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Modeling the diffusion of antibiotic-resistant bacteria along the Pays de la Loire healthcare network.

The Modelling, Epidemiology and Surveillance of Health Risks (MESuRS) laboratory of the Conservatoire National des Arts et Métiers (Cnam) and the University of Nantes are recruiting a PhD student for the fall of 2023, as part of an already funded research project.

PhD advisors: Gabriel Birgand (Université de Nantes) and Laura Temime (Cnam)

Context: In healthcare settings, antibiotic-resistant bacteria are responsible for infections for which treatment options are limited, with potentially important consequences in terms of morbidity and mortality. These bacteria can spread from one healthcare facility to another via patient transfers, facilitating their global spread. In recent years, research using transfer data has enabled the reconstruction of "healthcare networks" in the Netherlands, the United Kingdom, and France, for example1-3. This work has highlighted the role played by these networks in the dynamics of antimicrobial resistance, and shown how they can be used to improve surveillance and control strategies. However, the networks reconstructed to date have mostly been limited to hospitals - often acute care hospitals only.

PhD objectives: This project aims at reconstructing, at a regional scale, a healthcare network including short and long-stay hospitals, follow-up and rehabilitation care settings, as well as nursing homes, and at analyzing the spread of multi-resistant Enterobacteriaceae along this network. The final objective is to evaluate different surveillance and control strategies, based on a mathematical model of propagation on the network.

Proposed methodology: In a first step, the healthcare network of the Pays de la Loire region will be reconstructed from exhaustive chained data (PMSI, SNIIRAM) on all patient transfers over one year between different types of hospitals and long-term care facilities in the region. The properties of this network (average degree, clustering level, etc.) will then be described. The "hubs" (highly connected care facilities) will be identified within the network, and the determinants of this level of connection will be explored using multivariate statistical analyses.
In a second step, a mathematical model of the spread of multi-resistant bacteria to antibiotics will be developed on this network. This stochastic model will take into account both intra-institutional dynamics and patient transfers (metapopulation model). It will be informed by epidemiological data on episodes of multidrug-resistant Enterobacteriaceae infections in the region.
Finally, in the last part of the thesis, surveillance and control strategies based on the structure of the care network will be simulated and evaluated using the model: wastewater monitoring targeted at some healthcare institutions (to be identified); improvement of control measures in some institutions, also to be identified; better communication between healthcare institutions (in particularly between nursing homes and hospitals).

Candidate profile: Candidates should have a master or engineering degree in applied mathematics or biostatistics. They should master the main data analysis tools as well as at least one programming language (R or C++), and be motivated by applications in the health field and multidisciplinary work. Knowledge in epidemiology and/or life sciences would be useful.


  1. Donker T, Wallinga J, Grundmann H. Patient referral patterns and the spread of hospital-acquired infections through national health care networks. PLoS Comput Biol 2010; 6(3): e1000715.
  2. Donker T, Wallinga J, Grundmann H. Dispersal of antibiotic-resistant high-risk clones by hospital networks: changing the patient direction can make all the difference. The Journal of hospital infection 2014; 86(1): 34-41.
  3. Nekkab N, Astagneau P, Temime L, Crepey P. Spread of hospital-acquired infections: A comparison of healthcare networks. PLoS Comput Biol 2017; 13(8): e1005666.

Practical information:
The PhD student will be based in the MESuRS laboratory of the Cnam, located in the 3rd arrondissement of Paris. He/she will travel regularly to Nantes.
To apply, please send your CV and cover letter to Laura Temime ( and Gabriel Birgand (

PhD position
Conservatoire national des Arts et Métiers
Closing date
July 20th, 2023
Posted on
April 20th, 2023 13:55
Last updated
April 20th, 2023 13:55