Evaluation of the enterococci indicator in biosolids using culture-based and quantitative PCR assays

The risk of viable but non-culturable (VBNC) enterococci and antibiotic resistance transmission during simulated municipal sludge composting

Sludge composting is a sludge resource utilization method that can reduce pollutants, such as pathogens. Enterococci are regarded as more reliable and conservative indicators of pathogen inactivation than fecal coliforms, which are typically used as indicators of fecal pollution. Non-spore pathogenic bacteria may enter a viable but non-culturable (VBNC) state during composting, leading to residual risk. The VBNC status of bacteria is related to their survival during composting. However, the survival mechanisms of enterococci during sludge composting remain unclear. Therefore, this study aimed to investigate the VBNC state of enterococci in different phases of simulated sludge composting and the fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) during the composting process. This study is expected to provide a basis for subsequent exploration of possible methods to completely inactivate enterococci and reduce ARGs during sludge composting. Culturable enterococci were reduced in the thermophilic phase of sludge composting, but the proportion of VBNC subpopulation increased. It was reported for the first time that most VBNC enterococci were killed by extending the cooling phase of sludge compost, and by prolonging the cooling phase the types of ARG were reduced. However, there was a certain quantity (approximately 104/g dry weight) of culturable and VBNC enterococci in the compost products. In addition, MGEs and ARGs exist in both bacteria and compost products, leading to the risk of spreading antibiotic-resistant bacteria and antibiotic resistance when sludge compost products are used.

SARS-CoV-2 and other pathogens in municipal wastewater, landfill leachate, and solid waste: A review about virus surveillance, infectivity, and inactivation

This review discusses the techniques available for detecting and inactivating of pathogens in municipal wastewater, landfill leachate, and solid waste. In view of the current COVID-19 pandemic, SARS-CoV-2 is being given special attention, with a thorough examination of all possible transmission pathways linked to the selected waste matrices. Despite the lack of works focused on landfill leachate, a systematic review method, based on cluster analysis, allows to analyze the available papers devoted to sewage sludge and wastewater, allowing to focalize the work on technologies able to detect and treat pathogens. In this work, great attention is also devoted to infectivity and transmission mechanisms of SARS-CoV-2. Moreover, the literature analysis shows that sewage sludge and landfill leachate seem to have a remote chance to act as a virus transmission route (pollution-to-human transmission) due to improper collection and treatment of municipal wastewater and solid waste. However due to the incertitude about virus infectivity, these possibilities cannot be excluded and need further investigation. As a conclusion, this paper shows that additional research is required not only on the coronavirus-specific disinfection, but also the regular surveillance or monitoring of viral loads in sewage sludge, wastewater, and landfill leachate. The disinfection strategies need to be optimized in terms of dosage and potential adverse impacts like antimicrobial resistance, among many other factors. Finally, the presence of SARS-CoV-2 and other pathogenic microorganisms in sewage sludge, wastewater, and landfill leachate can hamper the possibility to ensure safe water and public health in economically marginalized countries and hinder the realization of the United Nations' sustainable development goals (SDGs).

Rural blackwater treatment by a full-scale Brazilian Biodigester Septic Tank: microbial indicators and pathogen removal efficiency

The Brazilian Biodigester Septic Tank (BBST) is an on-site appropriate technology for blackwater treatment, which was developed to yield an effluent suitable for agricultural use. Although several studies have proven its efficacy for secondary blackwater treatment, there are few published studies about the microbiological quality of its effluent, and most of them focus on the quantification of total or thermotolerant coliforms. This study evaluates the performance of a BBST for the removal of human adenovirus (HAdV), Enterococcus spp., Salmonella sp., and Escherichia coli. The results further clarify the safety and risks associated with the reuse of the obtained effluent. The full-scale system consists of three 1.2 m³ interconnected reactors, with a blackwater input of 0.045 m³/day, and hydraulic retention time of 80 days. Six sample campaigns were performed at different stages of the monthly operating cycle. The system presented an average removal efficiency of 5.09 log₁₀ for E. coli, 3.22 log₁₀ for Enterococcus spp., 1.2 log₁₀ for Salmonella sp., and 3.0 log₁₀ for HAdV. According to the World Health Organization standards, the obtained effluent is suitable for subsurface irrigation, and for use in crops that develop distant from the soil or highly mechanized crop systems.

Selection of indigenous indicator micro-organisms for validating desiccation-adapted Salmonella reduction in physically heat-treated poultry litter

AIMS

The thermal resistance of desiccation-adapted Salmonella Senftenberg 775/W was compared with those of indigenous enterococci and total aerobic bacteria in poultry litter.

METHODS AND RESULTS

Aged broiler litter and composted turkey litter with 20, 30, 40 and 50% moisture contents were inoculated with desiccation-adapted Salm. Senftenberg 775/W, and then heat-treated at 75 and 85°C. Compared to total aerobic bacteria, there were better correlations between mean log reductions of desiccation-adapted Salm. Senftenberg 775/W and indigenous enterococci in broiler litter samples with 20, 30, 40 and 50% moisture contents at 75°C (R²  > 0·91), and 20, 30 and 40% moisture contents at 85°C (R²  > 0·87). The mean log reductions of Salm. Senftenberg 775/W were better correlated with those of indigenous enterococci in turkey litter samples with 20, 30, 40 and 50% moisture contents at 75°C (R²  > 0·88), and 20 and 30% moisture contents at 85°C (R²  = 0·83) than those of total aerobic bacteria, which had a better correlation in turkey litter sample with 40% (R²  = 0·98) moisture content at 85°C.

CONCLUSION

Indigenous enterococci may be used to validate the thermal processing of poultry litter, as it predicts the survival behaviour of Salmonella under some treatment conditions.

SIGNIFICANCE AND THE IMPACT OF THE STUDY

This study provides some scientific data for poultry litter processors when validating the effectiveness of thermal processing.

Anaerobic Membrane Bioreactor Effluent Reuse: A Review of Microbial Safety Concerns

Broad and increasing interest in sustainable wastewater treatment has led a paradigm shift towards more efficient means of treatment system operation. A key aspect of improving overall sustainability is the potential for direct wastewater effluent reuse. Anaerobic membrane bioreactors (AnMBRs) have been identified as an attractive option for producing high quality and nutrient-rich effluents during the treatment of municipal wastewaters. The introduction of direct effluent reuse does, however, raise several safety concerns related to its application. Among those concerns are the microbial threats associated with pathogenic bacteria as well as the emerging issues associated with antibiotic-resistant bacteria and the potential for proliferation of antibiotic resistance genes. Although there is substantial research evaluating these topics from the perspectives of anaerobic digestion and membrane bioreactors separately, little is known regarding how AnMBR systems can contribute to pathogen and antibiotic resistance removal and propagation in wastewater effluents. The aim of this review is to provide a current assessment of existing literature on anaerobic and membrane-based treatment systems as they relate to these microbial safety issues and utilize this assessment to identify areas of potential future research to evaluate the suitability of AnMBRs for direct effluent reuse.

An investigation of the antibacterial ability and cytotoxicity of a novel cu-bearing 317L stainless steel

In order to solve the challenging problem of microbial infections caused by microorganisms on medical implants, it is imperative to develop novel antimicrobial biomaterials. This work demonstrated that 317L-Cu stainless steel (SS), created by adding copper through a solution and aging heat treatment process, exhibited good antibacterial properties against staphylococcus aureus, achieving 2 log reduction of planktonic cells after 5 days of incubation. In this study, the antibacterial test was performed using the plate count method, the fluorescence cell staining method and the quantitative polymerase chain reaction (qPCR) method. It is well known that a high concentration of copper ion can lead to cytotoxicity. This work explored the cytotoxicity of 317L-Cu SS through real-time cell analysis (RTCA). Experimental results demonstrated that the 317L-Cu SS possessed a satisfactory antibacterial ability against S. aureus, and the antibacterial rate based on the reduction of sessile cell count reached 98.3% after 24-hour treatment. The bacterial adhesion and the biofilm thickness were considerably reduced by the 317L-Cu SS. The results of RTCA suggested that 317L-Cu SS did not introduce cytotoxicity to mouse cells, indicating its suitability as a medical implant material.

Comparison of Methods to Identify Pathogens and Associated Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada

The use of treated municipal wastewater residues (biosolids) as fertilizers is an attractive, inexpensive option for growers and farmers. Various regulatory bodies typically employ indicator organisms (fecal coliforms, E. coli and Salmonella) to assess the adequacy and efficiency of the wastewater treatment process in reducing pathogen loads in the final product. Molecular detection approaches can offer some advantages over culture-based methods as they can simultaneously detect a wider microbial species range, including non-cultivable microorganisms. However, they cannot directly assess the viability of the pathogens. Here, we used bacterial enumeration methods together with molecular methods including qPCR, 16S rRNA and cpn60 gene amplicon sequencing and shotgun metagenomic sequencing to compare pre- and post-treatment biosolids from two Canadian wastewater treatment plants (WWTPs). Our results show that an anaerobic digestion WWTP was unsuccessful at reducing the live indicator organism load (coliforms, generic E. coli and Salmonella) below acceptable regulatory criteria, while biosolids from a dewatering/pelletization WWTP met these criteria. DNA from other pathogens was detected by the molecular methods, but these species were considered less abundant. Clostridium DNA increased significantly following anaerobic digestion treatments. In addition to pathogen DNA, genes related to virulence and antibiotic resistance were identified in treated biosolids. Shotgun metagenomics revealed the widest range of pathogen DNA and, among the approaches used here, was the only approach that could access functional gene information in treated biosolids. Overall, our results highlight the potential usefulness of amplicon sequencing and shotgun metagenomics as complementary screening methods that could be used in parallel with culture-based methods, although more detailed comparisons across a wider range of sites would be needed.

Fate of Viable but Non-culturable Listeria monocytogenes in Pig Manure Microcosms

The fate of two strains of Listeria monocytogenes and their ability to become viable but non-culturable (VBNC) was investigated in microcosms containing piggery effluents (two raw manures and two biologically treated manures) stored for 2 months at 8 and 20°C. Levels of L. monocytogenes were estimated using the culture method, qPCR, and propidium monoazide treatment combined with qPCR (qPCRPMA). The chemical composition and the microbial community structure of the manures were also analyzed. The strains showed similar decline rates and persisted up to 63 days. At day zero, the percentage of VBNC cells among viable cells was higher in raw manures (81.5-94.8%) than in treated manures (67.8-79.2%). The changes in their proportion over time depended on the temperature and on the type of effluent: the biggest increase was observed in treated manures at 20°C and the smallest increase in raw manures at 8°C. The chemical parameters had no influence on the behavior of the strains, but decrease of the persistence of viable cells was associated with an increase in the microbial richness of the manures. This study demonstrated that storing manure altered the culturability of L. monocytogenes, which rapidly entered the VBNC state, and underlines the importance of including VBNC cells when estimating the persistence of the pathogens in farm effluents.

Use of real-time PCR with propidium monoazide for enumeration of viable Escherichia coli in anaerobic digestion

A combination of propidium monoazide (PMA) with real-time quantitative polymerase chain reaction (PMA-qPCR) was optimized to enumerate only viable Escherichia coli in anaerobic digestion processes. Repeating the PMA treatment twice and a final concentration of 100 μM resulted in an effective exclusion of DNA from heat-treated E. coli cells. In three anaerobic digestion processes, real-time PCR, PMA-qPCR, and the most probable number method (MPN) were used to estimate the numbers of total, viable, and culturable E. coli cells, respectively. Culturable concentrations of fecal coliforms were also measured by the membrane filter method. For thermophilic digestion, the reductions in total and viable E. coli cells from the digester influent to the effluent were significantly lower than those in culturable cells and fecal coliforms by two to four orders of magnitude. For mesophilic digestion, the differences in the reductions in E. coli and fecal coliforms counts were less than two orders of magnitude. Based on the measurements of viable E. coli determined by the PMA-qPCR method, the microbial quality of digester effluents was discussed for agricultural application, and pasteurization after anaerobic digestion was suggested for the destruction of viable pathogens.

Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants

The propagation of antibiotic resistance genes (ARGs) is an emerging health concern worldwide. Thus, it is important to understand and mitigate their occurrence in different systems. In this study, 30 ARGs that confer resistance to tetracyclines, sulfonamides, quinolones or macrolides were detected in two activated sludge wastewater treatment plants (WWTPs) in northern China. Bacteria harboring ARGs persisted through all treatment units, and survived disinfection by chlorination in greater percentages than total Bacteria (assessed by 16S rRNA genes). Although the absolute abundances of ARGs were reduced from the raw influent to the effluent by 89.0%-99.8%, considerable ARG levels [(1.0 ± 0.2) × 10(3) to (9.5 ± 1.8) × 10(5) copies/mL)] were found in WWTP effluent samples. ARGs were concentrated in the waste sludge (through settling of bacteria and sludge dewatering) at (1.5 ± 2.3) × 10(9) to (2.2 ± 2.8) × 10(11) copies/g dry weight. Twelve ARGs (tetA, tetB, tetE, tetG, tetH, tetS, tetT, tetX, sul1, sul2, qnrB, ermC) were discharged through the dewatered sludge and plant effluent at higher rates than influent values, indicating overall proliferation of resistant bacteria. Significant antibiotic concentrations (2%-50% of raw influent concentrations) remained throughout all treatment units. This apparently contributed selective pressure for ARG replication since the relative abundance of resistant bacteria (assessed by ARG/16S rRNA gene ratios) was significantly correlated to the corresponding effluent antibiotic concentrations. Similarly, the concentrations of various heavy metals (which induce a similar bacterial resistance mechanism as antibiotics - efflux pumps) were also correlated to the enrichment of some ARGs. Thus, curtailing the release of antibiotics and heavy metals to sewage systems (or enhancing their removal in pre-treatment units) may alleviate their selective pressure and mitigate ARG proliferation in WWTPs.

Effect of solarization on the removal of indicator microorganisms from municipal sewage sludge

The effect of solarization on bacterial inactivation in sewage sludge was studied using thermotolerant coliforms, enterococci and Escherichia coli (E. coli) as the indicator organisms. Solarization significantly increased the sludge temperature. The maximum temperatures were achieved at the beginning of the second week, reaching 65, 58, 55 and 50 degrees C at depths of 0-10, 10-20, 20-30 and 30-40 cm, respectively. E. coli was found to be the most sensitive microorganism and was reduced to undetectable levels after 9 d at all monitored sludge depths. Thermotolerant coliforms were rapidly inactivated but were not reduced to below the detection limit. The inactivation curves of enterococci showed both shoulders and tailing, indicating a larger heat resistant fraction than with E. coli and the thermotolerant coliforms. Overall, the results suggest that the temperature regime produced by solarization was sufficient to reduce bacterial indicators to an acceptable level, meeting the pathogen regulation limit, in two weeks.

Removal of faecal indicator pathogens from waters and wastewaters by photoelectrocatalytic oxidation on TiO(2)/Ti films under simulated solar radiation

PURPOSE

The disinfection efficiency of water and secondary treated wastewater by means of photoelectrocatalytic oxidation (PEC) using reference strains of Enterococcus faecalis and Escherichia coli as faecal indicators was evaluated. Operating parameters such as applied potential (2-10 V), initial bacterial concentration (10(3)-10(7) CFU/mL), treatment time (up to 90 min) and aqueous matrix (pure water and treated effluent) were assessed concerning their impact on disinfection.

METHODS

PEC experiments were carried out using a TiO(2)/Ti film anode and a zirconium cathode in the presence of simulated solar radiation. Bacterial inactivation was monitored by the culture method and real-time SYBR green PCR.

RESULTS

A 6.2 log reduction in E. faecalis population was achieved after 15 min of PEC treatment in water at 10 V of applied potential and an initial concentration of 10(7) CFU/mL; pure photocatalysis (PC) led to only about 4.3 log reduction, whilst negligible inactivation was recorded when the respective electrochemical oxidation process was applied (i.e. without radiation). PEC efficiency was generally improved increasing the applied potential and decreasing initial bacterial concentration. Regarding real wastewater, E. coli was more susceptible than E. faecalis during treatment at a potential of 5 V. Wastewater disinfection was affected by its complex composition and the contained mixed bacterial populations, yielding lower inactivation rates compared to water treatment. Screening the results obtained from both applied techniques (culture method and real-time PCR), there was a discrepancy regarding the recorded time periods of total bacterial inactivation, with qPCR revealing longer periods for complete bacterial reduction.

CONCLUSIONS

PEC is superior to PC in terms of E. faecalis inactivation presumably due to a more efficient separation and utilization of the photogenerated charge carriers, and it is mainly affected by the applied potential, initial bacterial concentration and the aqueous matrix.

Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of enterococcus species in environmental samples

The detection of environmental enterococci has been determined primarily by using culture-based techniques that might exclude some enterococcal species as well as those that are nonculturable. To address this, the relative abundances of enterococci were examined by challenging fecal and water samples against a currently available genus-specific assay (Entero1). To determine the diversity of enterococcal species, 16S rRNA gene-based group-specific quantitative PCR (qPCR) assays were developed and evaluated against eight of the most common environmental enterococcal species. Partial 16S rRNA gene sequences of 439 presumptive environmental enterococcal strains were analyzed to study further the diversity of enterococci and to confirm the specificities of group-specific assays. The group-specific qPCR assays showed relatively high amplification rates with targeted species (>98%), although some assays cross-amplified with nontargeted species (1.3 to 6.5%). The results with the group-specific assays also showed that different enterococcal species co-occurred in most fecal samples. The most abundant enterococci in water and fecal samples were Enterococcus faecalis and Enterococcus faecium, although we identified more water isolates as Enterococcus casseliflavus than as any of the other species. The prevalence of the Entero1 marker was in agreement with the combined number of positive signals determined by the group-specific assays in most fecal samples, except in gull feces. On the other hand, the number of group-specific assay signals was lower in all water samples tested, suggesting that other enterococcal species are present in these samples. While the results highlight the value of genus- and group-specific assays for detecting the major enterococcal groups in environmental water samples, additional studies are needed to determine further the diversity, distributions, and relative abundances of all enterococcal species found in water.

A perspective on the prevalence of DNA enteric virus genomes in anaerobic-digested biological wastes

The major goal of this study is to gain a perspective on the prevalence of DNA enteric virus genomes in mesophilic anaerobic-digested (MAD) sewage sludge and manure by comparing their quantitative PCR (qPCR) concentrations and removals with traditional fecal indicators (Escherichia coli, enterococci, and Bacteroidetes). In addition, relationships between qPCR and culture measurements of fecal indicators (FIs) were determined. There was no significant difference between the qPCR concentrations of human adenovirus and E. coli/enterococci in MAD sewage sludge; however, the qPCR concentrations of bovine adenovirus were significantly lower than FIs and bovine polyomavirus (BPyV) in MAD manure. The qPCR concentrations of human polyomavirus were slightly lower than E. coli and enterococci (p  ≤  0.05), but no significant difference was observed between the qPCR concentrations of BPyV and FIs. The digestion treatment achieved higher genome removal of bovine DNA enteric viruses than FIs (p  ≤  0.05). Significant correlations were observed between qPCR and culture measurements of FIs, but the concentrations and removals of FIs determined by qPCR assays were still significantly different than those determined by culture assays. Overall, we determined that the prevalence of DNA enteric virus genomes in MAD biological wastes was high due to their comparable in qPCR concentrations to FIs, indicating that mesophilic anaerobic digestion treatment alone may not be effective enough to remove DNA viral pathogens in biological wastes.

Reactor performance and bacterial pathogen removal in response to sludge retention time in a mesophilic anaerobic digester treating sewage sludge

The effects of sludge retention time (SRT) on reactor performance and bacterial pathogen removal of sludge mesophilic anaerobic digestion (MAD) were investigated in a continuous stirred tank reactor. The average volatile solids removal remained around 20% and the biogas production rate varied from 100 to 132ml/ld. The MAD process was efficient to remove Salmonella sp. and Escherichia coli with removal efficiencies increased with SRT from 11d, 16d to 25d. However, the Shigella sp. removal was insignificant. The difference in the resistance of the three pathogens to sludge MAD process is helpful to the selection of pathogen indicators in the biosolids. Log reduction of pathogens determined by MPN was much higher than the data by quantitative PCR, suggesting the presence of viable but non-culturable pathogen cells. This study confirms that the control of appropriate SRT for sludge MAD should take both reactor performance and pathogen removal into account.

Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines interlaboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention was placed on the influence of the DNA isolation step and effect of simplex and multiplex amplification approaches on interlaboratory variability. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol.

Net energy production associated with pathogen inactivation during mesophilic and thermophilic anaerobic digestion of sewage sludge

The potential for anaerobic digester energy production must be balanced with the sustainability of reusing the resultant biosolids for land application. Mesophilic, thermophilic, temperature-phased, and high temperature (60 or 70 °C) batch pre-treatment digester configurations have been systematically evaluated for net energy production and pathogen inactivation potential. Energy input requirements and net energy production were modeled for each digester scheme. First-order inactivation rate coefficients for Escherichia coli, Enterococcus faecalis and bacteriophage MS-2 were measured at each digester temperature and full-scale pathogen inactivation performance was estimated for each indicator organism and each digester configuration. Inactivation rates were found to increase dramatically at temperatures above 55 °C. Modeling full-scale performance using retention times based on U.S. EPA time and temperature constraints predicts a 1-2 log inactivation in mesophilic treatment, and a 2-5 log inactivation in 50-55 °C thermophilic and temperature-phased treatments. Incorporating a 60 or 70 °C batch pre-treatment phase resulted in dramatically higher potency, achieving MS-2 inactivation of 14 and 16 logs respectively, and complete inactivation (over 100 log reduction) of E. coli and E. faecalis. For temperatures less than 70 °C, viability staining of thermally-treated E. coli showed significantly reduced inactivation relative to standard culture enumeration. Due to shorter residence times in thermophilic reactors, the net energy production for all digesters was similar (less than 20% difference) with the 60 or 70 °C batch treatment configurations producing the most net energy and the mesophilic treatment producing the least. Incorporating a 60 or 70 °C pre-treatment phase can dramatically increase pathogen inactivation performance without decreasing net energy capture from anaerobic digestion. Energy consumption is not a significant barrier against improving the pathogen quality of biosolids.

Toward a consensus view on the infectious risks associated with land application of sewage sludge

The science linking processed sewage sludge (biosolids) land application with human health has improved in the last ten years. The goal of this review is to develop a consensus view on the human health impacts associated with land-applying biosolids. Pre-existing risk studies are integrated with recent advances in biosolids pathogen exposure science and risk analysis. Other than accidental direct ingestion, the highest public risks of infection from land application are associated with airborne exposure. Multiple, independent risk assessments for enteroviruses similarly estimate the yearly probabilities of infection near 10(-4). However, the inclusion of other emerging pathogens, specifically norovirus, increases this yearly infectious risk by over 2 orders of magnitude. Quantitative microbial risk assessment for biosolids exposure more effectively operates as a tool for analyzing how exposure can be reduced rather than being used to assess "safety". Such analysis demonstrates that the tradition of monitoring pathogen quality by Salmonella spp. and enterovirus content underestimates the infectious risk to the public, and that a rigorous biosolids pathogen treatment process, rather than extending community separation distances, is the most efficient method for reducing pathogen exposure and infectious risk.

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

This study examined persistence and decay of bacterial pathogens, fecal indicator bacteria (FIB), and emerging real-time quantitative PCR (qPCR) genetic markers for rapid detection of fecal pollution in manure-amended agricultural soils. Known concentrations of transformed green fluorescent protein-expressing Escherichia coli O157:H7/pZs and red fluorescent protein-expressing Salmonella enterica serovar Typhimurium/pDs were added to laboratory-scale manure-amended soil microcosms with moisture contents of 60% or 80% field capacity and incubated at temperatures of -20°C, 10°C, or 25°C for 120 days. A two-stage first-order decay model was used to determine stage 1 and stage 2 first-order decay rate coefficients and transition times for each organism and qPCR genetic marker in each treatment. Genetic markers for FIB (Enterococcus spp., E. coli, and Bacteroidales) exhibited decay rate coefficients similar to that of E. coli O157:H7/pZs but not of S. enterica serovar Typhimurium/pDs and persisted at detectable levels longer than both pathogens. Concentrations of these two bacterial pathogens, their counterpart qPCR genetic markers (stx1 and ttrRSBCA, respectively), and FIB genetic markers were also correlated (r = 0.528 to 0.745). This suggests that these qPCR genetic markers may be reliable conservative surrogates for monitoring fecal pollution from manure-amended land. Host-associated qPCR genetic markers for microbial source tracking decayed rapidly to nondetectable concentrations, long before FIB, Salmonella enterica serovar Typhimurium/pDs, and E. coli O157:H7/pZs. Although good indicators of point source or recent nonpoint source fecal contamination events, these host-associated qPCR genetic markers may not be reliable indicators of nonpoint source fecal contamination events that occur weeks following manure application on land.

Comparison of genotypic and phylogenetic relationships of environmental Enterococcus isolates by BOX-PCR typing and 16S rRNA gene sequencing

Environmental Enterococcus spp. were compared by BOX-PCR genotyping and 16S rRNA gene sequencing to clarify the predictive relationship of BOX-PCR fingerprints to species designation. BOX-PCR and 16S rRNA gene relationships agreed for 77% of strains. BOX-PCR provided superior intraspecies discrimination but incorrectly identified some strains to the species level and divided some species into multiple groups.

Escherichia coli, enterococci, and Bacteroides thetaiotaomicron qPCR signals through wastewater and septage treatment

Fecal indicators such as Escherichia coli and enterococci are used as regulatory tools to monitor water with 24 h cultivation techniques for possible input of sewage or feces and presence of potential enteric pathogens yet their source (human or animal) cannot be determined with routine methods. This critical uncertainty has furthered water pollution science toward new molecular approaches. Members of Bacteroides genus, such as Bacteroides thetaiotaomicron are found to have features that allow their use as alternative fecal indicators and for Microbial Source Tracking (MST). The overall aim of this study was to evaluate the concentration and fate of B. thetaiotaomicron, throughout a wastewater treatment facility and septage treatment facility. A large number of samples were collected and tested for E. coli and enterococci by both cultivation and qPCR assays. B. thetaiotaomicron qPCR equivalent cells (mean: 1.8 × 10(7)/100 mL) were present in significantly higher concentrations than E. coli or enterococci in raw sewage and at the same levels in raw septage. The removal of B. thetaiotaomicron target qPCR signals was similar to E. coli and enterococci DNA during the treatment of these wastes and ranged from 3 to 5 log(10) for wastewater and was 7 log(10) for the septage. A significant correlation was found between B. thetaiotaomicron marker and each of the conventional indicators throughout the waste treatment process for both raw sewage and septage. A greater variability was found with enterococci when compared to E. coli, and CFU and equivalent cells could be contrasted by various treatment processes to examine removal and inactivation via septage and wastewater treatment. These results are compared and contrasted with other qPCR studies and other targets in wastewater samples providing a view of DNA targets in such environments.

Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids

Given the potential for a variety of bacterial pathogens to occur in variably stabilized sewage sludge (biosolids), an understanding of pathogen diversity and abundance is necessary for accurate assessment of infective risk when these products are land applied. 16S rDNA was PCR amplified from genomic DNA extracted from municipal wastewater residuals (mesophilic- and thermophilic-phased anaerobic digestion (MAD and TPAD), composting (COM)), and agricultural soil (SOIL), and these amplicons were sequenced using massively parallel pyrosequencing technology. Resulting libraries contained an average of 30,893 16S rDNA sequences per sample with an average length of 392 bases. FASTUNIFRAC-based comparisons of population phylogenetic distance demonstrated similarities between the populations of different treatment plants performing the same stabilization method (e.g. different MAD samples), and population differences among samples from different biosolids stabilization methods (COM, MAD, and TPAD). Based on a 0.03 Jukes-Cantor distance to 80 potential bacterial pathogens, all samples contained pathogens and enrichment ranged from 0.02% to 0.1% of sequences. Most (61%) species identified were opportunistic pathogens of the genera Clostridium and Mycobacterium. As risk sciences continue to evolve to address scenarios that include multiple pathogen exposure, the analysis described here can be used to determine the diversity of pathogens in an environmental sample. This work provides guidance for prioritizing subsequent culturable and quantitative analysis, and for the first time, ensuring that potentially significant pathogens are not left out of risk estimations.