AMRmap – antibiotic resistance surveillance system in Russia

Clinical Microbiology and Antimicrobial Chemotherapy. 2021; 23(2):198-204

​ Kuzmenkov A.Yu., Vinogradova A.G., Trushin I.V., Edelstein M.V., Avramenko A.A., Dekhnich A.V., Kozlov R.S.
10.36488/cmac.2021.2.198-204
antibiotic resistance surveillance online platform AMRmap
Section
Antimicrobial Resistance
Type
Original Article
Publication
Clinical Microbiology and Antimicrobial Chemotherapy. 2021; 23(2):198-204

Objective.

To review the basic principles and functionality of the AMRmap online resource.

Materials and Methods.

The AMRmap platform was developed using the R programming language and various downloadable modules – packages. The current annually updated version of EUCAST clinical breakpoints was applied for determination of categories of susceptibility to antimicrobial agents. Descriptive analysis includes calculation of absolute and relative frequencies, median values, and confidence intervals using the Wilson method. Categorical variables are compared using Fisher’s exact test and Holm correction method for multiple comparisons. The algorithms are used to visualize multiple comparisons, kernel regression for trend analysis, and algorithms for finding associative rules.

Results.

The developed surveillance system includes modules for filtering, analyzing and visualizing antibiotic resistance data. The filters allow creating a sample of data with a specific list of parameters. A tab-based separation of analysis and visualization options ensure efficient stepwise evaluation of results. Data saving and sharing functions are also provided.

Conclusions.

This web-based informatics system provides a convenient way to AMR data from prospective microbiological surveillance studies in Russia. AMRmap can be accessed at https://amrmap.ru.

Kuzmenkov Alexey Yuryevich

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Alina G. Vinogradova

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Ivan V. Trushin

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Mikhail V. Edelstein

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Andrey A. Avramenko

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Andrey V. Dekhnich

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

Roman S. Kozlov

Institute of Antimicrobial Chemotherapy, Smolensk, Russia

  • 1. Ferri M., Ranucci E., Romagnoli P., Giaccone V. Antimicrobial resistance: a global emerging threat to public health systems. Crit Rev Food Sci Nutr. 2017;57(13):28572876. DOI: 10.1080/10408398.2015.1077192
  • 2. Sultan I., Rahman S., Jan A.T., Siddiqui M.T., Mondal A.H., Haq Q.M. Antibiotics, resistome and resistance mechanisms: a bacterial perspective. Front Microbiol. 2018;9:2066. DOI: 10.3389/fmicb.2018.02066
  • 3. Chaudhary A.S. A review of global initiatives to fight antibiotic resistance and recent antibiotics’ discovery. Acta Pharm Sin B. 2016;6(6):552-556. DOI: 10.1016/j.apsb.2016.06.004
  • 4. Tacconelli E., Sifakis F., Harbarth S., Schrijver R., van Mourik M., Voss A., et al. Surveillance for control of antimicrobial resistance. Lancet Infect Dis. 2018;18(3):e99-e106. DOI: 10.1016/S14733099(17)30485-1
  • 5. Statens Serum Institut. The Danish Integrated Antimicrobial Resistance Monitoring and Research Programme. Available at: www.danmap.org. Accessed March 2021.
  • 6. The Public Health Agency of Sweden. A report on Swedish Antibiotic Sales and Resistance in Human Medicine and Swedish Veterinary Antibiotic Resistance Monitoring. Available at: www.sva.se/en/our-topics/antibiotics/svarmresistance-monitoring/swedres-svarm-reports/. Accessed March 2021.
  • 7. The Ministry of Health Labour and Welfare. Japan Nosocomial Infections Surveillance. Available at: https://janis.mhlw.go.jp/english/about/index.html. Accessed March 2021.
  • 8. European Centre for Disease Prevention and Control. Antimicrobial Resistance in the EU/EEA (EARS-Net). Annual Report 2019. Available at: www.euro.who.int/__data/assets/pdf_file/0003/418863/53373-WHO-CAESARannual-report-2019.pdf. Accessed March 24, 2021.
  • 9. The Center for Disease Dynamics Economics & Policy. ResistanceMap: Antibiotic resistance. Available at https://resistancemap.cddep.org/AntibioticResistance.php. Accessed March 21, 2021.
  • 10. WHO/Europe. Central Asian and European Surveillance of Antimicrobial Resistance. Annual report 2019. Available at www.euro.who.int/__data/assets/pdf_file/0003/418863/53373-WHO-CAESAR-annualreport-2019.pdf. Accessed March 24, 2021.
  • 11. R Core Team. A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: www.r-project.org. Accessed March 2021.
  • 12. Chang W., Cheng J., Allaire J., Sievert C., Schloerke C., Xie Y., et al. Web application framework for R. R package version 1.6.0. Available at: https://cran.r-project.org/package=shiny. Accessed March 2021.
  • 13. Wickham H., Chang W., Henry L., Pedersen T., Takahashi K., Wilke C., et al. Create elegant data visualisations using the grammar of graphics. R package version 3.3.3. Available at: https://cran.r-project.org/package=ggplot2. Accessed March 2021.
  • 14. Dowle M., Srinivasan A., Gorecki J., Chirico M., Stetsenko P., Short T., et al. Extension of «data.frame». R package version 1.14.0. Available at: https://r-datatable.com. Accessed March 2021.
  • 15. Xie Y., Cheng J., Tan X., Allaire J., Girlich M., Ellis G., et al. A wrapper of the JavaScript library «DataTables». R packages version 0.17. Available at: https://cran.r-project.org/package=DT. Accessed March 2021.
  • 16. Almende B., Benoit T., Titouan R. Network visualization using «vis.js» library. R package version 2.0.9. Available at: https://cran.r-project.org/package=visNetwork. Accessed March 2021.
  • 17. Cheng J., Karambelkar B., Xie Y., Wickham H., Russell K., Johnson K., et al. Create interactive web maps with the JavaScript «Leaflet» library. R package version 2.0.4.1. Available at: https://cran.r-project.org/package=leaflet. Accessed March 2021.
  • 18. Kunst J., Agostinho N., Noriega D., Hadley M., Flores E., Kilfoyle D., et al. Highcharter: a wrapper for the «Highcharts» library. R package version 0.8.2. Available at: https://cran.r-project.org/package=highcharter. Accessed March 2021.
  • 19. Hahsler M., Buchta C., Gruen B., Hornik K., Johnson I., Borgelt C. Mining association rules and frequent itemsets. R package version 1.6-6. Available at: https://cran.r-project.org/package=arules. Accessed March 2021.
  • 20. Kuzmenkov A.Y., Vinogradova A.G. Antimicrobial resistance monitoring: a review of information resources. Bull Sib Med. 2020;19(2):163-170. DOI: 10.20538/16820363-2020-2-163-170
  • 21. Diallo O.O., Baron S.A., Abat C., Colson P., Chaudet H., Rolain J-M. Antibiotic resistance surveillance systems: A review. J Glob Antimicrob Resist. 2020;23:430-438. DOI: 10.1016/j.jgar.2020.10.009
  • 22. Schnall J., Rajkhowa A., Ikuta K., Rao P., Moore C.E. Surveillance and monitoring of antimicrobial resistance: limitations and lessons from the GRAM project. BMC Med. 2019;17(1):176. DOI: 10.1186/s12916-019-1412-8
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