Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking

Seasonally recurring patterns of dominant Crenothrix spp. in a European alluvial drinking water well: Significance and potential indicator role

Iron and manganese (Fe/Mn) often lead to aesthetic quality issues in water supply. Strong and problematic black-brown particle formation was persistently observed in an alluvial drinking water well, even though oxygen enrichment probes, intended for in situ i.e., subsurface iron/manganese removal, were installed. To investigate the cause of the problem, a comparative and multiparametric approach was undertaken at the problematic well, seven additional wells (with 0.3 to 70 km distance to the affected well) and all the adjacent surface waters. Via a time-series investigation of up to 2.5 years, microbiological analysis (high-throughput 16S rRNA gene amplicon sequencing, total cell count) and chemical analysis (high-resolution elemental analysis using inductively coupled mass spectrometry and others) of the water samples were performed. Results revealed previously unreported, extremely dynamic, and seasonally recurring patterns of genus Crenothrix (a sheathed, filamentous bacterial population) in water samples obtained from the particle-affected well. Crenothrix spp. dominated the microbial community in summer months (up to 82 % relative abundance), being virtually absent in winter. Explanatory models for the high dynamics and association with bio-geochemical processes were established. These included methane formation and manganese mobilization in relation to riverbank filtration in the summer months, as well as changing aerobic and anaerobic conditions in the aquifer. Dominance of Crenothrix spp. in the affected well, low abundance in weak particle-affected wells, and total absence in non-affected wells was observed. This led to the suggestion of Crenothrix spp. as a technical indicator for Fe/Mn treatment failure for alluvial groundwater (e.g., genetic marker quantification by q/dPCR), to be evaluated in future studies regarding their applicability across a broader geographic context. Despite being first described in association with drinking water deterioration 150 years ago, this is the first study reporting seasonally recurring dominant patterns of Crenothrix spp. in association with operational/aesthetic issues for drinking water production.

Using a harmonised study design and quantitative tool-box reveals major inconsistencies when investigating the main drivers of water and biofilm antibiotic resistomes in different rivers

The spread of antibiotic resistance (ABR) via surface waters is of increasing concern. Large-scale studies investigating ABR drivers in different water bodies and habitats with uniform quantitative methods are largely missing. Here, we present a comprehensive investigation on ABR occurrence and drivers in water and biofilms of four Austrian rivers over a one-year-cycle using a harmonised quantitative tool-box and study-design. At the bacterial community level, human faecal pollution was a main factor driving the aquatic riverine resistome. Despite relatively low concentrations, also antibiotics and metals showed significant correlations, however to a different extent in the different rivers. At the organismic level, a decoupling of the Escherichia coli resistome from the bacterial community resistomes was observed. In biofilms, the relationships with anthropogenic pollution factors were heterogeneous and markedly dampened. Our results clearly show that general conclusions about the role of biofilms, the influence of pollution or the prevalence of resistance genes or phenotypic resistances must be drawn with caution. Results are dependent on the river and local situation of the sampling sites due to the large environmental heterogeneity. International harmonisation of the methodology and general awareness of this problem shall contribute to better understand environmental ABR to develop effective mitigation strategies.

Cultured and molecular measures of fecal indicator microbes in Gulf of Mexico recreational waters

Recreational waters are routinely assessed by enumeration of fecal indicator bacteria, such as enterococci, but research suggests viral indicators may be better suited for recreational water quality applications. Somatic and F+ coliphage were proposed as predictors of viral pathogens in recreational waters, but concurrent measurements of enterococci and coliphages and comparisons across different risk-based beach action values (BAVs) are limited. We collected paired measurements of enterococci, E. coli, somatic and F+ coliphage from three Gulf of Mexico beaches. Enterococci (colony forming units: CFU) were enumerated on mEI agar and by qPCR (Entero1a: target sequence [TS]). E. coli was enumerated by qPCR (EC23S587, TS). Coliphages (plaque forming units: PFU) were enumerated using dead-end hollowfiber ultrafiltration and single agar layer assay. The largest correlation observed was between Entero1a and cultured enterococci (r ≥ 0.51, p ≤ 0.0001) and the smallest (r ≤ 0.01, p = 1.0) between F+ coliphage and cultured enterococci. Applying equivalent BAVs for culturable enterococci (60 CFU/100 mL), Entero1a (9658 TS per 100 mL) and suggested somatic (14 PFU/100 mL) and F+ (3 PFU/100 mL) thresholds resulted in the overall greatest agreement in beach advisory status between coliphages and Entero1a (74-82 %) and lowest between cultured enterococci and somatic coliphage (65 %). This rich data set not only provides valuable insights on the incidence of coliphage and FIB in the Gulf of Mexico but will also provide a foundation for future research on fecal source identification and water quality forecast modeling in sub-tropical marine waters.

Assessing the impact of inland navigation on the faecal pollution status of large rivers: A novel integrated field approach

The contribution of ships to the microbial faecal pollution status of water bodies is largely unknown but frequently of human health concern. No methodology for a comprehensive and target-orientated system analysis was available so far. We developed a novel approach for integrated and multistage impact evaluation. The approach includes, i) theoretical faecal pollution source profiling (PSP, i.e., size and pollution capacity estimation from municipal vs. ship sewage disposal) for impact scenario estimation and hypothesis generation, ii) high-resolution field assessment of faecal pollution levels and chemo-physical water quality at the selected river reaches, using standardized faecal indicators (cultivation-based) and genetic microbial source tracking markers (qPCR-based), and iii) integrated statistical analyses of the observed faecal pollution and the number of ships assessed by satellite-based automated ship tracking (i.e., automated identification system, AIS) at local and regional scales. The new approach was realised at a 230 km long Danube River reach in Austria, enabling detailed understanding of the complex pollution characteristics (i.e., longitudinal/cross-sectional river and upstream/downstream docking area analysis). Faecal impact of navigation was demonstrated to be remarkably low at regional and local scale (despite a high local contamination capacity), indicating predominantly correct disposal practices during the investigated period. Nonetheless, faecal emissions were sensitively traceable, attributable to the ship category (discriminated types: cruise, passenger and freight ships) and individual vessels (docking time analysis) at one docking area by the link with AIS data. The new innovative and sensitive approach is transferrable to any water body worldwide with available ship-tracking data, supporting target-orientated monitoring and evidence-based management practices.

Quantitative fecal source characterization of urban municipal storm sewer system outfall 'wet' and 'dry' weather discharges

Urban areas are built environments containing substantial amounts of impervious surfaces (e.g., streets, sidewalks, roof tops). These areas often include elaborately engineered drainage networks designed to collect, transport, and discharge untreated stormwater into local surface waters. When left uncontrolled, these discharges may contain unsafe levels of fecal waste from sources such as sanitary sewage and wildlife even under dry weather conditions. This study evaluates paired measurements of host-associated genetic markers (log10 copies per reaction) indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal sources, 12-hour cumulative precipitation (mm), four catchment land use metrics determined by global information system (GIS) mapping, and Escherichia coli (MPN/100 ml) from seven municipal separate storm sewer system outfall locations situated at the southern portion of the Anacostia River Watershed (District of Columbia, U.S.A.). A total of 231 discharge samples were collected twice per month (n = 24 sampling days) and after rain events (n = 9) over a 13-month period. Approximately 50 % of samples (n = 116) were impaired, exceeding the local E. coli single sample maximum of 2.613 log10 MPN/100 ml. Genetic quality controls indicated the absence of amplification inhibition in 97.8 % of samples, however 14.7 % (n = 34) samples showed bias in DNA recovery. Of eligible samples, quantifiable levels were observed for avian (84.1 %), human (57.4 % for HF183/BacR287 and 40 % for HumM2), canine (46.7 %), and ruminant (15.9 %) host-associated genetic markers. Potential links between paired measurements are explored with a recently developed Bayesian qPCR censored data analysis approach. Findings indicate that human, pet, and urban wildlife all contribute to storm outfall discharge water quality in the District of Columbia, but pollutant source contributions vary based on 'wet' and 'dry' conditions and catchment land use, demonstrating that genetic-based fecal source identification methods combined with GIS land use mapping can complement routine E. coli monitoring to improve stormwater management in urban areas.

Improved SARS-CoV-2 RNA recovery in wastewater matrices using a CTAB-based extraction method

Wastewater-based epidemiology has allowed tracking the magnitude and distribution of SARS-CoV-2 in communities, allowing public health officials to prepare for impending outbreaks. While many factors influence recovery of SARS-CoV-2 from wastewater, proper extraction, concentration, and purification of RNA are key steps to ensure accurate detection of viral particles. The aim of this study was to compare the efficiency of four commonly used RNA extraction methods for detection of the SARS-CoV-2 RNA genome in sewage samples artificially inoculated with the virus, in order to identify a protocol that improves viral recovery. These methods included CTAB-based, TRIzol-based, and guanidinium thiocyanate (GTC)-based extraction procedures coupled with silica spin column-based purification, and an automated extraction/purification protocol using paramagnetic particles. Following RNA extraction, virus recovery rates were compared using RT-qPCR-based detection. The CTAB-based approach yielded the highest recovery rates and was the only method to consistently demonstrate stable virus recovery percentages regardless of the specific physicochemical characteristics of the samples tested. The TRIzol method proved to be the second most effective, yielding significantly higher recovery rates compared to both the GTC-based and the automated extraction methods. These results suggest that the CTAB-based approach could be a useful tool for the recovery of viral RNA from complex wastewater matrices.

A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements

Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.

Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River

The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are of particular concern as they are highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding of occurrence, spread and key drivers of AMR along whole river courses is largely lacking. We provide a holistic approach by studying spatiotemporal patterns and hotspots of antibiotic resistance genes (ARGs) along 2311 km of the navigable Danube River, combining a longitudinal and temporal monitoring campaign. The integration of advanced faecal pollution diagnostics and environmental and chemical key parameters allowed linking ARG concentrations to the major pollution sources and explaining the observed patterns. Nine AMR markers, including genes conferring resistance to five different antibiotic classes of clinical and environmental relevance, and one integrase gene were determined by probe-based qPCR. All AMR targets could be quantified in Danube River water, with intI1 and sul1 being ubiquitously abundant, qnrS, tetM, blaTEM with intermediate abundance and blaOXA-48like, blaCTX-M-1 group, blaCTX-M-9 group and blaKPC genes with rare occurrence. Human faecal pollution from municipal wastewater discharges was the dominant factor shaping ARG patterns along the Danube River. Other significant correlations of specific ARGs were observed with discharge, certain metals and pesticides. In contrast, intI1 was not associated with wastewater but was already established in the water microbiome. Animal contamination was detected only sporadically and was correlated with ARGs only in the temporal sampling set. During temporal monitoring, an extraordinary hotspot was identified emphasizing the variability within natural waters. This study provides the first comprehensive baseline concentrations of ARGs in the Danube River and lays the foundation for monitoring future trends and evaluating potential reduction measures. The applided holistic approach proved to be a valuable methodological contribution towards a better understanding of the environmental occurrence of AMR.

Rapid detection method of bacterial pathogens in surface waters and a new risk indicator for water pathogenic pollution

In this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 104 copies 100 mL-1. When the detection value is lower than 104 copy 100 mL-1, the bacteria in the water are rarely pathogenic bacteria, so the detection value of 104 copy 100 mL-1 can be used as a new indicator of waterborne pathogen pollution.

Low antimicrobial resistance in Escherichia coli isolates from two large Austrian alpine karstic spring catchments

The increasing occurrence of antibiotic resistant bacteria poses a threat to global public health. Clinically relevant resistances also spread through the environment. Aquatic ecosystems in particular represent important dispersal pathways. In the past, pristine water resources have not been a study focus, although ingestion of resistant bacteria through water consumption constitutes a potentially important transmission route. This study assessed antibiotic resistances in Escherichia coli populations in two large well-protected and well-managed Austrian karstic spring catchments representing essential groundwater resources for water supply. E. coli were detected seasonally only during the summer period. By screening a representative number of 551 E. coli isolates from 13 sites in two catchments, it could be shown that the prevalence of antibiotic resistance in this study area is low. 3.4 % of the isolates showed resistances to one or two antibiotic classes, 0.5 % were resistant to three antibiotic classes. No resistances to critical and last-line antibiotics were detected. By integrating fecal pollution assessment and microbial source tracking, we could infer that ruminants were the main hosts for antibiotic resistant bacteria in the studied catchment areas. A comparison with other studies on antibiotic resistances in karstic or mountainous springs highlighted the low contamination status of the model catchments studied here, most likely due to the high protection and careful management while other, less pristine catchments showed much higher antibiotic resistances. We demonstrate that studying easily accessible karstic springs allows a holistic view on large catchments concerning the extent and origin of fecal pollution as well as antibiotic resistance. This representative monitoring approach is also in line with the proposed update of the EU Groundwater Directive (GWD).

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

First report on the occurrence of Vibrio cholerae nonO1/nonO139 in natural and artificial lakes and ponds in Serbia: Evidence for a long-distance transfer of strains and the presence of Vibrio paracholerae

Vibrio cholerae are natural inhabitants of specific aquatic environments. Strains not belonging to serogroups O1 and O139 are usually unable to produce cholera toxin and cause cholera. However, non-toxigenic V. cholerae (NTVC) are able to cause a variety of mild-to-severe human infections (via seafood consumption or recreational activities). The number of unreported cases is considered substantial, as NTVC infections are not notifiable and physicians are mostly unaware of this pathogen. In the northern hemisphere, NTVC infections have been reported to increase due to global warming. In Eastern Europe, climatic and geological conditions favour the existence of inland water-bodies harbouring NTVC. We thus investigated the occurrence of NTVC in nine Serbian natural and artificial lakes and ponds, many of them used for fishing and bathing. With the exception of one highly saline lake, all investigated water-bodies harboured NTVC, ranging from 5.4 × 10¹ to 1.86 × 10⁴  CFU and 4.5 × 10² to 5.6 × 10⁶ genomic units per 100 ml. The maximum values observed were in the range of bathing waters in other countries, where infections have been reported. Interestingly, 7 out of 39 fully sequenced presumptive V. cholerae isolates were assigned as V. paracholerae, a recently described sister species of V. cholerae. Some clones and sublineages of both V. cholerae and V. paracholerae were shared by different environments indicating an exchange of strains over long distances. Important pathogenicity factors such as hlyA, toxR, and ompU were present in both species. Seasonal monitoring of ponds/lakes used for recreation in Serbia is thus recommended to be prepared for potential occurrence of infections promoted by climate change-induced rise in water temperatures.

Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment

We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log₁₀ 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.