Skip to content
1887

Microbiology Society logo Microbiology

Volume 171, Issue 1

A plasmid with the gene enhances the fitness of strains under laboratory conditions Open Access

Abstract

Antimicrobial resistance (AMR) is a major threat to global public health that continues to grow owing to selective pressure caused by the use and overuse of antimicrobial drugs. Resistance spread by plasmids is of special concern, as they can mediate a wide distribution of AMR genes, including those encoding extended-spectrum -lactamases (ESBLs). The CTX-M family of ESBLs has rapidly spread worldwide, playing a large role in the declining effectiveness of third-generation cephalosporins. This rapid spread across the planet is puzzling given that plasmids carrying AMR genes have been hypothesized to incur a fitness cost to their hosts in the absence of antibiotics. Here, we focus on a WT plasmid that carries the ESBL gene. We examine its conjugation rates and use head-to-head competitions to assay its associated fitness costs in both laboratory and wild strains. We found that the wild strains exhibit intermediate conjugation levels, falling between two high-conjugation and two low-conjugation laboratory strains, the latter being older and more ancestral. We also show that the plasmid increases the fitness of both WT and lab strains when grown in lysogeny broth and Davis–Mingioli media without antibiotics, which might stem from metabolic benefits conferred on the host, or from interactions between the host and the rifampicin-resistant mutation we used as a selective marker. Laboratory strains displayed higher conjugation frequencies compared to WT strains. The exception was a low-passage K-12 strain, suggesting that prolonged laboratory cultivation may have compromised bacterial defences against plasmids. Despite low transfer rates among WT , the plasmid carried low fitness cost in minimal medium but conferred improved fitness in enriched medium, indicating a complex interplay between plasmids, host genetics and environmental conditions. Our findings reveal an intricate relationship between plasmid carriage and bacterial fitness. Moreover, they show that resistance plasmids can confer adaptive advantages to their hosts beyond AMR. Altogether, these results highlight that a closer study of plasmid dynamics is critical for developing a secure understanding of how they evolve and affect bacterial adaptability that is necessary for combating resistance spread.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antibiotic-resistant burden , blaCTX-M , ESBL fitness cost , Escherichia coli , plasmid fitness cost and plasmid maintenance
Funding
This study was supported by the:
  • Universidad San Francisco de Quito
    • Principal Award Recipient: GabrielTrueba
  • National Institutes of Health (Award R01AI135118)
    • Principal Award Recipient: JayP. Graham
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.001525
2025-01-30
2026-02-19

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/micro/171/1/mic001525.html?itemId=/content/journal/micro/10.1099/mic.0.001525&mimeType=html&fmt=ahah

References

  1. Dadgostar P. Antimicrobial resistance: implications and costs. Infect Drug Resist 2019; 12:3903–3910 [View Article] [PubMed]
     [Google Scholar]
  2. Pitout JDD, DeVinney R. Escherichia coli ST131: a multidrug-resistant clone primed for global domination. F1000Res 2017; 6:F1000 Faculty Rev-195 [View Article] [PubMed]
     [Google Scholar]
  3. Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet 2022; 399:629–655 [View Article]
     [Google Scholar]
  4. O’Neill J. Tackling drug-resistant infections globally: final report and recommendations. Government of the United Kingdom; 2016
  5. Paterson DL, Bonomo RA. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev 2005; 18:657–686 [View Article] [PubMed]
     [Google Scholar]
  6. Zamudio R, Boerlin P, Beyrouthy R, Madec J-Y, Schwarz S et al. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nat Commun 2022; 13:7490 [View Article] [PubMed]
     [Google Scholar]
  7. Kawamura K, Nagano N, Suzuki M, Wachino JI, Kimura K et al. Esbl-producing Escherichia coli and its rapid rise among healthy people. Food Saf 2017; 5:122–150 [View Article] [PubMed]
     [Google Scholar]
  8. Knothe H, Shah P, Krcmery V, Antal M, Mitsuhashi S. Transferable resistance to cefotaxime, cefoxitin, cefamandole and cefuroxime in clinical isolates of Klebsiella pneumoniae and Serratia marcescens. Infection 1983; 11:315–317 [View Article] [PubMed]
     [Google Scholar]
  9. Cantón R, González-Alba JM, Galán JC. CTX-M enzymes: origin and diffusion. Front Microbiol 2012; 3:110 [View Article] [PubMed]
     [Google Scholar]
  10. Gniadkowski M. Evolution and epidemiology of extended-spectrum beta-lactamases (ESBLs) and ESBL-producing microorganisms. Clin Microbiol Infect 2001; 7:597–608 [View Article] [PubMed]
     [Google Scholar]
  11. Yang JT, Zhang LJ, Lu Y, Zhang RM, Jiang HX. Genomic insights into global blaCTX-M-55-positive Escherichia coli epidemiology and transmission characteristics. Microbiol Spectr 2023; 11:e0108923 [View Article] [PubMed]
     [Google Scholar]
  12. Salinas L, Loayza F, Cárdenas P, Saraiva C, Johnson TJ et al. Environmental spread of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and ESBL genes among children and domestic animals in Ecuador. Environ Health Perspect 2021; 129:27007 [View Article] [PubMed]
     [Google Scholar]
  13. Mattila S, Ruotsalainen P, Ojala V, Tuononen T, Hiltunen T et al. Conjugative ESBL plasmids differ in their potential to rescue susceptible bacteria via horizontal gene transfer in lethal antibiotic concentrations. J Antibiot 2017; 70:805–808 [View Article]
     [Google Scholar]
  14. Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 2018; 31:e00088–17 [View Article]
     [Google Scholar]
  15. Rawat D, Nair D. Extended-spectrum β-lactamases in gram negative bacteria. J Glob Infect Dis 2010; 2:263–274 [View Article] [PubMed]
     [Google Scholar]
  16. Yu K, Huang Z, Xiao Y, Gao H, Bai X et al. Global spread characteristics of CTX-M-type extended-spectrum β-lactamases: a genomic epidemiology analysis. Drug Resist Updat 2024; 73:101036 [View Article] [PubMed]
     [Google Scholar]
  17. San Millan A, MacLean RC. Fitness costs of plasmids: a limit to plasmid transmission. Microbiol Spectr 2017; 5: [View Article] [PubMed]
     [Google Scholar]
  18. Hernández-Beltrán JCR, San Millán A, Fuentes-Hernández A, Peña-Miller R. Mathematical models of plasmid population dynamics. Front Microbiol 2021; 12:606396 [View Article] [PubMed]
     [Google Scholar]
  19. Rajer F, Sandegren L. The role of antibiotic resistance genes in the fitness cost of multiresistance plasmids. mBio 2022; 13:e0355221 [View Article] [PubMed]
     [Google Scholar]
  20. Alonso-Del Valle A, León-Sampedro R, Rodríguez-Beltrán J, DelaFuente J, Hernández-García M et al. Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nat Commun 2021; 12:2653 [View Article] [PubMed]
     [Google Scholar]
  21. Bottery MJ. Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr Opin Microbiol 2022; 68:102152 [View Article] [PubMed]
     [Google Scholar]
  22. Wang T, Weiss A, Ha Y, You L. Predicting plasmid persistence in microbial communities by coarse-grained modeling. Bioessays 2021; 43:e2100084 [View Article] [PubMed]
     [Google Scholar]
  23. Brockhurst MA, Harrison E. Ecological and evolutionary solutions to the plasmid paradox. Trends Microbiol 2022; 30:534–543 [View Article] [PubMed]
     [Google Scholar]
  24. Carroll AC, Wong A. Plasmid persistence: costs, benefits, and the plasmid paradox. Can J Microbiol 2018; 64:293–304 [View Article] [PubMed]
     [Google Scholar]
  25. MacLean RC, San Millan A. Microbial evolution: towards resolving the plasmid paradox. Curr Biol 2015; 25:R764–7 [View Article] [PubMed]
     [Google Scholar]
  26. DelaFuente J, Toribio-Celestino L, Santos-Lopez A, León-Sampedro R, Alonso-del Valle A et al. Within-patient evolution of plasmid-mediated antimicrobial resistance. Nat Ecol Evol 2022; 6:1980–1991 [View Article]
     [Google Scholar]
  27. Salinas L, Cárdenas P, Graham JP, Trueba G. IS26 drives the dissemination of bla CTX-M genes in an ecuadorian community. Microbiol Spectr 2023; 12:e02504–23 [View Article]
     [Google Scholar]
  28. He L, Partridge SR, Yang X, Hou J, Deng Y et al. Complete nucleotide sequence of pHN7A8, an F33:A-:B-type epidemic plasmid carrying blaCTX-M-65, fosA3 and rmtB from China. J Antimicrob Chemother 2013; 68:46–50 [View Article]
     [Google Scholar]
  29. Yi H, Cho YJ, Yong D, Chun J. Genome sequence of Escherichia coli J53, a reference strain for genetic studies. J Bacteriol 2012; 194:3742–3743 [View Article] [PubMed]
     [Google Scholar]
  30. Calderón D, Cárdenas PA, Prado-Vivar B, Graham JP, Trueba G. A longitudinal study of dominant E. coli lineages and antimicrobial resistance in the gut of children living in an upper middle-income country. J Glob Antimicrob Resist 2022; 29:136–140 [View Article] [PubMed]
     [Google Scholar]
  31. López L, Calderón D, Cardenas P, Prado MB, Valle C et al. Evolutionary changes of an intestinal Lactobacillus reuteri during probiotic manufacture. Microbiologyopen 2020; 9:e972 [View Article] [PubMed]
     [Google Scholar]
  32. CLSI Performance Standards for Antimicrobial Susceptibility Testing, CLSI Supplement M100. 34th ed Clinical and Laboratory Standards Institute; 2024
     [Google Scholar]
  33. Mostafa HH, Cameron A, Taffner SM, Wang J, Malek A et al. Genomic surveillance of ceftriaxone-resistant Escherichia coli in western New York suggests the extended-spectrum β-lactamase bla CTX-M-27 is emerging on distinct plasmids in ST38. Front Microbiol 2020; 11:1747 [View Article] [PubMed]
     [Google Scholar]
  34. Huisman JS, Benz F, Duxbury SJN, de Visser JAGM, Hall AR et al. Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods. Plasmid 2022; 121:102627 [View Article] [PubMed]
     [Google Scholar]
  35. Lopatkin AJ, Huang S, Smith RP, Srimani JK, Sysoeva TA et al. Antibiotics as a selective driver for conjugation dynamics. Nat Microbiol 2016; 1:16044 [View Article] [PubMed]
     [Google Scholar]
  36. Alderliesten JB, Duxbury SJN, Zwart MP, de Visser JAGM, Stegeman A et al. Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis. BMC Microbiol 2020; 20:135 [View Article] [PubMed]
     [Google Scholar]
  37. Hu D, Fuller NR, Caterson ID, Holmes AJ, Reeves PR. Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Rep 2022; 38:110239 [View Article] [PubMed]
     [Google Scholar]
  38. Barrick JE, Blount ZD, Lake DM, Dwenger JH, Chavarria-Palma JE et al. Daily transfers, archiving populations, and measuring fitness in the long-term evolution experiment with Escherichia coli. J Vis Exp 202365342 [View Article] [PubMed]
     [Google Scholar]
  39. Wiser MJ, Lenski RE. A comparison of methods to measure fitness in Escherichia coli. PLoS One 2015; 10:e0126210 [View Article] [PubMed]
     [Google Scholar]
  40. Sprouffske K, Wagner A. Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves. BMC Bioinf 2016; 17:172 [View Article] [PubMed]
     [Google Scholar]
  41. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  42. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  43. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  44. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
     [Google Scholar]
  45. Choi Y, Lee J-Y, Lee H, Park M, Kang K et al. Comparison of fitness cost and virulence in chromosome- and plasmid-mediated colistin-resistant Escherichia coli. Front Microbiol 2020; 11:798 [View Article] [PubMed]
     [Google Scholar]
  46. Li F, Wang J, Jiang Y, Guo Y, Liu N et al. Adaptive evolution compensated for the plasmid fitness costs brought by specific genetic conflicts. Pathogens 2023; 12:137 [View Article]
     [Google Scholar]
  47. Liu Z, Zhang H, Xiao X, Liu Y, Li R et al. Comparison of fitness cost, stability, and conjugation frequencies of tet(X4)-positive plasmids in chicken and pig Escherichia coli. Antibiotics 2022; 11:1657 [View Article] [PubMed]
     [Google Scholar]
  48. Humphrey B, Thomson NR, Thomas CM, Brooks K, Sanders M et al. Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol 2012; 12:53 [View Article] [PubMed]
     [Google Scholar]
  49. Enne VI, Delsol AA, Davis GR, Hayward SL, Roe JM et al. Assessment of the fitness impacts on Escherichia coli of acquisition of antibiotic resistance genes encoded by different types of genetic element. J Antimicrob Chemother 2005; 56:544–551 [View Article]
     [Google Scholar]
  50. Dahlberg C, Chao L. Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12. Genetics 2003; 165:1641–1649 [View Article] [PubMed]
     [Google Scholar]
  51. Petersen A, Aarestrup FM, Olsen JE. The in vitro fitness cost of antimicrobial resistance in Escherichia coli varies with the growth conditions. FEMS Microbiol Lett 2009; 299:53–59 [View Article] [PubMed]
     [Google Scholar]
  52. Harrison E, Guymer D, Spiers AJ, Paterson S, Brockhurst MA. Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum. Curr Biol 2015; 25:2034–2039 [View Article] [PubMed]
     [Google Scholar]
  53. Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ et al. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225 [View Article] [PubMed]
     [Google Scholar]
  54. Lopatkin AJ, Meredith HR, Srimani JK, Pfeiffer C, Durrett R et al. Persistence and reversal of plasmid-mediated antibiotic resistance. Nat Commun 2017; 8:1689 [View Article] [PubMed]
     [Google Scholar]
  55. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453–1462 [View Article] [PubMed]
     [Google Scholar]
  56. Frost LS, Ippen-Ihler K, Skurray RA. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev 1994; 58:162–210 [View Article] [PubMed]
     [Google Scholar]
  57. Jeltsch A. Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?. Gene 2003; 317:13–16 [View Article] [PubMed]
     [Google Scholar]
  58. Koraimann G. Spread and persistence of virulence and antibiotic resistance genes: a ride on the F plasmid conjugation module. EcoSal Plus 2018; 8: [View Article] [PubMed]
     [Google Scholar]
  59. Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 2005; 3:711–721 [View Article] [PubMed]
     [Google Scholar]
  60. Pohlman RF, Genetti HD, Winans SC. Entry exclusion of the IncN plasmid pKM101 is mediated by a single hydrophilic protein containing a lipid attachment motif. Plasmid 1994; 31:158–165 [View Article] [PubMed]
     [Google Scholar]
  61. Gama JA, Zilhão R, Dionisio F. Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: plasmids promote the immigration of other plasmids but repress co-colonizing plasmids. Plasmid 2017; 93:6–16 [View Article] [PubMed]
     [Google Scholar]
  62. Palkovicova J, Sukkar I, Delafuente J, Valcek A, Medvecky M et al. Fitness effects of blaCTX-M-15-harbouring F2:A1:B- plasmids on their native Escherichia coli ST131 H30Rx hosts. J Antimicrob Chemother 2022; 77:2960–2963 [View Article] [PubMed]
     [Google Scholar]
  63. Ranjan A, Scholz J, Semmler T, Wieler LH, Ewers C et al. ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost. Gut Pathog 2018; 10:24 [View Article] [PubMed]
     [Google Scholar]
  64. Schaufler K, Semmler T, Pickard DJ, de Toro M, de la Cruz F et al. Carriage of extended-spectrum beta-lactamase-plasmids does not reduce fitness but enhances virulence in some strains of pandemic E. coli lineages. Front Microbiol 2016; 7:336 [View Article] [PubMed]
     [Google Scholar]
  65. Shin J, Ko KS. Effect of plasmids harbouring blaCTX-M on the virulence and fitness of Escherichia coli ST131 isolates. Int J Antimicrob Agents 2015; 46:214–218 [View Article] [PubMed]
     [Google Scholar]
  66. Dimitriu PA, Iker B, Malik K, Leung H, Mohn WW et al. New insights into the intrinsic and extrinsic factors that shape the human skin microbiome. mBio 2019; 10:e00839-19 [View Article] [PubMed]
     [Google Scholar]
  67. García-Bayona L, Comstock LE. Bacterial antagonism in host-associated microbial communities. Science 2018; 361:eaat2456 [View Article] [PubMed]
     [Google Scholar]
  68. Vanacker M, Lenuzza N, Rasigade JP. The fitness cost of horizontally transferred and mutational antimicrobial resistance in Escherichia coli. Front Microbiol 2023; 14: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1186920/full
     [Google Scholar]
  69. Jin DJ, Gross CA. Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J Mol Biol 1988; 202:45–58 [View Article] [PubMed]
     [Google Scholar]
  70. Giddey AD, Ganief TA, Ganief N, Koch A, Warner DF et al. Cell wall proteomics reveal phenotypic adaptation of drug-resistant Mycobacterium smegmatis to subinhibitory rifampicin exposure. Front Med 2021; 8: https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2021.723667
     [Google Scholar]
  71. Soley JK, Jago M, Walsh CJ, Khomarbaghi Z, Howden BP et al. Pervasive genotype-by-environment interactions shape the fitness effects of antibiotic resistance mutations. Proc Biol Sci 2023; 290:20231030 [View Article] [PubMed]
     [Google Scholar]
  72. Silva RF, Mendonça SCM, Carvalho LM, Reis AM, Gordo I et al. Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations. PLoS Genet 2011; 7:e1002181 [View Article] [PubMed]
     [Google Scholar]
  73. Cutugno L, Mc Cafferty J, Pané-Farré J, O’Byrne C, Boyd A. rpoB mutations conferring rifampicin-resistance affect growth, stress response and motility in Vibrio vulnificus. Microbiology 2020; 166:1160–1170 [View Article] [PubMed]
     [Google Scholar]
  74. Hughes D, Brandis G. Rifampicin resistance: fitness costs and the significance of compensatory evolution. Antibiotics 2013; 2:206–216 [View Article] [PubMed]
     [Google Scholar]
  75. Nair RR, Andersson DI, Warsi OM. Antibiotic resistance begets more resistance: chromosomal resistance mutations mitigate fitness costs conferred by multi-resistant clinical plasmids. Microbiol Spectr 2024; 12:e0420623 [View Article] [PubMed]
     [Google Scholar]
  76. Billane K, Harrison E, Cameron D, Brockhurst MA. Why do plasmids manipulate the expression of bacterial phenotypes?. Phil Trans R Soc B 2022; 377:20200461 [View Article]
     [Google Scholar]
  77. Carrilero L, Dunn SJ, Moran RA, McNally A, Brockhurst MA. Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse Escherichia coli lineages. mSystems 2023; 8:e0071322 [View Article] [PubMed]
     [Google Scholar]
  78. Hall RJ, Snaith AE, Thomas MJN, Brockhurst MA, McNally A. Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli. mSystems 2024; 9:e01193–23 [View Article]
     [Google Scholar]
  79. Palomino A, Gewurz D, DeVine L, Zajmi U, Moralez J et al. Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment. ISME J 2023; 17:151–162 [View Article] [PubMed]
     [Google Scholar]
  80. Yang J, Wang H-H, Lu Y, Yi L-X, Deng Y et al. A ProQ/FinO family protein involved in plasmid copy number control favours fitness of bacteria carrying mcr-1 -bearing IncI2 plasmids. Nucleic Acids Res 2021; 49:3981–3996 [View Article]
     [Google Scholar]
  81. Rodriguez-Valverde D, Giron JA, Hu Y, Nataro JP, Ruiz-Perez F et al. Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with master and global regulators. Sci Rep 2023; 13:7024 [View Article] [PubMed]
     [Google Scholar]
  82. Ho CS, Wong CTH, Aung TT, Lakshminarayanan R, Mehta JS et al. Antimicrobial resistance: a concise update. Lancet Microbe 2025; 6:100947 [View Article] [PubMed]
     [Google Scholar]
/content/journal/micro/10.1099/mic.0.001525
Loading
A plasmid with the blaCTX-M gene enhances the fitness of Escherichia coli strains under laboratory conditions
Microbiology 171, 001525 (2025); https://doi.org/10.1099/mic.0.001525
/content/journal/micro/10.1099/mic.0.001525
/content/journal/micro/10.1099/mic.0.001525
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error