Geographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.

The Complexity of Tobacco Smoke-Induced Mutagenesis in Head and Neck Cancer

Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). Here, we further explore how tobacco exposure contributes to cancer development by mutational signature analysis of 265 whole-genome sequenced HNC from eight countries. Six tobacco-associated mutational signatures were detected, including some not previously reported. Differences in HNC incidence between countries corresponded with differences in mutation burdens of tobacco-associated signatures, consistent with the dominant role of tobacco in HNC causation. Differences were found in the burden of tobacco-associated signatures between anatomical subsites, suggesting that tissue-specific factors modulate mutagenesis. We identified an association between tobacco smoking and three additional alcohol-related signatures indicating synergism between the two exposures. Tobacco smoking was associated with differences in the mutational spectra and repertoire of driver mutations in cancer genes, and in patterns of copy number change. Together, the results demonstrate the multiple pathways by which tobacco smoke can influence the evolution of cancer cell clones.

The Mutographs biorepository: A unique genomic resource to study cancer around the world

Large-scale biorepositories and databases are essential to generate equitable, effective, and sustainable advances in cancer prevention, early detection, cancer therapy, cancer care, and surveillance. The Mutographs project has created a large genomic dataset and biorepository of over 7,800 cancer cases from 30 countries across five continents with extensive demographic, lifestyle, environmental, and clinical information. Whole-genome sequencing is being finalized for over 4,000 cases, with the primary goal of understanding the causes of cancer at eight anatomic sites. Genomic, exposure, and clinical data will be publicly available through the International Cancer Genome Consortium Accelerating Research in Genomic Oncology platform. The Mutographs sample and metadata biorepository constitutes a legacy resource for new projects and collaborations aiming to increase our current research efforts in cancer genomic epidemiology globally.

Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health

For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.

Toward biophysical markers of depression vulnerability

A major difficulty with treating psychiatric disorders is their heterogeneity: different neural causes can lead to the same phenotype. To address this, we propose describing the underlying pathophysiology in terms of interpretable, biophysical parameters of a neural model derived from the electroencephalogram. We analyzed data from a small patient cohort of patients with depression and controls. Using DCM, we constructed biophysical models that describe neural dynamics in a cortical network activated during a task that is used to assess depression state. We show that biophysical model parameters are biomarkers, that is, variables that allow subtyping of depression at a biological level. They yield a low dimensional, interpretable feature space that allowed description of differences between individual patients with depressive symptoms. They could capture internal heterogeneity/variance of depression state and achieve significantly better classification than commonly used EEG features. Our work is a proof of concept that a combination of biophysical models and machine learning may outperform earlier approaches based on classical statistics and raw brain data.

A review of the selection process and decontamination methods with the use of face shields in UV phototherapy during the SARS‐CoV‐2 pandemic

Targeted ultraviolet (UV) phototherapy has been used in the management of a wide variety of dermatological clinical conditions including moderate to severe psoriasis unresponsive to topical therapies, vitiligo, severe atopic dermatitis and lymphoproliferative disorders. To date there are no uniform, standardised guidelines for the selection and decontamination process for UV personal protective equipment (PPE) and facial shields used in phototherapy. In the current climate, Coronavirus 2019 (COVID‐19) pandemic, standards regarding all decontamination and disinfection processes are under significant scrutiny. In terms of the UV‐PPE and facial shields used in phototherapy, careful disinfection procedures need to be implemented to ensure that the decontamination practice is effective enough to neutralise the virulent virus whilst maintaining maximal protection to the user from UV‐rays and safeguard the equipment from damage during the cleaning process. The aim of this report is to provide an evidence based review of the current and international practice standards guiding the selection, use and decontamination processes of UV facial shields in phototherapy. The complications and concerns that the COVID‐19 pandemic has had on this practice is highlighted. As such, we performed a comprehensive evaluation of the literature to provide recommendations as to the most effective, time efficient and safest practices for disinfection and decontamination of UV facial shields used in phototherapy during these unprecedented times.

259 IDENTIFYING THE TOP 10 RESEARCH PRIORITIES FOR FAMILY CARERS: THE INTERFACE PROJECT

Background

In assessing the global impact of the COVID-19 pandemic on society, it is important to understand the communities most affected and develop methods of support. Family carers provide a vital, yet often invisible role in our society and healthcare system. Identifying research priorities for carers helps establish overall gaps in the research agenda and increases awareness of the role of carers in the community.

Methods

A priority setting partnership methodology was engaged and through collaboration with carers, healthcare professionals and researchers, a participatory process was conducted to identify gaps in the current literature and prioritise research questions and uncertainties. Focus group discussions followed, the first consisted of family carers (n = 5). The second (n = 3) interviewed stakeholders namely healthcare professionals, researchers and policy makers. After collating the data, researchable questions were developed through an iterative process with a Multi Stakeholder Advisory Committee to identify the top 10 research priorities for Family Carers Ireland.

Results

The top 10 researchable questions were distilled from a list of 16 and fit into 7 broad categories. 1) economic impact and financial strain 2) Systemic issues, education, resources and policy 3) technology 4) support services and infrastructure 5) mental health and wellbeing of the carer 6) carers in society 7) Recognition and acknowledgment of the family carer.

Conclusion

The partnership focus of this project allowed the ‘ground-up’ development of research priorities for carers by carers. The COVID-19 pandemic served to magnify systemic issues already present in society, as well as highlight new burdens. As a result, the subsequent development of 10 researchable questions will guide further investigation to improve the support and wellbeing of family carers.

Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence

Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here we combine the fields of mutational signature analysis with cancer epidemiology to study 552 ESCC genomes from eight countries with varying incidence rates. Mutational profiles were similar across all countries studied. Associations between specific mutational signatures and ESCC risk factors were identified for tobacco, alcohol, opium and germline variants, with modest impacts on mutation burden. We find no evidence of a mutational signature indicative of an exogenous exposure capable of explaining differences in ESCC incidence. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signatures single-base substitution (SBS)2 and SBS13 were present in 88% and 91% of cases, respectively, and accounted for 25% of the mutation burden on average, indicating that APOBEC activation is a crucial step in ESCC tumor development.

1080 An Audit on Compliance with Recommended Duration of Surgical Antimicrobial Prophylaxis in St. Vincent’s University Hospital, Dublin, Ireland

Aim

Surgical site infection (SSI) is a common healthcare-associated infection, and a frequent cause of post-operative morbidity. SSI comprises any infection of the operative incision, cavity or involved organ, that occurs within the 30-day post-operative period. Antimicrobial prophylaxis is critical in reducing SSIs. Our aim was to assess adherence to the recommended surgical antimicrobial prophylaxis guidelines in St. Vincent’s University Hospital (SVUH), as part of the hospital antimicrobial stewardship programme. Compliance of surgical services was measured against the recommended regimens described in the SVUH Antimicrobial Guidelines.

Method

Data on duration and choice of prophylaxis were prospectively gathered on inpatients undergoing elective surgery during a three-week period between August-September 2020. Patients undergoing transplant procedures, inpatients in the intensive care unit, and patients who moved off-site postoperatively were excluded.

Results

Eighty-one patients were included. Sixty-four (79%) were compliant with prophylaxis duration, while seventeen (21%) were not. Reasons for extended prophylaxis included three (18%) cases where there were intra-operative complications and five (29%) cases of routine prescribing of an additional 24-hour coverage. Nine (53%) did not document the reason for extended cover.

Conclusions

Compliance with recommended duration of prophylaxis improved in comparison to prior audits. Among patients receiving extended prophylaxis, documentation of the indication was poor. Patients with evidence of post-operative infection may be better served with targeted antimicrobial therapy rather than extended prophylaxis. One reason for extended prophylaxis may be due to difficulty accessing guidelines on recommended prophylaxis duration, hence a targeted smartphone application was introduced to improve accessibility.

Are medical procedures that induce coughing or involve respiratory suctioning associated with increased generation of aerosols and risk of SARS-CoV-2 infection? A rapid systematic review

BACKGROUND

The risk of transmission of SARS-CoV-2 from aerosols generated by medical procedures is a cause for concern.

AIM

To evaluate the evidence for aerosol production and transmission of respiratory infection associated with procedures that involve airway suctioning or induce coughing/sneezing.

METHODS

The review was informed by PRISMA guidelines. Searches were conducted in PubMed for studies published between January 1st, 2003 and October 6th, 2020. Included studies examined whether nasogastric tube insertion, lung function tests, nasendoscopy, dysphagia assessment, or suctioning for airway clearance result in aerosol generation or transmission of SARS-CoV-2, SARS-CoV, MERS, or influenza. Risk of bias assessment focused on robustness of measurement, control for confounding, and applicability to clinical practice.

FINDINGS

Eighteen primary studies and two systematic reviews were included. Three epidemiological studies found no association between nasogastric tube insertion and acquisition of respiratory infections. One simulation study found low/very low production of aerosols associated with pulmonary lung function tests. Seven simulation studies of endoscopic sinus surgery suggested significant increases in aerosols but findings were inconsistent; two clinical studies found airborne particles associated with the use of microdebriders/drills. Some simulation studies did not use robust measures to detect particles and are difficult to equate to clinical conditions.

CONCLUSION

There was an absence of evidence to suggest that the procedures included in the review were associated with an increased risk of transmission of respiratory infection. In order to better target precautions to mitigate risk, more research is required to determine the characteristics of medical procedures and patients that increase the risk of transmission of SARS-CoV-2.

Iatrogenic Foreign Materials Associated with Retrieved Clot Tissue via Mechanical Thrombectomy

BACKGROUND AND PURPOSE

Hydrophilic polymers and polytetrafluoroethylene liners, commonly used in the construction of endovascular devices, occasionally separate from devices with subsequent embolization. We determined the frequency of such materials in thrombus specimens retrieved by mechanical thrombectomy in patients with stroke.

MATERIALS AND METHODS

We retrospectively reviewed H&E-stained thrombus sections for presence and types of foreign materials. We identified 4 types of foreign materials-Type I: material was light green with refraction and had a homogeneous texture; type II: material was light gray and/or dark gray, thin, and loose or attenuated in texture; type III: material was light green with refraction, solitary in texture, irregular in shape, and was often associated with round or oval bubblelike particles and/or diffuse black particles; and type IV: material had homogeneous texture and was light pink or red. In addition, polymer materials from different layers of used mechanical thrombectomy catheters were compared with the foreign materials found in thrombus specimens.

RESULTS

A total of 101 thrombi were evaluated. Foreign materials were found in 53 (52.5%) thrombus samples. The most common type was type I (92%), followed by type II (30%). The histopathologic features of the polymer materials from mechanical thrombectomy catheters were similar to the foreign materials found in thrombus specimens. The inner polytetrafluoroethylene liner and coating layer of catheters resembled type I and type II of the foreign materials, respectively.

CONCLUSIONS

Foreign polymer materials are present in approximately half of retrieved thrombi, most commonly polytetrafluoroethylene from catheter liners and less from hydrophilic coatings.

Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration

H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here, we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. Each clade is composed exclusively of either chromosome-encoded or plasmid-encoded proteins. On chromosomes, stpA and newly discovered hlpP are core genes in specific genera, whereas hfp and newly discovered hlpC are sporadically distributed. Six clades of H-NS plasmid proteins (Hpp) exhibit ancient and dedicated associations with plasmids, including three clades with fidelity for plasmid incompatibility groups H, F or X. A proliferation of H-NS homologs in Erwiniaceae includes the first observation of potentially co-dependent H-NS forms. Conversely, the observed diversification of oligomerization domains may facilitate stable co-existence of divergent homologs in a genome. Transcriptomic and proteomic analysis in Salmonella revealed regulatory crosstalk and hierarchical control of H-NS homologs. We also discovered that H-NS is both a repressor and activator of Salmonella Pathogenicity Island 1 gene expression, and both regulatory modes are restored by Sfh (HppH) in the absence of H-NS.

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

BACKGROUND

Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences.

RESULTS

Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

CONCLUSIONS

This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

Visual Immunoprecipitate Assay (VIP) for Listeria monocytogenes and Related Listeria Species Detection in Selected Foods: Collaborative Study

Six foods representing a variety of food products were analyzed by the Assurance Listeria polyclonal enzyme immunoassay (EIA) and by either the Bacteriological Analytical Manual or the U.S. Department of Agriculture culture method for detecting Listeria monocytogenes and related Listeria species. Samples of each food type, at each inoculation level, were analyzed simultaneously by both methods. A total of 19 laboratories representing federal government agencies and private industry in the United States and Canada participated. Food types were inoculated with Listeria species including L. monocytogenes, with the exception of 3 lots of green beans, which were naturally contaminated. During this study, 1764 samples and controls were analyzed and confirmed, of which 492 were positive and 947 were negative by both methods. There were 159 samples that were positive by culture method but negative by the EIA and 188 that were negative by culture method but positive by EIA. Twenty-two samples were negative by EIA and by culture method but confirmed positive when Assurance selective enrichment broths were subcultured to selective agar. The Assurance polyclonal EIA for detecting L. monocytogenes and related Listeria species in foods has been adopted first action by AOAC INTERNATIONAL.

Evaluation of the Assurance GDS® for Salmonella Method in Foods and Environmental Surfaces: Multilaboratory Collaborative Study

A multilaboratory collaborative study was conducted to compare the detection of Salmonella by the Assurance GDS® for Salmonella method and the Reference culture methods. Six foods, representing a variety of low microbial and high microbial load foods were analyzed. Seventeen laboratories in the United States and Canada participated in this study. No statistical differences (P &lt; 0.05) were observed between the Assurance GDS for Salmonella and the Reference culture methods for any inoculation level of any food type or naturally contaminated food, except for pasta, for which the Assurance GDS method had a higher number of confirmed test portions for Salmonella compared to the Reference method.

Method Extension Study to Validate Applicability of AOAC Official Method 996.14 Assurance® Polyclonal Enzyme Immunoassay for Detection of Listeria monocytogenes and Related Listeria spp. from Environmental Surfaces: Collaborative Study

Test portions from 3 environmental surface types, representative of typical surfaces found in a food production facility, were analyzed by the Assurance®Listeria Polyclonal Enzyme Immunoassay (EIA) and the U.S. Department of Agriculture/Food Safety and Inspection Service (USDA/FSIS) culture method for Listeria monocytogenes and related Listeria species. In all cases, naturally contaminated environmental test samples were collected from an actual food production facility by sponge or swab. Test samples from concrete surfaces were collected by both swab and sponge; sponge test samples were collected from rubber surfaces, and swabs were used to sample steel surfaces. Test portions from each surface type were simultaneously analyzed by both methods. A total of 23 collaborators, representing government agencies, as well as private industry in both the United States and Canada, participated in the study. During this study, a total of 550 test portions and controls was analyzed and confirmed, of which 207 were positive and 336 were negative by both methods. Six test portions were positive by culture, but negative by the EIA. Three test portions were negative by culture, but positive by the EIA. Two test portions were negative by EIA and by culture, but confirmed positive when EIA enrichment broths were subcultured to selective agars. The data reported here indicate that the Assurance®Listeria EIA method and the USDA/FSIS culture method are statistically equivalent for detection of L. monocytogenes and related Listeria species from environmental surfaces taken by sponges or swabs.

Method Extension Study to Validate Applicability of AOAC Official Method 997.03 Visual Immunoprecipitate Assay (VIP®) for Listeria monocytogenes and Related Listeria spp. from Environmental Surfaces: Collaborative Study

Test portions from 3 environmental surface types, representative of typical surfaces found in a food production facility, were analyzed by the Visual Immunoprecipitate assay (VIP®) and the U.S. Department of Agriculture/Food Safety and Inspection Service (USDA/FSIS) culture method for Listeria monocytogenes and related Listeria species. In all cases, naturally contaminated environmental test samples were collected from an actual food production facility by sponge or swab. Test samples from concrete surfaces were collected by both swab and sponge; sponge test samples were collected from rubber surfaces, and swabs were used to sample steel surfaces. Test portions from each surface type were simultaneously analyzed by both methods. A total of 27 laboratories, representing government agencies as well as private industry in both the United States and Canada, participated in the study. During this study, a total of 615 test portions and controls was analyzed and confirmed, of which 227 were positive and 378 were negative by both methods. Nine test portions were positive by culture, but negative by the VIP. Five test portions were negative by culture, but positive by the VIP. Four test portions were negative by VIP and by culture, but confirmed positive when VIP enrichment broths were subcultured to selective agars. The data reported here indicate that the VIP method and the USDA/FSIS culture method are statistically equivalent for detection of L. monocytogenes and related Listeria species from environmental surfaces taken by sponges or swabs.

Equivalence of Assurance® Gold Enzyme Immunoassay for Visual or Instrumental Detection of Motile and Nonmotile Salmonella in All Foods to AOAC Culture Method: Collaborative Study

Six foods representative of a wide variety of processed, dried powder processed, and raw food types were analyzed by the Assurance® Gold Salmonella Enzyme Immunoassay (EIA) and AOAC INTERNATIONAL culture method. Paired samples of each food type were simultaneously analyzed; one sample by the Assurance method and one by the AOAC culture method. The results for Assurance method were read visually and instrumentally with a microplate reader. A total of 24 laboratories representing federal government agencies and private industry, in the United States and Canada, participated in this collaborative study. Food types were inoculated with species of Salmonella with the exception of raw ground chicken, which was naturally contaminated. No statistical differences (p &lt; 0.05) were observed between Assurance Gold Salmonella EIA with either visual or instrumental interpretation and the AOAC culture method for any inoculation level of any food type or naturally contaminated food. The Assurance visual and instrumental options of reading sample reactions produced the same results for 1277 of the 1296 sample and controls analyzed.

Design Evaluation of a Novel Multicompartment Unloader Knee Brace

Knee osteoarthritis (OA) is a significant problem in the aging population, causing pain, impaired mobility, and decreased quality of life. Conservative treatment methods are necessary to reduce rapidly increasing rates of knee joint surgery. Recommended strategies include weight loss and knee bracing to unload knee joint forces. Although weight loss can be beneficial for joint unloading, knee OA patients often find it difficult to lose weight or begin exercise due to knee pain, and not all patients are overweight. Unicompartment offloader knee braces can redistribute joint forces away from one tibiofemoral (TF) compartment; however, <5% of patients have unicompartmental tibiofemoral osteoarthritis (TFOA), while patients with isolated patellofemoral or multicompartmental OA are much more common. By absorbing body weight (BW) and assisting the knee extension moment using a spring-loaded hinge, sufficiently powerful knee-extension-assist (KEA) braces could be useful for unloading the whole knee. This paper (1) describes the design of a spring-loaded tricompartment unloader (TCU) knee brace intended to provide unloading in all three compartments of the knee while weight-bearing, (2) measures and compares the force output of the TCU against the only published and commercially available KEA brace, and (3) calculates the static unloading capacity of each device. The TCU and KEA braces delivered maximum assistive moments equivalent to reducing BW by approximately 45 and 6 lbs, respectively. The paper concludes that sufficiently powerful spring-loaded knee braces show promise in a new class of multicompartment unloader knee orthoses, capable of providing a clinically meaningful unloading effect across all three knee compartments.

Histological stroke clot analysis after thrombectomy: Technical aspects and recommendations

The recent advent of endovascular procedures has created the unique opportunity to collect and analyze thrombi removed from cerebral arteries, instigating a novel subfield in stroke research. Insights into thrombus characteristics and composition could play an important role in ongoing efforts to improve acute ischemic stroke therapy. An increasing number of centers are collecting stroke thrombi. This paper aims at providing guiding information on thrombus handling, procedures, and analysis in order to facilitate and standardize this emerging research field.

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. We develop a workflow that uses machine learning to predict novel conserved protein-coding regions and efficiently guide their manual curation. We analyze more than 1000 high-scoring human PhyloCSF regions and confidently add 144 conserved protein-coding genes to the GENCODE gene set, as well as additional coding regions within 236 previously annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverged. The majority of these represent new discoveries, including 70 previously undetected protein-coding genes. The novel coding genes are additionally supported by single-nucleotide variant evidence indicative of continued purifying selection in the human lineage, coding-exon splicing evidence from new GENCODE transcripts using next-generation transcriptomic data sets, and mass spectrometry evidence of translation for several new genes. Our discoveries required simultaneous comparative annotation of other vertebrate genomes, which we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions. Our new coding regions help elucidate disease-associated regions by revealing that 118 GWAS variants previously thought to be noncoding are in fact protein altering. Altogether, our PhyloCSF data sets and algorithms will help researchers seeking to interpret these genomes, while our new annotations present exciting loci for further experimental characterization.

Safety in steep slope logging operations

Partial results of a NIOSH-funded study for "Protecting the Logging Workforce: Development of Innovative Logging Techniques for a Safer Work Environment" by a team of researchers at Oregon State University are presented that review safety in steep slope logging. Comparisons are made for hazards and exposures of "conventional" and new technologies for steep slopes. Hazards of new technologies are identified. Safety assessments are addressed for forestry sectors internationally, for the firm and for workers. Important questions of technical feasibility, economic viability and environmental performance are raised. Ongoing research on operators using tethered and untethered systems are described. Results will help inform training and selecting operators. New Best Operating Practices and safety code regulations will result from the research. New technologies will reduce worker hazards and exposures for steep slope logging.

Identification and Characterization of Novel Compounds Blocking Shiga Toxin Expression in Escherichia coli O157:H7

Infections caused by Shiga toxin (Stx)-producing E. coli strains constitute a health problem, as they are problematic to treat. Stx production is a key virulence factor associated with the pathogenicity of enterohaemorrhagic E. coli (EHEC) and can result in the development of haemolytic uremic syndrome in infected patients. The genes encoding Stx are located on temperate lysogenic phages integrated into the bacterial chromosome and expression of the toxin is generally coupled to phage induction through the SOS response. We aimed to find new compounds capable of blocking expression of Stx type 2 (Stx2) as this subtype of Stx is more strongly associated with human disease. High-throughput screening of a small-molecule library identified a lead compound that reduced Stx2 expression in a dose-dependent manner. We show that the optimized compound interferes with the SOS response by directly affecting the activity and oligomerization of RecA, thus limiting phage activation and Stx2 expression. Our work suggests that RecA is highly susceptible to inhibition and that targeting this protein is a viable approach to limiting production of Stx2 by EHEC. This type of approach has the potential to limit production and transfer of other phage induced and transduced determinants.

Hepatitis B and Hepatocellular Carcinoma Screening Practices in Chinese and African Immigrant-Rich Neighborhoods in New York City

BACKGROUND

Immigrants from China and Africa have high rates of hepatitis B virus infection (HBV) and hepatocellular carcinoma (HCC); however, primary care physician (PCP) adherence to screening guidelines in at-risk communities is not well understood.

METHODS

The New York City (NYC) neighborhood tabulation areas with the 25 greatest Chinese and African immigrant populations were determined based on US census data. The American Medical Association database was used to identify PCPs practicing in these neighborhoods. A Web-based survey designed to assess HBV and HCC knowledge and screening practices was distributed via e-mail to PCPs in these target areas.

RESULTS

A total of 2072 physicians were contacted, and 109 responded to the survey, for a response rate of 5.3 %. Among responding physicians, 73 % report routinely testing immigrant patients for HBV. However, if a patient tests positive for HBV, only 68 % of providers recommend screening for HCC. Over a quarter of PCPs (27 %), failed to correctly state that antiviral therapy can lower the risk of developing HCC, and only 56 % correctly replied that screening for liver cancer improves survival. Of responders, only 54 % answered correctly that a 25-year-old patient from Africa with HBV should be screened for HCC, whereas 53 % answered incorrectly that a 25-year-old patient from China with HBV should be screened, demonstrating a lack of awareness of the different age of onset of liver cancer in the two groups. The most commonly reported barrier to offering both HBV testing and HCC screening was a "lack of clear guidelines." Neither HBV nor HCC was among the top 3 health concerns of patients, as perceived by their physicians. There were no significant differences between provider responses in Chinese and African immigrant neighborhoods.

CONCLUSIONS

Providers serving Chinese and African immigrants in NYC often fail to recommend appropriate HBV and HCC screening. This appears to be due to significant gaps in provider knowledge and a lack of awareness of established screening guidelines. This study suggests the need for better distribution of existing guidelines to physicians serving immigrant-rich communities in order to improve HBV and HCC screening in high-risk individuals.

Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.

Ensembl comparative genomics resources

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.

Ensembl 2016

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

Re-engineering cellular physiology by rewiring high-level global regulatory genes

Knowledge of global regulatory networks has been exploited to rewire the gene control programmes of the model bacterium Salmonella enterica serovar Typhimurium. The product is an organism with competitive fitness that is superior to that of the wild type but tuneable under specific growth conditions. The paralogous hns and stpA global regulatory genes are located in distinct regions of the chromosome and control hundreds of target genes, many of which contribute to stress resistance. The locations of the hns and stpA open reading frames were exchanged reciprocally, each acquiring the transcription control signals of the other. The new strain had none of the compensatory mutations normally associated with alterations to hns expression in Salmonella; instead it displayed rescheduled expression of the stress and stationary phase sigma factor RpoS and its regulon. Thus the expression patterns of global regulators can be adjusted artificially to manipulate microbial physiology, creating a new and resilient organism.

Nutrition knowledge, diet quality and hypertension in a working population

OBJECTIVE

To examine if employees with higher nutrition knowledge have better diet quality and lower prevalence of hypertension.

METHOD

Cross-sectional baseline data were obtained from the complex workplace dietary intervention trial, the Food Choice at Work Study. Participants included 828 randomly selected employees (18-64 years) recruited from four multinational manufacturing workplaces in Ireland, 2013. A validated questionnaire assessed nutrition knowledge. Food Frequency Questionnaires (FFQ) measured diet quality from which a DASH (Dietary Approaches to Stop Hypertension) score was constructed. Standardised digital blood pressure monitors measured hypertension.

RESULTS

Nutrition knowledge was positively associated with diet quality after adjustment for age, gender, health status, lifestyle and socio-demographic characteristics. The odds of having a high DASH score (better diet quality) were 6 times higher in the highest nutrition knowledge group compared to the lowest group (OR = 5.8, 95% CI 3.5 to 9.6). Employees in the highest nutrition knowledge group were 60% less likely to be hypertensive compared to the lowest group (OR = 0.4, 95% CI 0.2 to 0.87). However, multivariate analyses were not consistent with a mediation effect of the DASH score on the association between nutrition knowledge and blood pressure.

CONCLUSION

Higher nutrition knowledge is associated with better diet quality and lower blood pressure but the inter-relationships between these variables are complex.

Ensembl 2015

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.

Pulmonary non-tuberculous mycobacteria in a general respiratory population

The prevalence of non-tuberculous mycobacterium (NTM) appears to be increasing. Much of the experience in the literature about this emerging organism comes from specialised units or populations such as cystic fibrosis patients. We, therefore, aim to evaluate the experience in a general respiratory population of dealing with patients with positive culture of NTM. We did a retrospective review of medical notes of general respiratory patients from whom NTM were isolated from January 2007 to July 2012. Cystic fibrosis patients were excluded. We reviewed 37 patients' (19 males, 18 females) medical records. A total of 73 positive cultures were reviewed. 28 isolates were from sputum samples alone, 34 isolates were from bronchoalveolar lavage alone and 11 isolates were from a combination of sputum and bronchoalveor lavage (11 isolates), We found that Mycobacterium avium was the most frequently isolated Mycobacterium in our laboratory with 22 (60%) patients had Mycobacterium avium in their pulmonary cultures. Interestingly, Mycobacterium gordonae and mycobacterium intracellulare were the second commonest mycobacterium (4, 11%) cultured. We noted 2 (5%), cases of Mycobacterium szulgai, 2 (5%) cases of Mycobacterium chelonae and 2 (5%) cases of Mycobacterium abscessus. There was 1(3%) case of Mycobacterium malmoense. There is prevalence of NTM in male COPD patients (7, 89%) and femal bronchiectasis (10, 77%) patients. Of our 8 COPD patients, 6 (75%) were on inhaled corticosteroids while 2 (25%) were not. 9 (24%) patients were smokers, 11 (30%) were ex-smokers, 14 (38%) were non-smokers and the smoking status of the remaining 3 (8%) was unknown. Of the 37 patients, only 6 (16%) received treatment. However, 2 patients stopped their treatment due to treatment toxicity. We concluded that the isolation of NTM is not uncommon. Defining NTM disease is difficult and deciding which patient to be treated needs careful evaluation as treatment can potentially be very toxic.

Investigation of the first outbreak of OXA-48-producing Klebsiella pneumoniae in Ireland

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) strains are encountered with increasing frequency in Europe. In November 2010 the European Centre for Disease Control (ECDC) graded Ireland as only having sporadic occurrence of CPE.

AIM

To describe the epidemiological and molecular typing analysis of the first outbreak of OXA-48-producing Klebsiella pneumoniae in an Irish tertiary care referral centre.

METHODS

Sixteen OXA-48-producing K. pneumoniae isolates were detected, from both clinical and screening specimens, and analysed by pulsed-field gel electrophoresis and by multi-locus sequence typing.

FINDINGS

Typing analysis revealed that two outbreak strains were circulating in the hospital, one among surgical patients and one among medical patients. The 'medical strain' ST13 had already been identified as an internationally disseminated clone, whereas the 'surgical strain' ST221 had not previously been reported as an OXA-48-carrying strain.

CONCLUSION

Although the outbreak on surgical wards was successfully controlled by implementing strict infection control measures, intermittent detection of individual patients carrying the 'medical strain' of OXA-48 K. pneumoniae has persisted since then. The experience from this outbreak suggests that OXA-48 K. pneumoniae is endemic at low level in the healthcare setting in the Dublin region.

Ensembl 2014

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

Ensembl 2013

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.