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Antimicrobial susceptibility and adaptative changes in MRSA lineages exposed to increasing concentrations of fluoroquinolones and chlorhexidine
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  • Published: 16 February 2026

Antimicrobial susceptibility and adaptative changes in MRSA lineages exposed to increasing concentrations of fluoroquinolones and chlorhexidine

  • Tamara Lopes Rocha de Oliveira1,3,
  • Ariane Faria de Souza1,
  • Bruna Marques de Souza1,
  • Marlei Gomes da Silva1,
  • Rafael Silva Duarte1,
  • Rosana Barreto Rocha Ferreira1,2 &
  • …
  • Kátia Regina Netto dos Santos1,3 

Scientific Reports , Article number:  (2026) Cite this article

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Subjects

  • Diseases
  • Microbiology
  • Molecular biology

Abstract

Selective pressure from antimicrobial use can drive the emergence of methicillin-resistant Staphylococcus aureus (MRSA) isolates. We evaluated resistance rates to fluoroquinolones and chlorhexidine digluconate (CD) and the effect of their selective pressure on lineages of MRSA. Minimum inhibitory concentrations (MICs) for fluoroquinolones and CD were determined for 75 isolates from 11 lineages. Phenotypic expression of efflux pumps was assessed by the Cartwheel method and associated genes were detected by PCR. Cross-resistance between antibiotics and CD and point gene mutations were investigated after exposure to increasing concentrations of fluoroquinolones and CD. The MIC90 values for ciprofloxacin, moxifloxacin, and CD in 75 MRSA isolates were 128, 8 and 1 mg/L, respectively. ST5-SCCmecII, ST239-III and ST1-IV lineages showed the highest resistance rates to fluoroquinolones, and ST5-II showed the highest MIC90 for CD. Among 17 (22.6%) MRSA isolates with detectable efflux pump activity, seven showed a higher efflux potential, including four ST5-II isolates. The qacA/B genes were found in 14 (18.6%) isolates, and 10 were ST5-II, while the smr gene was frequent among isolates with SCCmecIV (71.4%). Eight of 10 selected strains showed increased resistance to fluoroquinolones and/or tetracycline and increased phenotypic expression of efflux pumps. Point mutations in the gyrA, parC, norA, and/or norB genes emerged in three strains after exposure to higher doses of ciprofloxacin or CD. Resistance to fluoroquinolones was high among MRSA isolates, especially those from ST5-II. MRSA isolates subjected to in vitro selective pressure of antimicrobials showed increased MICs and gene mutations, reinforcing the importance of the rational use of antimicrobial agents in clinical practice.

Data availability

The data sets generated and analyzed during the current study, such as the patterns of genetic mutations identified after induction with ciprofloxacin and CD, are available in Genbank (Access number: PX432114 → PX432119).

References

  1. Haque, M., Sartelli, M., McKimm, J. & Bakar, M. A. Health care-associated infections–an overview. Infect. Drug Resist. 11, 2321–2333. https://doi.org/10.2147/IDR.S177247 (2018).

    Google Scholar 

  2. Bai, A. D. et al. Staphylococcus aureus bacteremia mortality across country income groups: A secondary analysis of a systematic review. Int. J. Infect. Dis. 122, 405–411. https://doi.org/10.1016/j.ijid.2022.06.026 (2022).

    Google Scholar 

  3. Hiramatsu, K. et al. Genomic basis for methicillin resistance in Staphylococcus aureus. Infect. Chemother. 45, 117–136. https://doi.org/10.3947/ic.2013.45.2.117 (2013).

    Google Scholar 

  4. Monteiro, A. D. S. et al. Phylogenetic and molecular profile of Staphylococcus aureus isolated from bloodstream infections in Northeast Brazil. Microorganisms 7, 210. https://doi.org/10.3390/microorganisms7070210 (2019).

    Google Scholar 

  5. De Oliveira Whitaker, C. et al. Clonal shift and impact of azithromycin use on antimicrobial resistance of Staphylococcus aureus isolated from bloodstream infection during the COVID-19 pandemic. Sci. Rep. 15, 597. https://doi.org/10.1038/s41598-024-84307-1 (2025).

    Google Scholar 

  6. Hushyar, S., Doghaheh, H. P. & Arzanlou, M. Evaluation of aminoglycoside- and methicillin-resistant Staphylococcus aureus: Phenotypic and genotypic insights from clinical specimens in Ardabil, Iran. BMC Infect. Dis. 25, 285. https://doi.org/10.1186/s12879-025-10659-2 (2025).

    Google Scholar 

  7. Kinoshita, T., Tokumasu, H., Tanaka, S., Kramer, A. & Kawakami, K. Policy implementation for methicillin-resistant Staphylococcus aureus in seven European countries: A comparative analysis from 1999 to 2015. J. Mark. Access Health Policy 5, 1351293. https://doi.org/10.1080/20016689.2017.1351293 (2017).

    Google Scholar 

  8. Fuzi, M., Rodriguez Baño, J. & Toth, A. Global evolution of pathogenic bacteria with extensive use of fluoroquinolone agents. Front. Microbiol. 11, 271. https://doi.org/10.3389/fmicb.2020.00271 (2020).

    Google Scholar 

  9. Redgrave, L. S., Sutton, S. B., Webber, M. A. & Piddock, L. J. Fluoroquinolone resistance: Mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol. 22, 438–445. https://doi.org/10.1016/j.tim.2014.04.007 (2014).

    Google Scholar 

  10. Lompo, P. et al. Bacterial contamination of antiseptics, disinfectants and hand hygiene products in healthcare facilities in high-income countries: A scoping review. Hygiene 3, 136–175. https://doi.org/10.3390/hygiene3020012 (2023).

    Google Scholar 

  11. Rozman, U., Pušnik, M., Kmetec, S., Duh, D. & Šostar Turk, S. Reduced susceptibility and increased resistance of bacteria against disinfectants: A systematic review. Microorganisms 9, 2550. https://doi.org/10.3390/microorganisms9122550 (2021).

    Google Scholar 

  12. Conceição, T., De Lencastre, H. & Aires-de-Sousa, M. Prevalence of biocide resistance genes and chlorhexidine and mupirocin non-susceptibility in Portuguese hospitals during a 31-year period (1985–2016). J. Glob. Antimicrob. Resist. 24, 169–174. https://doi.org/10.1016/j.jgar.2020.12.010 (2021).

    Google Scholar 

  13. Sarwar, S., Saleem, S., Shahzad, F. & Jahan, S. Identifying and elucidating the resistance of Staphylococcus aureus isolated from hospital environment to conventional disinfectants. Am. J. Infect. Control 51, 178–183. https://doi.org/10.1016/j.ajic.2022.05.018 (2023).

    Google Scholar 

  14. Garcia, Í. R. et al. Microbial resistance: The role of efflux pump superfamilies and their respective substrates. Life Sci. 295, 120391. https://doi.org/10.1016/j.lfs.2022.120391 (2022).

    Google Scholar 

  15. Coombs, K., Rodriguez-Quijada, C., Clevenger, J. O. & Sauer-Budge, A. F. Current understanding of potential linkages between biocide tolerance and antibiotic cross-resistance. Microorganisms 11, 2000. https://doi.org/10.3390/microorganisms11082000 (2023).

    Google Scholar 

  16. Horváth, A. et al. Varying fitness cost associated with resistance to fluoroquinolones governs clonal dynamic of methicillin-resistant Staphylococcus aureus. Eur. J. Clin. Microbiol. Infect. Dis. 31, 2029–2036. https://doi.org/10.1007/s10096-011-1536-z (2012).

    Google Scholar 

  17. De Oliveira, T. L. R., Cavalcante, F. S., Chamon, R. C., Ferreira, R. B. R. & Dos Santos, K. R. N. Genetic mutations in the quinolone resistance-determining region are related to changes in the epidemiological profile of methicillin-resistant Staphylococcus aureus isolates. J. Glob. Antimicrob. Resist. 19, 236–240. https://doi.org/10.1016/j.jgar.2019.05.026 (2019).

    Google Scholar 

  18. Milheiriço, C., Oliveira, D. C. & De Lencastre, H. Update to the multiplex PCR strategy for assignment of mec element types in Staphylococcus aureus. Antimicrob. Agents Chemother. 51, 3374–3377. https://doi.org/10.1128/AAC.00275-07 (2007).

    Google Scholar 

  19. De Oliveira, T. L. R. et al. High colonization by multidrug-resistant and virulent Staphylococcus aureus genotypes among critically ill patients in the COVID-19 pandemic in a Brazilian hospital. BMC Microbiol. 25, 810–823. https://doi.org/10.1186/s12866-025-04526-y (2025).

    Google Scholar 

  20. Enright, M. C., Day, N. P., Davies, C. E., Peacock, S. J. & Spratt, B. G. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J. Clin. Microbiol. 38, 1008–1015. https://doi.org/10.1128/JCM.38.3.1008-1015.2000 (2000).

    Google Scholar 

  21. CLSI. Clinical and Laboratory Standard Institute. Performance standards for antimicrobial susceptibility testing; Twentieth informational supplement. CLSI document M100- S20 & Wayne Pensylvania, USA (2020).

  22. Costa, S. et al. Resistance to antimicrobials mediated by efflux pumps in Staphylococcus aureus. Antibiotics 2, 83–99. https://doi.org/10.3390/antibiotics2010083 (2013).

    Google Scholar 

  23. Worthing, K. A., Marcus, A., Abraham, S., Trott, D. J. & Norris, J. M. Qac genes and biocide tolerance in clinical veterinary methicillin-resistant and methicillin-susceptible Staphylococcus aureus and Staphylococcus pseudintermedius. Vet. Microbiol. 216, 153–158. https://doi.org/10.1016/j.vetmic.2018.02.004 (2018).

    Google Scholar 

  24. Martins, M. et al. Identification of efflux pump-mediated multidrug-resistant bacteria by the ethidium bromide-agar cartwheel method. Vivo 25, 171–178 (2011).

    Google Scholar 

  25. Wu, D. et al. Study of cross-resistance mediated by antibiotics, chlorhexidine and Rhizoma coptidis in Staphylococcus aureus. J. Glob. Antimicrob. Resist. 7, 61–66. https://doi.org/10.1016/j.jgar.2016.07.011 (2016).

    Google Scholar 

  26. Pitcher, D. G., Saunders, N. A. & Owen, R. J. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8, 151–156. https://doi.org/10.1111/j.1472-765X.1989.tb00262.x (1989).

    Google Scholar 

  27. Alam, M. M., Kobayashi, N., Uehara, N. & Watanabe, N. Analysis on distribution and genomic diversity of high-level antiseptic resistance genes qac and qacB in human clinical isolates of Staphylococcus aureus. Microb. Drug Resist. 9, 109–121. https://doi.org/10.1089/107662903765826697 (2003).

    Google Scholar 

  28. Kwak, Y. G. et al. Association of norB overexpression and fluoroquinolone resistance in clinical isolates of Staphylococcus aureus from Korea. J. Antimicrob. Chemother. 68, 2766–2772. https://doi.org/10.1093/jac/dkt286 (2013).

    Google Scholar 

  29. Boyle-Vavra, S., Berke, S. K., Lee, J. C. & Daum, R. S. Reversion of the glycopeptide resistance phenotype in Staphylococcus aureus clinical isolates. Antimicrob. Agents Chemother. 44, 272–277. https://doi.org/10.1128/aac.44.2.272-277.2000 (2000).

    Google Scholar 

  30. Damasco, A. P. et al. Daptomycin and vancomycin non-susceptible methicillin-resistant Staphylococcus aureus clonal lineages from bloodstream infection in a Brazilian teaching hospital. Braz. J. Infect. Dis. 23, 139–142. https://doi.org/10.1016/j.bjid.2019.03.003 (2019).

    Google Scholar 

  31. Augusto, M. F. et al. Pandemic clone USA300 in a Brazilian hospital: Detection of an emergent lineage among methicillin-resistant Staphylococcus aureus isolates from bloodstream infections. Antimicrob. Resist. Infect. Control 11, 114. https://doi.org/10.1186/s13756-022-01154-3 (2022).

    Google Scholar 

  32. Fuzi, M. Dissimilar fitness associated with resistance to fluoroquinolones influences clonal dynamics of various multiresistant bacteria. Front. Microbiol. 7, 1017. https://doi.org/10.3389/fmicb.2016.01017 (2016).

    Google Scholar 

  33. Maris, A. S., Mody, P., Brewer, D. J. & Humphries, R. M. The fluoroquinolones: An update for the clinical microbiologist. Clin. Microbiol. Newsl. 43, 97–107. https://doi.org/10.1016/j.clinmicnews.2021.06.001 (2021).

    Google Scholar 

  34. Hashem, R. A., Yassin, A. S., Zedan, H. H. & Amin, M. A. Fluoroquinolone resistant mechanisms in methicillin-resistant Staphylococcus aureus clinical isolates in Cairo, Egypt. J. Infect. Dev. Ctries. 7, 796–803. https://doi.org/10.3855/jidc.3105 (2013).

    Google Scholar 

  35. Mohamad Farook, N. A. et al. Diversity and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) genotypes in Southeast Asia. Trop. Med. Infect. Dis. 7, 438. https://doi.org/10.3390/tropicalmed7120438 (2022).

    Google Scholar 

  36. Kumar, S. et al. Functional and structural roles of the major facilitator superfamily bacterial multidrug efflux pumps. Microorganisms 8, 266. https://doi.org/10.3390/microorganisms8020266 (2020).

    Google Scholar 

  37. Henderson, P. J. et al. Physiological functions of bacterial “multidrug” efflux pumps. Chem. Rev. 121, 5417–5478. https://doi.org/10.1021/acs.chemrev.0c01226 (2021).

    Google Scholar 

  38. Buffet-Bataillon, S., Tattevin, P., Maillard, J. Y., Bonnaure-Mallet, M. & Jolivet-Gougeon, A. Efflux pump induction by quaternary ammonium compounds and fluoroquinolone resistance in bacteria. Future Microbiol. 11, 81–92. https://doi.org/10.2217/fmb.15.131 (2016).

    Google Scholar 

  39. McNeil, J. C. et al. Clinical and molecular features of decreased chlorhexidine susceptibility among nosocomial Staphylococcus aureus isolates at Texas Children’s Hospital. Antimicrob. Agents Chemother. 60, 1121–1128. https://doi.org/10.1128/AAC.02011-15 (2016).

    Google Scholar 

  40. Zhang, C. et al. Distribution of biocide resistance genes and association with clonal complex genotypes in Staphylococcus aureus isolated from school-age children in Guangzhou. Infect. Drug Resist. 15, 7165–7175. https://doi.org/10.2147/IDR.S387528 (2022).

    Google Scholar 

  41. Sanfilippo, C. M., Hesje, C. K., Haas, W. & Morris, T. W. Topoisomerase mutations that are associated with high-level resistance to earlier fluoroquinolones in Staphylococcus aureus have less effect on the antibacterial activity of besifloxacin. Chemotherapy 57, 363–371. https://doi.org/10.1159/000330858 (2011).

    Google Scholar 

  42. Hardy, K. et al. Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of Staphylococcus aureus. mBio 9, e00894-18. https://doi.org/10.1128/mBio.00894-18 (2018).

    Google Scholar 

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Acknowledgements

We thank FIOCRUZ-INCQS, Rio de Janeiro, RJ for the donation of Staphylococcus aureus INCQS 00039 (ATCC 6538) strain of Collection of Reference Microorganisms in Health Surveillance-CRMVS. We also thank Dr. Renata Cristina Picão/UFRJ for the donation of P. aeruginosa PA01XY++ strain.

Funding

This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro [FAPERJ, Grants #E-26/203.296/2017; #E-26/200.419/2023, #E-26/010.000172/2016, #E-26/010.001463/2019, #E-26/010.101056/2018; #E-26/211.554/2019 (Projeto REDES); #E-26/201.071/2020; #E-26/211.284/2021; #E-26/201.454/2021 and #E-26/205.939/2022] and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Grants #307594/2021-1 [KRNS] and 405020/2023-6 [Universal-MSL]).

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Authors and Affiliations

  1. Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil

    Tamara Lopes Rocha de Oliveira, Ariane Faria de Souza, Bruna Marques de Souza, Marlei Gomes da Silva, Rafael Silva Duarte, Rosana Barreto Rocha Ferreira & Kátia Regina Netto dos Santos

  2. Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA

    Rosana Barreto Rocha Ferreira

  3. Laboratório de Infecção Hospitalar, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, CCS, Bloco I, Sala I2-010 - Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-590, Brazil

    Tamara Lopes Rocha de Oliveira & Kátia Regina Netto dos Santos

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  1. Tamara Lopes Rocha de Oliveira
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Contributions

TLRO and KRNS designed the study. TLRO, AFS, MGS and BMS analyzed the S. aureus isolates, conducted the experiments described in the “Methods” sections. TLRO gathered the data for the final statistical analysis as well as drafted the manuscript. RBRF and RSD critically reviewed the manuscript. KRNS supervised and critically reviewed the manuscript. All authors approved the final version.

Corresponding authors

Correspondence to Tamara Lopes Rocha de Oliveira or Kátia Regina Netto dos Santos.

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The authors declare no competing interests.

Ethics approval and consent to participate

This study was approved by the Human Research Ethics Committee of Universidade Federal do Rio de Janeiro (UFRJ) under numbers 159/07 and CAAE40652714.0.0000.5257, and by the Human Research Ethics Committee of Copa Dor hospital under number 088/07. In addition, all methods were performed in accordance with the relevant guidelines and regulations. All experimental protocols were approved by the Microbiology Institute/UFRJ.

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de Oliveira, T.L.R., de Souza, A.F., de Souza, B.M. et al. Antimicrobial susceptibility and adaptative changes in MRSA lineages exposed to increasing concentrations of fluoroquinolones and chlorhexidine. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40345-5

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  • Received: 01 October 2025

  • Accepted: 12 February 2026

  • Published: 16 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-40345-5

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Keywords

  • MRSA
  • Fluoroquinolones
  • Chlorhexidine
  • Cross-resistance
  • Gene mutations
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