A Targeted Genome-scale Overexpression Platform for Proteobacteria.

Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale overexpression face key limitations. Here, we develop a facile approach for genome-scale gene overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We create a platform for comprehensive gene targeting using CRISPR-associated transposition (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in Escherichia coli, recovering known antibiotic targets and genes with unexplored roles in antibiotic function. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.

Essential gene knockdowns reveal genetic vulnerabilities and antibiotic sensitivities in Acinetobacter baumannii.

The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing, they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that may explain synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.IMPORTANCEAcinetobacter baumannii is a hospital-acquired pathogen that is resistant to many common antibiotic treatments. To combat resistant A. baumannii infections, we need to identify promising therapeutic targets and effective antibiotic combinations. In this study, we comprehensively characterize the genes and pathways that are critical for A. baumannii viability. We show that genes involved in aerobic metabolism are central to A. baumannii physiology and may represent appealing drug targets. We also find antibiotic-gene interactions that may impact the efficacy of carbapenems, rifamycins, and polymyxins, providing a new window into how these antibiotics function in mono- and combination therapies. Our studies offer a useful approach for characterizing interactions between drugs and essential genes in pathogens to inform future therapies.

Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in Acinetobacter baumannii.

The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing (Tn-seq), they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that underpin synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.

The disparate impact of age-based COVID-19 vaccine prioritization by race/ethnicity in Denver, Colorado.

COVID-19 vaccines are an effective tool in preventing severe disease. Most states used an age-based prioritization for vaccine rollout. We examined the impact of a primarily age-based prioritization policy on reductions of severe disease in different racial and ethnic groups. We calculated age-specific rates of COVID-19 hospitalization and death by race/ethnicity in Denver, Colorado. To assess potentially averted hospitalizations and deaths by race/ethnicity, we then applied the first three phases of Colorado's primarily age-based vaccine rollout criteria to historical 2020 COVID-19 hospitalizations and deaths in Denver, Colorado. In the first 3 phases, 40% (1403/3473) of hospitalizations and 83% (503/604) of deaths occurred among those meeting age and long-term care facility criteria and could have been averted. Impacts varied by race/ethnicity with only 28% (440/1587) of hospitalizations and 74% (131/178) of deaths averted among Hispanic or Latino residents, compared to 57% (619/1094) of hospitalizations and 92% (252/274) of deaths among non-Hispanic White residents. We demonstrate using local data and policy that early age-based prioritization decisions disproportionately promoted reductions in severe disease among non-Hispanic White residents irrespective of COVID-19 risk in Denver, Colorado. These findings suggest that more equitable future vaccine prioritization policies, which lead with a goal of reducing health disparities through prioritizing susceptibility to adverse health outcomes rather than overall population-based cutoffs, are necessary. Our results have implications for future vaccination rollouts in limited vaccine resource conditions.

A process to deduplicate individuals for regional chronic disease prevalence estimates using a distributed data network of electronic health records.

Introduction: Learning health systems can help estimate chronic disease prevalence through distributed data networks (DDNs). Concerns remain about bias introduced to DDN prevalence estimates when individuals seeking care across systems are counted multiple times. This paper describes a process to deduplicate individuals for DDN prevalence estimates. Methods: We operationalized a two-step deduplication process, leveraging health information exchange (HIE)-assigned network identifiers, within the Colorado Health Observation Regional Data Service (CHORDS) DDN. We generated prevalence estimates for type 1 and type 2 diabetes among pediatric patients (0-17 years) with at least one 2017 encounter in one of two geographically-proximate DDN partners. We assessed the extent of cross-system duplication and its effect on prevalence estimates. Results: We identified 218 437 unique pediatric patients seen across systems during 2017, including 7628 (3.5%) seen in both. We found no measurable difference in prevalence after deduplication. The number of cases we identified differed slightly by data reconciliation strategy. Concordance of linked patients' demographic attributes varied by attribute. Conclusions: We implemented an HIE-dependent, extensible process that deduplicates individuals for less biased prevalence estimates in a DDN. Our null pilot findings have limited generalizability. Overlap was small and likely insufficient to influence prevalence estimates. Other factors, including the number and size of partners, the matching algorithm, and the electronic phenotype may influence the degree of deduplication bias. Additional use cases may help improve understanding of duplication bias and reveal other principles and insights. This study informed how DDNs could support learning health systems' response to public health challenges and improve regional health.

Missed appointments during COVID-19: The impact of telehealth for persons experiencing homelessness with substance use disorders.

We examined the impact of telehealth on appointment retention among individuals with substance use disorder (SUD) by housing status. We evaluated appointment status using multivariate logistic regression with primary predictor variables of visit modality, patient's housing status and interaction between these two variables. Between March 1 and September 30, 2020, there were 18,206 encounters among 1,626 clients with SUD. For telehealth encounters, the probability of an appointment no-show was significantly higher for persons experiencing homelessness compared to stably housed (37% versus 25%, p < 0.001). Housing status influences the effectiveness of telehealth as a modality of healthcare delivery for individuals with SUD.

Programmable Gene Knockdown in Diverse Bacteria Using Mobile-CRISPRi.

Facile bacterial genome sequencing has unlocked a veritable treasure trove of novel genes awaiting functional exploration. To make the most of this opportunity requires powerful genetic tools that can target all genes in diverse bacteria. CRISPR interference (CRISPRi) is a programmable gene-knockdown tool that uses an RNA-protein complex comprised of a single guide RNA (sgRNA) and a catalytically inactive Cas9 nuclease (dCas9) to sterically block transcription of target genes. We previously developed a suite of modular CRISPRi systems that transfer by conjugation and integrate into the genomes of diverse bacteria, which we call Mobile-CRISPRi. Here, we provide detailed protocols for the modification and transfer of Mobile-CRISPRi vectors for the purpose of knocking down target genes in bacteria of interest. We further discuss strategies for optimizing Mobile-CRISPRi knockdown, transfer, and integration. We cover the following basic protocols: sgRNA design, cloning new sgRNA spacers into Mobile-CRISPRi vectors, Tn7 transfer of Mobile-CRISPRi to Gram-negative bacteria, and ICEBs1 transfer of Mobile-CRISPRi to Bacillales. © 2020 The Authors. Basic Protocol 1: sgRNA design Basic Protocol 2: Cloning of new sgRNA spacers into Mobile-CRISPRi vectors Basic Protocol 3: Tn7 transfer of Mobile-CRISPRi to Gram-negative bacteria Basic Protocol 4: ICEBs1 transfer of Mobile-CRISPRi to Bacillales Support Protocol 1: Quantification of CRISPRi repression using fluorescent reporters Support Protocol 2: Testing for gene essentiality using CRISPRi spot assays on plates Support Protocol 3: Transformation of E. coli by electroporation Support Protocol 4: Transformation of CaCl2 -competent E. coli.

Evaluating Population Coverage in a Regional Distributed Data Network: Implications for Electronic Health Record-Based Public Health Surveillance.

OBJECTIVE: Electronic health records (EHRs) hold promise as a public health surveillance tool, but questions remain about how EHR patients compare with populations in health and demographic surveys. We compared population characteristics from a regional distributed data network (DDN), which securely and confidentially aggregates EHR data from multiple health care organizations in the same geographic region, with population characteristics from health and demographic surveys. METHODS: Ten health care organizations participating in a Colorado DDN contributed data for coverage estimation. We aggregated demographic and geographic data from 2017 for patients aged ≥18 residing in 7 counties. We used a cross-sectional design to compare DDN population size, by county, with the following survey-estimated populations: the county population, estimated by the American Community Survey (ACS); residents seeking any health care, estimated by the Colorado Health Access Survey; and residents seeking routine (eg, primary) health care, estimated by the Behavioral Risk Factor Surveillance System. We also compared data on the DDN and survey populations by sex, age group, race/ethnicity, and poverty level to assess surveillance system representativeness. RESULTS: The DDN population included 609 840 people in 7 counties, corresponding to 25% coverage of the general adult population. Population coverage ranged from 15% to 35% across counties. Demographic distributions generated by DDN and surveys were similar for many groups. Overall, the DDN and surveys assessing care-seeking populations had a higher proportion of women and older adults than the ACS population. The DDN included higher proportions of Hispanic people and people living in high-poverty neighborhoods compared with the surveys. CONCLUSION: The DDN population is not a random sample of the regional adult population; it is influenced by health care use patterns and organizations participating in the DDN. Strengths and limitations of DDNs complement those of survey-based approaches. The regional DDN is a promising public health surveillance tool.

Transcript decay mediated by RNase III in Borrelia burgdorferi.

The causative agent of Lyme disease, Borrelia burgdorferi, requires shifts in gene expression to undergo its natural enzootic cycle between tick and vertebrate hosts. mRNA decay mechanisms play significant roles in governing gene expression in other bacteria, but are not yet characterized in B. burgdorferi. RNase III is an important enzyme in processing ribosomal RNA, but it also plays a role in mRNA decay in many bacteria. We compared RNA decay profiles and steady-state abundances of transcripts in wild-type Borrelia burgdorferi strain B31 and in an RNase III null (rnc-) mutant. Transcripts encoding RNA polymerase subunits (rpoA and rpoS), ribosomal proteins (rpsD, rpsK, rpsM, rplQ, and rpsO), a nuclease (pnp), a flagellar protein (flaB), and a translational regulator (bpuR) decayed more rapidly in the wild-type strain than in the slow growing rnc- mutant indicating that RNA turnover is mediated by RNase III in the bacterium that causes Lyme disease. Additionally, in wild type bacteria, RNA decay rates of rpoS, rpoN, ospA, ospC, bpuR and dbpA transcripts are only modestly affected by changes in the osmolarity.

Racial/ethnic differences in treatment recommendations: lifestyle changes and medication prescriptions for high cholesterol.

Objective: High cholesterol is a common condition in the United States, affecting nearly one third of adults, and is a leading precursor to coronary heart disease. This study investigates race/ethnic differences in treatment recommendations for patients with high cholesterol, including prescription medication and lifestyle changes such as eating less fat, losing weight, or exercising more.Design: Data were obtained from the 2005 to 2010 National Health and Nutrition Examination Survey (N = 4846), a representative sample of adults in the United States, and the 2005-2010 National Ambulatory Medical Care Survey (N = 12,113), a representative sample of patient visits in the United States. Logistic regression analyses were used to assess whether health professionals recommended lifestyle changes or medication prescriptions differently by patient race/ethnicity and age. Models adjusted for demographic characteristics, socioeconomic status, health behaviors, health care access/utilization, and comorbidities.Results: Non-Hispanic Black and Hispanic patients with high cholesterol were significantly and substantially more likely to receive recommendations for lifestyle changes compared to non-Hispanic White patients. These differences were exacerbated at younger ages and largely diminished for adults over the age of 65. These patterns were reflected in both datasets. However, non-Hispanic Black patients from the NHANES analysis were less likely than non-Hispanic White patients to receive medication prescriptions for high cholesterol, particularly at younger ages. There were no race/ethnic differences in odds of medication prescriptions for Hispanic patients compared to White patients.Conclusions: Results suggest widespread and pervasive race/ethnic differences in recommending lifestyle changes for patients with high cholesterol. Although lifestyle changes may lower cholesterol they are often less effective than prescription medication. Because differences in lifestyle recommendations were not reflected in prescription practices, results may indicate a form of discrimination within physician-patient interactions that could be addressed by increased provider education about most effective treatment practices.

Developing a Regional Distributed Data Network for Surveillance of Chronic Health Conditions: The Colorado Health Observation Regional Data Service.

Electronic health records (EHRs) provide an alternative to traditional public health surveillance surveys and administrative data for measuring the prevalence and impact of chronic health conditions in populations. As the infrastructure for secondary use of EHR data improves, many stakeholders are poised to benefit from data partnerships for regional access to information. Electronic health records can be transformed into a common data model that facilitates data sharing across multiple organizations and allows data to be used for surveillance. The Colorado Health Observation Regional Data Service, a regional distributed data network, has assembled diverse data partnerships, flexible infrastructure, and transparent governance practices to better understand the health of communities through EHR-based, public health surveillance. This article describes attributes of regional distributed data networks using EHR data and the history and design of Colorado Health Observation Regional Data Service as an emerging public health surveillance tool for chronic health conditions. Colorado Health Observation Regional Data Service and our experience may serve as a model for other regions interested in similar surveillance efforts. While benefits from EHR-based surveillance are described, a number of technology, partnership, and value proposition challenges remain.

Effects of exposure to bodies of different sizes on perception of and satisfaction with own body size: two randomized studies.

Body dissatisfaction is prevalent among women and associated with subsequent obesity and eating disorders. Exposure to images of bodies of different sizes has been suggested to change the perception of 'normal' body size in others. We tested whether exposure to different-sized (otherwise identical) bodies changes perception of own and others' body size, satisfaction with body size and amount of chocolate consumed. In Study 1, 90 18-25-year-old women with normal BMI were randomized into one of three groups to complete a 15 min two-back task using photographs of women either of 'normal weight' (Body Mass Index (BMI) 22-23 kg m-2), or altered to appear either under- or over-weight. Study 2 was identical except the 96 participants had high baseline body dissatisfaction and were followed up after 24 h. We also conducted a mega-analysis combining both studies. Participants rated size of others' bodies, own size, and satisfaction with size pre- and post-task. Post-task ratings were compared between groups, adjusting for pre-task ratings. Participants exposed to over- or normal-weight images subsequently perceived others' bodies as smaller, in comparison to those shown underweight bodies (p < 0.001). They also perceived their own bodies as smaller (Study 1, p = 0.073; Study 2, p = 0.018; mega-analysis, p = 0.001), and felt more satisfied with their size (Study 1, p = 0.046; Study 2, p = 0.004; mega-analysis, p = 0.006). There were no differences in chocolate consumption. This study suggests that a move towards using images of women with a BMI in the healthy range in the media may help to reduce body dissatisfaction, and the associated risk of eating disorders.

Does the Hispanic health advantage extend to better management of hypertension? The role of socioeconomic status, sociobehavioral factors, and health care access.

Hispanics in the United States (and foreign-born Hispanics in particular) have relatively favorable health given their lower socioeconomic status compared to, for example, non-Hispanic whites. This phenomenon is often called the Hispanic health paradox (HHP). This study examines whether the previously documented HHP in hypertension prevalence extends to its management using clinical and self-reported measures from the 2007-2012 National Health and Nutrition Examination Surveys. Multivariate models adjusting for demographic, socioeconomic, and sociobehavioral characteristics show an advantage among foreign-born Mexicans in hypertension prevalence relative to non-Hispanic whites (adjusted OR = 0.85). However, compared to non-Hispanic whites, foreign-born Mexicans were 38% less likely to receive treatment recommendations and, when advised to undergo treatment, were 60% less likely to adhere to treatment. Adjusting for health care access and utilization dramatically reduces disparities in hypertension control between foreign-born Mexicans and non-Hispanic whites, suggesting that insufficient systematic access to and use of quality health care erodes the HHP and contributes to the deterioration of health throughout the immigrant experience. Without appropriate interventions, particularly in health care access and utilization, poorer hypertension management among foreign-born Mexicans may negatively affect the Hispanic health profile, increase risk of cardiovascular disease-related mortality, and erode the Hispanic health advantage in the future.

Tips and Troubleshooting for Use of the GlideScope Video Laryngoscope for Emergency Endotracheal Intubation.

Video laryngoscopy (VL) is still a relatively novel advancement in airway management that offers many potential benefits over direct laryngoscopy. These advantages include decreased time to intubation in difficulty airways, unique opportunities in teaching as the video screen allows for real time teaching points, increased first pass success, particularly with novice operators, and decreased cervical spine motion during intubation. Despite the advantages, the intubation procedure itself has some subtle but significant differences from direct laryngoscopy that change the expected motion as well as troubleshooting techniques, which might discourage the use of the GlideScope by practitioners less familiar with the product. With the hope of generating confidence in the video laryngoscopy procedure, we have compiled some basic tips that we have found helpful when intubating with the GlideScope. These tips include inserting the blade to the left of midline to improve space allowed for the endotracheal tube itself, backing the scope up a small amount to improve the view, holding the tube close to the connector to improve maneuverability, and withdrawing the tube with your thumb to improve advancement through the cords. We hope that, with these tips, in conjunction with ample practice, clinicians can gain comfort and experience with all the tools at our disposal in an effort to provide the best possible care for our patients.