Research

The STI Interactome Project investigates the complex network of interactions between sexually transmitted pathogens, commensal microbiota, and antimicrobial resistance mechanisms within the urogenital and rectal environments. By combining culturomics, metagenomics, and pathogen genomics, the project aims to map the ecological and functional relationships that define the STI interactome. Special attention is given to co-infections, microbial competition, and the selective pressures introduced by antimicrobial treatments, with the goal of advancing our understanding of STI persistence, transmission, and treatment response in diverse populations.

Nicole Borel, Enrique Rayo, Delia Onorini

The Microbial Mobilome Project investigates the frequent exchange of antimicrobial resistance determinants and virulence markers among bacteria. This exchange is facilitated, in part, by rapid evolutionary mechanisms that include transduction, conjugation and transformation, driven by bacteriophage infection, plasmid-donor-recipient interaction and bacteria-owned competence machineries, respectively.
We aim to unravel this complex microbial mobilome with a particular focus on facultative and obligate intracellular Gram-negative bacteria and their specific DNA exchange mechanisms. 

Hanna Marti

The Environmental Pathobiology Project takes a step beyond host-host, host-pathogen and pathogen-pathogen interaction by investigating the environment as a factor for microbial fitness and viability. This project takes a holistic approach to elucidate the influence of the environment on the interactome between hosts, pathogens and microbial communities. Our specific aims are to identify environmental factors that influence bacterial viability and to develop molecular tools for rapid distinction between live and dead bacteria in complex samples.

Nicole Borel, Hanna Marti, Enrique Rayo

This project examines the interactions between Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), focusing on their competitive and cooperative dynamics during co-infections of the urogenital tract. The research employs diverse methodologies, including in vitro co-culture models to elucidate the precise molecular mechanisms and cellular crosstalk that govern the interactions between CT and NG. Outcomes will provide insights into potential pathogen synergism or antagonism, informing better treatment strategies for dual infections.

This study investigates the impact of sexually transmitted infections (STIs) on microbiome composition, diversity, and resilience in the rectal niche, with an emphasis on co-infection scenarios. The project aims to elucidate how microbiome disruptions influence susceptibility, persistence, and clearance of STIs, potentially uncovering microbiota-based markers for disease prognosis.

The project focuses on understanding antimicrobial resistance (AMR) mechanisms in Neisseria gonorrhoeae through combined phenotypic resistance profiling and whole-genome sequencing approaches. The integrated phenotypic-genomic framework seeks to clarify genotype-to-phenotype correlations, informing surveillance and therapeutic guidelines for gonorrhea.

This project explores the inclusion fusion dynamics of Chlamydia suis employing high-resolution imaging approaches comprising confocal and electron microscopy, and characterizes the IncA protein of Chlamydia suis as an important factor of inclusion fusion.

Multiple Chlamydia suis strains infect the same pig. This project explores the co-infection dynamics of field samples by using a single-gene Nanopore sequencing approach targeting the ompA gene as well as the rrn-nqrF region for strain diversity and Tet-island presence, respectively.

This project adresses the antibiotic resistance uptake through natural competence by Chlamydia suis in a two-tier approach exploring the influence of outer membrane vesicles and the competence gene comEC in the process of AMR uptake by Chlamydia suis.

This project investigates the fitness of Chlamydia suis after faecal shedding by its porcine host, with a particular focus on its survival during manure processing. Viability is determined by extended cell culture methods, Nanopore Squiggle analysis and viability PCR.

This project determines the viability of Chlamydia abortus in the environment after being shed during abortion as well as normal births. Infected placentas are incubated at a constant temperature for up to one month and the decrease in viability is observed to determine safe working conditions for people working on farms.

This project explores how environmental conditions affect microbial fitness and viability, specifically focusing on the persistence and dynamics of antimicrobial resistance (AMR) genes in environmental reservoirs. By characterizing AMR using Oxford Nanopore sequencing (ONT), we can leverage real-time AMR detection and long-read metagenomics approaches.