Amplicon-based taxonomic characterization of bacteria in urban and peri-urban roof-harvested rainwater stored in tanks

Nocardia species distribution and antimicrobial susceptibility within Australia

BACKGROUND

Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation.

AIMS

To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program.

METHODS

Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022.

RESULTS

Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation.

CONCLUSIONS

We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Water quality and microecosystem of water tanks in karst mountainous area, Southwest China

Karst mountainous areas in Southwest China, the world's largest bare karst area, are faced with growing water shortages. Rainwater harvesting plays an important role in alleviating water shortage. However, there remains a substantial gap in the research regarding the water quality of tanks. Water samples were seasonally collected from ten tanks to investigate the physicochemical properties, microbial communities, and their key influencing factors. The result showed that pH, turbidity, chroma, DOC, and CODMn exceeded drinking water guidelines. The alkaline pH value and the deterioration of sensory properties was the main feature of tank water, from which the over-standard rate of the uncleaned water tanks was higher. Moreover, principal component analyses suggested that tank water quality was influenced by human activities, catchment areas, and material cycling processes within the tanks, of which in-tank microbial activities were the most important driving factors in water quality variation. Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Verrucomicrobia were the predominant bacterial phyla in water tanks. Acinetobacter, Cyanobium-PCC-6307, CL500-29-marine-group, Candidatus-Aquiluna, and Exiguobacterium were the most abundant genera. The bacterial communities were significantly affected by the management practices. Higher relative abundance of Cyanobacteria and lower relative abundance of Proteobacteria was detected in the uncleaned tanks, which was a sign of tank water quality deterioration. The microbial community structure was closely related to the environmental factors. There was evidence that the water quality was affected by the existence of a microecosystem dominated by photosynthetic microorganisms in the water tanks. In addition, Acinetobacter, Enterobacter, Pseudomonas, and Legionella identified as the potential opportunistic pathogenic genera were frequently detected but the relative abundances except Acinetobacter were low in the tanks. Overall, our findings indicated that management style influences water quality and bacterial communities of tank water.

Assessing Freshwater Microbiomes from Different Storage Sources in the Caribbean Using DNA Metabarcoding

Next-generation sequencing (NGS) and the technique of DNA metabarcoding have provided more efficient and comprehensive options for testing water quality compared to traditional methods. Recent studies have shown the efficacy of DNA metabarcoding in characterizing the bacterial microbiomes of varied sources of drinking water, including rivers, reservoirs, wells, tanks, and lakes. We asked whether DNA metabarcoding could be used to characterize the microbiome of different private sources of stored freshwater on the Caribbean Island nation of Antigua and Barbuda. Two replicate water samples were obtained from three different private residential sources in Antigua: a well, an above-ground tank, and a cistern. The bacterial microbiomes of different freshwater sources were assessed using 16S rRNA metabarcoding. We measured both alpha diversity (species diversity within a sample) and beta diversity (species diversity across samples) and conducted a taxonomic analysis. We also looked for the presence of potentially pathogenic species. Major differences were found in the microbiome composition and relative abundances depending on the water source. A lower alpha diversity was observed in the cistern sample compared to the others, and distinct differences in the microbiome composition and relative abundance were noted between the samples. Notably, pathogenic species, or genera known to harbor such species, were detected in all the samples. We conclude that DNA metabarcoding can provide an effective and comprehensive assessment of drinking water quality and has the potential to identify pathogenic species overlooked using traditional methods. This method also shows promise for tracing the source of disease outbreaks due to waterborne microorganisms. This is the first study from small island countries in the Caribbean where metabarcoding has been applied for assessing freshwater water quality.

Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers

Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Variation in the Structure and Composition of Bacterial Communities within Drinking Water Fountains in Melbourne, Australia

Modern drinking water distributions systems (DWDSs) have been designed to transport treated or untreated water safely to the consumer. DWDSs are complex environments where microorganisms are able to create their own niches within water, biofilm or sediment. This study was conducted on twelve drinking fountains (of three different types, namely types A, B and C) within the Melbourne (Australia) city area with the aim to (i) characterize the water quality and viable and total counts at each fountain, (ii) compare the differences in the structure and diversity of the bacterial community between bulk water and biofilm and (iii) determine differences between the bacterial communities based on fountain type. Samples of water and biofilm were assessed using both culture-dependent and culture-independent techniques. Heterotrophic plate counts of water samples ranged from 0.5 to 107.5 CFU mL−1, and as expected, total cell counts (cells mL−1) were, on average, 2.9 orders of magnitude higher. Based on the mean relative abundance of operational taxonomic units (OTUs), ANOSIM showed that the structure of the bacterial communities in drinking water and biofilm varied significantly (R = 0.58, p = 0.001). Additionally, ANOSIM showed that across fountain types (in water), the bacterial community was more diverse in fountain type C compared to type A (p < 0.001) and type B (p < 0.001). 16S rRNA next-generation sequencing revealed that the bacterial communities in both water and biofilm were dominated by only seven phyla, with Proteobacteria accounting for 71.3% of reads in water and 68.9% in biofilm. The next most abundant phylum was Actinobacteria (10.4% water; 11.7% biofilm). In water, the genus with the highest overall mean relative abundance was Sphingomonas (24.2%), while Methylobacterium had the highest mean relative abundance in biofilm samples (54.7%). At the level of genus and higher, significant differences in dominance were found across fountain types. In water, Solirubrobacterales (order) were present in type C fountains at a relative abundance of 17%, while the mean relative abundance of Sphingomonas sp. in type C fountains was less than half that in types A (25%) and B (43%). In biofilm, the relative abundance of Sphingomonas sp. was more than double in type A (10%) fountains compared to types B (4%) and C (5%), and Sandarakinorhabdus sp. were high in type A fountains (6%) and low in types B and C (1%). Overall this research showed that there were significant differences in the composition of bacterial communities in water and biofilm from the same site. Furthermore, significant variation exists between microbial communities present in the fountain types, which may be related to age. Long-established environments may lead to a greater chance of certain bacteria gaining abilities such as increased disinfection resistance. Variations between the structure of the bacterial community residing in water and biofilm and differences between fountain types show that it is essential to regularly test samples from individual locations to determine microbial quality.

Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

Human Pathogenic Bacteria Detected in Rainwater: Risk Assessment and Correlation to Microbial Source Tracking Markers and Traditional Indicators

Roof-harvested rainwater (RHRW) was investigated for the presence of the human pathogenic bacteria Mycobacterium tuberculosis (M. tuberculosis), Yersinia spp. and Listeria monocytogenes (L. monocytogenes). While Yersinia spp. were detected in 92% (n = 25) of the RHRW samples, and L. monocytogenes and M. tuberculosis were detected in 100% (n = 25) of the samples, a significantly higher mean concentration (1.4 × 10³ cells/100 mL) was recorded for L. monocytogenes over the sampling period. As the identification of appropriate water quality indicators is crucial to ensure access to safe water sources, correlation of the pathogens to traditional indicator organisms [Escherichia coli (E. coli) and Enterococcus spp.] and microbial source tracking (MST) markers (Bacteroides HF183, adenovirus and Lachnospiraceae) was conducted. A significant positive correlation was then recorded for E. coli versus L. monocytogenes (r = 0.6738; p = 0.000), and Enterococcus spp. versus the Bacteroides HF183 marker (r = 0.4071; p = 0.043), while a significant negative correlation was observed for M. tuberculosis versus the Bacteroides HF183 marker (r = −0.4558; p = 0.022). Quantitative microbial risk assessment indicated that the mean annual risk of infection posed by L. monocytogenes in the RHRW samples exceeded the annual infection risk benchmark limit (1 × 10^–4 infections per person per year) for intentional drinking (∼10^–4). In comparison, the mean annual risk of infection posed by E. coli was exceeded for intentional drinking (∼10^–1), accidental consumption (∼10^–3) and cleaning of the home (∼10^–3). However, while the risk posed by M. tuberculosis for the two relevant exposure scenarios [garden hosing (∼10^–5) and washing laundry by hand (∼10^–5)] was below the benchmark limit, the risk posed by adenovirus for garden hosing (∼10^–3) and washing laundry by hand (∼10^–3) exceeded the benchmark limit. Thus, while the correlation analysis confirms that traditional indicators and MST markers should be used in combination to accurately monitor the pathogen-associated risk linked to the utilisation of RHRW, the integration of QMRA offers a more site-specific approach to monitor and estimate the human health risks associated with the use of RHRW.

EMA-amplicon-based sequencing informs risk assessment analysis of water treatment systems

Illumina amplicon-based sequencing was coupled with ethidium monoazide bromide (EMA) pre-treatment to monitor the total viable bacterial community and subsequently identify and prioritise the target organisms for the health risk assessment of the untreated rainwater and rainwater treated using large-volume batch solar reactor prototypes installed in an informal settlement and rural farming community. Taxonomic assignments indicated that Legionella and Pseudomonas were the most frequently detected genera containing opportunistic bacterial pathogens in the untreated and treated rainwater at both sites. Additionally, Mycobacterium, Clostridium sensu stricto and Escherichia/Shigella displayed high (≥80%) detection frequencies in the untreated and/or treated rainwater samples at one or both sites. Numerous exposure scenarios (e.g. drinking, cleaning) were subsequently investigated and the health risk of using untreated and solar reactor treated rainwater in developing countries was quantified based on the presence of L. pneumophila, P. aeruginosa and E. coli. The solar reactor prototypes were able to reduce the health risk associated with E. coli and P. aeruginosa to below the 1 × 10^-4 annual benchmark limit for all the non-potable uses of rainwater within the target communities (exception of showering for E. coli). However, the risk associated with intentional drinking of untreated or treated rainwater exceeded the benchmark limit (E. coli and P. aeruginosa). Additionally, while the solar reactor treatment reduced the risk associated with garden hosing and showering based on the presence of L. pneumophila, the risk estimates for both activities still exceeded the annual benchmark limit. The large-volume batch solar reactor prototypes were thus able to reduce the risk posed by the target bacteria for non-potable activities rainwater is commonly used for in water scarce regions of sub-Saharan Africa. This study highlights the need to assess water treatment systems in field trials using QMRA.

Removal of CX3R-type disinfection by-product precursors from rainwater with conventional drinking water treatment processes

In addition to surface water and groundwater, rainwater is used as an important drinking water source in many parts of the world, especially in areas with serious water pollution or insufficient water resources. Conventional drinking water treatment technologies can remove dissolved organic matter and therefore reduce the formation of disinfection by-products (DBPs) during subsequent disinfection using surface water or groundwater as drinking water sources. However, little information has been known about the effect of conventional water treatment processes on DBP formation when rainwater is used as drinking water source. This study evaluated CX₃R-type DBP precursors removal from rainwater by conventional drinking water treatments and the corresponding decrease of CX₃R-type DBP (trihalomethanes (THMs), haloaldehydes (HALs), haloacetonitriles (HANs) and haloacetamides (HAMs)) formation and toxicity during the subsequent chlor(am)ination. The result showed that both sand filtration (SF) and activated carbon filtration (GAC) were able to remove DBP precursors and GAC outperformed SF, but no DBP precursors removal was observed during coagulation-sedimentation treatment. Among all treatments, SF + GAC was the most effective for DBP precursors removal, with removal efficiencies of 64.2% DOC, 98% DON and 76.6% UV₂₅₄. Correspondingly, both SF and GAC decreased the formation of THMs, HALs, HANs and HAMs, and GAC performed better than SF. The combination of SF and GAC, especially SF + GAC, greatly decreased DBP formation, with average reduction of 79.2% and 85% during chlorination and chloramination respectively. After different treatments, the comprehensive toxicity risk of CX₃R-type DBPs was all reduced, among which GAC + SF exhibited superior performance. Generally, the main contribution of integrated toxicity was HANs during chlor(am)ination. The formation potential of THMs, HALs, HANs and HAMs and the corresponding integrated toxicity were greater during chlorination than that during chloramination. Therefore, the combination of GAC and chloramination was promising in mitigating the comprehensive toxicity risk of THMs, HALs, HANs and HAMs for rainwater.

Quantitative Microbial Risk Assessment and Molecular Biology: Paths to Integration

Quantitative microbial risk assessment (QMRA) has now been in use for over 35 years and has formed the basis for developing criteria for ensuring public health related to water, food, and remediation, to name a few areas. The initial data for QMRA (both in exposure assessment and in dose response assessment) came from measurements using assays for viability, such as plate counts, plaque assays, or animal infectivity. With the increasing use of molecular methods for the measurement of microorganisms in the environment, it has become important to assess how to use such data to estimate infectious disease risks. The limitations to the use of such data and needs to resolve the limitations will be addressed.

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area

The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.

An examination of the microbial community and occurrence of potential human pathogens in rainwater harvested from different roofing materials

While harvested rainwater can serve as an alternative water supply, microbial contaminants within the collection system can negatively affect water quality. Here, we investigated the impact of roofing material on the microbial quality of rainwater freshly harvested from pilot-scale roofs (concrete tile, cool, green, Galvalume^® metal, and asphalt fiberglass shingle). The microbial quality of freshly harvested rainwater from six rain events over two years was analyzed by high-throughput sequencing and culture-dependent and -independent techniques. The concentrations of total coliform were significantly different among rainwaters harvested from the various roofing materials (p-value >0.05). However, the fecal coliform concentrations and the copy numbers of Enterococcus 23S rRNA genes and total Bacteria 16S rRNA genes did not vary by type of roofing material in a statistically significant way. Potential human pathogens such as Legionella, Escherichia coli O157:H7, Shiga-toxin-producing Escherichia coli, and adenovirus were detected at least once in rainwater harvested from the different roofing materials, even though the lowest occurrence of those potential human pathogens was noted from the metal roof. Also, substantial variation in the microbial communities from the different roofing materials was observed at the family and genus levels. These results demonstrate that the type of roofing material affects the microbial quality of freshly harvested rainwater, indicating that the choice of roofing material could shape the microbial community structure entering a rainwater storage tank. Given that detection of potential pathogens in the freshly harvested rainwater also differed between roofing materials, the type of roofing used to capture rainwater needs to be considered in rainwater harvesting system design, particularly if the water is intended for potable use.

Purification of harvested rainwater using slow sand filters with low-cost materials: Bacterial community structure and purifying effect

Slow sand filters (SSFs) have been shown to effectively improve water quality. The aim of the present study was to obtain low-cost materials (LCMs) as filter mediums (FMs) to efficiently purify harvested rainwater and to document the relationship between bacterial community structure and water purification. The red clay was mixed with crushed limestone and crushed brick, respectively. The mixtures or brick powder were used as the filter media for SSFs. Laboratory column tests were conducted in conjunction with the monitoring of representative water quality parameters (COD, NH₄⁺, CFU and total coliforms) to estimate the performance of low-cost material slow sand filters (LCM-SSFs), including the time needed for biofilm maturation. The relationship between bacterial community structure and SSF performance was determined using a combination of 16S rRNA gene sequencing and an array of statistical techniques. The results demonstrated that LCM-SSFs perform well in purifying harvested rainwater, and are of superior economic benefit. LCMs had a stronger adsorptivity than quartz sand, which enhanced the purification of harvested rainwater before the biofilms matured, and shorten the time required for biofilm maturation. During the 90-day laboratory experiment, a mixture of crushed limestone and red clay exhibited the best performance. The abundance of Opitutae could be used as a potential indicator of NH₄⁺ removal efficiency by SSFs. Schmutzdecke was characterized by abundant, diverse and evenly distributed bacterial communities that produced rich, stable and robust environmental functions, and that possessed an excellent purifying capacity. Environmental conditions associated with low ecological stress, such as neutral pH filter mediums and lucifugal experimental conditions, were conducive to the diversity and evenness of effluent bacterial communities and improved the performance of LCM-SSFs in purifying harvested rainwater.

The influence of climate change on waterborne disease and Legionella: a review

Climate change is predicted to have a major impact on people's lives with the recent extreme weather events and varying abnormal temperature profiles across the world raising concerns. The impacts of global warming are already being observed, from rising sea levels and melting snow and ice to changing weather patterns. Scientists state unequivocally that these trends cannot be explained by natural variability in climate alone. Human activities, especially the burning of fossil fuels, have warmed the earth by dramatically increasing concentrations of heat-trapping gases in the atmosphere; as these concentrations increase, the more the earth will warm. Climate change and related extreme weather events are being exacerbated sooner than has previously been considered and are already adversely affecting ecosystems and human health by increasing the burden and type of disease at a local level. Changes to the marine environment and freshwater supplies already affect significant parts of the world's population and warmer temperatures, especially in more temperate regions, may see an increased spread and transmission of diseases usually associated with warmer climes including, for example, cholera and malaria; these impacts are likely to become more severe in a greater number of countries. This review discusses the impacts of climate change including changes in infectious disease transmission, patterns of waterborne diseases and the likely consequences of climate change due to warmer water, drought, higher rainfall, rising sea levels and flooding.

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking

Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist. We investigated how the inclusion of bacterial overlap between sources in the library affects source prediction accuracy. To achieve this, large-scale sampling - including feces from seven species, raw sewage, and raw water samples from water treatment plants - was followed by 16S rRNA amplicon sequencing. The MST library was defined using three settings: (i) no raw water communities represented; (ii) raw water communities selected through clustering analysis; and (iii) local water communities collected across consecutive years. The results suggest that incorporating either the local background or representative bacterial composition improves MST analyses, as the results were positively correlated to measured levels of fecal indicator bacteria and the accuracy at which OTUs were assigned to the correct contamination source increased fourfold. Using the proportion of OTUs with high source origin probability, underpinning a contaminating signal, is a solid foundation in a framework for further deciphering and comparing contaminating signals derived in signature-based MST approaches. In conclusion, incorporating background bacterial composition of water in MST can improve mitigation efforts for minimizing the spread of pathogenic and antibiotic resistant bacteria into essential freshwater resources.

Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing

In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

Application of SourceTracker for Accurate Identification of Fecal Pollution in Recreational Freshwater: A Double-Blinded Study

The efficacy of SourceTracker software to attribute contamination from a variety of fecal sources spiked into ambient freshwater samples was investigated. Double-blinded samples spiked with ≤5 different sources (0.025-10% vol/vol) were evaluated against fecal taxon libraries characterized by next-generation amplicon sequencing. Three libraries, including an initial library (17 nonlocal sources), a blinded source library (5 local sources), and a composite library (local and nonlocal sources), were used with SourceTracker. SourceTracker's predictions of fecal compositions in samples were made, in part, based on distributions of taxa within abundant genera identified as discriminatory by discriminant analyses but also using a large percentage of low abundance taxa. The initial library showed poor ability to characterize blinded samples, but, using local sources, SourceTracker showed 91% accuracy (31/34) at identifying the presence of source contamination, with two false positives for sewage and one for horse. Furthermore, sink predictions of source contamination were positively correlated (Spearman's ρ ≥ 0.88, P < 0.001) with spiked source volumes. Using the composite library did not significantly affect sink predictions ( P > 0.79) compared to those made using the local sources alone. Results of this study indicate that geographically associated fecal samples are required for SourceTracker to assign host sources accurately.

Microfluidic quantification of multiple enteric and opportunistic bacterial pathogens in roof-harvested rainwater tank samples

Potable and non-potable uses of roof-harvested rainwater (RHRW) are increasing due to water shortages. To protect human health risks, it is important to identify and quantify disease-causing pathogens in RHRW so that appropriate treatment options can be implemented. We used a microfluidic quantitative PCR (MFQPCR) system for the quantitative detection of a wide array of fecal indicator bacteria (FIB) and pathogens in RHRW tank samples along with culturable FIB and conventional qPCR analysis of selected pathogens. Among the nine pathogenic bacteria and their associated genes tested with the MFQPCR, 4.86 and 2.77% samples were positive for Legionella pneumophila and Shigella spp., respectively. The remaining seven pathogens were absent. MFQPCR and conventional qPCR results showed good agreement. Therefore, direct pathogen quantification by MFQPCR systems may be advantageous for circumstances where a thorough microbial analysis is required to assess the public health risks from multiple pathogens that occur simultaneously in the target water source.

A Review of Roof Harvested Rainwater in Australia

To address concern regarding water sustainability, the Australian Federal Government and many state governments have implemented regulatory mechanisms and incentives to support households to purchase and install rainwater harvesting systems. This has led to an increase in rainwater harvesting in regional and urban Australia. This review examines the implementation of the regulatory mechanisms across Australia. In addition, the literature investigating the potential health consequences of rainwater consumption in Australia was explored. Studies demonstrated that although trace metals such as arsenic, cadmium, chromium, lead, and iron were present in Australian rainwater, these metallic elements were generally found below the health limit guideline, except in high industrial areas. In addition, pathogenic or indicator microorganisms that include, but are not limited to, Escherichia coli, total and faecal coliforms, Campylobacter, Salmonella, Legionella, Pseudomonas, Cryptosporidium, Enterococci, Giardia, Aeromonas, and Mycobacterium avium Complex (MAC) have been detected in rainwater collected in Australia. However, epidemiological evidence suggests that drinking rainwater does not increase the risk of gastrointestinal disease. It was also identified that there is a need for further research investigating the potential for rainwater to be a source of infection for opportunistic pathogens.

Toward Forensic Uses of Microbial Source Tracking

The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary

Current microbial source-tracking (MST) methods, employed to determine sources of fecal contamination in waterways, use molecular markers targeting host-associated bacteria in animal or human feces. However, there is a lack of knowledge about fecal microbiome composition in several animals and imperfect marker specificity and sensitivity. To overcome these issues, a community-based MST method has been developed. Here, we describe a study done in the Lake Superior-Saint Louis River estuary using SourceTracker, a program that calculates the source contribution to an environment. High-throughput DNA sequencing of microbiota from a diverse collection of fecal samples obtained from 11 types of animals (wild, agricultural, and domesticated) and treated effluent (n = 233) was used to generate a fecal library to perform community-based MST. Analysis of 319 fecal and environmental samples revealed that the community compositions in water and fecal samples were significantly different, allowing for the determination of the presence of fecal inputs and identification of specific sources. SourceTracker results indicated that fecal bacterial inputs into the Lake Superior estuary were primarily attributed to wastewater effluent and, to a lesser extent, geese and gull wastes. These results suggest that a community-based MST method may be another useful tool for determining sources of aquatic fecal bacteria.

Rainwater harvesting in American Samoa: current practices and indicative health risks

Roof-harvested rainwater (RHRW) is an important alternative source of water that many island communities can use for drinking and other domestic purposes when groundwater and/or surface water sources are contaminated, limited, or simply not available. The aim of this pilot-scale study was to investigate current RHRW practices in American Samoa (AS) and to evaluate and compare the quality of water from common potable water sources including RHRW stored in tanks, untreated stream water, untreated municipal well water, and treated municipal tap water samples. Samples were analyzed using culture-based methods, quantitative polymerase chain reaction (qPCR), and 16S amplicon sequencing-based methods. Based on indicator bacteria (total coliform and Escherichia coli) concentrations, the quality of RHRW was slightly lower than well and chlorinated tap water but exceeded that of untreated stream water. Although no Giardia or Leptospira spp. were detected in any of the RHRW samples, 86% of the samples were positive for Cryptosporidium spp. All stream water samples tested positive for Cryptosporidium spp. Opportunistic pathogens (Pseudomonas aeruginosa and Mycobacterium intracellulare) were also detected in the RHRW samples (71 and 21% positive samples, respectively). Several potentially pathogenic genera of bacteria were also detected in RHRW by amplicon sequencing. Each RHRW system was characterized by distinct microbial communities, 77% of operational taxonomic units (OTUs) were detected only in a single tank, and no OTU was shared by all the tanks. Risk of water-borne illness increased in the following order: chlorinated tap water/well water < RHRW < stream water. Frequent detection of opportunistic pathogens indicates that RHRW should be treated before use. Stakeholder education on RHRW system design options as well as on importance of regular cleaning and proper management techniques could improve the quality of the RHRW in AS.