Postdoctoral position in bacterial genomics

About this position

A Genomic Time Machine: Reconstructing the Lost Diversity of Salmonella Typhi

Location: Institut Pasteur, Paris, France

Duration: 2-3 years

Principal Investigator: François-Xavier Weill

We are seeking an outstanding postdoctoral researcher with a strong background in bacterial genomics and evolutionary biology to join an ambitious project that will reconstruct the twentieth-century global evolution of Salmonella enterica serotype Typhi ( S. Typhi), the human-restricted pathogen causing typhoid fever. This project offers a rare opportunity to work on a unique historical genomic resource and to answer fundamental questions in pathogen evolution by reconnecting classical epidemiology with modern bacterial genomics.

The project

Before the genomic era, the worldwide surveillance of typhoid fever relied on Vi phage typing, which served for decades as the international standard for strain discrimination. Beginning in 1947, laboratories around the world published regular inventories documenting the geographical and temporal distribution of S. Typhi phage types. Together, these reports constitute an extraordinary historical record of the global circulation of this pathogen.

However, because phage typing has now disappeared from routine practice, this remarkable epidemiological resource has become largely inaccessible to contemporary microbiology. Our goal is to bring it back to life.

The project is built around an exceptional collection of more than 500 historical S. Typhi isolates collected worldwide between 1950 and 1980 . Importantly, almost all isolates have already been whole-genome sequenced , allowing the successful candidate to focus immediately on biological discovery. Every isolate also has its original Vi phage-type designation, providing a unique bridge between historical surveillance and modern genomics.

By integrating these genomes with decades of published phage-typing surveys, the project aims to convert an extensive — but now largely unusable — historical atlas of S. Typhi diversity into a comprehensive genomic framework. The resulting resource will enable the reinterpretation of more than seventy years of epidemiological observations in light of bacterial evolution.

This work will address fundamental questions including:

• How was the global population structure of S. Typhi organized before the emergence of modern antimicrobial-resistant lineages?
• What are the genomic determinants underlying the classical Vi phage types?
• Which historical lineages have disappeared, persisted or given rise to present-day populations?
• How can historical phage-type surveillance be translated into modern genomic epidemiology?

The project combines comparative genomics, phylogenomics, bacterial population genomics and evolutionary analyses, with considerable scope for developing original methodological and biological insights.

Candidate profile

We seek a creative and ambitious scientist who enjoys addressing biological questions using large genomic datasets. Applicants should have:

• a PhD in microbial genomics, evolutionary biology, bioinformatics, computational biology or a related discipline;
• demonstrated experience in bacterial whole-genome analyses;
• expertise in phylogenetics and/or population genomics;
• proficiency with Linux, Python and/or R;
• excellent communication skills and fluent English.

Experience with bacterial pathogens, microbial evolution, genome-wide association studies, or comparative genomics will be considered an asset.

Research environment

The project will be conducted under the supervision of Prof. François-Xavier Weill ( https://research.pasteur.fr/fr/member/francois-xavier-weill/ ) at the Institut Pasteur in Paris, a world-leading institute for infectious disease research. The successful candidate will join an internationally recognized research environment with expertise in bacterial genomics, evolution, and public health microbiology. The project offers substantial opportunities for high-impact publications and international collaborations (as in Hawkey, Frézal et al. Nat Commun 2024 or Frézal et al. Research Square 2026 ).

Application

Please submit to François-Xavier Weill ( fxweill@pasteur.fr )

• a cover letter describing your research interests and motivation;
• a curriculum vitae including publication list;
• contact details for two or three referees.

Applications will be reviewed on a rolling basis until the position is filled. The host laboratory is located within a controlled-access area, and appointment is subject to a favourable security vetting process.