Parisi, A. et al. Health outcomes from multidrug-resistant Salmonella infections in high-income countries: a systematic review and meta-analysis. Foodborne Pathog. Dis. 15, 428–436 (2018).
Wright, G. D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5, 175–186 (2007).
Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Q. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. Rev. Microbiol. 14, 320–330 (2016).
Fridman, O., Goldberg, A., Ronin, I., Shoresh, N. & Balaban, N. Q. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 513, 418–421 (2014).
Claudi, B. et al. Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell 158, 722–733 (2014).
Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204–208 (2014).
Kaiser, P. et al. Cecum lymph node dendritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment. PLoS Biol. 12, e1001793 (2014).
Dolowschiak, T. et al. IFN-γ hinders recovery from mucosal inflammation during antibiotic therapy for Salmonella gut infection. Cell Host Microbe 20, 238–249 (2016).
Balaban, N. Q. et al. Definitions and guidelines for research on antibiotic persistence. Nat. Rev. Microbiol. 17, 441–448 (2019).
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004).
Levin-Reisman, I. et al. Antibiotic tolerance facilitates the evolution of resistance. Science 355, 826–830 (2017).
Wotzka, S. Y. et al. Microbiota stability in healthy individuals after single-dose lactulose challenge–a randomized controlled study. PLoS ONE 13, e0206214 (2018).
Coque, T. M., Baquero, F. & Canton, R. Increasing prevalence of ESBL-producing Enterobacteriaceae in Europe. Eurosurveillance 13, 19044 (2008).
Crump, J. A., Sjölund-Karlsson, M., Gordon, M. A. & Parry, C. M. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin. Microbiol. Rev. 28, 901–937 (2015).
Wilcock, B. P., Armstrong, C. H. & Olander, H. J. The significance of the serotype in the clinical and pathological features of naturally occurring porcine salmonellosis. Can. J. Comp. Med. 40, 80–88 (1976).
Wood, R. L., Pospischil, A. & Rose, R. Distribution of persistent Salmonella typhimurium infection in internal organs of swine. Am. J. Vet. Res. 50, 1015–1021 (1989).
San Román, B. et al. Relationship between Salmonella infection, shedding and serology in fattening pigs in low–moderate prevalence areas. Zoonoses Public Health 65, 481–489 (2018).
Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).
Apperloo-Renkema, H. Z., Van der Waaij, B. D. & Van der Waaij, D. Determination of colonization resistance of the digestive tract by biotyping of Enterobacteriaceae. Epidemiol. Infect. 105, 355–361 (1990).
Stecher, B. et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc. Natl Acad. Sci. USA 109, 1269–1274 (2012).
Diard, M. et al. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 355, 1211–1215 (2017).
Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 544, 498–502 (2017).
Monack, D. M., Bouley, D. M. & Falkow, S. Salmonella typhimurium persists within macrophages in the mesenteric lymph nodes of chronically infected Nramp1 +/+ mice and can be reactivated by IFNγ neutralization. J. Exp. Med. 199, 231–241 (2004).
Diard, M. et al. Antibiotic treatment selects for cooperative virulence of Salmonella Typhimurium. Curr. Biol. 24, 2000–2005 (2014).
Sampei, G. et al. Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid 64, 92–103 (2010).
Hensel, M. et al. Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400–403 (1995).
Stapels, D. A. C. et al. Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 362, 1156–1160 (2018).
Moor, K. et al. Peracetic acid treatment generates potent inactivated oral vaccines from a broad range of culturable bacterial species. Front. Immunol. 7, 34 (2016).
Fauvart, M., De Groote, V. N. & Michiels, J. Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J. Med. Microbiol. 60, 699–709 (2011).
Roberts, M. E. & Stewart, P. S. Modelling protection from antimicrobial agents in biofilms through the formation of persister cells. Microbiology 151, 75–80 (2005).
Knodler, L. A. et al. Noncanonical inflammasome activation of caspase-4/caspase-11 mediates epithelial defenses against enteric bacterial pathogens. Cell Host Microbe 16, 249–256 (2014).
Sellin, M. E. et al. Epithelium-intrinsic NAIP/NLRC4 inflammasome drives infected enterocyte expulsion to restrict Salmonella replication in the intestinal mucosa. Cell Host Microbe 16, 237–248 (2014).
Defraine, V., Fauvart, M. & Michiels, J. Fighting bacterial persistence: current and emerging anti-persister strategies and therapeutics. Drug Resist. Updat. 38, 12–26 (2018).
Grant, A. J. et al. Modelling within-host spatiotemporal dynamics of invasive bacterial disease. PLoS Biol. 6, e74 (2008).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Sternberg, N. L. & Maurer, R. Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204, 18–43 (1991).
Stecher, B. et al. Chronic Salmonella enterica serovar Typhimurium-induced colitis and cholangitis in streptomycin-pretreated Nramp1 +/+ mice. Infect. Immun. 74, 5047–5057 (2006).
Barthel, M. et al. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect. Immun. 71, 2839–2858 (2003).
Johansson, M. E. & Hansson, G. C. Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH. Methods Mol. Biol. 842, 229–235 (2012).
Marjoram, P., Molitor, J., Plagnol, V. & Tavare, S. Markov chain Monte Carlo without likelihoods. Proc. Natl Acad. Sci. USA 100, 15324–15328 (2003).
Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).