A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions

Assessing the nucleic acid decay of human wastewater markers and enteric viruses in estuarine waters in Sydney, Australia

This research investigated the in-situ decay rates of four human wastewater-associated markers (Bacteroides HF183 (HF183), Lachnospiraceae Lachno3 (Lachno3), cross-assembling phage (crAssphage), pepper mild mottle virus (PMMoV) and three enteric viruses (human adenovirus 40/41 (HAdV 40/41), enterovirus (EV) and human norovirus GII (HNoV GII) in two estuarine water environments (Davidson Park (DP) and Hen and Chicken Bay (HCB) in temperate Sydney, NSW, Australia, employing qPCR and RT-qPCR assays. The study also aimed to compare decay rates observed in mesocosms with previously published laboratory microcosms, providing insights into the persistence of markers and viruses in estuarine environments. Results indicated varying decay rates between DP and HCB mesocosms, with HF183 exhibiting relatively faster decay rates compared to other markers and enteric viruses in sunlight and dark mesocosms. In DP mesocosms, HF183 decayed the fastest, contrasting with PMMoV, which exhibited the slowest. Sunlight induced higher decay rates for all markers and viruses in DP mesocosms. In HCB sunlight mesocosms, HF183 nucleic acid decayed most rapidly compared to other markers and enteric viruses. In dark mesocosms, crAssphage showed the fastest decay, while PMMoV decayed at the slowest rate in both sunlight and dark mesocosms. Comparisons with laboratory microcosms revealed faster decay of markers and enteric viruses in laboratory microcosms than the mesocosms, except for crAssphage and HAdV 40/41 in dark, and PMMoV in sunlight mesocosms. The study concludes that decay rates of markers and enteric viruses vary between estuarine mesocosms, emphasizing the impact of sunlight exposure, which was potentially influenced by the elevated turbidity at HCB estuarine waters. The generated decay rates contribute valuable insights for establishing site-specific risk-based thresholds of human wastewater-associated markers.

Spatio-Temporal Variation in the Exceedance of Enterococci in Lake Burley Griffin: An Analysis of 16 Years' Recreational Water Quality Monitoring Data

Recreational waterbodies with high levels of faecal indicator bacteria (FIB) pose health risks and are an ongoing challenge for urban-lake managers. Lake Burley Griffin (LBG) in the Australian Capital city of Canberra is a popular site for water-based recreation, but analyses of seasonal and long-term patterns in enterococci that exceed alert levels (>200 CFU per 100 mL, leading to site closures) are lacking. This study analysed enterococci concentrations from seven recreational sites from 2001-2021 to examine spatial and temporal patterns in exceedances during the swimming season (October-April), when exposure is highest. The enterococci concentrations varied significantly across sites and in the summer months. The frequency of the exceedances was higher in the 2009-2015 period than in the 2001-2005 and 2015-2021 periods. The odds of alert-level concentrations were greater in November, December, and February compared to October. The odds of exceedance were higher at the Weston Park East site (swimming beach) and lower at the Ferry Terminal and Weston Park West site compared to the East Basin site. This preliminary examination highlights the need for site-specific assessments of environmental and management-related factors that may impact the public health risks of using the lake, such as inflows, turbidity, and climatic conditions. The insights from this study confirm the need for targeted monitoring efforts during high-risk months and at specific sites. The study also advocates for implementing measures to minimise faecal pollution at its sources.

Village Settlements in Mountainous Tropical Areas, Hotspots of Fecal Contamination as Evidenced by Escherichia coli and Stanol Concentrations in Stormwater Pulses

Fecal bacteria in surface water may indicate threats to human health. Our hypothesis is that village settlements in tropical rural areas are major hotspots of fecal contamination because of the number of domestic animals usually roaming in the alleys and the lack of fecal matter treatment before entering the river network. By jointly monitoring the dynamics of Escherichia coli and of seven stanol compounds during four flood events (July-August 2016) at the outlet of a ditch draining sewage and surface runoff out of a village of Northern Lao PDR, our objectives were (1) to assess the range of E. coli concentration in the surface runoff washing off from a village settlement and (2) to identify the major contributory sources of fecal contamination using stanol compounds during flood events. E. coli pulses ranged from 4.7 × 104 to 3.2 × 106 most probable number (MPN) 100 mL-1, with particle-attached E. coli ranging from 83 to 100%. Major contributory feces sources were chickens and humans (about 66 and 29%, respectively), with the highest percentage switching from the human pole to the chicken pole during flood events. Concentrations indicate a severe fecal contamination of surface water during flood events and suggest that villages may be considered as major hotspots of fecal contamination pulses into the river network and thus as point sources in hydrological models.

Microbial source tracking of fecal pollution to coral reef lagoons of Norfolk Island, Australia

Fecal pollution contributes to global degradation of water quality and requires identification of the source(s) for predicting human health risk, tracking disease, and developing management strategies. While fecal indicator bacteria are commonly used to detect fecal pollution, they cannot identify sources. Novel approaches, such as microbial source tracking (MST), can be applied to evaluate the origin of fecal pollution. This study examined fecal pollution in the coral reef lagoons of Norfolk Island, Australia where reef health decline has been related to nutrient input. The primary objective of this study was to evaluate the host sensitivity and specificity of two human wastewater-associated marker genes (Bacteroides HF183 (HF183) and cross-assembly phage (crAssphage)) and four animal feces associated marker genes targeting avian, ruminant, dog, and pig (Helicobacter-associated GFD (GFD), Bacteroides BacR (BacR), Bacteroides DogBact (DogBact), and Bacteroides Pig-2-Bac (Pig-2-Bac)) in wastewater and animal fecal samples collected from Norfolk Island. The prevalence and concentrations of these marker genes along with enterococci genetic marker (ENT 23S rRNA) of general fecal pollution and human adenovirus (HAdV), which is considered predominantly a pathogen but also a human-wastewater associated marker gene, were determined in surface, ground, and marine water resources. A secondary objective of this study was to assess the sources and pathways of fecal pollution to a sensitive marine environment under rainfall events. HF183, crAssphage, HAdV, and BacR demonstrated absolute host sensitivity values of 1.00, while GFD and Pig-2-Bac had host sensitivity values of 0.60, and 0.20, respectively. Host specificity values were > 0.94 for all marker genes. Human and animal (avian, ruminant, dog) fecal sources were present in the coral reef lagoons and surface water whereas groundwater was polluted by human wastewater markers. This study provides understanding of fecal pollution in water resources on Norfolk Island, Australia after precipitation events. The results may aid in effective water quality management, mitigating potential adverse effects on both human and environmental health.

Effects of chlorination on the survival of sewage bacteria in seawater microcosms

Chlorination is a commonly used disinfection method in sewage treatment process. However, resistant bacteria may survive chlorination and enter the receiving aquatic environment upon effluent discharge. There has been limited research on the effects of chlorination on bacterial survival in seawater. To address this knowledge gap, microcosm experiments were conducted to simulate the discharge of chlorinated effluents into coastal seawater. The results revealed that bacterial communities in seawater-based effluents survived better in seawater than those in freshwater-based effluents. High chlorine dosages could significantly reduce the viable bacterial populations and their chance of regrowth in seawater. Additionally, faecal indicator bacteria (FIB) that entered the viable but non-culturable (VBNC) state under chlorination tended to persist in the VBNC state without resuscitation during seawater incubation. Because of the prevalence of VBNC indicator bacteria, qPCR quantification of FIB was more effective than conventional culture-based methods in tracing viable pathogenic chlorine-resistant bacteria, although the correlation strength varied depending on the type of effluent. This study sheds light on how chlorine dosages and the intrinsic properties of effluents affect bacterial survival in seawater and highlights the potential and limitations of using FIB in monitoring the health risks associated with the discharge of chlorinated effluents.

Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches

BACKGROUND

Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources.

RESULTS

Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples.

CONCLUSION

This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.

Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes

Background

Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.

Methods

This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.

Results

The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g-1, and was about one order higher than in the water column (1 to 2,300 cfu mL-1). The habitat transition rates ranged from 0.03 to 0.41 h-1. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h-1. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.

Discussion

Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.

Anthropogenic activity remains the main contributor to fecal pollution in managed tropical watersheds as unraveled by PhyloChip microarray-based microbial source tracking

The spread of disease by enteric pathogens associated with fecal contamination is a major concern for the management of urban watersheds. So far, the relative contribution of natural and anthropogenic sources to fecal pollution in managed tropical watersheds remains poorly evaluated. In this study, the microbiomes of water samples collected from managed watersheds in Singapore were elicited using the PhyloChip, a dense 16S rRNA gene-based DNA microarray, and fecal impairment was inferred using a machine-learning classification algorithm (SourceTracker). The predicted contribution of wildlife fecal sources to environmental samples was generally negligible (< 0.01 ± 0.01), indicating a low likelihood of fecal impairment from natural sources. However, sewage showed considerably higher contribution (0.09 ± 0.05) to microbial communities in a subset of watershed samples from canals and rivers, suggesting persistent impairment of certain areas by anthropogenic activity although being managed. Interestingly, the contribution of sewage microbial communities showed decreasing trends from canals/rivers to the connected reservoirs, indicating meaningful auto-mitigation of fecal pollution in canals and rivers. Notably, exclusion of locally derived fecal samples and source categories from the training data set impaired the predictive performance of the classification algorithm despite a high degree of similarity in the phylogenetic composition of microbiomes in biologically similar but geographically distinct sources.

Land use and rainfall influences on bacterial levels and sources in stormwater ponds

Urban stormwater runoff is a known source of microbial contamination of stormwater ponds. However, less is known about the influences of land use and rainfall on microbial quality over time in these receiving waters. In this study, two fecal indicator bacteria (FIB), namely Escherichia coli and thermotolerant coliforms, were monitored in three stormwater ponds in Calgary, Alberta, Canada. The stormwater ponds were selected due to their potential as water sources for beneficial uses such as irrigation, which requires lower water quality than drinking water, thereby alleviating the pressure on the city's potable water demands. The selected stormwater ponds vary in size and shape, contribution catchment size, and percentages of several primary land use types. Microbial source tracking for human, dog, seagull, Canada goose, ruminant, and muskrat was also conducted to determine sources of bacterial contamination in the stormwater ponds. Sampling was conducted near the pond surface and adjacent to the shoreline, specifically near the outfalls that discharge stormwater runoff into the ponds and the inlets that convey water out of the ponds. Overall, the FIB concentrations in the vicinity of pond outfalls were significantly or relatively higher than those near pond inlets. The contamination in the McCall Lake and the Country Hills stormwater ponds showed higher amounts of human markers (40 to 60%) compared to the Inverness stormwater pond (< 20%), which coincided with their higher FIB concentration medians. The results revealed that stormwater drained from catchments with a higher percentage of commercial land use was more contaminated than those with primary residential land use, while the impacts of residential development on the FIB levels in the Inverness stormwater pond were not obvious. Furthermore, FIB concentrations in the ponds increased in response to both rain events and inter-event dry periods, with human-specific markers being predominant despite the high levels of animal markers during inter-event dry periods. Human-origin sources might be among the main microbial loading contributors in the pond catchments in general. All these findings can inform the development or improvement of measures for mitigating microbial pollution, strategies for reusing stormwater, and maintenance programs.

A simple and rapid method for detecting fecal pollution in urban rivers by measuring the intrinsic β-D-glucuronidase activity of Escherichia coli

As urban rivers are domestic, industrial, and agricultural water resources, fecal pollution poses human health and environmental risks. In this study, we developed a simple and rapid method to detect fecal pollution in urban rivers. Water samples were mixed with liquid medium, including a fluorescent substrate and fluorescence intensity (F.I.) was measured using a microplate reader to determine Escherichia coli (E. coli) β-D-glucuronidase (GUS) activity instead of E. coli concentration. GUS activities measurements in pure E. coli cultures revealed that E. coli incubated with a GUS substrate accumulated GUS enzymes in their cells, whereas those incubated without a GUS substrate did not. The increase in GUS activity corresponded to the proliferation of E. coli and the GUS activity increased linearly even during the lag growth phase of E. coli, indicating the presence of intrinsic GUS (iGUS) in E. coli cells before incubation. iGUS activity persisted at 81 % in the chlorinated samples, even though the E. coli concentration was reduced by a factor of 106. The iGUS activity persisted for approximately three days. Therefore, we assumed that E. coli present in fecal contaminants, in which GUS substrates are present, could be distinguished from those surviving in the natural environment for three days or longer by measuring iGUS activity. River water samples were collected upstream and downstream of the discharge outlets of municipal wastewater treatment plants and a combined sewer outlet. The iGUS activities were <0.24 mMFU/mL for the upstream samples and >0.21 mMFU/mL for the downstream samples. Interestingly, E. coli concentrations were not necessarily associated with fecal pollution. This indicates that by setting a threshold for iGUS activity, our method can be used as a simple and rapid method for detecting fecal pollution in urban rivers. Because the limit of detection for our method is 20 CFU/mL, our method is applicable to detecting high fecal pollution in a small river.

Enhanced Escherichia coli removal from stormwater with bermudagrass-derived activated biochar filtration systems

Stormwater treatment and reuse can alleviate water pollution and scarcity while current sand filtration systems showed low treatment performance for stormwater. For enhancing E. coli removal in stormwater, this study applied the bermudagrass-derived activated biochars (BCs) in the BC-sand filtration systems for E. coli removal. Compared with the pristine BC (without activation), the FeCl3 and NaOH activations increased the BC carbon content from 68.02% to 71.60% and 81.22% while E. coli removal efficiency increased from 77.60% to 81.16% and 98.68%, respectively. In all BCs, the BC carbon content showed a highly positive correlation with E. coli removal efficiency. The FeCl3 and NaOH activations also led to the enhancement of roughness of BC surface for enhancing E. coli removal by straining (physical entrapment). The main mechanisms for E. coli removal by BC-amended sand column were found to be hydrophobic attraction and straining. Additionally, under 105-107 CFU/mL of E. coli, final E. coli concentration in NaOH activated BC (NaOH-BC) column was one order of magnitude lower than those in pristine BC and FeCl3 activated BC (Fe-BC) columns. The presence of humic acid remarkably lowered the E. coli removal efficiency from 77.60% to 45.38% in pristine BC-amended sand column while slightly lowering the E. coli removal efficiencies from 81.16% and 98.68% to 68.65% and 92.57% in Fe-BC and NaOH-BC-amended sand columns, respectively. Moreover, compared to pristine BC, the activated BCs (Fe-BC and NaOH-BC) also resulted in the lower antibiotics (tetracycline and sulfamethoxazole) concentrations in the effluents from the BC-amended sand columns. Therefore, for the first time, this study indicated NaOH-BC showed high potential for effective treatment of E. coli from stormwater by the BC-amended sand filtration system compared with pristine BC and Fe-BC.

Gastropods as a source for fecal indicator bacteria in drinking water

Microbial water quality is routinely examined using the fecal indicator bacteria Escherichia coli, coliform bacteria and enterococci. Several practical cases in German drinking water distribution systems indicated invertebrates such as insects or gastropods as a source for the microbiological deterioration. Therefore, we examined three genera of Gastropoda (Arion, Helix and Cepaea) for the presence of fecal indictor bacteria in excreta using standard methods. Enterococci and coliform bacteria were detected in high concentrations (mean values of 1.5 × 106 and 6.3 × 106 per gram feces, respectively). E. coli was also detected, still specification revealed that what was assigned by standard ISO-methods to be E. coli was indeed a novel species of Buttiauxella, exhibiting β-D-glucuronidase activity, thus, explaining the false-positive results. Microbiome analyses confirmed the cultural results. Enterobacteriaceae were dominant in the samples, yet only very few sequences could be assigned to Escherichia. Our study suggests, that enterococci and coliform bacteria are an integral component in the gastropod microbiome, whereas E. coli might be derived from other sources with gastropods being a vector. The results further indicate, that the current concept of fecal indicator bacteria needs to be extended, as not only humans and homeothermic animals could be a source for fecal indictor bacteria, but also gastropods need to be taken into consideration.

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

Microbial contamination in the coastal aquaculture zone of the Ba Lat river mouth, Vietnam

Contamination of aquaculture products by pathogenic organisms is a major concern in areas where this activity is of high economic importance. The abundances of total coliforms (TC), Escherichia coli (EC) and faecal streptococci (FS) (in CFU.100 mL^-1) in seawater in the Red River coastal aquaculture zone were determined. The results showed TC numbers (200 to 9100; average 1822), EC (<100 to 3400; average 469) and FS (<100 to 2100; average 384), of which TC exceeded the allowable threshold of the Vietnam regulation for coastal aquaculture water. TC and EC numbers in 4 wastewater types (domestic, livestock farming sewage, agricultural runoff, and mixed sewage canals) were investigated and revealed the importance of point sources of faecal contamination in seawater. These results underline the need to reduce the release of untreated wastewater and to put into place seawater microbial quality monitoring in areas where the development of sustainable aquaculture is an objective.

Microbial source tracking to elucidate the impact of land-use and physiochemical water quality on fecal contamination in a mixed land-use watershed

Escherichia coli has been widely used as a fecal indicator bacterium (FIB) for monitoring water quality in drinking water sources and recreational water. However, fecal contamination sources remain difficult to identify and mitigate, as millions of cases of infectious diseases are reported yearly due to swimming and bathing in recreational water. The objective of this study was to apply molecular techniques for microbial source tracking (MST) to identify sources of fecal contamination in a representative mixed land-use watershed located in the Appalachian Mountains of the United States of America (USA). Monthly samples were collected over one year at 11 sites, including the confluence of key first-order streams in the study watershed representing distinct land-use types and anticipated fecal sources. Results indicated that coupled monitoring of host-specific MST markers with the FIB E. coli effectively identified sources and quantified fecal contamination in the study watershed. Human-associated MST markers were abundant primarily at developed sites, suggesting septic or sewer failure is a key source of fecal input to the watershed. Across the dataset, samples positive for E. coli and human MST markers were associated with a higher pH than those samples from which each target was not detected, thereby suggesting that acid mine drainage in the watershed likely contributed to inactivation or loss of culturability in E. coli. In addition, this research provides the first evidence that the BacCan-UCD marker is present in fox feces and can influence MST results in areas where substantial wildlife activity is present. Identifying the sources of fecal contamination and better understanding the impact of in-stream physiochemistry throughout this study will help to develop sustainable and effective watershed management plans to control fecal contamination to protect drinking water sources and recreational water.

Huge anthropogenic microbial load during southwest monsoon season in coastal waters of Kakinada, Bay of Bengal

To examine the influence of anthropogenic activities on the marine ecosystem near the coastal waters of the port city, Kakinada, a study was conducted to investigate the abundance of heterotrophic, indicator and pathogenic bacteria during the spring inter monsoon (SIM) and southwest monsoon (SWM) seasons. A drastic change in the marine bacteria due to the input of allochthonous bacteria during SWM was noticed. An order of magnitude higher abundance of indicators (Escherichia coli and Enterococcus faecalis) and bacterial pathogens (Proteus mirabilis and Pseudomonas aeruginosa) was observed during SWM. In contrast, Chlorophyll-a, heterotrophic bacterial abundance, Aeromonas hydrophila and Klebsiella pneumoniae were higher during SIM. A significant increase in some of the indicator and pathogenic bacterial abundance due to moderate rainfall suggests that the improper drainage system in the city could spread these bacteria, posing a considerable threat to both environment and human health.

Evaluation of physicochemical and microbiological parameters, and their correlation in Himalayan Spring Water Systems: A case study of District Kulgam of Kashmir Valley, India, Western Himalaya

Total coliforms, E. coli, and fecal streptococci are the important indicators linked to the human health. This study investigated presence of these indicator bacteria in the Himalayan springs at various locations in the district Kulgam of Kashmir valley. A total of 30 spring water samples were collected from rural, urban, and forest areas during post-melting season 2021 and pre-melting season 2022. The springs in the area originate from the alluvium deposit, Karewa, and hard rock formations. The physicochemical parameters were found within the acceptable limits. However, nitrate and phosphate were found above the permissible limit at few sites, thus indicating the presence of anthropogenic activities in the area. Majority of the samples during both the seasons were found highly loaded with total coliforms with maximum limit of greater than 180 MPN/100 ml. E. coli and fecal streptococci were found in the range of less than 1 to more than 180 MPN/100 ml. The results of Pearson correlation of physicochemical parameters with indicator bacteria showed that chemical oxygen demand, rainfall, spring discharge, nitrate, and phosphate are the main factors affecting the concentration of indicator bacteria in the spring water at each site. Principal component analysis showed the most influencing factors of water quality in most of the spring sites are total coliforms, E. coli, fecal streptococci, rainfall, discharge, and chemical oxygen demand. The results of this study showed that the spring water is unfit for drinking purpose because of high concentration of fecal indicator bacteria.

Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers

The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH₃-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.

Water Resources in Africa under Global Change: Monitoring Surface Waters from Space

ABSTRACT

The African continent hosts some of the largest freshwater systems worldwide, characterized by a large distribution and variability of surface waters that play a key role in the water, energy and carbon cycles and are of major importance to the global climate and water resources. Freshwater availability in Africa has now become of major concern under the combined effect of climate change, environmental alterations and anthropogenic pressure. However, the hydrology of the African river basins remains one of the least studied worldwide and a better monitoring and understanding of the hydrological processes across the continent become fundamental. Earth Observation, that offers a cost-effective means for monitoring the terrestrial water cycle, plays a major role in supporting surface hydrology investigations. Remote sensing advances are therefore a game changer to develop comprehensive observing systems to monitor Africa's land water and manage its water resources. Here, we review the achievements of more than three decades of advances using remote sensing to study surface waters in Africa, highlighting the current benefits and difficulties. We show how the availability of a large number of sensors and observations, coupled with models, offers new possibilities to monitor a continent with scarce gauged stations. In the context of upcoming satellite missions dedicated to surface hydrology, such as the Surface Water and Ocean Topography (SWOT), we discuss future opportunities and how the use of remote sensing could benefit scientific and societal applications, such as water resource management, flood risk prevention and environment monitoring under current global change.

ARTICLE HIGHLIGHTS

The hydrology of African surface water is of global importance, yet it remains poorly monitored and understoodComprehensive review of remote sensing and modeling advances to monitor Africa's surface water and water resourcesFuture opportunities with upcoming satellite missions and to translate scientific advances into societal applications.

Distribution of faecal indicator bacteria in tropical waters of Peninsular Malaysia and their decay rates in tropical seawater

We investigated the appropriateness of faecal indicator bacteria in tropical waters. We compared total coliform (undetectable to 7.2 × 10⁵ cfu 100 mL^-1), faecal coliform (undetectable to 6.1 × 10⁵ cfu 100 mL^-1) and enterococci (undetectable to 3.1 × 10⁴ cfu 100 mL^-1) distribution in Peninsular Malaysia. Faecal indicator bacteria was highest in freshwater, and lowest in seawater (q > 4.18, p < 0.01). We also measured the decay rates of Escherichia coli and Enterococcus faecium in microcosms. In seawater, average decay rate for E. coli was 0.084 ± 0.029 h^-1, and higher than E. faecium (0.048 ± 0.024 h^-1) (t = 2.527, p < 0.05). Grazing accounted for 54 % of both E. coli and E. faecium decay. E. coli decayed in the <0.02 μm seawater fraction (0.023 ± 0.012 h^-1) but E. faecium sometimes grew. Seawater warming further uncoupled the response from both E. coli and E. faecium as E. faecium grew and E. coli decayed with warming. Our results suggested that the prevalence of faecal indicator bacteria in tropical waters was not due to faecal pollution alone, and this will have serious implications towards the use of these faecal indicator bacteria.

Fecal indicators and antibiotic resistance genes exhibit diurnal trends in the Chattahoochee River: Implications for water quality monitoring

Water bodies that serve as sources of drinking or recreational water are routinely monitored for fecal indicator bacteria (FIB) by state and local agencies. Exceedances of monitoring thresholds set by those agencies signal likely elevated human health risk from exposure, but FIB give little information about the potential source of contamination. To improve our understanding of how within-day variation could impact monitoring data interpretation, we conducted a study at two sites along the Chattahoochee River that varied in their recreational usage and adjacent land-use (natural versus urban), collecting samples every 30 min over one 24-h period. We assayed for three types of microbial indicators: FIB (total coliforms and Escherichia coli); human fecal-associated microbial source tracking (MST) markers (crAssphage and HF183/BacR287); and a suite of clinically relevant antibiotic resistance genes (ARGs; blaCTX-M, blaCMY, MCR, KPC, VIM, NDM) and a gene associated with antibiotic resistance (intl1). Mean levels of FIB and clinically relevant ARGs (blaCMY and KPC) were similar across sites, while MST markers and intI1 occurred at higher mean levels at the natural site. The human-associated MST markers positively correlated with antibiotic resistant-associated genes at both sites, but no consistent associations were detected between culturable FIB and any molecular markers. For all microbial indicators, generalized additive mixed models were used to examine diurnal variability and whether this variability was associated with environmental factors (water temperature, turbidity, pH, and sunlight). We found that FIB peaked during morning and early afternoon hours and were not associated with environmental factors. With the exception of HF183/BacR287 at the urban site, molecular MST markers and intI1 exhibited diurnal variability, and water temperature, pH, and turbidity were significantly associated with this variability. For blaCMY and KPC, diurnal variability was present but was not correlated with environmental factors. These results suggest that differences in land use (natural or urban) both adjacent and upstream may impact overall levels of microbial contamination. Monitoring agencies should consider matching sample collection times with peak levels of target microbial indicators, which would be in the morning or early afternoon for the fecal associated indicators. Measuring multiple microbial indicators can lead to clearer interpretations of human health risk associated with exposure to contaminated water.

Can water composition and weather factors predict fecal indicator bacteria removal in retention ponds in variable weather conditions?

Retention ponds provide benefits including flood control, groundwater recharge, and water quality improvement, but changes in weather conditions could limit the effectiveness in improving microbial water quality metrics. The concentration of fecal indicator bacteria (FIB), which is used as regulatory standards to assess microbial water quality in retention ponds, could vary widely based on many factors including local weather and influent water chemistry and composition. In this critical review, we analyzed 7421 data collected from 19 retention ponds across North America listed in the International Stormwater BMP Database to examine if variable FIB removal in the field conditions can be predicted based on changes in these weather and water composition factors. Our analysis confirms that FIB removal in retention ponds is sensitive to weather conditions or seasons, but temperature and precipitation data may not describe the variable FIB removal. These weather conditions affect suspended solid and nutrient concentrations, which in turn could affect FIB concentration in the ponds. Removal of total suspended solids and total P only explained 5% and 12% of FIB removal data, respectively, and TN removal had no correlation with FIB removal. These results indicate that regression-based modeling with a single parameter as input has limited use to predict FIB removal due to the interactive nature of their effects on FIB removal. In contrast, machine learning algorithms such as the random forest method were able to predict 65% of the data. The overall analysis indicates that the machine learning model could play a critical role in predicting microbial water quality of surface waters under complex conditions where the variation of both water composition and weather conditions could deem regression-based modeling less effective.

A comparison of soil Staphylococcus aureus and fecal indicator bacteria concentrations across land uses in a Hawaiian watershed

Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and fecal indicator bacteria (FIB; Enterococcus spp., Clostridium perfringens) concentrations increase in Hawaiian streams and estuaries following storms and pose a health threat to recreational water users. To reduce this risk, watershed bacteria sources need to be identified for management actions. This study's goals were to identify soil bacteria sources among different land uses and to determine if their concentrations were associated with different soil properties. Soil samples were collected three times on 24 d between October 2017 and November 2018 at urban, agriculture, and native-forest land uses in the Hilo Bay watershed, Hawai'i Island, Hawai'i. Soil bacteria concentrations were quantified using culturing techniques with selective media. Staphylococcus aureus, MRSA, and FIB were present in soil from all land uses. Bacteria concentrations were highest in urban soils and lowest in native-forest soils, with up to three orders of magnitude differences among land uses. Staphylococcus aureus, MRSA, and FIB soil concentrations were positively correlated with each other and with soil temperature and pH, but inversely correlated with soil moisture and organic matter content. Our results demonstrate that soils are a watershed bacteria source and that some soil properties affect their concentrations. Identifying these sources is critical for implementing management actions to reduce pathogen loads to estuaries and transmission to recreational water users.

Temporal Variation of Meropenem Resistance in E. coli Isolated from Sewage Water in Islamabad, Pakistan

The WHO has classified carbapenem-resistant Enterobacteriaceae in most critical priority pathogens that pose a threat to human health. The present study investigated the prevalence of meropenem-resistant Escherichia coli (E. coli) in relation to its temporal variation in different seasons along with its resistance markers in sewage water. E. coli was selected on MacConkey agar containing meropenem (3 µg/mL). There were 27% of sites/sewage samples carrying meropenem-resistant E. coli. All E. coli were confirmed through the amplification of the uidA gene. All isolated E. coli were multidrug-resistant (MDR), and among them, 51% were extensively drug-resistant (XDR). An antibiogram determined against 15 antibiotics showed the highest resistance to ampicillin and cefotaxime (98% each) and lowest resistance to fosfomycin (2%). Phylogenetic groups and resistance gene analysis through PCR showed a significant co-occurrence of carbapenemases with extended spectrum beta lactamases (ESBLs), plasmid encoded quinolone, and colistin resistance genes. The higher number of resistance genes in E. coli isolates in community sewage indirectly indicate that these isolates circulate abundantly in the community.

Evaluation of crAssphage as a human-specific microbial source-tracking marker in the Republic of Korea

CrAssphage is a novel and by far the most abundant bacteriophage in the human gut and has been proposed as a human-specific microbial source tracking (MST) marker. However, its global use as a human-specific MST marker requires validation in more extensive regions. The purpose of this study was to evaluate the specificity and abundance of the human-specific MST marker crAssphage with PCR and RT-PCR assays in human and animal feces in Korea. The prevalence of crAssphage was confirmed in 94 human feces samples (subjects: 19 to 45 years old) and 56 animal feces samples (from birds, raccoons, squirrels, weasels, deer, wild boars, hares, cats, and dogs). CrAssphage showed sensitivity of 0.39 and specificity of 1.00 in Korea, with a sequencing analysis showing that genotype II was dominant at 71.9%. The quantitative analysis showed that crAssphage is sufficiently abundant in human feces given the high concentration range of 4.26 to 8.25 log gene copies (GC)/ng in human feces. In conclusion, this study confirmed the crAssphage as a specific and abundant MST marker with which to identify human fecal contamination in Korea.

Interpretable tree-based ensemble model for predicting beach water quality

Tree-based machine learning models based on environmental features offer low-cost and timely solutions for predicting microbial fecal contamination in beach water to inform the public of the health risk. However, many of these models are black boxes that are difficult for humans to understand, which may cause severe consequences such as unexplained decisions and failure in accountability. To develop interpretable predictive models for beach water quality, we evaluate five tree-based models, namely classification tree, random forest, CatBoost, XGBoost, and LightGBM, and employ a state-of-the-art explanation method SHAP to explain the models. When tested on the Escherichia coli (E. coli) concentration data collected from three beach sites along Lake Erie shores, LightGBM, followed by XGBoost, achieves the highest averaged precision and recall scores. For all three sites, both models suggest lake turbidity as the most important predictor, and elucidate the crucial role of accurate local data of wave height and rainfall in the model development. Local SHAP values further reveal the robustness of the importance of lake turbidity as its SHAP value increases nearly monotonically with its value and is minimally affected by other environmental factors. Moreover, we found an intriguing interaction between lake turbidity and day-of-year. This work suggests that the combination of LightGBM and SHAP has a promising potential to develop interpretable models for predicting microbial water quality in freshwater lakes.

Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments

Escherichia coli not only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, cryptic Escherichia clades that were often misidentified as E. coli by conventional diagnostic methods were discovered. Failure to distinguish them from E. coli sensu stricto could lead to inaccurate conclusions about the population genetics of E. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity of E. coli and cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated with E. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades and E. coli showed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typical E. coli; some may even represent novel environmental Escherichia clades that were closely related to the original clade II strains of fecal origins. E. coli of diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonal E. coli. Notably, environmental E. coli were less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution of E. coli and clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and new E. coli genotypes reduces, while E. coli bearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity of E. coli and cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.

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.

Biodigester Cookstove Interventions and Child Diarrhea in Semirural Nepal: A Causal Analysis of Daily Observations

BACKGROUND

Hundreds of thousands of biodigesters have been constructed in Nepal. These household-level systems use human and animal waste to produce clean-burning biogas used for cooking, which can reduce household air pollution from woodburning cookstoves and prevent respiratory illnesses. The biodigesters, typically operated by female caregivers, require the handling of animal waste, which may increase domestic fecal contamination, exposure to diarrheal pathogens, and the risk of enteric infections, especially among young children.

OBJECTIVE

We estimated the effect of daily reported biogas cookstove use on incident diarrhea among children < 5 y old in the Kavrepalanchok District of Nepal. Secondarily, we assessed effect measure modification and statistical interaction of individual- and household-level covariates (child sex, child age, birth order, exclusive breastfeeding, proof of vaccination, roof type, sanitation, drinking water treatment, food insecurity) as well as recent 14-d acute lower respiratory infection (ALRI) and season.

METHODS

We analyzed 300,133 person-days for 539 children in an observational prospective cohort study to estimate the average effect of biogas stove use on incident diarrhea using cross-validated targeted maximum likelihood estimation (CV-TMLE).

RESULTS

Households reported using biogas cookstoves in the past 3 d for 23% of observed person-days. The adjusted relative risk of diarrhea for children exposed to biogas cookstove use was 1.31 (95% confidence interval (CI): 1.00, 1.71) compared to unexposed children. The estimated effect of biogas stove use on diarrhea was stronger among breastfed children (2.09; 95% CI: 1.35, 3.25) than for nonbreastfed children and stronger during the dry season (2.03; 95% CI: 1.17, 3.53) than in the wet season. Among children exposed to biogas cookstove use, those with a recent ALRI had the highest mean risk of diarrhea, estimated at 4.53 events (95% CI: 1.03, 8.04) per 1,000 person-days.

DISCUSSION

This analysis provides new evidence that child diarrhea may be an unintended health risk of biogas cookstove use. Additional studies are needed to identify exposure pathways of fecal pathogen contamination associated with biodigesters to improve the safety of these widely distributed public health interventions. https://doi.org/10.1289/EHP9468.

Genetic characterization of ESBL/pAmpC-producing Escherichia coli isolated from forest, urban park and cereal culture soils

Little is known about the role of forestland and non-fertilized agriculture soils as reservoirs of extended-spectrum beta-lactamase (ESBL) and plasmid-borne AmpC (pAmpC)-producing Escherichia coli isolates. Thus, in the present study, 210 soil samples from various origins (forest of Oued Zen (Ain Drahem), non-agriculture soils from different park gardens in Tunis City, cereal culture soils and home gardens) were investigated to characterize cefotaxime-resistant E. coli isolates. A total of 22 ESBL/pAmpC-producing E. coli were collected, and all harbored variants of the blaCTX-M gene (15 blaCTX-M-1, 5 blaCTX-M-55 and 2 blaCTX-M-15). A total of seven and two isolates harbored also blaEBC and blaDHA-like genes, respectively. Resistances to tetracycline, sulfonamides and fluoroquinolones were encoded by tetA (n = 4)/tetB (n = 12), sul1 (n = 17)/sul2 (n = 19) and aac(6')-Ib-cr (n = 2)/qnrA (n = 1)/qnrS (n = 1) genes, respectively. A total of seven isolates were able to transfer by conjugation cefotaxime-resistance in association or not with other resistance markers. PFGE showed that ten and two isolates were clonally related (pulsotypes P1 and P2). The 10 P1 isolates had been collected from forestland, cereal culture soils and an urban park garden in Tunis City, arguing for a large spread of clonal strains. Our findings highlight the occurrence of ESBL/pAmpC-E. coli isolates in soils under limited anthropogenic activities and the predominance of CTX-M enzymes that are largely disseminated in E. coli from humans and animals in Tunisia.

Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review

Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.

Microbial Contamination Survey of Environmental Fresh and Saltwater Resources of Upolu Island, Samoa

Analysis of microbe diversity in freshwater resources and nearshore seawater samples of Upolu Island was performed to investigate the distribution of harmful bacteria. For this, 124 samples were collected from 23 river systems, two volcanic lakes, and 45 locations inside and outside the barrier reef of Upolu Island, Samoa. Physicochemical parameters for general water quality, detection of coliform bacteria and 16S rRNA amplicon sequencing were performed on all samples. Fecal indicator bacteria (FIB) testing indicated a wide distribution of coliform bacteria in all sampled freshwater sites with evidence of fecal coliform in most locations. Importantly, evidence of coliform bacteria was found in most seawater samples inside and along the reef, apart from those samples taken ~20 km offshore. Illumina 16S rRNA amplicon sequencing of the V4 hypervariable region confirmed the presence of various types of harmful bacterial species, namely from the Enterobacteriaceae, Enterococcae, Streptococcaceae, and Vibrionacea families. By combining the sensitivity of FIB testing and next-generation sequencing, we were able to show the extent of potential contaminations in fresh and seawater samples and simultaneously identify the potential pathogenic bacterial genera present. The wide distribution of potential harmful bacteria from river runoff or direct sewage dumping has an impact on human health, leading to many skin and intestinal diseases, and is potentially detrimental to coral reef community health.

Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador

In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The bla_CTX–M–55, bla_{CTX–M 65}, and bla_{CTX–M 15} genes were the most frequently found gene associated with the ESBL phenotype and coincided with the bla_CTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.

Human Polyomaviruses (HPyV) in Wastewater and Environmental Samples from the Lisbon Metropolitan Area: Detection and Genetic Characterization of Viral Structural Protein-Coding Sequences

Due to the lack of reliable epidemiological information regarding the geographic distribution and genetic diversity of human polyomaviruses (HPyV) in Portugal, we addressed these issues in this initial study by focusing on the Lisbon Metropolitan area, the most populated and culturally diverse hub in the country. The HPyV structural protein-coding sequence was partially amplified using two touch-down PCR multiplex protocols, starting from water samples, collected between 2018 and 2020, where viral genomes were detected. The obtained results disclosed the frequent detection of HPyV1, HPyV2, HPyV5, and HPyV6 in 35.3% (n = 6), 29.4% (n = 5), 47.1% (n = 8) and 29.4% (n = 5), respectively, of the water samples analyzed. The sequences assigned to a given viral species did not segregate to a single genotype, this being especially true for HPyV2 for which five genotypes (including a putative new genotype 9) could be identified. The phylogenetic trees obtained for HPyV5 and HPyV6 had less resolving power than those obtained for HPyV1/HPyV2, but both viruses were shown to be genetically diverse. This analysis emphasizes the epidemiological helpfulness of these detection/genetic characterization studies in addition to being relevant tools for assessment of human waste contamination.

Mapping the Terrain for Pathogen Persistence and Proliferation in Non-potable Reuse Distribution Systems: Interactive Effects of Biofiltration, Disinfection, and Water Age

Diverse pathogens can potentially persist and proliferate in reclaimed water distribution systems (RWDSs). The goal of this study was to evaluate interactive effects of reclaimed water treatments and water age on persistence and proliferation of multiple fecal (e.g., Klebsiella, Enterobacter) and non-fecal (e.g., Legionella, mycobacteria) gene markers in RWDSs. Six laboratory-scale RWDSs were operated in parallel receiving the influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. After 3 years of operation, the RWDSs were subject to sacrificial sampling and shotgun metagenomic sequencing. We developed an in-house metagenome-derived pathogen quantification pipeline, validated by quantitative polymerase chain reaction and mock community analysis, to estimate changes in abundance of ∼30 genera containing waterborne pathogens. Microbial community composition in the RWDS bulk water, biofilm, and sediments was clearly shaped by BAC filtration, disinfectant conditions, and water age. Key commonalities were noted in the ecological niches occupied by fecal pathogen markers in the RWDSs, while non-fecal pathogen markers were more varied in their distribution. BAC-filtration + chlorine was found to most effectively control the widest range of target genera. However, filtration alone or chlorine secondary disinfection alone resulted in proliferation of some of these genera containing waterborne pathogens.

Environmental determinants of E. coli, link with the diarrheal diseases, and indication of vulnerability criteria in tropical West Africa (Kapore, Burkina Faso)

In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak environmental and health monitoring infrastructures. Escherichia coli (E. coli) is an indicator for the enteric pathogens that cause many diarrheal diseases. The links between E. coli, diarrheal diseases and environmental parameters have not received much attention in West Africa, and few studies have assessed health risks by taking into account hazards and socio-health vulnerabilities. This case study, carried out in Burkina Faso (Bagre Reservoir), aims at filling this knowledge gap by analyzing the environmental variables that play a role in the dynamics of E. coli, cases of diarrhea, and by identifying initial vulnerability criteria. A particular focus is given to satellite-derived parameters to assess whether remote sensing can provide a useful tool to assess the health hazard. Samples of surface water were routinely collected to measure E. coli, enterococci and suspended particulate matter (SPM) at a monitoring point (Kapore) during one year. In addition, satellite data were used to estimate precipitation, water level, Normalized Difference Vegetation Index (NDVI) and SPM. Monthly epidemiological data for cases of diarrhea from three health centers were also collected and compared with microbiological and environmental data. Finally, semi-structured interviews were carried out to document the use of water resources, contact with elements of the hydrographic network, health behavior and condition, and water and health policy and prevention, in order to identify the initial vulnerability criteria. A positive correlation between E. coli and enterococci in surface waters was found indicating that E. coli is an acceptable indicator of fecal contamination in this region. E. coli and diarrheal diseases were strongly correlated with monsoonal precipitation, in situ SPM, and Near Infra-Red (NIR) band between March and November. Partial least squares regression showed that E. coli concentration was strongly associated with precipitation, Sentinel-2 reflectance in the NIR and SPM, and that the cases of diarrhea were strongly associated with precipitation, NIR, E. coli, SPM, and to a lesser extent with NDVI. Moreover, E. coli dynamics were reproduced using satellite data alone, particularly from February to mid-December (R2 = 0.60) as were cases of diarrhea throughout the year (R2 = 0.76). This implies that satellite data could provide an important contribution to water quality monitoring. Finally, the vulnerability of the population was found to increase during the rainy season due to reduced accessibility to healthcare and drinking water sources and increased use of water of poor quality. During this period, surface water is used because it is close to habitations, easy to use and free from monetary or political constraints. This vulnerability is aggravated by marginality and particularly affects the Fulani, whose concessions are often close to surface water (river, lake) and far from health centers.

The single-tube quantitative rapid detection of coliform bacteria based on enzyme-specific technology

To detect coliform bacteria (CB) with simplicity and portability, a novel, single-tube quantitative rapid detection method was developed based on CB-specific enzymatic technology. This technology involved a simple multi-channel spectrometer which could detect 7 cfu mL-1 CB specifically, and the approach was applied to various food and water samples.

Decay Rate of Escherichia coli in a Mountainous Tropical Headwater Wetland

Surface water contamination by pathogen bacteria remains a threat to public health in the rural areas of developing countries. Fecal indicator bacteria (FIB) like Escherichia coli (E. coli) are widely used to assess water contamination, but their behavior in tropical ecosystems is poorly documented. Our study focused on headwater wetlands which are likely to play a key role in stream water purification of fecal pollutants. Our main objectives were to: (i) evaluate decay rates (k) of the total, particle-attached and free-living E. coli; (ii) quantify the relative importance of solar radiation exposition and suspended particles deposition on k; and (iii) investigate E. coli survival in the deposited sediment. We installed and monitored 12 mesocosms, 4500 mL each, across the main headwater wetland of the Houay Pano catchment, northern Lao People’s Democratic Republic (Lao PDR), for 8 days. The four treatments with triplicates were: sediment deposition-light (DL); sediment deposition-dark (DD); sediment resuspension-light (RL); and sediment resuspension-dark (RD). Particle-attached bacteria predominated in all mesocosms (97 ± 6%). Decay rates ranged from 1.43 ± 0.15 to 1.17 ± 0.13 day−1 for DL and DD treatments, and from 0.50 ± 0.15 to −0.14 ± 0.37 day−1 for RL and RD treatments. Deposition processes accounted for an average of 92% of E. coli stock reduction, while solar radiation accounted for around 2% over the experiment duration. The sampling of E. coli by temporary resuspension of the deposited sediment showed k values close to zero, suggesting potential survival or even growth of bacteria in the sediment. The present findings may help parameterizing hydrological and water quality models in a tropical context.

Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network

Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.

Inactivation of waterborne fungal spores by 1-bromo-3-chloro-5,5-dimethylhydantoin: Kinetics, influencing factors and mechanisms

Fungal contamination in drinking water source has become a problem worth studying, as waterborne fungi may cause deterioration of water quality and outbreak of diseases. Various disinfection methods have been explored to control fungal spores in drinking water, such as chlor(am)ination, ozonation, chlorine dioxide treatment, but these methods are not appropriate for remote areas, owing to the difficulties in preparation, carriage and storage. In this study, a powdery disinfectant of 1-bromo-3-chloro-5,5-dimethylhydantoin (BCDMH), which facilitated transportation and preservation, was firstly chosen to inactivate opportunistic pathogens of Aspergillus niger (A. niger) and Penicillium polonicum (P. polonicum). The results revealed that the inactivation kinetics of fungal spores by BCDMH fitted to Chick-Watson model well, with the inactivation rate constant of 0.011 and 0.034 L mg^-1 min^-1 for A. niger and P. polonicum, respectively. Acidic condition and high temperature promoted the inactivation by BCDMH. Compared with chlorine, BCDMH showed relative weaker ability on inactivation of fungal spores. However, it was demonstrated that the inactivation efficiency of BCDMH was obviously enhanced by adding halide ions, with 11 or 36 folds for A. niger and 4 or 15 folds for P. polonicum by adding 40 μM Br^- or I^-. The inactivation mechanisms were detected by flow cytometry and scanning electron microscope. Fungal spores lost their culturability firstly, then membrane integrity was damaged. Meanwhile, the esterase activity and intracellular reactive oxygen species level changed, and finally intracellular adenosine triphosphate released.

The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China

Background

Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.

Results

We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (COD_Mn) and (NH₄⁺ )were the dominant environmental drivers affecting the bacterial community variance.

Conclusions

The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02252-9.

Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except bla_VIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

Performance of faecal indicator bacteria, microbial source tracking, and pollution risk mapping in tropical water

Faecal indicator bacteria (FIB) are used for the assessment of faecal pollution and possible water quality deterioration. There is growing evidence that FIB used in temperate regions are not adequate and reliable to detect faecal pollution in tropical regions. Hence, this study evaluated the adequacy of FIB, including total coliforms (TC), Escherichia coli (EC), Enterococci (IEC), and Clostridium perfringens (CP) in the high-altitude, tropical country of Ethiopia. In addition to FIB, for microbial source tracking (MST), a ruminant-associated molecular marker was applied at different water types and altitudes, and faecal pollution risk mapping was conducted based on consensus FIB. The performances of the indicators were evaluated at 22 sites from different water types. The results indicate that EC cell enumeration and CP spore determination perform well for faecal contamination monitoring. Most of the sub-basins of Lake Tana were found to be moderately to highly polluted, and the levels of pollution were demonstrated to be higher in the rainy season than in the post-rainy season. Markers associated with ruminants (BacR) were identified in more than three quarters of the sites. A bacterial pollution risk map was developed for sub-basins of Lake Tana, including the un-gauged sub-basins. We demonstrate how bacterial pollution risk mapping can aid in improvements to water quality testing and reduce risk to the general population from stream bacteria.

Experimental and modelling evidence of splash effects on manure borne Escherichia coli washoff

In tropical montane South-East Asia, recent changes in land use have induced increased runoff, soil erosion and in-stream suspended sediment loads. Land use change is also contributing to increased microbial pathogen dissemination and contamination of stream waters. Escherichia coli (E. coli) is frequently used as an indicator of faecal contamination. Field rain simulations were conducted to examine how E. coli is exported from the surface of upland, agricultural soils during runoff events. The objectives were to characterize the loss dynamics of this indicator from agricultural soils contaminated with livestock waste, and to identify the effect of splash on washoff. Experiments were performed on nine 1 m2 plots, amended or not with pig or poultry manure. Each plot was divided into two 0.5 m2 sub-plots. One of the two sub-plots was protected with a mosquito net for limiting the raindrop impact effects. Runoff, soil detachment by raindrop impact and its entrainment by runoff, and E. coli loads and discharge were measured for each sub-plot. The results show that raindrop impact strongly enhances runoff generation, soil detachment and entrainment and E. coli export. When the impact of raindrops was reduced with a mosquito net, total runoff was reduced by more than 50%, soil erosion was on average reduced by 90% and E. coli export from the amended soil surface was on average 3 to 8 times lower. A coupled physics-based approach was performed using the Cast3M platform for modelling the time evolutions of runoff, solid particles detachment and transfer and bacteria transport that were measured for one of the nine plots. After estimation of the saturated hydraulic conductivity, soil erodibility and attachment rate of bacteria, model outputs were consistent with measured runoff coefficients, suspended sediment and E. coli loads. This work therefore underlines the need to maintain adequate vegetation at the soil surface to avoid the erosion and export of soil borne potential pathogens towards downstream aquatic systems.

Water quality prospective in Twenty First Century: Status of water quality in major river basins, contemporary strategies and impediments: A review

Water quality improvement is one of the top priorities in the global agenda endorsed by United Nation. In this review manuscript, a holistic view of water quality degradation such as concerned pollutants, source of pollution, and its consequences in major river basins around the globe (at least 1 from each continent and a total of 16 basins) is presented. Additionally, nine contemporary techniques such as field scale evaluation, watershed scale evaluation, strategies to identify critical source areas, optimization strategies for placement of best management practices (BMPs), social component in watershed modeling, machine learning algorithms to address water quality problems in complex natural systems concomitant with spatial heterogeneity, establishing a total maximum daily loads (TMDLs), remote sensing in monitoring water quality, and developing water quality index are discussed. Next, the existing barriers to improve water quality are classified into primary and secondary impediments. A detail discussion of three primary impediments (climate change, urbanization and industrial activities, and agriculture) and ten secondary impediments (availability of water quality data, complexity of system, lack of skilled person, environmental legislation, fragmented mandate, limitation in resources, environmental awareness, resistance to change, alteration of nutrient ratio by river damming, and emerging pollutants) are illustrated. Finally, considering all the existing knowledge gaps pertaining to contemporary strategies, a future direction of water quality research is outlined to significantly improve the water quality around the globe.

Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR

In the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination using Escherichia coli as fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extreme E. coli concentrations occurring during the rainy season. The highest E. coli concentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province.

The relationship between environmental parameters and microbial water quality at two Costa Rican beaches from 2002 to 2017

Environmental conditions influence fecal indicator bacteria (FIB) levels, which are routinely used to characterize recreational water quality. This study examined 15 years of environmental and FIB data at Puntarenas and Jacó beach, Costa Rica. FIB relationships with sea level, wave height, precipitation, direct normal irradiance (DNI), wind, and turbidity were analyzed. Pearson's correlations identified lags between 24 and 96 h among environmental parameters and FIB. Multiple linear regression models composed of environmental parameters explained 24% and 27% of fecal coliforms and enterococci variability in Jacó, respectively. Puntarenas's models explained 17-26% of fecal coliforms and 12-18% enterococci variability. Precipitation, sea level anomalies, and wave height most frequently explained FIB variability. Hypothesis testing often identified significant differences in precipitation, wave height, daily sea level anomalies, and maximum sea level 24 h prior between days with and without FIB threshold exceedance. Unexpected FIB interactions with DNI, sea level, and turbidity highlight the importance of future investigations.

Using Land Runoff to Survey the Distribution and Genetic Diversity of Burkholderia pseudomallei in Vientiane, Laos

Melioidosis is a disease of significant public health importance that is being increasingly recognized globally. The majority of cases arise through direct percutaneous exposure to its etiological agent, Burkholderia pseudomallei In the Lao People's Democratic Republic (Laos), the presence and environmental distribution of B. pseudomallei are not well characterized, though recent epidemiological surveys of the bacterium have indicated that B. pseudomallei is widespread throughout the environment in the center and south of the country and that rivers can act as carriers and potential sentinels for the bacterium. The spatial and genetic distribution of B. pseudomallei within Vientiane Capital, from where the majority of cases diagnosed to date have originated, remains an important knowledge gap. We sampled surface runoff from drain catchment areas throughout urban Vientiane to determine the presence and local population structure of the bacterium. B. pseudomallei was detected in drainage areas throughout the capital, indicating it is widespread in the environment and that exposure rates in urban Vientiane are likely more frequent than previously thought. Whole-genome comparative analysis demonstrated that Lao B. pseudomallei isolates are highly genetically diverse, suggesting the bacterium is well-established and not a recent introduction. Despite the wide genome diversity, one environmental survey isolate was highly genetically related to a Lao melioidosis patient isolate collected 13 years prior to the study. Knowledge gained from this study will augment understanding of B. pseudomallei phylogeography in Asia and enhance public health awareness and future implementation of infection control measures within Laos.IMPORTANCE The environmental bacterium B. pseudomallei is the etiological agent of melioidosis, a tropical disease with one model estimating a global annual incidence of 165,000 cases and 89,000 deaths. In the Lao People's Democratic Republic (Laos), the environmental distribution and population structure of B. pseudomallei remain relatively undefined, particularly in Vientiane Capital from where most diagnosed cases have originated. We used surface runoff as a proxy for B. pseudomallei dispersal in the environment and performed whole-genome sequencing (WGS) to examine the local population structure. Our data confirmed that B. pseudomallei is widespread throughout Vientiane and that surface runoff might be useful for future environmental monitoring of the bacterium. B. pseudomallei isolates were also highly genetically diverse, suggesting the bacterium is well-established and endemic in Laos. These findings can be used to improve awareness of B. pseudomallei in the Lao environment and demonstrates the epidemiological and phylogeographical insights that can be gained from WGS.

What Environmental Factors Influence the Concentration of Fecal Indicator Bacteria in Groundwater? Insights from Explanatory Modeling in Uganda and Bangladesh

Information about microbial water quality is critical for managing water safety and protecting public health. In low-income countries, monitoring all drinking water supplies is impractical because financial resources and capacity are insufficient. Data sets derived from satellite imagery, census, and hydrological models provide an opportunity to examine relationships between a suite of environmental risk factors and microbial water quality over large geographical scales. We investigated the relationships between groundwater fecal contamination and different environmental parameters in Uganda and Bangladesh. In Uganda, groundwater contamination was associated with high population density (p < 0.001; OR = 1.27), high cropland coverage (p < 0.001; OR = 1.47), high average monthly precipitation (p < 0.001; OR = 1.14), and high surface runoff (p < 0.001; OR = 1.37), while low groundwater contamination was more likely in areas further from cities (p < 0.001; OR = 0.66) and with higher forest coverage (p < 0.001; OR = 0.70). In Bangladesh, contamination was associated with higher weekly precipitation (p < 0.001; OR = 1.44) and higher livestock density (p = 0.05; OR = 1.11), while low contamination was associated with low forest coverage (p < 0.001; OR = 1.23) and high cropland coverage (p < 0.001; OR = 0.80). We developed a groundwater contamination index for each country to help decision-makers identify areas where groundwater is most prone to fecal contamination and prioritize monitoring activities. Our approach demonstrates how to harness satellite-derived data to guide water safety management.