{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T13:28:51Z","timestamp":1791984531798,"version":"4.4.0"},"reference-count":91,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T00:00:00Z","timestamp":1732233600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T00:00:00Z","timestamp":1732233600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-024-01859-8","type":"journal-article","created":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T10:09:28Z","timestamp":1732270168000},"page":"3345-3361","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6380-627X","authenticated-orcid":false,"given":"Lukas","family":"Hafner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0675-8815","authenticated-orcid":false,"given":"Enzo","family":"Gadin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"Frouin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2509-3293","authenticated-orcid":false,"given":"Fabien","family":"Laporte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Gaultier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afonso","family":"Vieira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8856-0819","authenticated-orcid":false,"given":"Claire","family":"Maudet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3980-4463","authenticated-orcid":false,"given":"Hugo","family":"Varet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Moura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9l\u00e8ne","family":"Bracq-Dieye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Tessaud-Rita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myl\u00e8ne","family":"Maury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7319-3809","authenticated-orcid":false,"given":"Melody","family":"Dazas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Legendre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6579-2756","authenticated-orcid":false,"given":"Pauline","family":"Gastineau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1374-2359","authenticated-orcid":false,"given":"Yu-Huan","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Yves","family":"Copp\u00e9e","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Charlier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9911-4459","authenticated-orcid":false,"given":"Etienne","family":"Patin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayan","family":"Chikhi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7704-822X","authenticated-orcid":false,"given":"Eduardo P. C.","family":"Rocha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3778-7313","authenticated-orcid":false,"given":"Alexandre","family":"Leclercq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Disson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7554-6783","authenticated-orcid":false,"given":"Hugues","family":"Aschard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4491-1063","authenticated-orcid":false,"given":"Marc","family":"Lecuit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,11,22]]},"reference":[{"key":"1859_CR1","doi-asserted-by":"crossref","first-page":"E3801","DOI":"10.1073\/pnas.1523199113","volume":"113","author":"E Bosi","year":"2016","unstructured":"Bosi, E. et al. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proc. Natl Acad. Sci. USA 113, E3801\u2013E3809 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1859_CR2","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1126\/science.1134933","volume":"314","author":"P Roumagnac","year":"2006","unstructured":"Roumagnac, P. et al. Evolutionary history of Salmonella Typhi. Science 314, 1301\u20131304 (2006).","journal-title":"Science"},{"key":"1859_CR3","doi-asserted-by":"crossref","first-page":"16185","DOI":"10.1038\/nmicrobiol.2016.185","volume":"2","author":"A Moura","year":"2016","unstructured":"Moura, A. et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2, 16185 (2016).","journal-title":"Nat. Microbiol."},{"key":"1859_CR4","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1038\/ng.3501","volume":"48","author":"MM Maury","year":"2016","unstructured":"Maury, M. M. et al. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat. Genet. 48, 308\u2013313 (2016).","journal-title":"Nat. Genet."},{"key":"1859_CR5","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1128\/JCM.02036-10","volume":"49","author":"RMK Stewart","year":"2011","unstructured":"Stewart, R. M. K. et al. Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections. J. Clin. Microbiol. 49, 993\u20131003 (2011).","journal-title":"J. Clin. Microbiol."},{"key":"1859_CR6","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/s41467-021-20988-w","volume":"12","author":"L Mageiros","year":"2021","unstructured":"Mageiros, L. et al. Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nat. Commun. 12, 765 (2021).","journal-title":"Nat. Commun."},{"key":"1859_CR7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1890-1","volume":"20","author":"A Vasquez-Rifo","year":"2019","unstructured":"Vasquez-Rifo, A., Veksler-Lublinsky, I., Cheng, Z., Ausubel, F. M. & Ambros, V. The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. Genome Biol. 20, 1\u201322 (2019).","journal-title":"Genome Biol."},{"key":"1859_CR8","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1084\/jem.20092594","volume":"207","author":"A Tazi","year":"2010","unstructured":"Tazi, A. et al. The surface protein HvgA mediates group B streptococcus hypervirulence and meningeal tropism in neonates. J. Exp. Med. 207, 2313\u20132322 (2010).","journal-title":"J. Exp. Med."},{"key":"1859_CR9","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1093\/infdis\/jir389","volume":"204","author":"JJC Nienaber","year":"2011","unstructured":"Nienaber, J. J. C. et al. Methicillin-susceptible Staphylococcus aureus endocarditis isolates are associated with clonal complex 30 genotype and a distinct repertoire of enterotoxins and adhesins. J. Infect. Dis. 204, 704\u2013713 (2011).","journal-title":"J. Infect. Dis."},{"key":"1859_CR10","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1093\/femsre\/fux023","volume":"41","author":"M Diard","year":"2017","unstructured":"Diard, M. & Hardt, W.-D. Evolution of bacterial virulence. FEMS Microbiol. Rev. 41, 679\u2013697 (2017).","journal-title":"FEMS Microbiol. Rev."},{"key":"1859_CR11","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.tim.2012.04.005","volume":"20","author":"SP Brown","year":"2012","unstructured":"Brown, S. P., Cornforth, D. M. & Mideo, N. Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control. Trends Microbiol. 20, 336\u2013342 (2012).","journal-title":"Trends Microbiol."},{"key":"1859_CR12","doi-asserted-by":"crossref","first-page":"e00259","DOI":"10.1128\/mBio.00259-17","volume":"8","author":"JJ Quereda","year":"2017","unstructured":"Quereda, J. J. et al. Listeriolysin S is a streptolysin S-like virulence factor that targets exclusively prokaryotic cells in vivo. mBio 8, e00259\u201317 (2017).","journal-title":"mBio"},{"key":"1859_CR13","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1016\/j.chom.2019.10.016","volume":"26","author":"N Rolhion","year":"2019","unstructured":"Rolhion, N. et al. A Listeria monocytogenes bacteriocin can target the commensal Prevotella copri and modulate intestinal infection. Cell Host Microbe 26, 691\u2013701.e5 (2019).","journal-title":"Cell Host Microbe"},{"key":"1859_CR14","doi-asserted-by":"crossref","first-page":"e1002229","DOI":"10.1371\/journal.pbio.1002229","volume":"13","author":"M Laabei","year":"2015","unstructured":"Laabei, M. et al. Evolutionary trade-offs underlie the multi-faceted virulence of Staphylococcus aureus. PLoS Biol. 13, e1002229 (2015).","journal-title":"PLoS Biol."},{"key":"1859_CR15","doi-asserted-by":"crossref","first-page":"6826","DOI":"10.1038\/s41467-021-27069-y","volume":"12","author":"L Hafner","year":"2021","unstructured":"Hafner, L. et al. Listeria monocytogenes faecal carriage is common and depends on the gut microbiota. Nat. Commun. 12, 6826 (2021).","journal-title":"Nat. Commun."},{"key":"1859_CR16","doi-asserted-by":"crossref","first-page":"4420","DOI":"10.1128\/AEM.00282-12","volume":"78","author":"BD Sauders","year":"2012","unstructured":"Sauders, B. D. et al. Diversity of Listeria species in urban and natural environments. Appl. Environ. Microbiol. 78, 4420\u20134433 (2012).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR17","doi-asserted-by":"crossref","first-page":"4458","DOI":"10.1128\/AEM.70.8.4458-4467.2004","volume":"70","author":"KK Nightingale","year":"2004","unstructured":"Nightingale, K. K. et al. Ecology and transmission of Listeria monocytogenes infecting ruminants and in the farm environment. Appl. Environ. Microbiol. 70, 4458\u20134467 (2004).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR18","doi-asserted-by":"crossref","DOI":"10.1038\/srep36419","volume":"6","author":"M Dreyer","year":"2016","unstructured":"Dreyer, M. et al. Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis. Sci. Rep. 6, 36419 (2016).","journal-title":"Sci. Rep."},{"key":"1859_CR19","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/S1473-3099(16)30521-7","volume":"17","author":"C Charlier","year":"2017","unstructured":"Charlier, C. et al. Clinical features and prognostic factors of listeriosis: the MONALISA national prospective cohort study. Lancet Infect. Dis. 17, 510\u2013519 (2017).","journal-title":"Lancet Infect. Dis."},{"key":"1859_CR20","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1093\/cid\/ciab337","volume":"74","author":"C Charlier","year":"2022","unstructured":"Charlier, C. et al. Neonatal listeriosis presentation and outcome: a prospective study of 189 cases. Clin. Infect. Dis. 74, 8\u201316 (2022).","journal-title":"Clin. Infect. Dis."},{"key":"1859_CR21","doi-asserted-by":"crossref","first-page":"e02948","DOI":"10.1128\/mBio.02948-19","volume":"10","author":"A Louie","year":"2019","unstructured":"Louie, A., Zhang, T., Becattini, S., Waldor, M. K. & Portnoy, D. A. A multiorgan trafficking circuit provides purifying selection of Listeria monocytogenes virulence genes. mBio 10, e02948\u201319 (2019).","journal-title":"mBio"},{"key":"1859_CR22","doi-asserted-by":"crossref","first-page":"6334","DOI":"10.1073\/pnas.1702077114","volume":"114","author":"T Zhang","year":"2017","unstructured":"Zhang, T. et al. Deciphering the landscape of host barriers to Listeria monocytogenes infection. Proc. Natl Acad. Sci. USA 114, 6334\u20136339 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1859_CR23","doi-asserted-by":"crossref","first-page":"5273","DOI":"10.1007\/s00253-016-7552-2","volume":"100","author":"RH Orsi","year":"2016","unstructured":"Orsi, R. H. & Wiedmann, M. Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009. Appl. Microbiol. Biotechnol. 100, 5273\u20135287 (2016).","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"1859_CR24","doi-asserted-by":"crossref","first-page":"e1000146","DOI":"10.1371\/journal.ppat.1000146","volume":"4","author":"M Ragon","year":"2008","unstructured":"Ragon, M. et al. A new perspective on Listeria monocytogenes evolution. PLoS Pathog. 4, e1000146 (2008).","journal-title":"PLoS Pathog."},{"key":"1859_CR25","first-page":"e00396","volume":"9","author":"S Lee","year":"2018","unstructured":"Lee, S. et al. Listeria monocytogenes source distribution analysis indicates regional heterogeneity and ecological niche preference among serotype 4b clones. mBio 9, e00396\u201318 (2018).","journal-title":"mBio"},{"key":"1859_CR26","doi-asserted-by":"crossref","first-page":"e0164283","DOI":"10.1371\/journal.pone.0164283","volume":"11","author":"S Bertrand","year":"2016","unstructured":"Bertrand, S. et al. Diversity of Listeria monocytogenes strains of clinical and food chain origins in Belgium between 1985 and 2014. PLoS ONE 11, e0164283 (2016).","journal-title":"PLoS ONE"},{"key":"1859_CR27","doi-asserted-by":"crossref","first-page":"e0213621","DOI":"10.1128\/aem.02136-21","volume":"88","author":"A Fagerlund","year":"2022","unstructured":"Fagerlund, A. et al. Whole-genome sequencing analysis of Listeria monocytogenes from rural, urban, and farm environments in Norway: genetic diversity, persistence, and relation to clinical and food isolates. Appl. Environ. Microbiol. 88, e0213621 (2022).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR28","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nprot.2009.66","volume":"4","author":"O Disson","year":"2009","unstructured":"Disson, O. et al. Modeling human listeriosis in natural and genetically engineered animals. Nat. Protoc. 4, 799\u2013810 (2009).","journal-title":"Nat. Protoc."},{"key":"1859_CR29","volume":"10","author":"MM Maury","year":"2019","unstructured":"Maury, M. M. et al. Hypervirulent Listeria monocytogenes clones\u2019 adaption to mammalian gut accounts for their association with dairy products. Nat. Commun. 10, 2488 (2019).","journal-title":"Nat. Commun."},{"key":"1859_CR30","doi-asserted-by":"crossref","first-page":"e00541","DOI":"10.1128\/IAI.00541-17","volume":"85","author":"MM Maury","year":"2017","unstructured":"Maury, M. M. et al. Spontaneous loss of virulence in natural populations of Listeria monocytogenes. Infect. Immun. 85, e00541\u201317 (2017).","journal-title":"Infect. Immun."},{"key":"1859_CR31","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ijfoodmicro.2014.02.018","volume":"177","author":"VB Ribeiro","year":"2014","unstructured":"Ribeiro, V. B. et al. Contributions of \u03c3B and PrfA to Listeria monocytogenes salt stress under food relevant conditions. Int. J. Food Microbiol. 177, 98\u2013108 (2014).","journal-title":"Int. J. Food Microbiol."},{"key":"1859_CR32","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1038\/nature08080","volume":"459","author":"A Toledo-Arana","year":"2009","unstructured":"Toledo-Arana, A. et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459, 950\u2013956 (2009).","journal-title":"Nature"},{"key":"1859_CR33","doi-asserted-by":"crossref","first-page":"3948","DOI":"10.1128\/IAI.70.7.3948-3952.2002","volume":"70","author":"CA Nadon","year":"2002","unstructured":"Nadon, C. A., Bowen, B. M., Wiedmann, M. & Boor, K. J. Sigma B contributes to PrfA-mediated virulence in Listeria monocytogenes. Infect. Immun. 70, 3948\u20133952 (2002).","journal-title":"Infect. Immun."},{"key":"1859_CR34","doi-asserted-by":"crossref","first-page":"4216","DOI":"10.1128\/AEM.00031-10","volume":"76","author":"HF Oliver","year":"2010","unstructured":"Oliver, H. F., Orsi, R. H., Wiedmann, M. & Boor, K. J. Listeria monocytogenes \u03c3B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains. Appl. Environ. Microbiol. 76, 4216 (2010).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR35","first-page":"289905","volume":"8","author":"Y Liu","year":"2017","unstructured":"Liu, Y., Orsi, R. H., Boor, K. J., Wiedmann, M. & Guariglia-Oropeza, V. Home alone: elimination of all but one alternative sigma factor in Listeria monocytogenes allows prediction of new roles for \u03c3B. Front. Microbiol. 8, 289905 (2017).","journal-title":"Front. Microbiol."},{"key":"1859_CR36","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1126\/science.1059852","volume":"292","author":"M Lecuit","year":"2001","unstructured":"Lecuit, M. et al. A transgenic model for listeriosis: role of internalin in crossing the intestinal barrier. Science 292, 1722\u20131725 (2001).","journal-title":"Science"},{"key":"1859_CR37","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1038\/s41586-022-04505-7","volume":"603","author":"C Maudet","year":"2022","unstructured":"Maudet, C. et al. Bacterial inhibition of Fas-mediated killing promotes neuroinvasion and persistence. Nature 603, 900\u2013906 (2022).","journal-title":"Nature"},{"key":"1859_CR38","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/S0092-8674(02)00905-4","volume":"110","author":"J Johansson","year":"2002","unstructured":"Johansson, J. et al. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110, 551\u2013561 (2002).","journal-title":"Cell"},{"key":"1859_CR39","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/nature14029","volume":"517","author":"ML Reniere","year":"2015","unstructured":"Reniere, M. L. et al. Glutathione activates virulence gene expression of an intracellular pathogen. Nature 517, 170\u2013173 (2015).","journal-title":"Nature"},{"key":"1859_CR40","doi-asserted-by":"crossref","first-page":"eabj9805","DOI":"10.1126\/sciadv.abj9805","volume":"7","author":"A Moura","year":"2021","unstructured":"Moura, A. et al. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Sci. Adv. 7, eabj9805 (2021).","journal-title":"Sci. Adv."},{"key":"1859_CR41","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1746-6148-5-2","volume":"5","author":"JI Esteban","year":"2009","unstructured":"Esteban, J. I., Oporto, B., Aduriz, G., Juste, R. A. & Hurtado, A. Faecal shedding and strain diversity of Listeria monocytogenes in healthy ruminants and swine in Northern Spain. BMC Vet. Res. 5, 2 (2009).","journal-title":"BMC Vet. Res."},{"key":"1859_CR42","doi-asserted-by":"crossref","first-page":"7617","DOI":"10.1111\/1462-2920.15860","volume":"23","author":"C Palacios-Gorba","year":"2021","unstructured":"Palacios-Gorba, C. et al. Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms. Environ. Microbiol. 23, 7617\u20137631 (2021).","journal-title":"Environ. Microbiol."},{"key":"1859_CR43","doi-asserted-by":"crossref","first-page":"e43801","DOI":"10.1371\/journal.pone.0043801","volume":"7","author":"L Mikonranta","year":"2012","unstructured":"Mikonranta, L., Friman, V.-P. & Laakso, J. Life history trade-offs and relaxed selection can decrease bacterial virulence in environmental reservoirs. PLoS ONE 7, e43801 (2012).","journal-title":"PLoS ONE"},{"key":"1859_CR44","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1111\/j.1420-9101.2008.01658.x","volume":"22","author":"S Alizon","year":"2009","unstructured":"Alizon, S., Hurford, A., Mideo, N. & Van Baalen, M. Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. J. Evol. Biol. 22, 245\u2013259 (2009).","journal-title":"J. Evol. Biol."},{"key":"1859_CR45","doi-asserted-by":"crossref","first-page":"5273","DOI":"10.1098\/rsif.2020.0600","volume":"17","author":"I Sultan","year":"2020","unstructured":"Sultan, I., Fromion, V., Schbath, S. & Nicolas, P. Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application to Listeria monocytogenes. J. R. Soc. Interface 17, 5273\u20135287 (2020).","journal-title":"J. R. Soc. Interface"},{"key":"1859_CR46","doi-asserted-by":"crossref","first-page":"5722","DOI":"10.1128\/JB.185.19.5722-5734.2003","volume":"185","author":"MJ Kazmierczak","year":"2003","unstructured":"Kazmierczak, M. J., Mithoe, S. C., Boor, K. J. & Wiedmann, M. Listeria monocytogenes \u03c3B regulates stress response and virulence functions. J. Bacteriol. 185, 5722\u20135734 (2003).","journal-title":"J. Bacteriol."},{"key":"1859_CR47","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s00284-003-4020-x","volume":"48","author":"A Ferreira","year":"2004","unstructured":"Ferreira, A., Gray, M., Wiedmann, M. & Boor, K. J. Comparative genomic analysis of the sigB operon in Listeria monocytogenes and in other Gram-positive bacteria. Curr. Microbiol. 48, 39\u201346 (2004).","journal-title":"Curr. Microbiol."},{"key":"1859_CR48","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1146\/annurev.micro.61.080706.093445","volume":"61","author":"M Hecker","year":"2007","unstructured":"Hecker, M., Pan\u00e9-Farr\u00e9, J. & Uwe, V. SigB-dependent general stress response in Bacillus subtilis and related Gram-positive bacteria. Annu. Rev. Microbiol. 61, 215\u2013236 (2007).","journal-title":"Annu. Rev. Microbiol."},{"key":"1859_CR49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-319-46503-6_1","volume":"83","author":"J Pan\u00e9-Farr\u00e9","year":"2017","unstructured":"Pan\u00e9-Farr\u00e9, J., Quin, M. B., Lewis, R. J. & Marles-Wright, J. Structure and function of the stressosome signalling hub. Subcell. Biochem. 83, 1\u201341 (2017).","journal-title":"Subcell. Biochem."},{"key":"1859_CR50","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1126\/science.1208144","volume":"334","author":"JCW Locke","year":"2011","unstructured":"Locke, J. C. W., Young, J. W., Fontes, M., Jim\u00e9nez, M. J. H. & Elowitz, M. B. Stochastic pulse regulation in bacterial stress response. Science 334, 366\u2013369 (2011).","journal-title":"Science"},{"key":"1859_CR51","doi-asserted-by":"crossref","first-page":"4140","DOI":"10.1073\/pnas.1213060110","volume":"110","author":"JW Young","year":"2013","unstructured":"Young, J. W., Locke, J. C. W. & Elowitz, M. B. Rate of environmental change determines stress response specificity. Proc. Natl Acad. Sci. USA 110, 4140\u20134145 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1859_CR52","doi-asserted-by":"crossref","first-page":"5197","DOI":"10.1128\/AEM.03058-05","volume":"72","author":"S Chaturongakul","year":"2006","unstructured":"Chaturongakul, S. & Boor, K. J. \u03c3B activation under environmental and energy stress conditions in Listeria monocytogenes. Appl. Environ. Microbiol. 72, 5197 (2006).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR53","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.1038\/s41467-019-10782-0","volume":"10","author":"AH Williams","year":"2019","unstructured":"Williams, A. H. et al. The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation. Nat. Commun. 10, 3005 (2019).","journal-title":"Nat. Commun."},{"key":"1859_CR54","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1128\/AEM.69.4.2015-2022.2003","volume":"69","author":"KR Fraser","year":"2003","unstructured":"Fraser, K. R., Sue, D., Wiedmann, M., Boor, K. & O\u2019Byrne, C. P. Role of \u03c3B in regulating the compatible solute uptake systems of Listeria monocytogenes: osmotic induction of opuC is \u03c3B dependent. Appl. Environ. Microbiol. 69, 2015\u20132022 (2003).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR55","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1101\/gr.276747.122","volume":"32","author":"MA Fischer","year":"2022","unstructured":"Fischer, M. A. et al. Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection. Genome Res. 32, 1711\u20131726 (2022).","journal-title":"Genome Res."},{"key":"1859_CR56","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1111\/mmi.12966","volume":"96","author":"VK K\u00f6seo\u011flu","year":"2015","unstructured":"K\u00f6seo\u011flu, V. K. et al. Listeria monocytogenes exopolysaccharide: origin, structure, biosynthetic machinery and c-di-GMP-dependent regulation. Mol. Microbiol. 96, 728\u2013743 (2015).","journal-title":"Mol. Microbiol."},{"key":"1859_CR57","doi-asserted-by":"crossref","first-page":"6827","DOI":"10.1128\/JB.182.23.6827-6830.2000","volume":"182","author":"S Mahapatra","year":"2000","unstructured":"Mahapatra, S., Crick, D. C. & Brennan, P. J. Comparison of the UPD-N-acetylmuramate:l-alanine ligase enzymes from Mycobacterium tuberculosis and Mycobacterium leprae. J. Bacteriol. 182, 6827\u20136830 (2000).","journal-title":"J. Bacteriol."},{"key":"1859_CR58","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41576-018-0081-3","volume":"20","author":"J Beaulaurier","year":"2019","unstructured":"Beaulaurier, J., Schadt, E. E. & Fang, G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat. Rev. Genet. 20, 157\u2013172 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"1859_CR59","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41579-019-0286-2","volume":"18","author":"MA S\u00e1nchez-Romero","year":"2019","unstructured":"S\u00e1nchez-Romero, M. A. & Casades\u00fas, J. The bacterial epigenome. Nat. Rev. Microbiol. 18, 7\u201320 (2019).","journal-title":"Nat. Rev. Microbiol."},{"key":"1859_CR60","doi-asserted-by":"crossref","first-page":"e1004823","DOI":"10.1371\/journal.ppat.1004823","volume":"11","author":"S Abel","year":"2015","unstructured":"Abel, S., Wiesch, P. A., zur, Davis, B. M. & Waldor, M. K. Analysis of bottlenecks in experimental models of infection. PLoS Pathog. 11, e1004823 (2015).","journal-title":"PLoS Pathog."},{"key":"1859_CR61","doi-asserted-by":"crossref","first-page":"e16151","DOI":"10.1371\/journal.pone.0016151","volume":"6","author":"N Ondrusch","year":"2011","unstructured":"Ondrusch, N. & Kreft, J. Blue and red light modulates SigB-dependent gene transcription, swimming motility and invasiveness in Listeria monocytogenes. PLoS ONE 6, e16151 (2011).","journal-title":"PLoS ONE"},{"key":"1859_CR62","doi-asserted-by":"publisher","unstructured":"Frouin, A. et al. ChoruMM: a versatile multi-components mixed model for bacterial-GWAS. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.03.28.534531 (2023) .","DOI":"10.1101\/2023.03.28.534531"},{"key":"1859_CR63","doi-asserted-by":"crossref","first-page":"e1007758","DOI":"10.1371\/journal.pgen.1007758","volume":"14","author":"M Jaillard","year":"2018","unstructured":"Jaillard, M. et al. A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events. PLoS Genet. 14, e1007758 (2018).","journal-title":"PLoS Genet."},{"key":"1859_CR64","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1101\/gr.241455.118","volume":"29","author":"JA Lees","year":"2019","unstructured":"Lees, J. A. et al. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res. 29, 304\u2013316 (2019).","journal-title":"Genome Res."},{"key":"1859_CR65","doi-asserted-by":"crossref","first-page":"e1009761","DOI":"10.1371\/journal.pgen.1009761","volume":"17","author":"M-V Mazzuoli","year":"2021","unstructured":"Mazzuoli, M.-V. et al. The CovR regulatory network drives the evolution of Group B Streptococcus virulence. PLoS Genet. 17, e1009761 (2021).","journal-title":"PLoS Genet."},{"key":"1859_CR66","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1038\/nrmicro1446","volume":"4","author":"EV Sokurenko","year":"2006","unstructured":"Sokurenko, E. V., Gomulkiewicz, R. & Dykhuizen, D. E. Source\u2013sink dynamics of virulence evolution. Nat. Rev. Microbiol. 4, 548\u2013555 (2006).","journal-title":"Nat. Rev. Microbiol."},{"key":"1859_CR67","doi-asserted-by":"crossref","first-page":"4283","DOI":"10.1038\/s41467-019-12072-1","volume":"10","author":"Y Yin","year":"2019","unstructured":"Yin, Y. et al. A hybrid sub-lineage of Listeria monocytogenes comprising hypervirulent isolates. Nat. Commun. 10, 4283 (2019).","journal-title":"Nat. Commun."},{"key":"1859_CR68","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/j.chom.2018.03.004","volume":"23","author":"R Drolia","year":"2018","unstructured":"Drolia, R., Tenguria, S., Durkes, A. C., Turner, J. R. & Bhunia, A. K. Listeria adhesion protein induces intestinal epithelial barrier dysfunction for bacterial translocation. Cell Host Microbe 23, 470\u2013484.e7 (2018).","journal-title":"Cell Host Microbe"},{"key":"1859_CR69","doi-asserted-by":"crossref","first-page":"112515","DOI":"10.1016\/j.celrep.2023.112515","volume":"42","author":"D Liu","year":"2023","unstructured":"Liu, D. et al. Cell-surface anchoring of Listeria adhesion protein on L. monocytogenes is fastened by internalin B for pathogenesis. Cell Rep. 42, 112515 (2023).","journal-title":"Cell Rep."},{"key":"1859_CR70","doi-asserted-by":"crossref","first-page":"4566","DOI":"10.1111\/1462-2920.12980","volume":"17","author":"RB Vasanthakrishnan","year":"2015","unstructured":"Vasanthakrishnan, R. B. et al. PrfA regulation offsets the cost of Listeria virulence outside the host. Environ. Microbiol. 17, 4566\u20134579 (2015).","journal-title":"Environ. Microbiol."},{"key":"1859_CR71","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.tree.2015.02.009","volume":"30","author":"S Alizon","year":"2015","unstructured":"Alizon, S. & Michalakis, Y. Adaptive virulence evolution: the good old fitness-based approach. Trends Ecol. Evol. 30, 248\u2013254 (2015).","journal-title":"Trends Ecol. Evol."},{"key":"1859_CR72","doi-asserted-by":"crossref","first-page":"e0033022","DOI":"10.1128\/aem.00330-22","volume":"88","author":"DN Guerreiro","year":"2022","unstructured":"Guerreiro, D. N. et al. In vitro evolution of Listeria monocytogenes reveals selective pressure for loss of SigB and AgrA function at different incubation temperatures. Appl. Environ. Microbiol. 88, e0033022 (2022).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR73","first-page":"e01370","volume":"85","author":"BH Lee","year":"2019","unstructured":"Lee, B. H. et al. Exploring Listeria monocytogenes transcriptomes in correlation with divergence of lineages and virulence as measured in Galleria mellonella. Appl. Environ. Microbiol. 85, e01370\u201319 (2019).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR74","first-page":"e00863","volume":"10","author":"A Casadevall","year":"2019","unstructured":"Casadevall, A. & Pirofski, L. A. Benefits and costs of animal virulence for microbes. mBio 10, e00863\u201319 (2019).","journal-title":"mBio"},{"key":"1859_CR75","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/0966-842X(94)90538-X","volume":"2","author":"BR Levin","year":"1994","unstructured":"Levin, B. R. & Bull, J. J. Short-sighted evolution and the virulence of pathogenic microorganisms. Trends Microbiol. 2, 76\u201381 (1994).","journal-title":"Trends Microbiol."},{"key":"1859_CR76","doi-asserted-by":"crossref","first-page":"4085","DOI":"10.1128\/JB.186.13.4085-4099.2004","volume":"186","author":"M Bischoff","year":"2004","unstructured":"Bischoff, M. et al. Microarray-based analysis of the Staphylococcus aureus \u03c3B regulon. J. Bacteriol. 186, 4085\u20134099 (2004).","journal-title":"J. Bacteriol."},{"key":"1859_CR77","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s41576-018-0069-z","volume":"20","author":"JL Payne","year":"2018","unstructured":"Payne, J. L. & Wagner, A. The causes of evolvability and their evolution. Nat. Rev. Genet. 20, 24\u201338 (2018).","journal-title":"Nat. Rev. Genet."},{"key":"1859_CR78","doi-asserted-by":"crossref","first-page":"eadi0908","DOI":"10.1126\/science.adi0908","volume":"385","author":"A Weimann","year":"2024","unstructured":"Weimann, A. et al. Evolution and host-specific adaptation of Pseudomonas aeruginosa. Science 385, eadi0908 (2024).","journal-title":"Science"},{"key":"1859_CR79","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691\u20133693 (2015).","journal-title":"Bioinformatics"},{"key":"1859_CR80","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"1859_CR81","doi-asserted-by":"crossref","first-page":"641647","DOI":"10.1155\/2014\/641647","volume":"2014","author":"M Utratna","year":"2014","unstructured":"Utratna, M., Cosgrave, E., Baustian, C., Ceredig, R. H. & O\u2019Byrne, C. P. Effects of growth phase and temperature on \u03c3B activity within a Listeria monocytogenes population: evidence for RsbV-independent activation of \u03c3B at refrigeration temperatures. Biomed. Res. Int. 2014, 641647 (2014).","journal-title":"Biomed. Res. Int."},{"key":"1859_CR82","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"1859_CR83","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","volume":"16","author":"S Berg","year":"2019","unstructured":"Berg, S. et al. ilastik: interactive machine learning for (bio)image analysis. Nat. Methods 16, 1226\u20131232 (2019).","journal-title":"Nat. Methods"},{"key":"1859_CR84","doi-asserted-by":"crossref","first-page":"5309","DOI":"10.1128\/iai.65.12.5309-5319.1997","volume":"65","author":"M Lecuit","year":"1997","unstructured":"Lecuit, M., Ohayon, H., Braun, L., Mengaud, J. & Cossart, P. Internalin of Listeria monocytogenes with an intact leucine-rich repeat region is sufficient to promote internalization. Infect. Immun. 65, 5309\u20135319 (1997).","journal-title":"Infect. Immun."},{"key":"1859_CR85","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460\u20132461 (2010).","journal-title":"Bioinformatics"},{"key":"1859_CR86","doi-asserted-by":"crossref","first-page":"3921","DOI":"10.1128\/AEM.00314-08","volume":"74","author":"IR Monk","year":"2008","unstructured":"Monk, I. R., Gahan, C. G. M. & Hill, C. Tools for functional postgenomic analysis of Listeria monocytogenes. Appl. Environ. Microbiol. 74, 3921\u20133934 (2008).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR87","doi-asserted-by":"crossref","first-page":"e02927","DOI":"10.1128\/AEM.02927-16","volume":"83","author":"T Argov","year":"2017","unstructured":"Argov, T., Rabinovich, L., Sigal, N. & Herskovits, A. A. An effective counterselection system for Listeria monocytogenes and its use to characterize the monocin genomic region of strain 10403S. Appl. Environ. Microbiol. 83, e02927\u201316 (2017).","journal-title":"Appl. Environ. Microbiol."},{"key":"1859_CR88","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"1859_CR89","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586\u20131591 (2007).","journal-title":"Mol. Biol. Evol."},{"key":"1859_CR90","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422\u20131423 (2009).","journal-title":"Bioinformatics"},{"key":"1859_CR91","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","volume":"43","author":"TL Bailey","year":"2015","unstructured":"Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. The MEME suite. Nucleic Acids Res. 43, W39\u2013W49 (2015).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-024-01859-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-024-01859-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-024-01859-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T16:13:50Z","timestamp":1732724030000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-024-01859-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,22]]},"references-count":91,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1859"],"URL":"https:\/\/doi.org\/10.1038\/s41564-024-01859-8","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,22]]},"assertion":[{"value":"21 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 October 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 November 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}