The seasonality of fecal coliform bacteria pollution and its influence on closures of shellfish harvesting areas in Mississippi Sound

Assessing the utility of shellfish sanitation monitoring data for long-term estuarine water quality analysis

Regular testing of coastal waters for fecal coliform bacteria by shellfish sanitation programs could provide data to fill large gaps in existing coastal water quality monitoring, but research is needed to understand the opportunities and limitations of using these data for inference of long-term trends. In this study, we analyzed spatiotemporal trends from multidecadal fecal coliform concentration observations collected by a shellfish sanitation program, and assessed the feasibility of using these monitoring data to infer long-term water quality dynamics. We evaluated trends in fecal coliform concentrations for a 20-year period (1999-2021) using data collected from spatially fixed sampling sites (n = 466) in North Carolina (USA). Findings indicated that shellfish sanitation data can be used for long-term water quality inference under relatively stationary management conditions, and that salinity trends can be used to investigate management-driven bias in fecal coliform observations collected in a particular area.

Short-term forecasting of fecal coliforms in shellfish growing waters

This study sought to develop models for predicting near-term (1-3 day) fecal contamination events in coastal shellfish growing waters. Using Random Forest regression, we (1) developed fecal coliform (FC) concentration models for shellfish growing areas using watershed characteristics and antecedent hydrologic and meteorologic observations as predictors, (2) tested the change in model performance associated when forecasted, as opposed to measured, rainfall variables were used as predictors, and (3) evaluated model predictor importance in relation to shellfish sanitation management criteria. Models were trained to 10 years of coastal FC measurements (n = 1285) for 5 major shellfish management areas along the Florida (USA) coast. Model performance varied between the 5 management areas with R2 ranging from 0.36 to 0.72. Antecedent precipitation variables were among the most important predictors in the day-of forecast models in all management areas. When forecasted rainfall was included in the models, wind components became increasingly important.

Assessment of Bacterial Accumulation and Environmental Factors in Sentinel Oysters and Estuarine Water Quality from the Phang Nga Estuary Area in Thailand

This study characterized microbiological and chemical contamination of oyster meat and estuarine water in Phang Nga, Thailand. Pooled oyster meats (n = 144), estuarine waters (n = 96) and environmental parameters were collected from March, 2016 to February, 2017, and assessed for levels of total coliforms (TC), fecal coliforms (FC), Escherichia coli (EC), and Vibrio parahaemolyticus (VP), presence of Salmonella and Shigella and levels of heavy metals (Mn, Pb and Cd). The prevalence of TC, FC and EC were in 99.3%, 94.4% and 93.1% of oyster meat and 94.8%, 79.2%, and 78.1% of water, respectively. The average VP levels was 8.5 × 10⁷ most probable number (MPN)/g oyster. Prevalence of Shigella and Salmonella in the pooled oysters were 7.6% and 30.6%, respectively. The dominant Salmonella serovars were Paratyphi B followed by Seremban, and Kentucky. In contrast, the prevalence of Shigella were 27.1%, but Salmonella was not detected in estuarine water. Factors statistically associated with EC accumulation in oyster were level of FC, 7-day average precipitation, temperature, relative humidity, and presence of Salmonella in the sample. The optimal cutoff value of EC to predict Salmonella in oyster was 420 MPN/g. Results indicate this area has relatively safe levels of heavy metals, whereas bacterial contamination was very high for oysters.

Do the Escherichia coli European Union shellfish safety standards predict the presence of Arcobacter spp., a potential zoonotic pathogen?

The genus Arcobacter comprises Campylobacter-related species, considered zoonotic emergent pathogens, the presence of which in water has been associated with fecal pollution. Discharges of fecal polluted water into the sea have been considered as one of the main reasons for the presence of Arcobacter in shellfish, and this may represent a risk for public health. In this study, the European Union shellfish food safety criteria based on levels of Escherichia coli were studied in relation to their capacity to predict the presence of Arcobacter species. In addition, the accumulation factor (AF) that measures the concentration ratio between the microbes present in the shellfish and in the water, was also studied for both bacteria. The results show that the presence of E. coli correlated with the presence of the potentially pathogenic species A. butzleri and A. cryaerophilus. However, in 26.1% of the shellfish samples (corresponding to those taken during summer months) E. coli failed to predict the presence of, for instance A. butzleri and A. skirrowii, among other species. In the rest of the samples a significant correlation between the concentration of E. coli and Arcobacter spp. (mussels and oyster; R²=0.744) was found. This study indicates that the presence of E. coli can predict the presence of pathogenic Arcobacter species in shellfish samples harvested from water with temperatures lower than 26.2°C. Consumption of shellfish collected at higher temperatures which may not be permissive to the growth of E. coli but does allow growth of Arcobacter spp., may represent a risk for consumers.

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

Bacteriological quality evaluation of seawater and oysters from the Hansan-Geojeman area in Korea, 2011-2013: impact of inland pollution sources

From 2011 to 2013, we conducted a full sanitary survey of pollution sources in proximity to a shellfish growing area in the Hansan-Geojeman region in Korea, which includes a designated shellfish growing area. In the sea area, 1152 seawater and 209 oyster samples were collected and examined to evaluate their bacteriological quality. There were 758 potential pollution sources in the drainage area, including 40 sources discharging water in 2013. Fecal coliform (FC) concentrations and impact radii of discharges ranged from 1.8 to 700,000 MPN/100 mL and from 3 to 600 m, respectively; however, the pollutants did not reach the designated area. This demonstrates that the dilution of waste was sufficient such that no significant impact occurred within the designated shellfish growing area. The variation in the FC levels of seawater was closely related to season and rainfall. The FC levels of seawater and oysters from the designated area met the regulation limits set by various countries. No pathogens were found in any oysters. The results of the survey indicate that the oysters produced in this area are apparently safe for raw consumption based on their bacterial quality.

Climate relationships to fecal bacterial densities in Maryland shellfish harvest waters

Coastal states of the United States (US) routinely monitor shellfish harvest waters for types of bacteria that indicate the potential presence of fecal pollution. The densities of these indicator bacteria in natural waters may be related to climate in several ways, including through runoff from precipitation and survival related to water temperatures. The relationship between interannual precipitation and air temperature patterns and the densities of fecal indicator bacteria in shellfish harvest waters in Maryland's portion of the Chesapeake Bay was quantified using 34 years of data (1979-2013). Annual and seasonal precipitation totals had a strong positive relationship with average fecal coliform levels (R(2) = 0.69) and the proportion of samples with bacterial densities above the FDA regulatory criteria (R(2) = 0.77). Fecal coliform levels were also significantly and negatively related to average annual air temperature (R(2) = -0.43) and the average air temperature of the warmest month (R(2) = -0.57), while average seasonal air temperature was only significantly related to fecal coliform levels in the summer. River and regional fecal coliform levels displayed a wide range of relationships with precipitation and air temperature patterns, with stronger relationships in rural areas and mainstem Bay stations. Fecal coliform levels tended to be higher in years when the bulk of precipitation occurred throughout the summer and/or fall (August to September). Fecal coliform levels often peaked in late fall and winter, with precipitation peaking in summer and early fall. Continental-scale sea level pressure (SLP) analysis revealed an association between atmospheric patterns that influence both extratropical and tropical storm tracks and very high fecal coliform years, while regional precipitation was found to be significantly correlated with the Atlantic Multidecadal Oscillation and the Pacific North American Pattern. These findings indicate that management of shellfish harvest waters should account for changes in climate conditions and that SLP patterns may be particularly important for predicting years with extremely high levels of fecal coliforms.

Bacterial community composition and physiological shifts associated with the El Niño Southern Oscillation (ENSO) in the Patos Lagoon estuary

The Patos Lagoon estuary is a microtidal system that is strongly regulated by atmospheric forces, including remote large-scale phenomena such as the El Niño Southern Oscillation (ENSO), which affects precipitation patterns in the region. In this study, we investigated whether the bacterial community composition (BCC), community-level physiological profiles (CLPP), and a set of environmental variables were affected by the transition from a moderate El Niño to a strong La Niña event (June 2010 to May 2011). We identified two distinct periods: a period following El Niño that was characterized by low salinity and high concentrations of NO3(-) and PO4(-3) and low molecular weight (LMW) substances and a period following La Niña during which salinity, temperature, and transparency increased and the concentrations of nutrients and LMW substances decreased. The BCC and CLPP were significantly altered in response to this transition. This is the first study addressing the effect of ENSO on bacteria at the community level in an estuarine system. Our results suggest that there is a link between ENSO and bacteria, indicating the role of climate variability in bacterial activities and, hence, the cycling of organic matter by these microorganisms.

Differentiating Enterococcus concentration spatial, temporal, and analytical variability in recreational waters

Monitoring recreational waters for fecal contamination is an important responsibility of water resource management agencies throughout the world, yet fecal indicator bacteria (FIB)-based recreational water quality assessments rarely distinguish between analytical, spatial, and temporal variability. To address this gap in water resources research and management protocol, we compare two methods for quantifying FIB concentration variability at a frequently-used beach on Lake Huron (Michigan, USA). The first method calculates differences between most probable number (MPN) and colony-forming unit (CFU) values derived from conventional analysis procedures. The second method uses the "raw data" from these analysis procedures in a Bayesian hierarchical model to explicitly acknowledge analytical variability and subsequently infer the relative significance of the effect of sampling location and time on in situ FIB concentrations. Results of the Bayesian analysis indicate that in situ FIB concentrations do not vary significantly over small spatial and temporal scales, and that observed differences in MPN and CFU values over these same spatial and temporal scales are due almost entirely to intrinsic variability introduced by laboratory analysis procedures. Our findings underscore potential opportunities for incorporating Bayesian statistical models directly into routine recreational water quality assessments and for advancing the state of the art in methods for protecting humans from waterborne disease.

Temporal genetic variability and host sources of Escherichia coli associated with fecal pollution from domesticated animals in the shellfish culture environment of Xiangshan Bay, East China Sea

This study was conducted to analyze the genetic variability of Escherichia coli from domesticated animal wastes for microbial source tracking (MST) application in fecal contaminated shellfish growing waters of Xiangshan Bay, East China Sea. (GTG)(5) primer was used to generate 1363 fingerprints from E. coli isolated from feces of known 9 domesticated animal sources around this shellfish culture area. Jackknife analysis of the complete (GTG)(5)-PCR DNA fingerprint library indicated that isolates were assigned to the correct source groups with an 84.28% average rate of correct classification. Based on one-year source tracking data, the dominant sources of E. coli were swine, chickens, ducks and cows in this water area. Moreover, annual and spatial changes of E. coli concentrations and host sources may affect the level and distribution of zoonotic pathogen species in waters. Our findings will further contribute to preventing fecal pollution in aquatic environments and quality control of shellfish.

Calibrating and validating bacterial water quality models: a Bayesian approach

Water resource management decisions often depend on mechanistic or empirical models to predict water quality conditions under future pollutant loading scenarios. These decisions, such as whether or not to restrict public access to a water resource area, may therefore vary depending on how models reflect process, observation, and analytical uncertainty and variability. Nonetheless, few probabilistic modeling tools have been developed which explicitly propagate fecal indicator bacteria (FIB) analysis uncertainty into predictive bacterial water quality model parameters and response variables. Here, we compare three approaches to modeling variability in two different FIB water quality models. We first calibrate a well-known first-order bacterial decay model using approaches ranging from ordinary least squares (OLS) linear regression to Bayesian Markov chain Monte Carlo (MCMC) procedures. We then calibrate a less frequently used empirical bacterial die-off model using the same range of procedures (and the same data). Finally, we propose an innovative approach to evaluating the predictive performance of each calibrated model using a leave-one-out cross-validation procedure and assessing the probability distributions of the resulting Bayesian posterior predictive p-values. Our results suggest that different approaches to acknowledging uncertainty can lead to discrepancies between parameter mean and variance estimates and predictive performance for the same FIB water quality model. Our results also suggest that models without a bacterial kinetics parameter related to the rate of decay may more appropriately reflect FIB fate and transport processes, regardless of how variability and uncertainty are acknowledged.

Microbial co-habitation and lateral gene transfer: what transposases can tell us

Interactions between microbial communities are revealed using a network of lateral gene transfer events.

Background

Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?

Results

All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.

Conclusions

We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.