Ahmed, S. K. et al. Antimicrobial resistance: impacts, challenges, and future prospects. J. Med. Surg. Public Health 2, 100081 (2024).
Naghavi, M. et al. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. Lancet 404, 1199–1226 (2024).
Jonas, O. B., Irwin, A., Berthe, F. C. J., Le Gall, F. G. & Marquez, P. V. Drug-resistant infections: a threat to our economic future. World Bank Report https://documents.worldbank.org/en/publication/documents-reports/documentdetail/323311493396993758 (2017).
Helaine, S., Conlon, B. P., Davis, K. M. & Russell, D. G. Host stress drives tolerance and persistence: the bane of anti-microbial therapeutics. Cell Host Microbe 32, 852–862 (2024).
Cox, G. & Wright, G. D. Intrinsic antibiotic resistance: mechanisms, origins, challenges and solutions. Int. J. Med. Microbiol. 303, 287–292 (2013).
Balaban, N. Q. et al. Definitions and guidelines for research on antibiotic persistence. Nat. Rev. Microbiol. 17, 441–448 (2019).
Darby, E. M. et al. Molecular mechanisms of antibiotic resistance revisited. Nat. Rev. Microbiol. 21, 280–295 (2023).
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).
Ronneau, S., Hill, P. W. & Helaine, S. Antibiotic persistence and tolerance: not just one and the same. Curr. Opin. Microbiol. 64, 76–81 (2021).
Araten, A. H. et al. Cephalosporin resistance, tolerance, and approaches to improve their activities. J. Antibiot. 77, 135–146 (2024).
Fang, X. & Allison, K. R. Resuscitation dynamics reveal persister partitioning after antibiotic treatment. Mol. Syst. Biol. 19, e11320 (2023).
Marques, C. N. H., Morozov, A., Planzos, P. & Zelaya, H. M. The fatty acid signaling molecule cis-2-decenoic acid increases metabolic activity and reverts persister cells to an antimicrobial-susceptible state. Appl. Env. Microbiol. 80, 6976–6991 (2014).
Moyed, H. S. & Bertrand, K. P. hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J. Bacteriol. 155, 768–775 (1983).
Lacerda Mariano, L. & Ingersoll, M. A. The immune response to infection in the bladder. Nat. Rev. Urol. 17, 439–458 (2020).
Kochanowski, K., Morinishi, L., Altschuler, S. J. & Wu, L. F. Drug persistence — from antibiotics to cancer therapies. Curr. Opin. Syst. Biol. 10, 1–8 (2018).
Ma, M. & Kim, M. High-resolution, high-throughput detection of hidden antibiotic resistance with the dilution-and-delay (DnD) susceptibility assay. Nat. Commun. 17, 3641 (2026).
Olivares Pacheco, J. A. et al. The intrinsic resistome of bacterial pathogens. Front. Microbiol. 4, 103 (2013).
Kadeřábková, N., Mahmood, A. J. S. & Mavridou, D. A. I. Antibiotic susceptibility testing using minimum inhibitory concentration (MIC) assays. npj Antimicrob. Resist. 2, 37 (2024).
Neuhaus, S. et al. Towards a harmonized terminology: a glossary for biocide susceptibility testing. Pathogens 11, 1455 (2022).
Fernández, L. & Hancock, R. E. W. Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin. Microbiol. Rev. 25, 661–681 (2012).
Niu, H., Gu, J. & Zhang, Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct. Target. Ther. 9, 174 (2024).
Orman, M. A. & Brynildsen, M. P. Dormancy is not necessary or sufficient for bacterial persistence. Antimicrob. Agents Chemother. 57, 3230–3239 (2013).
Hill, P. W. S. et al. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 29, 1757–1773.e10 (2021).
Mouton, J. W. et al. The role of pharmacokinetics/pharmacodynamics in setting clinical MIC breakpoints: the EUCAST approach. Clin. Microbiol. Infect. 18, E37–E45 (2012).
MacLean, R. C. & San Millan, A. The evolution of antibiotic resistance. Science 365, 1082–1083 (2019).
Kolář, M., Urbánek, K. & Látal, T. Antibiotic selective pressure and development of bacterial resistance. Int. J. Antimicrob. Agents 17, 357–363 (2001).
Pandey, S. et al. Antibiotic resistance in livestock, environment and humans: One Health perspective. J. Anim. Sci. Technol. 66, 266–278 (2024).
Djordjevic, S. P. et al. Genomic surveillance for antimicrobial resistance — a One Health perspective. Nat. Rev. Genet. 25, 142–157 (2024).
von Wintersdorff, C. J. H. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).
Li, D. et al. Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids. Microb. Genom. 9, 001068 (2023).
Hossain, M. et al. Genotype–phenotype correlation of β-lactamase-producing uropathogenic Escherichia coli (UPEC) strains from Bangladesh. Sci. Rep. 10, 14549 (2020).
Li, D. et al. Genomic comparisons of Escherichia coli ST131 from Australia. Microb. Genom. 7, 000721 (2021).
Hussain, A. et al. Multiresistant uropathogenic Escherichia coli from a region in India where urinary tract infections are endemic: genotypic and phenotypic characteristics of sequence type 131 isolates of the CTX-M-15 extended-spectrum-β-lactamase-producing lineage. Antimicrob. Agents Chemother. 56, 6358–6365 (2012).
Li, D., Reid, C. J., Kudinha, T., Jarocki, V. M. & Djordjevic, S. P. Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections. Microb. Genom. 6, e000475 (2020).
Poey, M. E., de los Santos, E., Aznarez, D., García-Laviña, C. X. & Laviña, M. Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes. Front. Microbiol. 15, 1395953 (2024).
Blahna, M. T. et al. The role of horizontal gene transfer in the spread of trimethoprim–sulfamethoxazole resistance among uropathogenic Escherichia coli in Europe and Canada. J. Antimicrob. Chemother. 57, 666–672 (2006).
Kneis, D. et al. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. ISME J. 17, 1455–1466 (2023).
Venkatesan, M. et al. Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat. Commun. 14, 4031 (2023).
Yu, K. et al. Global spread characteristics of CTX-M-type extended-spectrum β-lactamases: a genomic epidemiology analysis. Drug Resist. Updates 73, 101036 (2024).
Tooke, C. L. et al. β-lactamases and β-lactamase inhibitors in the 21st century. J. Mol. Biol. 431, 3472–3500 (2019).
Yun, M.-K. et al. Catalysis and sulfa drug resistance in dihydropteroate synthase. Science 335, 1110–1114 (2012).
Krucinska, J. et al. Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Commun. Biol. 5, 459 (2022).
Li, Y., Green, K. D., Johnson, B. R. & Garneau-Tsodikova, S. Inhibition of aminoglycoside acetyltransferase resistance enzymes by metal salts. Antimicrob. Agents Chemother. 59, 4148–4156 (2015).
Cowan, S. W. et al. Crystal structures explain functional properties of two E. coli porins. Nature 358, 727–733 (1992).
Pagès, J.-M., James, C. E. & Winterhalter, M. The porin and the permeating antibiotic: a selective diffusion barrier in gram-negative bacteria. Nat. Rev. Microbiol. 6, 893–903 (2008).
Hernández-Allés, S. et al. Porin expression in clinical isolates of Klebsiella pneumoniae. Microbiology 145, 673–679 (1999).
Choi, U. & Lee, C.-R. Distinct roles of outer membrane porins in antibiotic resistance and membrane integrity in Escherichia coli. Front. Microbiol. 10, 953 (2019).
Masi, M. et al. Cephalosporin translocation across enterobacterial OmpF and OmpC channels, a filter across the outer membrane. Commun. Biol. 5, 1059 (2022).
Lou, H. et al. Altered antibiotic transport in OmpC mutants isolated from a series of clinical strains of multi-drug resistant E. coli. PLoS ONE 6, e25825 (2011).
Goessens, W. H. F. et al. Antibiotic trapping by plasmid-encoded CMY-2 β-lactamase combined with reduced outer membrane permeability as a mechanism of carbapenem resistance in Escherichia coli. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.02459-12 (2013).
Kaczmarek, F. M., Dib-Hajj, F., Shang, W. & Gootz, T. D. High-level carbapenem resistance in a Klebsiella pneumoniae clinical isolate is due to the combination of blaACT-1 β-lactamase production, porin OmpK35/36 insertional inactivation, and down-regulation of the phosphate transport porin PhoE. Antimicrob. Agents Chemother. 50, 3396–3406 (2006).
Teelucksingh, T., Thompson, L. K. & Cox, G. The evolutionary conservation of Escherichia coli drug efflux pumps supports physiological functions. J. Bacteriol. https://doi.org/10.1128/jb.00367-20 (2020).
McMurry, L., Petrucci, R. E. & Levy, S. B. Active efflux of tetracycline encoded by four genetically different tetracycline resistance determinants in Escherichia coli. Proc. Natl Acad. Sci. 77, 3974–3977 (1980).
Okusu, H., Ma, D. & Nikaido, H. AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J. Bacteriol. 178, 306–308 (1996).
Li, X.-Z., Plésiat, P. & Nikaido, H. The challenge of efflux-mediated antibiotic resistance in gram-negative bacteria. Clin. Microbiol. Rev. 28, 337–418 (2015).
Grimsey, E. M., Weston, N., Ricci, V., Stone, J. W. & Piddock, L. J. V. Overexpression of RamA, which regulates production of the multidrug resistance efflux pump AcrAB-TolC, increases mutation rate and influences drug resistance phenotype. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.02460-19 (2020).
Padilla, E. et al. Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrob. Agents Chemother. 54, 177–183 (2010).
Swick, M. C., Morgan-Linnell, S. K., Carlson, K. M. & Zechiedrich, L. Expression of multidrug efflux pump genes acrAB-tolC, mdfA, and norE in Escherichia coli clinical isolates as a function of fluoroquinolone and multidrug resistance. Antimicrob. Agents Chemother. 55, 921–924 (2011).
Keeney, D., Ruzin, A., McAleese, F., Murphy, E. & Bradford, P. A. MarA-mediated overexpression of the AcrAB efflux pump results in decreased susceptibility to tigecycline in Escherichia coli. J. Antimicrob. Chemother. 61, 46–53 (2008).
He, F. et al. Tigecycline susceptibility and the role of efflux pumps in tigecycline resistance in KPC-producing Klebsiella pneumoniae. PLoS ONE 10, e0119064 (2015).
Baucheron, S., Imberechts, H., Chaslus-Dancla, E. & Cloeckaert, A. The AcrB multidrug transporter plays a major role in high-level fluoroquinolone resistance in Salmonella enterica Serovar typhimurium phage type DT204. Microb. Drug Resist. 8, 281–289 (2002).
Andersson, D. I., Nicoloff, H. & Hjort, K. Mechanisms and clinical relevance of bacterial heteroresistance. Nat. Rev. Microbiol. 17, 479–496 (2019).
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).
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).
Band, V. I. et al. Carbapenem-resistant Klebsiella pneumoniae exhibiting clinically undetected colistin heteroresistance leads to treatment failure in a murine model of infection. mBio 9, e02448-17 https://doi.org/10.1128/mbio.02448-17 (2018).
Kon, H. et al. Prevalence and clinical consequences of colistin heteroresistance and evolution into full resistance in carbapenem-resistant Acinetobacter baumannii. Microbiol. Spectr. 11, e05093-22 (2023).
Heyman, G. et al. Prevalence, misclassification, and clinical consequences of the heteroresistant phenotype in Escherichia coli bloodstream infections in patients in Uppsala, Sweden: a retrospective cohort study. Lancet Microbe 6, 101010 (2025).
Claeys, K. C. et al. Pneumonia caused by methicillin-resistant Staphylococcus aureus: does vancomycin heteroresistance matter? Antimicrob. Agents Chemother. 60, 1708–1716 (2016).
Tan, K. et al. Prevalence of the carbapenem-heteroresistant phenotype among ESBL-producing Escherichia coli and Klebsiella pneumoniae clinical isolates. J. Antimicrob. Chemother. 75, 1506–1512 (2020).
Dao, T. H. et al. Vancomycin heteroresistance and clinical outcomes in bloodstream infections caused by coagulase-negative Staphylococci. Antimicrob. Agents Chemother. 64, e00944-20 https://doi.org/10.1128/aac.00944-20 (2020).
Tomasz, A., Albino, A. & Zanati, E. Multiple antibiotic resistance in a bacterium with suppressed autolytic system. Nature 227, 138–140 (1970).
Forsberg, C. & Rogers, H. J. Autolytic enzymes in growth of bacteria. Nature 229, 272–273 (1971).
Michaux, C., Ronneau, S., Giorgio, R. T. & Helaine, S. Antibiotic tolerance and persistence have distinct fitness trade-offs. PLoS Pathog. 18, e1010963 (2022).
Fisher, R. A., Gollan, B. & Helaine, S. Persistent bacterial infections and persister cells. Nat. Rev. Microbiol. 15, 453–464 (2017).
Wiuff, C. & Andersson, D. I. Antibiotic treatment in vitro of phenotypically tolerant bacterial populations. J. Antimicrob. Chemother. 59, 254–263 (2007).
Dengler Haunreiter, V. et al. In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance. Nat. Commun. 10, 1149 (2019).
Pontes, M. H. & Groisman, E. A. Slow growth determines nonheritable antibiotic resistance in Salmonella enterica. Sci. Signal. 12, eaax3938 (2019).
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).
Pu, Y. et al. Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Mol. Cell 62, 284–294 (2016).
Fanous, J. et al. Limited impact of Salmonella stress and persisters on antibiotic clearance. Nature 639, 181–189 (2025).
Beam, J. E. et al. Inflammasome-mediated glucose limitation induces antibiotic tolerance in Staphylococcus aureus. iScience 26, 107942 (2023).
Rowe, S. E. et al. Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection. Nat. Microbiol. 5, 282–290 (2020).
Beam, J. E. et al. Macrophage-produced peroxynitrite induces antibiotic tolerance and supersedes intrinsic mechanisms of persister formation. Infect. Immun. 89, e0028621 (2021).
Acocella, G., Carlone, N. A., Cuffini, A. M. & Cavallo, G. The penetration of rifampicin, pyrazinamide, and pyrazinoic acid into mouse macrophages. Am. Rev. Respir. Dis. 132, 1268–1273 (1985).
Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204–208 (2014).
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).
Baek, S.-H., Li, A. H. & Sassetti, C. M. Metabolic regulation of mycobacterial growth and antibiotic sensitivity. PLoS Biol. 9, e1001065 (2011).
Levin-Reisman, I. et al. Antibiotic tolerance facilitates the evolution of resistance. Science 355, 826–830 (2017).
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).
Hobby, G. L., Meyer, K. & Chaffee, E. Observations on the mechanism of action of penicillin. Proc. Soc. Exp. Biol. Med. 50, 281–285 (1942).
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004).
Claudi, B. et al. Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell 158, 722–733 (2014).
Blattman, S. B. et al. Identification and genetic dissection of convergent persister cell states. Nature 636, 438–446 (2024).
Umetani, M. et al. Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence. eLife 14, e79517 (2025).
Miyahara, Y. et al. Survival of ampicillin-treated uropathogenic Escherichia coli is independent of single-cell growth rates. npj Antimicrob. Resist. 4, 7 (2026).
Goormaghtigh, F. & Van Melderen, L. Single-cell imaging and characterization of Escherichia coli persister cells to ofloxacin in exponential cultures. Sci. Adv. 5, eaav9462 (2019).
Brown, D. R. Nitrogen starvation induces persister cell formation in Escherichia coli. J. Bacteriol. 201, e00622-18 https://doi.org/10.1128/jb.00622-18 (2019).
Mina, E. G. & Marques, C. N. H. Interaction of Staphylococcus aureus persister cells with the host when in a persister state and following awakening. Sci. Rep. 6, 31342 (2016).
Vega, N. M., Allison, K. R., Khalil, A. S. & Collins, J. J. Signaling-mediated bacterial persister formation. Nat. Chem. Biol. 8, 431–433 (2012).
Dörr, T., Vulić, M. & Lewis, K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol. 8, e1000317 (2010).
Dörr, T., Lewis, K. & Vulić, M. SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet. 5, e1000760 (2009).
Wiradiputra, M. R. D., Khuntayaporn, P., Thirapanmethee, K. & Chomnawang, M. T. Toxin-antitoxin systems: a key role on persister formation in Salmonella enterica Serovar Typhimurium. Infect. Drug Resist. 15, 5813–5829 (2022).
Nashier, P. et al. Deep phosphoproteomics of Klebsiella pneumoniae reveals HipA-mediated tolerance to ciprofloxacin. PLoS Pathog. 20, e1012759 (2024).
Yang, Q. E. & Walsh, T. R. Toxin–antitoxin systems and their role in disseminating and maintaining antimicrobial resistance. FEMS Microbiol. Rev. 41, 343–353 (2017).
Wolfson, J. S., Hooper, D. C., McHugh, G. L., Bozza, M. A. & Swartz, M. N. Mutants of Escherichia coli K-12 exhibiting reduced killing by both quinolone and β-lactam antimicrobial agents. Antimicrob. Agents Chemother. 34, 1938–1943 (1990).
Nguyen, D. et al. Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria. Science 334, 982–986 (2011).
Fung, D. K. C., Chan, E. W. C., Chin, M. L. & Chan, R. C. Y. Delineation of a bacterial starvation stress response network which can mediate antibiotic tolerance development. Antimicrob. Agents Chemother. 54, 1082–1093 (2010).
Pacios, O. et al. (p)ppGpp and its role in bacterial persistence: new challenges. Antimicrob. Agents Chemother. 64, e01283-20 https://doi.org/10.1128/aac.01283-20 (2020).
Hauryliuk, V., Atkinson, G. C., Murakami, K. S., Tenson, T. & Gerdes, K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat. Rev. Microbiol. 13, 298–309 (2015).
Svenningsen, M. S., Veress, A., Harms, A., Mitarai, N. & Semsey, S. Birth and resuscitation of (p)ppGpp induced antibiotic tolerant persister cells. Sci. Rep. 9, 6056 (2019).
Manina, G., Dhar, N. & McKinney, J. D. Stress and host immunity amplify Mycobacterium tuberculosis phenotypic heterogeneity and induce nongrowing metabolically active forms. Cell Host Microbe 17, 32–46 (2015).
Mouton, J. M., Helaine, S., Holden, D. W. & Sampson, S. L. Elucidating population-wide mycobacterial replication dynamics at the single-cell level. Microbiology 162, 966–978 (2016).
Peyrusson, F. et al. Intracellular Staphylococcus aureus persisters upon antibiotic exposure. Nat. Commun. 11, 2200 (2020).
Demarre, G. et al. The Crohn’s disease-associated Escherichia coli strain LF82 relies on SOS and stringent responses to survive, multiply and tolerate antibiotics within macrophages. PLoS Pathog. 15, e1008123 (2019).
Peyrusson, F., Nguyen, T. K., Najdovski, T. & Van Bambeke, F. Host cell oxidative stress induces dormant Staphylococcus aureus persisters. Microbiol. Spectr. 10, e02313-21 (2022).
Ronneau, S., Michaux, C. & Helaine, S. Decline in nitrosative stress drives antibiotic persister regrowth during infection. Cell Host Microbe 31, 993–1006.e6 (2023).
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).
Helaine, S. et al. Dynamics of intracellular bacterial replication at the single cell level. Proc. Natl Acad. Sci. USA 107, 3746–3751 (2010).
Dadole, I., Blaha, D. & Personnic, N. The macrophage–bacterium mismatch in persister formation. Trends Microbiol. 32, 944–956 (2024).
Windels, E. M. et al. Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME J. 13, 1239–1251 (2019).
Barrett, T. C., Mok, W. W. K., Murawski, A. M. & Brynildsen, M. P. Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat. Commun. 10, 1177 (2019).
Giorgio, R. T. & Helaine, S. Antibiotic-recalcitrant Salmonella during infection. Nat. Rev. Microbiol. 23, 276–287 (2025).
Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015).
Rotem, E. et al. Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc. Natl Acad. Sci. USA 107, 12541–12546 (2010).
Zeng, Z., Zhan, J., Zhang, K., Chen, H. & Cheng, S. Global, regional, and national burden of urinary tract infections from 1990 to 2019: an analysis of the global burden of disease study 2019. World J. Urol. 40, 755–763 (2022).
Assumpcao, C. Some urinary tract disease in Australian aboriginal inpatients in 1980. Aust. N. Z. J. Med. 18, 17–20 (1988).
Wojszel, Z. B. & Toczyńska-Silkiewicz, M. Urinary tract infections in a geriatric sub-acute ward-health correlates and atypical presentations. Eur. Geriatr. Med. 9, 659–667 (2018).
Medina, M. & Castillo-Pino, E. An introduction to the epidemiology and burden of urinary tract infections. Ther. Adv. Urol. 11, 1756287219832172 (2019).
Kaur, N., Sharma, S., Malhotra, S., Madan, P. & Hans, C. Urinary tract infection: aetiology and antimicrobial resistance pattern in infants from a tertiary care hospital in Northern India. J. Clin. Diagn. Res. 8, DC01–DC03 (2014).
Foxman, B. The epidemiology of urinary tract infection. Nat. Rev. Urol. 7, 653–660 (2010).
EAU Guidelines on Urological Infections Edn. presented at the EAU Annual Congress Madrid, Spain. European Association of Urology https://uroweb.org/guidelines/urological-infections/chapter/the-guideline (2025).
Flores-Mireles, A. L., Walker, J. N., Caparon, M. & Hultgren, S. J. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat. Rev. Microbiol. 13, 269–284 (2015).
Lupo, F. & Ingersoll, M. A. Is bacterial prostatitis a urinary tract infection. Nat. Rev. Urol. 16, 203–204 (2019).
Kass, E. H. Asymptomatic infections of the urinary tract. J. Urol. 167, 1016–1020 (2002).
Doiron, R. C. & Cotechini, T. The 2025 AUA Guideline Update on Recurrent Urinary Tract Infections: important new recommendations reflecting progress in an often-ignored disease space. J. Urol. https://doi.org/10.1097/JU.0000000000005079.
Lawrenson, R. A. & Logie, J. W. Antibiotic failure in the treatment of urinary tract infections in young women. J. Antimicrob. Chemother. 48, 895–901 (2001).
Cuningham, W. et al. Repurposing antibiotic resistance surveillance data to support treatment of recurrent infections in a remote setting. Sci. Rep. 14, 2414 (2024).
Cohen, J. E., Chen, L. & Schaeffer, A. J. Algorithms using previous resistance, prior antimicrobial prescriptions, and patient place of residence enhance empirical therapy for women with uncomplicated urinary tract infections. Urology 137, 72–78 (2020).
Honda, T. et al. The impact of inter-infection time on antimicrobial resistance profiles in women with multiple urinary tract infections over time. J. Antimicrob. Chemother. 80, 2234–2240 (2025).
Zhu, N. J. et al. Economic burden of community-acquired antibiotic-resistant urinary tract infections: systematic review and meta-analysis. JMIR Public. Health Surveill. 10, e53828 (2024).
Flower, A., Bishop, F. L. & Lewith, G. How women manage recurrent urinary tract infections: an analysis of postings on a popular web forum. BMC Family Pract. 15, 162 (2014).
Newlands, A. F. et al. Evaluating the quality of life impact of recurrent urinary tract infection: validation and refinement of the Recurrent UTI Impact Questionnaire (RUTIIQ). Neurourol. Urodyn. 43, 902–914 (2024).
Gupta, K. & Stamm, W. E. Outcomes associated with trimethoprim/sulphamethoxazole (TMP/SMX) therapy in TMP/SMX resistant community-acquired UTI. Int. J. Antimicrob. Agents 19, 554–556 (2002).
Kot, B. Antibiotic resistance among uropathogenic Escherichia coli. Pol. J. Microbiol. 68, 403–415 (2019).
Sati, H. et al. The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance. Lancet Infect Dis 25, 1033–1043 (2025).
Murray, C. J. L. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).
Mulvey, M. A. et al. Induction and evasion of host defenses by type 1-piliated uropathogenic Escherichia coli. Science 282, 1494–1497 (1998).
Melican, K. et al. Uropathogenic Escherichia coli P and type 1 fimbriae act in synergy in a living host to facilitate renal colonization leading to nephron obstruction. PLoS Pathog. 7, e1001298 (2011).
Wurpel, D. J., Beatson, S. A., Totsika, M., Petty, N. K. & Schembri, M. A. Chaperone-usher fimbriae of Escherichia coli. PLoS ONE 8, e52835 (2013).
Eto, D. S., Jones, T. A., Sundsbak, J. L. & Mulvey, M. A. Integrin-mediated host cell invasion by type 1–piliated uropathogenic Escherichia coli. PLoS Pathog. 3, e100 (2007).
Martinez, J. J., Mulvey, M. A., Schilling, J. D., Pinkner, J. S. & Hultgren, S. J. Type 1 pilus-mediated bacterial invasion of bladder epithelial cells. EMBO J. 19, 2803–2812 (2000).
Anderson, G. G. et al. Intracellular bacterial biofilm-like pods in urinary tract infections. Science 301, 105–107 (2003).
Pokhrel, A. et al. Uropathogenic Escherichia coli proliferate as a coccoid morphotype inside human host cells. PLoS Biol. 23, e3003366 (2025).
Justice, S. S. et al. Differentiation and developmental pathways of uropathogenic Escherichia coli in urinary tract pathogenesis. Proc. Natl Acad. Sci. USA 101, 1333–1338 (2004).
Le Blanc, L. et al. Bacterial growth under confinement requires transcriptional adaptation to resist turgor pressure build-up. Nat. Commun. 17, 10434 (2026).
Anderson, G. G., Goller, C. C., Justice, S., Hultgren, S. J. & Seed, P. C. Polysaccharide capsule and sialic acid-mediated regulation promote biofilm-like intracellular bacterial communities during cystitis. Infect. Immun. 78, 963–975 (2010).
Mulvey, M. A., Schilling, J. D. & Hultgren, S. J. Establishment of a persistent Escherichia coli reservoir during the acute phase of a bladder infection. Infect. Immun. 69, 4572–4579 (2001).
Abell-King, C., Costas, A., Duggin, I. G. & Söderström, B. Bacterial filamentation during urinary tract infections. PLoS Pathog. 18, e1010950 (2022).
Iosifidis, G. & Duggin, I. G. Distinct morphological fates of uropathogenic Escherichia coli intracellular bacterial communities: dependency on urine composition and pH. Infect. Immun. 88, e00884-19 https://doi.org/10.1128/iai.00884-19 (2020).
Mysorekar, I. U. & Hultgren, S. J. Mechanisms of uropathogenic Escherichia coli persistence and eradication from the urinary tract. Proc. Natl Acad. Sci. USA 103, 14170–14175 (2006).
Fromer, D. L. et al. Risk factors for empiric treatment failure in US female outpatients with uncomplicated urinary tract infection: an observational study. J. Gen. Intern. Med. 40, 862–870 (2025).
Wurpel, D. J., Moriel, D. G., Totsika, M., Easton, D. M. & Schembri, M. A. Comparative analysis of the uropathogenic Escherichia coli surface proteome by tandem mass-spectrometry of artificially induced outer membrane vesicles. J. Proteom. 115, 93–106 (2015).
Kishii, R. & Takei, M. Relationship between the expression of ompF and quinolone resistance in Escherichia coli. J. Infect. Chemother. 15, 361–366 (2009).
da Silva Ribeiro, Á. C. et al. Exposure to sub-inhibitory ciprofloxacin and nitrofurantoin concentrations increases recA gene expression in uropathogenic Escherichia coli: the role of RecA protein as a drug target. Eur. J. Pharm. Sci. 146, 105268 (2020).
Yasufuku, T. et al. Correlation of overexpression of efflux pump genes with antibiotic resistance in Escherichia coli strains clinically isolated from urinary tract infection patients. J. Clin. Microbiol. 49, 189–194 (2011).
Sung, K. et al. Comprehensive genomic analysis of uropathogenic e. coli: virulence factors, antimicrobial resistance, and mobile genetic elements. Pathogens 13, 794 (2024).
Choi, N. et al. A shared mechanism of multidrug resistance in laboratory-evolved uropathogenic Escherichia coli. Virulence 15, 2367648 (2024).
Goneau, L. W. et al. Selective target inactivation rather than global metabolic dormancy causes antibiotic tolerance in uropathogens. Antimicrob. Agents Chemother. 58, 2089–2097 (2014).
Kerkez, I., Tulkens, P. M., Tenson, T., Van Bambeke, F. & Putrinš, M. Uropathogenic Escherichia coli Shows antibiotic tolerance and growth heterogeneity in an in vitro model of intracellular infection. Antimicrob. Agents Chemother. 65, e01468-21 https://doi.org/10.1128/aac.01468-21 (2021).
Sharma, K. et al. Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection. eLife 10, e66481 (2021).
Leatham-Jensen, M. P. et al. Uropathogenic Escherichia coli metabolite-dependent quiescence and persistence may explain antibiotic tolerance during urinary tract infection. mSphere 1, e00055-15 https://doi.org/10.1128/msphere.00055-15 (2016).
Zheng, E. J. et al. Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies. Nat. Commun. 13, 2525 (2022).
Amoura, A. et al. Variability in cell division among anatomical sites shapes Escherichia coli antibiotic survival in a urinary tract infection mouse model. Cell Host Microbe 32, 900–912.e4 (2024).
Blango, M. G. & Mulvey, M. A. Persistence of uropathogenic Escherichia coli in the face of multiple antibiotics. Antimicrob. Agents Chemother. 54, 1855–1863 (2010).
Norton, J. P. & Mulvey, M. A. Toxin-antitoxin systems are important for niche-specific colonization and stress resistance of uropathogenic Escherichia coli. PLoS Pathog. 8, e1002954 (2012).
Zahir, T. et al. Image-based dynamic phenotyping reveals genetic determinants of filamentation-mediated β-lactam tolerance. Front. Microbiol. 11, 374 (2020).
Chung, H. S. et al. Rapid β-lactam-induced lysis requires successful assembly of the cell division machinery. Proc. Natl Acad. Sci. USA 106, 21872–21877 (2009).
Söderström, B., Pittorino, M. J., Daley, D. O. & Duggin, I. G. Assembly dynamics of FtsZ and DamX during infection-related filamentation and division in uropathogenic E. coli. Nat. Commun. 13, 3648 (2022).
Köhn, R.-M. et al. A simple ex vivo bladder infection model permits study of host–pathogen interactions in urinary tract infection. FEMS Microbes 7, xtag012 (2026).
Sulaiman, J. E. & Lam, H. Proteomic study of the survival and resuscitation mechanisms of filamentous persisters in an evolved Escherichia coli population from cyclic ampicillin treatment. mSystems 5, e00462-20 https://doi.org/10.1128/msystems.00462-20 (2020).
Rosen, D. A., Hooton, T. M., Stamm, W. E., Humphrey, P. A. & Hultgren, S. J. Detection of intracellular bacterial communities in human urinary tract infection. PLoS Med. 4, e329 (2007).
Abell-King, C., Pokhrel, A., Rice, S. A., Duggin, I. G. & Söderström, B. Multispecies bacterial invasion of human host cells. Pathog. Dis. 82, ftae012 (2024).
Conner, J. F., Coleman, S. E., Davis, J. L. & McGaughey, F. S. Bacterial L-forms from urinary-tract infections in a veterans hospital population. J. Am. Geriatr. Soc. 16, 893–900 (1968).
Mickiewicz, K. M. et al. Possible role of L-form switching in recurrent urinary tract infection. Nat. Commun. 10, 4379 (2019).
Petrovic Fabijan, A. et al. L-form switching in Escherichia coli as a common β-lactam resistance mechanism. Microbiol. Spectr. 10, e02419-22 (2022).
Mercier, R., Kawai, Y. & Errington, J. General principles for the formation and proliferation of a wall-free (L-form) state in bacteria. eLife 3, e04629 (2014).
Paduthol, G. et al. A microphysiological human mini-bladder reveals urine-urothelium interplay in tissue resilience and UPEC recurrence in urinary tract infections. Nat. Commun. 17, 2322 (2026).
Kawai, Y., Mickiewicz, K. & Errington, J. Lysozyme counteracts β-lactam antibiotics by promoting the emergence of L-form bacteria. Cell 172, 1038–1049.e10 (2018).
Lacerda Mariano, L. et al. Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder. Sci. Adv. 6, eabc5739 (2020).
Mora-Bau, G. et al. Macrophages subvert adaptive immunity to urinary tract infection. PLoS Pathog. 11, e1005044 (2015).
Anderson, G. G., Martin, S. M. & Hultgren, S. J. Host subversion by formation of intracellular bacterial communities in the urinary tract. Microbes Infect. 6, 1094–1101 (2004).
Brooun, A., Liu, S. & Lewis, K. A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms. Antimicrob. Agents Chemother. 44, 640–646 (2000).
Spoering, A. L. & Lewis, K. Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J. Bacteriol. 183, 6746–6751 (2001).
Verstraete, L. et al. In vitro persistence level reflects in vivo antibiotic survival of natural Pseudomonas aeruginosa isolates in a murine lung infection model. Microbiol. Spectr. 11, e0497022 (2023).
Schilling, J. D., Lorenz, R. G. & Hultgren, S. J. Effect of trimethoprim-sulfamethoxazole on recurrent bacteriuria and bacterial persistence in mice infected with uropathogenic Escherichia coli. Infect. Immun. 70, 7042–7049 (2002).
Negrete, H. O., Lavelle, J. P., Berg, J., Lewis, S. A. & Zeidel, M. L. Permeability properties of the intact mammalian bladder epithelium. Am. J. Physiol. Renal Physiol. 271, F886–F894 (1996).
Wientjes, M. G., Badalament, R. A., Wang, R. C., Hassan, F. & Au, J. L. Penetration of mitomycin C in human bladder. Cancer Res. 53, 3314–3320 (1993).
Labbaf, S. et al. An encapsulated drug delivery system for recalcitrant urinary tract infection. J. R. Soc. Interface 10, 20130747 (2013).
Lau, W. K. et al. Novel antibiotic-loaded particles conferring eradication of deep tissue bacterial reservoirs for the treatment of chronic urinary tract infection. J. Control. Rel. 328, 490–502 (2020).
GuhaSarkar, S. & Banerjee, R. Intravesical drug delivery: challenges, current status, opportunities and novel strategies. J. Control. Rel. 148, 147–159 (2010).
Morrison, J. J. et al. Metabolic flux regulates growth transitions and antibiotic tolerance in uropathogenic Escherichia coli. J. Bacteriol. 206, e00162-24 (2024).
Valencia, E. Y., de Moraes Gomes, F., Ospino, K. & Spira, B. RpoS role in antibiotic resistance, tolerance and persistence in E. coli natural isolates. BMC Microbiol. 24, 72 (2024).
Molina-Quiroz, R. C., Lazinski, D. W., Camilli, A. & Levy, S. B. Transposon-sequencing analysis unveils novel genes involved in the generation of persister cells in uropathogenic Escherichia coli. Antimicrob. Agents Chemother. 60, 6907–6910 (2016).
Zhang, S. et al. Small Non-coding RNA RyhB mediates persistence to multiple antibiotics and stresses in uropathogenic Escherichia coli by reducing cellular metabolism. Front. Microbiol. 9, 136 (2018).
Keren, I., Shah, D., Spoering, A., Kaldalu, N. & Lewis, K. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J. Bacteriol. 186, 8172–8180 (2004).
Schumacher, M. A. et al. HipBA–promoter structures reveal the basis of heritable multidrug tolerance. Nature 524, 59–64 (2015).
Michaux, C., Ronneau, S. & Helaine, S. Studying antibiotic persistence during infection. Methods Mol. Biol. 2357, 273–289 (2021).
Gefen, O., Chekol, B., Strahilevitz, J. & Balaban, N. Q. TDtest: easy detection of bacterial tolerance and persistence in clinical isolates by a modified disk-diffusion assay. Sci. Rep. 7, 41284 (2017).
Lazarovits, G. et al. Prevalence of antibiotic tolerance and risk for reinfection among Escherichia coli bloodstream isolates: a prospective cohort Study. Clin. Infect. Dis. 75, 1706–1713 (2022).
Zheng, E. J., Stokes, J. M. & Collins, J. J. Eradicating bacterial persisters with combinations of strongly and weakly metabolism-dependent antibiotics. Cell Chem. Biol. 27, 1544–1552.e3 (2020).
Clinical Breakpoint Tables. European Committee on Antimicrobial Susceptibility Testing https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/ (2025).
Patel, P. & Preuss, C. V. Cephalosporins. StatPearls [Internet] https://www.ncbi.nlm.nih.gov/sites/books/NBK551517/ (updated 17 February 2024).
Silver, L. L. Fosfomycin: mechanism and resistance. Cold Spring Harb. Perspect. Med. 7, a025262 (2017).
Hawkins, B. K., Ding, H., Harriott, M. M. & Wang, J. L. New perspectives on antimicrobial agents: pivmecillinam. Antimicrob. Agents Chemother. 69, e0182424 (2025).
Kemnic, T. R., Patel, P. & Nicolas, S. Trimethoprim-sulfamethoxazole. StatPearls [Internet] https://www.ncbi.nlm.nih.gov/sites/books/NBK513232/ (updated 19 June 2026).
Khamari, B. & Bulagonda, E. P. Unlocking nitrofurantoin: understanding molecular mechanisms of action and resistance in Enterobacterales. Med. Princ. Pract. 34, 121–137 (2024).