Application of library-independent microbial source tracking methods for identifying the sources of faecal contamination in coastal areas

Temporal variations in fecal indicator bacteria in bathing water and sediment in a coastal ecosystem (Aytré Bay, Charente-Maritime, France)

This study presents the fecal contamination dynamic at the two bathing sites of Aytré Bay (Charente Maritime, France). We quantified fecal indicator bacteria (FIB) abundances (Escherichia coli and enterococci) from water and sediment samples over one-year survey. Then we measured biological (bacterial abundance, chlorophyll-a), physico-chemical (dissolved nutrients and oxygen, salinity, pH …) and climatic (temperatures, rainfall and tidal coefficient) parameters. Results showed that FIB abundances were occasionally higher than the European regulatory threshold during winter, summer and fall. The "poor quality" of the bathing water was due to high enterococci abundance. We found negative significant correlations between FIB and water temperature and salinity, and positive significant correlations between FIB and rainfall, PO₄, NO₃, NO₂, and SiO₂ mainly in water. Relationships between parameters showed that during summer and spring the main environmental drivers were temperature and salinity, while in fall and winter they were rainfall and dissolved nutrients.

Use of coliphages to investigate norovirus contamination in a shellfish growing area in Republic of Korea

A number of severe norovirus outbreaks due to the consumption of contaminated shellfish have been reported recently. In this study, we evaluated the distribution of coliphage densities to determine their efficacy as fecal indicators of enteric viruses, including noroviruses, in water samples collected from a shellfish growing area in Republic of Korea over a period of approximately 1 year. Male-specific and somatic coliphages in water samples were analyzed using the single agar layer method, and norovirus genogroups I and II, which infect mainly humans, were analyzed using duplex reverse transcription quantitative PCR. Male-specific and somatic coliphages were detected widely throughout the study area. Several environmental parameters, including salinity, precipitation, temperature, and wind speed were significantly correlated with coliphage concentrations (P < 0.05). Moreover, the concentrations of male-specific coliphages were positively correlated with the presence of human noroviruses (r = 0.443; P < 0.01). The geospatial analysis with coliphage concentrations using a geographic information system revealed that densely populated residential areas were the major source of fecal contamination. Our results indicate that coliphage monitoring in water could be a useful approach to prevent norovirus contamination in shellfish.

Host-Specific Bacteroides Markers-Based Microbial Source Tracking in Aquaculture Areas

Various waterborne pathogens originate from human or animal feces and may cause severe gastroenteric outbreaks. Bacteroides spp. that exhibit strong host- or group-specificities are promising markers for identifying fecal sources and their origins. In the present study, 240 water samples were collected from two major aquaculture areas in Republic of Korea over a period of approximately 1 year, and the concentrations and occurrences of four host-specific Bacteroides markers (human, poultry, pig, and ruminant) were evaluated in the study areas. Host-specific Bacteroides markers were detected widely in the study areas, among which the poultry-specific Bacteroides marker was detected at the highest concentration (1.0-1.2 log₁₀ copies L^-1). During the sampling period, high concentrations of host-specific Bacteroides markers were detected between September and December 2015. The host-specific Bacteroides marker-combined geospatial map revealed the up-to-downstream gradient of fecal contamination, as well as the effects of land-use patterns on host-specific Bacteroides marker concentrations. In contrast to traditional bacterial indicators, the human-specific Bacteroides marker correlated with human specific pathogens, such as noroviruses (r=0.337; P<0.001). The present results indicate that host-specific Bacteroides genetic markers with an advanced geospatial analysis are useful for tracking fecal sources and associated pathogens in aquaculture areas.

Norwegian study on microbial source tracking for water quality control and pollution removal in constructed wetland treating catchment run-off

This study describes the first Norwegian microbial source tracking (MST) approach for water quality control and pollution removal from catchment run-off in a nature-based treatment system (NBTS) with a constructed wetland. The applied MST tools combined microbial analyses and molecular tests to detect and define the source(s) and dominant origin(s) of faecal water contamination. Faecal indicator bacteria Escherichia coli and host-specific Bacteroidales 16 s rRNA gene markers have been employed. The study revealed that the newly developed contribution profiling of faecal origin derived from the Bacteroidales DNA could quantitatively distinguish between human and non-human pollution origins. Further, the outcomes of the MST test have been compared with the results of both physicochemical analyses and tests of pharmaceutical and personal care products (PPCPs). A strong positive correlation was discovered between the human marker and PPCPs. Gabapentin was the most frequently detected compound and it showed the uppermost positive correlation with the human marker. The study demonstrated that the NBTS performs satisfactorily with the removal of E. coli but not PPCPs. Interestingly, the presence of PPCPs in the water samples was not correlated with high concentrations of E. coli. Neither has the latter an apparent correlation with the human marker.

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

BACKGROUND

Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.

RESULTS

We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.

CONCLUSION

This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

The emerging microbial source tracking (MST) methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes high throughput sequencing (HTS) to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU) analysis was then performed, from which sequences were retained for downstream quantitative polymerase chain reaction (qPCR) marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae, and other bacteria. Two assays (Av4143 and Av163) identified most of the avian fecal samples and demonstrated sensitivity values of 91 and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216) identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

Male-specific coliphages for source tracking fecal contamination in surface waters and prevalence of Shiga-toxigenic Escherichia coli in a major produce production region of the Central Coast of California

To provide data for traditional trace-back studies from fork to farm, it is necessary to determine the environmental sources for Shiga-toxigenic Escherichia coli. We developed SYBR green based reverse-transcriptase PCR methods to determine the prevalence of F+ RNA coliphages (FRNA) as indicators of fecal contamination. Male-specific coliphages, determined using a single-agar overlay method, were prevalent in all surface waters sampled for 8 months. F+ DNA coliphages (FDNA) were predominant compared to FRNA in water samples from majority of sampling locations. Most (90%) of the FRNA were sourced to humans and originated from human-impacted sites. Members of genogroup III represented 77% of FRNA originated from human sources. Furthermore, 93% of FRNA sourced to animals were also detected in water samples from human-impacted sites. Eighty percent of all FRNA were isolated during the winter months indicating seasonality in prevalence. In contrast, FDNA were more prevalent during summer months. E. coli O157:H7 and Shiga-toxigenic E. coli were detected in water samples from locations predominantly influenced by agriculture. Owing to their scarcity, their numbers could not be correlated with the prevalence of FRNA or FDNA in water samples. Both coliform bacteria and generic E. coli from agricultural or human-impacted sites were similar in numbers and thus could not be used to determine the sources of fecal contamination. Data on the prevalence of male-specific coliphages may be invaluable for predicting the sources of fecal contamination and aid in developing methods to prevent enteric pathogen contamination from likely sources during produce production.

Microbial Source Tracking in Adjacent Karst Springs

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment.

Incorporating expert judgments in utility evaluation of bacteroidales qPCR assays for microbial source tracking in a drinking water source

Several assays for the detection of host-specific genetic markers of the order Bacteroidales have been developed and used for microbial source tracking (MST) in environmental waters. It is recognized that the source-sensitivity and source-specificity are unknown and variable when introducing these assays in new geographic regions, which reduces their reliability and use. A Bayesian approach was developed to incorporate expert judgments with regional assay sensitivity and specificity assessments in a utility evaluation of a human and a ruminant-specific qPCR assay for MST in a drinking water source. Water samples from Lake Rådasjön were analyzed for E. coli, intestinal enterococci and somatic coliphages through cultivation and for human (BacH) and ruminant-specific (BacR) markers through qPCR assays. Expert judgments were collected regarding the probability of human and ruminant fecal contamination based on fecal indicator organism data and subjective information. Using Bayes formula, the conditional probability of a true human or ruminant fecal contamination given the presence of BacH or BacR was determined stochastically from expert judgments and regional qPCR assay performance, using Beta distributions to represent uncertainties. A web-based computational tool was developed for the procedure, which provides a measure of confidence to findings of host-specific markers and demonstrates the information value from these assays.

Are fecal stanols suitable to record and identify a pulse of human fecal contamination in short-term exposed shellfish? A microcosm study

In this study, the capacity of oysters to bioaccumulate fecal stanols and to record a source-specific fingerprint was investigated by the short-term contamination of seawater microcosms containing oysters with a human effluent. Contaminated oysters bioaccumulated the typical fecal stanols coprostanol and 24-ethylcoprostanol and their bioaccumulation kinetics were similar to that of the Fecal Indicator Bacteria Escherichia coli used in European legislation. Although stanol fingerprints of contaminated water allowed the identification of the human specific fingerprint, this was not the case for oysters. This discrepancy is attributed to (i) high concentrations of endogenous cholestanol and sitostanol, responsible for "unbalanced" stanol fingerprints, (ii) different accumulation/depuration kinetics of fecal coprostanol and 24-ethylcoprostanol and (iii) the limits of the analytical pathway used. These results show that fecal stanols bioaccumulated by oysters are useful to record fecal contamination but the usefulness of stanol fingerprints to identify specific sources of contamination in shellfish currently seems limited.

Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

Quantitative multi-year elucidation of fecal sources of waterborne pathogen contamination in the South Nation River basin using bacteroidales microbial source tracking markers

Over a seven-year period (2004-2010) 1095 water samples were obtained from the South Nation River basin at multiple watershed monitoring sites (Ontario, Canada). Real-time PCR using Bacteroidales specific markers was used to identify the origin (human (10% prevalence), ruminant (22%), pig (~2%), Canada goose (4%) and muskrat (7%)) of fecal pollution. In parallel, the distribution of fecal indicator bacteria and waterborne pathogens (Cryptosporidium oocysts, Giardia cysts, Escherichia coli O157:H7, Salmonella enterica and Campylobacter spp.) was evaluated. Associations between the detection of specific Bacteroidales markers and the presence of fecal indicator bacteria, pathogens, and distinct land use or environmental variables were evaluated. Linear correlations between Bacteroidales markers and fecal indicator bacteria were weak. However, mean marker densities, and the presence and absence of markers could be discriminated on the basis of threshold fecal indicator densities. The ruminant-specific Bacteroidales marker was the most frequently detected marker in water, consistent with the large number of dairy farms in the study area. Detection of the human or the ruminant markers were associated with a slightly higher risk of detecting S. enterica. Detection of the muskrat marker was related to more frequent Campylobacter spp. detections. Important positive associations between markers and pathogens were found among: i) total Bacteroidales and Cryptosporidium and Giardia, ii) ruminant marker and S. enterica, and iii) muskrat and Campylobacter spp.

Recent innovation in microbial source tracking using bacterial real-time PCR markers in shellfish

We assessed the capacity of real-time PCR markers to identify the origin of contamination in shellfish. Oyster, cockles or clams were either contaminated with fecal materials and host-associated markers designed from Bacteroidales or Catellicoccus marimammalium 16S RNA genes were extracted from their intravalvular liquid, digestive tissues or shellfish flesh. Extraction of bacterial DNA from the oyster intravalvular liquid with FastDNA spin kit for soil enabled the selected markers to be quantified in 100% of artificially contaminated samples, and the source of contamination to be identified in 13 out of 38 naturally contaminated batches from European Class B and Class C areas. However, this protocol did not enable the origin of the contamination to be identified in cockle or clam samples. Although results are promising for extracts from intravalvular liquid in oyster, it is unlikely that a single protocol could be the best across all bacterial markers and types of shellfish.