Humans

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 is a good way to get started and can be useful to quickly assess the current situation. It is also possible to find evidence of the resistance situation from for example scientific studies or initiatives within countries. Efforts can be scaled up over time and eventually act as inputs to national surveillance.

Point prevalence studies

Point prevalence studies (PPS) are 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. The European Committee on Antimicrobial Susceptibility testing (EUCAST) works to define, harmonize and standardize antimicrobial breakpoints and testing methods, which are openly available. The Clinical and Laboratory and Standards Institute (CLSI) also provides break point values (with a fee for use in some cases). 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

Hospitals and laboratories undertaking surveillance activities should also participate in an external quality assessment (EQA) program. EQA is used to assure quality of clinical testing and enable comparing results from individual laboratories in the network with reference results.

One Health resources are found on the Antibiotic resistance page. For more on measuring the burden of resistance see MEASURE – Burden.

Selected Resources

Tools and guidelines

Resource	Description
Global Point Prevalence Survey on Antimicrobial Consumption and Resistance	Methodology, templates and support. This open to join initiative allows participating healthcare centres to monitor antimicrobial prescribing and resistance in patients through a “one day survey” and helps design interventions to promote prudent use (provides a personalized report). There is a module for inpatients and a module for outpatients. 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.
Antibiogo	Mobile app. A free app for healthcare professionals for measurement and interpretation of antibiotic susceptibility tests. Developed by Doctors Without Borders. Described and evaluated in an article in Nature communications.
Global Antimicrobial Resistance and Use Surveillance System (GLASS)	Informational and resource portal. GLASS provides a standardized approach to collection, analysis, interpretation and sharing of antibiotic resistance and use data by countries. Guidelines and tools can be found in the GLASS Resource Centre and the data is also visualized through the GLASS dashboard.
PARN website	Information & resource portal. Website of the Pakistan Antimicrobial Resistance Network (PARN). Provides tools and information for laboratory personnel and antibiotic resistance data of bacterial isolates collected at Pakistani hospitals. Also provides online courses (upon registration).
WHONET Software	Data software for the management and analysis of antibiotic resistance data. The software is free to download and use. Provides an online training center and webinars. See for example an introduction to facility and national “Antibiograms” in WHONET. Developed and maintained by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance.
The AMR Package for R	Data 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.
Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data	Framework for reporting and interpreting clinical microbiological data. The purpose is to achieve comparability between studies to inform policy and practice. Table 4 includes a checklist of 20 items. Developed by an international working group.
AMR Register	Data sharing platform with data shared from biotech and pharmaceutical companies. Researchers can request access to AMR surveillance datasets.

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