Skip to main navigation menu Skip to main content Skip to site footer

Original article

Vol. 149 No. 2930 (2019)

Antimicrobial resistance trends in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis urinary isolates from Switzerland: retrospective analysis of data from a national surveillance network over an 8-year period (2009–2016)

  • Veronica Zanichelli
  • Angela Huttner
  • Stephan Harbarth
  • Andreas Kronenberg
  • Benedikt Huttner
  • the Swiss Centre for Antibiotic Resistance (ANRESIS)
Cite this as:
Swiss Med Wkly. 2019;149:w20110



Most urinary tract infections (UTIs) are treated empirically with antibiotics, making comprehensive resistance surveillance data essential to guide empiric regimens. We describe trends in the antibiotic resistance of urinary Enterobacteriaceae isolates in Switzerland between 2009 and 2016.


We analysed data from routinely collected Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis urinary samples from community and hospital settings in Switzerland. The data were collected by ANRESIS, the national laboratory-based antimicrobial resistance surveillance system. Our analyses focused on resistance to antibiotics commonly prescribed for UTIs for the period 2009–2016. Only the first isolate per patient per year was included.


297,200 urinary samples were included in the analysis, of which 246,656 (83.0%) were E. coli isolates. Overall, E. coli showed high susceptibility to 3rd/4th-generation cephalosporins, nitrofurantoin and fosfomycin, with the annual proportions of resistant isolates <6%, <5% and <2%, respectively, for all study years. Resistance to fluoroquinolones was >14% and increased over time (from 14.5% in 2009 to 19.3% in 2016). Resistance to cotrimoxazole was >20% for the whole study period. K. pneumoniae (n = 32,757; 11.0%) showed low resistance to cotrimoxazole and quinolones (<11% and <12%, respectively), while for P. mirabilis (n = 17,787; 6.0%) the proportion of resistant isolates was <35% for cotrimoxazole and <18% for quinolones. Even though quinolone resistance remained low for both pathogens (<12% for K. pneumoniae and <18% for P. mirabilis), it increased significantly over time. Proportions of isolates resistant to 3rd/4th generation cephalosporins remained low (<5% for K. pneumoniae and <2% for P. mirabilis), but in the case of K. pneumoniae they increased over time.


Swiss surveillance data confirm that resistance among uropathogenic E. coli isolates to nitrofurantoin and fosfomycin remains low. While resistance to 3rd/4th-generation cephalosporins also remains relatively low, it has been increasing and needs further surveillance. As for K. pneumoniae and P. mirabilis, high levels of susceptibility to 3rd-generation cephalosporins and quinolones were confirmed, while high prevalences of resistance to nitrofurantoin and fosfomycin discourage their use as first-line therapies for these pathogens.


  1. Tan C, Graves E, Lu H, Chen A, Li S, Schwartz KL, et al. A decade of outpatient antimicrobial use in older adults in Ontario: a descriptive study. CMAJ Open. 2017;5(4):E878–85. doi:.
  2. Aabenhus R, Hansen MP, Siersma V, Bjerrum L. Clinical indications for antibiotic use in Danish general practice: results from a nationwide electronic prescription database. Scand J Prim Health Care. 2017;35(2):162–9. doi:.
  3. Foxman B. Epidemiology of urinary tract infections: incidence, morbidity, and economic costs. Am J Med. 2002;113(1, Suppl 1A):5–13. doi:.
  4. Huttner A, Kowalczyk A, Turjeman A, Babich T, Brossier C, Eliakim-Raz N, et al. Effect of 5-day nitrofurantoin vs single-dose fosfomycin on clinical resolution of uncomplicated lower urinary tract infection in women: A randomized clinical trial. JAMA. 2018;319(17):1781–9. doi:.
  5. Blaettler L, Mertz D, Frei R, Elzi L, Widmer AF, Battegay M, et al. Secular trend and risk factors for antimicrobial resistance in Escherichia coli isolates in Switzerland 1997-2007. Infection. 2009;37(6):534–9. doi:.
  6. Seiffert SN, Hilty M, Kronenberg A, Droz S, Perreten V, Endimiani A. Extended-spectrum cephalosporin-resistant Escherichia coli in community, specialized outpatient clinic and hospital settings in Switzerland. J Antimicrob Chemother. 2013;68(10):2249–54. doi:.
  7. Kronenberg A, Hilty M, Endimiani A, Muhlemann K. Temporal trends of extended-spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in in- and outpatients in Switzerland, 2004 to 2011. Euro Surveill. 2013;18(21):18.
  8. Woerther PL, Burdet C, Chachaty E, Andremont A. Trends in human fecal carriage of extended-spectrum β-lactamases in the community: toward the globalization of CTX-M. Clin Microbiol Rev. 2013;26(4):744–58. doi:.
  9. Gupta K, Hooton TM, Naber KG, Wullt B, Colgan R, Miller LG, et al.; Infectious Diseases Society of America; European Society for Microbiology and Infectious Diseases. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: A 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin Infect Dis. 2011;52(5):e103–20. doi:.
  10. Bonkat G, Müller G, Braissant O, Frei R, Tschudin-Suter S, Rieken M, et al. Increasing prevalence of ciprofloxacin resistance in extended-spectrum-β-lactamase-producing Escherichia coli urinary isolates. World J Urol. 2013;31(6):1427–32. doi:.
  11. Sanchez GV, Baird AM, Karlowsky JA, Master RN, Bordon JM. Nitrofurantoin retains antimicrobial activity against multidrug-resistant urinary Escherichia coli from US outpatients. J Antimicrob Chemother. 2014;69(12):3259–62. doi:.
  12. Stewardson AJ, Vervoort J, Adriaenssens N, Coenen S, Godycki-Cwirko M, Kowalczyk A, et al.; SATURN WP1 Study Group; SATURN WP3 Study Group. Effect of outpatient antibiotics for urinary tract infections on antimicrobial resistance among commensal Enterobacteriaceae: a multinational prospective cohort study. Clin Microbiol Infect. 2018;24(9):972–9. doi:.
  13. Sommerstein R, Atkinson A, Lo Priore EF, Kronenberg A, Marschall J, Burnens A, et al.; Swiss Centre for Antibiotic Resistance (ANRESIS). Characterizing non-linear effects of hospitalisation duration on antimicrobial resistance in respiratory isolates: an analysis of a prospective nationwide surveillance system. Clin Microbiol Infect. 2018;24(1):45–52. doi:.
  14. Olearo F, Albrich WC, Vernaz N, Harbarth S, Kronenberg A, Swiss C ; Swiss Centre For Antibiotic Resistance Anresis. Staphylococcus aureus and methicillin resistance in Switzerland: regional differences and trends from 2004 to 2014. Swiss Med Wkly. 2016;146:w14339. doi:.
  15. Anresis Swiss Center for Antibiotic Resistance. Definitions selection criteria; [cited 2019, February 20]. Available from:
  16. The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of mics and zone diameters; [cited 2019, May 3]. Available from:
  17. Clinical & Laboratory Standards Institute. Clsi guidelines; [cited 2019, May 3]. Available from:
  18. Vernaz N, Huttner B, Muscionico D, Salomon JL, Bonnabry P, López-Lozano JM, et al. Modelling the impact of antibiotic use on antibiotic-resistant Escherichia coli using population-based data from a large hospital and its surrounding community. J Antimicrob Chemother. 2011;66(4):928–35. doi:.
  19. Kronenberg A, Koenig S, Droz S, Mühlemann K. Active surveillance of antibiotic resistance prevalence in urinary tract and skin infections in the outpatient setting. Clin Microbiol Infect. 2011;17(12):1845–51. doi:.
  20. Swiss Society for Infectious Diseases. Guidelines urinary tract infections [cited 2019, February 20]. Available from:
  21. Costelloe C, Metcalfe C, Lovering A, Mant D, Hay AD. Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. BMJ. 2010;340(may18 2):c2096. doi:.
  22. Bell BG, Schellevis F, Stobberingh E, Goossens H, Pringle M. A systematic review and meta-analysis of the effects of antibiotic consumption on antibiotic resistance. BMC Infect Dis. 2014;14(1):13. doi:.
  23. Falagas ME, Kotsantis IK, Vouloumanou EK, Rafailidis PI. Antibiotics versus placebo in the treatment of women with uncomplicated cystitis: a meta-analysis of randomized controlled trials. J Infect. 2009;58(2):91–102. doi:.
  24. Chastain DB, King ST, Stover KR. Rethinking urinary antibiotic breakpoints: analysis of urinary antibiotic concentrations to treat multidrug resistant organisms. BMC Res Notes. 2018;11(1):497. doi:.

Most read articles by the same author(s)