Fecal indicator bacteria and Salmonella in ponds managed as bird habitat, San Francisco Bay, California, USA

Occurrence of Fecal Bacteria and Zoonotic Pathogens in Different Water Bodies: Supporting Water Quality Management

Water contaminated with microbiological and chemical constituents can cause a variety of diseases. Water bodies may become contaminated by wild and domestic animal feces, agricultural runoff or sewage, and are often overlooked as a reservoir and source of human infection by pathogenic microorganisms. The objectives of this study were to evaluate the presence of the zoonotic pathogens, Salmonella spp. and Listeria monocytogenes, in various water bodies located in urban and rural areas in the north of Portugal. Water samples were collected from six sites, including natural and artificial ponds, in two different time periods. Several water quality physicochemical parameters, as well as fecal indicator bacteria, were evaluated. High levels of total coliforms (>1.78 log CFU/100 mL) were detected in all samples, and substantial numbers of Enterococcus (>2.32 log CFU/100 mL) were detected in two ponds located in a city park and in an urban garden. Escherichia coli counts ranged from undetectable to 2.76 log CFU/100 mL. Salmonella spp. was isolated from two sites, the city park and the natural pond, while L. monocytogenes was isolated from three sites: the city garden, the natural pond and the artificial pond, both in the rural area. These data show that artificial and natural ponds are a reservoir of fecal indicator bacteria and enteric and zoonotic pathogens. This may impact the potential risks of human infections by potential contaminants during recreational activities, being important for assessing the water quality for strategic management of these areas.

Distribution and Antibiotic Resistance Profiles of Salmonella enterica in Rural Areas of North Carolina After Hurricane Florence in 2018

In this study, water samples were analyzed from a rural area of North Carolina after Hurricane Florence in 2018 and the distribution of the ttrC virulence gene of Salmonella enterica were investigated. We also examined the distribution of culturable S. enterica and determined their antibiotic resistance profiles. Antibiotic resistance genes (ARGs) in the classes of aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin B (MLSB) were targeted in this study. The ttrC gene was detected in 23 out of 25 locations. There was a wider and higher range of the ttrC gene in flooded water versus unflooded water samples (0-2.12 × 105 copies/L vs. 0-4.86 × 104 copies/L). Culturable S. enterica was isolated from 10 of 25 sampling locations, which was less prevalent than the distribution of the ttrC gene. The antibiotic resistance profiles were not distinct among the S. enterica isolates. The aminoglycoside resistance gene aac(6')-Iy had the highest relative abundance (around 0.05 copies/16S rRNA gene copy in all isolates) among all ARGs. These findings suggested that the 2018 flooding event led to higher copy numbers of the ttrC genes of S. enterica in some flooded water bodies compared to those in unflooded water bodies. The high ARG level and similar ARG profiles were observed in all S. enterica isolates from both flooded and unflooded samples, suggesting that the antibiotic resistance was prevalent in S. enterica within this region, regardless of flooding.

Antimicrobial Drug-Resistant Gram-Negative Saprophytic Bacteria Isolated from Ambient, Near-Shore Sediments of an Urbanized Estuary: Absence of β-Lactamase Drug-Resistance Genes

We assessed the prevalence of antimicrobial resistance and screened for clinically relevant β-lactamase resistance determinants in Gram-negative bacteria from a large urbanized estuary. In contrast to the broad literature documenting potentially hazardous resistance determinants near wastewater treatment discharge points and other local sources of aquatic pollution, we employed a probabilistic survey design to examine ambient, near-shore sediments. We plated environmental samples from 40 intertidal and shallow subtidal areas around San Francisco Bay (California, USA) on drug-supplemented MacConkey agar, and we tested isolates for antimicrobial resistance and presence of clinically relevant β-lactamase resistance determinants. Of the 74 isolates identified, the most frequently recovered taxa were Vibrio spp. (40%), Shewanella spp. (36%), Pseudomonas spp. (11%), and Aeromonas spp. (4%). Of the 55 isolates tested for antimicrobial resistance, the Vibrio spp. showed the most notable resistance profiles. Most (96%) were resistant to ampicillin, and two isolates showed multidrug-resistant phenotypes: V. alginolyticus (cefotaxime, ampicillin, gentamicin, cefoxitin) and V. fluvialis (cefotaxime, ampicillin, cefoxitin). Targeted testing for class 1 integrons and presence of β-lactam-resistance gene variants TEM, SHV, OXA, CTX-M, and Klebsiella pneumonia carbapenemase (KPC) did not reveal any isolates harboring these resistance determinants. Thus, while drug-resistant, Gram-negative bacteria were recovered from ambient sediments, neither clinically relevant strains nor mobile β-lactam resistance determinants were found. This suggests that Gram-negative bacteria in this well-managed, urbanized estuary are unlikely to constitute a major human exposure hazard at this time.

Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment

Fecal contamination of recreational waters with cattle manure can pose a risk to public health due to the potential presence of various zoonotic pathogens. Fecal indicator bacteria (FIB) have a long history of use in the assessment of recreational water quality, but FIB quantification provides no information about pollution sources. Microbial source tracking (MST) markers have been developed in response to a need to identify pollution sources, yet factors that influence their decay in ambient waters are often poorly understood. We investigated the influence of water type (freshwater versus marine) and select environmental parameters (indigenous microbiota, ambient sunlight) on the decay of FIB and MST markers originating from cattle manure. Experiments were conducted in situ using a submersible aquatic mesocosm containing dialysis bags filled with a mixture of cattle manure and ambient water. Culturable FIB (E. coli, enterococci) were enumerated by membrane filtration and general fecal indicator bacteria (GenBac3, Entero1a, EC23S857) and MST markers (Rum2Bac, CowM2, CowM3) were estimated by qPCR. Water type was the most significant factor influencing decay (three-way ANOVA, p: 0.006 to <0.001), although the magnitude of the effect differed among microbial targets and over time. The presence of indigenous microbiota and exposure to sunlight were significantly correlated (three-way ANOVA, p: 0.044 to <0.001) with decay of enterococci and CowM2, while E. coli, EC23S857, Rum2Bac, and CowM3 (three-way ANOVA, p: 0.044 < 0.001) were significantly impacted by sunlight or indigenous microbiota. Results indicate extended persistence of both cultivated FIB and genetic markers in marine and freshwater water types. Findings suggest that multiple environmental stressors are important determinants of FIB and MST marker persistence, but their magnitude can vary across indicators. Selective exclusion of natural aquatic microbiota and/or sunlight typically resulted in extended survival, but the effect was minor and limited to select microbial targets.

A Constructed Wetland for Treatment of an Impacted Waterway and the Influence of Native Waterfowl on its Perceived Effectiveness

A constructed, variable-flow treatment wetland was evaluated for its ability to reduce microbial loads from the Banklick Creek, an impacted recreational waterway in Northern Kentucky. For this study, levels of traditional (Escherichia coli and enterococci measured by culture and molecular techniques) and alternative fecal indicators (infectious somatic and F+ coliphage, Clostridium spp. and Clostridium perfringens by culture), potential pathogens (molecular signal of Campylobacter spp.) as well as various microbial source tracking (MST) markers (human fecal marker HF183 and avian fecal marker GFD) were monitored during the summer and early fall through five treatment stages within the Banklick Creek Wetland. No difference in concentrations of traditional or alternative fecal indicators were observed in any of the sites monitored. Microbial source tracking markers were employed to identify sources of fecal contamination within the wetland. Human marker HF183 concentrations at beginning stages of treatment were found to be significantly higher (P value range: 0.0016-0.0003) than levels at later stages. Conversely, at later stages of treatment where frequent bird activity was observed, Campylobacter and avian marker (GFD) signals were detected at significantly higher frequencies (P value range: 0.024 to <0.0001), and both signals were strongly correlated (P = 0.0001). Our study suggests constructed wetlands are an effective means for removal of microbial contamination in ambient waters, but reliance on general fecal indicators is not ideal for determining system efficacy or assessing appropriate remediation efforts.

Association between wetland presence and incidence of Salmonella enterica serotype Javiana infections in selected US sites, 2005–2011

Salmonella causes an estimated 1·2 million illnesses annually in the USA. Salmonella enterica serotype Javiana (serotype Javiana) is the fourth most common serotype isolated from humans, with the majority of illnesses occurring in southeastern states. The percentage of wetland cover by wetland type and the average incidence rates of serotype Javiana infection in selected counties of the Foodborne Disease Active Surveillance Network (FoodNet) were examined. This analysis explored the relationship between wetland environments and incidence in order to assess whether regional differences in environmental habitats may be associated with observed variations in incidence. Findings suggest that environmental habitats may support reservoirs or contribute to the persistence of serotype Javiana, and may frequently contribute to the transmission of infection compared with other Salmonella serotypes.

Salmonella enterica diversity in central Californian coastal waterways

Salmonella enterica is one of the most important bacterial enteric pathogens worldwide. However, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over 2 years from 12 coastal waterways in central California. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found, including 18 newly described STs. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium, and other frequently detected STs were associated with the serovars Heidelberg and Enteritidis; all of these serovars are important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxon-time relationship but no taxon-area or taxon-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest that the lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.

Impact of mixed land-use practices on the microbial water quality in a subtropical coastal watershed

Surface runoff water is an important non-point source of fecal pollution to downstream water; however, there is a lack of systematic studies on the microbial quality of surface runoff water from watersheds with mixed land uses. In this study water samples from 12 surface runoff holding water bodies (SRW), which collected runoff from various patterns of land use within the St. Lucie watershed along the southeastern coastline of Florida, were collected monthly for 22 months. The concentration of fecal indicator bacteria (FIB) and frequency of detection of Salmonella and host specific markers (HF183, CF128, CF193, and HS-esp) were determined, and their associations with land use, rainfall, and water physico-chemical parameters were investigated. Higher FIB concentrations were observed from urban land and cattle ranch sites. Within the same primary land use pattern, different sub-patterns did not have the same level of FIB: golf communities contributed less to fecal pollution than residential areas, and plant nursery sites contained relative higher FIB concentrations than other agricultural sites. Salmonella, CF128, and CF193 markers were more frequently detected from the cattle ranch sites. In contrast the frequency of detecting human specific markers (HF183 and HS-esp) was much higher in residential sites. Rainfall positively affected the concentration of FIB and occurrence of Salmonella, possibly by providing more inputs or mobilizing the sources from sediments. Water temperature, dissolved organic carbon (DOC), and nutrient levels were positively correlated with FIB concentrations and occurrence in SRW, possibly by promoting their growth and survival. This study indicated the need for site specific mitigation strategies to improve SRW and downstream water quality.

Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources

Using in situ subtropical aquatic mesocosms, fecal source (cattle manure versus sewage) was shown to be the most important contributor to differential loss in viability of fecal indicator bacteria (FIB), specifically enterococci in freshwater and Escherichia coli in marine habitats. In this study, sunlight exposure and indigenous aquatic microbiota were also important contributors, whose effects on FIB also differed between water types.

Occurrence and persistence of bacterial pathogens and indicator organisms in beach sand along the California coast

This report documents the presence of fecal indicators and bacterial pathogens in sand at 53 California marine beaches using both culture-dependent and -independent (PCR and quantitative PCR [QPCR]) methods. Fecal indicator bacteria were widespread in California beach sand, with Escherichia coli and enterococci detected at 68% and 94% of the beaches surveyed, respectively. Somatic coliphages and a Bacteroidales human-specific fecal marker were detected at 43% and 13% of the beaches, respectively. Dry sand samples from almost 30% of the beaches contained at least one of the following pathogens: Salmonella spp., Campylobacter spp., Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA), which were detected at 15%, 13%, 14%, and 3% of tested beaches, respectively. Fecal indicators and pathogens were poorly correlated to one another and to land cover. Sands were dry at the time of collection, and those with relatively high moisture tended to have higher concentrations or a more frequent occurrence of both indicators and pathogens. Using culture-dependent assays, fecal indicators decayed faster than pathogens in microcosm experiments using unaltered beach sand seeded with sewage and assessed by culture-dependent assays. The following order of persistence was observed (listed from most to least persistent): Campylobacter > Salmonella > somatic coliphages > enterococci > E. coli > F(+) phages. In contrast, pathogens decayed faster than fecal indicators in culture-independent assays: enterococci > Bacteroidales human-specific marker > Salmonella > Campylobacter. Microcosm experiments demonstrated that both indicators and pathogens were mobilized by wetting with seawater. Decay rates measured by QPCR were lower than those measured with culture-dependent methods. Enterococcal persistence and possible growth were observed for wetted microcosms relative to unwetted controls.

Bacterial pathogens in Hawaiian coastal streams--associations with fecal indicators, land cover, and water quality

This work aimed to understand the distribution of five bacterial pathogens in O'ahu coastal streams and relate their presence to microbial indicator concentrations, land cover of the surrounding watersheds, and physical-chemical measures of stream water quality. Twenty-two streams were sampled four times (in December and March, before sunrise and at high noon) to capture seasonal and time of day variation. Salmonella, Campylobacter, Staphylococcus aureus, Vibrio vulnificus, and V. parahaemolyticus were widespread -12 of 22 O'ahu streams had all five pathogens. All stream waters also had detectable concentrations of four fecal indicators and total vibrio with log mean ± standard deviation densities of 2.2 ± 0.8 enterococci, 2.7 ± 0.7 Escherichia coli, 1.1 ± 0.7 Clostridium perfringens, 1.2 ± 0.8 F(+) coliphages, and 3.6 ± 0.7 total vibrio per 100 ml. Bivariate associations between pathogens and indicators showed enterococci positively associated with the greatest number of bacterial pathogens. Higher concentrations of enterococci and higher incidence of Campylobacter were found in stream waters collected before sunrise, suggesting these organisms are sensitive to sunlight. Multivariate regression models of microbes as a function of land cover and physical-chemical water quality showed positive associations between Salmonella and agricultural and forested land covers, and between S. aureus and urban and agricultural land covers; these results suggested that sources specific to those land covers may contribute these pathogens to streams. Further, significant associations between some microbial targets and physical-chemical stream water quality (i.e., temperature, nutrients, turbidity) suggested that organism persistence may be affected by stream characteristics. Results implicate streams as a source of pathogens to coastal waters. Future work is recommended to determine infectious risks of recreational waterborne illness related to O'ahu stream exposures and to mitigate these risks through control of land-based runoff sources.

Impact of urbanization and agriculture on the occurrence of bacterial pathogens and stx genes in coastal waterbodies of central California

Fecal pollution enters coastal waters through multiple routes, many of which originate from land-based activities. Runoff from pervious and impervious land surfaces transports pollutants from land to sea and can cause impairment of coastal ocean waters. To understand how land use practices and water characteristics influence concentrations of fecal indicator bacteria (FIB) and pathogens in natural waters, fourteen coastal streams, rivers, and tidal lagoons, surrounded by variable land use and animal densities, were sampled every six weeks over two years (2008 & 2009). Fecal indicator bacteria (FIB; Escherichia coli and Enterococci) and Salmonella concentrations, the occurrence of Bacteroidales human, ruminant, and pig-specific fecal markers, E. coli O157:H7, and Shiga toxin (stx) genes present in E. coli, were measured. In addition, environmental and climatic variables (e.g., temperature, salinity, rainfall), as well as human and livestock population densities and land cover were quantified. Concentrations of FIB and Salmonella were correlated with each other, but the occurrence of host-specific Bacteroidales markers did not correlate with FIB or pathogens. FIB and Salmonella concentrations, as well as the occurrence of E. coli harboring stx genes, were positively associated with the fraction of the surrounding subwatershed that was urban, while the occurrence of E. coli O157:H7 was positively associated with the agricultural fraction. FIB and Salmonella concentrations were negatively correlated to salinity and temperature, and positively correlated to rainfall. Areal loading rates of FIB, Salmonella and E. coli O157:H7 to the coastal ocean were calculated for stream and river sites and varied with land cover, salinity, temperature, and rainfall. Results suggest that FIB and pathogen concentrations are influenced, in part, by their flux from the land, which is exacerbated during rainfall; once waterborne, bacterial persistence is affected by water temperature and salinity.

Beach boundary layer: a framework for addressing recreational water quality impairment at enclosed beaches

Nearshore waters in bays, harbors, and estuaries are frequently contaminated with human pathogens and fecal indicator bacteria. Tracking down and mitigating this contamination is complicated by the many point and nonpoint sources of fecal pollution that can degrade water quality along the shore. From a survey of the published literature, we propose a conceptual and mathematical framework, the "beach boundary layer model", for understanding and quantifying the relative impact of beach-side and bay-side sources of fecal pollution on nearshore water quality. In the model, bacterial concentration in ankle depth water C(ankle) [bacteria L(-3)] depends on the flux m'' [bacteria L(-2) T(-1)] of fecal bacteria from beach-side sources (bather shedding, bird and dog feces, tidal washing of sediments, decaying vegetation, runoff from small drains, and shallow groundwater discharge), a cross-shore mass transfer velocity k [L T(-1)] that accounts for the physics of nearshore transport and mixing, and a background concentration C(bay) [bacteria L(-3)] attributable to bay-side sources of pollution that impact water quality over large regions (sewage outfalls, creeks and rivers): C(ankle) = m''/k + C(bay). We demonstrate the utility of the model for identifying risk factors and pollution sources likely to impact shoreline water quality, and evaluate the model's underlying assumptions using computational fluid dynamic simulations of flow, turbulence, and mass transport in a trapezoidal channel.

Reduction of fecal indicator bacteria (FIB) in the Ballona Wetlands saltwater marsh (Los Angeles County, California, USA) with implications for restoration actions

A benefit of wetland preservation and restoration is the ecosystem service of improving water quality, typically assessed based on bacterial loading. The Ballona Wetlands, a degraded salt marsh of approximately 100 ac located on the southern border of Marina Del Rey (Los Angeles County, California, USA) are currently the focus of publicly funded restoration planning. The wetlands receive tidal water, usually contaminated with fecal indicator bacteria (FIB: total and fecal coliforms, Escherichia coli, enterococci) from the adjacent Ballona Creek and Estuary. During the summer of 2007, two 24-h studies were conducted to determine FIB tidal dynamics within the wetland. Measurements of water flow and mean FIB concentrations (n = 3) were measured every 1.5 h to determine total FIB load estimates. FIB loading rates (MPN/s) were greatest during flood tides as water entered the wetlands, and then again during spring tide conditions when sediments were resuspended during swifter spring ebb flows. During daylight hours, the wetland acted as a sink for these bacteria as loads diminished, presumably by sunlight and other processes. Conversely, during late afternoon and night, the wetlands shifted to being a source as excess FIB departed on ebb flows. Therefore, the wetlands act as both a source and sink for FIB depending on tidal conditions and exposure to sunlight. Future restoration actions would result in a tradeoff - increased tidal channels offer a greater surface area for FIB inactivation, but also would result in a greater volume of FIB-contaminated resuspended sediments carried out of the wetlands on stronger ebb flows. As levels of FIB in Ballona Creek and Estuary diminish through recently established regulatory actions, the wetlands could shift into a greater sink for FIB.

Water quality in South San Francisco Bay, California: current condition and potential issues for the South Bay Salt Pond Restoration Project

The SBSPRP is an extensive tidal wetland restoration project that is underway at the margin of South San Francisco Bay, California. The Project, which aims to restore former salt ponds to tidal marsh and manage other ponds for water bird support, is taking place in the context of a highly urbanized watershed and an Estuary already impacted by chemical contaminants. There is an intimate relationship between water quality in the watershed, the Bay, and the transitional wetland areas where the Project is located. The Project seeks to restore habitat for endangered and endemic species and to provide recreational opportunities for people. Therefore, water quality and bioaccumulation of contaminants in fish and wildlife is an important concern for the success of the Project. Mercury, PCBs, and PBDEs are the persistent contaminants of greatest concern in the region. All of these contaminants are present at elevated concentrations both in the abiotic environment and in wildlife. Dioxins, pyrethroids, PAHs, and selenium are also problematic. Organochlorine insecticides have historically impacted the Bay, and they remain above thresholds for concern in a small proportion of samples. Emerging contaminants, such as PFCs and non-PBDE flame retardants, are also an important water quality issue. Beyond chemical pollutants, other concerns for water quality in South San Francisco Bay exist, and include biological constituents, especially invasive species, and chemical attributes, such as dissolved oxygen and salinity. Future changes, both from within the Project and from the Bay and watershed, are likely to influence water quality in the region. Project actions to restore wetlands could worsen, improve, or not affect the already impaired water quality in South Bay. Accelerated erosion of buried sediment as a consequence of Project restoration actions is a potentially serious regional threat to South Bay water and sediment quality. Furthermore, the planned restoration of salt ponds to tidal marsh has raised concerns about possible increased net production of methylmercury and its subsequent accumulation in the food web. This concern applies not only to the restored marshes, but also to the South Bay as a whole, which could be affected on a regional scale. The ponds that are converted to tidal marsh will sequester millions of cubic meters of sediment. Sequestration of sediment in marshes could remove contaminated sediment from the active zone of the Bay but could also create marshes with contaminated food webs. Some of the ponds will not be restored to marsh but will be managed for use by water birds. Therefore, the effect of dense avian populations on eutrophication and the introduction of pathogens should be considered. Water quality in the Project also could be affected by external changes, such as human population growth and climate change. To address these many concerns related to water quality, the SBSPRP managers, and others faced with management of wetland restoration at a regional scale, should practice adaptive management and ongoing monitoring for water quality, particularly monitoring bioaccumulation of contaminants in the food web.