Rework EUCAST Expert Rules

[Matthijs Berends]

• add new version numbering for the HORRIBLE new versions of EUCAST expert rules (e.g., Enterobacterales has v3.2 but date January 2023, while the older Enterobacterales also has v3.2 but date June 2019 on the website and October 2021 in its PDF file; it's a mess)

See https://www.eucast.org/expert_rules_and_expected_phenotypes/expected_phenotypes.

There's now a document 'Expected Resistant Phenotypes' Version 1.2 January 2023 here. This document is based on previous document “Intrinsic Resistance and Unusual Phenotypes” version 3.3, October 2021. Since then EUCAST has decided to abandon the term “intrinsic resistance” because of the difficulties identified when discussing the term “intrinsic”. The document has been divided into “Expected resistant phenotypes” and “Expected susceptible phenotypes” organised by species, and together with “Expert rules” they are available on https://www.eucast.org/expert_rules_and_intrinsic_resistance/.

Expected Phenotypes

Definitions of “Expected Phenotypes”

The purpose of the Expected phenotypes tables is to serve as a tool for the validation of species identification, to aid in the validation of susceptibility test results and to prevent unnecessary susceptibility testing. The presence of an unexpected phenotype indicates that the laboratory should check the species identification, the susceptibility test results or both.
A microorganism is listed as an “expected phenotype” for an agent (or group of agents) because the vast majority of isolates are resistant (expected resistant phenotype) or in another case, susceptible (expected susceptible phenotype).

Expected Resistant phenotype (previously categorized as “intrinsic resistance”). When isolates of a species (or group of species) are generally and universally resistant (>90% of all isolates irrespective of origin exhibit a characteristic resistance mechanism or MIC values above the PK/PD breakpoint listed in the EUCAST tables), a susceptible result should be viewed with suspicion (Tables below). Testing should normally be avoided, and laboratories are expected to either not report a result at all, or if a result is desired, to report the isolate as resistant without testing. Clinical colleagues should be advised against using the agent for the species in question. In the tables, where there is an “R”, any other result is unexpected.

Expected Susceptible phenotype. When isolates of a species (or group of species) are generally and universally expected to be susceptible (>99% of all isolates susceptible to the agent irrespective of origin because resistance mechanisms of clinical significance have not been reported and/or because MIC-values are consistently below the PK/PD breakpoint listed in EUCAST tables), a resistant result should be viewed with suspicion. If testing is performed, unexpected test results indicate a problem with species identification and/or susceptibility testing and results should be confirmed with alternative methods. When the resistant result is thought to reflect an acquired resistance mechanism this must be confirmed by reference methodology and preferably also by sequencing of the genome.

[Matthijs Berends]

.. (e.g., current Enterobacterales has v3.2 but date January 2023, while the older Enterobacterales also has v3.2 but date June 2019 on the website and October 2021 in its PDF file; it's a mess) …

Especially for this part, we will not fix this for now. It’s undoable with their current versioning system. Or lack thereof.