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, European Food Safety Authority & European Centre for Disease Prevention and Control. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2015, EFSA J, vol.14, 2016.

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, Annexe 2 b. Distribution phylogénétique des CMI pour l'ampicilline et la penicilline G, sur une sélection de 67 isolats de S. enterica sérotype Typhimurium

, Le premier cercle indique les souches productrices de ?-lactamase, avec quatre gènes différents en bleu, vert, violet et rose représentant blaTEM-1B, blaTEM-1A, blaOXA-1 et blaOXA-2 repectivement. Le second cercle indique les isolats testés pour la CMI pour l

, Annexe 2 c. Fréquence de transfert des différents plasmides de S. enterica sérotype Typhimurium. Les statistiques ont été obtenues en faisant l

, Characterisation of the ampicillin-resistant isolates The 11 ampicillin-resistant S. enterica serotype Typhimurium isolates detected by the disk diffusion method and shown in Table 2 had penicillin MICs (for ampicillin or penicillin G) ? 256 mg/L (table S1, figure 2). The genomic analysis identified a ?-lactamase gene, either blaTEM (n = 9) or blaOXA (n = 2) in all these isolates. In a selection of 56 S. enterica serotype Typhimurium isolates devoid of ?-lactamase genes and belonging to the different genomic clades of the collection (see below and Appendix, total, 123 CRISPOL types were observed, with CT117 the most frequently represented (4.9%, 11/225)

, The most frequent ?-lactamase gene, blaTEM-1B, carried by transposon Tn2, 26 was found in eight (72.7%) ampicillin-resistant S. enterica serotype Typhimurium isolates, The Tn2 transposon was located on plasmids from incompatibility groups IncF (n = 5) and IncX1

, In two ST313 isolates, STM 232-68 and STM 266-68, collected in France and Tunisia in 1968, the Tn2 integration site was identical to that of pSLT-BT, a multidrug resistance plasmid found in lineage II of the ST313 clone, a serotype Typhimurium population associated with invasive infections in Africa. 25 Furthermore, as observed in pSLT-BT, a Tn21like element was also found integrated into the Tn2 of the STM 232-68 and STM 266-68 IncF plasmids. However, these two plasmids differed slightly from pSLT-BT in having a 6.8 kb IS1mediated deletion (corresponding to region 41,666-48,543 of GenBank accession number FN432031) encompassing the integron (In2) region of the Tn21-like element. The IncF plasmid of the fifth isolate, An analysis of Tn2 transposon junctions revealed that, in four isolates, Tn2 was located on pSLT, a 93 kb IncF plasmid known as the S. enterica serotype Typhimurium type strain LT2 virulence plasmid

, These plasmids had only 45-77% of their DNA sequences (98-99% nucleotide identity) in common with pExPB5-59-1. Interestingly, the oldest of these isolates was collected during a foodborne outbreak of disease in Newcastle, United Kingdom in 1911. The three S. enterica serotype Typhimurium isolates collected in France and Tunisia before the release of ampicillin contained the Tn2 transposon, in the IncX1 (n = 1) and pSLT-derived IncF (n = 2) plasmids. Tn2 was found inserted at two different sites within IncF. AUTHOR CONTRIBUTIONS Conceived and designed the experiments: FXW. Performed the experiments: ATD. Contributed reagents/materials/analysis tools: SLH, CB. Analysed the data: ATD and FXW. Wrote the paper: ATD and FXW. Reviewed, critiqued and, The 45 kb Tn2-containing IncX1 plasmid pExPB5-59-1 was also sequenced with the PacBio platform. This plasmid was present in a clonal bacterial population (ST19-CT160) isolated in France over a 10-year period, 1959.

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E. S. Anderson, E. J. Threlfall, J. M. Carr, M. M. Mcconnell, and H. R. Smith, Clonal distribution of resistance plasmid-carrying Salmonella Typhimurium, mainly in the Middle East, J Hyg (Lond), vol.79, pp.425-473, 1977.

J. N. Grindley and D. Nakada, The nucleotide sequence of the replication origin of plasmid NTP1, Nucleic Acids Res, vol.9, pp.4355-66, 1981.

E. Kelterborn, Salmonella-species. First isolations, names and occurrence, 1967.

, The European Union summary report on trends and sources of zoonoses, 2017.

, EFSA Journal, vol.14, p.4634, 2016.

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H. Gounelle and A. Szakvary, Antibiotics and food. IV. Use of antibiotics outside medical

, Bull Acad Natl Med, vol.150, pp.149-56, 1966.

K. E. Webb and J. P. Fontenot, Medicinal drug residues in broiler litter and tissues from cattle fed litter, J Anim Sci, vol.41, pp.1212-1219, 1975.

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, Title: Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

, Unité des Bactéries Pathogènes Entériques, Institut Pasteur

, Wellcome Trust, p.5020

M. T. ,

Z. Z. , zhemin.zhou@warwick.ac.uk ?Present addresses: Molecular Microbiology

, Gastrointestinal Bacteria Reference Unit

, Here we compare a draft Paratyphi C genome from the 800-year-old skeleton of a young woman in Trondheim, Norway, against a new database of related modern genomes. We demonstrate that Paratyphi C is descended from the ancestors of swine pathogens, serovars Choleraesuis and Typhisuis, and may have evolved after zoonotic transfer from swine during the Neolithic synteny of the pan genome was reconstructed as described in Supplementary Materials of Zhou et al. 13 and can be examined in detail in a publicly accessible, interactive local version of Anvi'o server Pan-genome, Salmonella enterica serovar Paratyphi C is the causative agent in Africa and Asia of enteric (paratyphoid) fever 1,2 , a potentially lethal infection of humans