Assessment of sensitivity and specificity of bacterial culture and the VetMAX™ MastiType Multi Kit in detecting Streptococcus uberis and Escherichia coli in milk samples from dairy cows with clinical mastitis in subtropical Australia.

Mastitis, a prevalent and economically important disease in the dairy industry, poses substantial challenges to dairy cow health, milk quality, and farm profitability worldwide. Mastitis is predominantly caused by bacterial infections. The objective of this study was to estimate the sensitivity (Se) and specificity (Sp) of bacterial culture and the VetMAX™ MastiType Multi Kit PCR in identified clinical mastitis pathogens.

Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast.

Gut bacterial communities play a vital role in a host's digestion and fermentation of complex carbohydrates, absorption of nutrients, and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay.

Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species.

Dermatological conditions may be complicated by Staphylococcus spp. infections influencing skin and nasal microbiota. We investigated the associations between the resident nasal microbiota of shelter dogs with and without dermatological conditions carrying methicillin-resistant and -sensitive Staphylococcus spp.

Documenting patients' and providers' preferences when proposing a randomized controlled trial: a qualitative exploration.

Background: With advances in cancer diagnosis and treatment, women with early-stage breast cancer (ESBC) are living longer, increasing the number of patients receiving post-treatment follow-up care. Best-practice survivorship models recommend transitioning ESBC patients from oncology-provider (OP) care to community-based care. While developing materials for a future randomized controlled trial (RCT) to test the feasibility of a nurse-led Telephone Survivorship Clinic (TSC) for a smooth transition of ESBC survivors to follow-up care, we explored patients' and OPs' reactions to several of our proposed methods.

Medications and Patient Factors Associated With Increased Readmission for Alcohol-Related Diagnoses.

Objective: To investigate medication factors and patient characteristics associated with readmissions following alcohol-related hospitalizations.

Patients And Methods: Adult patients admitted from September 1, 2016, through August 31, 2019, who had an alcohol-related hospitalization were identified through electronic health records. Patient characteristics and medications of interest administered during hospitalization or prescribed at discharge were identified.

"Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures.

Background: Surgical site infection is a major source of morbidity in patients undergoing pancreatic head resection and is often from organisms in intraoperative bile duct cultures. As such, many institutions use prolonged prophylactic antibiotics and tailor based on bile duct cultures. However, standard cultures take days, leaving many patients unnecessarily on prolonged antibiotics.

Intraoperative bile duct cultures in patients undergoing pancreatic head resection: Prospective comparison of bile duct swab versus bile duct aspiration.

Background: Postoperative surgical site infection is a major source of morbidity after pancreatic head resections, and data suggest bacterobilia as a leading cause. Some centers use intraoperative bile duct cultures to guide postoperative antimicrobial prophylaxis. This prospective study evaluates culture differences between traditional bile duct swab versus bile duct aspiration intraoperative samples.

Environmental Recovery of Nosocomial Bacteria in a Companion Animal Shelter Before and After Infection Control Procedures.

While the effects of cleaning and disinfection practices on the reduction of environmental nosocomial bacteria are well-established in human and large animal veterinary hospitals, how animal movements within animal health care facilities influence environmental bacterial recovery is poorly understood. During three consecutive weeks, 155 electrostatic wipes were collected from the environment pre- and post-cleaning only or following disinfection from seven target locations within an animal shelter. All samples were cultured, and isolates were identified using a matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Skin Toxicity in Early Breast Cancer Patients Treated with Field-In-Field Breast Intensity-Modulated Radiotherapy versus Helical Inverse Breast Intensity-Modulated Radiotherapy: Results of a Phase III Randomised Controlled Trial.

Aims: Skin toxicity is a common adverse effect of breast radiotherapy. We investigated whether inverse-planned intensity-modulated radiotherapy (IMRT) would reduce the incidence of skin toxicity compared with forward field-in-field breast IMRT (FiF-IMRT) in early stage breast cancer.

Materials And Methods: This phase III randomised controlled trial compared whole-breast irradiation with either FiF-IMRT or helical tomotherapy IMRT (HT-IMRT), with skin toxicity as the primary end point.

Induction of humoral immune response in piglets after perinatal or post-weaning immunization against porcine circovirus type-2 or keyhole limpet hemocyanin.

The objective of this study was to test the hypothesis that porcine circovirus type-2 (PCV2) vaccination is efficacious when administered in the first week of life. Three groups of pigs were vaccinated with Circumvent either early (at the end of week 1), late (at the end of week 4), or not at all. All 3 groups were later challenged intranasally with PCV2 (at the end of week 5).

Treatment variation in stent choice in patients with stable or unstable coronary artery disease.

Aim: Variations in treatment are the result of differences in demographic and clinical factors (e.g. anatomy), but physician and hospital factors may also contribute to treatment variation.

Acute BVDV-2 infection in beef calves delays humoral responses to a non-infectious antigen challenge.

Immunosuppressive effects of an intranasal challenge with non-cytopathic bovine viral diarrhea virus (BVDV) 2a (strain 1373) were assessed through acquired and innate immune system responses to ovalbumin (OVA). Concurrent BVDV infection was hypothesized to delay and reduce the humoral response to ovalbumin (administered on days 3 and 15 post-inoculation). Infected animals followed the expected clinical course.

ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS.

Background: Sequence analysis of immunoglobulin heavy chain (IGH) gene rearrangements and frequency analysis is a powerful tool for studying the immune repertoire, immune responses and immune dysregulation in health and disease. The challenge is to provide user friendly, secure and reproducible analytical services that are available for both small and large laboratories which are determining VDJ repertoire using NGS technology.

Results: In this study we describe ImmunoGlobulin Galaxy (IGGalaxy)- a convenient web based application for analyzing next-generation sequencing results and reporting IGH gene rearrangements for both repertoire and clonality studies.

Circulating cells as predictors of secondary manifestations of cardiovascular disease: design of the CIRCULATING CELLS study.

Biomarkers for primary or secondary risk prediction of cardiovascular disease (CVD) are urgently needed to improve individual treatment and clinical trial design. The vast majority of biomarker discovery studies has concentrated on plasma/serum as an easily accessible source. Although numerous markers have been identified, their added predictive value on top of traditional risk factors has been limited, as the biological specimen does not specifically reflect expression profiles related with CVD progression and because the signal is often diluted by marker release from other organs.

Extracellular DNA-induced antimicrobial peptide resistance in Salmonella enterica serovar Typhimurium.

Background: The Salmonella enterica serovar Typhimurium PhoPQ two component system (TCS) is activated by low Mg2+ levels, low pH and by antimicrobial peptides (AP). Under Mg2+ limitation, the PhoPQ system induces pmrD expression, which post-translationally activates the PmrAB TCS. PhoPQ and PmrAB control many genes required for intracellular survival and pathogenesis.

iFUSE: integrated fusion gene explorer.

Unlabelled: We present iFUSE (integrated fusion gene explorer), an online visualization tool that provides a fast and informative view of structural variation data and prioritizes those breaks likely representing fusion genes. This application uses calculated break points to determine fusion genes based on the latest annotation for genomic sequence information, and where relevant the structural variation (SV) events are annotated with predicted RNA and protein sequences. iFUSE takes as input a Complete Genomics (CG) junction file, a FusionMap fusion detection report file or a file already analysed and annotated by the iFUSE application on a previous occasion.

Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.

Background: Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection.

Calcium chelation by alginate activates the type III secretion system in mucoid Pseudomonas aeruginosa biofilms.

The extracellular biofilm matrix includes primarily DNA and exopolysaccharides (EPS), which function to maintain aggregate structures and to protect biofilms from antibiotics and the immune response. Both polymers are anionic and have cation binding activity, however the impact of this activity on biofilms is not fully understood. Host cell contact is considered the primary signal for activation of most type III secretion systems (T3SS), although calcium limitation is frequently used as a trigger of contact-independent T3SS expression.

Inhibition of bacterial biofilm formation and swarming motility by a small synthetic cationic peptide.

Biofilms cause up to 80% of infections and are difficult to treat due to their substantial multidrug resistance compared to their planktonic counterparts. Based on the observation that human peptide LL-37 is able to block biofilm formation at concentrations below its MIC, we screened for small peptides with antibiofilm activity and identified novel synthetic cationic peptide 1037 of only 9 amino acids in length. Peptide 1037 had very weak antimicrobial activity, but at 1/30th the MIC the peptide was able to effectively prevent biofilm formation (>50% reduction in cell biomass) by the Gram-negative pathogens Pseudomonas aeruginosa and Burkholderia cenocepacia and Gram-positive Listeria monocytogenes.

Symptom assessment in ambulatory oncology: initial validation of the nurse-developed Modified Ambulatory Care Flow Sheet (MACFS).

Purpose: This paper reports relationships between symptoms assessed using a newly developed instrument for assessing patient-reported symptoms, the Modified Ambulatory Care Flow Sheet (MACFS), and other symptom assessment measures.

Methods: Using a cross-sectional design, patients on active treatment for colorectal cancer were recruited in an ambulatory setting of a tertiary care cancer center in western Canada. Participants completed the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire--Cancer 30, the Rotterdam Symptom Checklist Modified, Linear analog scales for pain and coping, and the MACFS, all at a single time point.

Overexpression of hns in the plant growth-promoting bacterium Enterobacter cloacae UW5 increases root colonization.

Aims: Plant growth-promoting rhizobacteria (PGPR) introduced into soil often do not compete effectively with indigenous micro-organisms for plant colonization. The aim of this study was to identify novel genes that are important for root colonization by the PGPR Enterobacter cloacae UW5.

Methods And Results: A library of transposon mutants of Ent.

SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels.

Background: Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. In fact, obtaining an integrated view of both large scale SNP genotyping and gene expression is currently complicated since only a limited number of appropriate software tools are available.

Results: We present SNPExpress, a software tool to accurately analyze Affymetrix and Illumina SNP genotype calls, copy numbers, polymorphic copy number variations (CNVs) and Affymetrix gene expression in a combinatorial and efficient way.