in Coastal Ecosystems

Co-Culturing Seaweed with Scallops Can Inhibit the Occurrence of Vibrio by Increasing Dissolved Oxygen and pH

Seaweeds are critically important for the maintenance of biodiversity in marine aquaculture ecosystems, as they can inhibit the growth of Vibrio. Here, we determined the optimal environmental parameters for co-culturing green macroalgae (Ulva pertusa) and red macroalgae (Gracilariopsis lemaneiformis) with Chinese scallop (Chlamys farreri) by measuring dissolved oxygen (DO), pH, and the strength of Vibrio inhibition under laboratory conditions and validating the effectiveness of this optimal co-culture system from the perspectives of nutrient levels, enzyme activities, and microbial diversity. The results show that co-culturing 30 g of seaweed and three scallops in 6 L of seawater with aeration in the dark (1.25 L min-1, 12:12 h L:D) significantly decreased the number and abundance of Vibrio after 3 days. The activities of superoxide dismutase, catalase, pyruvate kinase, and lactate dehydrogenase in C. farreri were significantly higher, indicating that its immune defense and metabolism enhanced in this optimal co-culture system. High DO and pH levels significantly decreased the alpha diversity of microorganisms, and the abundance of pathogenic microorganisms decreased. The optimal co-culture system was effective for the control of vibriosis. Generally, our findings suggest that seaweeds could be used to enhance the aquaculture environment by conferring healthy and sustainable functions in the future.

Analysis on Bacterial Community of Noctiluca scintillans Algal Blooms Near Pingtan Island, China

Noctiluca scintillans, known as a global red tide species, is a common red tide species found in Pingtan Island. To examine the bacterial community structure in different environments during the red tide period of N. scintillans on Pingtan Island, samples were collected from the Algal Bloom Area (ABA), Transition Area (TA), and Non-Algal Bloom Area (NBA) on 6 April 2022, and the environmental physicochemical factors and bacterial community were determined. The outbreak of N. scintillans red tide significantly impacted the water quality and bacterial community structure in the affected sea area. The water quality in the ABA has deteriorated markedly, with the contents of COD, NH4+-N, and PO43- in the ABA being significantly higher than those in the TA and NBA, while the pH is significantly lower than that in the TA and NBA. The richness, diversity, and evenness of the bacterial community in the ABA are all lower than those of the TA and NBA. For instance, the Shannon index values of the three sampling points are 4.41, 5.41, and 6.37, respectively. At the phylum level, the dominant bacterial phyla in the ABA are Proteobacteria, Firmicutes, and Cyanobacteria; in the TA, they are Proteobacteria, Bacteroidetes, and Firmicutes; and in the NBA, they are Proteobacteria, Bacteroidetes, and Cyanobacteria. At the genus level, the dominant bacterial genera in the ABA are Vibrio, Carnobacterium, Candidatus_Megaira, Planktomarina, and Pseudoalteromonas; in the TA, they are Vibrio, Planktomarina, Lentibacter, Glaciecola, and Jannaschia; and in the NBA, they are Planktomarina, Amylibacter, NS5_marine_group, Aurantivirga, and marine_metagenome. In the ABA, the combined proportion of Vibrio and Carnobacterium exceeds 50%, with Vibrio_splendidus accounting for 93% of the total Vibrio population. These research results can provide a scientific basis for clarifying the environmental characteristics and bacterial composition during the large-scale N. scintillans red tide in Pingtan Island.

Machine learning to predict the relationship between Vibrio spp. concentrations in seawater and oysters and prevalent environmental conditions

Vibrio parahaemolyticus and Vibrio vulnificus are bacteria with a significant public health impact. Identifying factors impacting their presence and concentrations in food sources could enable the identification of significant risk factors and prevent incidences of foodborne illness. In recent years, machine learning has shown promise in modeling microbial presence based on prevalent external and internal variables, such as environmental variables and gene presence/absence, respectively, particularly with the generation and availability of large amounts and diverse sources of data. Such analyses can prove useful in predicting microbial behavior in food systems, particularly under the influence of the constant changes in environmental variables. In this study, we tested the efficacy of six machine learning regression models (random forest, support vector machine, elastic net, neural network, k-nearest neighbors, and extreme gradient boosting) in predicting the relationship between environmental variables and total and pathogenic V. parahaemolyticus and V. vulnificus concentrations in seawater and oysters. In general, environmental variables were found to be reliable predictors of total and pathogenic V. parahaemolyticus and V. vulnificus concentrations in seawater, and pathogenic V. parahaemolyticus in oysters (Acceptable Prediction Zone >70 %) when analyzed using our machine learning models. SHapley Additive exPlanations, which was used to identify variables influencing Vibrio concentrations, identified chlorophyll a content, seawater salinity, seawater temperature, and turbidity as influential variables. It is important to note that different strains were differentially impacted by the same environmental variable, indicating the need for further research to study the causes and potential mechanisms of these variations. In conclusion, environmental variables could be important predictors of Vibrio growth and behavior in seafood. Moreover, the models developed in this study could prove invaluable in assessing and managing the risks associated with V. parahaemolyticus and V. vulnificus, particularly in the face of a changing environment.

Public health aspects of Vibrio spp. related to the consumption of seafood in the EU

Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.

Nested Spatial and Temporal Modeling of Environmental Conditions Associated With Genetic Markers of Vibrio parahaemolyticus in Washington State Pacific Oysters

The Pacific Northwest (PNW) is one of the largest commercial harvesting areas for Pacific oysters (Crassostrea gigas) in the United States. Vibrio parahaemolyticus, a bacterium naturally present in estuarine waters accumulates in shellfish and is a major cause of seafood-borne illness. Growers, consumers, and public-health officials have raised concerns about rising vibriosis cases in the region. Vibrio parahaemolyticus genetic markers (tlh, tdh, and trh) were estimated using an most-probable-number (MPN)-PCR technique in Washington State Pacific oysters regularly sampled between May and October from 2005 to 2019 (N = 2,836); environmental conditions were also measured at each sampling event. Multilevel mixed-effects regression models were used to assess relationships between environmental measures and genetic markers as well as genetic marker ratios (trh:tlh, tdh:tlh, and tdh:trh), accounting for variation across space and time. Spatial and temporal dependence were also accounted for in the model structure. Model fit improved when including environmental measures from previous weeks (1-week lag for air temperature, 3-week lag for salinity). Positive associations were found between tlh and surface water temp, specifically between 15 and 26°C, and between trh and surface water temperature up to 26°C. tlh and trh were negatively associated with 3-week lagged salinity in the most saline waters (> 27 ppt). There was also a positive relationship between tissue temperature and tdh, but only above 20°C. The tdh:tlh ratio displayed analogous inverted non-linear relationships as tlh. The non-linear associations found between the genetic targets and environmental measures demonstrate the complex habitat suitability of V. parahaemolyticus. Additional associations with both spatial and temporal variables also suggest there are influential unmeasured environmental conditions that could further explain bacterium variability. Overall, these findings confirm previous ecological risk factors for vibriosis in Washington State, while also identifying new associations between lagged temporal effects and pathogenic markers of V. parahaemolyticus.

Remnants of horizontal transfers of Wolbachia genes in a Wolbachia-free woodwasp

Background

Wolbachia is a bacterial endosymbiont of many arthropod and nematode species. Due to its capacity to alter host biology, Wolbachia plays an important role in arthropod and nematode ecology and evolution. Sirex noctilio is a woodwasp causing economic loss in pine plantations of the Southern Hemisphere. An investigation into the genome of this wasp revealed the presence of Wolbachia sequences. Due to the potential impact of Wolbachia on the populations of this wasp, as well as its potential use as a biological control agent against invasive insects, this discovery warranted investigation.

Results

In this study we first investigated the presence of Wolbachia in S. noctilio and demonstrated that South African populations of the wasp are unlikely to be infected. We then screened the full genome of S. noctilio and found 12 Wolbachia pseudogenes. Most of these genes constitute building blocks of various transposable elements originating from the Wolbachia genome. Finally, we demonstrate that these genes are distributed in all South African populations of the wasp.

Conclusions

Our results provide evidence that S. noctilio might be compatible with a Wolbachia infection and that the bacteria could potentially be used in the future to regulate invasive populations of the wasp. Understanding the mechanisms that led to a loss of Wolbachia infection in S. noctilio could indicate which host species or host population should be sampled to find a Wolbachia strain that could be used as a biological control against S. noctilio.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01995-x.

Detection and correlation analysis of shellfish pathogens in Dadeng Island, Xiamen

Food poisoning is caused by pathogenic bacteria in water and aquatic products, especially bivalves (e.g., oysters, clams), which can bioaccumulate pathogenic bacteria. Polluted water and aquatic products thus pose a serious threat to human health and safety. In this study, the types of pathogenic bacteria in water samples and shellfish collected from the Dadeng offshore area in Xiamen were examined. We also analyzed the relationships between dominant pathogens and major climate and water quality parameters. Our objective was to provide reference data that may be used to help prevent bacterial infections and to improve aquatic food hygiene in Xiamen and its surrounding areas to safe levels, thus ensuring the health of Xiamen residents. We found that the main pathogenic bacteria were Vibrio and Bacillus, with the dominant pathogen being Vibrio parahaemolyticus. Physical and chemical indexes (water temperature, salinity, pH, dissolved oxygen, and turbidity) of water bodies and the 3-day accumulated rainfall were found to be important factors affecting the occurrence and abundance of V. parahaemolyticus.

Impact of heavy precipitation events on pathogen occurrence in estuarine areas of the Puzi River in Taiwan

Pathogen populations in estuarine areas are dynamic, as they are subject to multiple natural and anthropogenic challenges. Heavy rainfall events bring instability to the aquatic environment in estuaries, causing changes in pathogen populations and increased environmental sanitation and public health concerns. In this study, we investigated the effects of heavy precipitation on the occurrence of pathogens in the Puzi River estuary, which is adjacent to the largest inshore oyster farming area in Taiwan. Our results indicated that Vibrio parahaemolyticus and adenovirus were the most frequently detected pathogens in the area. There was a significant difference (Mann-Whitney U test, p < 0.01) in water quality parameters, including total coliform, Escherichia coli, water temperature, turbidity, salinity, and dissolved oxygen, between groups with and without V. parahaemolyticus. In addition, the detection rate was negatively correlated with the average daily rainfall (r2 > 0.8). There was no significant difference between water quality parameters and the presence/absence of adenovirus, but a positive correlation was observed between the average daily rainfall and the detection rate of adenovirus (r2 ≥ 0.75). We conclude that heavy precipitation changes estuarine water quality, causing variations in microbial composition, including pathogens. As extreme weather events become more frequent due to climate change, the potential impacts of severe weather events on estuarine environments require further investigation.

Biochemical and Virulence Characterization of Vibrio vulnificus Isolates From Clinical and Environmental Sources

Vibrio vulnificus is a deadly human pathogen for which infections occur via seafood consumption (foodborne) or direct contact with wounds. Virulence is not fully characterized for this organism; however, there is evidence of biochemical and genotypic correlations with virulence potential. In this study, biochemical profiles and virulence genotype, based on 16S rRNA gene (rrn) and virulence correlated gene (vcg) types, were determined for 30 clinical and 39 oyster isolates. Oyster isolates were more biochemically diverse than the clinical isolates, with four of the 20 tests producing variable (defined as 20–80% of isolates) results. Whereas, for clinical isolates only mannitol fermentation, which has previously been associated with virulence potential, varied among the isolates. Nearly half (43%) of clinical isolates were the more virulent genotype (rrnB/vcgC); this trend was consistent when only looking at clinical isolates from blood. The majority (64%) of oyster isolates were the less virulent genotype (rrnA or AB/vcgE). These data were used to select a sub-set of 27 isolates for virulence testing with a subcutaneously inoculated, iron-dextran treated mouse model. Based on the mouse model data, 11 isolates were non-lethal, whereas 16 isolates were lethal, indicating a potential for human infection. Within the non-lethal group there were eight oyster and three clinical isolates. Six of the non-lethal isolates were the less virulent genotype (rrnA/vcgE or rrnAB/vcgE) and two were rrnB/vcgC with the remaining two of mixed genotype (rrnAB/vcgC and rrnB/vcgE). Of the lethal isolates, five were oysters and 11 were clinical. Eight of the lethal isolates were the less virulent genotype and seven the more virulent genotype, with the remaining isolate a mixed genotype (rrnA/vcgC). A discordance between virulence genotype and individual mouse virulence parameters (liver infection, skin infection, skin lesion score, and body temperature) was observed; the variable most strongly associated with mouse virulence parameters was season (warm or cold conditions at time of strain isolation), with more virulent strains isolated from cold conditions. These results indicate that biochemical profiles and genotype are not significantly associated with virulence potential, as determined by a mouse model. However, a relationship with virulence potential and seasonality was observed.

Modeling and Forecasting Vibrio Parahaemolyticus Concentrations in Oysters

Vibrio parahaemolyticus (V.p) is an epidemiologically significant pathogen that thrives in coastal waters where oysters are harvested, posing high risks to human health and shellfish industry and requiring effective forecasting models for emergency preparedness and interventions. This study sought to develop forecasting models with differing lead times, which are able to predict the level of V.p in oysters in advance to mitigate the health risk to the general public and the economic loss to the shellfish industry. The Random Forest method along with 227 sampling datasets from two different geographic locations were utilized to: (1) Identify the most critical environmental predictors controlling the level of V.p in oysters, (2) Select the most important time lags for the environmental predictors as model input variables, and (3) Develop four forecasting models (RF-1Day, RF-2Day, RF-3Day, and RF-4Day) with the lead time of one to four days. The uncertainty involved in model predictions was quantified using the bootstrapping method. Results showed that V.p abundance in oysters is controlled by antecedent environmental conditions 1-11 days before. The antecedent environmental conditions can be described using time-lagged Sea Surface Temperature (SST) and salinity. The V.p abundance can well be forecasted 1 - 4 days in advance using the four models. The performance of the models decreases with increasing lead time. The RF-3Day and RF-4Day models can be employed primarily for emergency preparedness due to their relatively long lead time while the RF-1Day and RF-2Day models can be used primarily for management interventions due to their relatively high predictive performance.

A case-control analysis of traceback investigations for Vibrio parahaemolyticus infections (vibriosis) and pre-harvest environmental conditions in Washington State, 2013-2018

BACKGROUND

Vibrio parahaemolyticus is a major cause of seafood-borne illness. It is naturally prevalent in brackish waters and accumulates in shellfish. Vibriosis cases are rising globally, likely due to rising temperatures.

OBJECTIVES

To identify associations between vibriosis in Washington State and pre-harvest environmental and V. parahaemolyticus genetic measurements sampled from shellfish.

METHODS

Successful vibriosis traceback investigations were spatiotemporally matched to routine intertidal oyster (Crassostrea gigas) sampling events, which included measurements of temperature, salinity, and V. parahaemolyticus genetic targets (thermolabile hemolysin: tlh; thermostable direct hemolysin: tdh; thermostable direct-related hemolysin: trh). Unmatched sampling events were treated as controls. Associations were evaluated using logistic regression models.

RESULTS

Systematic differences were observed across Washington harvesting zones. These included positive associations between the odds of vibriosis and all three genetic targets in South Puget Sound, with a large odds ratio (OR) = 13.0 (95% CI: 1.5, 115.0) for a 1-log₁₀ increase in tdh when total bacterium abundance was low (tlh < 1 log₁₀ MPN/g). A positive association also occurred for a 1 °C increase in tissue temperature OR = 1.20 (95% CI: 1.10, 1.30) while a negative association occurred for a similar increase in water temperature OR = 0.70 (95% CI: 0.59, 0.81). In contrast, the coastal bays displayed positive associations for water temperature OR = 2.16 (95% CI, 1.15, 4.05), and for a 1-log₁₀ increase in the tdh:trh ratio OR = 5.85 (95% CI, 1.06, 32.26).

DISCUSSION

The zonal variation in associations indicates unique pathogenic strain prominence, suggesting tdh+/trh+ strains in South Puget Sound, such as the O4:K12 serotype, and tdh+/trh- strains in the coastal bays. The temperature discrepancy between water and oyster tissue suggests that South Puget Sound pathogenic strains flourish with exposure to relatively warm air during low tide. These findings identify new ecological risk factors for vibriosis in Washington State that can be used in future prevention efforts.

A systematic review of post-harvest interventions for Vibrio parahaemolyticus in raw oysters

BACKGROUND

Non-cholera Vibrio bacteria are a major cause of foodborne illness in the United States. Raw oysters are commonly implicated in gastroenteritis caused by pathogenic Vibrio parahaemolyticus. In response to outbreaks in 1997-1998, the US Food and Drug Administration developed a nation-wide quantitative microbial risk assessment (QMRA) of V. parahaemolyticus in raw oysters in 2005. The QMRA identified information gaps that new research may address. Incidence of sporadic V. parahaemolyticus illness has recently increased and, as oyster consumption increases and sea temperatures rise, V. parahaemolyticus outbreaks may become more frequent, posing health concerns. Updated and region-specific QMRAs will improve the accuracy and precision of risk of infection estimates.

OBJECTIVES

We identify research to support an updated QMRA of V. parahaemolyticus from oysters harvested in Chesapeake Bay and Puget Sound, focusing on observational and experimental research on post-harvest practices (PHPs) published from 2004 to 2019.

METHODS

A predefined search strategy was applied to PubMed, Embase, Scopus, Science.gov, NAL Agricola, and Google Scholar. Study eligibility criteria were defined using a population, intervention, comparator, and outcome statement. Reviewers independently coded abstracts for inclusion/exclusion using predefined criteria. Data were extracted and study quality and relevance evaluated based on published guidance for food safety risk assessments. Findings were synthesized using a weight of evidence approach.

RESULTS

Of 12,174 articles retrieved, 93 were included for full-text review. Twenty-seven studies were found to be high quality and high relevance, including studies on cold storage, high hydrostatic pressure, depuration, and disinfectant, and other PHPs. High hydrostatic pressure consistently emerged as the most effective PHP in reducing abundance of V. parahaemolyticus.

DISCUSSION

Limitations of the knowledge base and review approach involve the type and quantity of data reported. Future research should focus on PHPs for which few or no high quality and high relevance studies exist, such as irradiation and relaying.

Potentially human pathogenic Vibrio spp. in a coastal transect: Occurrence and multiple virulence factors

An increase in human Vibrio spp. infections has been linked to climate change related events, in particular to seawater warming and heatwaves. However, there is a distinct lack of research of pathogenic Vibrio spp. occurrences in the temperate North Sea, one of the fastest warming seas globally. Particularly in the German Bight, Vibrio investigations are still scarce. This study focuses on the spatio-temporal quantification and pathogenic characterization of V. parahaemolyticus, V. vulnificus and V. cholerae over the course of 14 months. Species-specific MPN-PCR (Most probable number - polymerase chain reaction) conducted on selectively enriched surface water samples revealed seasonal patterns of all three species with increased abundances during summer months. The extended period of warm seawater coincided with prolonged Vibrio spp. occurrences in the German Bight. Temperature and nitrite were the factors explaining variations in Vibrio spp. abundances after generalized additive mixed models. The specific detection of pathogenic markers via PCR revealed trh-positive V. parahaemolyticus, pathogenic V. vulnificus (nanA, manIIA, PRXII) and V. cholerae serotype O139 presence. Additionally, spatio-temporally varying virulence profiles of V. cholerae with multiple accessory virulence-associated genes, such as the El Tor variant hemolysin (hlyAET), acyltransferase of the repeats-in-toxin cluster (rtxC), Vibrio 7th pandemic island II (VSP-II), Type III Secretion System (TTSS) and the Cholix Toxin (chxA) were detected. Overall, this study highlights that environmental human pathogenic Vibrio spp. comprise a reservoir of virulence-associated genes in the German Bight, especially in estuarine regions. Due to their known vast genetic plasticity, we point to the possible emergence of highly pathogenic V. cholerae strains. Particularly, the presence of V. cholerae serotype O139 is unusual and needs urgent continuous surveillance. Given the predictions of further warming and more frequent heatwave events, human pathogenic Vibrio spp. should be seriously considered as a developing risk to human health in the German Bight.

High abundance of Vibrio in tarball-contaminated seawater from Vagator beach, Goa, India

Tarballs are semi-solid remnants of crude oil and they are formed in marine environment after oil-spill incidents. They are composed of diverse hydrocarbons; some of which are recalcitrant in nature. Recent studies based on amplicon sequencing of 16S rRNA gene suggested that tarballs support hundreds of bacterial genera and provided insights into their role as hydrocarbon degraders and potential human pathogens. In this study, bacterial composition of tarball-contaminated seawater from Vagator beach, Goa, India was characterized by amplicon sequencing of V₃-V₄ regions of 16S rRNA gene. The DNA data revealed an unusual surge of Vibrio in sea-water contaminated with tarballs in May 2018 (16.16% OTUs), compared to tarball-free seawater samples collected in March 2018 (no detectable OTUs) and September 2018 (0.17% OTUs). Further studies are required to investigate if Vibrio species form biofilms on tarballs which may act as good reservoirs for their survival and transmission success.

Associations of Environmental Conditions and Vibrio parahaemolyticus Genetic Markers in Washington State Pacific Oysters

Vibrio parahaemolyticus is a naturally occurring bacterium in estuarine waters and is a major cause of seafood-borne illness. The bacterium has been consistently identified in Pacific Northwest waters and elevated illness rates of vibriosis in Washington State have raised concerns among growers, risk managers, and consumers of Pacific oysters (Crassostrea gigas). In order to better understand pre-harvest variation of V. parahaemolyticus in the region, abundance of total and potentially pathogenic strains of the bacterium in a large number of Washington State Pacific oyster samples were compared with environmental conditions at the time of sampling. The Washington Department of Health regularly sampled oysters between June and September at over 21 locations from 2014 to 2018, resulting in over 946 samples. V. parahaemolyticus strains carrying three genetic markers, tlh, trh, and tdh, were enumerated in oyster tissue using a most probable number-PCR analysis. Tobit regressions and seemingly unrelated estimations were used to formally assess relationships between environmental measures and genetic markers. All genetic markers were found to be positively associated with temperature, independent of the abundance of other genetic markers. Surface water temperature displayed a non-linear relationship, with no association observed between any genetic marker in the warmest waters. There were also stark differences between surface and shore water temperature models. Salinity was not found to be substantially associated with any of the genetic variables. The relative abundance of tdh+ strains given total V. parahaemolyticus abundance (pathogenic ratio tdh:tlh) was negatively associated with water temperature in colder waters and decreased exponentially as total V. parahaemolyticus abundance increased. Strains carrying the trh gene had a pronounced positive association with strains carrying the tdh gene but was also negatively associated with the tdh:tlh pathogenic ratio. These results suggest that there are ecological relationships of competition, growth, and survival for V. parahaemolyticus strains in the oyster tissue matrix. This work also improves the overall understanding of environmental associations with V. parahaemolyticus in Washington State Pacific oysters, laying the groundwork for future risk mitigation efforts in the region.

Vibrio parahaemolyticus in the Chesapeake Bay: Operational In Situ Prediction and Forecast Models Can Benefit from Inclusion of Lagged Water Quality Measurements

Vibrio parahaemolyticus is a leading cause of seafood-borne gastroenteritis. Given its natural presence in brackish waters, there is a need to develop operational forecast models that can sufficiently predict the bacterium's spatial and temporal variation. This work attempted to develop V. parahaemolyticus prediction models using frequently measured time-indexed and -lagged water quality measures. Models were built using a large data set (n = 1,043) of surface water samples from 2007 to 2010 previously analyzed for V. parahaemolyticus in the Chesapeake Bay. Water quality variables were classified as time indexed, 1-month lag, and 2-month lag. Tobit regression models were used to account for V. parahaemolyticus measures below the limit of quantification and to simultaneously estimate the presence and abundance of the bacterium. Models were evaluated using cross-validation and metrics that quantify prediction bias and uncertainty. Presence classification models containing only one type of water quality parameter (e.g., temperature) performed poorly, while models with additional water quality parameters (i.e., salinity, clarity, and dissolved oxygen) performed well. Lagged variable models performed similarly to time-indexed models, and lagged variables occasionally contained a predictive power that was independent of or superior to that of time-indexed variables. Abundance estimation models were less effective, primarily due to a restricted number of samples with abundances above the limit of quantification. These findings indicate that an operational in situ prediction model is attainable but will require a variety of water quality measurements and that lagged measurements will be particularly useful for forecasting. Future work will expand variable selection for prediction models and extend the spatial-temporal extent of predictions by using geostatistical interpolation techniques.IMPORTANCEVibrio parahaemolyticus is one of the leading causes of seafood-borne illness in the United States and across the globe. Exposure often occurs from the consumption of raw shellfish. Despite public health concerns, there have been only sporadic efforts to develop environmental prediction and forecast models for the bacterium preharvest. This analysis used commonly sampled water quality measurements of temperature, salinity, dissolved oxygen, and clarity to develop models for V. parahaemolyticus in surface water. Predictors also included measurements taken months before water was tested for the bacterium. Results revealed that the use of multiple water quality measurements is necessary for satisfactory prediction performance, challenging current efforts to manage the risk of infection based upon water temperature alone. The results also highlight the potential advantage of including historical water quality measurements. This analysis shows promise and lays the groundwork for future operational prediction and forecast models.

Performance of Cold Chains for Chesapeake Bay Farmed Oysters and Modeled Growth of Vibrio parahaemolyticus

Temperature-controlled supply chains (cold chains) require an unbroken chain of refrigeration to maintain product quality and safety. This study investigated cold chains for farmed oysters raised in the Chesapeake Bay, one of the largest shellfish-growing regions in the United States, and sold live to the half-shell market in surrounding states. Temperature sensors were used in boxes of oysters from February to September 2017, which generated 5,250 h of temperature data. Thirty-nine businesses participated in the temperature sensor study, and 26 of those businesses participated in interviews to further understand how cold chains function. Internal oyster temperatures were measured above 50°F (10°C) for over 1 h in 19% (7 of 36) of shipments, which is a temperature that exceeds National Shellfish Sanitation Program criteria. The highest internal oyster temperature recorded in any shipment was 54.5°F (12.5°C). Some parts of the cold chain had difficulty maintaining storage temperatures below 45°F (7.2°C) in warmer months when Vibrio control plans were in effect. We modeled the effects of temperature on Vibrio parahaemolyticus. The model predicted moderate bacterial growth before oysters were under temperature control, but cold chains prevented further bacterial growth and provided a moderate drop-off in V. parahaemolyticus abundance.

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts

In the current report, we describe the identification of three genetically distinct groups of prophages integrated into three different chromosomal sites of human gut-associated Bifidobacterium breve and Bifidobacterium longum strains. These bifidobacterial prophages are distantly related to temperate actinobacteriophages of several hosts. Some prophages, integrated within the dnaJ₂ gene, are competent for induction, excision, replication, assembly and lysis, suggesting that they are fully functional and can generate infectious particles, even though permissive hosts have not yet been identified. Interestingly, several of these phages harbor a putative phase variation shufflon (the Rin system) that generates variation of the tail-associated receptor binding protein (RBP). Unlike the analogous coliphage-associated shufflon Min, or simpler Cin and Gin inversion systems, Rin is predicted to use a tyrosine recombinase to promote inversion, the first reported phage-encoded tyrosine-family DNA invertase. The identification of bifidobacterial prophages with RBP diversification systems that are competent for assembly and lysis, yet fail to propagate lytically under laboratory conditions, suggests dynamic evolution of bifidobacteria and their phages in the human gut.

Temporal and Environmental Factors Driving Vibrio Vulnificus and V. Parahaemolyticus Populations and Their Associations With Harmful Algal Blooms in South Carolina Detention Ponds and Receiving Tidal Creeks

Incidences of harmful algal blooms (HABs) and Vibrio infections have increased over recent decades. Numerous studies have tried to identify environmental factors driving HABs and pathogenic Vibrio populations separately. Few have considered the two simultaneously, though emerging evidence suggests that algal blooms enhance Vibrio growth and survival. This study examined various physical, nutrient, and temporal factors associated with incidences of HABs, V. vulnificus, and V. parahaemolyticus in South Carolina coastal stormwater detention ponds, managed systems where HABs often proliferate, and their receiving tidal creek waters. Five blooms occurred during the study (2008-2009): two during relatively warmer months (an August 2008 cyanobacteria bloom and a November 2008 dinoflagellate bloom) followed by increases in both Vibrio species and V. parahaemolyticus, respectively, and three during cooler months (December 2008 through February 2009) caused by dinoflagellates and euglenophytes that were not associated with marked changes in Vibrio abundances. Vibrio concentrations were positively and significantly associated with temperature and dissolved organic matter, dinoflagellate blooms, negatively and significantly associated with suspended solids, but not significantly correlated with chlorophyll or nitrogen. While more research involving longer time series is needed to increase robustness, findings herein suggest that certain HAB species may augment Vibrio occurrences during warmer months.

Environmental Determinants of Vibrio parahaemolyticus in the Chesapeake Bay

Vibrio parahaemolyticus naturally occurs in brackish and marine waters and is one of the leading causes of seafood-borne illness. Previous work studying the ecology of V. parahaemolyticus has often been limited in geographic extent and lacked a full range of environmental measures. This study used a unique large data set of surface water samples in the Chesapeake Bay (n = 1,385) collected from 148 monitoring stations from 2007 to 2010. Water was analyzed for more than 20 environmental parameters, with additional meteorological and surrounding land use data. The V. parahaemolyticus-specific genetic markers thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) were assayed using quantitative PCR (qPCR), and interval-censored regression models with nonlinear effects were estimated to account for limits of detection and quantitation. tlh was detected in 19.6% of water samples; tdh or trh markers were not detected. The results confirmed previously reported positive associations for V. parahaemolyticus abundance with temperature and turbidity and negative associations with high salinity (>10 to 23‰). Furthermore, the salinity relationship was determined to be a function of both low temperature and turbidity, with an increase of either nullifying the high salinity effect. Associations with dissolved oxygen and phosphate also appeared stronger when samples were taken near human developments. A renewed focus on the V. parahaemolyticus ecological paradigm is warranted to protect public health.IMPORTANCE Vibrio parahaemolyticus is one of the leading causes of seafood-borne illness in the United States and across the globe. Exposure is often through consuming raw or undercooked shellfish. Given the natural presence of the bacterium in the marine environment, an improved understanding of its environmental determinants is necessary for future preventative measures. This analysis of environmental Vibrio parahaemolyticus is one of only a few that utilize a large data set measured over a wide geographic and temporal range. The analysis also includes a large number of environmental parameters for Vibrio modeling, many of which have previously only been tested sporadically, and some of which have not been considered before. The results of the analysis revealed previously unknown relationships between salinity, turbidity, and temperature that provide significant insight into the abundance and persistence of V. parahaemolyticus bacterium in the environment. This information will be essential for developing environmental forecast models for the bacterium.

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.