M. Achtman, How old are bacterial pathogens?, Proc Biol Sci, vol.283, 2016.

M. Achtman and Z. Zhou, Distinct genealogies for plasmids and chromosome, PLoS Genet, vol.10, p.1004874, 2014.

M. Achtman and Z. Zhou, Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi, 2019.

M. Achtman, J. Wain, F. X. Weill, S. Nair, Z. Zhou et al., Multilocus sequence typing as a replacement for serotyping in Salmonella enterica, PLoS Pathog, vol.8, p.1002776, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01117433

C. A. Ahlstrom, J. Bonnedahl, H. Woksepp, J. Hernandez, B. Olsen et al., Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis, Sci Rep, vol.8, p.7361, 2018.

C. A. Ahlstrom, J. Bonnedahl, H. Woksepp, J. Hernandez, J. A. Reed et al., Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska. Mol Ecol, vol.28, pp.2531-2545, 2019.

C. A. Ahlstrom, A. M. Ramey, H. Woksepp, and J. Bonnedahl, Repeated detection of carbapenemase-producing Escherichia coli in gulls inhabiting Alaska, Antimicrob Agents Chemother, vol.63, pp.758-777, 2019.

N. F. Alikhan, Z. Zhou, M. J. Sergeant, and M. Achtman, A genomic overview of the population structure of Salmonella, PLoS Genet, vol.14, p.1007261, 2018.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.80360-80362, 1990.

S. Argimón, K. Abudahab, R. J. Goater, A. Fedosejev, J. Bhai et al., Microreact: visualizing and sharing data for genomic epidemiology and phylogeography, Microb Genom, vol.2, p.93, 2016.

P. M. Ashton, S. V. Owen, L. Kaindama, W. Rowe, C. R. Lane et al., Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa, Genome Med, vol.9, p.92, 2017.

J. Beghain, A. Bridier-nahmias, N. H. Le, E. Denamur, and O. Clermont, ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping, Microb Genom, vol.4, p.192, 2018.

S. Bird, E. Klein, and E. Loper, Natural language processing with Python: analyzing text with the Natural Language Toolkit, 2009.

K. I. Bos, V. J. Schuenemann, G. B. Golding, H. A. Burbano, N. Waglechner et al., A draft genome of Yersinia pestis from victims of the Black Death, Nature, vol.478, pp.506-510, 2011.

K. I. Bos, A. Herbig, J. Sahl, N. Waglechner, M. Fourment et al., Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus, vol.5, p.12994, 2016.

K. Clark, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers, GenBank. Nucleic Acids Res, vol.44, pp.67-72, 2016.

O. Clermont, J. K. Christenson, E. Denamur, and D. M. Gordon, The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environ Microbiol Rep, vol.5, pp.58-65, 2013.

T. R. Connor, S. V. Owen, G. Langridge, S. Connell, S. Nair et al., What's in a name? Species-wide whole-genome sequencing resolves invasive and noninvasive lineages of Salmonella enterica serotype Paratyphi B, MBio, vol.7, pp.527-543, 2016.

Y. Cui, C. Yu, Y. Yan, D. Li, Y. Li et al., Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis, Proc Natl Acad Sci, vol.110, pp.577-582, 2013.

T. Dallman, T. Inns, T. Jombart, P. Ashton, N. Loman et al., Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network, Microb Genom, vol.2, p.70, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01524578

P. B. Damgaard, N. Marchi, S. Rasmussen, M. Peyrot, G. Renaud et al., 137 ancient human genomes from across the Eurasian steppes, Nature, vol.557, pp.369-374, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02277549

S. Diemert and T. Yan, Clinically unreported salmonellosis outbreak detected via comparative genomic analysis of municipal wastewater Salmonella isolates, Appl Environ Microbiol, vol.85, pp.139-158, 2019.

R. C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, pp.2460-2461, 2010.

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, and T. A. Cebula, Genome signatures of Escherichia coli O157:H7 from the bovine host reservoir, Appl Environ Microbiol, vol.77, pp.2916-2925, 2011.

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, and T. A. Cebula, Genomic anatomy of Escherichia coli O157:H7 outbreaks, Proc Natl Acad Sci, vol.108, pp.20142-20147, 2011.

G. A. Eroshenko, N. Y. Nosov, Y. M. Krasnov, Y. G. Oglodin, L. M. Kukleva et al., Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan, PLoS One, vol.12, p.187230, 2017.

E. J. Feil, B. C. Li, D. M. Aanensen, W. P. Hanage, and B. G. Spratt, eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data, J Bacteriol, vol.186, pp.1518-1530, 2004.

M. Feldman, M. Harbeck, M. Keller, M. A. Spyrou, A. Rott et al., A high-coverage Yersinia pestis genome from a sixth-century Justinianic plague victim, Mol Biol Evol, vol.33, pp.2911-2923, 2016.

M. Frentrup, Z. Zhou, M. Steglich, J. P. Meier-kolthoff, M. Göker et al., Global genomic population structure of Clostridioides difficile, 2019.

D. M. Gordon, S. Geyik, O. Clermont, C. L. O'brien, S. Huang et al., Fine-scale structure analysis shows epidemic patterns of clonal complex 95, a cosmopolitan Escherichia coli lineage responsible for extraintestinal infection, vol.2, pp.168-185, 2017.

M. H. Green, Putting Africa on the Black Death map: narratives from genetics and history. Afriques [Online] 9, 2018.

D. Griffiths, W. Fawley, M. Kachrimanidou, R. Bowden, D. W. Crook et al., Multilocus sequence typing of Clostridium difficile, J Clin Microbiol, vol.48, pp.770-778, 2010.

M. Guibourdenche, P. Roggentin, M. Mikoleit, P. I. Fields, J. Bockemühl et al., 47) to the White-Kauffmann-Le Minor scheme, Res Microbiol, vol.161, pp.26-29, 2003.
URL : https://hal.archives-ouvertes.fr/pasteur-02019334

B. J. Haley, S. W. Kim, J. Haendiges, E. Keller, D. Torpey et al., Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, Zoonoses Public Health, vol.66, pp.382-392, 2011.

M. Hall, M. A. Chattaway, S. Reuter, C. Savin, E. Strauch et al., Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels, J Clin Microbiol, vol.53, pp.35-42, 2015.

S. Issenhuth-jeanjean, P. Roggentin, M. Mikoleit, M. Guibourdenche, D. Pinna et al., 48) to the White-Kauffmann-Le Minor scheme, Res Microbiol, vol.165, pp.526-530, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-01104894

T. J. Johnson, E. Elnekave, E. A. Miller, J. Munoz-aguayo, F. C. Flores et al., Phylogenomic analysis of extraintestinal pathogenic Escherichia coli sequence type 1193, an emerging multidrug-resistant clonal group, Antimicrob Agents Chemother, vol.63, pp.1913-1931, 2019.

K. A. Jolley, C. M. Bliss, J. S. Bennett, H. B. Bratcher, C. Brehony et al., Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain, Microbiology, vol.158, pp.1005-1015, 2012.

G. Jones, S. Lefèvre, M. P. Donguy, A. Nisavanh, G. Terpant et al., Outbreak of Shiga toxinproducing Escherichia coli (STEC) O26 paediatric haemolytic uraemic syndrome (HUS) cases associated with the consumption of soft raw cow's milk cheeses, Euro Surveill, vol.24, p.1900305, 2019.
URL : https://hal.archives-ouvertes.fr/pasteur-02482068

G. Jones, P. De-la-gandaro, M. Herrera-leon, L. Herrera-leon, S. et al., Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, Euro Surveill, vol.24, p.1900161, 2018.

M. Keller, M. A. Spyrou, C. L. Scheib, G. U. Neumann, A. Kröpelin et al., Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750), Proc Natl Acad Sci, vol.116, pp.12363-12372, 2019.

C. Kidgell, U. Reichard, J. Wain, B. Linz, M. Torpdahl et al., Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old, Infect Genet Evol, vol.2, pp.89-97, 2002.

V. V. Kutyrev, G. A. Eroshenko, V. L. Motin, N. Y. Nosov, J. M. Krasnov et al., Phylogeny and classification of Yersinia pestis through the lens of strains from the plague foci of Commonwealth of Independent States, Front Microbiol, vol.9, p.1106, 2018.

G. C. Langridge, M. Fookes, T. R. Connor, T. Feltwell, N. Feasey et al., Patterns of genome evolution that have accompanied host adaptation in Salmonella, Proc Natl Acad Sci, vol.112, pp.863-868, 2015.

R. Laukkanen-ninios, X. Didelot, K. A. Jolley, G. Morelli, V. Sangal et al., Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing, Environ Microbiol, vol.13, pp.3114-3127, 2011.

H. Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, vol.34, pp.3094-3100, 2018.

S. Liu, J. D. Lan, R. Wang, Y. Meng, Q. Dai et al., Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana, Int J Syst Evol Microbiol, vol.65, pp.2130-2134, 2015.

C. M. Liu, M. Stegger, M. Aziz, T. J. Johnson, K. Waits et al., Escherichia coli ST131-H22 as a foodborne uropathogen, MBio, vol.9, pp.470-488, 2018.

C. Luo, S. T. Walk, D. M. Gordon, M. Feldgarden, J. M. Tiedje et al.,

, Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species, Proc Natl Acad Sci, vol.108, pp.7200-7205

M. Maiden, J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell et al., Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc Natl Acad Sci, vol.95, pp.3140-3145, 1998.

M. C. Maiden, M. J. Van-rensburg, J. E. Bray, S. G. Earle, S. A. Ford et al., MLST revisited: the gene-by-gene approach to bacterial genomics, Nat Rev Microbiol, vol.11, pp.728-736, 2013.

A. Margaryan, H. B. Hansen, S. Rasmussen, M. Sikora, V. Moiseyev et al., Ancient pathogen DNA in human teeth and petrous bones, Ecol Evol, vol.8, pp.3534-3542, 2018.

J. L. Mcdonald, A. Robertson, and M. J. Silk, Wildlife disease ecology from the individual to the population: insights from a long-term study of a naturally infected European badger population, J Anim Ecol, vol.87, pp.101-112, 2018.

A. Mellmann, D. Harmsen, C. A. Cummings, E. B. Zentz, S. R. Leopold et al., Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology, PLoS One, vol.6, p.22751, 2011.

E. A. Miller, E. Elnekave, C. F. Figueroa, A. Johnson, A. Kearney et al., Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America, 2019.

G. Morelli, Y. Song, C. J. Mazzoni, M. Eppinger, P. Roumagnac et al., Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity, Nature Genet, vol.42, pp.1140-1143, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-00836130

A. Namouchi, M. Guellil, O. Kersten, S. Hänsch, C. Ottoni et al., Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period, Proc Natl Acad Sci, vol.115, pp.11790-11797, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02118066

D. G. Newell, L. Ragione, and R. M. , Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies?, Transbound Emerg Dis, vol.65, pp.49-71, 2018.

D. Numberger, T. Riedel, G. Mcewen, U. Nübel, M. Frentrup et al., Genomic analysis of three Clostridioides difficile isolates from urban water sources, Anaerobe, vol.56, pp.22-26, 2019.

H. Ochman and R. K. Selander, Standard reference strains of Escherichia coli from natural populations, J Bacteriol, vol.157, pp.690-693, 1984.

B. O'farrell, J. K. Haase, V. Velayudhan, R. A. Murphy, and M. Achtman, Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains, PLoS One, vol.7, p.48022, 2012.

J. Parkhill, B. W. Wren, N. R. Thomson, R. W. Titball, M. T. Holden et al., Genome sequence of Yersinia pestis, the causative agent of plague, Nature, vol.413, pp.523-527, 2001.

G. M. Pupo, R. Lan, and P. R. Reeves, Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics, Proc Natl Acad Sci, vol.97, pp.10567-10572, 2000.

S. Rasmussen, M. E. Allentoft, K. Nielsen, L. Orlando, M. Sikora et al., Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago, Cell, vol.163, pp.571-582, 2015.

J. Robertson, C. Yoshida, P. Kruczkiewicz, C. Nadon, A. Nichani et al., Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR), 2018.

L. Roer, V. Tchesnokova, R. Allesøe, M. Muradova, S. Chattopadhyay et al., Development of a web tool for Escherichia coli subtyping based on fimH alleles, J Clin Microbiol, vol.55, pp.2538-2543, 2017.

L. M. Rogers, R. Delahay, C. L. Cheeseman, S. Langton, G. C. Smith et al., Movement of badgers (Meles meles) in a high-density population: individual, population and disease effects, Proc Biol Sci, vol.265, pp.1269-1276, 1998.

M. Sanaa, R. Pouillot, F. G. Vega, E. Strain, and J. M. Van-doren, GenomeGraphR: a user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization, PLoS One, vol.14, p.213039, 2019.

L. Sandegren, J. Stedt, U. Lustig, J. Bonnedahl, D. I. Andersson et al., Long-term carriage and rapid transmission of extended spectrum ?-lactamase-producing E. coli within a flock of Mallards in the absence of antibiotic selection, Environ Microbiol Rep, vol.10, pp.576-582, 2018.

R. K. Selander, D. A. Caugant, T. S. Whittam, and F. C. Neidhardt, Genetic structure and variation in natural populations of Escherichia coli, Escherichia coli and Salmonella typhimurium cellular and molecular biology, vol.II, pp.1625-1648, 1987.

M. Simonsen, T. Mailund, and C. Pedersen, Inference of large phylogenies using neighbour-joining, Biomedical Engineering Systems and Technologies: 3rd International Joint Conference, BIOSTEC 2010, pp.334-344, 2011.

M. A. Spyrou, R. I. Tukhbatova, M. Feldman, J. Drath, S. Kacki et al., Historical Y. pestis genomes reveal the European Black Death as the source of ancient and modern plague pandemics, Cell Host Microbe, vol.19, pp.874-881, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01842544

M. A. Spyrou, R. I. Tukhbatova, C. C. Wang, A. A. Valtueña, A. K. Lankapalli et al., Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague, Nat Commun, vol.9, p.2234, 2018.

M. A. Spyrou, M. Keller, R. I. Tukhbatova, C. L. Scheib, E. A. Nelson et al., Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes, Nat Commun, vol.10, p.4470, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02315966

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014.

J. Stedt, J. Bonnedahl, J. Hernandez, B. J. Mcmahon, B. Hasan et al., Antibiotic resistance patterns in Escherichia coli from gulls in nine European countries, Infect Ecol Epidemiol, vol.4, p.21565, 2014.

N. Stoesser, A. E. Sheppard, L. Pankhurst, D. Maio, N. Moore et al., Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131, MBio, vol.7, p.2162, 2016.

B. Van-der-putten, S. Matamoros, . Consortium, and C. Schultsz, Genomic evidence for revising the Escherichia genus and description of Escherichia ruysiae sp, 2019.

D. M. Wagner, J. Klunk, M. Harbeck, A. Devault, N. Waglechner et al., Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis, Lancet Infect Dis, vol.14, pp.319-326, 2014.

A. Waldram, G. Dolan, P. M. Ashton, C. Jenkins, and T. J. Dallman, Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, Food Microbiol, vol.71, pp.39-45, 2014.

S. T. Walk, E. W. Alm, D. M. Gordon, J. L. Ram, G. A. Toranzos et al., Cryptic lineages of the genus Escherichia, Appl Environ Microbiol, vol.75, pp.6534-6544, 2009.

B. J. Walker, T. Abeel, T. Shea, M. Priest, A. Abouelleil et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, vol.9, p.112963, 2014.

N. R. Waters, A. F. Brennan, F. Holmes, A. Pritchard, and L. , Easily phylotyping E. coli via the EzClermont web app and command-line tool, 2018.

J. S. Wilson, S. M. Hazel, N. J. Williams, A. Phiri, N. P. French et al., Nontyphoidal salmonellae in United Kingdom badgers: prevalence and spatial distribution, Appl Environ Microbiol, vol.69, pp.4312-4315, 2003.

T. Wirth, D. Falush, R. Lan, F. Colles, P. Mensa et al., Sex and virulence in Escherichia coli: an evolutionary perspective, Mol Microbiol, vol.60, pp.1136-1151, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00174910

T. Wirth, G. Morelli, B. Kusecek, A. Van-belkum, C. Van-der-schee et al., The rise and spread of a new pathogen: seroresistant Moraxella catarrhalis, Genome Res, vol.17, pp.1647-1656, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00173850

V. K. Wong, S. Baker, T. R. Connor, D. Pickard, A. J. Page et al., An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid, Nat Commun, vol.7, p.12827, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01422000

J. Worley, J. Meng, M. W. Allard, E. W. Brown, and R. E. Timme, Salmonella enterica phylogeny based on whole-genome sequencing reveals two new clades and novel patterns of horizontally acquired genetic elements, MBio, vol.9, pp.2303-2321, 2018.

C. Wray, K. Baker, J. Gallagher, and P. Naylor, Salmonella infection in badgers in the South West of England, Br Vet J, vol.133, issue.17, pp.33996-34005, 1977.

C. E. Yoshida, P. Kruczkiewicz, C. R. Laing, E. J. Lingohr, V. P. Gannon et al., The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies, PLoS One, vol.11, 2016.

S. Zhang, H. C. Den-bakker, S. Li, J. Chen, B. A. Dinsmore et al., SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data, Appl Environ Microbiol, vol.85, pp.1746-1765, 2019.

Z. Zhou, A. Mccann, E. Litrup, R. Murphy, M. Cormican et al., Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona, PLoS Genet, vol.9, p.1003471, 2013.

Z. Zhou, A. Mccann, F. X. Weill, C. Blin, S. Nair et al., Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever, Proc Natl Acad Sci, vol.111, pp.12199-12204, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01104820

Z. Zhou, N. Alikhan, M. J. Sergeant, N. Luhmann, C. Vaz et al., GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens, Genome Res, vol.28, pp.1395-1404, 2018.

Z. Zhou, N. Luhmann, N. F. Alikhan, C. Quince, and M. Achtman, Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes, RECOMB 2018, pp.225-240, 2018.

. Springer,

Z. Zhou, I. Lundstrøm, A. Tran-dien, S. Duchêne, N. F. Alikhan et al., Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia, Curr Biol, vol.28, pp.2420-2428, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-02006054


, Access the most recent version at doi: 2020, vol.30, pp.138-152, 2019.

, Genome Res. References