Latest work
Emerging AMR Campylobacter in LMICs
Attributing the source of Campylobacter infections
Attributing the source of Campylobacter infections
Cooper et al (2024)
Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter in the Peruvian Amazon
mBio
Attributing the source of Campylobacter infections
Attributing the source of Campylobacter infections
Attributing the source of Campylobacter infections
Pascoe et al (2024)
Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data
Journal of Infection
Asymptomatic carriage of Campylobacter
Attributing the source of Campylobacter infections
Asymptomatic carriage of Campylobacter
Schiaffino & Colson et al
(2024)
The epidemiology and impact of persistent Campylobacter infections on childhood growth
The Lancet Discovery Science
Zoonotic transfer of AMR
Attributing the source of Campylobacter infections
Asymptomatic carriage of Campylobacter
Mourkas & Valdebenito et al
(2024)
Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes
Current Biology
research themes
Global pathogen genomics
Our research tackles some of the world’s most pressing health issues, focusing on diseases that disproportionately impact low- and middle-income countries (LMICs). Diarrheal disease, for example, is the second leading cause of death among children under five in these regions. By combining expertise in microbiology, genomics, and systems biology, we aim to better understand how these diseases spread, persist, and cause harm.
Current Focus Areas: We collaborate with partners across South America, West Africa, and Southeast Asia to fill critical gaps in our understanding of local disease dynamics, particularly in regions where data is scarce.
The evolution and spread of AMR
A Growing Global Threat: Antimicrobial resistance (AMR) in gut infections poses a major challenge to effective treatment. Our team has identified novel genetic mechanisms behind resistance to key antibiotics used in LMICs, including macrolides and fluoroquinolones. These discoveries are vital for shaping future treatment strategies.
The Bigger Picture: Resistance evolves differently depending on the mechanism—sometimes through subtle genetic mutations, and other times through the transfer of entire resistance genes between species. Our work explores these dynamics, aiming to prevent the spread of resistance through the food chain.
Current Efforts: We are investigating how resistance develops in pathogens like Campylobacter and Salmonella, particularly concerning the widely used antibiotic azithromycin.
Key Question: Can resistance genes jump from livestock to humans, driving new outbreaks of food borne illnesses?
Predicting disease outcomes from microbial genomes
The Power of Genomics: Advances in DNA sequencing have transformed how we study microbes, allowing us to explore how specific genetic differences influence the severity of diseases. However, working with large genome datasets can be daunting. Our team has developed tools and infrastructure to support researchers worldwide, including building bioinformatics capabilities in places like Viet Nam and The Gambia.
Impactful Discoveries: Our genomic studies have linked specific bacterial strains to severe conditions like gastrointestinal cancer, irritable bowel syndrome, and Guillain-Barre syndrome. These insights are not only advancing science but also informing practical solutions, such as tailored veterinary treatments and improved disease surveillance.
Current Initiatives: We’re using cutting-edge methods to identify genetic markers in Campylobacter jejuni that increase the risk of post-infection complications like Guillain-Barre syndrome.
Key Question: Can we pinpoint genetic traits that make certain strains more dangerous and use this knowledge to predict or prevent severe disease outcomes?