Resistance data can be used to support decisions on antibiotic therapy and may facilitate development or revision of treatment guidelines. Data can further be used to inform key stakeholders of the scale of the problem. Here you find guidance, methods and tools to measure antibiotic resistance patterns in bacteria isolated from humans, and can access selected databases and reports on the topic.
Data can be generated on a small or large scale. Conducting point prevalence studies or surveys is a good way to get started and can be useful to quickly assess the current situation. It is usually also possible to find some evidence of the resistance situation from for example scientific studies or initiatives within countries. Over time efforts can be scaled up and eventually act as inputs to national surveillance.
GARP Situation Analyses
The Global Antibiotic Resistance Partnership (GARP) has in collaboration with specific countries conducted national situation analyses focusing on antibiotic use and resistance. Click on the respective country to access the reports:
Point prevalence studies
Point prevalence studies (PPS) can be used for measuring a variety of components related to antibiotic resistance. Several parameters are usually measured during a limited period of time, for example one day. It can hence provide comprehensive results with relatively little effort. The studies can be repeated and thereby also provide useful data on trends and outcomes of interventions. Data from point prevalence studies can be used and analyzed independently or can be an input to larger surveillance efforts.
National surveillance systems
Broad-scale surveillance of antibiotic resistant bacteria of public health importance allows tracking of resistance trends and identification of new resistant strains. The WHO Global Antimicrobial Resistance Surveillance System (GLASS) was launched by WHO in 2015 in an effort to standardize surveillance across the world. Resources and information for setting up national surveillance can be found in POLICY: Implement the national action plan – Surveillance of antibiotic resistance.
Selecting pathogens and antibiotics
Selection of key pathogens and which antibiotics that should be tested on each isolate should be made prior to collecting antibiotic resistance data. It is also important to monitor which types of infections are prevalent within different settings to be able to choose relevant pathogens to monitor for resistance, see MEASURE – Infections for more information.
Susceptibility testing of bacteria
The most frequently used tests to determine if bacteria are susceptible or resistant to antibiotics are disc diffusion tests and minimum inhibitory concentration (MIC) tests. The MIC is the lowest concentration of an antibiotic that inhibits the growth of a bacterium. In order to determine if a bacterial strain is resistant to a specific antibiotic, clinical MIC break point values are used as guidelines. For example, the European Committee on Antimicrobial Susceptibility testing (EUCAST) provides break point values used in the European countries and are free of charge. The Clinical and Laboratory and Standards Institute (CLSI) also provides break point values, however, there is a fee for use. All results should be reported, whether bacteria are susceptible or resistant.
Please note that it is very important that all products used in susceptibility testing are of good quality. EUCAST issues warnings about known quality issues on their website.
The microbiology laboratory
The clinical microbiology laboratory is an essential component of work to measure and monitor resistance in bacteria and for correct treatment of infectious diseases. For accurate results, the collection of patient samples should be standardized and follow good laboratory practice. Samples should be handled according to the methods described in manuals for basic laboratory procedures. It is important to take into consideration if the samples need to be transported to other laboratories for analysis, and make suitable preparations. Also, for monitoring bacterial resistance rates, an adequate number of samples is needed.
External quality assessment tools
Hospitals and laboratories undertaking surveillance activities should also participate in an external quality assessment (EQA) program. EQA is used for comparing the results from individual laboratories in the network with reference results. The WHO/NICD Microbiology EQAs program in Africa developed a manual that contains summaries of surveys and technical documents for setting up EQA programs.
Resources below have been divided into the following tables:
- Tools and guidelines
- Surveillance systems
- Databases & interactive maps
- Data and reports
Tools and guidelines
|GLASS method for estimating attributable mortality of antimicrobial resistant bloodstream infections||Protocol. Master template protocol from WHO GLASS for estimating in-hospital mortality attributable to resistant blood stream infections. Focuses on ESBL E. coli and MRSA infections of both community and hospital-origin. Can be expanded to other bacteria as well. Can also support tracking of progress towards the sustainable development goals and specifically the antimicrobial resistance indicator.|
|Global Point Prevalence Survey on Antimicrobial Consumption and Resistance||Survey protocol and support. This open to join initiative allows participating hospitals to monitor antimicrobial prescribing and resistance in patients through a “one day survey” and helps design hospital interventions to promote prudent use (provides a personalized report). Hospitals are welcome to join survey and network (already more than 300 institutions from over 50 countries have participated). For documents such as protocols and data collection templates in different languages (incl. Spanish, French and Arabic) click here. Numerous scientific publications with results from the project have been published.|
|Antimicrobial susceptibility testing by EUCAST||Step by step guidance on how to do susceptibility tests, including clinical breakpoint tables, developed by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). See also Instruction videos for antimicrobial susceptibility testing (AST) by EUCAST in collaboration with the WHO that describes the methods and interpretation. Subtitles available in several languages, including French, Spanish, Chinese, Russian and Arabic.|
|Methods of Antimicrobial Susceptibility Testing Educational Resource (MASTER) eLearning Curriculum||Online course on antimicrobial susceptibility testing for bacteria isolated from clinical specimens. For laboratory professionals with knowledge of basic medical microbiology and others responsible for microbiology laboratories. Based on CLSI guidelines, requires registration.|
|Antibiogo||Mobile app. A free app for measurement and interpretation of antibiotic susceptibility tests. Developed by Doctors Without Border. Described and evaluated in an article published in Nature communications.|
|Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute||Journal article discussing things to keep in mind when creating and reading antibiograms (based on CLSI-standards).|
|WHONET Software||Database software for the management and analysis of antibiotic resistance data. The software is free to download and use and is developed and maintained by WHO.|
|The AMR Package for R||Software. Free, open-source and independent package for R for easy analysis of microbial and antimicrobial data, and prediction of antimicrobial resistance (AMR). A manual on how to use the AMR package can be found here. See also The epidemiologist R handbook, a reference tool for using R code. Designed for people working in applied epidemiology, public health practice, and disease control.|
|PARN website||Information portal. Website of the Pakistan Antimicrobial Resistance Network (PARN). Provides online courses upon registration, tools and information for laboratory personnel and antibiotic resistance data of bacterial isolates collected at Pakistani hospitals.|
|Community-Based Surveillance of Antimicrobial Use and Resistance in Resource-constrained settings: Report on five pilot projects (PDF, 1MB)||Manual describing implementation of community-based surveillance of antibiotic resistance and use through five pilot projects in resource‐constrained settings.|
|Protocol: a ‘One health’ two year follow-up, mixed methods study on antibiotic resistance, focusing children under 5 and their environment in rural India||Protocol. A published protocol for studying antibiotic resistance in children and their environment.|
|Proposed Minimum Reporting Guidelines for Research on Antimicrobial Resistance, Appendix in: A review of 40 years of enteric antimicrobial resistance research in Eastern Africa: what can be done better?||Review discussing research on antimicrobial resistance in enteric bacteria conducted in Eastern Africa up until March 2014. Suggests minimum reporting guidelines for designing antibiotic resistance studies to allow accurate conclusions and comparisons between studies. Also discusses how inadequate study design and a bias towards hospital sampling rather than community-wide sampling often make conclusions about the magnitude and trends of resistance difficult. While article discusses African studies, the proposed guidelines should be applicable in any setting.|
|Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data||Journal article proposing a framework (MICRO) for reporting and interpreting clinical micobiological data. The purpose is to achieve comparability between studies to inform policy and practice. Table 4 includes a checklist of 20 items that should be adressed. Developed by an international working group and was based on datasets from LMICs in South and South East Asia.|
Databases & interactive maps
|GLASS reports||Reports. Collection of all reports from the Global Antimicrobial Resistance and Use Surveillance System (GLASS) managed by WHO.
|AMR Register||Global AMR surveillance platform based on data shared by biotech and pharmaceutical companies. Researchers can request access to AMR surveillance datasets.|
|ResistanceMap||Interactive charts and maps summarizing national and sub-national data on antimicrobial use and resistance around the world.|
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