowpat. Mobilization of fecal markers from rainfall-impacted cowpats, however, was markedly reduced compared with fecal markers in the cowpat. Overall, the Bacteroidales bovine-associated MST markers were less persistent than E. coli in the cowpat and rainfall runoff. The ten fecal steroids, including the major herbivore steroid, 24-ethylcoprostanol, are shown to be stable markers of bovine pollution due to statistically similar degradation rates among all steroids. The mobilizable fraction for each FST marker in the rainfall runoff allowed generation of mobilization decline curves and the derived decline rate constants can be incorporated into source attribution models for agricultural contaminants. Findings from this study of aged bovine pollution sources will enable water managers to improve attribution of elevated E. coli to the appropriate fecal source in rural environments.

Quantitative microbial risk assessment associated with ready-to-eat salads following the application of farmyard manure and slurry or anaerobic digestate to arable lands

Farmyard manure and slurry (FYM&S) and anaerobic digestate are potentially valuable soil conditioners providing important nutrients for plant development and growth. However, these organic fertilisers may pose a microbial health risk to humans. A quantitative microbial risk assessment (QMRA) model was developed to investigate the potential human exposure to pathogens following the application of FYM&S and digestate to agricultural land. The farm-to-fork probabilistic model investigated the fate of microbial indicators (total coliforms and enterococci) and foodborne pathogens in the soil with potential contamination of ready-to-eat salads (RTEs) at the point of human consumption. The processes examined included pathogen inactivation during mesophilic anaerobic digestion (M-AD), post-AD pasteurisation, storage, dilution while spreading, decay in soil, post-harvest washing processes, and finally, the potential growth of the pathogen during refrigeration/storage at the retail level in the Irish context. The QMRA highlighted a very low annual probability of risk (P_annual) due to Clostridium perfringens, norovirus, and Salmonella Newport across all scenarios. Mycobacterium avium may result in a very high mean P_annual for the application of raw FYM&S, while Cryptosporidium parvum and pathogenic E. coli showed high P_annual, and Listeria monocytogenes displayed moderate P_annual for raw FYM&S application. The use of AD reduces this risk; however, pasteurisation reduces the P_annual to an even greater extent posing a very low risk. An overall sensitivity analysis revealed that mesophilic-AD's inactivation effect is the most sensitive parameter of the QMRA, followed by storage and the decay on the field (all negatively correlated to risk estimate). The information generated from this model can help to inform guidelines for policymakers on the maximum permissible indicator or pathogen contamination levels in the digestate. The QMRA can also provide the AD industry with a safety assessment of pathogenic organisms resulting from the digestion of FYM&S.

Rapid quantification of fecal indicator bacteria in water using the most probable number - loop-mediated isothermal amplification (MPN-LAMP) approach on a polymethyl methacrylate (PMMA) microchip

Fecal contamination of water and its associated pathogens are a major public health concern in both developing and industrialized areas. Fecal indicator bacteria (FIB) are commonly used to assess microbial water quality, but they require a relatively long period of incubation time. Currently, molecular techniques have been applied to rapidly detect FIB. However, these molecular techniques require expensive and sophisticated equipment. In this study, we developed a rapid on-chip gene quantification method based on loop-mediated isothermal amplification (LAMP) PCR. The LAMP assays can measure the target genes of the fecal indicator bacteria (FIB), including E. coli and Enterococcus spp, using the most probable number (MPN) approach. The colorimetric LAMP assay allows for naked-eye observation of the PCR reaction as few as 4 gene copies / well. When the reaction ends, MPN measurement of positive outcomes on the white-based PMMA (polymethacrylic acid) microchips provides the concentrations of the target genes of FIB with a confidence interval. We validated the feasibility of the MPN-LAMP approach by obtaining a strong correlation between the results of the MPN estimations and the qPCR analysis. Moreover, the MPN-LAMP approach was used to quantify the FIB in different environmental water collected from the freshwater reservoirs, beach, agriculture farm, and sewage. Our research demonstrates that the MPN- LAMP method enables us to easily and quickly quantifying FIB genes isolated from the environment without expensive qPCR instruments.

Characterisation and control of the biosolids storage environment: Implications for E. coli dynamics

E. coli survival in biosolids storage may present a risk of non-compliance with guidelines designed to ensure a quality product safe for agricultural use. The storage environment may affect E. coli survival but presently, storage characteristics are not well profiled. Typically biosolids storage environments are not actively controlled or monitored to support increased product quality or improved microbial compliance. This two-phased study aimed to identify the environmental factors that control bacterial concentrations through a long term, controlled monitoring study (phase 1) and a field-scale demonstration trial modifying precursors to bacterial growth (phase 2). Digested and dewatered biosolids were stored in operational-scale stockpiles to elucidate factors controlling E. coli dynamics. E. coli concentrations, stockpile dry solids, temperature, redox and ambient weather data were monitored. Results from ANCOVA analysis showed statistically significant (p < 0.05) E. coli reductions across storage periods with greater die-off in summer months. Stockpile temperature had a statistically significant effect on E. coli survival. A 4.5 Log reduction was measured in summer (maximum temperature 31 °C). In the phase 2 modification trials, covered stockpiles were able to maintain a temperature >25 °C for a 28 day period and achieved a 3.7 Log E. coli reduction. In winter months E. coli suppression was limited with concentrations >6 Log₁₀ CFU g^-1 DS maintained. The ANCOVA analysis has identified the significant role that physical environmental factors, such as stockpile temperature, has on E. coli dynamics and the opportunities for control.

Epidemiology of Campylobacter jejuni in raccoons (Procyon lotor) on swine farms and in conservation areas in southern Ontario

Campylobacter is a leading cause of foodborne illness in humans worldwide. Sources of infection are often difficult to identify, and are, generally, poorly understood. Recent work suggests that wildlife may represent a source of Campylobacter for human infections. Using a repeated cross-sectional study design, raccoons were trapped on five swine farms and five conservation areas in southern Ontario from 2011 to 2013. Our objectives were to: (a) assess the impact of seasonal, climatic, location, annual and raccoon demographic factors on the occurrence of Campylobacter jejuni in these animals; and (b) identify clusters of C. jejuni in space, time and space-time using spatial scan statistics. Multi-level multivariable logistic regression was used to examine the odds of isolating C. jejuni, with site and animal modelled as random intercepts. The following independent variables were examined: raccoon age and sex, year, location type, season, temperature and rainfall. A total of 1,096 samples were obtained from 627 raccoons; 46.3% were positive for C. jejuni. The following interactions and their main effects were significant (p < .05) and retained in the final model: season × temperature, year × rainfall, year × temperature. Based on the results from our multivariable model and spatial scan statistics, climatic variables (i.e. rainfall, temperature and season) were associated with the carriage of C. jejuni by raccoons, but the effects were not consistent, and varied by location and year. Although raccoons may pose a zoonotic risk due to their carriage of Campylobacter, further work is required to characterize the transmission and movement of this microorganism within the ecosystem.

Molecular detection of opportunistic pathogens and insights into microbial diversity in private well water and premise plumbing

Private well water systems in rural areas that are improperly maintained will result in poor drinking water quality, loss of water supply, and pose human health risk. The purpose of this study was to investigate the occurrence of fecal indicator bacteria (FIB) and opportunistic pathogens in private well water in rural areas surrounding New Orleans, Louisiana. Our results confirmed the ubiquitous nature of Legionella (86.7%) and mycobacteria (68.1%) in private well water in the study area, with gene concentration ranged from 0.60 to 5.53 and 0.67 to 5.95 Log₁₀ of GC/100 mL, respectively. Naegleria fowleri target sequence was detected in 16.8% and Escherichia coli was detected in 43.4% of the water samples. Total coliform, as well as Legionella and mycobacteria genetic markers' concentrations were significantly reduced by 3-minute flushing. Next-generation sequencing (NGS) data indicated that the abundance of bacterial species was significantly increased in water collected in kitchens compared with samples from wells directly. This study provided integrated knowledge on the persistence of pathogenic organisms in private well water. Further study is needed to explore the presence of clinical species of those opportunistic pathogens in private well water systems to elucidate the health risk.

Implementation and integration of microbial source tracking in a river watershed monitoring plan

Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess their usefulness as an effective management tool of water quality. First, the potential of the selected markers to track the source was evaluated using fresh fecal samples. Subsequently, we evaluated their performance in a catchment with different impacts, considering land use and environmental conditions. All MST markers showed high sensitivity and specificity, although none achieved 100% for both. Although some of the MST markers were detected in hosts other than the intended ones, their abundance in the target group was always several orders of magnitude higher than in the non-target hosts, demonstrating their suitability to distinguish between sources of pollution. The MST analysis matched the land use in the watershed allowing an accurate assessment of the main sources of pollution, in this case mainly human and ruminant pollution. Correlating environmental parameters including temperature and rainfall with MST markers provided insight into the dynamics of the pollution in the catchment. The levels of the human marker showed a significant negative correlation with rainfall in human polluted areas suggesting a dilution of the pollution, whereas at agricultural areas the ruminant marker increased with rainfall. There were no seasonal differences in the levels of human marker, indicating human pollution as a constant pressure throughout the year, whereas the levels of the ruminant marker was influenced by the seasons, being more abundant in summer and autumn. MST analysis integrated with land use and environmental data can improve the management of fecal polluted areas and set up best practice.

A Predictive Model for Survival of Escherichia coli O157:H7 and Generic E. coli in Soil Amended with Untreated Animal Manure

This study aimed at developing a predictive model that captures the influences of a variety of agricultural and environmental variables and is able to predict the concentrations of enteric bacteria in soil amended with untreated Biological Soil Amendments of Animal Origin (BSAAO) under dynamic conditions. We developed and validated a Random Forest model using data from a longitudinal field study conducted in mid-Atlantic United States investigating the survival of Escherichia coli O157:H7 and generic E. coli in soils amended with untreated dairy manure, horse manure, or poultry litter. Amendment type, days of rain since the previous sampling day, and soil moisture content were identified as the most influential agricultural and environmental variables impacting concentrations of viable E. coli O157:H7 and generic E. coli recovered from amended soils. Our model results also indicated that E. coli O157:H7 and generic E. coli declined at similar rates in amended soils under dynamic field conditions.The Random Forest model accurately predicted changes in viable E. coli concentrations over time under different agricultural and environmental conditions. Our model also accurately characterized the variability of E. coli concentration in amended soil over time by providing upper and lower prediction bound estimates. Cross-validation results indicated that our model can be potentially generalized to other geographic regions and incorporated into a risk assessment for evaluating the risks associated with application of untreated BSAAO. Our model can be validated for other regions and predictive performance also can be enhanced when data sets from additional geographic regions become available.

Formation of Escherichia coli O157:H7 Persister Cells in the Lettuce Phyllosphere and Application of Differential Equation Models To Predict Their Prevalence on Lettuce Plants in the Field

Escherichia coli O157:H7 (EcO157) infections have been recurrently associated with produce. The physiological state of EcO157 cells surviving the many stresses encountered on plants is poorly understood. EcO157 populations on plants in the field generally follow a biphasic decay in which small subpopulations survive over longer periods of time. We hypothesized that these subpopulations include persister cells, known as cells in a transient dormant state that arise through phenotypic variation in a clonal population. Using three experimental regimes (with growing, stationary at carrying capacity, and decaying populations), we measured the persister cell fractions in culturable EcO157 populations after inoculation onto lettuce plants in the laboratory. The greatest average persister cell fractions on the leaves within each regime were 0.015, 0.095, and 0.221%, respectively. The declining EcO157 populations on plants incubated under dry conditions showed the largest increase in the persister fraction (46.9-fold). Differential equation models were built to describe the average temporal dynamics of EcO157 normal and persister cell populations after inoculation onto plants maintained under low relative humidity, resulting in switch rates from a normal cell to a persister cell of 7.7 × 10-6 to 2.8 × 10-5 h-1 Applying our model equations from the decay regime, we estimated model parameters for four published field trials of EcO157 survival on lettuce and obtained switch rates similar to those obtained in our study. Hence, our model has relevance to the survival of this human pathogen on lettuce plants in the field. Given the low metabolic state of persister cells, which may protect them from sanitization treatments, these cells are important to consider in the microbial decontamination of produce.IMPORTANCE Despite causing outbreaks of foodborne illness linked to lettuce consumption, E. coli O157:H7 (EcO157) declines rapidly when applied onto plants in the field, and few cells survive over prolonged periods of time. We hypothesized that these cells are persisters, which are in a dormant state and which arise naturally in bacterial populations. When lettuce plants were inoculated with EcO157 in the laboratory, the greatest persister fraction in the population was observed during population decline on dry leaf surfaces. Using mathematical modeling, we calculated the switch rate from an EcO157 normal to persister cell on dry lettuce plants based on our laboratory data. The model was applied to published studies in which lettuce was inoculated with EcO157 in the field, and switch rates similar to those obtained in our study were obtained. Our results contribute important new knowledge about the physiology of this virulent pathogen on plants to be considered to enhance produce safety.

Comparison of microbial source tracking efficacy for detection of cattle fecal contamination by quantitative PCR

Identification of fecal contamination sources in surface water has become heavily dependent on quantitative PCR (qPCR) because this technique allows for the rapid enumeration of fecal indicator bacteria as well as the detection and quantification of fecal source-associated genetic markers in the environment. Identification of contamination sources in impaired waters is a prerequisite for developing best management practices to reduce future pollution. Proper management decisions rely on the quality and interpretation of qPCR data. In this study, we developed a method to determine analytical and process lower limits of detection (LLOD) and quantification (LLOQ) using two cattle-associated genetic markers targeting Bacteroidales. Analytical LLOD (A_LLOD) for both CowM2 and CowM3 genetic markers in the qPCR assay were five gene copies per reaction. Using composite fecal DNA, the analytical LLOQ (A_LLOQ) determined for CowM2 and CowM3 were 78 and 195 gene copies/reaction, respectively. When plasmid DNA was used, the A_LLOQ for CowM2 and CowM3 were 46 and 20 gene copies/reaction, respectively. The process LLOD (P_LLOD) for CowM2 and CowM3 were 0.4 and 0.02 mg feces/filter (wet weight), respectively. Using the standard deviation value of 0.25 as a cut-off point for LLOQ in regression analysis, the process LLOQ (P_LLOQ) for CowM2 and CowM3 were 3.2 and 0.3 mg feces/filter, respectively. These results indicate that CowM3 exhibited superior performance characteristics compared with CowM2 for fecal samples collected from our geographical region. Moreover, the method for calculating LLOD and LLOQ developed here can be applied to other microbial source tracking studies.

Phenotypic variations in persistence and infectivity between and within environmentally transmitted pathogen populations impact population-level epidemic dynamics

BACKGROUND

Human pathogens transmitted through environmental pathways are subject to stress and pressures outside of the host. These pressures may cause pathogen pathovars to diverge in their environmental persistence and their infectivity on an evolutionary time-scale. On a shorter time-scale, a single-genotype pathogen population may display wide variation in persistence times and exhibit biphasic decay.

METHODS

We use a transmission modeling framework to develop an infectious disease model with biphasic pathogen decay. We take a differential algebra approach to assessing model identifiability, calculate basic reproduction numbers by the next generation method, and use simulation to explore model dynamics.

RESULTS

For both long and short time-scales, we demonstrate that epidemic-potential-preserving trade-offs have implications for epidemic dynamics: less infectious, more persistent pathogens cause epidemics to progress more slowly than more infectious, less persistent (labile) pathogens, even when the overall risk is the same. Using identifiability analysis, we show that the usual disease surveillance data does not sufficiently inform these underlying pathogen population dynamics, even when combined with basic environmental monitoring data. However, risk could be indirectly ascertained by developing methods to separately monitor labile and persistent subpopulations. Alternatively, determining the relative infectivity of persistent pathogen subpopulations and the rates of phenotypic conversion will help ascertain how much disease risk is associated with the long tails of biphasic decay.

CONCLUSION

A better understanding of persistence-infectivity trade-offs and associated dynamics can improve our ecological understanding of environmentally transmitted pathogens, as well as our risk assessment and disease control strategies.

Methodology for Determining the Die-Off Coefficient of Enterococci in the Conditions of Transport through the Karst Aquifer—Case Study: Bokanjac–Poličnik Catchment

This paper presents the methodology for determining the die-off coefficient of faecal indicator bacteria (enterococci) when transported in a karst environment. The main problem in exploring karst environments, which this methodology strives to cope with, is lack of field measurements, poor data on karst rock formation, fractures and channels within it, and groundwater level dynamics. The analysed karst catchment (Bokanjac–Poličnik) is situated in the hinterland of the city of Zadar (Republic of Croatia) and covers an area of 235.07 km2. In the water supply wells within the analysed catchment, a frequent occurrence of enterococci was observed. The proposed methodology consists of two basic steps. Preliminary analyses as the initial step were used in the accumulation of certain assumptions related to the detection of increased concentrations of enterococci as well as in determination of the potential source of pollution. In the second step, the analytical model was constructed with the aim of resolving processes of sorption and die-off and determining the dominant factor in the process of natural removal of enterococci when transported in karst environment. Within the model, two parts of the pollutant transport are integrated: vertical percolation and horizontal seepage flow and transport. The mean value of the total die-off coefficient by transport through the unsaturated zone in the analysed case is k t o t = 8.25. Within the saturated zone the total die-off coefficient k t o t is within the limits of 0.1 and 0.5.

Removal of fecal indicator bacteria and antibiotic resistant genes in constructed wetlands

Wastewater discharge evidently increased bacterial diversity in the receiving waterbodies. The objective of this study was to evaluate the effectiveness of a constructed wetland in reducing fecal indicator bacteria (FIB) and antibiotic resistant genes (ARGs). We determined the prevalence and attenuation of fecal indicator bacteria including Escherichia coli and enterococci, along with ARGs, and human-associated Bacteroidales (HF183) markers by quantitative polymerase chain reaction (qPCR) method. Three types of water samples (inlet, intermediate, and outlet) from a constructed wetland were collected once a month from May to December in 2013. The overall reduction of E. coli was 50.0% based on culture method. According to the qPCR result, the overall removal rate of E. coli was only 6.7%. Enterococci were found in 62.5% of the wetland samples. HF183 genetic marker was detected in all final effluent samples with concentration ranging from 1.8 to 4.22 log₁₀ gene copies (GC)/100 ml. Of the ARGs tested, erythromycin resistance genes (ermF) were detected in 79.2% of the wetland samples. The class 1 integrase (intI1) was detected in all water samples with concentration ranging from 0.83 to 5.54 log₁₀ GC/100 ml. The overall removal rates of enterococci, HF183, intI1, and ermF were 84.0%, 66.6%, 67.2%, and 13.1%, respectively.

Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment

Fecal contamination of recreational waters with cattle manure can pose a risk to public health due to the potential presence of various zoonotic pathogens. Fecal indicator bacteria (FIB) have a long history of use in the assessment of recreational water quality, but FIB quantification provides no information about pollution sources. Microbial source tracking (MST) markers have been developed in response to a need to identify pollution sources, yet factors that influence their decay in ambient waters are often poorly understood. We investigated the influence of water type (freshwater versus marine) and select environmental parameters (indigenous microbiota, ambient sunlight) on the decay of FIB and MST markers originating from cattle manure. Experiments were conducted in situ using a submersible aquatic mesocosm containing dialysis bags filled with a mixture of cattle manure and ambient water. Culturable FIB (E. coli, enterococci) were enumerated by membrane filtration and general fecal indicator bacteria (GenBac3, Entero1a, EC23S857) and MST markers (Rum2Bac, CowM2, CowM3) were estimated by qPCR. Water type was the most significant factor influencing decay (three-way ANOVA, p: 0.006 to <0.001), although the magnitude of the effect differed among microbial targets and over time. The presence of indigenous microbiota and exposure to sunlight were significantly correlated (three-way ANOVA, p: 0.044 to <0.001) with decay of enterococci and CowM2, while E. coli, EC23S857, Rum2Bac, and CowM3 (three-way ANOVA, p: 0.044 < 0.001) were significantly impacted by sunlight or indigenous microbiota. Results indicate extended persistence of both cultivated FIB and genetic markers in marine and freshwater water types. Findings suggest that multiple environmental stressors are important determinants of FIB and MST marker persistence, but their magnitude can vary across indicators. Selective exclusion of natural aquatic microbiota and/or sunlight typically resulted in extended survival, but the effect was minor and limited to select microbial targets.

Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region

There is a growing move towards using the quantitative polymerase chain (qPCR)-based sewage-associated marker genes to assess surface water quality. However, a lack of understanding about the persistence of many sewage-associated markers creates uncertainty for those tasked with investigating microbial water quality. In this study, we investigated the decay of two qPCR FIB [E. coli (EC), and Enterococcus spp. (ENT) 23S rRNA genes] and four sewage-associated microbial source tracking (MST) marker genes [human Bacteroides HF183 16S rRNA, adenovirus (HAdV), and polyomavirus (HPyV), and crAssphage, a recently described bacteriophage in feces], in outdoor mesocosms containing fresh and marine waters and their corresponding sediments. Decay rates of EC 23S rRNA, ENT 23S rRNA, and HF183 16S rRNA were significantly (p < 0.05) faster than the HAdV, HPyV and crAssphage markers in water samples from all mesocosms. In general, decay rates of bacterial targets were similar in the water columns of the studied mesocosms. Similarly, decay rates of viral targets were also alike in mesocosm water columns in relation to each other. The decay rates of FIB and sewage-associated markers were significantly faster in water samples compared to sediments in all three mesocosms. In the event of resuspension, FIB and marker genes from sediments can potentially recontaminate overlying waters. Thus, care should be taken when interpreting the occurrence of FIB and sewage-associated MST markers in water, which may have originated from sediments. The differential decay of these targets may also influence health outcomes and need to be considered in risk assessment models.

Safe surface concept in vertical flow constructed wetland design to mitigate infection hazard

Decentralized wastewater management based on vertical flow constructed wetlands (VFCWs) can be an effective solution for minimizing sanitation problems also in urban landscapes, especially when considering rapidly expanding cities in developing countries. Yet, the mass implementation of VFCWs in urbanized areas first needs improvement of a few design drawbacks - among them, the control of infection hazard is of primary importance. Therefore, in this study, the possibility of mitigation of the VFCW-derived infection hazard was assessed, through analysis of bacteriostatic properties of top filtration layer materials, according to clinical experiences based on "safe" antimicrobial surfaces. The experiment was carried out on a daily operating VFCW. Coliform bacteria survival rates were measured for known VFCW construction materials such as Pinus bark, gravel, slag, charcoal and LECA. The calculated die-off rates expressed as 12-h first-order inactivation coefficients ranged between 6.91 h^-1 (slag/summer) and 0.58 h^-1 (Pinus bark/autumn). The obtained die-off curves showed charcoal, Pinus bark and LECA to have little bacteriostatic properties - even occasionally providing conditions promoting the growth of the coliform population. Meanwhile, slag and gravel were strictly inhibiting bacteria growth, reducing the population up to 99% within the first 3 h of contact time. The research showed that it is possible to significantly mitigate the infection hazard of VFCW by means of proper top-layer substrate material, similar or equal to slag or gravel.

Evaluating the long-term persistence of Bacillus spores on common surfaces

Bacillus spores resist inactivation, but the extent of their persistence on common surfaces is unclear. This work addresses knowledge gaps regarding biothreat agents in the environment to reduce uncertainty in risk assessment models. Studies were conducted to investigate the long-term inactivation of Bacillus anthracis and three commonly used surrogate organisms - B. cereus, B. atrophaeus and B. thuringiensis on three materials: laminate countertop, stainless steel and polystyrene Petri dishes. Viable spores were measured at 1, 30, 90, 196, 304 and 1038 days. Twelve different persistence models were fit to the data using maximum likelihood estimation and compared. The study found that (1) spore inactivation was not log-linear, as commonly modelled; (2) B. thuringiensis counts increased at 24 h on all materials, followed by a subsequent decline; (3) several experiments showed evidence of a 'U' shape, with spore counts apparently decreasing and then increasing between 1 and 304 days; (4) spores on polystyrene showed little inactivation; and (5) the maximum inactivation of 56% was observed for B. atrophaeus spores on steel at 196 days. Over the range of surfaces, time durations and conditions (humidity controlled vs. uncontrolled) examined, B. thuringiensis most closely matched the behaviour of B. anthracis.

Effects of irrigation with secondary treated wastewater on physicochemical and microbial properties of soil and produce safety in a semi-arid area

Water scarcity is becoming one of the largest problems worldwide. Agricultural reuse of wastewater has been considered a valuable and reliable alternative, alleviating the pressure on freshwater resources in arid and semi-arid regions such as the Middle East. Inadequate microbial quality of treated wastewater is a challenge for developing countries, which limits agricultural reuse of wastewater. This study assessed the impact of irrigation with secondary treated wastewater (STWW) on soil properties as well as the safety of various types of crops as compared with tap water (TW) irrigation through a furrow system. Total and fecal coliforms and Escherichia coli were monitored as indicator bacteria in STWW, irrigated soil and harvested crops. The presence of pathogenic E. coli O157, Salmonella and Shigella was also monitored in all samples using a combination of culture and molecular methods. The microbial quality of wastewater in terms of E. coli concentration (4.18 Log MPN/100 ml) failed to meet the world health organization (WHO) recommendation for irrigation of root and leafy crops (≤103 and ≤ 104E. coli per 100 ml for root and leafy crops, respectively). No significant effects on physicochemical properties of the soil irrigated with STWW was found in comparison with control plots, except for electrical conductivity (EC) and sodium adsorption ratio (SAR), which were slightly higher in STWW soil samples. Although the microbial quality of soil was affected by STWW irrigation, a relatively low concentration of E. coli was detected in soil. No microbial contamination in terms of E. coli was found on harvested maize and onion. E. coli contamination of lettuce and spring onion was found for both irrigation schemes. No STWW, soil or crop samples were found positive for pathogenic bacteria. According to the analyzed parameters, STWW could be safely used as an alternative source for irrigation of root and leafy crops.

Modelling of ultraviolet light inactivation kinetics of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, Clostridium difficile spores and murine norovirus on fomite surfaces

AIMS

Quantitative data on the doses needed to inactivate micro-organisms on fomites are not available for ultraviolet applications. The goal of this study was to determine the doses of UV light needed to reduce bacteria and murine norovirus (MNV) on hard surface fomites through experimentation and to identify appropriate models for predicting targeted levels of reduction.

METHODS AND RESULTS

Stainless steel and Formica laminate coupons were selected as they are common surfaces found in healthcare settings. Test organisms included methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Clostridium difficile and MNV. The fomites were inoculated with 10⁵ -10⁷ bacteria or virus and exposed to a range of UV doses. The order of resistance to UV irradiation was virus, bacterial spore and vegetative cell. The best fitting inactivation curves suggested nonlinear responses to increasing doses after a 3-4 log reduction in the test organisms. The average UV doses required for a 3 log reduction in the C. difficile, MRSA and VRE were 16 000, 6164 and 11 228 (mJ-s cm^-2 ) for stainless steel, respectively, and 16 000, 11 727 and 12 441 (mJ-s cm^-2 ) for Formica laminate, respectively.

CONCLUSIONS

Higher UV light doses are required to inactivate bacteria and viruses on hard surfaces than in suspension. Greater doses are needed to inactivate bacterial spores and MNV compared to vegetative bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Quantitative data and models on UV light doses needed to inactivate bacteria and MNV on hard surfaces are now available. The generalizable results of this study can be used to estimate required UV dosages to achieve targeted levels of inactivation based on estimated levels of contamination or to support quantitative microbial risk assessments.

Fecal Fingerprints of Enteric Pathogen Contamination in Public Environments of Kisumu, Kenya, Associated with Human Sanitation Conditions and Domestic Animals

Young children are infected by a diverse range of enteric pathogens in high disease burden settings, suggesting pathogen contamination of the environment is equally diverse. This study aimed to characterize across- and within-neighborhood diversity in enteric pathogen contamination of public domains in urban informal settlements of Kisumu, Kenya, and to assess the relationship between pathogen detection patterns and human and domestic animal sanitation conditions. Microbial contamination of soil and surface water from 166 public sites in three Kisumu neighborhoods was measured by enterococcal assays and quantitative reverse transcription polymerase chain reaction (qRT-PCR) for 19 enteric pathogens. Regression was used to assess the association between observed sanitary indicators of contamination with enterococci and pathogen presence and concentration, and pathogen diversity. Seventeen types of pathogens were detected in Kisumu public domains. Enteric pathogens were codetected in 33% of soil and 65% of surface water samples. Greater pathogen diversity was associated with the presence of domestic animal feces but not with human open defecation, deteriorating latrines, flies, or disposal of human feces. Sanitary conditions were not associated with enterococcal bacteria, specific pathogen concentrations, or "any pathogen". Young children played at 40% of observed sites. Managing domestic animal feces may be required to reduce enteric pathogen environmental contamination in high-burden settings.

Persistence of bacterial pathogens, antibiotic resistance genes, and enterococci in tidal creek tributaries

Intertidal creeks form the primary hydrologic link between estuaries and land-based activities on barrier islands. Fecal indicators Enterococcus spp. (Entero1), pathogens Shigella spp. (ipaH), Salmonella spp. (invA), E. coli of EHEC/EPEC groups (eaeA), E. coli of EAEC, EIEC, and UPEC groups (set1B), E. coli of STEC group (stx1); and tetracycline resistance genes (tet(B), tet(C), tet(D), tet(E), tet(K), tet(Q), tet(W), and tet(X); TRG) were detected in the headwater of Oakdale Creek (Sapelo Island, GA) receiving runoffs from Hog Hammock village. Excavation of drainage ditches around the village caused a high increase in the incidence of the above determinants. Water samples were collected from the headwater, transferred to diffusion chambers, submersed in the headwater, saltmarsh, and mouth of the creek; and the determinants were monitored for 3 winter months. With some exceptions, their persistence decreased in order headwater > saltmarsh > mouth. Genes associated with Enterococcus spp. were the most persistent at all the sites, following in the headwater with determinants for Salmonella spp. and E. coli of EAEC, EIEC, and UPEC groups. In the mouth, the most persistent gene was eaeA indicating EHEC, EPEC, and STEC. Tet(B) and tet(C) persisted the longest in headwater and saltmarsh. No TRG persisted after 11 days in the mouth. Most determinants revealed correlations with temperature and pH, and inverse correlations with dissolved oxygen. Decay rates of the above determinants varied in the range of -0.02 to -0.81/day, and were up to 40 folds higher in the saltmarsh and mouth than in the headwater. Our data demonstrated that water parameters could to some extent predict a general trend in the fate of virulence and antibiotic resistance determinants in tidal creek tributaries but strongly suggested that their persistence in these tributaries cannot be predicted from that of enterococci, or extrapolated from one biological contaminant to another.

Quantification of Leptospira interrogans Survival in Soil and Water Microcosms

Leptospira interrogans is the etiological agent of leptospirosis, a globally distributed zoonotic disease. Human infection usually occurs through skin exposure with water and soil contaminated with the urine of chronically infected animals. In this study, we aimed to quantitatively characterize the survival of Leptospira interrogans serovar Copenhageni in environmental matrices. We constructed laboratory microcosms to simulate natural conditions and determined the persistence of DNA markers in soil, mud, spring water and sewage using a quantitative PCR (qPCR) and a propidium monoazide (PMA)-qPCR assay. We found that L. interrogans does not survive at high concentrations in the tested matrices. No net growth was detected in any of the experimental conditions and in all cases the concentration of the DNA markers targeted decreased from the beginning of the experiment following an exponential decay with a decreasing decay rate over time. After 12 and 21 days of incubation the spiked concentration of 10⁶L. interrogans cells/ml or g decreased to approximately 100 cells/ml or g in soil and spring water microcosms, respectively. Furthermore, culturable L. interrogans persisted at concentrations under the limit of detection by PMA-qPCR or qPCR for at least 16 days in soil and 28 days in spring water. Altogether, our findings suggest that the environment is not a multiplication reservoir but a temporary carrier of L. interrogans Copenhageni, although the observed prolonged persistence at low concentrations may still enable the transmission of the disease.IMPORTANCE Leptospirosis is a zoonotic disease caused by spirochetes of the genus Leptospira that primarily affects impoverished populations worldwide. Although leptospirosis is transmitted by contact with water and soil, little is known about the ability of the pathogen to survive in the environment. In this study, we quantitatively characterized the survival of L. interrogans in environmental microcosms and found that although it cannot multiply in water, soil or sewage, it survives for extended time periods (days to weeks depending on the matrix). The survival parameters obtained here may help to better understand the distribution of pathogenic Leptospira in the environment and improve the predictions of human infection risks in areas where such infections are endemic.

Does Size Matter? An Experimental Evaluation of the Relative Abundance and Decay Rates of Aquatic Environmental DNA

Environmental DNA (eDNA) is increasingly used to monitor aquatic macrofauna. Typically, short mitochondrial DNA fragments are targeted because these should be relatively more abundant in the environment as longer fragments will break into smaller fragments over time. However, longer fragments may permit more flexible primer design and increase taxonomic resolution for eDNA metabarcoding analyses, and recent studies have shown that long mitochondrial eDNA fragments can be extracted from environmental water samples. Nuclear eDNA fragments have also been proposed as targets, but little is known about their persistence in the aquatic environment. Here we measure the abundance of mitochondrial eDNA fragments of different lengths and of short nuclear eDNA fragments, originating from captive fish in experimental tanks, and we test whether longer mitochondrial and short nuclear fragments decay faster than short mitochondrial fragments following fish removal. We show that when fish are present, shorter mitochondrial fragments are more abundant in water samples than both longer mitochondrial fragments and short nuclear eDNA fragments. However, the rate of decay following fish removal was similar for all fragment types, suggesting that the differences in abundance resulted from differences in the rates at which different fragment types were produced rather than differences in their decay rates.

Quantitative assessment of Naegleria fowleri and fecal indicator bacteria in brackish water of Lake Pontchartrain, Louisiana

Brackish water samples from Lake Pontchartrain in Louisiana were assessed for the presence of pathogenic amoeba Naegleria fowleri, which causes primary amoebic meningoencephalitis (PAM). In our study, quantitative polymerase chain reaction (qPCR) methods were used to determine N. fowleri, E. coli, and enterococci in water collected from Lake Pontchartrain. N. fowleri target sequence was detected in 35.4% (56/158) of the water samples from ten sites around the lake. Statistically significant positive correlations between N. fowleri concentration and water temperature as well as E. coli (qPCR) were observed. Multiple linear regression (MLR) model shows seasonal factor (summer or winter) has significant effect on the concentration of N. fowleri, E. coli and enterococci (qPCR) concentration. Significant positive relationships between E. coli and enterococci was observed from both qPCR (r=0.25) and culture based method (r=0.54). Meanwhile, significant positive correlation between qPCR and culture based methods for enterococci concentration was observed (r=0.33). In our study, water temperature and E. coli concentration were indicative of N. fowleri concentrations in brackish water environment. Future research is needed to determine whether sediment is a source of N. fowleri found in the water column.

Assessment of fecal pollution in Lake Pontchartrain, Louisiana

Water quality in Lake Pontchartrain was deteriorating and recreational activities along the beach were restricted by the end of the 20th Century. A microbial source tracking (MST) study was conducted to determine the fecal contamination sources at public beach of the lake, so that effective pollution control strategies can be developed. Water samples were collected over an eight-month period at ten locations along the lake in 2016 and 2017. E. coli and Enterococcus were detected in 90.6% (culture) and 97.5% (qPCR), 95.8% (culture) and 91.8% (qPCR) of water samples from all sampling sites, respectively. Significant positive relationship between E. coli and Enterococcus results was observed for both qPCR and culture methods. HF183 marker was detected in 94.3% water samples (149 of 158), with concentrations ranging from 29.0 to 6073.5GC/100ml and from 129.8 to 38,465.6GC/100ml in summer and winter, respectively. The results also indicate that significant rainfall events have the potential to supply considerable loads of fecal bacteria to lake waters. Further research is needed to determine the contribution of other animals to fecal contamination in the region.

Validation and application of quantitative PCR assays using host-specific Bacteroidales genetic markers for swine fecal pollution tracking

Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing. After challenged against fecal DNA extracted from different animal sources, four sequences from the clone libraries targeting two Bacteroidales- (genes 1-38 and 3-53), a Clostridia- (gene 2-109) as well as a Bacilli-like sequence (gene 2-95), respectively, showed high specificity to swine feces based on PCR analysis. Host-specificity and host-sensitivity analysis confirmed that oligonucleotide primers and probes capable of annealing to select Bacteroidales-like sequences (1-38 and 3-53) exhibited high specificity (>90%) in quantitative PCR assays with 71 fecal DNAs from non-target animal sources. The two assays also demonstrated broad distributions of corresponding genetic markers (>94% positive) among 72 swine feces. After evaluation with environmental water samples from different areas, swine-targeted assays based on two Bacteroidales-like GFE sequences appear to be suitable quantitative tracing tools for swine fecal pollution.

The effect of anaerobic digestion and storage on indicator microorganisms in swine and dairy manure

The aim of this experimental study was to evaluate the influence of anaerobic digestion and storage on indicator microorganisms in swine and dairy excreta. Samples were collected every 90 days for 15 months at eight farms, four pig, and four dairy farms, four of them having a biogas plant. Moreover, to evaluate storage effects on samples, 20 l of manure and slurry taken at each farm (digested manure only in farms with a biogas plant) were stored in a controlled climatic chamber at 18 °C, for 6 months. The bacterial load and the chemical-physical characteristics of excreta were evaluated at each sampling time, stored slurry, and manure were sampled and analyzed every 2 months. A high variability of the concentration of bacteria in the different excreta types was observed during the experiment, mainly depending on the type and time of treatment. No sample revealed either the presence of Escherichia coli O157:H7 or of Salmonella, usually linked to the temporary rearing of infected animals in facilities. Anaerobic digestion and storage affected in a significant way the reduction of indicator bacteria like lactobacilli, coliforms, and streptococci. Anaerobic digestion lowered coliforms in pig slurry (- 2.80 log, P < 0.05), streptococci in dairy manure (- 2.44 log, P < 0.001) and in pig slurry (- 1.43 log, P < 0.05), and lactobacilli in pig slurry (- 3.03 log, P < 0.05). Storage lowered coliforms and the other indicators counts, in particular in fresh wastes, while clostridia did not show a reduction in concentration.

Survival of Escherichia coli on Lettuce under Field Conditions Encountered in the Northeastern United States

Although wildlife intrusion and untreated manure have been associated with microbial contamination of produce, relatively few studies have examined the survival of Escherichia coli on produce under field conditions following contamination (e.g., via splash from wildlife feces). This experimental study was performed to estimate the die-off rate of E. coli on preharvest lettuce following contamination with a fecal slurry. During August 2015, field-grown lettuce was inoculated via pipette with a fecal slurry that was spiked with a three-strain cocktail of rifampin-resistant nonpathogenic E. coli. Ten lettuce heads were harvested at each of 13 time points following inoculation (0, 2.5, 5, and 24 h after inoculation and every 24 h thereafter until day 10). The most probable number (MPN) of E. coli on each lettuce head was determined, and die-off rates were estimated. The relationship between sample time and the log MPN of E. coli per head was modeled using a segmented linear model. This model had a breakpoint at 106 h (95% confidence interval = 69, 142 h) after inoculation, with a daily decrease of 0.70 and 0.19 log MPN for 0 to 106 h and 106 to 240 h following inoculation, respectively. These findings are consistent with die-off rates obtained in similar studies that assessed E. coli survival on produce following irrigation. Overall, these findings provide die-off rates for E. coli on lettuce that can be used in future quantitative risk assessments.

Sources and persistence of fecal indicator bacteria and Bacteroidales in sand as measured by culture-based and culture-independent methods: A case study at Santa Monica Pier, California

This study investigated causes of persistent fecal indicator bacteria (FIB) in beach sand under the pier in Santa Monica, CA. FIB levels were up to 1,000 times higher in sand underneath the pier than that collected from adjacent to the pier, with the highest concentrations under the pier in spring and fall. Escherichia coli (EC) and enterococci (ENT) under the pier were significantly positively correlated with moisture (ρ = 0.61, p < 0.001, n = 59; ρ = 0.43, p < 0.001, n = 59, respectively), and ENT levels measured by qPCR (qENT) were much higher than those measured by membrane filtration (cENT). Microcosm experiments tested the ability of EC, qENT, cENT, and general Bacteroidales (GenBac) to persist under in-situ moisture conditions (10% and 0.1%). Decay rates of qENT, cENT, and GenBac were not significantly different from zero at either moisture level, while decay rates for EC were relatively rapid during the microcosm at 10% moisture (k = 0.7 days-1). Gull/pelican marker was detected at eight of 12 sites and no human-associated markers (TaqHF183 and HumM2) were detected at any site during a one-day site survey. Results from this study indicate that the high levels of FIB observed likely stem from environmental sources combined with high persistence of FIB under the pier.

Modeling Biphasic Environmental Decay of Pathogens and Implications for Risk Analysis

As the appreciation for the importance of the environment in infectious disease transmission has grown, so too has interest in pathogen fate and transport. Fate has been traditionally described by simple exponential decay, but there is increasing recognition that some pathogens demonstrate a biphasic pattern of decay-fast followed by slow. While many have attributed this behavior to population heterogeneity, we demonstrate that biphasic dynamics can arise through a number of plausible mechanisms. We examine the identifiability of a general model encompassing three such mechanisms: population heterogeneity, hardening off, and the existence of viable-but-not-culturable states. Although the models are not fully identifiable from longitudinal sampling studies of pathogen concentrations, we use a differential algebra approach to determine identifiable parameter combinations. Through case studies using Cryptosporidium and Escherichia coli, we show that failure to consider biphasic pathogen dynamics can lead to substantial under- or overestimation of disease risks and pathogen concentrations, depending on the context. More reliable models for environmental hazards and human health risks are possible with an improved understanding of the conditions in which biphasic die-off is expected. Understanding the mechanisms of pathogen decay will ultimately enhance our control efforts to mitigate exposure to environmental contamination.

Persistence analysis of poliovirus on three different types of fomites

AIMS

The goal of this study was to explore various models for describing viral persistence (infectivity) on fomites and identify the best fit models.

METHODS AND RESULTS

The persistence of poliovirus over time was studied on three different fomite materials: steel, cotton and plastic. Known concentrations of poliovirus type 1 were applied to the surface coupons in an indoor environment for various lengths of time. Viruses were recovered from the surfaces by vortexing in phosphate buffer. Seven different mathematical models of relative persistence over time were fit to the data, and the preferred model for each surface was selected based on the Bayesian information criterion.

CONCLUSIONS

While the preferred model varied by fomite type, the virus showed a rapid initial decay on all of the fomite types, followed by a transition to a more gradual decay after about 4-8 days. Estimates of the time for 99% reduction ranged from 81 h for plastic to 143 h for cotton. A 6 log reduction of recoverable infectivity of poliovirus did not occur during the 3-week duration of the experiment for any of the fomites.

SIGNIFICANCE AND IMPACT OF THE STUDY

In protected indoor environments poliovirus can remain infective for weeks. The models identified by this study can be used in risk assessments to identify appropriate strategies for managing this risk.

Decay rates of zoonotic pathogens and viral surrogates in soils amended with biosolids and manures and comparison of qPCR and culture derived rates

AIMS

The purpose of this study was to establish inactivation decay constants of foodborne pathogens and coliphage in clay and sandy soils for future "downstream" analyses such as quantitative microbial risk analysis and to compare cultivation-dependent and -independent (e.g. qPCR) methods.

METHODS AND RESULTS

Salmonella enterica, Campylobacter jejuni, Listeria monocytogenes, Escherichia coli O157:H7, and Clostridium perfringens, were seeded together with MS2 and ØX174 phages, into three waste matrices (Class B biosolids, swine lagoon effluent, cattle manure), and phosphate buffered saline (PBS) as a control, and applied to two soil types (sandy loam, clay loam) using two management practices (incorporated, surface applied). S. enterica and L. monocytogenes inactivation rates were positively affected (e.g. slower rate) by solid wastes, while C. jejuni was quickly inactivated by day 7 regardless of waste type. The use of qPCR provided more conservative inactivation rates, with qPCR-based rates typically twice as slow as cultivation-based. The effect of soil type and management were less apparent as rates were variably affected. For instance, incorporation of waste negatively impacted (e.g. faster rate) inactivation of Salmonella when measured by qPCR, while the opposite was true when measured by cultivation. Inactivation rates were organism∗waste∗soil∗management dependent since the interactions of these main effects significantly affected most combinations.

CONCLUSIONS

Class B biosolids and cattle manure most often slowed inactivation when measured by cultivation, but the complex interactions between variables and organism made sweeping conclusions difficult. On the contrary cultivation-independent inactivation rates were negatively affected by solid wastes. Inactivation rates developed by cultivation-dependent and -independent assays needs further scrutiny as interprerations can vary by orders of magnitude depending on the organism∗environment combination.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study compares decay rate data based on waste, soil, management and assay type which can be further used in risk assessments.

Decay of Coliphages in Sewage-Contaminated Freshwater: Uncertainty and Seasonal Effects

Understanding the fate of enteric viruses in water is vital for protection of water quality. However, the decay of enteric viruses is not well characterized, and its uncertainty has not been examined yet. In this study, the decay of coliphages, an indicator for enteric viruses, was investigated in situ under both sunlit and shaded conditions as well as in summer and winter. The decay rates of coliphages and their uncertainties were analyzed using a Bayesian approach. The results from the summer experiments revealed that the decay rates of somatic coliphages were significantly higher in sunlight (1.29 ± 0.06 day^-1) than in shade (0.96 ± 0.04 day^-1), but the decay rates of male-specific (F+) coliphages were not significantly different between sunlight (1.09 ± 0.09 day^-1) and shaded treatments (1.11 ± 0.08 day^-1). The decay rates of both F+ coliphages (0.25 ± 0.02 day^-1) and somatic coliphages (0.12 ± 0.01 day^-1) in winter were considerably lower than those in summer. Temperature and chlorophyll a (chla) concentration varied significantly (p < 0.001) between the two seasons, suggesting that these parameters might be important contributors to the seasonal variation of coliphage decay. Additionally, the Bayesian approach provided full distributions of decay rates and reduced the uncertainty, offering useful information for comparing decay rates under different conditions.

Evaluation of five microbial and four mitochondrial DNA markers for tracking human and pig fecal pollution in freshwater

This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84.0-88.8%) except Pig-2-Bac (100%). Specificities of the human mtDNA markers (99.1 and 98.1%) were higher than those of the human-associated microbial ones (57.0-88.8%). But this pattern was not observed in the pig-associated markers where Pig-2-Bac had 100% specificity. The reliability of H-ND6 and H-ND5 was further evidenced to identify locations of the most polluted within the Taihu Lake watershed of China. In general, the microbial DNA markers demonstrated a higher fecal concentration than the mtDNA ones; increasing temperature and sunlight exposure accelerated significantly the decay of all the DNA markers. Results of this study suggest that DNA markers H-ND6, H-ND5, and Pig-2-Bac may be among the best for fecal source tracking in water.

Quantitative detection of viable helminth ova from raw wastewater, human feces, and environmental soil samples using novel PMA-qPCR methods

In this study, we have evaluated the efficacy of propidium monoazide quantitative polymerase chain reaction (PMA-qPCR) to differentiate between viable and non-viable Ancylostoma caninum ova. The newly developed method was validated using raw wastewater seeded with known numbers of A. caninum ova. Results of this study confirmed that PMA-qPCR has resulted in average of 88 % reduction (P < 0.05) in gene copy numbers for 50 % viable +50 % non-viable when compared with 100 % viable ova. A reduction of 100 % in gene copies was observed for 100 % non-viable ova when compared with 100 % viable ova. Similar reductions (79-80 %) in gene copies were observed for A. caninum ova-seeded raw wastewater samples (n = 18) collected from wastewater treatment plants (WWTPs) A and B. The newly developed PMA-qPCR method was applied to determine the viable ova of different helminths (A. caninum, A. duodenale, Necator americanus and Ascaris lumbricoides) in raw wastewater, human fecal and soil samples. None of the unseeded wastewater samples were positive for the above-mentioned helminths. N. americanus and A. lumbricoides ova were found in unseeded human fecal and soil samples. For the unseeded human fecal samples (1 g), an average gene copy concentration obtained from qPCR and PMA-qPCR was found to be similar (6.8 × 10(5) ± 6.4 × 10(5) and 6.3 × 10(5) ± 4.7 × 10(5)) indicating the presence of viable N. americanus ova. Among the 24 unseeded soil samples tested, only one was positive for A. lumbricoides. The mean gene copy concentration in the positively identified soil sample was 1.0 × 10(5) ± 1.5 × 10(4) (determined by qPCR) compared to 4.9 × 10(4) ± 3.7 × 10(3) (determined by PMA-qPCR). The newly developed PMA-qPCR methods were able to detect viable helminth ova from wastewater and soil samples and could be adapted for health risk assessment.

Historical Associations of Molecular Measurements of Escherichia coli and Enterococci to Anthropogenic Activities and Climate Variables in Freshwater Sediment Cores

This study investigated the long-term associations of anthropogenic (sedimentary P, C, and N concentrations, and human population in the watershed), and climatic variables (air temperature, and river discharge) with Escherichia coli uidA and enterococci 23S rRNA concentrations in sediment cores from Anchor Bay (AB) in Lake St. Clair, and near the mouth of the Clinton River (CR), Michigan. Calendar year was estimated from vertical abundances of (137)Cs. The AB and CR cores spanned c.1760-2012 and c.1895-2012, respectively. There were steady state concentrations of enterococci in AB during c.1760-c.1860 and c.1910-c.2003 at ∼0.1 × 10(5) and ∼2.0 × 10(5) cell equivalents (CE) per g-dry wt, respectively. Enterococci concentrations in CR increased toward present day, and ranged from ∼0.03 × 10(5) to 9.9 × 10(5) CE/g-dry wt. The E. coli concentrations in CR and AB increased toward present day, and ranged from 0.14 × 10(7) to 1.7 × 10(7) CE/g-dry wt, and 1.8 × 10(6) to 8.5 × 10(6) CE/g-dry wt, respectively. Enterococci was associated with population and river discharge, while E. coli was associated with population, air temperature, and N and C concentrations (p < 0.05). Sediments retain records of the abundance of fecal indicator bacteria, and offer a way to evaluate responses to increased population, nutrient loading, and environmental policies.

Survival of Manure-borne and Fecal Coliforms in Soil: Temperature Dependence as Affected by Site-Specific Factors

Understanding pathogenic and indicator bacteria survival in soils is essential for assessing the potential of microbial contamination of water and produce. The objective of this work was to evaluate the effects of soil properties, animal source, experimental conditions, and the application method on temperature dependencies of manure-borne generic , O157:H7, and fecal coliforms survival in soils. A literature search yielded 151 survival datasets from 70 publications. Either one-stage or two-stage kinetics was observed in the survival datasets. We used duration and rate of the logarithm of concentration change as parameters of the first stage in the two-stage kinetics data. The second stage of the two-stage kinetics and the one-stage kinetics were simulated with the model to find the dependence of the inactivation rate on temperature. Classification and regression trees and linear regressions were applied to parameterize the kinetics. Presence or absence of two-stage kinetics was controlled by temperature, soil texture, soil water content, and for fine-textured soils by setting experiments in the field or in the laboratory. The duration of the first stage was predominantly affected by soil water content and temperature. In the model dependencies of inactivation rates on temperature, parameter estimates were significantly affected by the laboratory versus field conditions and by the application method, whereas inactivation rates at 20°C were significantly affected by all survival and management factors. Results of this work can provide estimates of coliform survival parameters for models of microbial water quality.

Effects of tillage and poultry manure application rates on Salmonella and fecal indicator bacteria concentrations in tiles draining Des Moines Lobe soils

Application of poultry manure (PM) to cropland as fertilizer is a common practice in artificially drained regions of the Upper Midwest United States. Tile-waters have the potential to contribute pathogenic bacteria to downstream waters. This 3-year study (2010-2012) was designed to evaluate the impacts of manure management and tillage practices on bacteria losses to drainage tiles under a wide range of field conditions. PM was applied annually in spring, prior to planting corn, at application rates ranging from 5 to 40 kg/ha to achieve target rates of 112 and 224 kg/ha nitrogen (PM1 and PM2). Control plots received no manure (PM0). Each treatment was replicated on three chisel-plowed (CP) plots and one no-till (NT) plot. Tile-water grab samples were collected weekly when tiles were flowing beginning 30 days before manure application to 100 days post application, and additional grab samples were obtained to target the full spectrum of flow conditions. Manure and tile-water samples were analyzed for the pathogen, Salmonella spp. (SALM), and fecal indicator bacteria (FIB), Escherichia coli (EC), and enterococci (ENT). All three bacterial genera were detected more frequently, and at significantly higher concentrations, in tile-waters draining NT plots compared to CP plots. Transport of bacteria to NT tiles was most likely facilitated by macropores, which were significantly more numerous above tiles in NT plots in 2012 as determined by smoke-testing. While post-manure samples contained higher concentrations of bacteria than pre-manure samples, significant differences were not seen between low (PM1) and high (PM2) rates of PM application. The highest concentrations were observed under the NT PM2 plot in 2010 (6.6 × 10(3) cfu/100 mL EC, 6.6 × 10(5) cfu/100 mL ENT, and 2.8 × 10(3) cfu/100 mL SALM). Individual and 30-day geometric mean ENT concentrations correlated more strongly to SALM than EC; however, SALM were present in samples with little or no FIB.

Effects of Temperature and Trophic State on Degradation of Environmental DNA in Lake Water

Degradation of environmental DNA (eDNA) in aquatic habitats can affect the interpretation of eDNA data and the ability to detect aquatic organisms. The effect of temperature and trophic state on the decay of Common Carp (Cyprinus carpio) eDNA was evaluated using lake water microcosms and quantitative PCR for a Common Carp-specific genetic marker in two experiments. The first experiment tested the effect of temperature on Common Carp eDNA decay. Common Carp eDNA exhibited exponential decay that increased with temperature. The slowest decay rate was observed at 5 °C, with a T90 value (time to 90% reduction from initial concentration) of 6.6 days, as opposed to ∼1 day at higher temperatures. In a second experiment, decay was compared across waters from lakes of different trophic states. In this experiment, Common Carp eDNA exhibited biphasic exponential decay, characterized by rapid decay for 3-8 days followed by slow decay. Decay rate was slowest in dystrophic water and fastest in oligotrophic water, and decay rate was negatively correlated to dissolved organic carbon concentration. The overall rapid decay of eDNA and the effects of temperature and water quality should be considered in protocols for water sample storage and field sampling design.

Persistence of mitochondrial DNA markers as fecal indicators in water environments

Mitochondrial DNA (mtDNA) polymerase chain reaction (PCR) technology has recently been developed to identify sources of fecal contamination, but information regarding environmental fate of mtDNA is limited. In this study, quantitative real-time PCR was used to determine the persistence of three species-specific mtDNA markers (human, pig and chicken) in river microcosms under different laboratory conditions and in dialysis tubes incubated in river environments during different seasons. Human feces had a higher abundance of mtDNA marker than pig and chicken feces. A biphasic decay pattern was observed for the mtDNA markers in microcosms incubated in darkness, and T90 (time needed for 90% reduction) ranged from 2.03 to 13.83 d. Each species-specific mtDNA marker persisted for relatively longer time at lower temperatures, and light exposure and predation increased the decay rates. Field experiments showed that the mtDNA markers could survive for longer time in winter (T90: 1.79-4.37 d) than in summer (T90: 0.60-0.75 d). Field application of mtDNA technology indicated that the markers were mainly distributed on the sites near animal breeding plants and had lower abundance in downstream water of the receiving river. This study expands our knowledge of the environmental fate of mtDNA markers and the results may be useful for practical application of the technology in fecal source tracking.

Emission and Dispersion of Bioaerosols from Dairy Manure Application Sites: Human Health Risk Assessment

In this study, we report the human health risk of gastrointestinal infection associated with inhalation exposure to airborne zoonotic pathogens emitted following application of dairy cattle manure to land. Inverse dispersion modeling with the USEPA's AERMOD dispersion model was used to determine bioaerosol emission rates based on edge-of-field bioaerosol and source material samples analyzed by real-time quantitative polymerase chain reaction (qPCR). Bioaerosol emissions and transport simulated with AERMOD, previously reported viable manure pathogen contents, relevant exposure pathways, and pathogen-specific dose-response relationships were then used to estimate potential downwind risks with a quantitative microbial risk assessment (QMRA) approach. Median 8-h infection risks decreased exponentially with distance from a median of 1:2700 at edge-of-field to 1:13 000 at 100 m and 1:200 000 at 1000 m; peak risks were considerably greater (1:33, 1:170, and 1:2500, respectively). These results indicate that bioaerosols emitted from manure application sites following manure application may present significant public health risks to downwind receptors. Manure management practices should consider improved controls for bioaerosols in order to reduce the risk of disease transmission.

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms

Laboratory microcosm experiments were conducted to determine the decay kinetics of wastewater bacteria and the change of microbial communities in beach sand and seawater. Cultivation-based methods showed that common fecal indicator bacteria (FIBs; Escherichia coli, enterococci, and Clostridium perfringens) exhibited biphasic decay patterns in all microcosms. Enterococci and C. perfringens, but not E. coli, showed significantly smaller decay rates in beach sand than in seawater. Cultivation-independent qPCR quantification of 16S rRNA gene also showed significantly slower decrease of total bacterial densities in beach sand than in seawater. Microbial community analysis by next-generation sequencing (NGS) further illustrated that the decreasing relative abundance of wastewater bacteria was contrasted by the increase in indigenous beach sand and seawater microbiota, and the overall microbial community dynamics corresponded well with the decay of individual FIB populations. In summary, the differential decay of wastewater bacteria in beach sand and in seawater provides a kinetic explanation to the often-observed higher abundance of FIBs in beach sand, and the NGS-based microbial community analysis can provide valuable insights to understanding the fate of wastewater bacteria in the context of indigenous microbial communities in natural environments.

Analysis of the persistence of enteric markers in sewage polluted water on a solid matrix and in liquid suspension

Addressing the persistence of bacterial indicators using qPCR and their respective DNA targets under various conditions is a critical part of risk assessment for water quality monitoring. The goal of this study was to examine the persistence of fecal indicator bacteria (FIB) via Escherichia coli uidA, enterococci 23S rDNA and Bacteroides thetataiotaomicron 1,6 alpha mannanase from cells attached to a solid matrix and in suspension. Raw sewage (10% vol/vol) was seeded into autoclaved river water with half of the sample volume in suspension and the other half was filtered onto membranes and stored at 4°, 27° and 37°C for up to 28 days. At various time points, DNA from cells was extracted, markers were quantified, and were fit to linear and non-linear models (first order exponential, biphasic (double) exponential, two-staged, log-logistic, and Gompertz 3-parameter). First order and biphasic exponential models fit 73% of the experimental data. Persistence increased significantly when the cells were stored in an attached state (p < 0.001). Increasing temperature had an inverse effect on persistence for the cells in suspension. Bacterial cells could be stored on a solid matrix at 4°, 27° and 37 °C for up to 27, 18, and 3 days, respectively, with <90% decay. The least stable indicator at 4°, 27° and 37 °C was B. thetataiotaomicron in suspension with T90 = 9.6, 1.8, and 1.1 days, respectively. The most persistent indicator was enterococci, with T90 > 28 days in an attached state at all temperatures.

Depth-Dependent Survival of Escherichia coli and Enterococci in Soil after Manure Application and Simulated Rainfall

Once released, manure-borne bacteria can enter runoff via interaction with the thin mixing layer near the soil surface. The objectives of this work were to document temporal changes in profile distributions of manure-borne Escherichia coli and enterococci in the near-surface soil layers after simulated rainfalls and to examine differences in survival of the two fecal indicator bacteria. Rainfall simulations were performed in triplicate on soil-filled boxes with grass cover and solid manure application for 1 h with rainfall depths of 30, 60, and 90 mm. Soil samples were collected weekly from depth ranges of 0 to 1, 1 to 2, 2 to 5, and 5 to 10 cm for 1 month. Rainfall intensity was found to have a significant impact on the initial concentrations of fecal indicator bacteria in the soil. While total numbers of enterococci rapidly declined over time, E. coli populations experienced initial growth with concentration increases of 4, 10, and 25 times the initial levels at rainfall treatment depths of 30, 60, and 90 mm, respectively. E. coli populations grew to the approximately the same level in all treatments. The 0- to 1-cm layer contained more indicator bacteria than the layers beneath it, and survival of indicator bacteria was better in this layer, with decimation times between 12 and 18 days after the first week of growth. The proportion of bacteria in the 0- to 1-cm layer grew with time as the total number of bacteria in the 0- to 10-cm layer declined. The results of this work indicate the need to revisit the bacterial survival patterns that are assumed in water quality models.