A cross-sectional study of MRI features and the gut microbiome in pediatric-onset multiple sclerosis

OBJECTIVE

To identify gut microbiome features associated with MRI lesion burden in persons with pediatric-onset multiple sclerosis (symptom onset <18 years).

METHODS

A cross-sectional study involving the Canadian Paediatric Demyelinating Disease Network study participants. Gut microbiome features (alpha diversity, phylum- and genus-level taxa) were derived using 16S rRNA sequencing from stool samples. T1- and T2-weighted lesion volumes were measured on brain MRI obtained within 6 months of stool sample procurement. Associations between the gut microbiota and MRI metrics (cube-root-transformed) were assessed using standard and Lasso regression models.

RESULTS

Thirty-four participants were included; mean ages at symptom onset and MRI were 15.1 and 19.0 years, respectively, and 79% were female. The T1- and T2-weighted lesion volumes were not significantly associated with alpha diversity (age and sex-adjusted p > 0.08). At the phylum level, high Tenericutes (relative abundance) was associated with higher T1 and T2 volumes (β coefficient = 0.25, 0.37) and high Firmicutes, Patescibacteria or Actinobacteria with lower lesion volumes (β coefficient = -0.30 to -0.07). At the genus level, high Ruminiclostridium, whereas low Coprococcus 3 and low Erysipelatoclostridium were associated with higher lesion volumes.

INTERPRETATION

Our study characterized the gut microbiota features associated with MRI lesion burden in pediatric-onset MS, shedding light onto possible pathophysiological mechanisms.

Cryptococcal laryngitis in an immunocompetent asthmatic patient using inhaled corticosteroids

We present a case of laryngeal cryptococcosis caused by cryptococcosis neoformans var. grubii affecting a patient using excessive inhaled corticosteroids. The patient experienced symptoms for several months prior to specialist review and the visualization of a mass lesion by nasopharyngoscopy. Fortunately a biopsy was performed and through histopathology & microbiological assessment a diagnosis of cryptococcal laryngitis was made. Treatment with 6 months of fluconazole resulted in clinical cure and resolution of symptoms. It is important to raise awareness of the risk of non-Candida fungal infections in patients on high dose corticosteroids, especially in the post covid era were steroids are more commonly prescribed.

Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach

BACKGROUND

The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users. In this study, we aimed to assess the performance of a foodborne pathogen (FBP)-specific reference database (taxon-specific) relative to a universal reference database (taxon-agnostic). We tested our FBP-specific reference database's performance for detecting Listeria monocytogenes in two complex food matrices-ready-to-eat (RTE) turkey deli meat and prepackaged spinach-using three popular read-based DNA-to-DNA metagenomic classifiers: Centrifuge, Kraken 2 and KrakenUniq.

RESULTS

In silico host sequence removal led to substantially fewer false positive (FP) classifications and higher classification precision in RTE turkey deli meat datasets using the FBP-specific reference database. No considerable improvement in classification precision was observed following host filtering for prepackaged spinach datasets and was likely a consequence of a higher microbe-to-host sequence ratio. All datasets classified with Centrifuge using the FBP-specific reference database had the lowest classification precision compared to Kraken 2 or KrakenUniq. When a confidence-scoring threshold was applied, a nearly equivalent precision to the universal reference database was achieved for Kraken 2 and KrakenUniq. Recall was high for both reference databases across all datasets and classifiers. Substantially fewer computational resources were required for metagenomics-based detection of L. monocytogenes using the FBP-specific reference database, especially when combined with Kraken 2.

CONCLUSIONS

A universal (taxon-agnostic) reference database is not essential for accurate and reliable metagenomics-based pathogen detection of L. monocytogenes in complex food matrices. Equivalent classification performance can be achieved using a taxon-specific reference database when the appropriate quality control measures, classification software, and analysis parameters are applied. This approach is less computationally demanding and more attainable for the broader scientific and food safety communities.

Proksee: in-depth characterization and visualization of bacterial genomes

Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, or GenBank format. Alternatively, users can supply a GenBank accession or a previously generated Proksee map in JSON format. Proksee then performs assembly (for raw sequence data), generates a graphical map, and provides an interface for customizing the map and launching further analysis jobs. Notable features of Proksee include unique and informative assembly metrics provided via a custom reference database of assemblies; a deeply integrated high-performance genome browser for viewing and comparing analysis results at individual base resolution (developed specifically for Proksee); an ever-growing list of embedded analysis tools whose results can be seamlessly added to the map or searched and explored in other formats; and the option to export graphical maps, analysis results, and log files for data sharing and research reproducibility. All these features are provided via a carefully designed multi-server cloud-based system that can easily scale to meet user demand and that ensures the web server is robust and responsive.

Monkeypox in Montréal: Epidemiology, Phylogenomics, and Public Health Response to a Large North American Outbreak

BACKGROUND

Monkeypox, a viral zoonotic disease, is causing a global outbreak outside of endemic areas.

OBJECTIVE

To characterize the outbreak of monkeypox in Montréal, the first large outbreak in North America.

DESIGN

Epidemiologic and laboratory surveillance data and a phylogenomic analysis were used to describe and place the outbreak in a global context.

SETTING

Montréal, Canada.

PATIENTS

Probable or confirmed cases of monkeypox.

MEASUREMENTS

Epidemiologic, clinical, and demographic data were aggregated. Whole-genome sequencing and phylogenetic analysis were performed for a set of outbreak sequences. The public health response and its evolution are described.

RESULTS

Up to 18 October 2022, a total of 402 cases of monkeypox were reported mostly among men who have sex with men (MSM), most of which were suspected to be acquired through sexual contact. All monkeypox genomes nested within the B.1 lineage. Montréal Public Health worked closely with the affected communities to control the outbreak, becoming the first jurisdiction to offer 1 dose of the Modified Vaccinia Ankara-Bavarian Nordic vaccine as preexposure prophylaxis (PrEP) to those at risk in early June 2022. Two peaks of cases were seen in early June and July (43 and 44 cases per week, respectively) followed by a decline toward near resolution of the outbreak in October. Reasons for the biphasic peak are not fully elucidated but may represent the tempo of vaccination and/or several factors related to transmission dynamics and case ascertainment.

LIMITATIONS

Clinical data are self-reported. Limited divergence among sequences limited genomic epidemiologic conclusions.

CONCLUSION

A large outbreak of monkeypox occurred in Montréal, primarily among MSM. Successful control of the outbreak rested on early and sustained engagement with the affected communities and rapid offer of PrEP vaccination to at-risk persons.

PRIMARY FUNDING SOURCE

None.

183 DEVELOPING AND FACILITATING ONLINE INTERGENERATIONAL CAFÉS

Background

Many older people throughout their lives will require nursing care, consequentially most nurses will care for older people during their career. It is important that older people and student nurses are provided with shared learning opportunities so that professional caring partnerships can be nurtured and realised for mutual benefit. Intergenerational projects offer opportunities for intergenerational learning. However, few projects explore student nurse-older person dyads and how these can be integrated within undergraduate pre-registration programmes. This paper describes the development and facilitation of online older person-student nurse intergenerational cafés.

Methods

The project was managed by a design team comprising senior administration, lecturers in BSc Nursing programmes and a lecturer in Design for Health and Wellbeing. The ‘world café’ concept along with values of enablement and participation underpinned the design. The initiative was planned to align with a year three community care module. Regular online team meetings were held to agree the aims and outcomes for student nurse-older person cohorts, decide recruitment strategies, agree the process and format of facilitation. Older people were recruited through retirement, church, volunteer, social and sporting organisations, media and also using snowballing methods.

Results

Both student nurse and older person cohorts were offered support on how to access and participate in the café. Participants attended one of three online cafés hosted through Microsoft Teams. Each café followed the same format: 1) Group meeting convened with all participants; 2) Breakout small group ‘table’ discussions with student nurse-older people participants and design team facilitation; 3) The café was reconvened to whole group meeting where feedback was collated to elicit shared learning.

Conclusion

The initiative proved successful and there is merit in embedding intergenerational cafés into professionally accredited health care programmes. Through sharing life experiences and perspectives, intergenerational barriers can be reduced and new insights developed on person-centred gerontological care.

Source of human milk (mother or donor) is more important than fortifier type (human or bovine) in shaping the preterm infant microbiome

Milk fortifiers help meet the nutritional needs of preterm infants receiving their mother’s own milk (MOM) or donor human milk. We conducted a randomized clinical trial (NCT03214822) in 30 very low birth weight premature neonates comparing bovine-derived human milk fortifier (BHMF) versus human-derived fortifier (H2MF). We found that fortifier type does not affect the overall microbiome, although H2MF infants were less often colonized by an unclassified member of Clostridiales Family XI. Secondary analyses show that MOM intake is strongly associated with weight gain and microbiota composition, including Bifidobacterium, Veillonella, and Propionibacterium enrichment. Finally, we show that while oxidative stress (urinary F2-isoprostanes) is not affected by fortifier type or MOM intake, fecal calprotectin is higher in H2MF infants and lower in those consuming more MOM. Overall, the source of human milk (mother versus donor) appears more important than the type of milk fortifier (human versus bovine) in shaping preterm infant gut microbiota.

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Milk fortifier type (human versus bovine) has little impact on the preterm microbiome

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Milk source (mother versus donor) is strongly associated with microbiome composition

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Feeding mother’s own milk is linked to better weight gain and less gut inflammation

Stability of the gut microbiota in persons with paediatric-onset multiple sclerosis and related demyelinating diseases

Objective:

Examine if the gut microbiota composition changes across repeated samples in paediatric-onset multiple sclerosis (MS) or monophasic-acquired demyelinating syndromes (monoADS).

Methods:

A total of 36 individuals (18 MS/18 monoADS) with ⩾2 stool samples were included. Stool sample-derived DNA was sequenced. Alpha/beta diversities and genus-level taxa were analysed.

Results:

Mean ages at first sample procurement (MS/monoADS) = 18.0/13.8 years. Median time (months) between first/second samples = 11.2 and second/third = 10.3. Alpha/beta diversities did not differ between stool samples (p > 0.09), while one genus – Solobacterium did (p = 0.001).

Conclusions:

The gut microbiota composition in paediatric-onset MS and monoADS exhibited stability, suggesting that single stool sample procurement is a reasonable first approach.

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

BACKGROUND AND OBJECTIVES

Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.

METHODS

Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha diversity, relative abundance, and prevalence using Wilcoxon rank sum, ALDEx2, and Fisher exact tests, respectively.

RESULTS

Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD-naive. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha diversity of enzymes and proteins did not differ by disease or DMD status (p > 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log₂ fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033).

DISCUSSION

The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.

The gut microbiota in pediatric multiple sclerosis and demyelinating syndromes

Objective

To examine the gut microbiota in individuals with and without pediatric‐onset multiple sclerosis (MS).

Methods

We compared stool‐derived microbiota of Canadian Pediatric Demyelinating Disease Network study participants ≤21 years old, with MS (disease‐modifying drug [DMD] exposed and naïve) or monophasic acquired demyelinating syndrome [monoADS] (symptom onset <18 years), and unaffected controls. All were ≥30 days without antibiotics or corticosteroids. V4 region 16S RNA gene‐derived amplicon sequence variants (Illumina MiSeq) were assessed using negative binomial regression and network analyses; rate ratios were age‐ and sex‐adjusted (aRR).

Results

Thirty‐two MS, 41 monoADS (symptom onset [mean] = 14.0 and 6.9 years) and 36 control participants were included; 75%/56%/58% were female, with mean ages at stool sample = 16.5/13.8/15.1 years, respectively. Nine MS cases (28%) were DMD‐naïve. Although microbiota diversity (alpha, beta) did not differ between participants (p > 0.1), taxa‐level and gut community networks did. MS (vs. monoADS) exhibited > fourfold higher relative abundance of the superphylum Patescibacteria (aRR = 4.2;95%CI:1.6–11.2, p = 0.004, Q = 0.01), and lower abundances of short‐chain fatty acid (SCFA)‐producing Lachnospiraceae (Anaerosporobacter) and Ruminococcaceae (p, Q < 0.05). DMD‐naïve MS cases were depleted for Clostridiales vadin‐BB60 (unnamed species) versus either DMD‐exposed, controls (p, Q < 0.01), or monoADS (p = 0.001, Q = 0.06) and exhibited altered community connectedness (p < 10⁻⁹ Kruskal–Wallis), with SCFA‐producing taxa underrepresented. Consistent taxa‐level findings from an independent US Network of Pediatric MS Centers case/control (n = 51/42) cohort included >eightfold higher abundance for Candidatus Stoquefichus and Tyzzerella (aRR = 8.8–12.8, p < 0.05) in MS cases and 72%–80% lower abundance of SCFA‐producing Ruminococcaceae‐NK4A214 (aRR = 0.38–0.2, p ≤ 0.01).

Interpretation

Gut microbiota community structure, function and connectivity, and not just individual taxa, are of likely importance in MS.

NSW Cannabis Medicines Advisory Service preliminary survey results - Enquirer perceptions and patient outcomes

Background

In 2018, an innovative, State government‐funded cannabis medicines drug information service was established for health professionals in New South Wales (NSW). The NSW Cannabis Medicines Advisory Service (CMAS) provides expert clinical guidance and support to medical practitioners considering prescribing a cannabis medicine to their patient(s).

Aims

This research examines quality assurance and patient outcomes related to enquirers' experience with NSW CMAS.

Methods

Data collection involved an online, anonymous survey with two components. Following a health professional enquiry, quality assurance data were collected about the enquirers' experience with NSW CMAS. The second survey focussed on patient outcomes and provides real‐world observational data about cannabis medicines safety and effectiveness across a wide range of indications.

Results

Data collection occurred between January 2020 and June 2021. Preliminary analyses were based on 68 quality assurance and 50 patient outcomes survey responses. General practitioners represented the highest proportion of survey responses (n = 33; 49%). The most common enquiry involved ‘patient‐specific advice’ (n = 50; 74%). Patient‐specific information provided by the service was mainly used for prescribing decision support (n = 45; 90%).

Conclusions

Preliminary findings highlight the impact of an innovative cannabis medicines drug information service in supporting health professional clinical practice in an area of rapid knowledge translation. Quality assurance data indicate that the service is perceived well by the majority of enquirers. Patient outcomes data across a wide range of indications suggest some effectiveness and a reasonable safety profile for prescribed cannabis medicines for most patients.

Trends in cardiovascular mortality of cancer patients in the US over two decades 1999–2019

Background

Cancer is the second most common cause of death globally after cardiovascular (CV) disease. The present study sought to compare the trends in CV mortality between patients with and without cancer in the US over two decades (1999 to 2019), stratified by sociodemographic factors such as age, sex and geographical location.

Methods

In this retrospective study, the number of deaths, crude- and age-adjusted mortality rates between January 1, 1999, and December 31, 2019, were obtained from the Centers for Disease Control and Prevention Wide-Ranging Online Data for Epidemiologic Research (CDC WONDER) data set

Results

We examined a total of 53,422,612 deaths between 1999 and 2019; of which 33.4% were defined as CV mortality and 25.6% had malignancy. During this period, among patients with cancer, the age-adjusted mortality rate dropped by 52%. (Vs, 38% in patients with no malignancy). CV mortality was highest in patients with gastrointestinal and prostate malignancy where CV mortality accounts together for over 40% of all CV mortality in patients with cancer in 1999 and 33.6% in 2019. The age-adjusted CV mortality rate (per 100,000 people) of patients with GI and prostate cancer nearly halved over twenty years from 2.7 to 1.0 and 2.5 to 1.0.

The CV age-adjusted mortality rate dropped more significantly among patients with gastrointestinal, breast, and prostate malignancy than among patients with hematological malignancy (59–63% vs. 41%. We observed that crude CV mortality rates amongst patients with cancer declined over the study period in all age groups but was more prominent among patients over 65 years old than those aged 55–64 and under 55 (51%-55% Vs. 41%, 25%, respectively).Similar reductions in mortality in men and women (54% and 53% reduction) were observed

During the study period the decline in cardiovascular mortality was more prominent in metro areas which led to lower age adjusted CV mortality in Metro compared to non-Metro areas (5.7–6.3 vs 7.2). The decline in age adjusted CV mortality in patients with cancer differed significantly in different states

Conclusions

In our temporal analysis we show a 50% decline in CV mortality in the US over two decades in both male and female patients with cancer, that has exceeded the reduction in CV mortality seen in the non-cancer population. The greatest reductions in CV mortality were observed in patients with GI, breast and prostate malignancies, those residing in metro areas and in patients aged 65 and over.

Funding Acknowledgement

Type of funding sources: None. CV death among cancer patients

Sugar prevalence in Aedes albopictus differs by habitat, sex and time of day on Masig Island, Torres Strait, Australia

Background

Sugar feeding is a fundamental behaviour of many mosquito species. For Aedes albopictus, an important vector of dengue virus and chikungunya virus, little is known about its sugar-feeding behaviour, and no studies have been conducted on this in the southern hemisphere. This knowledge is pivotal for determining the potential of attractive targeted sugar baits (ATSBs) to control this important vector.

Methods

The prevalence of sugar was assessed in 1808 Ae. albopictus from Masig Island, Torres Strait, Australia collected between 13 and 25 March 2020. Fructose presence and content in field-collected Ae. albopictus were quantified using the cold anthrone assay.

Results

Significantly more male (35.8%) than female (28.4%) Ae. albopictus were sugar fed. There was a significant interaction between sex and time of day on the probability of capturing sugar-fed Ae. albopictus. For both sexes, fructose prevalence and content were higher in mosquitoes caught in the morning than in the afternoon. Female Ae. albopictus collected in the residential habitat were significantly more likely to be sugar fed than those collected in the woodland habitat.

Conclusions

These findings provide baseline information about the sugar-feeding patterns of Ae. albopictus and provide essential information to enable an assessment of the potential of ATSBs for vector suppression and control on Masig Island, with relevance to other locations where this species occurs.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-05020-w.

Longitudinal evaluation of laboratory-based serological assays for SARS-CoV-2 antibody detection

Serological assays for SARS-CoV-2 infection are now widely available for use in diagnostic laboratories. Limited data are available on the performance characteristics in different settings, and at time periods remote from the initial infection. Validation of the Abbott (Architect SARS-CoV-2 IgG), DiaSorin (Liaison SARS-CoV-2 S1/S2 IgG) and Roche (Cobas Elecsys Anti-SARS-CoV-2) assays was undertaken utilising 217 serum samples from 131 participants up to 7 months following COVID-19 infection. The Abbott and DiaSorin assays were implemented into routine laboratory workflow, with outcomes reported for 2764 clinical specimens. Sensitivity and specificity were concordant with the range reported by the manufacturers for all assays. Sensitivity across the convalescent period was highest for the Roche at 95.2-100% (95% CI 81.0-100%), then the DiaSorin at 88.1-100% (95% CI 76.0-100%), followed by the Abbott 68.2-100% (95% CI 53.4-100%). Sensitivity of the Abbott assay fell from approximately 5 months; on this assay paired serum samples for 45 participants showed a significant drop in the signal-to-cut-off ratio and 10 sero-reversion events. When used in clinical practice, all samples testing positive by both DiaSorin and Abbott assays were confirmed as true positive results. In this low prevalence setting, despite high laboratory specificity, the positive predictive value of a single positive assay was low. Comprehensive validation of serological assays is necessary to determine the optimal assay for each diagnostic setting. In this low prevalence setting we found implementation of two assays with different antibody targets maximised sensitivity and specificity, with confirmatory testing necessary for any sample which was positive in only one assay.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn's Disease and Ulcerative Colitis

Background

In studies evaluating the microbiome, numerous factors can contribute to technical variability. These factors include DNA extraction methodology, sequencing protocols, and data analysis strategies. We sought to evaluate the impact these factors have on the results obtained when the sequence data are independently generated and analyzed by different laboratories.

Methods

To evaluate the effect of technical variability, we used human intestinal biopsy samples resected from individuals diagnosed with an inflammatory bowel disease (IBD), including Crohn’s disease (n = 12) and ulcerative colitis (n = 10), and those without IBD (n = 10). Matched samples from each participant were sent to three laboratories and studied using independent protocols for DNA extraction, library preparation, targeted-amplicon sequencing of a 16S rRNA gene hypervariable region, and processing of sequence data. We looked at two measures of interest – Bray–Curtis PERMANOVA R² values and log2 fold-change estimates of the 25 most-abundant taxa – to assess variation in the results produced by each laboratory, as well the relative contribution to variation from the different extraction, sequencing, and analysis steps used to generate these measures.

Results

The R² values and estimated differential abundance associated with diagnosis were consistent across datasets that used different DNA extraction and sequencing protocols, and within datasets that pooled samples from multiple protocols; however, variability in bioinformatic processing of sequence data led to changes in R² values and inconsistencies in taxonomic assignment and abundance estimates.

Conclusion

Although the contribution of DNA extraction and sequencing methods to variability were observable, we find that results can be robust to the various extraction and sequencing approaches used in our study. Differences in data processing methods have a larger impact on results, making comparison among studies less reliable and the combined analysis of bioinformatically processed samples nearly impossible. Our results highlight the importance of making raw sequence data available to facilitate combined and comparative analyses of published studies using common data processing protocols. Study methodologies should provide detailed data processing methods for validation, interpretability, reproducibility, and comparability.

The SLAC RCE Platform for ProtoDUNE

The ProtoDUNE-SP is a single-phase liquid argon time projection chamber (LArTPC) prototype for the Deep Underground Neutrino Experiment (DUNE). Signals from 15,360 electronic channels are received by 60 Reconfigurable Cluster Elements (RCEs), which are processing elements designed at SLAC for a wide range of applications and are based upon the “system-onchip” Xilinx Zynq family of FPGAs. The RCEs are housed in industry-standard ATCA shelves on a custom blade, called the Cluster on Board (COB). The RCE platform and its processing functions for the ProtoDUNE-SP will be presented.

The evolving nature of Bordetella pertussis in Ontario, Canada, 2009-2017: strains with shifting genotypes and pertactin deficiency

This study examined the evolving nature of Bordetella pertussis in Ontario, Canada, by characterizing isolates for their genotypes and expression of pertactin (PRN). From 2009 to 2017, 413 B. pertussis were cultured from pertussis cases at the Public Health Ontario Laboratory. Their genotypes were determined by partial gene sequence analysis of their virulence and (or) vaccine antigens: filamentous haemagglutinin, PRN, fimbriae 3, and pertussis toxin, including the promoter region. Expression of PRN was measured by Western immunoblot. Two predominant genotypes, ST-1 and ST-2, were found throughout the study and were responsible for 47.5% and 46.3% of all case isolates, respectively. The prevalence of ST-1 appeared to fluctuate from 80.3% in 2009 to 20.0% in 2014 and 58.5% in 2017, while the prevalence of ST-2 changed from 18.4% in 2009 to 80.0% in 2014 and 26.2% in 2017. A PRN-deficient strain was first noted in 2011 (16.7%), and its prevalence increased to 70.8% in 2016 but decreased to 46.2% in 2017. More ST-2 (46.6%) than ST-1 (16.8%) strains were associated with PRN deficiency. Newer ST-21 and ST-22 found in 2015-2017 were uniformly PRN deficient. The impact of the evolving nature of B. pertussis on disease epidemiology requires further longitudinal studies.

A comparison of four risk models for the prediction of cardiovascular complications in patients with a history of atrial fibrillation undergoing non-cardiac surgery

It is unclear how best to predict peri-operative cardiovascular risk in patients with atrial fibrillation undergoing non-cardiac surgery. This study examined the accuracy of the revised cardiac risk index and three atrial fibrillation thrombo-embolic risk models for predicting 30-day cardiovascular events after non-cardiac surgery in patients with a pre-operative history of atrial fibrillation. We conducted a prospective cohort study in 28 centres from 2007 to 2013 of 40,004 patients ≥ 45 years of age undergoing inpatient non-cardiac surgery who were followed until 30 days after surgery for cardiovascular events (defined as myocardial injury, heart failure, stroke, resuscitated cardiac arrest or cardiovascular death). The 2088 patients with a pre-operative history of atrial fibrillation were at higher risk of peri-operative cardiovascular events compared with the 34,830 patients without a history of atrial fibrillation (29% vs. 13%, respectively, adjusted odds ratio 1.30 (95%CI 1.17-1.45). Compared with the revised cardiac risk index (c-index 0.60), all atrial fibrillation thrombo-embolic risk scores were significantly better at predicting peri-operative cardiovascular events: CHADS₂ (c-index 0.62); CHA₂ DS₂ -VASc (c-index 0.63); and R₂ CHADS₂ (c-index 0.65), respectively. Although the three thrombo-embolic risk prediction models were significantly better than the revised cardiac risk index for prediction of peri-operative cardiovascular events, none of the four models exhibited strong discrimination metrics. There remains a need to develop a better peri-operative risk prediction model.

Lesion distribution in cases of canine atopic dermatitis in South Australia

OBJECTIVE

To determine the lesion distribution patterns in different breeds of dogs affected by atopic dermatitis in South Australia.

METHODS

The presence or absence of erythematous skin lesions in 267 cases of canine atopic dermatitis (CAD) was recorded across 36 anatomical sites. Breeds represented by ≥ 9 dogs were included in the analysis. The percentage of dogs showing lesions at each of the body sites was calculated and illustrated on colour-coded diagrams. Variations in affected body sites within and between breeds were compared using Kruskal-Wallis ANOVA and Dunn's multiple comparison tests.

RESULTS

The prevalence of skin lesions at different body sites differed significantly both in the population as a whole and within breeds. The sites affected in ≥ 75% dogs were the dorsal and ventral aspects of the front and hind paws. The sites affected in 50-74% were the medial pinnae, axillae, ventral chest, abdomen and perineum. Sites affected in 25-49% of dogs included the face, periocular region and forelimb. Remaining body sites were affected in < 25% of dogs. Analysis at the breed level revealed some differences from this standard distribution pattern.

CONCLUSION

The results of this study confirmed the typical lesion distributions seen in CAD and highlighted some subtle differences in breeds commonly seen in South Australia. This will be useful for clinical practitioners in prioritising differential diagnoses for pruritic skin conditions.

Septic pericarditis and pericardial abscess secondary to a migrating foreign body in a dog

Abscess formation in the pericardial space has been described as a rare complication of trauma, congenital defects, penetrating foreign body, or extension of local myocardial infection in the dog. Presented here is a case of a juvenile dog with septic pericardial effusion secondary to an isolated intrapericardial abscess. Surgical pericardiectomy was successful in removing the abscess and nidus for septic effusion in this patient, and histopathology of the abscess tissue was suggestive of foreign plant material migration as the nidus for abscess formation. Recheck echocardiogram at the six-month postoperative period showed no recurrence of pericardial effusion or abscessation. Although abscess formation and septic pericarditis secondary to foreign body migration is an uncommon cause for large volume pericardial effusion, this should be considered as a differential particularly in a young and previously healthy dog.

Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria

The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.

Whole genome sequencing and phylogenetic analysis of strains of the agent of Lyme disease Borrelia burgdorferi from Canadian emergence zones

Lyme disease is emerging in southern Canada due to range expansion of the tick vector, followed by invasion of the agent of Lyme disease Borrelia burgdorferi sensu stricto. Strain diversity, as determined by Multi Locus Sequence Typing, occurs in this zone of emergence, and this may have its origins in adaptation to ecological niches, and have phenotypic consequences for pathogenicity and serological test performance. Sixty-four unique strains were cultured from ticks collected in southern Canada and the genomes sequenced using the Illumina MiSeq platform. A maximum likelihood phylogenetic tree of the chromosome revealed two large clades with multiple subclades. Consistent with previous studies on this species, the clades were not geographically defined, and some Canadian strains were highly divergent from previously sequenced US strains. There was evidence for recombination in the chromosome but this did not affect the phylogeny. Analysis of chromosomal genes indicated that these are under intense purifying selection. Phylogenies of the accessory genome and chromosome were congruent. Therefore strain differences identified in the phylogeny of chromosomal genes likely act as a proxy for genetic determinants of phenotypic differences amongst strains that are harboured in the accessory genome. Further studies on health implications of strain diversity are needed.

Nanoencapsulation of phase change materials for advanced thermal energy storage systems

Phase change materials (PCMs) allow the storage of large amounts of latent heat during phase transition. They have the potential to both increase the efficiency of renewable energies such as solar power through storage of excess energy, which can be used at times of peak demand; and to reduce overall energy demand through passive thermal regulation. 198.3 million tons of oil equivalent were used in the EU in 2013 for heating. However, bulk PCMs are not suitable for use without prior encapsulation. Encapsulation in a shell material provides benefits such as protection of the PCM from the external environment and increased specific surface area to improve heat transfer. This review highlights techniques for the encapsulation of both organic and inorganic PCMs, paying particular attention to nanoencapsulation (capsules with sizes <1 μm). We also provide insight on future research, which should focus on (i) the development of multifunctional shell materials to improve lifespan and thermal properties and (ii) advanced mass manufacturing techniques for the economically viable production of PCM capsules, making it possible to utilize waste heat in intelligent passive thermal regulation systems, employing controlled, "on demand" energy release/uptake.

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance

Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called “contextual data”) to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment. However, current multi-jurisdictional pathogen surveillance and investigation efforts are complicated by time-consuming data re-entry, curation and integration of contextual information owing to a lack of interoperable standards and inconsistent reporting. A solution to these challenges is the use of ‘ontologies’ - hierarchies of well-defined and standardized vocabularies interconnected by logical relationships. Terms are specified by universal IDs enabling integration into highly regulated areas and multi-sector sharing (e.g., food and water microbiology with the veterinary sector). Institution-specific terms can be mapped to a given standard at different levels of granularity, maximizing comparability of contextual information according to jurisdictional policies. Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation. Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well as existing food resources. These efforts are supported by a global consortium of researchers and stakeholders worldwide. Since foodborne diseases do not respect international borders, uptake of such vocabularies will be crucial for multi-jurisdictional interpretation of WGS results and data sharing.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology

The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is a bioinformatics pipeline for identifying high-quality single-nucleotide variants (SNVs) and constructing a whole-genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity, and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. SNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.

Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing

Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13) in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD) has declined from 55% (n = 1492) in 2010 to 31% (n = 764) in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183) to 11% (n = 283). Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005-2015. Six phylogenetic lineages (n = 117) were identified among a serotype 22F/ST433 clonal complex (CC), including a recently expanding erythromycin-resistant clone. Erythromycin-resistance was observed in 25 isolates possessing ermB, mef or a 23S rRNA A2061G point mutation; 2 penicillin-resistant isolates had recombinant pbp1a, pbp2a and/or pbp2x; 3 tetracycline-resistant isolates contained tetM; and 1 isolate was multidrug-resistant. Virulence factor analysis indicated a high level of homogeneity among the 22F/ST433 clonal complex strains. A group of 6 phylogenetic outlier strains had differing MLST, antimicrobial resistance and molecular profiles suggestive of capsule switching events. While capsule switch events among S. pneumoniae serotype 22F has been observed, increasing prevalence of S. pneumoniae serotype 22F can be attributed to an evolving homogenous clone expanding nationally through local transmission events.

A randomized trial to determine the impact of a digestion resistant starch composition on the gut microbiome in older and mid-age adults

BACKGROUND

The elderly often have a diet lacking resistant starch (RS) which is thought to lead to gut microbiome dysbiosis that may result in deterioration of gut colonocytes.

OBJECTIVE

The primary objective was to assess if elderly (ELD; ≥ 70 years age) had microbiome dysbiosis compared to mid-age (MID; 30-50 years age) adults and then determine the impact of daily consumption of MSPrebiotic^® (a RS) or placebo over 3 months on gut microbiome composition. Secondary objectives included assessment of stool short-chain fatty acids (SCFA) and inflammatory markers in ELD and MID Canadian adults.

DESIGN

This was a prospective, placebo controlled, randomized, double-blinded study. Stool was collected at enrollment and 6, 10 and 14 weeks after randomization to placebo or MSPrebiotic^®. Microbiome analysis was done using 16S rRNA sequencing of DNA extracted from stool. SCFA analysis of stool was performed using gas chromatography.

RESULTS

There were 42 ELD and 42 MID participants randomized to either placebo or MSPrebiotic^® who completed the study. There was significantly higher abundance of Proteobacteria (Escherichia coli/Shigella) in ELD compared to MID at enrollment (p < 0.001) that was not observed after 12 weeks of MSPrebiotic^® consumption. There was a significant increase in Bifidobacterium in both ELD and MID compared to placebo (p = 0.047 and 0.006, respectively). There was a small but significant increase in the stool SCFA butyrate levels in the ELD on MSPrebiotic^® versus placebo.

CONCLUSIONS

The study data demonstrated that MSPrebiotic^® meets the criteria of a prebiotic and can stimulate an increased abundance of endogenous Bifidobacteria in both ELD and MID without additional probiotic supplementation. MSPrebiotic^® consumption also eliminated the dysbiosis of gut Proteobacteria observed in ELD at baseline.

CLINICAL TRIAL REGISTRY NUMBER

NCT01977183 listed on NIH website: ClinicalTrials.gov. The full trial protocol is available on request from the corresponding author.

NUCLEOTIDE SEQUENCE ACCESSION NUMBERS

The 16S rRNA sequencing data and metadata generated in this study have been submitted to the NCBI Sequence Read Archive (SRA: http://www.ncbi.nlm.nih.gov/bioproject/381931).

PABPN1 gene therapy for oculopharyngeal muscular dystrophy

Oculopharyngeal muscular dystrophy (OPMD) is an autosomal dominant, late-onset muscle disorder characterized by ptosis, swallowing difficulties, proximal limb weakness and nuclear aggregates in skeletal muscles. OPMD is caused by a trinucleotide repeat expansion in the PABPN1 gene that results in an N-terminal expanded polyalanine tract in polyA-binding protein nuclear 1 (PABPN1). Here we show that the treatment of a mouse model of OPMD with an adeno-associated virus-based gene therapy combining complete knockdown of endogenous PABPN1 and its replacement by a wild-type PABPN1 substantially reduces the amount of insoluble aggregates, decreases muscle fibrosis, reverts muscle strength to the level of healthy muscles and normalizes the muscle transcriptome. The efficacy of the combined treatment is further confirmed in cells derived from OPMD patients. These results pave the way towards a gene replacement approach for OPMD treatment.

Oculopharyngeal muscular dystrophy is caused by trinucleotide repeat expansions in the PABPN1 gene. Here the authors use AAV-based gene therapy to knockdown the mutant gene and replace it with a wild-type allele, and show effectiveness in mice and in patient cells.

Abstract OT3-04-01: BRE12-158: A phase II randomized controlled trial of genomically directed therapy after preoperative chemotherapy in patients with triple negative breast cancer (TNBC)

Background: About 1/3 of patients with TNBC who receive preoperative therapy will experience a pathological complete response (pCR). Patients with residual disease have a markedly inferior overall survival (OS) compared to those who experience pCR. Recently, the CREATE-X trial demonstrated an improvement in disease free survival (DFS) and OS for post-neoadjuvant capecitebine; although the addition of capecitebine to standard therapy has not previously improved outcome across other non-selected adjuvant or neo-adjuvant trials. Prior data have also demonstrated that the residual tumors are genomically diverse and that these genetic changes are reflected at time of relapse.

Trial Design: This trial is a randomized phase II trial to determine whether a genomically guided therapy in the setting of incomplete response to standard neoadjuvant therapy will improve outcomes compared to standard of care. DNA from archived tumor samples collected at the time of surgery will be extracted and sequenced. The sequencing data will be interrogated for known genomic drivers of sensitivity or resistance to existing FDA approved agents. A cancer genomic tumor board (CGTB) will consider the genomic data along with the patient's prior treatment history, toxicities, and comorbidities and select the optimal therapy. Participants with a CGTB recommendation will be randomized to Experimental Arm A (genomically directed monotherapy) or Control Arm B (standard of care). Participants may have no CGTB recommendation either because sequencing did not identify a matched drug or because the drug was contraindicated and will be assigned to Control Arm B.

Eligibility criteria: Patients must have histologically confirmed TNBC with completion of all definitive local therapy and no evidence of metastatic disease. There must be significant residual disease characterized by &gt;2cm primary tumor, or lymph node positivity or RCB classification II or III. An FFPE tumor block with tumor cellularity &gt;20% is required. All patients must have completed preoperative chemotherapy including a taxane or anthracycline or both.

Specific aims: The Primary Aim is to compare 2-year DFS with a genomically directed therapy vs. standard of care. Secondary Aims include 1-year DFS, 5-year OS, collection of archival specimens for correlative studies, and to describe toxicities. Exploratory Aims are to describe the evolution of genomically directed therapies during the course of the study and to evaluate the drug specific effect on efficacy and toxicity.

Statistical methods: In order to detect an improvement in the fraction of patients free from disease at 2-year from 40% in the control Arm B to 63.2% in the genomically directed Experimental Arm A (corresponding to an HR=0.5), 136 participants will have 80% power to detect a difference in DFS using a two-side log-rank test with 0.05 level of significance.

Present accrual/target accrual: 38 accrued of 136 to be randomized.

Citation Format: Schneider B, Miller KD, Badve S, O'Neil B, Helft P, Chitambar C, Falkson C, Nanda R, McCormick M, Danso M, Blaya M, Langdon R, Lippman M, Paplomata E, Walling R, Thompson M, Robin E, Aggarwal L, Shalaby I, Canfield V, Adesunloye B, Lee T, Daily K, Ma C, Erban J, Radhakrishnan N, Bruetman D, Graham M, Reddy NA, Lynce FC, Radovich M. BRE12-158: A phase II randomized controlled trial of genomically directed therapy after preoperative chemotherapy in patients with triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-04-01.

The prediction of postoperative stroke or death in patients with preoperative atrial fibrillation undergoing non-cardiac surgery: a VISION sub-study

BACKGROUND

The optimal means of pre-operative risk stratification in patients with atrial fibrillation (AF) is uncertain.

OBJECTIVE

To examine the accuracy of AF thromboembolic risk models (the CHADS2, CHA2DS2-VASc, and R2CHADS2 scores) for predicting 30-day stroke and/or all-cause mortality after non-cardiac surgery in patients with preoperative AF, and to compare these risk scores with the Revised Cardiac Risk Index (RCRI).

PATIENTS/METHODS

A multicentre (8 countries, 2007-2011) prospective cohort study of patients ≥ 45 years of age undergoing inpatient non-cardiac surgery, who were followed until 30 days after surgery. We calculated c-statistics for each risk prediction model and net reclassification improvements (NRIs) compared with the RCRI.

RESULTS

The 961 patients with preoperative AF were at higher risk of any cardiovascular event in the 30 days postoperatively compared with the 13 001 patients without AF: 26.6% vs. 9.0%; adjusted odds ratio, 1.58; 95% confidence interval [CI], 1.33-1.88. All thromboembolic risk scores predicted postoperative death just as well as the RCRI (with c-indices between 0.67 and 0.72). Compared with the RCRI (which had a c-index of 0.64 for 30-day stroke/death), the CHADS2 (c-index, 0.67; NRI, 0.31; 95% CI, 0.02-0.61) significantly improved postoperative stroke/mortality risk prediction, largely due to improved discrimination of patients who did not subsequently have an event.

CONCLUSIONS

In AF patients, the three thromboembolic risk scores performed similarly to the RCRI in predicting death within 30 days and the CHADS2 score was the best predictor of postoperative stroke/death regardless of type of surgery.