, Conceived and designed the experiments: FXW. Performed the experiments: ATD

, Wrote the paper: ATD and FXW. Reviewed, critiqued and offered comments on the text: SLH, CB. ACKNOWLEDGMENTS We thank G. Costilhes, L. Ma, and A. Rivasseau for expert technical assistance. We thank all corresponding laboratories of the French National, Contributed reagents/materials/analysis tools: SLH, CB. Analysed the data: ATD and FXW

, The French National Reference Centre for E. coli, Shigella, and Salmonella is funded by the

, Institut Pasteur and Santé Publique France. A. Tran-Dien

F. Mousquetaires and . The, Integrative Biology of Emerging Infectious Diseases" Laboratory of Excellence funded by the French Government "Investissement d'Avenir" programme (grant no. ANR-10-LABX-62-IBEID). The Genomics Platform is member of the

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