For determining if an antibiotic treatment will be effective and appropriate, a species-level identification is not sufficient. With some bacteria and in some settings, it can be easy to determine which antibiotic is most appropriate. For example, penicillin resistance among Group A streptococci has never been reported, and as a consequence strep throats can be treated successfully without susceptibility testing. But as resistance among bacteria increases, so does the factual need for susceptibility testing in order to find the best available antibiotic. But susceptibility testing is also a central component of surveillance that can feed information about resistance levels both to clinicians to guide empiric therapy, as well as national or international surveillance systems that monitor resistance levels and trends.
There are two main categories of measures to describe the susceptibility of bacteria to antibiotics: MICs and SIR categories. The MIC, or minimal inhibitory concentration is defined as the lowest concentration of an antibiotic that inhibits the visible growth of a bacterium under standardized conditions. This value is then related to predefined breakpoint values, either clinical breakpoints or epidemiological cutoffs.
Clinical breakpoints: values of MIC set for each bacteria-antibiotic combination based on expected clinical effect under normal circumstances.
Epidemiological cutoffs (ECOFFs): values of MIC set for each bacteria-antibiotic combination to identify shifts in resistance levels in the wild-type, “normal”, population.
Clinical breakpoints often coincide with ECOFFs, but not always.
The SIR system is a classification of the susceptibility in relation to expected clinical effect. A bacterium found in a patient sample can be tested and classified as either “S”, susceptible, “I” susceptible with increased exposure, or “R”, resistant. The terminology used by EUCAST was updated in 2019, when the former definition of “I” as “intermediate” was changed to “susceptible, increased exposure”.
The most common methods to determine the susceptibility of a bacterium to antibiotics are based on growing the bacteria in a laboratory. The gold standard method is still broth dilution, a method where the bacterium is exposed to a series of antibiotic concentrations in liquid culture media. While the original method was done in test tubes, the current standard is microdilution with smaller volumes in a handy microplate format. Once the dilution series is prepared and the bacteria are added, the plates or tubes are incubated in 35 degrees Celsius for 16-20 hours. After incubation, the lowest concentration where no visible growth is seen is the MIC.
As this method is laborious, a simpler method called disk-diffusion is used in most clinical laboratories. The test is done on a solid agar medium with paper disks containing antibiotics. The bacteria are spread evenly onto the plate surface before adding the disks. After 16-20 hours incubation, the bacteria will have grown on the plate, except around the disks that contain antibiotics that have an effect on the bacteria. The zone of inhibition is measured and related to breakpoint measures. The size of the zone will vary depending on the bacterium, but also on the antibiotic and the amount of antibiotic in the disk. This method will not give a MIC, but the SIR category.
A variant of this method is the gradient test. In this test, a plastic strip contains a gradient of the antibiotic that is transferred to the surface of the medium. A scale on the plastic strip can then be used to read the MIC after incubation.
Nucleic acid amplification tests (NAAT)
The above described methods determine the resistance of the bacterium to the antibiotic based on its phenotype, or ability to grow while being exposed to the antibiotic. But in many cases, antibiotic resistance is caused by a gene, or a mutation in a gene, that causes the resistance. Examples are mutations in the DNA gyrase gene that cause ciprofloxacin resistance and ESBL-genes that cause resistance to beta-lactam antibiotics. A wide variety of genetic tools can thus be used to detect these genes and mutations, from amplification of the gene of interest to whole genome sequencing. These types of methods are especially valuable for bacteria that are difficult to culture, such as Mycobacterium tuberculosis, or in epidemiological studies that aim to track the prevalence or spread of said genes.
The major downsides of DNA-based methods is that not all resistance is directly linked to a specific gene – and any new genes that emerge are of course not identified by these tests. This leads to the conclusion that DNA-based methods tend to err towards missing resistance if the resistance mechanism is not sought for.
In recent years, rapid diagnostics have also entered the field of susceptibility testing. A new protocol from EUCAST is, in some cases, able to identify susceptibility in a disk diffusion test within 4-8 hours. Many DNA based methods also give results within a few hours, and a MALDI-TOF can detect some known resistance mechanisms within hours. Newer advances include microfluidics, cellular level imaging and image processing as well as detection of cell-level responses to antibiotics. The field has picked up pace as the consequences of antibiotic resistance have become more evident also among non-specialists.
Considerations for adoption
Aside the more mundane considerations such as cost and laboratory capacity, deciding which diagnostic method(s) to implement depend on factors like throughput, perceived need for rapid diagnosis and, most importantly, what the diagnostic is needed for. For some bacteria, NAAT is the only viable option, but for most bacteria encountered in a clinical laboratory the choice is open. It is important to remember that a diagnostic test only answers the specific question that is asked by the design of the test – in the case of most NAATs, the question is “Is this genetic element present in the sample?”. In the case of culture-based methods, the question is “Is this bacterium susceptible or resistant to these antibiotics?”.
The difference between these questions has led many clinical microbiologists to advocate for culture-based diagnostic methods. As for the new rapid diagnostic tests, an additional question is: “How rapid is rapid – how will the increased speed translate into improved clinical outcomes or prescription?” As an example, the standard methods described in this and previous articles require approximately 48-72 hours from sampling to final diagnosis – for some blood cultures even longer. Even if a new test can shave off for example 12 hours from this, a patient with a severe infection will receive antibiotics before the culture results. However, if a combination of rapid detection and resistance testing could reduce time in each step, or even run species identification and susceptibility tests simultaneously, time savings may be significant. But will that be enough?
ReAct Policy Brief
Read more about diagnostics
Learn more in the ReAct Toolbox
Knowledge about antibiotic resistance levels in bacteria from both humans and animals and how common these bacteria are, is key to guide appropriate treatment of patients and animals, as well as for understanding the scale of the problem and address it appropriately. Go to ReAct Toolbox and section Measure.
More news and opinion from 2019
- ReAct’s 2019 wrap up and 2020 expectations
- Blog post by UNDP and ReAct: Antimicrobial resistance: An emerging crisis
- Water, sanitation and hygiene services critical to curbing antibiotic quick fix
- Diagnostics: Antibiotic susceptibility
- ReAct highlights during World Antibiotic Awareness week 2019
- 2019 AMR photo competition prizes announced
- Launch of UNICEF’s institutional guidance on antimicrobial resistance
- Proposed ban on colistin for animal use announced in Indonesia
- School children led celebration of World Toilet Day and World Antibiotic Awareness Week
- 10 Innovate4AMR-winning teams enjoyed 3-day workshop in Geneva
- After 4 collaborative meeting days: Actions for the future in Latin America
- Four key points from joint comments to One Health Global Leaders Group on AMR
- Why are children more vulnerable to AMR?
- Dr Yoel Lubell, Health Economist, on Thailand, AMR, UCH and cultural factors driving AMR
- UHC and AMR: The Thai Experience
- Why do effective antibiotics matter for quality of care and patient safety?
- New ReAct policy brief: Antimicrobial resistance and universal health coverage – What’s the deal?
- Three key takeaways from the ReAct Africa conference
- Diagnostics: Species identification
- AMR-specific indicator proposed for monitoring Sustainable Development Goals
- Five focus areas at the 2nd Ministerial Conference on AMR hosted by the Netherlands
- Safety concerns of fecal microbiota transplants
- Upcoming ReAct Africa Conference: universal health coverage and antimicrobial resistance in focus
- Mother Earth conference in Argentina – the environment in focus
- Diagnostics: What are we talking about?
- Connecting global to local civil-society-agenda on AMR at CSO convening in Geneva
- ReAct colleagues featured in WHO Bulletin as leading profiles in the work on reacting to antibiotic resistance
- RAN stakeholder at WHO IPC consultation – for standards and guidelines in African Union member states
- WHA conversation on Antibiotic Resistance as a Global Development Problem co-organized by ReAct
- Insights from ReAct Asia Pacific project on antibiotic stewardship in secondary level hospitals in India
- Open letter to UN Member States from former IACG members Anthony So and Otto Cars
- ReAct UHC Intervention at UNGA Multi-stakeholder Hearing for High-level Meeting on UHC
- ReAct Latin America honors Earth Day
- Medicines Patent Pool’s view on the role of licenses for antibiotics – World Intellectual Property Day
- Second time for Innovate4AMR competition!
- World Health Day 2019: Universal Health Coverage
- Diagnostics: Constraints for successful implementation
- Antibiotic Shortages: magnitude, causes and possible solutions: A new WHO meeting report
- Erry Setyawan, FAO, on Indonesian NAP: We need to work together to make it possible to manage AMR
- ReAct’s new 5-year strategic plan receives funding from Sida
- How infections spread and how to stop them
- Generating data for policy and practice