The genomic epidemiology of shigellosis in South Africa.

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei.

Corridor-based approach with spatial cross-validation reveals scale-dependent effects of geographic distance, human footprint and canopy cover on grizzly bear genetic connectivity.

Understanding how human infrastructure and other landscape attributes affect genetic differentiation in animals is an important step for identifying and maintaining dispersal corridors for these species. We built upon recent advances in the field of landscape genetics by using an individual-based and multiscale approach to predict landscape-level genetic connectivity for grizzly bears (Ursus arctos) across ~100,000 km in Canada's southern Rocky Mountains. We used a genetic dataset with 1156 unique individuals genotyped at nine microsatellite loci to identify landscape characteristics that influence grizzly bear gene flow at multiple spatial scales and map predicted genetic connectivity through a matrix of rugged terrain, large protected areas, highways and a growing human footprint.

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among .

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences.

Synchronous Hürthle cell and medullary thyroid carcinomas.

Hürthle cell carcinoma (HCC) and medullary thyroid carcinomas (MTC) are uncommon histological subtypes of thyroid cancers, each accounting for around 3% of all thyroid cancers. A septuagenarian woman with a history of multiple primary cancer diagnoses presented with a growing left-sided neck lump. A diagnostic left thyroid lobectomy was performed, and pathological examination found two separate malignant foci: one HCC and an MTC.

Machine learning outperforms clinical experts in classification of hip fractures.

Hip fractures are a major cause of morbidity and mortality in the elderly, and incur high health and social care costs. Given projected population ageing, the number of incident hip fractures is predicted to increase globally. As fracture classification strongly determines the chosen surgical treatment, differences in fracture classification influence patient outcomes and treatment costs.

Protein biomarkers in serum as a conservation tool to assess reproduction: a case study on brown bears ().

Monitoring the reproductive characteristics of a species can complement existing conservation strategies by understanding the mechanisms underlying demography. However, methodology to determine important aspects of female reproductive biology is often absent in monitoring programs for large mammals. Protein biomarkers may be a useful tool to detect physiological changes that are indicative of reproductive state.

Ten-year survival outcomes after radical nephroureterectomy with a risk-stratified approach using prior diagnostic ureteroscopy: a single-institution observational retrospective cohort study.

Objectives: To evaluate the long-term oncological outcomes of patients with upper tract urothelial carcinoma (UTUC) undergoing radical nephroureterectomy (RNU) and the impact of diagnostic ureteroscopy (URS) on survival outcomes.

Materials And Methods: A retrospective analysis of all consecutive patients undergoing RNU for suspected UTUC at a UK tertiary referral centre from a prospectively maintained database was conducted. The primary outcome measures were 5- and 10-year cancer-specific survival (CSS).

Correcting for enzyme immunoassay changes in long term monitoring studies.

Enzyme immunoassays (EIAs) are a common tool for measuring steroid hormones in wildlife due to their low cost, commercial availability, and rapid results. Testing technologies improve continuously, sometimes requiring changes in protocols or crucial assay components. Antibody replacement between EIA kits can cause differences in EIA sensitivity, which can hinder monitoring hormone concentration over time.

Landscape condition influences energetics, reproduction, and stress biomarkers in grizzly bears.

Environmental change has been shown to influence mammalian distribution, habitat use, and behavior; however, few studies have investigated the impact on physiological function. This study aimed to determine the influence of landscape condition on the expression of target proteins related to energetics, reproduction, and stress in grizzly bears. We hypothesized that changes in landscape condition explains protein expression.

Cortisol levels in blood and hair of unanesthetized grizzly bears (Ursus arctos) following intravenous cosyntropin injection.

Hair cortisol concentration (HCC) is being used increasingly to evaluate long-term stress in many mammalian species. Most of the cortisol is assumed to passively diffuse from circulating blood into hair follicles and gradually accumulate in growing hair. However, our research with free-ranging grizzly bears (Ursus arctos) suggests HCC increases significantly within several hours following capture, a time too brief to be explained by this mechanism alone.

Accessory Genome Dynamics and Structural Variation of from Persistent Infections.

Shigellosis is a diarrheal disease caused mainly by and Infection is thought to be largely self-limiting, with short- to medium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated and isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection.

Quantifying energetic costs and defining energy landscapes experienced by grizzly bears.

Animal movements are major determinants of energy expenditure and ultimately the cost-benefit of landscape use. Thus, we sought to understand those costs and how grizzly bears () move in mountainous landscapes. We trained captive grizzly bears to walk on a horizontal treadmill and up and down 10% and 20% slopes.

Response of grizzly bears (Ursus arctos) to pipelines in Alberta.

This research provides the first in-depth analysis of fine-scale grizzly bear habitat selection and movement patterns in response to the linear footprints cleared for below-ground pipelines in Alberta. Using an extensive set of GPS location data from collared grizzly bears, we were able to determine that grizzly bears selected for younger pipelines (mean age since last construction~6.5 years), which are known to have a greater abundance of important bear foods.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa.

Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear.

Meniscal scaffold for the treatment of partial meniscal defect-clinical and radiological outcomes in a two-year follow-up.

Purpose: The aim of meniscal scaffolds is to fill the defect, allow regeneration of meniscal-like tissues, and to prevent long-term risk of cartilage wear and tear. The aim of this study was to evaluate clinical results after two years and magnetic resonance imaging (MRI) results a year after implantation of a meniscal scaffold.

Methods: Fifteen patients were recruited into a prospective, single-arm, single-center study, and treated with meniscal scaffolds as a result of segmental meniscal defect due to previous partial meniscectomy.

Changing spring snow cover dynamics and early season forage availability affect the behavior of a large carnivore.

Changing climates are altering wildlife habitats and wildlife behavior in complex ways. Here, we examine how changing spring snow cover dynamics and early season forage availability are altering grizzly bear (Ursus arctos) behavior postden emergence. Telemetry data were used to identify spring activity dates for 48 individuals in the Yellowhead region of Alberta, Canada.

The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator.

Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether ease-of-travel or access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features.

Development and validation of protein biomarkers of health in grizzly bears.

Large carnivores play critical roles in the maintenance and function of natural ecosystems; however, the populations of many of these species are in decline across the globe. Therefore, there is an urgent need to develop novel techniques that can be used as sensitive conservation tools to detect new threats to the health of individual animals well in advance of population-level effects. Our study aimed to determine the expression of proteins related to energetics, reproduction and stress in the skin of grizzly bears () using a liquid chromatography and multiple reaction monitoring mass spectrometry assay.

Grizzly bear response to fine spatial and temporal scale spring snow cover in Western Alberta.

Snow dynamics influence seasonal behaviors of wildlife, such as denning patterns and habitat selection related to the availability of food resources. Under a changing climate, characteristics of the temporal and spatial patterns of snow are predicted to change, and as a result, there is a need to better understand how species interact with snow dynamics. This study examines grizzly bear (Ursus arctos) spring habitat selection and use across western Alberta, Canada.

EcoAnthromes of Alberta: An example of disturbance-informed ecological regionalization using remote sensing.

Humans influence ecosystems on magnitudes that often exceed that of natural forces such as climate and geology; however, frameworks rarely include anthropogenic disturbance when delineating unique ecological regions. A critical step toward understanding, managing and monitoring human-altered ecosystems is to incorporate disturbance into ecological regionalizations. Furthermore, quantitative regionalization approaches are desirable to provide cost-effective, repeatable and statistically sound stratification for environmental monitoring.

Motorized Activity on Legacy Seismic Lines: A Predictive Modeling Approach to Prioritize Restoration Efforts.

Natural regeneration of seismic lines, cleared for hydrocarbon exploration, is slow and often hindered by vegetation damage, soil compaction, and motorized human activity. There is an extensive network of seismic lines in western Canada which is known to impact forest ecosystems, and seismic lines have been linked to declines in woodland caribou (Rangifer tarandus caribou). Seismic line restoration is costly, but necessary for caribou conservation to reduce cumulative disturbance.

Natural regeneration on seismic lines influences movement behaviour of wolves and grizzly bears.

Across the boreal forest of Canada, habitat disturbance is the ultimate cause of caribou (Rangifer tarandus caribou) declines. Habitat restoration is a focus of caribou recovery efforts, with a goal to finding ways to reduce predator use of disturbances, and caribou-predator encounters. One of the most pervasive disturbances within caribou ranges in Alberta, Canada are seismic lines cleared for energy exploration.

Using spatial mark-recapture for conservation monitoring of grizzly bear populations in Alberta.

One of the challenges in conservation is determining patterns and responses in population density and distribution as it relates to habitat and changes in anthropogenic activities. We applied spatially explicit capture recapture (SECR) methods, combined with density surface modelling from five grizzly bear (Ursus arctos) management areas (BMAs) in Alberta, Canada, to assess SECR methods and to explore factors influencing bear distribution. Here we used models of grizzly bear habitat and mortality risk to test local density associations using density surface modelling.