US CDC
Division of Bacterial Diseases

Moderator Of 2 Sessions

Workshop 02: Tools for Genomic Data Analysis and Visualisation

Session Type
On-site Pre-Symposium Workshop
Date
Sun, 19.06.2022
Session Time
09:00 - 16:00
Room
Grand Ballroom West
Session Description
A highly interactive hands-on workshop that aims for you to understand the basic principles of WGS strain characterization and subsequent typing analysis and data visualization. During the workshop, participants will be able to upload genomic sequences to local and web-based platforms and use analysis tools to characterize, visualize, and explore genomic data with metadata variables.
Target audience: Public health professionals, clinicians and researchers

Please note: All ISPPD-12 Workshops are highly interactive and designed to allow at least 25% active learning for the maximum registrants anticipated.
Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Session Description
Please note: Each presentation is followed by about 3 minutes of Q&A. The audience is encouraged to send questions to the speakers from the beginning of their presentations. Q&A time is included in each speaker’s presentation duration, accounting for at least 25% active learning for the maximum registrants anticipated.

Presenter Of 1 Presentation

O037 - BACTERIAL MUTATIONS ASSOCIATED WITH MENINGITIS AMONG INVASIVE PNEUMOCOCCAL DISEASE PATIENTS, USA, 2016-2019 (ID 252)

Session Type
Parallel Session
Date
Tue, 21.06.2022
Session Time
14:50 - 16:20
Room
Grand Ballroom West
Lecture Time
15:05 - 15:15

Abstract

Background

Previous studies have identified several pneumococcal gene mutations that disproportionally affect meningitis patients. Here we aim to confirm previously reported associations and identify additional genes linked to meningitis.

Methods

Non-synonymous mutations in previously reported candidate genes, including pbp1B, pspC, zmpB, and pde1, were determined by whole genome sequencing. The association between a candidate mutation and syndrome (meningitis vs. non-meningitis) was evaluated using a linear mixed-effects model (LMM), implemented in the FaST-LMM software, to control for population structure. All k-mers of length 15 were identified from draft genome assemblies. The k-mers present in >5% but <95% of isolates, representing common variants, were evaluated for association with meningitis using LMM.

Results

Of the 11,015 invasive pneumococcal isolates identified in 2016-2019, 763 (7%) were cultured from meningitis patients. Compared to non-meningitis isolates, meningitis isolates had a higher proportion of pbp1B641C (21% vs. 10%), pspC1360A (34% vs. 31%), and zmpB638A (5% vs. 2%) variants. After controlling for population structure, each of the three variants was significantly associated with meningitis (p<0.05). LMM analysis on 2,083,856 k-mers estimated a heritability (h2) of 0.08. K-mers that showed genome-wide significant association (p<1×10-8) with meningitis were identified in genes encoding ABC transporter ATP-binding protein (H020_RS0107080), AraC family transcriptional regulator (H020_RS0107070), and bacteriocin-associated integral membrane family protein (H020_RS0100550), among others.

Conclusions

The pneumococcal genome explained a modest amount of variation in clinical manifestations (meningitis vs. non-meningitis), although a larger proportion of such variation could be due to host and host-pathogen interactions. Further depiction of underlying mechanisms could help better understand bacterial pathogenesis.

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