Impact of Hurricane Irene on Vibrio vulnificus and Vibrio parahaemolyticus concentrations in surface water, sediment, and cultured oysters in the Chesapeake Bay, MD, USA

To determine if a storm event (i.e., high winds, large volumes of precipitation) could alter concentrations of Vibrio vulnificus and V. parahaemolyticus in aquacultured oysters (Crassostrea virginica) and associated surface water and sediment, this study followed a sampling timeline before and after Hurricane Irene impacted the Chesapeake Bay estuary in late August 2011. Aquacultured oysters were sampled from two levels in the water column: surface (0.3 m) and near-bottom (just above the sediment). Concentrations of each Vibrio spp. and associated virulence genes were measured in oysters with a combination of real-time PCR and most probable number (MPN) enrichment methods, and in sediment and surface water with real-time PCR. While concentration shifts of each Vibrio species were apparent post-storm, statistical tests indicated no significant change in concentration for either Vibrio species by location (surface or near bottom oysters) or date sampled (oyster tissue, surface water, and sediment concentrations). V. vulnificus in oyster tissue was correlated with total suspended solids (r = 0.41, P = 0.04), and V. vulnificus in sediment was correlated with secchi depth (r = −0.93, P < 0.01), salinity (r = −0.46, P = 0.02), tidal height (r = −0.45, P = 0.03), and surface water V. vulnificus (r = 0.98, P < 0.01). V. parahaemolyticus in oyster tissue did not correlate with environmental measurements, but V. parahaemolyticus in sediment and surface water correlated with several measurements including secchi depth [r = −0.48, P = 0.02 (sediment); r = −0.97, P < 0.01 (surface water)] and tidal height [r = −0.96, P < 0.01 (sediment), r = −0.59, P < 0.01 (surface water)]. The concentrations of Vibrio spp. were higher in oysters relative to other studies (average V. vulnificus 4 × 10⁵ MPN g⁻¹, V. parahaemolyticus 1 × 10⁵ MPN g⁻¹), and virulence-associated genes were detected in most oyster samples. This study provides a first estimate of storm-related Vibrio density changes in oyster tissues, sediment, and surface water at an aquaculture facility in the Chesapeake Bay.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/microbiology

Recreational swimmers' exposure to Vibrio vulnificus and Vibrio parahaemolyticus in the Chesapeake Bay, Maryland, USA

Vibrio vulnificus and Vibrio parahaemolyticus are ubiquitous in the marine–estuarine environment, but the magnitude of human non-ingestion exposure to these waterborne pathogens is largely unknown. We evaluated the magnitude of dermal exposure to V. vulnificus and V. parahaemolyticus among swimmers recreating in Vibrio-populated waters by conducting swim studies at four swimming locations in the Chesapeake Bay in 2009 and 2011. Volunteers (n = 31) swam for set time periods, and surface water (n = 25) and handwash (n = 250) samples were collected. Samples were analyzed for Vibrio concentrations using quantitative PCR. Linear and logistic regressions were used to evaluate factors associated with recreational exposures. Mean surface water V. vulnificus and V. parahaemolyticus concentrations were 1128 CFU mL⁻¹ (95% confidence interval (CI): 665.6, 1591.4) and 18 CFU mL⁻¹ (95% CI: 9.8, 26.1), respectively, across all sampling locations. Mean Vibrio concentrations in handwash samples (V. vulnificus, 180 CFU cm⁻² (95% CI: 136.6, 222.5); V. parahaemolyticus, 3 CFU cm⁻² (95% CI: 2.4, 3.7)) were significantly associated with Vibrio concentrations in surfacewater (V. vulnificus, p < 0.01; V. parahaemolyticus, p < 0.01), but not with salinity or temperature (V. vulnificus, p = 0.52, p = 0.17; V. parahaemolyticus, p = 0.82, p = 0.06). Handwashing reduced V. vulnificus and V. parahaemolyticus on subjects' hands by approximately one log (93.9%, 89.4%, respectively). It can be concluded that when Chesapeake Bay surface waters are characterized by elevated concentrations of Vibrio, swimmers and individuals working in those waters could experience significant dermal exposures to V. vulnificus and V. parahaemolyticus, increasing their risk of infection.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/environment-internationalKeywords: Vibrio parahaemolyticus, Recreational exposure, Vibrio vulnificus, Chesapeake Bay, Exposure assessment, Waterborne illnes

Antimicrobial Susceptibility of Vibrio vulnificus and Vibrio parahaemolyticus Recovered from Recreational and Commercial Areas of Chesapeake Bay and Maryland Coastal Bays

Vibrio vulnificus and V. parahaemolyticus in the estuarine-marine environment are of human health significance and may be increasing in pathogenicity and abundance. Vibrio illness originating from dermal contact with Vibrio laden waters or through ingestion of seafood originating from such waters can cause deleterious health effects, particularly if the strains involved are resistant to clinically important antibiotics. The purpose of this study was to evaluate antimicrobial susceptibility among these pathogens. Surface-water samples were collected from three sites of recreational and commercial importance from July to September 2009. Samples were plated onto species-specific media and resulting V. vulnificus and V. parahaemolyticus strains were confirmed using polymerase chain reaction assays and tested for antimicrobial susceptibility using the Sensititre® microbroth dilution system. Descriptive statistics, Friedman two-way Analysis of Variance (ANOVA) and Kruskal-Wallis one-way ANOVA were used to analyze the data. Vibrio vulnificus (n = 120) and V. parahaemolyticus (n = 77) were isolated from all sampling sites. Most isolates were susceptible to antibiotics recommended for treating Vibrio infections, although the majority of isolates expressed intermediate resistance to chloramphenicol (78% of V. vulnificus, 96% of V. parahaemolyticus). Vibrio parahaemolyticus also demonstrated resistance to penicillin (68%). Sampling location or month did not significantly impact V. parahaemolyticus resistance patterns, but V. vulnificus isolates from St. Martin's River had lower overall intermediate resistance than that of the other two sampling sites during the month of July (p = 0.0166). Antibiotics recommended to treat adult Vibrio infections were effective in suppressing bacterial growth, while some antibiotics recommended for pediatric treatment were not effective against some of the recovered isolates. To our knowledge, these are the first antimicrobial susceptibility data of V. vulnificus and V. parahaemolyticus recovered from the Chesapeake Bay. These data can serve as a baseline against which future studies can be compared to evaluate whether susceptibilities change over time

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

CrumpByronCEOASRecreationalSwimmersExposure.pdf

Vibrio vulnificus and Vibrio parahaemolyticus are ubiquitous in the marine–estuarine environment, but the magnitude of human non-ingestion exposure to these waterborne pathogens is largely unknown. We evaluated the magnitude of dermal exposure to V. vulnificus and V. parahaemolyticus among swimmers recreating in Vibrio-populated waters by conducting swim studies at four swimming locations in the Chesapeake Bay in 2009 and 2011. Volunteers (n = 31) swam for set time periods, and surface water (n = 25) and handwash (n = 250) samples were collected. Samples were analyzed for Vibrio concentrations using quantitative PCR. Linear and logistic regressions were used to evaluate factors associated with recreational exposures. Mean surface water V. vulnificus and V. parahaemolyticus concentrations were 1128 CFU mL⁻¹ (95% confidence interval (CI): 665.6, 1591.4) and 18 CFU mL⁻¹ (95% CI: 9.8, 26.1), respectively, across all sampling locations. Mean Vibrio concentrations in handwash samples (V. vulnificus, 180 CFU cm⁻² (95% CI: 136.6, 222.5); V. parahaemolyticus, 3 CFU cm⁻² (95% CI: 2.4, 3.7)) were significantly associated with Vibrio concentrations in surfacewater (V. vulnificus, p < 0.01; V. parahaemolyticus, p < 0.01), but not with salinity or temperature (V. vulnificus, p = 0.52, p = 0.17; V. parahaemolyticus, p = 0.82, p = 0.06). Handwashing reduced V. vulnificus and V. parahaemolyticus on subjects' hands by approximately one log (93.9%, 89.4%, respectively). It can be concluded that when Chesapeake Bay surface waters are characterized by elevated concentrations of Vibrio, swimmers and individuals working in those waters could experience significant dermal exposures to V. vulnificus and V. parahaemolyticus, increasing their risk of infection.Keywords: Chesapeake Bay, Recreational exposure, Exposure assessment, Waterborne illness, Vibrio vulnificus, Vibrio parahaemolyticusKeywords: Chesapeake Bay, Recreational exposure, Exposure assessment, Waterborne illness, Vibrio vulnificus, Vibrio parahaemolyticusKeywords: Chesapeake Bay, Recreational exposure, Exposure assessment, Waterborne illness, Vibrio vulnificus, Vibrio parahaemolyticusKeywords: Chesapeake Bay, Recreational exposure, Exposure assessment, Waterborne illness, Vibrio vulnificus, Vibrio parahaemolyticu

CrumpByronCEOASRecreationalSwimmersExposure_AppendixA.pdf

Vibrio vulnificus and Vibrio parahaemolyticus are ubiquitous in the marine–estuarine environment, but the magnitude of human non-ingestion exposure to these waterborne pathogens is largely unknown. We evaluated the magnitude of dermal exposure to V. vulnificus and V. parahaemolyticus among swimmers recreating in Vibrio-populated waters by conducting swim studies at four swimming locations in the Chesapeake Bay in 2009 and 2011. Volunteers (n = 31) swam for set time periods, and surface water (n = 25) and handwash (n = 250) samples were collected. Samples were analyzed for Vibrio concentrations using quantitative PCR. Linear and logistic regressions were used to evaluate factors associated with recreational exposures. Mean surface water V. vulnificus and V. parahaemolyticus concentrations were 1128 CFU mL⁻¹ (95% confidence interval (CI): 665.6, 1591.4) and 18 CFU mL⁻¹ (95% CI: 9.8, 26.1), respectively, across all sampling locations. Mean Vibrio concentrations in handwash samples (V. vulnificus, 180 CFU cm⁻² (95% CI: 136.6, 222.5); V. parahaemolyticus, 3 CFU cm⁻² (95% CI: 2.4, 3.7)) were significantly associated with Vibrio concentrations in surfacewater (V. vulnificus, p < 0.01; V. parahaemolyticus, p < 0.01), but not with salinity or temperature (V. vulnificus, p = 0.52, p = 0.17; V. parahaemolyticus, p = 0.82, p = 0.06). Handwashing reduced V. vulnificus and V. parahaemolyticus on subjects' hands by approximately one log (93.9%, 89.4%, respectively). It can be concluded that when Chesapeake Bay surface waters are characterized by elevated concentrations of Vibrio, swimmers and individuals working in those waters could experience significant dermal exposures to V. vulnificus and V. parahaemolyticus, increasing their risk of infection.Keywords: Vibrio parahaemolyticus, Exposure assessment, Vibrio vulnificus, Waterborne illness, Chesapeake Bay, Recreational exposureKeywords: Vibrio parahaemolyticus, Exposure assessment, Vibrio vulnificus, Waterborne illness, Chesapeake Bay, Recreational exposur