Individualized decision aid for diverse women with lupus nephritis (IDEA-WON): A randomized controlled trial.

BackgroundTreatment decision-making regarding immunosuppressive therapy is challenging for individuals with lupus. We assessed the effectiveness of a decision aid for immunosuppressive therapy in lupus nephritis.Methods and findingsIn a United States multicenter, open-label, randomized controlled trial (RCT), adult women with lupus nephritis, mostly from racial/ethnic minority backgrounds with low socioeconomic status (SES), seen in in- or outpatient settings, were randomized to an individualized, culturally tailored, computerized decision aid versus American College of Rheumatology (ACR) lupus pamphlet (1:1 ratio), using computer-generated randomization. We hypothesized that the co-primary outcomes of decisional conflict and informed choice regarding immunosuppressive medications would improve more in the decision aid group. Of 301 randomized women, 298 were analyzed; 47% were African-American, 26% Hispanic, and 15% white. Mean age (standard deviation [SD]) was 37 (12) years, 57% had annual income of <$40,000, and 36% had a high school education or less. Compared with the provision of the ACR lupus pamphlet (n = 147), participants randomized to the decision aid (n = 151) had (1) a clinically meaningful and statistically significant reduction in decisional conflict, 21.8 (standard error [SE], 2.5) versus 12.7 (SE, 2.0; p = 0.005) and (2) no difference in informed choice in the main analysis, 41% versus 31% (p = 0.08), but clinically meaningful and statistically significant difference in sensitivity analysis (net values for immunosuppressives positive [in favor] versus negative [against]), 50% versus 35% (p = 0.006). Unresolved decisional conflict was lower in the decision aid versus pamphlet groups, 22% versus 44% (p < 0.001). Significantly more patients in the decision aid versus pamphlet group rated information to be excellent for understanding lupus nephritis (49% versus 33%), risk factors (43% versus 27%), medication options (50% versus 33%; p ≤ 0.003 for all); and the ease of use of materials was higher in the decision aid versus pamphlet groups (51% versus 38%; p = 0.006). Key study limitations were the exclusion of men, short follow-up, and the lack of clinical outcomes, including medication adherence.ConclusionsAn individualized decision aid was more effective than usual care in reducing decisional conflict for choice of immunosuppressive medications in women with lupus nephritis.Trial registrationClinicaltrials.gov, NCT02319525

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Error baseline rates of five sample preparation methods used to characterize RNA virus populations.

Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic "no amplification" method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a "targeted" amplification method, sequence-independent single-primer amplification (SISPA) as a "random" amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced "no amplification" method, and Illumina TruSeq RNA Access as a "targeted" enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4-5) of all compared methods

Impact of universal gowning and gloving on health care worker clothing contamination

OBJECTIVE: To determine whether gowning and gloving for all patient care reduces contamination of healthcare worker (HCW) clothing, compared to usual practice. DESIGN: Cross-sectional surveys. SETTING: Five study sites were recruited from intensive care units (ICUs) randomized to the intervention arm of the Benefits of Universal Gown and Glove (BUGG) study. PARTICIPANTS: All HCWs performing direct patient care in the study ICUs were eligible to participate. METHODS: Surveys were performed first during the BUGG intervention study period (July-September 2012) with universal gowning/gloving and again after BUGG study conclusion (October-December 2012), with resumption of usual care. During each phase, HCW clothing was sampled at the beginning and near the end of each shift. Cultures were performed using broth enrichment followed by selective media. Acquisition was defined as having a negative clothing culture for samples taken at the beginning of a shift and positive clothing culture at for samples taken at the end of the shift. RESULTS: A total of 348 HCWs participated (21-92 per site), including 179 (51%) during the universal gowning/gloving phase. Overall, 51 (15%) HCWs acquired commonly pathogenic bacteria on their clothing: 13 (7.1%) HCWs acquired bacteria during universal gowning/gloving, and 38 (23%) HCWs acquired bacteria during usual care (odds ratio [OR], 0.3; 95% confidence interval [CI], 0.2-0.6). Pathogens identified included S. aureus (25 species, including 7 methicillin-resistant S. aureus [MRSA]), Enterococcus spp. (25, including 1 vancomycin-resistant Enterococcus [VRE]), Pseudomonas spp. (4), Acinetobacter spp. (4), and Klebsiella (2). CONCLUSION: Nearly 25% of HCWs practicing usual care (gowning and gloving only for patients with known resistant bacteria) contaminate their clothing during their shift. This contamination was reduced by 70% by gowning and gloving for all patient interactions

Percentage of errors by type of acquired diversity determined during sample preparation.

<p>(A) Percentage of error attributed to synonymous vs. non-synonymous variants. (B) Percentage of errors attributed to transitions vs. transversions. (C) Percentage of errors attributed to insertions or deletions vs. Intra-host single nucleotide variants (iSNV).</p

Study sample diagram.

<p>Study sample diagram.</p

Sources of error per sample preparation method.

<p>(A) Intra-host single nucleotide variants (iSNVs) that were present in multiple samples at greater than 1% of population are shown in a heat map format to visualize patterned diversity acquired during sample preparation. The total number of samples containing iSNVs in greater than 1% of population are summarized in the column “#> 1% of Pop” in green. “Codon” column (second column from right) provides both the nucleotide and protein translation of the site. (B) The detected mean error rates of iSNVs greater than 0. 2% of population (error/site/copy) are stratified by presence in the plasmid (Origin), detection after transcription/reverse transcription (Transc) or preparation, and preparation/sequencer error (Prep). (C) Error profiles are expressed as the number of iSNVs per percent of population obtained from each of the 5 sample preparation methods.</p