Updating Breakpoints in Antimicrobial Susceptibility Testing

Dec. 13, 2023

This article was originally published on Feb. 22, 2022 and has been updated by the author.

In Jan. 2022, a publication was released that summarized the worldwide impact of antimicrobial resistance (AMR) in 2019. This study concluded that there were an estimated 4.95 million deaths associated with bacterial AMR across the globe in 2019, considerably more than previously estimated. This highlights the importance of antimicrobial susceptibility testing, reporting and surveillance in preventing and managing infections caused by resistant organisms. Data transparency and susceptibility testing in the clinical laboratory are more important than ever before. 

Antimicrobial Susceptibility Testing in the Clinical Lab Is Essential to Patient Care 

Imagine that a patient comes to a hospital seeking care for a bloodstream infection. Blood cultures are collected and sent to the microbiology laboratory, where microbiologists identify the organism causing the infection and set up susceptibility testing, the process by which the organism will be tested against antibiotics in varying dilutions to determine which dilutions prevent growth. The lowest dilution with no growth is known as the minimum inhibitory concentration (MIC) or, in the case of disk diffusion, a zone of inhibition. Alone, these numbers may not mean much to a clinician, but when paired with clinical breakpoints (a pre-determined range that classifies an organism as susceptible or not), they provide information that helps determine which antibiotic is best for their patient. In this patient’s case, the MIC of the clinician's drug of choice is interpreted as “susceptible,” and the drug is used to treat the patient. 
Now imagine the patient’s health worsens, and they are moved to another hospital to receive the care they need. New blood cultures are collected and are positive with the same organism. This time, the interpretation of the MIC is resistant. Based on this, the provider switches the antibiotic therapy to a drug to which the isolate is susceptible. This intervention is life-saving for the patient, since the organism was not susceptible to the original antibiotic used. The same bacterial isolate was tested at 2 different locations; how could the results be different? The answer is the use of different breakpoints. In this scenario, the first hospital used outdated breakpoints that classified the organism as susceptible to a particular antibiotic when it was not. Evidence about optimal treatment approaches and antimicrobial resistance within organisms evolve over time, and so too should clinical breakpoints. While this story serves as an example, it is not fiction. It is estimated that each year, thousands of patients become colonized by drug resistant organisms, and using outdated clinical breakpoints introduces the risk of mismanaging those patients. 

Left to right: Disk diffusion susceptibility testing and microbroth dilution panels for automated susceptibility testing.
Left to right: Disk diffusion susceptibility testing and microbroth dilution panels for automated susceptibility testing.
Source: Wikimedia

Clinical Breakpoints and How They Relate to Minimum Inhibitory Concentrations 

Clinical breakpoints are used to establish MICs for different “bug-drug” combinations into 3 primary interpretive categories based on clinical data and research. These categories are: susceptible, intermediate (or in the case of the European Committee on Antimicrobial Susceptibility Testing (EUCAST), "susceptible, increased exposure") and resistant. An additional category, “susceptible-dose dependent" suggests that the organism can be treated with a higher or more frequent dosing of antibiotics. Breakpoints may change when new data or resistance mechanisms emerge. 

Challenges of Updating Breakpoints in the Microbiology Laboratory 

Four primary agencies determine these interpretive categories: the U.S. Food and Drug Administration (FDA), Center for Drug Evaluation and Research (CDER), the Clinical and Laboratory Standards Institute (CLSI) and EUCAST. In the U.S., the FDA regulates drugs and devices used in medical practice. The regulations around automated susceptibility testing (AST) devices used in the microbiology laboratory can be challenging because each time a drug is added to the system or changed, FDA clearance is required. In addition, processes may seem disjointed between the FDA, CLSI and AST systems manufacturers. For example, the process for setting breakpoints for new drugs is different from the process for revising breakpoints for an antimicrobial that is already in use clinically. The time it takes a manufacturer to perform an internal study and receive approval from the FDA can be years and varies between manufacturers. Sometimes, manufacturers may even have to reformulate their test because what is currently available does not have a MIC range that accommodates new breakpoints. Testing in the clinical microbiology laboratory never stops, and while FDA clearance for new breakpoints is underway, laboratories have to decide whether to use outdated breakpoints on their device, perform a labor-intensive validation of the current breakpoints or switch to another method altogether

New College of American Pathologists (CAP) Checklist Requirement for AST Breakpoints 

Due to the safety concerns and impact on patient care associated with using obsolete breakpoints, the College of American Pathologists (CAP) has developed a new checklist item that requires all clinical laboratories to update their systems and AST processes to use current breakpoints by Jan. 1, 2024. Laboratories will have 3 years from the time a new breakpoint is published by a standards development organization (e.g., FDA) to make updates and will be required to be aware of which breakpoints (e.g., FDA, CLSI or EUCAST breakpoints) they are applying. Although the process can seem overwhelming, it is imperative for quality patient care. 
The following resources provide additional context and background on AST Breakpoints: 

Validation and Verification Steps for Updating Breakpoints     

Recently, several scientific and standards organizations (CLSI, Association of Public Health Laboratories [APHL], ASM, CAP and CDC) collaborated to create a breakpoint implementation toolkit. This toolkit provides instructions for performing breakpoint assessments and updates, templates for data collection and protocol development and instructions for ordering isolates for testing. Additionally, CAP has developed a website with resources, which include educational materials and frequently asked questions, for laboratory use. Overall, the following steps should be followed when updating AST breakpoints in the microbiology laboratory: 

Step 1: Identify Which Breakpoints Are Obsolete  

The first step in this process is identifying the method of MIC interpretation in your laboratory. For example, it is possible that interpretations could be driven by the AST instrument, the laboratory information system (LIS), the electronic medical record (EMR) or manual entry. Understanding which system is responsible for MIC interpretations will help laboratorians identify where updates are needed. Once identified: 

  1. Compare breakpoints to those listed in the CLSI M100 document or provided on the EUCAST website

  1. Check the breakpoints posted on the FDA STIC website if they do not match with CLSI M100 or EUCAST. 

  1. If the breakpoints routinely reported by the laboratory do not match CLSI, EUCAST or FDA, they are obsolete and must be updated to at least 2021 breakpoints before Jan. 1, 2024. Breakpoints Matter: Understanding CLSI Efforts and New CAP Requirements to Ensure Appropriate Antimicrobial Treatment for all Patients further discusses how to identify obsolete breakpoints.   

Step 2: Engage Industry Partners 

If the laboratory is using a commercial AST system, reaching out to the manufacturer for guidance can be helpful. For example, manufacturers can inform laboratories of which breakpoints are FDA cleared and expound upon the testing capabilities of their current system. In addition, it is essential to discuss the following with a manufacturer: 

  1. Which breakpoints (identified in step 1) are FDA cleared, and which are not. Updating breakpoints to those cleared by the FDA on an automated system is considered on-label use. Labs should perform verification to demonstrate that assay performance is comparable to what was shown by the manufacturer during the FDA clearance process. 

  2. Updating breakpoints to those not FDA cleared on a device is considered off-label use and a modification of the test. Laboratories must perform a validation, which is a more extensive evaluation than a verification. Laboratories may choose to validate breakpoints that are not FDA-cleared due to clinical relevance or local needs. 

  3. Whether the current formulation of the susceptibility panel or card has a testing range that can accommodate the new breakpoints. If not, the manufacturer may provide information about when new panels or cards may be available or provide alternative testing options until the appropriate testing range is available. 

Some manufacturers have developed supportive tools for laboratorians that provide information on the drug-bug combinations with breakpoints that have been cleared on the system (or are located in their software), and for which scenarios a verification or validation may be necessary. This information is very helpful for clinical microbiologists because determining which drug-bug combinations have clearance with the most recently published breakpoints can be challenging. Sometimes, breakpoint update clearance information is sent out via a customer notification (rather than a software update) and may be misplaced or lost altogether. Communicating with medical or scientific representatives of the device company may help ensure all necessary information is obtained to complete the breakpoint update process. 

Step 3: Make a Plan With the Clinical Team 

  1. Prioritize which breakpoints should be updated first. For example, updating carbapenem breakpoints for the Enterobacterales is considered a top priority, as the adverse clinical and public health outcomes associated with not doing so are significant.  

  1. Identifying whether an antibiotic is used at an institution, dosing requirements and understanding use in different patient populations can help determine whether breakpoint updates need to be performed. Not reporting the drug MIC might be a preferable option to completing a verification or validation. All decisions to not report a drug should be documented in the laboratory standard operating procedure. 

The Journal of Clinical Microbiology articles below describe tactics to help develop a plan for updating breakpoints in your laboratory: 

Step 4: Perform Validation or Verification Testing and Update Breakpoints 

Once a plan of action has been decided, the laboratory can perform validation or verification testing. All data from steps 1-3, and data collected during validation or verification, must be documented and will likely be required during future CAP inspections.  

 The following resources contain additional information about how to plan for and perform validation and verification testing: 

Step 5: Monitor for Quality and Repeat 

The CAP checklist update (found specifically under MIC.11385) requires that laboratories do breakpoint updates within 3 years of the most recent update by the FDA, CLSI or EUCAST. This means that by Jan. 1, 2024, all breakpoints must be up-to-date, with breakpoints considered current as of 2021 (at a minimum). This will be an iterative process, requiring the laboratory to review their breakpoints in use annually, and updating as appropriate. For each year that breakpoints are reviewed, any newly published breakpoints should be implemented within three years of the publication date. This review process should occur yearly, and laboratories should update breakpoints regularly. 

Patient Care at the Core of All Clinical Microbiology Practices 

In light of the COVID-19 pandemic, clinical microbiology laboratories are grappling with burnout, staffing shortages and high demand. Updating AST breakpoints may feel like an overwhelming task that is difficult to accomplish under these conditions. While it is true that AST validation is a challenging task for clinical microbiology laboratories, there are a wealth of resources available to provide guidance and support throughout the process. Providing accurate and up-to-date susceptibility data is one of the many key roles the microbiology laboratory plays in public health and direct patient care. In the face of a looming AMR crisis, it is imperative that laboratories take the lead in preventing and mitigating the spread of drug resistant organisms, as well as helping ensure that patients receive optimal antimicrobial therapy and high-quality care. 

The statements and opinions expressed in this article are those of the author and do not necessarily reflect those of bioMerieux, Inc., nor of the American Society for Microbiology.

Author: Andrea Prinzi, Ph.D., MPH, SM(ASCP)

Andrea Prinzi, Ph.D., MPH, SM(ASCP)
Andrea Prinzi, Ph.D., MPH, SM(ASCP) is a field medical director of U.S. medical affairs and works to bridge the gap between clinical diagnostics and clinical practice.