David John Bradshaw

The prevalence of Salmonella enterica serovar Enteritidis encoding a GyrA D87Y substitution, associated with decreased susceptibility to ciprofloxacin, has increased since 2018 in the United States. Here, we provide three Salmonella Enteritidis reference genomes belonging to an SNP cluster of interest with ( n = 2) or without (n = 1) the GyrA D87Y substitution.

Salmonella enterica serovar Enteritidis ( S . Enteritidis) is a major cause of foodborne illness linked to poultry across the globe, and its decreased susceptibility to quinolone antibiotics such as ciprofloxacin poses a significant threat to public health. Yet, the ecological and genetic pressures that drive the fitness of this pathogen in poultry environments remain poorly defined. In this study, we combined broiler chicken litter microcosm experiments, whole-genome sequencing, and machine learning to investigate factors that shape the fitness and antimicrobial resistance development of S . Enteritidis. We analyzed more than 10,000 genomes to assess the role bacteriophages, plasmids, and chromosomal mutations play in driving S . Enteritidis fitness. Our findings reveal that an underreported bacteriophage named ESSI-2 and IncX1 plasmids strongly influenced whether strains carried the gyrA mutations associated with decreased ciprofloxacin susceptibility. Strains of S . Enteritidis lacking both ESSI-2 phage and IncX1 plasmid harbored parallel mutations in genes linked to DNA topology, antimicrobial peptide resistance, and virulence. We found that ESSI-2 phage persistence in litter was shaped by distinct ecological community structures rather than random occurrence and that reused litter reduced S . Enteritidis survival compared to fresh pine wood shavings, suggesting that microbiome-based interventions could be leveraged to limit the spread of antibiotic-resistant Enteritidis strains. IMPORTANCE: Foodborne illnesses linked to Salmonella enterica serovar Enteritidis strains with decreased susceptibility to quinolones, including ciprofloxacin, are on the rise in the United States, Canada, and Europe. In this study, we report for the first time that the gyrA mutation responsible for this phenotype is associated with a bacteriophage and a particular plasmid group. We demonstrated that when either of the two mobile genetic elements is carried by a S. Enteritidis strain, the likelihood of having gyrA mutation was negligible. Using broiler chicken litter microcosms, we provided insights into how the microbiome could be harnessed to limit the continued spread of these fitter lineages of S. Enteritidis strains. Our study shows that the survival and evolution of S. Enteritidis in poultry environments are strongly shaped by interactions among bacteriophages, plasmids, and the microbial community.

Introduction: Salinity presents economic and technical challenges in land-based recirculating aquaculture systems (RAS) in the U.S. warm water marine finfish aquaculture industry. Many studies have shown euryhaline fish reared at salinities closer to their iso-osmotic salinity can yield enhanced production performance as well as potential reduced costs to farms. However, there is potential for osmotic stress in fish larvae to negatively impact larvae microbiome and innate immune system. Florida pompano (Trachinotus carolinus) is a popular sportfish has been targeted for land-based RAS due to its impressive market value and euryhaline capacity. This study investigated the impacts of rearing Florida pompano larvae at salinities closer to their iso-osmotic salinity.Materials and methods: Larvae were cultured at 10, 20, and 30 ppt in triplicates, and larvae samples were collected for histopathology, microbiome, and whole transcriptomics analysis every three days from hatching until the time of weaning (24 days post hatch [DPH]). Water samples were also taken for microbiome analysis on every other larval sampling day. Discussion: These changes were driven more by metamorphosis, causing an increase in expression of antioxidant genes (cat, gss, gsto1, and scara3) than by the presence of potentially pathogenic genera, which failed to induce an immune response (low or unchanged expression of downstream elements of the NOD1 or TLR5 pathways). These findings provide baseline information on Florida pompano low salinity tolerance in larviculture during early developmental stages. In addition, we have shown minimal effects on the immune system at salinities as low as 10 ppt. This work has important implications for larval health management and can be used to refine and direct future research regarding improving commercial production of warm water marine species

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes.

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of a anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment microbiome. In general, the Indian River Lagoon exhibited a microbiome that was consistent with other estuarine studies. Statistically different microbiomes were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious microbial seasonality, such as higher Betaproteobacteriales, a freshwater associated organism, in wet season and higher Flavobacteriales in dry season samples. Distance-based linear models revealed these microbiomes were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic organisms, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic organisms, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon microbiome and serves as an important baseline for possible future changes due to human impacts or environmental changes.

The protein kinase C family of enzymes is thought to be important in mediating signal transduction. Ro 31-8830 is a novel, potent inhibitor of protein kinase C, derived from the non-selective protein kinase inhibitor staurosporine. In this paper we demonstrate the selectivity of Ro 31-8830 for protein kinase C over other protein kinases and its ability to inhibit protein kinase-C-mediated events in platelets and lymphocytes. In addition, we describe a novel system for thein vivo evaluation of inhibitors of protein kinase C, and we demonstrate the oral anti-inflammatory activity of Ro 31-8830. This finding has implications for the treatment of inflammatory disorders in the clinic.