Personal clinical history predicts antibiotic resistance of urinary tract infections

Nature Medicine

Volumn 25, Issue 7, 2019, Pages 1143-1152

  Yelin, Idan ^a   Snitser, Olga ^a   Novich, Gal ^a   Katz, Rachel ^b   Tal, Ofir ^a   Parizade, Miriam ^b   Chodick, Gabriel ^b,c   Koren, Gideon ^b,c   Shalev, Varda ^b,c   Kishony, Roy ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b MACCABI HEALTHCARE SERVICES   (Israel)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AMOXICILLIN; ANTIBIOTIC AGENT; AZITHROMYCIN; CEFALEXIN; CEFUROXIME; CIPROFLOXACIN; NITROFURANTOIN; OFLOXACIN; PENICILLIN DERIVATIVE; ROXITHROMYCIN; TRIMETHOPRIM; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC THERAPY; ARTICLE; BOOTSTRAPPING; CIPROFLOXACIN RESISTANCE; CLINICAL EFFECTIVENESS; HUMAN; KLEBSIELLA PNEUMONIAE; MACHINE LEARNING; MAJOR CLINICAL STUDY; PATIENT CARE; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROTEUS MIRABILIS; URINARY TRACT INFECTION; URINE CULTURE; ALGORITHM; ANTIBIOTIC SENSITIVITY; BACTERIURIA; CALCULATION; DECISION TREE; DRUG CHOICE; DRUG PURCHASE; FEMALE; GRADIENT BOOSTING DECISION TREE; HEALTH CARE QUALITY; MALE; MEDICAL HISTORY; MISMATCH REPAIR; PERSONALIZED MEDICINE; PRESCRIPTION; PREVALENCE; RETROSPECTIVE STUDY; ADOLESCENT; ADULT; AGED; CHILD; INFANT; MIDDLE AGED; NEWBORN; PRESCHOOL CHILD; VERY ELDERLY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; ALGORITHMS; ANTI-BACTERIAL AGENTS; CHILD; CHILD, PRESCHOOL; DRUG RESISTANCE, BACTERIAL; FEMALE; HUMANS; INFANT; INFANT, NEWBORN; MALE; MIDDLE AGED; RETROSPECTIVE STUDIES; URINARY TRACT INFECTIONS; YOUNG ADULT;

EID: 85068773007     PISSN: 10788956     EISSN: 1546170X     Source Type: Journal    
DOI: 10.1038/s41591-019-0503-6     Document Type: Article

References (53)

1. Ventola, C. L. The antibiotic resistance crisis: part 1: causes threats. P T. 40, 277–283 (2015).
2. Rossolini, G. M., Arena, F., Pecile, P. & Pollini, S. Update on the antibiotic resistance crisis. Curr. Opin. Pharmacol. 18, 56–60 (2014).
3. Goossens, H., Ferech, M., Vander Stichele, R. & Elseviers, M., ESAC Project Group. Outpatient antibiotic use in Europe and association with resistance: a cross-national database study. Lancet 365, 579–587 (2005).
4. Bronzwaer, S. L. A. M. et al. A European study on the relationship between antimicrobial use and antimicrobial resistance. Emerg. Infect. Dis. 8, 278–282 (2002).
5. Costelloe, C., Metcalfe, C., Lovering, A., Mant, D. & Hay, A. D. Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. BMJ 340, c2096 (2010).
6. Fridkin, S. K. et al. The effect of vancomycin and third-generation cephalosporins on prevalence of vancomycin-resistant enterococci in 126 U.S. adult intensive care units. Ann. Intern. Med. 135, 175–183 (2001).
7. Malhotra-Kumar, S., Lammens, C., Coenen, S., Van Herck, K. & Goossens, H. Effect of azithromycin and clarithromycin therapy on pharyngeal carriage of macrolide-resistant streptococci in healthy volunteers: a randomised, double-blind, placebo-controlled study. Lancet 369, 482–490 (2007).
8. Kang, C.-I. et al. Bloodstream infections caused by antibiotic-resistant Gram-negative bacilli: risk factors for mortality and impact of inappropriate initial antimicrobial therapy on outcome. Antimicrob. Agents Chemother. 49, 760–766 (2005).
9. Kumar, A. et al. Initiation of inappropriate antimicrobial therapy results in a fivefold reduction of survival in human septic shock. Chest 136, 1237–1248 (2009).
10. Huang, A. M. et al. Impact of rapid organism identification via matrix-assisted laser desorption/ionization time-of-flight combined with antimicrobial stewardship team intervention in adult patients with bacteremia and candidemia. Clin. Infect. Dis. 57, 1237–1245 (2013).
11. Stamm, W. E. & Norrby, S. R. Urinary tract infections: disease panorama and challenges. J. Infect. Dis. 183, S1–4 (2001).
12. Engel, J. D. & Schaeffer, A. J. Evaluation of and antimicrobial therapy for recurrent urinary tract infections in women. Urol. Clin. North. Am. 25, 685–701 (2005).
13. Geerlings, S. E. Clinical presentations and epidemiology of urinary tract infections. Microbiol. Spectr. 4 10.1128/microbiolspec.UTI-0002-2012 (2016).
14. Shapiro, D. J., Hicks, L. A., Pavia, A. T. & Hersh, A. L. Antibiotic prescribing for adults in ambulatory care in the USA, 2007–09. J. Antimicrob. Chemother. 69, 234–240 (2014).
15. Low, M. et al. Infectious disease burden and antibiotic prescribing in primary care in Israel. Ann. Clin. Microbiol. Antimicrob. 17, 26 (2018).
16. Kahlmeter, G. An international survey of the antimicrobial susceptibility of pathogens from uncomplicated urinary tract infections: the ECO/textperiodcentered SENS Project. J. Antimicrob. Chemother. 51, 69–76 (2003).
17. Farrell, D. J., Morrissey, I., De Rubeis, D., Robbins, M. & Felmingham, D. A UK multicentre study of the antimicrobial susceptibility of bacterial pathogens causing urinary tract infection. J. Infect. 46, 94–100 (2003).
18. Foxman, B. Epidemiology of urinary tract infections: incidence, morbidity, and economic costs. Am. J. Med. 113, 5S–13S (2002).
19. 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).
20. Pouwels, K. B. et al. Association between use of different antibiotics and trimethoprim resistance: going beyond the obvious crude association. J. Antimicrob. Chemother. 73, 1700–1707 (2018).
21. Ashkenazi, S., Even-Tov, S., Samra, Z. & Dinari, G. Uropathogens of various childhood populations and their antibiotic susceptibility. Pediatr. Infect. Dis. J. 10, 742–746 (1991).
22. Kahan, N. R. et al. Empiric treatment of uncomplicated urinary tract infection with fluoroquinolones in older women in Israel: another lost treatment option? Ann. Pharmacother. 40, 2223–2227 (2006).
23. Hooton, T. M., Besser, R., Foxman, B., Fritsche, T. R. & Nicolle, L. E. Acute uncomplicated cystitis in an era of increasing antibiotic resistance: a proposed approach to empirical therapy. Clin. Infect. Dis. 39, 75–80 (2004).
24. Arslan, H., Azap, O. K., Ergönül, O. & Timurkaynak, F. Urinary Tract Infection Study Group. Risk factors for ciprofloxacin resistance among Escherichia coli strains isolated from community-acquired urinary tract infections in Turkey. J. Antimicrob. Chemother. 56, 914–918 (2005).
25. Ikram, R., Psutka, R., Carter, A. & Priest, P. An outbreak of multi-drug resistant Escherichia coli urinary tract infection in an elderly population: a case-control study of risk factors. BMC Infect. Dis. 15, 224 (2015).
26. Foxman, B. & Brown, P. Epidemiology of urinary tract infections: transmission and risk factors, incidence, and costs. Infect. Dis. Clin. North Am. 17, 227–241 (2003).
27. Tenney, J., Hudson, N., Alnifaidy, H., Li, J. T. C. & Fung, K. H. Risk factors for aquiring multidrug-resistant organisms in urinary tract infections: a systematic literature review. Saudi Pharm J. 26, 678–684 (2018).
28. Colgan, R., Johnson, J. R., Kuskowski, M. & Gupta, K. Risk factors for trimethoprim-sulfamethoxazole resistance in patients with acute uncomplicated cystitis. Antimicrob. Agents Chemother. 52, 846–851 (2008).
29. Burman, W. J. et al. Conventional and molecular epidemiology of trimethoprim-sulfamethoxazole resistance among urinary Escherichia coli isolates. Am. J. Med. 115, 358–364 (2003).
30. Kang, M.-S., Lee, B.-S., Lee, H.-J., Hwang, S.-W. & Han, Z.-A. Prevalence of and risk factors for multidrug-resistant bacteria in urine cultures of spinal cord injury patients. Ann. Rehabil. Med. 39, 686–695 (2015).
31. Lee, G., Cho, Y.-H., Shim, B. S. & Lee, S. D. Risk factors for antimicrobial resistance among the Escherichia coli strains isolated from Korean patients with acute uncomplicated cystitis: a prospective and nationwide study. J. Korean Med. Sci. 25, 1205–1209 (2010).
32. Johnson, L. et al. Emergence of fluoroquinolone resistance in outpatient urinary Escherichia coli isolates. Am. J. Med. 121, 876–884 (2008).
33. Paul, M. et al. Improving empirical antibiotic treatment using TREAT, a computerized decision support system: cluster randomized trial. J. Antimicrob. Chemother. 58, 1238–1245 (2006).
34. MacFadden, D. R., Ridgway, J. P., Robicsek, A., Elligsen, M. & Daneman, N. Predictive utility of prior positive urine cultures. Clin. Infect. Dis. 59, 1265–1271 (2014).
35. Olesen, S. W., Barnett, M. L., MacFadden, D. R., Lipsitch, M. & Grad, Y. H. Trends in outpatient antibiotic use and prescribing practice among US older adults, 2011–15: observational study. BMJ 362, k3155 (2018).
36. Ena, J., Amador, C., Martinez, C. & Ortiz de la Tabla, V. Risk factors for acquisition of urinary tract infections caused by ciprofloxacin resistant Escherichia coli. J. Urol. 153, 117–120 (1995).
37. Brown, P. D., Freeman, A. & Foxman, B. Prevalence and predictors of trimethoprim-sulfamethoxazole resistance among uropathogenic Escherichia coli isolates in Michigan. Clin. Infect. Dis. 34, 1061–1066 (2002).
38. Metlay, J. P., Strom, B. L. & Asch, D. A. Prior antimicrobial drug exposure: a risk factor for trimethoprim-sulfamethoxazole-resistant urinary tract infections. J. Antimicrob. Chemother. 51, 963–970 (2003).
39. Low, M. et al. Association between urinary community-acquired fluoroquinolone-resistant Escherichia coli and neighbourhood antibiotic consumption: a population-based case-control study. Lancet Infect. Dis. 19, 419–428 (2019).
40. Wang, A., Daneman, N., Tan, C., Brownstein, J. S. & MacFadden, D. R. Evaluating the relationship between hospital antibiotic use and antibiotic resistance in common nosocomial pathogens. Infect. Control Hosp. Epidemiol. 38, 1457–1463 (2017).
41. Gupta, K. et al. 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. 52, e103–e120 (2011).
42. Lipsky, B. A. Urinary tract infections in men. Epidemiology, pathophysiology, diagnosis, and treatment. Ann. Intern. Med. 110, 138–150 (1989).
43. Ginsburg, C. M. & McCracken, G. H. Jr. Urinary tract infections in young infants. Pediatrics 69, 409–412 (1982).
44. Edlin, R. S., Shapiro, D. J., Hersh, A. L. & Copp, H. L. Antibiotic resistance patterns of outpatient pediatric urinary tract infections. J. Urol. 190, 222–227 (2013).
45. Kahlmeter, G. & Menday, P. Cross-resistance and associated resistance in 2478 Escherichia coli isolates from the Pan-European ECO/textperiodcentered SENS Project surveying the antimicrobial susceptibility of pathogens from uncomplicated urinary tract infections. J. Antimicrob. Chemother. 52, 128–131 (2003).
46. Hanley, J. A. & McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29–36 (1982).
47. Lieberman, T. D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat. Genet. 43, 1275–1280 (2011).
48. Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. A. & Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13, 601–612 (2012).
49. Bradley, P. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun. 6, 10063 (2015).
50. Khoury, M. J. & Ioannidis, J. P. A. Medicine. Big data meets public health. Science 346, 1054–1055 (2014).
51. Beam, A. L. & Kohane, I. S. Big data and machine learning in health care. JAMA 319, 1317–1318 (2018).
52. Grad, Y. H. & Lipsitch, M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 15, 538 (2014).
53. Sandora, T. J., Gerner-Smidt, P. & McAdam, A. J. What’s your subtype? The epidemiologic utility of bacterial whole-genome sequencing. Clin. Chem. 60, 586–588 (2014).