What makes Candida auris pan-drug resistant? Integrative insights from genomic, transcriptomic, and phenomic analysis of clinical strains resistant to all four major classes of antifungal drugs.

The global epidemic of drug-resistant Candida auris continues unabated. We do not know what caused the unprecedented appearance of pan-drug resistant (PDR) Candida auris strains in a hospitalized patient in New York; the initial report highlighted both known and unique mutations in the prominent gene targets of azoles, amphotericin B, echinocandins, and flucytosine antifungal drugs. However, the factors that allow C. auris to acquire multi-drug resistance and pan-drug resistance are not known. Therefore, we conducted a comprehensive genomic, transcriptomic, and phenomic analysis to better understand PDR C. auris . Among 1,570 genetic variants in drug-resistant C. auris , 299 were unique to PDR strains. The whole genome sequencing results suggested perturbations in genes associated with nucleotide biosynthesis, mRNA processing, and nuclear export of mRNA. Whole transcriptome sequencing of PDR C. auris revealed two genes to be significantly differentially expressed - a DNA repair protein and DNA replication-dependent chromatin assembly factor 1. Of 59 novel transcripts, 12 candidate transcripts had no known homology among expressed transcripts found in other organisms. We observed no fitness defects among multi-drug resistant (MDR) and PDR C. auris strains grown in nutrient-deficient or - enriched media at different temperatures. Phenotypic profiling revealed wider adaptability to nitrogenous nutrients with an uptick in the utilization of substrates critical in upper glycolysis and tricarboxylic acid cycle. Structural modelling of 33-amino acid deletion in the gene for uracil phosphoribosyl transferase suggested an alternate route in C. auris to generate uracil monophosphate that does not accommodate 5-fluorouracil as a substrate. Overall, we find evidence of metabolic adaptations in MDR and PDR C. auris in response to antifungal drug lethality without deleterious fitness costs.

The ATCC genome portal: 3,938 authenticated microbial reference genomes.

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC's biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.

The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI's RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI's core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an "elephant in the room" for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. IMPORTANCE The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI's RefSeq database. We present a comparative analysis of de novo-assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.

The ATCC Genome Portal: Microbial Genome Reference Standards with Data Provenance.

Lack of data provenance negatively impacts scientific reproducibility and the reliability of genomic data. The ATCC Genome Portal (https://genomes.atcc.org) addresses this by providing data provenance information for microbial whole-genome assemblies originating from authenticated biological materials. To date, we have sequenced 1,579 complete genomes, including 466 type strains and 1,156 novel genomes.

The effectiveness of a Web-based personalized feedback and social norms alcohol intervention on United Kingdom university students: randomized controlled trial.

BACKGROUND: Alcohol consumption in the student population continues to be cause for concern. Building on the established evidence base for traditional brief interventions, interventions using the Internet as a mode of delivery are being developed. Published evidence of replication of initial findings and ongoing development and modification of Web-based personalized feedback interventions for student alcohol use is relatively rare. The current paper reports on the replication of the initial Unitcheck feasibility trial. OBJECTIVE: To evaluate the effectiveness of Unitcheck, a Web-based intervention that provides instant personalized feedback on alcohol consumption. It was hypothesized that use of Unitcheck would be associated with a reduction in alcohol consumption. METHODS: A randomized control trial with two arms (control=assessment only; intervention=fully automated personalized feedback delivered using a Web-based intervention). The intervention was available week 1 through to week 15. Students at a UK university who were completing a university-wide annual student union electronic survey were invited to participate in the current study. Participants (n=1618) were stratified by sex, age group, year of study, self-reported alcohol consumption, then randomly assigned to one of the two arms, and invited to participate in the current trial. Participants were not blind to allocation. In total, n=1478 (n=723 intervention, n=755 control) participants accepted the invitation. Of these, 70% were female, the age ranged from 17-50 years old, and 88% were white/white British. Data were collected electronically via two websites: one for each treatment arm. Participants completed assessments at weeks 1, 16, and 34. Assessment included CAGE, a 7-day retrospective drinking diary, and drinks consumed per drinking occasion. RESULTS: The regression model predicted a monitoring effect, with participants who completed assessments reducing alcohol consumption over the final week. Further reductions were predicted for those allocated to receive the intervention, and additional reductions were predicted as the number of visits to the intervention website increased. CONCLUSIONS: Unitcheck can reduce the amount of alcohol consumed, and the reduction can be sustained in the medium term (ie, 19 weeks after intervention was withdrawn). The findings suggest self-monitoring is an active ingredient to Web-based personalized feedback.

Prevalence of depression symptoms in outpatients with a complaint of headache.

PURPOSE: This case-control study was designed to determine whether adults who present to a primary care office with a chief complaint of headache have more reported symptoms of depression than adults presenting with other problems. METHODS: Adult, English-speaking patients who presented to a primary care office with a chief complaint of headache were matched to adult patients of the same age and sex who presented with problems other than headache. All participants completed the PRIME-MD 9-item Patient Health Questionnaire as a screen for depression. RESULTS: A total of 200 participants entered the study. The mean age of the participants was 43.8 years (range, 18-87 years). Women constituted 84% of the participants. Of those patients who presented with headache, 32% had a likelihood of possible major depressive disorder compared with 12% in the patients presenting without headache. CONCLUSIONS: Almost one-third of adult patients who present to a primary care office with a complaint of headache report moderate symptoms of depression when screened compared with approximately 10% of patients presenting with a complaint other than headache. Given such a high prevalence of these symptoms, primary care physicians should screen all adult patients who present with headache for depression.

Measuring awareness, interest, and involvement in the osteopathic community through board certification: a survey of DO residents in ACGME-accredited training programs.

Currently, close to 50% of osteopathic medical graduates receive residency training from programs accredited by the Accreditation Council for Graduate Medical Education (ACGME) rather than those approved by the American Osteopathic Association (AOA). As a result, leaders within the osteopathic medical profession have expressed ongoing concerns about the viability of the profession's distinct osteopathic identity. Using a one-page, 12-item survey, the authors queried ACGME-trained family practice residents (N=1354) regarding their interest in formal membership, continuing medical education activities, and specialty board certification options within the osteopathic medical profession. Four hundred twenty-six completed surveys were returned and usable for analysis for an overall response rate of 31.4%. A majority of survey participants indicated an interest "in continuing [their] osteopathic skills and training during residency" (376 [88.5%]), membership in osteopathic organizations and participating in continuing medical education programs (325 [77.2%]), and completing the American Osteopathic Board of Family Physicians certification examination (267 [63.7%]). Unfortunately, actual involvement may be limited by lack of communication or understanding, as in the case of lack of awareness regarding eligibility criteria for AOA board certification (311 [74.2%]). A variety of recommendations are offered to osteopathic organizations to improve involvement in and commitment to the profession among ACGME-trained DOs.

The economic impact of acute sunburn.

OBJECTIVE: To estimate the economic impact of sunburn in a beachgoing population during the summer. DESIGN: Survey. SETTING: Galveston, Tex, beachfront. PARTICIPANTS: Convenience sample of 56 sunburned beachgoers. Intervention None. MAIN OUTCOME MEASURES: Days of work lost as a result of sunburn in the previous year. RESULTS: Thirty-eight respondents (68%) reported painful sunburn. Sunscreen use did not prevent painful sunburn (23/38 [60%]). Those consuming alcohol at the beach had more severe sunburns than nondrinkers and had a higher frequency of analgesic use after sunburn (69% vs 26%, P =.007). Five men (5/18 [28%]) and 4 women (4/38 [10%]) missed a total of 9 and 8 days of work, respectively, because of sunburn within the prior year. Based on these findings and attendant assumptions, it is estimated that sunburn may account for as many as 92 720 lost workdays by Galveston beachgoers each year. The annual economic impact for lost work and treatment may exceed $10 million. CONCLUSION: Sunburn is a costly and preventable skin injury.