Samir Méchaï

Function and Biography

I am an epidemiologist specializing in the study of emerging infectious diseases and health risk assessment in rural settings. My research focuses on the interactions among climate change, ecosystems, vectors, pathogens, and human populations. 

Before joining the Centre Ruralités durables at INRS, I worked as a research scientist at the National Microbiology Laboratory of the Public Health Agency of Canada (PHAC), within the Modelling Hub Division. There, I contributed to several national research and surveillance programs on vector-borne and zoonotic diseases, as well as projects involving genomics, metagenomics, phylogenomics, and emerging health risk assessment. 

My research aims to better understand the ecological, evolutionary, and environmental processes that drive the emergence, adaptation, and spread of infectious diseases. By integrating epidemiology, genomics, entomology, bioinformatics, and modelling, I seek to improve health risk assessment, support evidence-informed public health decision-making, and strengthen the resilience of communities and territories facing emerging health threats.

Scientific Activities

My research activities aim to improve our understanding of the ecological, environmental, evolutionary, and climatic determinants that influence the emergence, transmission, and spread of infectious diseases in rural environments. 

I am particularly interested in the evolutionary history of pathogens and the mechanisms underlying their diversification, adaptation, and dispersal across human, animal, and environmental systems. By reconstructing their origins, evolutionary trajectories, and transmission dynamics, my research contributes to a better understanding of emerging health risks in the context of environmental and climate change. 

My research program is organized around five complementary themes: 

• Epidemiology of vector-borne and zoonotic diseases; 

• Pathogen genomics, metagenomics, and phylogenomics; 

• Evolutionary history, diversification, and adaptation of pathogens; 

• Spatial modeling and health risk assessment; 

• Impacts of climate change on rural population health. 

My research also focuses on the development and application of innovative genomic approaches for the surveillance and study of emerging infectious diseases. Through projects investigating mosquito-borne disease surveillance in Canada, I explore the potential of DNA metabarcoding and metagenomics to simultaneously characterize vector communities and the pathogens they carry. These approaches enable the identification of mosquito species present in complex samples, the estimation of their relative abundance, and the improvement of our capacity to detect and characterize pathogens of public health importance. This work is conducted in collaboration with several federal and academic partners, including the Public Health Agency of Canada, the Canadian Food Inspection Agency, Agriculture and Agri-Food Canada, Environment and Climate Change Canada, the National Research Council Canada, and Carleton University (ECOBIOMICS and GRDI-7 projects). 

I am also interested in the functional organization and evolution of bacterial genomes through integrative approaches combining comparative genomics, phylogenomics, and network biology. My research on Borrelia burgdorferi, the causative agent of Lyme disease, seeks to understand how interactions among genes, proteins, and biological systems shape pathogen adaptation to vectors and hosts, as well as its evolutionary history and population genetic structure. By integrating protein-protein interaction networks, protein domain architecture, and evolutionary signatures, these studies identify mechanisms associated with strain diversification, host adaptation, and the emergence of new health risks. This work is conducted in collaboration with the Public Health Agency of Canada and the National Microbiology Laboratory, particularly through projects focused on whole-genome analyses of Borrelia burgdorferi. 

I am also interested in the ecology, diversity, and health significance of fly communities associated with livestock production systems through integrative approaches combining entomology, genomics, metagenomics, and the One Health framework. My research aims to better understand the composition of dipteran communities associated with sheep farms, their spatial and temporal dynamics, and their potential role as vectors or biological sentinels of veterinary and zoonotic pathogens. By integrating traditional taxonomic identification methods, DNA barcoding, environmental metabarcoding, targeted molecular detection, and metagenomic approaches, these studies characterize both fly communities and the microorganisms they carry, while improving our understanding of interactions among animals, pathogens, and the environment. This work contributes to the development of innovative biosurveillance tools and sustainable strategies for managing health risks in livestock systems. These projects will be conducted in collaboration with the Centre d’expertise en production ovine du Québec (CEPOQ) and the Faculty of Veterinary Medicine at the University of Montreal. 

These complementary research areas are integrated within a broader framework of genomic surveillance and health risk assessment aimed at understanding the interactions among pathogens, vectors, hosts, and the environment. 

I use a multidisciplinary approach combining epidemiology, genomics, metagenomics, applied entomology, bioinformatics, phylogenomics, and statistical modeling to investigate how interactions among vectors, hosts, pathogens, and environmental factors shape current and future health risks. My research aims to generate the knowledge required to anticipate emerging infectious disease threats, support evidence-based decision-making, and strengthen the resilience of rural communities facing environmental and climatic change.

Chairs, Groups, and Networks

I conduct my research within interdisciplinary networks involving academic, governmental, and international partners. These collaborations enable me to investigate emerging infectious diseases at the intersection of epidemiology, genomics, pathogen evolution, and health risk assessment in the context of environmental and climate change. 

My main research networks and affiliations include, the Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), the Pôle de recherche en épidémiologie des zoonoses et en santé publique (PRECRISA), the Canadian Food Animal Zoonotic Diseases Network (CFAZID), and the Modelling Hub Division of the Public Health Agency of Canada, where I worked as a research scientist at the National Microbiology Laboratory. 

I also collaborate with several federal organizations, including the Public Health Agency of Canada, Environment and Climate Change Canada, National Research Council Canada (NRC), and the Canadian Food Inspection Agency. Internationally, my collaborations include the National Reference Centre for Borrelia and the Bavarian Health and Food Safety Authority (Germany), as well as the Milner Centre for Evolution at the University of Bath (United Kingdom). 

My research contributes to initiatives that integrate One Health approaches, pathogen genomics and evolution, vector-borne disease surveillance, and the assessment of emerging health risks.

Publications and scientific contributions

My research has contributed to advancing knowledge on emerging infectious diseases, vector-borne diseases, and pathogen evolution. 

Among my main scientific contributions are: 

• Whole-genome characterization of Borrelia burgdorferi, the bacterium responsible for Lyme disease, providing new insights into its genetic diversity and evolutionary history in Canada; 

• Development and validation of metabarcoding approaches for the identification of medically important mosquito species and vector surveillance; 

• Development of metagenomic approaches for the detection and characterization of mosquito-borne pathogens; 

• Investigation of the genetic diversity, population structure, and evolution of tick-borne pathogens; 

• Contribution to the generation of genomic reference resources and open-access datasets for public health research. 

My findings have been published in international peer-reviewed journals and have contributed to improving our understanding of the genetic diversity, evolutionary history, and geographic distribution of Borrelia burgdorferi strains associated with Lyme disease. They have also demonstrated the potential of genomic and metagenomic approaches to transform vector and pathogen surveillance while providing new insights into the factors that influence the emergence of health risks in the context of environmental and climate change. 

Selected Publications 

1. Phylogeographic Structure ofBorrelia burgdorferiin Canada 

Complex population structure of Borrelia burgdorferi in southeastern and south-central Canada as revealed by phylogeographic analysis (Applied and Environmental Microbiology, 2015) 

This study characterized the genetic diversity of Borrelia burgdorferi in southeastern and south-central Canada using multilocus sequence typing (MLST). The analyses revealed a complex phylogeographic structure and identified several novel sequence types previously unknown in Canada. The findings suggest that this diversity is shaped by ecological processes associated with reservoir hosts and the geographic expansion of the tick Ixodes scapularis. The study was highlighted by the journal as an important contribution to understanding the emergence of Lyme disease in Canada. 

2. Landscape Connectivity and the Spread of Lyme Disease

Evidence for an effect of landscape connectivity on Borrelia burgdorferi sensu stricto dispersion in a zone of range expansion (Ticks and Tick-Borne Diseases, 2018) 

This work demonstrated that the dispersal of Borrelia burgdorferi strains is influenced by landscape connectivity and local ecological conditions. The analyses described the genetic landscape of the bacterium in an emerging region and established links between patterns of genetic diversity and the ecological processes shaping its spread. 

3. Whole-Genome Sequencing ofBorrelia burgdorferi

Whole-genome sequencing of Canadian Borrelia burgdorferi isolates (Scientific Reports, 2018) 

This publication generated the first comprehensive collection of whole-genome sequences from Canadian Borrelia burgdorferi isolates. The results confirmed and refined evolutionary relationships previously identified through MLST analyses while providing a valuable genomic resource for Lyme disease research in Canada. 

4. Genetic Landscape of Lyme Disease in Canada(Scientific Reports,2025) 

By integrating a large collection of isolates and genomic data, this study refined our understanding of the genetic structure and geographic distribution of Borrelia burgdorferi strains across Canada, providing a more comprehensive view of the genetic diversity associated with Lyme disease emergence. 

5. Mosquito Metabarcoding and Genomic Surveillance

Development and validation of a metabarcoding approach for mosquito identification from mixed samples (Journal of Medical Entomology, 2021) 

This study demonstrated that mosquito species can be accurately identified from mixed samples while simultaneously estimating their relative abundance. The work laid the methodological foundation for the GRDI-7 project, which aims to develop integrated genomic approaches capable of simultaneously identifying mosquito species and detecting the pathogens they carry from a single mixed sample. 

Teaching activities and service to the scientific community

I actively contribute to the training of future scientists through my involvement in graduate student evaluation and academic mentorship. I have served as a PhD comprehensive examination evaluator, a member of doctoral dissertation committees, and the chair of a master’s thesis defense committee at the Université de Montréal. 

I also contribute to the scientific community through peer review of manuscripts submitted to international journals in the fields of epidemiology, infectious diseases, genomics, and public health. 

Journals reviewed include:

• Scientific Reports (Springer Nature)
• PLOS ONE
• Emerging Infectious Diseases (CDC)
• Frontiers in Bioscience-Scholar
• Bulletin of Entomological Research
• Parasites & Vectors
• Ticks and Tick-Borne Diseases
• IEEE Journal of Translational Engineering in Health and Medicine