Plaseval: a framework for comparing and evaluating plasmid detection tools.

Background: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid.

Microbiological analysis of tunneled hemodialysis catheters isolated from patients receiving hemodialysis in Saskatchewan.

To compare the microbial communities inside hemodialysis catheters from symptomatic and asymptomatic patients to determine their differences. Catheters ( = 41) were removed from patients in the Saskatchewan Health Authority over an 18-month period. The catheter section inside the body was flushed and the contents were evaluated using culture-dependent and culture-independent analysis.

Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.

Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach.

Exploring patterns of alcohol use and alcohol use disorder among Asian Americans with a finer lens.

Background: National survey data suggest Asian Americans (AA) are less likely to consume alcohol and develop AUD than Americans in other groups. However, it is common for AA to be born outside of the US and carry gene variants that alter alcohol metabolism, both of which can lead to lower levels of alcohol involvement. The current study examined differences in alcohol use and AUD between AA and other groups before and after controlling for birth location and gene variants.

Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing.

Background: Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E.

Features and algorithms: facilitating investigation of secreted effectors in Gram-negative bacteria.

Gram-negative bacteria deliver effector proteins through type III, IV, or VI secretion systems (T3SSs, T4SSs, and T6SSs) into host cells, causing infections and diseases. In general, effector proteins for each of these distinct secretion systems lack homology and are difficult to identify. Sequence analysis has disclosed many common features, helping us to understand the evolution, function, and secretion mechanisms of the effectors.

Solidified saturated fats coating subunit vaccines greatly extended vaccine booster release and contributed to a Th1/Th2 mixed immune response in mice.

Delayed release of vaccine coupled with a soluble vaccine acts as a primer and a booster with only a single administration, which would be very beneficial to livestock producers. We developed a subdermal pellet consisting of solid-phase pure stearic acid (SA) or palmitic acid (PA) that was used to encapsulate a small volume liquid vaccine consisting of fluorescently labeled *Ovalbumin (Cy5-*OVA) formulated with Emulsigen-D +/- Poly I:C (EMP) adjuvants. Mice were also immunized via the subcutaneous route with Cy5-*OVA-EMP (soluble liquid).

Hybrid Genome Assemblies of 245 Avian and Broiler Barn Environment-Associated Escherichia coli Strains Isolated from Saskatchewan Broiler Farms.

Escherichia coli infections in poultry cause significant morbidity and economic losses for producers each year. In a 3-year period, we collected and sequenced the whole genomes of E. coli disease isolates ( = 91), isolates from presumed healthy birds ( = 61), and isolates from 8 barn sites ( = 93) on broiler farms in Saskatchewan.

A Multipronged Unbiased Strategy Guides the Development of an Anti-EGFR/EPHA2-Bispecific Antibody for Combination Cancer Therapy.

Purpose: Accumulating analyses of pro-oncogenic molecular mechanisms triggered a rapid development of targeted cancer therapies. Although many of these treatments produce impressive initial responses, eventual resistance onset is practically unavoidable. One of the main approaches for preventing this refractory condition relies on the implementation of combination therapies.

Control of Line Complications with KiteLock (CLiCK) in the critical care unit: study protocol for a multi-center, cluster-randomized, double-blinded, crossover trial investigating the effect of a novel locking fluid on central line complications in the critical care population.

Background: Insertion of a central venous access device (CVAD) allows clinicians to easily access the circulation of a patient to administer life-saving interventions. Due to their invasive nature, CVADs are prone to complications such as bacterial biofilm production and colonization, catheter-related bloodstream infection, occlusion, and catheter-related venous thrombosis. A CVAD is among the most common interventions for patients in the intensive care unit (ICU), exposing this vulnerable population to the risk of nosocomial infection and catheter occlusion.

Characterization of colonization kinetics and virulence potential of Enteritidis in chickens by photonic detection.

The light emitting module operon () of can be integrated into a "dark" bacterium for expression under a suitable promoter. The technique has been used to monitor kinetics of infection, e.g.

Alcohol and aging - An area of increasing concern.

Alcohol use is increasing among adults 65 and older and the size of this population is expanding rapidly. Aging is associated with systemic inflammation, sleep disturbances, cancers, cognitive decline, and increased risk of injury and death from falls and other accidents. Alcohol misuse exacerbates and accelerates these age-related changes.

Purification of the Bacterial Amyloid "Curli" from Serovar Typhimurium and Detection of Curli from Infected Host Tissues.

Microbiologists are learning to appreciate the importance of "functional amyloids" that are produced by numerous bacterial species and have impacts beyond the microbial world. These structures are used by bacteria to link together, presumably to increase survival, protect against harsh conditions, and perhaps to influence cell-cell communication. Bacterial functional amyloids are also beginning to be appreciated in the context of host-pathogen interactions, where there is evidence that they can trigger the innate immune system and are recognized as non-self-molecular patterns.

Biofilm Formation and Antimicrobial Susceptibility of Associated With Colibacillosis Outbreaks in Broiler Chickens From Saskatchewan.

The global poultry industry has grown to the extent that the number of chickens now well exceeds the number of humans on Earth. infections in poultry cause significant morbidity and economic losses for producers each year. We obtained 94 isolates from 12 colibacillosis outbreaks on Saskatchewan farms and screened them for antimicrobial resistance and biofilm formation.

High Affinity Iron Acquisition Systems Facilitate but Are Not Essential for Colonization of Chickens by Enteritidis.

The roles of TonB mediated Fe (ferric iron) uptake via enterobactin (involving biosynthesis genes ) and Fe (ferrous iron) uptake through the FeoABC transporter are poorly defined in the context of chicken- interactions. Both uptake systems are believed to be the major contributors of iron supply in the life cycle. Current evidence suggests that these iron uptake systems play a major role in pathogenesis in mammals and as such, they represent promising antibacterial targets with therapeutic potential.

Alcohol-Related Deaths During the COVID-19 Pandemic.

This study uses mortality data from the National Center for Health Statistics to assess whether alcohol-related deaths increased during the COVID-19 pandemic.

Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes in .

Bacterial porin-encoding genes are often found under positive selection. Local recombination has also been identified in a few of them to facilitate bacterial rapid adaptation, although it remains unknown whether it is a common evolutionary mechanism for the porins or outer membrane proteins in Gram-negative bacteria. In this study, we investigated the beta-barrel (β-barrel) porin-encoding genes in Escherichia coli that were reported under positive Darwinian selection.

Nitrate Is an Environmental Cue in the Gut for Salmonella enterica Serovar Typhimurium Biofilm Dispersal through Curli Repression and Flagellum Activation via Cyclic-di-GMP Signaling.

Curli, a major component of the bacterial biofilms in the intestinal tract, activates pattern recognition receptors and triggers joint inflammation after infection with Salmonella enterica serovar Typhimurium. The factors that allow Typhimurium to disperse from biofilms and invade the epithelium to establish a successful infection during acute inflammation remain unknown. Here, we studied Typhimurium biofilms and to understand how the inflammatory environment regulates the switch between multicellular and motile Typhimurium in the gut.

Draft Genome Sequences of Multiple Isolates from Arizona.

strains are bacteria that are well known for their distinctive physiology, behaviors, and ecology, as well as for being prodigious producers of diverse antibiotics. Here, we report draft genome sequences for eight strains that were isolated from multiple sky islands in Arizona and sequenced using an Oxford Nanopore Technologies Flongle adapter and MinION system.

A GMMA-CPS-Based Vaccine for Non-Typhoidal .

Non-typhoidal are a major cause of gastroenteritis worldwide, as well as causing bloodstream infections in sub-Saharan Africa with a high fatality rate. No vaccine is currently available for human use. Current vaccine development strategies are focused on capsular polysaccharides (CPS) present on the surface of non-typhoidal .

Phosphoinositide 3-Kinase (PI3K) Reactive Oxygen Species (ROS)-Activated Prodrug in Combination with Anthracycline Impairs PI3K Signaling, Increases DNA Damage Response and Reduces Breast Cancer Cell Growth.

RIDR-PI-103 is a novel reactive oxygen species (ROS)-induced drug release prodrug with a self-cyclizing moiety linked to a pan-PI3K inhibitor (PI-103). Under high ROS, PI-103 is released in a controlled manner to inhibit PI3K. The efficacy and bioavailability of RIDR-PI-103 in breast cancer remains unexplored.

A SNP in the Cache 1 Signaling Domain of Diguanylate Cyclase STM1987 Leads to Increased Fitness of Invasive Strains.

Nontyphoidal (NTS) strains are associated with gastroenteritis worldwide but are also the leading cause of bacterial bloodstream infections in sub-Saharan Africa. The invasive NTS (iNTS) strains that cause bloodstream infections differ from standard gastroenteritis-causing strains by >700 single-nucleotide polymorphisms (SNPs). These SNPs are known to alter metabolic pathways and biofilm formation and to contribute to serum resistance and are thought to signify iNTS strains becoming human adapted, similar to typhoid fever-causing strains.

Synergistic activity of tetrasodium EDTA, ethanol and chlorhexidine hydrochloride against planktonic and biofilm cells of clinically relevant pathogens.

Objectives: Biofilms associated with implantable medical devices and wounds are clinically relevant, often requiring repeated use of antibiotics without success. A search for non-antibiotic antimicrobial and antibiofilm solutions is warranted, in line with antimicrobial stewardship. Our study aimed to evaluate the broad-spectrum antimicrobial efficacy of tetrasodium EDTA, ethanol and chlorhexidine hydrochloride (HCl) alone and in combination against clinically relevant planktonic and biofilm cells of bacterial and fungal pathogens.