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, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just 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 (LD) based haplotypes and association genetics analyses link Watkins genomes to the thousands of high-resolution quantitative trait loci (QTL), and significant marker-trait associations identified. 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 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

(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.

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.

Characterization of reported legionellosis outbreaks associated with buildings served by public drinking water systems: United States, 2001-2017.

This study examined 184 legionellosis outbreaks in the United States reported to the Centers for Disease Control and Prevention's Waterborne Disease and Outbreak Surveillance System, from 2001 to 2017. Drinking water characteristics examined include source water type, disinfectant type, exposure setting, geographical distribution by U.S. Census Divisions, and the public water system size (population served). This study found that most of the reported drinking water-associated legionellosis outbreaks occurred in eastern United States, including 35% in the South Atlantic, 32% in the Middle Atlantic, and 16% in the East North Central Census Divisions were linked with building water systems in healthcare and hotel settings; and were associated with buildings receiving drinking water from public water systems serving >10,000 people. Targeted evaluations and interventions may be useful to further determine the combination of factors, such as disinfectant residual type and drinking water system size that may lead to legionellosis outbreaks.

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.

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.

Evolving Epidemiology of Reported Giardiasis Cases in the United States, 1995-2016.

BACKGROUND: Giardiasis is the most common intestinal parasitic disease of humans identified in the United States (US) and an important waterborne disease. In the United States, giardiasis has been variably reportable since 1992 and was made a nationally notifiable disease in 2002. Our objective was to describe the epidemiology of US giardiasis cases from 1995 through 2016 using National Notifiable Diseases Surveillance System data. METHODS: Negative binomial regression models were used to compare incidence rates by age group (0-4, 5-9, 10-19, 20-29, 30-39, 40-49, 50-64, and ≥ 65 years) during 3 time periods (1995-2001, 2002-2010, and 2011-2016). RESULTS: During 1995-2016, the average number of reported cases was 19 781 per year (range, 14 623-27 778 cases). The annual incidence of reported giardiasis in the United States decreased across all age groups. This decrease differs by age group and sex and may reflect either changes in surveillance methods (eg, changes to case definitions or reporting practices) or changes in exposure. Incidence rates in males and older age groups did not decrease to the same extent as rates in females and children. CONCLUSIONS: Trends suggest that differences in exposures by sex and age group are important to the epidemiology of giardiasis. Further investigation into the risk factors of populations with higher rates of giardiasis will support prevention and control efforts.

Economic Burden of Legionnaires' Disease, United States, 2014.

Through the use of published estimates of medical costs and new calculations of productivity losses, we estimate the lifetime economic burden of 2014 Legionnaires' disease cases in the United States at ≈$835 million. This total includes $21 million in productivity losses caused by absenteeism and $412 million in productivity losses caused by premature deaths.

Geographic Range of Recreational Water-Associated Primary Amebic Meningoencephalitis, United States, 1978-2018.

Naegleria fowleri is a free-living ameba that causes primary amebic meningoencephalitis (PAM), a rare but usually fatal disease. We analyzed trends in recreational water exposures associated with PAM cases reported during 1978-2018 in the United States. Although PAM incidence remained stable, the geographic range of exposure locations expanded northward.

Attribution of Illnesses Transmitted by Food and Water to Comprehensive Transmission Pathways Using Structured Expert Judgment, United States.

Illnesses transmitted by food and water cause a major disease burden in the United States despite advancements in food safety, water treatment, and sanitation. We report estimates from a structured expert judgment study using 48 experts who applied Cooke's classical model of the proportion of disease attributable to 5 major transmission pathways (foodborne, waterborne, person-to-person, animal contact, and environmental) and 6 subpathways (food handler-related, under foodborne; recreational, drinking, and nonrecreational/nondrinking, under waterborne; and presumed person-to-person-associated and presumed animal contact-associated, under environmental). Estimates for 33 pathogens were elicited, including bacteria such as Salmonella enterica, Campylobacter spp., Legionella spp., and Pseudomonas spp.; protozoa such as Acanthamoeba spp., Cyclospora cayetanensis, and Naegleria fowleri; and viruses such as norovirus, rotavirus, and hepatitis A virus. The results highlight the importance of multiple pathways in the transmission of the included pathogens and can be used to guide prioritization of public health interventions.

Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States.

Provision of safe drinking water in the United States is a great public health achievement. However, new waterborne disease challenges have emerged (e.g., aging infrastructure, chlorine-tolerant and biofilm-related pathogens, increased recreational water use). Comprehensive estimates of the health burden for all water exposure routes (ingestion, contact, inhalation) and sources (drinking, recreational, environmental) are needed. We estimated total illnesses, emergency department (ED) visits, hospitalizations, deaths, and direct healthcare costs for 17 waterborne infectious diseases. About 7.15 million waterborne illnesses occur annually (95% credible interval [CrI] 3.88 million-12.0 million), results in 601,000 ED visits (95% CrI 364,000-866,000), 118,000 hospitalizations (95% CrI 86,800-150,000), and 6,630 deaths (95% CrI 4,520-8,870) and incurring US $3.33 billion (95% CrI 1.37 billion-8.77 billion) in direct healthcare costs. Otitis externa and norovirus infection were the most common illnesses. Most hospitalizations and deaths were caused by biofilm-associated pathogens (nontuberculous mycobacteria, Pseudomonas, Legionella), costing US $2.39 billion annually.

Demographic differences in use of household tap water in a representative sample of US adults, FallStyles 2019.

Tap water that is safe to consume may cause respiratory illness (e.g., Legionnaires' disease) when water conditions allow for proliferation and aerosolization of biofilm-associated pathogens. This study assessed household tap water consumption, exposure to aerosolized tap water, and associated demographics. A nationally representative FallStyles survey administered by Porter Novelli Public Services was sent to 4,677 US adult panelists in October 2019. There were 3,624 adults who completed the survey (77.5% response rate). Respondents were asked about self-reported use of household tap water for consumption (i.e., drinking, rinsing produce, or making ice) and use through water-aerosolizing devices (e.g., showerheads, humidifiers). Demographics included gender, age, race/ethnicity, education, income, region, and health status. Weighted analyses using complex sample survey procedures were used to assess tap water exposure by route and demographics. Most US adults are exposed to aerosolized tap water through showering (80.6%), and one in five are exposed through other water-aerosolizing devices (20.3%). Consumption and showering were greatest among older, White, higher educated, and higher-income adults. Aerosolized tap water can transmit waterborne pathogens and cause respiratory illness, especially among older age groups and people with weakened immune systems. These results will help target health messages for using water-aerosolizing devices safely.

American Academy of Optometry Microbial Keratitis Think Tank.

SIGNIFICANCE: Think Tank 2019 affirmed that the rate of infection associated with contact lenses has not changed in several decades. Also, there is a trend toward more serious infections associated with Acanthamoeba and fungi. The growing use of contact lenses in children demands our attention with surveillance and case-control studies. PURPOSE: The American Academy of Optometry (AAO) gathered researchers and key opinion leaders from around the world to discuss contact lens-associated microbial keratitis at the 2019 AAO Annual Meeting. METHODS: Experts presented within four sessions. Session 1 covered the epidemiology of microbial keratitis, pathogenesis of Pseudomonas aeruginosa, and the role of lens care systems and storage cases in corneal disease. Session 2 covered nonbacterial forms of keratitis in contact lens wearers. Session 3 covered future needs, challenges, and research questions in relation to microbial keratitis in youth and myopia control, microbiome, antimicrobial surfaces, and genetic susceptibility. Session 4 covered compliance and communication imperatives. RESULTS: The absolute rate of microbial keratitis has remained very consistent for three decades despite new technologies, and extended wear significantly increases the risk. Improved oxygen delivery afforded by silicone hydrogel lenses has not impacted the rates, and although the introduction of daily disposable lenses has minimized the risk of severe disease, there is no consistent evidence that they have altered the overall rate of microbial keratitis. Overnight orthokeratology lenses may increase the risk of microbial keratitis, especially secondary to Acanthamoeba, in children. Compliance remains a concern and a significant risk factor for disease. New insights into host microbiome and genetic susceptibility may uncover new theories. More studies such as case-control designs suited for rare diseases and registries are needed. CONCLUSIONS: The first annual AAO Think Tank acknowledged that the risk of microbial keratitis has not decreased over decades, despite innovation. Important questions and research directions remain.

Shigella sonnei Outbreak Investigation During a Municipal Water Crisis-Genesee and Saginaw Counties, Michigan, 2016.

Objectives. To investigate a shigellosis outbreak in Genesee County, Michigan (including the City of Flint), and Saginaw County, Michigan, in 2016 and address community concerns about the role of the Flint water system.Methods. We met frequently with community members to understand concerns and develop the investigation. We surveyed households affected by the outbreak, analyzed Shigella isolate data, examined the geospatial distribution of cases, and reviewed available water quality data.Results. We surveyed 83 households containing 158 cases; median age was 10 years. Index case-patients from 55 of 83 households (66%) reported contact with a person outside their household who wore diapers or who had diarrhea in the week before becoming ill; results were similar regardless of household drinking water source. Genomic diversity was not consistent with a point source. In Flint, no space-time clustering was identified, and average free chlorine residual values remained above recommended levels throughout the outbreak period.Conclusions. The outbreak was most likely caused by person-to-person contact and not by the Flint water system. Consistent community engagement was essential to the design and implementation of the investigation.

The Epidemiology and Clinical Features of Balamuthia mandrillaris Disease in the United States, 1974-2016.

BACKGROUND: Balamuthia mandrillaris is a free-living ameba that causes rare, nearly always fatal disease in humans and animals worldwide. B. mandrillaris has been isolated from soil, dust, and water. Initial entry of Balamuthia into the body is likely via the skin or lungs. To date, only individual case reports and small case series have been published. METHODS: The Centers for Disease Control and Prevention (CDC) maintains a free-living ameba (FLA) registry and laboratory. To be entered into the registry, a Balamuthia case must be laboratory-confirmed. Several sources were used to complete entries in the registry, including case report forms, CDC laboratory results, published case reports, and media information. SAS© version 9.3 software was used to calculate descriptive statistics and frequencies. RESULTS: We identified 109 case reports of Balamuthia disease between 1974 and 2016. Most (99%) had encephalitis. The median age was 36 years (range 4 months to 91 years). Males accounted for 68% of the case patients. California had the highest number of case reports, followed by Texas and Arizona. Hispanics constituted 55% for those with documented ethnicity. Exposure to soil was commonly reported. Among those with a known outcome, 90% of patients died. CONCLUSIONS: Balamuthia disease in the United States is characterized by a highly fatal encephalitis that affects patients of all ages. Hispanics were disproportionately affected. The southwest region of the United States reported the most cases. Clinician awareness of Balamuthia as a cause of encephalitis might lead to earlier diagnosis and initiation of treatment, resulting in better outcomes.

Healthy Contact Lens Behaviors Communicated by Eye Care Providers and Recalled by Patients - United States, 2018.

An estimated 45 million U.S. residents enjoy the benefits of contact lens wear, but many of them might be at increased risk for complications stemming from improper wear and care behaviors (1). One of the most serious complications of contact lens wear is a corneal infection known as microbial keratitis, which can sometimes result in reduced vision or blindness (2). In 2014, 50% of contact lens wearers reported ever sleeping in contact lenses, and 55% reported topping off* their contact lens solutions (3), which put them at greater risk for a contact lens-related eye infection (2,4). Data on communication between eye care providers and contact lens wearers on contact lens wear and care recommendations are limited. Two surveys were conducted to better understand and assess contact lens education about nine recommendations: the first assessed contact lens wearer experiences regarding recommendations received from eye care providers during their most recent appointment; the second evaluated provider-reported practices for communicating contact lens wear and care recommendations to their patients. One third (32.9%) of contact lens wearers aged ≥18 years recalled never hearing any lens wear and care recommendations. Fewer than half (47.9%) recalled hearing their provider recommend not sleeping in lenses at their last visit, and 19.8% recalled being told to avoid topping off their contact lens solution. A majority of providers reported sharing recommendations always or most of the time at initial visits, regular checkups, and complication-related visits. Providers reported sharing nearly all recommendations more frequently at initial and complication-related visits than at regular checkups. Of the nine recommendations for safe contact lens wear and care, eye care providers at regular checkups most often recommend complying with the recommended lens replacement schedules (85% of regular visits), not sleeping in lenses (79.0% of regular visits), and not topping off solutions (64.4% of regular visits). Eye care providers play an important role in the health of their contact lens-wearing patients and can share health communication messages with their patients to help educate them about healthy wear and care habits. These findings can assist in the creation of health communication messages to help encourage eye care providers to communicate more effectively with their patients.

Underestimation of N2 O emissions in a comparison of the DayCent, DNDC, and EPIC models.

Process-based models are increasingly used to study agroecosystem interactions and N2 O emissions from agricultural fields. The widespread use of these models to conduct research and inform policy benefits from periodic model comparisons that assess the state of agroecosystem modeling and indicate areas for model improvement. This work provides an evaluation of simulated N2 O flux from three process-based models: DayCent, DNDC, and EPIC. The models were calibrated and validated using data collected from two research sites over five years that represent cropping systems and nitrogen fertilizer management strategies common to dairy cropping systems. We also evaluated the use of a multi-model ensemble strategy, which inconsistently outperformed individual model estimations. Regression analysis indicated a cross-model bias to underestimate high magnitude daily and cumulative N2 O flux. Model estimations of observed soil temperature and water content did not sufficiently explain model underestimations, and we found significant variation in model estimates of heterotrophic respiration, denitrification, soil NH4+ , and soil NO3- , which may indicate that additional types of observed data are required to evaluate model performance and possible biases. Our results suggest a bias in the model estimation of N2 O flux from agroecosystems that limits the extension of models beyond calibration and as instruments of policy development. This highlights a growing need for the modeling and measurement communities to collaborate in the collection and analysis of the data necessary to improve models and coordinate future development.

Risk Factors for Acanthamoeba Keratitis-A Multistate Case-Control Study, 2008-2011.

OBJECTIVE: To identify modifiable risk factors contributing to Acanthamoeba keratitis (AK) infection. METHODS: A case-control investigation was conducted. Case patients were soft contact lens wearers with laboratory-confirmed AK. Control were soft contact lens wearers ≥12 years of age, with no history of AK. Case patients were recruited from 14 ophthalmology referral centers and a clinical laboratory. Control were matched on state of residence and type of primary eye care provider (ophthalmologist or optometrist). Participants were interviewed using a standardized questionnaire. Univariable and multivariable conditional logistic regression analyses were conducted. Matched odds ratios (mORs) were calculated. RESULTS: Participants included 88 case patients and 151 matched control. Case patients were more likely to be aged <25 years (unadjusted mOR 2.7, 95% confidence interval 1.3-5.5) or aged >53 years (mOR 2.5, 1.1-5.7), and more likely to be men (mOR 2.6, 1.4-4.8). Unadjusted analyses identified multiple risk factors: rinsing (mOR 6.3, 1.3-29.9) and storing lenses in tap water (mOR 3.9, 1.2-12.3), topping off solution in the lens case (mOR 4.0, 2.0-8.0), having worn lenses ≤5 years (mOR 2.4, 1.3-4.4), rinsing the case with tap water before storing lenses (mOR 2.1, 1.1-4.1), and using hydrogen peroxide (mOR 3.6, 1.1-11.7) versus multipurpose solution. Significant risk factors in multivariable modeling included age >53 years, male sex, topping off, and using saline solution. CONCLUSIONS: Numerous modifiable risk factors for AK were identified, mostly involving hygiene practices. To reduce the risk of AK, lens wearers should observe recommended lens care practices.

Giardiasis and Subsequent Irritable Bowel Syndrome: A Longitudinal Cohort Study Using Health Insurance Data.

Background: Giardia intestinalis is the most commonly reported human intestinal parasite in the United States. Increased incidence of chronic gastrointestinal complaints has been reported after some giardiasis outbreaks. We examined the relationship between giardiasis diagnosis and irritable bowel syndrome (IBS) diagnosis. Methods: We used the 2006-2010 MarketScan commercial insurance database. Persons with at least 1 giardiasis diagnosis were individually matched on age group, sex, and enrollment length in months to 5 persons without a giardiasis diagnosis. Persons diagnosed with IBS before the date of study entry were excluded. We calculated crude incidence rates (IRs) and developed Cox proportional hazards models. Results: The matched cohort included 3935 persons with giardiasis and 19663 persons without giardiasis. One-year incidence of IBS was higher in persons with giardiasis (IR = 37.7/1000 person-years vs 4.4/1000 person-years). The unadjusted hazard ratio was 4.8 (95% confidence interval [CI] = 3.6-6.4), attenuated slightly to 3.9 (95% CI = 2.9-5.4) after adjusting for anxiety, depression, and healthcare utilization. Conclusions: In a large insurance database, individuals diagnosed with giardiasis were more likely to have a subsequent IBS diagnosis, despite accounting for confounders. Future research on risk factors for IBS among giardiasis patients and the pathophysiology of postinfectious IBS is needed.

Giardiasis Diagnosis and Treatment Practices Among Commercially Insured Persons in the United States.

Background: Giardiasis, the most common enteric parasitic infection in the United States, causes an estimated 1.2 million episodes of illness annually. Published clinical recommendations include readily available Giardia-specific diagnostic testing and antiparasitic drugs. We investigated sequences of giardiasis diagnostic and treatment events using MarketScan, a large health insurance claims database. Methods: We created a longitudinal cohort of 2995 persons diagnosed with giardiasis (International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9-CM] code 007.1) from 2006 to 2010, and analyzed claims occurring 90 days before to 90 days after initial diagnosis. We evaluated differences in number and sequence of visits, diagnostic tests, and prescriptions by age group (children 1-17 years, adults 18-64 years) using χ2 tests and data visualization software. Results: Among 2995 patients (212433 claims), 18% had a Giardia-specific test followed by or concurrent with an effective antiparasitic drug, without ineffective antibiotics. Almost two-thirds of patients had an antiparasitic and 27% had an antibiotic during the study window. Compared with children, adults more often had ≥3 visits before diagnosis (19% vs 15%; P = .02). Adults were also less likely to have a Giardia-specific diagnostic test (48% vs 58%; P < .001) and more likely to have an antibiotic prescription (28% vs 25%; P = .04). When Giardia-specific tests and antiparasitic and antibiotic prescriptions were examined, pediatric clinical event sequences most frequently began with a Giardia-specific test, whereas adult sequences most frequently began with an antiparasitic prescription. Conclusions: Giardiasis care infrequently follows all aspects of clinical recommendations. Multiple differences between pediatric and adult care, despite age-agnostic recommendations, suggest opportunities for provider education or tailored guidance.