University of British Columbia

Author Of 3 Presentations

Biomarkers and Bioinformatics Poster Presentation

P0171 - The gut mycobiome in pediatric multiple sclerosis: establishing a bioinformatics pipeline (ID 876)

Speakers
Presentation Number
P0171
Presentation Topic
Biomarkers and Bioinformatics

Abstract

Background

Studies examining the role of the microbiota in multiple sclerosis (MS) often focus on the gut bacteria; few have considered a potential role of gut mycobiota. Methods for evaluating gut mycobiota are lacking and require systematic evaluation of sequencing protocols, reference databases, and bioinformatics pipelines to properly investigate possible gut mycobiome influences on MS.

Objectives

We set out to evaluate the performance of different sequencing conditions and analytical approaches for characterizing the gut mycobiome in a cohort of healthy individuals and cases with monophasic acquired demyelinating syndrome (mono ADS) or pediatric-onset MS.

Methods

We first assessed a mock-community control pool of known, staggered quantities of 19 defined fungal organisms. We then assessed 201 stool samples obtained from our cohort of 52 healthy individuals, 49 individuals with mono ADS, and 46 participants with pediatric-onset MS. The fungal internal transcribed spacer (ITS) 2 region was sequenced using the Illumina® MiSeq platform. Varying concentrations of PhiX Control v3 Library spike-in were tested to address low-complexity amplicon sequencing. Generated sequences were characterized by the UNITE database—a curated collection of eukaryotic ITS sequences—in conjunction with three distinct fungal sequence analysis pipelines: LotuS, mothur, and PIPITS.

Results

Taxa identified in our mock-community differed across sequencing conditions but were similar between technical replicates. LotuS correctly classified 7 taxa at species-level, 7 taxa at genus-level, whereas 5 remained unclassified. Mothur correctly identified 5 species-level taxa, 11 genus-level taxa, whereas 3 remained unclassified. Lastly, PIPITS correctly identified only 3 species-level taxa, 12 genus-level, while 4 remained unclassified. We successfully generated sequence data for 112 of 147 (76%) individuals (70 females; 42 males). The mean age at stool sample collection was 17.3 (SD 5.1) years. Of the tested sequencing conditions, a spike-in of 50% PhiX produced the highest-quality reads.

Conclusions

The LotuS pipeline best identified fungal taxa in our mock-community, with optimal resolution to species level. Sequencing read quality was optimal when 50% PhiX was used for sequencing ITS2 amplicon libraries of stool samples. Establishment of this validated sequencing pipeline, confirmed using a mock-community with known fungal identities, will aid characterization of gut mycobiomes for our cohort of individuals with/without pediatric-onset MS.

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Epidemiology Poster Presentation

P0443 - Characteristics of a population exposed to a disease-modifying drug for multiple sclerosis in the real-world setting (1996-2017) (ID 200)

Speakers
Presentation Number
P0443
Presentation Topic
Epidemiology

Abstract

Background

The efficacy of a disease-modifying drug (DMD) is typically established via brief clinical trials in highly selected groups. However, in clinical practice, DMDs are used for many years in a more diverse population of persons with multiple sclerosis (MS).

Objectives

The aim of the study was to describe the characteristics of a population with MS who are exposed to their first DMD in the real-world setting.

Methods

Using linked population-based health administrative data, we identified all individuals with MS aged 18 years who filled a prescription for a MS DMD in the province of British Columbia, Canada between 1996 and 2017. Individuals were followed from their first recorded demyelinating event to the earliest of death, emigration from the province, or study end (December 2017). We summarized cohort characteristics at their first filled DMD prescription (sex, age, socioeconomic status) and over the preceding year (comorbidity burden measured by the Charlson Comorbidity Index [CCI]).

Results

Overall, 4283 with MS filled a DMD prescription during the study period. Most were women (n=3132, 73%), with a mean (SD) age at the time of the first DMD prescription fill of 39.9 (9.9) years, and the socioeconomic status was distributed evenly across the income-based quintiles (neighborhood-level). Seventeen percent (n=741) had a CCI score 1. The most prevalent comorbidity was chronic pulmonary disease (n=235, 5%), followed by cerebrovascular disease (n=157, 4%) and diabetes (n=128, 3%). At the first DMD prescription fill, the proportion of women ranged from 63% (n=177/282) for dimethyl fumarate to 83% (n=15/18) for fingolimod. The mean (SD) age at first DMD prescription fill ranged from 37.2 (10.0) years for alemtuzumab to 43.0 (10.6) years for teriflunomide. Nearly 20% (n=724) were 50 years of age when they filled their first DMD prescription and 3% (n=108) were 60 years of age. From 1996-2012, the most common first DMD prescription filled was for either beta-interferon (n=2548/3190, 80%) or glatiramer acetate (n=612/3190, 19%). From 2013-2017, the most common first DMD prescription filled was for glatiramer acetate (n=379/1093, 35%), dimethyl fumarate (n=282/1093, 26%) or teriflunomide (n=182/1093, 17%).

Conclusions

Almost 1 in 5 persons with MS had at least some comorbidity at the time of initiation of their first DMD, while a minority were 60 years of age. As these individuals are often excluded from clinical trials, our data show an unmet need to understand the harms and benefits of DMD use in these understudied groups.

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Microbiome Poster Presentation

P0679 - The gut microbiota: a case-control study of children with multiple sclerosis, monophasic acquired demyelinating syndromes and unaffected controls (ID 102)

Abstract

Background

The gut microbiota may influence multiple sclerosis (MS) onset. Pediatric MS offers the opportunity to examine pathological processes close to risk acquisition.

Objectives

To examine the gut microbiota from stool samples of persons with pediatric onset MS, or monophasic acquired demyelinating syndromes (ADS) and unaffected controls in a case-control study.

Methods

Persons ≤21 years old with symptom onset <18 years of age with either MS (McDonald criteria) or ADS were eligible, as were unaffected controls with no known neurological or immune-mediated condition (migraine, asthma/allergies were permissible) were enrolled via the Canadian Pediatric Demyelinating Disease Network. Stools were collected between Nov/2015–Mar/2018, shipped on ice, and stored at -80°C. The 16S ribosomal RNA gene (V4 region) was amplified from extracted DNA and sequenced via the Illumina MiSeq platform. Amplicon sequence variants were used to compare the gut microbiota by disease status (MS/ADS/controls). The MS cases were also compared by disease-modifying drug (DMD) status (exposed/naïve). Negative binomial regression was used for genus-level analyses, with rate ratios adjusted (aRR) for age and sex.

Results

Of the 32/41/36 included MS/ADS/control participants, 24/23/21 were girls, averaging age 16.5/13.8/15.1 years at stool sample, respectively. The MS/ADS cases were 14.0/6.9 years at symptom onset. The 3 groups (MS/ADS/controls) were relatively similar for: body mass index (median: 22.8/19.7/19.9), presence of constipation (number of participants with a Bristol Stool Scale score of 1 or 2=8/9/7) and diet (% caloric intake for fat (median)=34/35/34 and for fibre (median)=9/10/11 g/day). Nine MS cases (28%) were DMD naïve. Gut microbiota diversity (alpha and beta) did not differ by disease (MS/ADS/controls), or DMD status (all p>0.1), while taxa-level findings did. For example, relative abundance of the Proteobacteria, Sutterella was depleted for MS cases vs controls and MS vs ADS cases (aRR:0.13;95%CI:0.03–0.59 and 0.21;95%CI:0.05–0.98), but did not differ for the ADS cases vs controls or by DMD status for the MS cases (all p>0.1). Several of the butyrate-producing genera within the Clostridia class (Firmicutes phylum) —Ruminococcaceae UCG−003, Lachnospiraceae UCG−008 and UCG−004—exhibited similar patterns.

Conclusions

Gut microbiota diversity was similar for individuals with pediatric MS relative to either monophasic ADS or unaffected controls. However, at the taxa-level, differences were observed which differentiated the MS cases from the monophasic ADS cases and controls.

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