Harnessing landrace diversity empowers wheat breeding.

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.

Effect of Ground Beef Irradiation on Annual Nontyphoidal Salmonella and Escherichia coli O157 Burden and Direct Healthcare Costs in the United States: A Simulation Study.

Over 20% of E. coli O157 illnesses and over 5% of Salmonella illnesses are estimated to be attributable to beef consumption in the United States. Irradiating ground beef is one possible method to reduce disease burden. We simulated the effect of ground beef irradiation on illnesses, hospitalizations, deaths, and direct healthcare costs from ground beef-associated E. coli O157 and Salmonella illnesses in the United States. To estimate the fraction of illnesses, hospitalizations, deaths, and direct healthcare costs preventable by ground beef irradiation, we multiplied the disease burden attributable to ground beef; the estimated percentage of ground beef sold that is not currently irradiated; the percentage of unirradiated ground beef that would be irradiated; and the percentage reduction in risk of illness after irradiation. We multiplied this fraction by estimates of burden and direct healthcare costs to calculate the numbers or amounts averted. Model inputs were obtained from the literature and expert opinion. We used Monte Carlo simulation to incorporate uncertainty in inputs into model estimates. Simulation outcomes were summarized with means and 95% uncertainty intervals (UI). Irradiating 50% of the currently unirradiated ground beef supply would avert 3,285 (95% UI: 624-9,977) E. coli O157 illnesses, 135 (95% UI: 24-397) hospitalizations, 197 (95% UI: 34-631) hemolytic uremic syndrome cases, 2 (95% UI: 0-16) deaths, and $2,972,656 (95% UI: $254,708-$14,496,916) in direct healthcare costs annually. For Salmonella, irradiation would avert 20,308 (95% UI: 9,858-38,903) illnesses, 400 (95% UI: 158-834) hospitalizations, 6 (95% UI: 0-18) deaths, and $7,318,632 (95% UI: $1,436,141-$26,439,493) in direct healthcare costs. Increasing ground beef irradiation could reduce E. coli O157 and Salmonella burden in the United States. Additional studies should assess whether targeted irradiation of higher-risk ground beef products could prevent similar numbers of illnesses with less total product irradiated.

A thematic analysis of staff perspectives on the impact of a mental health nurse (RMN) in a critical care unit.

Background: Recent guidelines in the UK have shaped Critical Care Units (CCUs) to bring the mental health needs of patients, and staff wellbeing to the forefront of service provision. A health board based in NHS Wales has trialled the secondment of a Mental Health Nurse (RMN) within a CCU to help service provision adhere to such guidelines. Methods: Critical care staff were invited to attend focus groups to share their experiences of how the RMN influenced service provision. Results: Thematic analysis identified five main themes; including 'smoother care pathways', 'a holistic approach to care', 'co-production', 'knowledge and confidence' and 'staff wellbeing'. Each of these themes reflected how the RMN had both direct and indirect benefits on patient and staff wellbeing. Conclusion: This qualitative exploration suggests that staff perceived value in the role of the RMN for both staff and patient outcomes, although further measures were considered necessary to improve staff-wellbeing within a critical care environment. This service evaluation supports recommendations for commissioning a RMN permanently in a CCU.

Estimating Waterborne Infectious Disease Burden by Exposure Route, United States, 2014.

More than 7.15 million cases of domestically acquired infectious waterborne illnesses occurred in the United States in 2014, causing 120,000 hospitalizations and 6,600 deaths. We estimated disease incidence for 17 pathogens according to recreational, drinking, and nonrecreational nondrinking (NRND) water exposure routes by using previously published estimates. In 2014, a total of 5.61 million (95% credible interval [CrI] 2.97-9.00 million) illnesses were linked to recreational water, 1.13 million (95% CrI 255,000-3.54 million) to drinking water, and 407,000 (95% CrI 72,800-1.29 million) to NRND water. Recreational water exposure was responsible for 36%, drinking water for 40%, and NRND water for 24% of hospitalizations from waterborne illnesses. Most direct costs were associated with pathogens found in biofilms. Estimating disease burden by water exposure route helps direct prevention activities. For each exposure route, water management programs are needed to control biofilm-associated pathogen growth; public health programs are needed to prevent biofilm-associated diseases.

(Mis)perception and Use of Unsterile Water in Home Medical Devices, PN View 360+ Survey, United States, August 20211.

Tap water is not sterile, and its use in home medical devices can result in infections from waterborne pathogens. However, many participants in a recent survey in the United States said tap water could safely be used for home medical devices. These results can inform communication materials to reduce the high consequence of infections.

More than Our Enemy: Making Space for the Microbiome in Pharmacy Education.

The microbiome is the collection of commensal microorganisms along with their genomes inhabiting the human body. Despite the many known beneficial effects of these microbes on human health, the 2016 ACPE Standards for Doctor of Pharmacy curricula describe Medical Microbiology in Appendix 1 with a pathogen-centered focus. Over the last twenty years, evolving biotechnology has enabled a deeper understanding of the microbiome in the context of both wellness and disease. Retail stores are allocating increasing shelf space to commercial probiotic products, while the approach to PharmD training on the selection and use of these natural care products remains static, creating a disproportionate footprint between PharmD curricula and consumer markets. Looking to the future of patient care, we brief pharmacy educators on the current evidence and invite discussion around a proposed revision to the 2025 ACPE Standards that would add language recognizing the beneficial role of the commensal microbiota and expanding therapeutic applications of microbiome supplementation. We suggest a variety of opportunities within Doctor of Pharmacy curricula as leverage points for including relevant aspects of the microbiome in the training of future pharmacists.

Community structured model for vaccine strategies to control COVID19 spread: A mathematical study.

Initial efforts to mitigate the COVID-19 pandemic have relied heavily on non-pharmaceutical interventions (NPIs), including physical distancing, hand hygiene, and mask-wearing. However, an effective vaccine is essential to containing the spread of the virus. We developed a compartmental model to examine different vaccine strategies for controlling the spread of COVID-19. Our framework accounts for testing rates, test-turnaround times, and vaccination waning immunity. Using reported case data from the city of Toronto, Canada between Mar-Dec, 2020 we defined epidemic phases of infection using contact rates as well as the probability of transmission upon contact. We investigated the impact of vaccine distribution by comparing different permutations of waning immunity, vaccine coverage and efficacy throughout various stages of NPI's relaxation in terms of cases and deaths. The basic reproduction number is also studied. We observed that widespread vaccine coverage substantially reduced the number of cases and deaths. Under phases with high transmission, an early or late reopening will result in new resurgence of the infection, even with the highest coverage. On the other hand, under phases with lower transmission, 60% of coverage is enough to prevent new infections. Our analysis of R0 showed that the basic reproduction number is reduced by decreasing the tests turnaround time and transmission in the household. While we found that household transmission can decrease following the introduction of a vaccine, public health efforts to reduce test turnaround times remain important for virus containment.

Direct Outpatient Health Care Costs Among Commercially Insured Persons for Common Foodborne Pathogens and Acute Gastroenteritis, 2012-2015.

Foodborne illness is common in the United States with most, but not all, foodborne pathogens causing symptoms of acute gastroenteritis (AGI). Outpatient care is the most frequent type of medical care sought; however, more accurate estimates of outpatient costs are needed to inform food safety policy decision. Using the U.S. MarketScan Commercial Claims and Encounters database, we quantified the per-visit cost of outpatient visits with any AGI-related diagnosis (including pathogen-specific and nonspecific or symptom-based diagnoses) and for those with a pathogen-specific diagnosis for 1 of 29 pathogens commonly transmitted through food (including pathogens that cause AGI and some that do not). Our estimates included the per-case cost of office visits and associated laboratory tests and procedures as well as the conservative estimates of prescription cost. Most AGI outpatient visits were coded using nonspecific codes (e.g., infectious gastroenteritis), rather than pathogen-specific codes (e.g., Salmonella). From 2012 to 2015, we identified more than 3.4 million initial outpatient visits with any AGI diagnosis and 45,077 with a foodborne pathogen-specific diagnosis. As is typical of treatment cost data, severe cases of illness drove mean costs above median. The mean cost of an outpatient visit with any AGI was $696 compared with the median of $162. The mean costs of visits with pathogen-specific diagnoses ranged from $254 (median $131; interquartile range [IQR]: $98-184) for Streptococcus spp. Group A (n = 22,059) to $1761 (median $161; IQR: $104-$1101) for Clostridium perfringens (n = 30). Visits with two of the most common causes of foodborne illness, nontyphoidal Salmonella and norovirus, listed as a diagnosis, had mean costs of $841 and $509, respectively. Overall, the median per-case costs of outpatient visits increased with age, with some variation by pathogen. More empirically based estimates of outpatient costs for AGI and specific pathogens can enhance estimates of the economic cost of foodborne illness used to guide food policy and focus prevention efforts.

Antibiotic prescribing for acute gastroenteritis during ambulatory care visits-United States, 2006-2015.

OBJECTIVE: To describe national antibiotic prescribing for acute gastroenteritis (AGE). SETTING: Ambulatory care. METHODS: We included visits with diagnoses for bacterial and viral gastrointestinal infections from the National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey (NAMCS/NHAMCS; 2006-2015) and the IBM Watson 2014 MarketScan Commercial Claims and Encounters Database. For NAMCS/NHAMCS, we calculated annual percentage estimates and 99% confidence intervals (CIs) of visits with antibiotics prescribed; sample sizes were too small to calculate estimates by pathogen. For MarketScan, we used Poisson regression to calculate the percentage of visits with antibiotics prescribed and 95% CIs, including by pathogen. RESULTS: We included 10,210 NAMCS/NHAMCS AGE visits; an estimated 13.3% (99% CI, 11.2%-15.4%) resulted in antibiotic prescriptions, most frequently fluoroquinolones (28.7%; 99% CI, 21.1%-36.3%), nitroimidazoles (20.2%; 99% CI, 14.0%-26.4%), and penicillins (18.9%; 99% CI, 11.6%-26.2%). In NAMCS/NHAMCS, antibiotic prescribing was least frequent in emergency departments (10.8%; 99% CI, 9.5%-12.1%). Among 1,868,465 MarketScan AGE visits, antibiotics were prescribed for 13.8% (95% CI, 13.7%-13.8%), most commonly for Yersinia (46.7%; 95% CI, 21.4%-71.9%), Campylobacter (44.8%; 95% CI, 41.5%-48.1%), Shigella (39.7%; 95% CI, 35.9%-43.6%), typhoid or paratyphoid fever (32.7%; (95% CI, 27.2%-38.3%), and nontyphoidal Salmonella (31.7%; 95% CI, 29.5%-33.9%). Antibiotics were prescribed for 12.3% (95% CI, 11.7%-13.0%) of visits for viral gastroenteritis. CONCLUSIONS: Overall, ∼13% of AGE visits resulted in antibiotic prescriptions. Antibiotics were unnecessarily prescribed for viral gastroenteritis and some bacterial infections for which antibiotics are not recommended. Antibiotic stewardship assessments and interventions for AGE are needed in ambulatory settings.

Mathematical modelling of vaccination rollout and NPIs lifting on COVID-19 transmission with VOC: a case study in Toronto, Canada.

BACKGROUND: Since December 2020, public health agencies have implemented a variety of vaccination strategies to curb the spread of SARS-CoV-2, along with pre-existing Nonpharmaceutical Interventions (NPIs). Initial strategies focused on vaccinating the elderly to prevent hospitalizations and deaths, but with vaccines becoming available to the broader population, it became important to determine the optimal strategy to enable the safe lifting of NPIs while avoiding virus resurgence. METHODS: We extended the classic deterministic SIR compartmental disease-transmission model to simulate the lifting of NPIs under different vaccine rollout scenarios. Using case and vaccination data from Toronto, Canada between December 28, 2020, and May 19, 2021, we estimated transmission throughout past stages of NPI escalation/relaxation to compare the impact of lifting NPIs on different dates on cases, hospitalizations, and deaths, given varying degrees of vaccine coverages by 20-year age groups, accounting for waning immunity. RESULTS: We found that, once coverage among the elderly is high enough (80% with at least one dose), the main age groups to target are 20-39 and 40-59 years, wherein first-dose coverage of at least 70% by mid-June 2021 is needed to minimize the possibility of resurgence if NPIs are to be lifted in the summer. While a resurgence was observed for every scenario of NPI lifting, we also found that under an optimistic vaccination coverage (70% coverage by mid-June, along with postponing reopening from August 2021 to September 2021) can reduce case counts and severe outcomes by roughly 57% by December 31, 2021. CONCLUSIONS: Our results suggest that focusing the vaccination strategy on the working-age population can curb the spread of SARS-CoV-2. However, even with high vaccination coverage in adults, increasing contacts and easing protective personal behaviours is not advisable since a resurgence is expected to occur, especially with an earlier reopening.