Title
The role of the environment in the dynamics and evolution of microbial populations
Abstract
Pneumococcal disease (PD) is a major driver of meningitis and bacteremia globally. PD epidemiology is characterized by seasonal spikes in disease with evidence for increased rates of disease in winter months. The precise environmental drivers and biological mechanisms of environment-PD interactions are poorly characterised. Here we work to disentangle these disease drivers and their mechanisms. We included >4000 pneumococcal genomes (causing disease) matched with patient metadata from 2005-2020 in South Africa. We harmonize this with meteorological and air quality models and data. We use Bayesian hierarchical space-time models to identify environmental drivers of disease accounting for underlying genomic diversity. We include lag times for the environmental effects and bacterial genome-environment interactions. We then explore signatures of environmental selection among the microbial population using a range of methods including an elastic net (predicting gene presence given the environment) and genome wide association studies (with particulate matter concentration as the phenotype). We find variability in seasonal magnitude, timing, and the importance of particular environmental factors between lineages – also varying by geographic region. The performance of models with different lag times help elucidate the affected epidemiological stage of carriage, transmission, or disease. We identify several genes which appear to be predictable by environmental factors. Further validation and exploration of these methods is ongoing.
Bio
Dr. Sophie Belman is a Schmidt Science Fellow in the Global Health Resilience group at the Barcelona Supercomputing Center in Barcelona Spain. Her current research focus is towards understanding the impact of our environment (air quality and meteorological datasets) in bacterial respiratory disease dynamics and evolution. She was previously at the Wellcome Sanger Institute,UK and the University of Cambridge, UK where she leveraged microbial genomic data together with human mobility and other data types to quantify the extent and mechanisms of long range microbial transmission. She is visiting the Oslo Center of Biostatistics and Epidemiology to explore a range of different methods towards identifying genomic signatures of environmental selection.
Speaker is presenting in person.
Practical
This seminar is organised by Integreat research theme (3) Scalable Approximation of Models and Algorithms and Department of Mathematics, statistics section, as part of the seminar series in Statistics and Data Science.
The Tuesday seminar series explores a wide range of topics relevant to our research themes. Each week, invited researchers present for 40 minutes, followed by a group discussion.
Seminars are open for attendance for everybody.
For those unable to attend in person: https://uio.zoom.us/j/62535744013
Point of contacts:
- Organisers and moderators: Geir Storvik and Jukka Corander, University of Oslo
- Integreat Administrative Leader Maria Dikova, University of Oslo