Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review

High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.

Assessment of multiple fecal contamination sources in surface waters using environmental mitochondrial DNA metabarcoding

Waterborne diseases are transmitted to humans through the fecal contamination of water, where homeothermic species are the main reservoir. Fecal indicator bacteria (FIB) are often used to determine the occurrence of fecal contamination. However, FIB cannot provide the source of fecal contamination. Furthermore, as fecal inputs and contamination could originate from multiple sources (e.g., human, livestock, wildlife), multiple source tracking markers are required to identify fecal sources. From a previous study, we developed a mitochondrial DNA (mtDNA) metabarcoding approach to assess the presence of multiple homeotherms in four surface waters. Here, we have broadened our approach by sampling 86 surface water samples from the L'Assomption River and Ville-Marie watersheds (Province of Quebec, Canada). Fecal coliform levels were higher than the expected sanitary recommendations for recreational water (> 200 CFU/100 mL) in 73 % samples. The occurrence of mtDNA from human, livestock, domestic animals, wild mammals and wild birds was found in 40-88 % of the samples. Multivariate analyses showed significant covariations between homeothermic taxa and fecal coliforms, enterococci, β-D-glucuronidase, conductivity, the human-specific Bacteroidales Hf183 genetic marker, and the human population, in the watersheds of L'Assomption River (p = 0.001) and Ville-Marie (p = 0.015) (Province of Quebec, Canada). Through the application of Bayes Theorem, it was determined that fecal coliforms co-occurred with the detection of bovine, beaver, robin and chicken mtDNA in 100 % of cases in the L'Assomption River watershed, and human mtDNA co-occurred with fecal coliforms in 93 % and 76 % of cases in L'Assomption River watershed and Ville-Marie sub-catchment, respectively. This study suggests that fecal contamination could be the result of multiple species, among which some wild animals may contribute to fecal inputs in surface waters, resulting in potential risk to human health. This reinforces the necessity of using the mtDNA metabarcoding method to monitor multi-animal species.

Microbial source tracking using molecular and cultivable methods in a tropical mixed-use drinking water source to support water safety plans

Microbial contamination deteriorates source water quality, posing a severe problem for drinking water suppliers worldwide and addressed by the Water Safety Plan framework to ensure high-quality and reliable drinking water. Microbial source tracking (MST) is used to examine different microbial pollution sources via host-specific intestinal markers for humans and different types of animals. However, the application of MST in tropical surface water catchments that provide raw water for drinking water supplies is limited. We analyzed a set of MST markers, namely, three cultivable bacteriophages and four molecular PCR and qPCR assays, together with 17 microbial and physicochemical parameters, to identify fecal pollution from general, human-, swine-, and cattle-specific sources. Seventy-two river water samples at six sampling sites were collected over 12 sampling events during wet and dry seasons. We found persistent fecal contamination via the general fecal marker GenBac3 (100 % detection; 2.10-5.42 log₁₀ copies/100 mL), with humans (crAssphage; 74 % detection; 1.62-3.81 log₁₀ copies/100 mL) and swine (Pig-2-Bac; 25 % detection; 1.92-2.91 log₁₀ copies/100 mL). Higher contamination levels were observed during the wet season (p < 0.05). The conventional PCR screening used for the general and human markers showed 94.4 % and 69.8 % agreement with the respective qPCR results. Specifically, in the studied watershed, coliphage could be a screening parameter for the crAssphage marker (90.6 % and 73.7 % positive and negative predictive values; Spearman's rank correlation coefficient = 0.66; p < 0.001). The likelihood of detecting the crAssphage marker significantly increased when total and fecal coliforms exceeded 20,000 and 4000 MPN/100 mL, respectively, as Thailand Surface Water Quality Standards, with odds ratios and 95 % confidence intervals of 15.75 (4.43-55.98) and 5.65 (1.39-23.05). Our study confirms the potential benefits of incorporating MST monitoring into water safety plans, supporting the use of this approach to ensure high-quality drinking water supplies worldwide.

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.

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla _CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla _CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla _CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.

Aptasensor Based on Microfluidic for Foodborne Pathogenic Bacteria and Virus Detection: A Review

In today's world, which is entangled with numerous foodborne pathogenic bacteria and viruses, it appears to be essential to rethink detection methods of these due to the importance of food safety in our lives. The vast majority of detection methods for foodborne pathogenic bacteria and viruses have suffered from sensitivity and selectivity due to the small size of these pathogens. Besides, these types of sensing approaches can improve on-site detection platforms in the fields of food safety. In recent, microfluidics systems as new emerging types of portable sensing approaches can introduce efficient and simple biodevice by integration with several analytical methods such as electrochemical, optical and colorimetric techniques. Additionally, taking advantage of aptamer as a selective bioreceptor in the sensing of microfluidics system has provided selective, sensitive, portable and affordable sensing approaches. Furthermore, some papers use increased data transferability ability and computational power of these sensing platforms by exploiting smartphones. In this review, we attempted to provide an overview of the current state of the recent aptasensor based on microfluidic for screening of foodborne pathogenic bacteria and viruses. Working strategies, benefits and disadvantages of these sensing approaches are briefly discussed.

Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach

Freshwater bodies receive waste, feces, and fecal microorganisms from agricultural, urban, and natural activities. In this study, the probable sources of fecal contamination were determined. Also, antibiotic resistant bacteria (ARB) were detected in the two main rivers of central Chile. Surface water samples were collected from 12 sampling sites in the Maipo (n = 8) and Maule Rivers (n = 4) every 3 months, from August 2017 until April 2019. To determine the fecal contamination level, fecal coliforms were quantified using the most probable number (MPN) method and the source of fecal contamination was determined by Microbial Source Tracking (MST) using the Cryptosporidium and Giardia genotyping method. Separately, to determine if antimicrobial resistance bacteria (AMB) were present in the rivers, Escherichia coli and environmental bacteria were isolated, and the antibiotic susceptibility profile was determined. Fecal coliform levels in the Maule and Maipo Rivers ranged between 1 and 130 MPN/100-ml, and 2 and 30,000 MPN/100-ml, respectively. Based on the MST results using Cryptosporidium and Giardia host-specific species, human, cattle, birds, and/or dogs hosts were the probable sources of fecal contamination in both rivers, with human and cattle host-specific species being more frequently detected. Conditional tree analysis indicated that coliform levels were significantly associated with the river system (Maipo versus Maule), land use, and season. Fecal coliform levels were significantly (p < 0.006) higher at urban and agricultural sites than at sites immediately downstream of treatment centers, livestock areas, or natural areas. Three out of eight (37.5%) E. coli isolates presented a multidrug-resistance (MDR) phenotype. Similarly, 6.6% (117/1768) and 5.1% (44/863) of environmental isolates, in Maipo and Maule River showed and MDR phenotype. Efforts to reduce fecal discharge into these rivers should thus focus on agriculture and urban land uses as these areas were contributing the most and more frequently to fecal contamination into the rivers, while human and cattle fecal discharges were identified as the most likely source of this fecal contamination by the MST approach. This information can be used to design better mitigation strategies, thereby reducing the burden of waterborne diseases and AMR in Central Chile.

Risk assessment of Escherichia coli in bioaerosols generated following land application of farmyard slurry

Transfer of Escherichia coli in bioaerosols to humans during and shortly after the land application of farmyard slurry may pose human health hazards, but it has not been extensively explored to date. The present study developed a quantitative risk assessment model for E. coli through the air exposure route. The probabilistic model assessed the predicted number of microorganisms in the air (PN_air) to which humans may be exposed. A Gaussian air dispersion model was used to calculate the concentration of E. coli transmitted through aerosols. Human exposure (HE) to E. coli was estimated using a Monte Carlo simulation approach. This research predicted the mean HE as 26 CFU day^-1 (95th percentile 263 CFU day^-1) and suggests the importance of keeping a distance of at least 100 m for the residential population from land spreading activities. However, the simulated mean daily or annual (once a year application) risk of 2.65 × 10^-7 person^-1 year^-1 due to land application of slurry indicates very low occupational risk for farmworkers not equipped with the personal protective equipment (PPE), who are potentially exposed to E. coli indirectly. The model found that the decay constant of E. coli in air, duration of decay, and bio-aerosolisation efficiency factor (top three) could influence HE to airborne E. coli. Furthermore, this research recommends an average time lag of at least 2.5 h following the application of farmyard slurry to the field before humans access the field again without PPE, allowing the airborne pathogen to decay, thereby ensuring occupational safety. The model suggested that the bio-aerosolisation efficiency factor (E) for other pathogens requires further investigation. The information generated from this model can help to assess likely exposure from bioaerosols triggered by land application of farmyard slurry.

Tracing sewage contamination based on sterols and stanols markers within the mainland aquatic ecosystem: a case study of Linggi catchment, Malaysia

Sewage contamination is a principal concern in water quality management as pathogens in sewage can cause diseases and lead to detrimental health effects in humans. This study examines the distribution of seven sterol compounds, namely coprostanol, epi-coprostanol, cholesterol, cholestanol, stigmasterol, campesterol, and β-sitosterol in filtered and particulate phases of sewage treatment plants (STPs), groundwater, and river water. For filtered samples, solid-phase extraction (SPE) was employed while for particulate samples were sonicated. Quantification was done by using gas chromatography-mass spectrometer (GC-MS). Faecal stanols (coprostanol and epi-coprostanol) and β-sitosterol were dominant in most STP samples. Groundwater samples were influenced by natural/biogenic sterol, while river water samples were characterized by a mixture of sources. Factor loadings from principal component analysis (PCA) defined fresh input of biogenic sterol and vascular plants (positive varimax factor (VF)1), aged/treated sewage sources (negative VF1), fresh- and less-treated sewage and domestic sources (positive VF2), biological sewage effluents (negative VF2), and fresh-treated sewage sources (VF3) in the samples. Association of VF loadings and factor score values illustrated the correlation of STP effluents and the input of biogenic and plant sterol sources in river and groundwater samples of Linggi. This study focuses on sterol distribution and its potential sources; these findings will aid in sewage assessment in the aquatic environment.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand

AIM

The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources.

METHODS AND RESULTS

A serial cross-sectional study with a risk-based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011-2012 and 2012-2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter-positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance.

CONCLUSIONS

Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in-depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides evidence that drinking water without treatment or filter-only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.

Microbial Water Quality Conditions Associated with Livestock Grazing, Recreation, and Rural Residences in Mixed-Use Landscapes

Contamination of surface waters with microbial pollutants from fecal sources is a significant human health issue. Identification of relative fecal inputs from the mosaic of potential sources common in rural watersheds is essential to effectively develop and deploy mitigation strategies. We conducted a cross-sectional longitudinal survey of fecal indicator bacteria (FIB) concentrations associated with extensive livestock grazing, recreation, and rural residences in three rural, mountainous watersheds in California, USA during critical summer flow conditions. Overall, we found that 86% to 87% of 77 stream sample sites across the study area were below contemporary Escherichia coli-based microbial water quality standards. FIB concentrations were lowest at recreation sites, followed closely by extensive livestock grazing sites. Elevated concentrations and exceedance of water quality standards were highest at sites associated with rural residences, and at intermittently flowing stream sites. Compared to national and state recommended E. coli-based water quality standards, antiquated rural regional policies based on fecal coliform concentrations overestimated potential fecal contamination by as much as four orders of magnitude in this landscape, hindering the identification of the most likely fecal sources and thus the efficient targeting of mitigation practices to address them.

What are the main factors influencing the presence of faecal bacteria pollution in groundwater systems in developing countries?

Groundwater is the major source of drinking water in most rural areas in developing countries. This resource is threatened by the potential presence of faecal bacteria coming from a variety of sources and pollution paths, the former including septic tanks, landfills, and crop irrigation with untreated, or insufficiently treated, sewage effluent. Accurately assessing the microbiological safety of water resources is essential to reduce diseases caused by waterborne faecal exposure. The objective of this study is to discern which are the most significant sanitary, hydrogeological, geochemical, and physical variables influencing the presence of faecal bacterial pollution in groundwater by means of statistical multivariate analyses. The concentration of Escherichia coli was measured in a number of waterpoints of different types in a rural area located in the coast of Kenya, assessing both a dry and a wet season. The results from the analyses reaffirm that the design of the well and their maintenance, the distance to latrines, and the geological structure of the waterpoints are the most significant variables affecting the presence of E. coli. Most notably, the presence of faecal bacteria in the study area correlates negatively with the concentration of ion Na⁺ (being an indirect indicator of fast recharge in the study site), and also negatively with the length of the water column inside the well.

Veterinary pharmaceutical residues in water resources and tap water in an intensive husbandry area in France

In intensive livestock areas, veterinary pharmaceutical residues (VPRs) can occur in water resources, but also in tap water because treatment processes are not designed to remove these contaminants. The main objective of this study is to assess the occurrence of VPRs in water resources and tap waters in Brittany. As several identical compounds are used in both veterinary and human medicine, a toolbox (stanols and pharmaceuticals) is used to help determine the origin of contamination in the case of mixed-use molecules. Water resources samples were collected from 25 sites (23 surface waters and two groundwaters) used for tap water production and located in watersheds considered as sensitive due to intensive husbandry activities. Samples were also taken at 23 corresponding tap water sites. A list of 38 VPRs of interest was analyzed. In water resources, at least one VPR was quantified in 32% of the samples. 17 different VPRs were quantified, including antibiotics, antiparasitic drugs and anti-inflammatory drugs. Concentration levels ranged between 5 ng/L and 2946 ng/L. Mixed-use pharmaceuticals were quantified in twelve samples of water resources and among these samples nine had a mixed overall fecal contamination. In the context of this large-scale study, it appeared difficult to determine precisely the factors impacting the occurrence of VPRs. VPRs were quantified in 20% of the tap water samples. Twelve VPRs were quantified, including ten compounds exclusively used in veterinary medicine and two mixed-use compounds. Concentration levels are inferior to 40 ng/L for all compounds, with the exception of the antibiotic florfenicol which was quantified at 159 ng/L and 211 ng/L. The population of Brittany may therefore be exposed to these contaminants through tap water. These observations should be put into perspective with the detection frequencies per compound which are all below 10% in both water resources and tap water.

Relationships between chemical and microbial faecal source tracking markers in urban river water and sediments during and post-discharge of human sewage

This study explores the relationships between faecal source tracking (FST) markers (quantitative Polymerase Chain Reaction (qPCR) markers and steroids), microbial indicators, the faecal ageing ratio of atypical colonies/total coliforms (AC/TC) and potential human pathogens (Giardia, Cryptosporidium and Campylobacter). Faecal source PCR markers tested were GenBac3, HumM3, HumBac (HF183-Bac708R); Bifidobacterium adolescentis, wildfowl and canine-associated markers. Sediment and water samples from the Avon River were collected during and post-discharge of untreated human sewage inputs, following a series of earthquakes, which severely damaged the Christchurch sewerage system. Significant, positive Spearman Ranks (r_s) correlations were observed between human-associated qPCR markers and steroid FST markers and Escherichia coli and F-specific RNA bacteriophage (r_s 0.57 to 0.84, p < 0.001) in water samples. These human source indicative FST markers demonstrated that they were also effective predictors of potentially pathogenic protozoa in water (r_s 0.43-0.74, p ≤ 0.002), but correlated less well with Campylobacter. Human-associated qPCR and steroid markers showed significant, substantial agreement between the two FST methods (Cohen's kappa, 0.78, p = 0.023), suggesting that water managers could be confident in the results using either method under these contamination conditions. Low levels of fluorescent whitening agents (FWA) (mean 0.06 μg/L, range 0.01-0.40 μg/L) were observed in water throughout the study, but steroids and FWA appeared to be retained in river sediments, months after continuous sewage discharges had ceased. No relationship was observed between chemical FST markers in sediments and the overlying water, and few correlations in sediment between chemical FST markers and target microorganisms. The low values observed for the faecal ageing ratio, AC/TC in water, were significantly, negatively correlated with increasing pathogen detection. This study provides support for the use of the AC/TC ratio, and qPCR and steroid FST markers as indicators of health risks associated with the discharge of raw human sewage into a freshwater system.

Human and animal microbial source tracking in a tropical river with multiple land use activities

The enhancement and restoration of the water quality of deteriorating surface water resources can be challenging, particularly for rivers with multiple usages, such as agriculture, animal husbandry, human residence, and industries. Recently, the performance of DNA-based microbial source tracking (MST) indicators detected by end-point and quantitative PCR assays for identifying sources of fecal pollution from human sewage, swine, and cattle and non-host-specific (universal) fecal pollution in the Tha Chin River basin, Thailand, was evaluated. The present study monitored these validated MST markers and various physicochemical and microbial water quality parameters in samples collected from twelve stations along the Tha Chin River during four sampling events in the wet and dry seasons. No significant difference in precipitation was observed between the wet and dry samplings. Universal markers (both PCR and qPCR) were detected in all 48 samples, indicating persistent and continuing fecal contamination. The sewage- and swine-specific qPCR marker concentrations did not vary among the sampling events, whereas cattle-specific qPCR markers were detected only in the wet season. Animal-specific markers were detected in the lower Tha Chin River section, which is characterized by intensive animal farming. Sewage-specific markers were also found in the lower section and near an upstream residential area. The high agreement (87.5-100%) between the PCR and qPCR results suggested that PCR could serve as a lower-cost MST screening test that requires less technical expertise. A multivariate analysis conducted using the survival analysis procedure to include censored data also emphasized the high pollution in the lower section of the river at all sampling events. Universal and swine-specific markers showed moderate correlations with microbial indicators, including total coliforms, fecal coliforms, E. coli, and enterococci. None of the MST markers or microbial parameters were associated with the measured physicochemical parameters. This study provides the first evaluation of MST markers for monitoring surface freshwater in Thailand, and the findings might aid the pollution surveillance of impaired water bodies and the development of strategies for improving their water quality.

How can we improve understanding of faecal indicator dynamics in karst systems under changing climatic, population, and land use stressors? - Research opportunities in SW China

Human exposure to water contaminated with faeces is a leading cause of worldwide ill-health. Contaminated water can be transmitted rapidly in karst terrain as a result of the connectivity of surface and groundwater systems, high transmissivity of aquifers over large areas, and well-developed underground conduit systems. Faecal indicator organisms (FIOs) are the most widely-used indicator of faecal contamination and microbial water quality; however, the conceptualisation of FIO risk and associated sources, pathways, and survival dynamics of FIOs in karst landscapes requires a degree of modification from traditional conceptual models of FIO fate and transfer in non-karst systems. While a number of reviews have provided detailed accounts of the state-of-the-science concerning FIO dynamics in catchments, specific reference to the uniqueness of karst and its influence on FIO fate and transfer is a common omission. In response, we use a mixed methods approach of critical review combined with a quantitative survey of 372 residents of a typical karst catchment in the southwest China karst region (SWCKR) to identify emerging research needs in an area where much of the population lives in poverty and is groundwater dependent. We found that the key research needs are to understand: 1) overland and subsurface FIO export pathways in karst hydrology under varying flow conditions; 2) urban and agricultural sources and loading in mixed land-use paddy farming catchments; 3) FIO survival in paddy farming systems and environmental matrices in karst terrain; 4) sediment-FIO interactions and legacy risk in karst terrain; and 5) key needs for improved hydrological modelling and risk assessment in karst landscapes. Improved knowledge of these research themes will enable the development of evidence-based faecal contamination mitigation strategies for managing land and water resources in the SWCKR, which is highly vulnerable to climate change impacts on water supply and quality of water resources.

Application of lactic acid derived from food waste on pathogen inactivation in fecal sludge: a review on the alternative use of food waste

Food waste generation and disposal have led to several environmental problems, especially in developing countries. This phenomenon is partly because most cities rapidly urbanize, which results in population increase, urban settlement and waste generation. Improper management of waste has continued to create environmental problems. These problems have indeed interfered with the inadequate measures in managing other organic waste such as food waste. Food waste can be fermented and used for pathogen inactivation in fecal sludge (FS). The continual decrease in global crop production due to soil erosion, nutrient runoff and loss of organic matter has generated interest in using FS for soil amendment. However, due to the high number of pathogens in FS that are harmful to humans, FS must be treated before being used in agriculture. Thus, given the high amounts of food waste generated globally and the lactic acid potential of fermented food waste, several researchers have recently proposed the use of fermented food waste to suppress pathogens in FS. This review presents the various approaches in pathogen inactivation in FS using different types of food waste. On the basis of the literature review, the major problems associated with the generation, collection and application of food waste in pathogen inactivation in FS are discussed. Moreover, the trends and challenges that concern the applicability of each method are critically reviewed.