Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Antibiotic-recalcitrant Salmonella during infection

Abstract

Antibiotic-recalcitrant infections, defined as the prolonged carriage of pathogenic bacteria even in the presence of antibiotics, are often caused by bacteria that are genetically susceptible to the drug. These recalcitrant bacteria fail to proliferate in the presence of antibiotics but remain viable such that they may recolonize their niche following antibiotic withdrawal. Significant progress has been made in our understanding of antibiotic-recalcitrant Salmonella, which are thought to be the source of infection relapse. In recent years, it has been shown that recalcitrant bacteria manipulate host immune defences and could directly contribute to the spread of antimicrobial resistance. In this Review, we provide an overview of what is currently known about the antibiotic recalcitrance of Salmonella during infection and highlight knowledge gaps requiring additional research in the future.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Bacterial mechanisms of antibiotic evasion.
Fig. 2: Intramacrophage persister physiology.
Fig. 3: Salmonella dissemination patterns in the murine model of systemic infection.
Fig. 4: Outcomes and implications of recalcitrant Salmonella infection.

Similar content being viewed by others

References

  1. Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).

    Article  CAS  Google Scholar 

  2. Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations (HM Government & Wellcome Trust, 2014).

  3. Levin-Reisman, I. et al. Antibiotic tolerance facilitates the evolution of resistance. Science 355, 826–830 (2017). This study provides some of the earliest evidence that antibiotic tolerance leads to resistance.

    Article  CAS  PubMed  Google Scholar 

  4. Windels, E. M. et al. Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME J. 13, 1239 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Santi, I., Manfredi, P., Maffei, E., Egli, A. & Jenal, U. Evolution of antibiotic tolerance shapes resistance development in chronic Pseudomonas aeruginosa infections. mBio 12, e03482-20 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bigger, J. W. Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 244, 497–500 (1944).

    Article  Google Scholar 

  7. Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004).

    Article  CAS  PubMed  Google Scholar 

  8. Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ. Front. Microbiol. 5, 102622 (2014).

    Article  Google Scholar 

  9. Hughes, M., Appiah, G. & Watkins, L. F. Typhoid & Paratyphoid Fever. In CDC Yellow Book 2024: Health Information for International Travel (Oxford Univ. Press, 2023).

  10. Plumb, I., Fields, P. & Bruce, B. Salmonellosis, nontyphoidal. In CDC Yellow Book 2024: Health Information for International Travel (Oxford Univ. Press, 2023).

  11. Roth, G. A. et al. Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet 392, 1736–1788 (2018).

    Article  Google Scholar 

  12. Medalla, F. et al. Increased incidence of antimicrobial-resistant nontyphoidal Salmonella infections, United States, 2004–2016. Emerg. Infect. Dis. 27, 1662–1672 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Takem, E. N., Roca, A. & Cunnington, A. The association between malaria and nontyphoid Salmonella bacteraemia in children in sub-Saharan Africa: a literature review. Malar. J. 13, 400 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Brent, A. J. et al. Salmonella bacteremia in Kenyan children. J. Pediatr. Infect. Dis. 25, 230–236 (2006).

    Article  Google Scholar 

  15. Marchello, C. S. et al. Complications and mortality of non-typhoidal Salmonella invasive disease: a global systematic review and meta-analysis. Lancet Infect. Dis. 22, 692–705 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Nyirenda, T. S., Mandala, W. L., Gordon, M. A. & Mastroeni, P. Immunological bases of increased susceptibility to invasive nontyphoidal Salmonella infection in children with malaria and anaemia. Microbes Infect. 20, 589–598 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Griffin, A. J., Li, L. X., Voedisch, S., Pabst, O. & McSorley, S. J. Dissemination of persistent intestinal bacteria via the mesenteric lymph nodes causes typhoid relapse. Infect. Immun. 79, 1479–1488 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204–208 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Balaban, N. Q. et al. Definitions and guidelines for research on antibiotic persistence. Nat. Rev. Microbiol. 17, 441–448 (2019). This review provides a comprehensive overview of the terms and definitions used throughout the field as agreed upon by a consensus of interested laboratories.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Weinstein, M. P. & Lewis, J. S. The Clinical and Laboratory Standards Institute Subcommittee on Antimicrobial Susceptibility Testing: background, organization, functions, and processes. J. Clin. Microbiol. 58, e01864-19 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Giske, C. G. et al. Update from the European Committee on Antimicrobial Susceptibility Testing (EUCAST). J. Clin. Microbiol. 60, e0027621 (2022).

    Article  PubMed  Google Scholar 

  22. Darby, E. M. et al. Molecular mechanisms of antibiotic resistance revisited. Nat. Rev. Microbiol. 21, 280–295 (2022).

    Article  PubMed  Google Scholar 

  23. Britto, C. D., Wong, V. K., Dougan, G. & Pollard, A. J. A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid. PLoS Negl. Trop. Dis. 12, e0006779 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kariuki, S., Gordon, M. A., Feasey, N. & Parry, C. M. Antimicrobial resistance and management of invasive Salmonella disease. Vaccine 33, C21 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Dewachter, L., Fauvart, M. & Michiels, J. Bacterial heterogeneity and antibiotic survival: understanding and combatting persistence and heteroresistance. Mol. Cell 76, 255–267 (2019).

    Article  CAS  PubMed  Google Scholar 

  26. Andersson, D. I., Nicoloff, H. & Hjort, K. Mechanisms and clinical relevance of bacterial heteroresistance. Nat. Rev. Microbiol. 17, 479–496 (2019).

    Article  CAS  PubMed  Google Scholar 

  27. Nicoloff, H., Hjort, K., Levin, B. R. & Andersson, D. I. The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat. Microbiol. 4, 504–514 (2019).

    Article  CAS  PubMed  Google Scholar 

  28. Hjort, K., Nicoloff, H. & Andersson, D. I. Unstable tandem gene amplification generates heteroresistance (variation in resistance within a population) to colistin in Salmonella enterica. Mol. Microbiol. 102, 274–289 (2016).

    Article  CAS  PubMed  Google Scholar 

  29. El-Halfawy, O. M. & Valvano, M. A. Antimicrobial heteroresistance: an emerging field in need of clarity. Clin. Microbiol. Rev. 28, 191–207 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pereira, C., Larsson, J., Hjort, K., Elf, J. & Andersson, D. I. The highly dynamic nature of bacterial heteroresistance impairs its clinical detection. Commun. Biol. 4, 521 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Pontes, M. H. & Groisman, E. A. Slow growth determines nonheritable antibiotic resistance in Salmonella enterica. Sci. Signal. 12, eaax3938 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Michaux, C., Ronneau, S., Giorgio, R. T. & Helaine, S. Antibiotic tolerance and persistence have distinct fitness trade-offs. PLoS Pathog. 18, e1010963 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Rossi, O. et al. Within-host spatiotemporal dynamics of systemic Salmonella infection during and after antimicrobial treatment. J. Antimicrob. Chemother. 72, 3390–3397 (2017). This study relies on DNA barcodes to provide one of the only quantitative measures to date of Salmonella dissemination patterns following antibiotic withdrawal.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Rizvanovic, A. et al. The RNA-binding protein ProQ promotes antibiotic persistence in Salmonella. mBio 13, e0289122 (2022).

    Article  PubMed  Google Scholar 

  35. Helaine, S. et al. Dynamics of intracellular bacterial replication at the single cell level. Proc. Natl Acad. Sci. USA 107, 3746–3751 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Beam, J. E. et al. Inflammasome-mediated glucose limitation induces antibiotic tolerance in Staphylococcus aureus. iScience 26, 107942 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Liu, J., Gefen, O., Ronin, I., Bar-Meir, M. & Balaban, N. Q. Effect of tolerance on the evolution of antibiotic resistance under drug combinations. Science 367, 200–204 (2020).

    Article  CAS  PubMed  Google Scholar 

  38. Hill, P. W. S. et al. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 29, 1757–1773.e10 (2021).

    Article  CAS  PubMed  Google Scholar 

  39. Manuse, S. et al. Bacterial persisters are a stochastically formed subpopulation of low-energy cells. PLoS Biol. 19, e3001194 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Peyrusson, F. et al. Intracellular Staphylococcus aureus persisters upon antibiotic exposure. Nat. Commun. 11, 2200 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Cotten, K. L. & Davis, K. M. Bacterial heterogeneity and antibiotic persistence: bacterial mechanisms utilized in the host environment. Microbiol. Mol. Biol. Rev. 87, e00174-22 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Nguyen, D. et al. Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria. Science 334, 982–986 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Irving, S. E., Choudhury, N. R. & Corrigan, R. M. The stringent response and physiological roles of (pp)pGpp in bacteria. Nat. Rev. Microbiol. 19, 256–271 (2020).

    Article  PubMed  Google Scholar 

  44. Conlon, B. P. et al. Persister formation in Staphylococcus aureus is associated with ATP depletion. Nat. Microbiol. 1, 16051 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Cox, M. M. Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 8, 127–138 (2007).

    Article  CAS  PubMed  Google Scholar 

  46. Podlesek, Z. & Žgur Bertok, D. The DNA damage inducible SOS response is a key player in the generation of bacterial persister cells and population wide tolerance. Front. Microbiol. 11, 1785 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Luk, C. H. et al. Salmonella enters a dormant state within human epithelial cells for persistent infection. PLoS Pathog. 17, e1009550 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Schulte, M., Olschewski, K. & Hensel, M. The protected physiological state of intracellular Salmonella enterica persisters reduces host cell-imposed stress. Commun. Biol. 4, 520 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Pizarro-Cerdá, J. & Tedin, K. The bacterial signal molecule, ppGpp, regulates Salmonella virulence gene expression. Mol. Microbiol. 52, 1827–1844 (2004).

    Article  PubMed  Google Scholar 

  50. Henard, C. A., Bourret, T. J., Song, M. & Vázquez-Torres, A. Control of redox balance by the stringent response regulatory protein promotes antioxidant defenses of Salmonella. J. Biol. Chem. 285, 36785–36793 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Henard, C. A. & Vázquez-Torres, A. DksA-dependent resistance of Salmonella enterica serovar Typhimurium against the antimicrobial activity of inducible nitric oxide synthase. Infect. Immun. 80, 1373–1380 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Azriel, S., Goren, A., Rahav, G. & Gal-Mor, O. The stringent response regulator DksA is required for Salmonella enterica serovar Typhimurium growth in minimal medium, motility, biofilm formation, and intestinal colonization. Infect. Immun. 84, 375–384 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Gruber, C. C. & Walker, G. C. Incomplete base excision repair contributes to cell death from antibiotics and other stresses. DNA Repair. 71, 108–117 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Husain, M. et al. Nitric oxide evokes an adaptive response to oxidative stress by arresting respiration. J. Biol. Chem. 283, 7682–7689 (2008).

    Article  CAS  PubMed  Google Scholar 

  55. Richardson, A. R. et al. Multiple targets of nitric oxide in the tricarboxylic acid (TCA) cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 10, 33 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Ronneau, S., Michaux, C. & Helaine, S. Decline in nitrosative stress drives antibiotic persister regrowth during infection. Cell Host Microbe 31, 993–1006.e6 (2023). This study is built on previous research about the effect of host-derived reactive nitrogen species on antibiotic recalcitrance, demonstrating the contribution of nitrosative stress to Salmonella persister regrowth in vivo.

    Article  CAS  PubMed  Google Scholar 

  57. Liu, Y. et al. Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. J. Exp. Med. 213, 809–825 (2016). This study identifies reactive nitrogen species as an inducer of antibiotic recalcitrance.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Rowe, S. E. et al. Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection. Nat. Microbiol. 5, 282–290 (2019). This study presents evidence that intoxication of the tricarboxylic acid cycle leads to antibiotic recalcitrance.

    Article  PubMed  PubMed Central  Google Scholar 

  59. Jurėnas, D., Fraikin, N., Goormaghtigh, F. & Van Melderen, L. Biology and evolution of bacterial toxin–antitoxin systems. Nat. Rev. Microbiol. 20, 335–350 (2022).

    Article  PubMed  Google Scholar 

  60. LeRoux, M., Culviner, P. H., Liu, Y. J., Littlehale, M. L. & Laub, M. T. Stress can induce transcription of toxin–antitoxin systems without activating toxin. Mol. Cell 79, 280–292.e8 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Cheverton, A. M. et al. A Salmonella toxin promotes persister formation through acetylation of tRNA. Mol. Cell 63, 86–96 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Dörr, T., Vulić, M. & Lewis, K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol. 8, e1000317 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Ronneau, S., Michaux, C., Giorgio, R. T. & Helaine, S. Intoxication of antibiotic persisters by host RNS inactivates their efflux machinery during infection. PLoS Pathog. 20, e1012033 (2024). This paper corroborates previous in vitro findings regarding the role of drug efflux pumps in persister survival and highlights the existence of phenotypic heterogeneity even within a persister subpopulation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Pu, Y. et al. Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Mol. Cell 62, 284 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Byrd, B. A. et al. The AcrAB-TolC efflux pump impacts persistence and resistance development in stationary-phase Escherichia coli following delafloxacin treatment. Antimicrob. Agents Chemother. 65, e0028121 (2021).

    Article  PubMed  Google Scholar 

  66. Stapels, D. A. C. et al. Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 362, 1156–1160 (2018).

    Article  CAS  PubMed  Google Scholar 

  67. Jennings, E., Thurston, T. L. M. & Holden, D. W. Salmonella SPI-2 type III secretion system effectors: molecular mechanisms and physiological consequences. Cell Host Microbe 22, 217–231 (2017).

    Article  CAS  PubMed  Google Scholar 

  68. Panagi, I. et al. Salmonella effector SteE converts the mammalian serine/threonine kinase GSK3 into a tyrosine kinase to direct macrophage polarization. Cell Host Microbe 27, 41–53.e6 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. McCoy, M. W., Moreland, S. M. & Detweiler, C. S. Hemophagocytic macrophages in murine typhoid fever have an anti-inflammatory phenotype. Infect. Immun. 80, 3642–3649 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Eisele, N. A. et al. Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long term persistence. Cell Host Microbe 14, 171 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Personnic, N. et al. Quorum sensing modulates the formation of virulent Legionella persisters within infected cells. Nat. Commun. 10, 5216 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  72. 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).

    Article  CAS  PubMed  Google Scholar 

  73. Hoiseth, S. K. & Stocker, B. A. D. Aromatic-dependent Salmonella typhimurium are non-virulent and effective as live vaccines. Nature 291, 238–239 (1981).

    Article  CAS  PubMed  Google Scholar 

  74. Richardson, E. J. et al. Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well-defined virulence in food-producing animals. J. Bacteriol. 193, 3162–3163 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Ramanadane, K., Straub, M. S., Dutzler, R. & Manatschal, C. Structural and functional properties 1 of a magnesium transporter of the SLC11/NRAMP family. eLife 11, e74589 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Cunrath, O. & Bumann, D. Host resistance factor SLC11A1 restricts Salmonella growth through magnesium deprivation. Science 366, 995–999 (2019).

    Article  CAS  PubMed  Google Scholar 

  77. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Scoggin, K. et al. Elucidating mechanisms of tolerance to Salmonella Typhimurium cross long-term infections using the collaborative cross. mBio 13, e01120-22 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  79. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. World Health Organization. World Health Organization model List of Essential Medicines, 23rd List. The Selection and Use of Essential Medicines 2023: Web Annex 4 (WHO, 2023).

  81. World Health Organization. World Health Organization Model List of Essential Medicines for Children, 9th list. The Selection and Use of Essential Medicines 2023: Web Annex B (WHO, 2023).

  82. Watson, K. G. & Holden, D. W. Dynamics of growth and dissemination of Salmonella in vivo. Cell Microbiol. 12, 1389–1397 (2010).

    Article  CAS  PubMed  Google Scholar 

  83. Salcedo, S. P., Noursadeghi, M., Cohen, J. & Holden, D. W. Intracellular replication of Salmonella typhimurium strains in specific subsets of splenic macrophages in vivo. Cell Microbiol. 3, 587–597 (2001).

    Article  CAS  PubMed  Google Scholar 

  84. Hopkins, S. A., Niedergang, F., Corthesy-Theulaz, I. E. & Kraehenbuhl, J. P. A recombinant Salmonella typhimurium vaccine strain is taken up and survives within murine Peyer’s patch dendritic cells. Cell. Microbiol. 2, 59–68 (2000).

    Article  CAS  PubMed  Google Scholar 

  85. Niedergang, F., Sirard, J. C., Blanc, C. T. & Kraehenbuhl, J. P. Entry and survival of Salmonella typhimurium in dendritic cells and presentation of recombinant antigens do not require macrophage-specific virulence factors. Proc. Natl Acad. Sci. USA 97, 14650–14655 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Hill, P. W. S. & Helaine, S. in Persister Cells and Infectious Disease (ed. Lewis, K.) 19–38 (Springer, 2019).

  87. Kaiser, P. et al. Cecum lymph node dendritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment. PLoS Biol. 12, e100793 (2014). This study corroborates previous findings that the caecal lymph node is a reservoir for antibiotic-recalcitrant Salmonella, with the bacteria primarily residing within classic dendritic cells.

    Article  Google Scholar 

  88. Pham, T. H. M. et al. Single-cell profiling identifies ACE+ granuloma macrophages as a nonpermissive niche for intracellular bacteria during persistent Salmonella infection. Sci. Adv. 9, eadd4333 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Nix, R. N., Altschuler, S. E., Henson, P. M. & Detweiler, C. S. Hemophagocytic macrophages harbor Salmonella enterica during persistent infection. PLoS Pathog. 3, e193 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  90. Pham, T. H. M. et al. Salmonella-driven polarization of granuloma macrophages antagonizes TNF-mediated pathogen restriction during persistent infection. Cell Host Microbe 27, 54–67.e5 (2020).

    Article  CAS  PubMed  Google Scholar 

  91. Kanvatirth, P. et al. Dual role of splenic mononuclear and polymorphonuclear cells in the outcome of ciprofloxacin treatment of Salmonella enterica infections. J. Antimicrob. Chemother. 75, 2914–2918 (2020).

    Article  CAS  PubMed  Google Scholar 

  92. Li, J. et al. Tissue compartmentalization enables Salmonella persistence during chemotherapy. Proc. Natl Acad. Sci. USA 118, e2113951118 (2021). This innovative study relies on the use of serial dual-photon microscopy to directly observe antibiotic-recalcitrant bacteria in the entire spleen.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Kurtz, J. R. et al. Salmonella persistence and host immunity is dictated by the anatomical microenvironment. Infect. Immun. 88, e00026-20 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  94. Bakkeren, E. et al. Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. Nature 573, 276–280 (2019). This paper provides evidence that Salmonella persisters can engage in horizontal gene transfer in vivo with luminal bacteria.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Aleksandrowicz, A. et al. Better together – Salmonella biofilm-associated antibiotic resistance. Gut Microbes 15, 2229937 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Crawford, R. W. et al. Gallstones play a significant role in Salmonella spp. gallbladder colonization and carriage. Proc. Natl Acad. Sci. USA 107, 4353–4358 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Gonzalez-Escobedo, G. & Gunn, J. S. Gallbladder epithelium as a niche for chronic Salmonella carriage. Infect. Immun. 81, 2920 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. González, J. F., Alberts, H., Lee, J., Doolittle, L. & Gunn, J. S. Biofilm formation protects Salmonella from the antibiotic ciprofloxacin in vitro and in vivo in the mouse model of chronic carriage. Sci. Rep. 8, 222 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  99. Ponder, R. G., Fonville, N. C. & Rosenberg, S. M. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell 19, 791–804 (2005).

    Article  CAS  PubMed  Google Scholar 

  100. Shee, C., Gibson, J. L., Darrow, M. C., Gonzalez, C. & Rosenberg, S. M. Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli. Proc. Natl Acad. Sci. USA 108, 13659–13664 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Pribis, J. P. et al. Gamblers: an antibiotic-induced evolvable cell subpopulation differentiated by reactive-oxygen-induced general stress response. Mol. Cell 74, 785–800.e7 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Moore, J. M., Correa, R., Rosenberg, S. M. & Hastings, P. J. Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli. PLoS Genet. 13, e1006733 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Long, H. et al. Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc. Natl Acad. Sci. USA 113, E2498–E2505 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Sebastian, J. et al. De novo emergence of genetically resistant mutants of Mycobacterium tuberculosis from the persistence phase cells formed against antituberculosis drugs in vitro. Antimicrob. Agents Chemother. 61, e01343-16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  105. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Bakkeren, E. et al. Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut. eLife 10, e69744 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Wain, J. et al. Molecular typing of multiple-antibiotic-resistant Salmonella enterica serovar Typhi from Vietnam: application to acute and relapse cases of typhoid fever. J. Clin. Microbiol. 37, 2466–2472 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Gordon, M. A. et al. Non-typhoidal Salmonella bacteraemia among HIV-infected Malawian adults: high mortality and frequent recrudescence. AIDS 16, 1633–1641 (2002).

    Article  PubMed  Google Scholar 

  109. Okoro, C. K. et al. High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease. Clin. Infect. Dis. 54, 955–963 (2012). This study reports the use of single nucleotide polymorphism-based phylogenetic analysis to distinguish between reinfection and infection relapse in human patient samples.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Caygill, C. P., Hill, M. J., Braddick, M. & Sharp, J. C. Cancer mortality in chronic typhoid and paratyphoid carriers. Lancet 343, 83–84 (1994).

    Article  CAS  PubMed  Google Scholar 

  111. Mughini-Gras, L. et al. Increased colon cancer risk after severe Salmonella infection. PLoS ONE 13, e0189721 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  112. van Elsland, D. M. et al. Repetitive non-typhoidal Salmonella exposure is an environmental risk factor for colon cancer and tumor growth. Cell Rep. Med. 3, 100852 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  113. Scanu, T. et al. Salmonella manipulation of host signaling pathways provokes cellular transformation associated with gallbladder carcinoma. Cell Host Microbe 17, 763–774 (2015).

    Article  CAS  PubMed  Google Scholar 

  114. Forbes, N. S., Munn, L. L., Fukumura, D. & Jain, R. K. Sparse initial entrapment of systemically injected Salmonella typhimurium leads to heterogeneous accumulation within tumors. Cancer Res. 63, 5188–5193 (2003).

    CAS  PubMed  Google Scholar 

  115. Pawelek, J. M., Low, K. B. & Bermudes, D. Tumor-targeted Salmonella as a novel anticancer vector. Cancer Res. 57, 4537–4544 (1997).

    CAS  PubMed  Google Scholar 

  116. Väyrynen, J. P. et al. The prognostic role of macrophage polarization in the colorectal cancer microenvironment. Cancer Immunol. Res. 9, 8–19 (2021).

    Article  PubMed  Google Scholar 

  117. Defraine, V., Fauvart, M. & Michiels, J. Fighting bacterial persistence: current and emerging anti-persister strategies and therapeutics. Drug. Resist. Updat. 38, 12–26 (2018).

    Article  PubMed  Google Scholar 

  118. Rishi, P., Bhagat, N. R., Thakur, R. & Pathania, P. Tackling Salmonella persister cells by antibiotic–nisin combination via mannitol. Indian. J. Microbiol. 58, 239–243 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Reens, A. L. et al. A cell-based infection assay identifies efflux pump modulators that reduce bacterial intracellular load. PLoS Pathog. 14, e1007115 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  120. Sandala, J. L. et al. A dual-therapy approach for the treatment of biofilm-mediated Salmonella gallbladder carriage. PLoS Pathog. 16, e1009192 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Stanley, S. A., Barczak, A. K., Silvis, M. R., Luo, S. S. & Sogi, K. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 10, e1003946 (2014). This study proposes a novel mechanism of persister control whereby host immune pathways are stimulated to restrict bacterial growth.

    Article  PubMed  PubMed Central  Google Scholar 

  122. Lin, J. S. et al. Anti-persister and anti-biofilm activity of self-assembled antimicrobial peptoid ellipsoidal micelles. ACS Infect. Dis. 8, 1823–1830 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Wollesen, M. et al. Polyether ionophore antibiotics target drug-resistant clinical isolates, persister cells, and biofilms. Microbiol. Spectr. 11, e00625-23 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  124. 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).

    Article  CAS  PubMed  Google Scholar 

  125. Lim, C. H. et al. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by Salmonella. PLoS Pathog. 10, e1004270 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Thiemann, S. et al. Enhancement of IFNγ production by distinct commensals ameliorates Salmonella-induced disease. Cell Host Microbe 21, 682–694.e5 (2017).

    Article  CAS  PubMed  Google Scholar 

  127. Al Shoyaib, A., Archie, S. R. & Karamyan, V. T. Intraperitoneal route of drug administration: should it be used in experimental animal studies? Pharm. Res. 37, 12 (2020).

    Article  CAS  Google Scholar 

  128. Vlazaki, M. et al. A data-based mathematical modelling study to quantify the effects of ciprofloxacin and ampicillin on the within-host dynamics of Salmonella enterica during treatment and relapse. J. R. Soc. Interface 17, 20200299 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Claudi, B. et al. Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell 158, 722–733 (2014).

    Article  CAS  PubMed  Google Scholar 

  130. Leiba, J. et al. Dynamics of macrophage polarization support Salmonella persistence in a whole living organism. eLife 13, e89828 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Contributions

R.T.G. researched data for the manuscript. R.T.G. and S.H. discussed, wrote and edited the manuscript.

Corresponding author

Correspondence to Sophie Helaine.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Microbiology thanks Kim Lewis and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Giorgio, R.T., Helaine, S. Antibiotic-recalcitrant Salmonella during infection. Nat Rev Microbiol 23, 276–287 (2025). https://doi.org/10.1038/s41579-024-01124-z

Download citation

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41579-024-01124-z

Search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology