senaite.ast 1.1.0

Antibiotic Sensitivity Testing (AST) for SENAITE

Antibiotic Sensitivity Testing (AST) for SENAITE

About

This add-on enables Antibiotic Sensitivity Testing (AST) for SENAITE LIMS by allowing the user to add analyses to a sample that are specifically designed for the measurement of the susceptibility of microorganisms to antibiotics. These analyses can be added either by means of pre-defined AST Panels or by direct assignment of Antibiotics and Microorganisms through a matrix.

senaite.ast also incorporates a default analysis for the identification of microorganisms present in a given sample. Once microorganisms are identified by means of this identification analysis, the system automatically populates the list of available AST Panels for selection with those that fit better with the identified microorganism(s).

Resistance analyses are qualitative and the supported results are in accordance with the new definitions of susceptibility testing categories by EUCAST 2019:

• S: Susceptible, standard dosing regimen

• I: Susceptible, increased exposure

• R: Resistant

Although user can configure AST Panels for the automatic addition of analyses for the capture of diameter of the zone of inhibition, the system does not automatically calculate the qualitative results based on the diameter of zone and the minimum inhibitory concentrations (MICs). However, system can infere the susceptibility testing category automatically based on pre-defined Breakpoints Tables, along with the diameter of the inhibitory zone or the MIC value.

Once installed, this add-on allows the laboratory to:

• Maintain microorganisms (via senaite.microorganism)

• Maintain antibiotics and antibiotic classes (via senaite.abx)

• Maintain pre-defined AST Panels

• Maintain pre-defined Breakpoints Tables

• Analysis for the identification of microorganisms

• Assignment of pre-defined AST Panels to a sample

• Sample-level customization of AST Panel

• Selective reporting of resistance results

• Support for and selective reporting of extrapolated antibiotics

Documentation

• https://senaiteast.readthedocs.io

Contribute

We want contributing to SENAITE.AST to be fun, enjoyable, and educational for anyone, and everyone. This project adheres to the Contributor Covenant.

By participating, you are expected to uphold this code. Please report unacceptable behavior.

Contributions go far beyond pull requests and commits. Although we love giving you the opportunity to put your stamp on SENAITE.AST, we also are thrilled to receive a variety of other contributions.

Please, read Contributing to senaite.ast document.

If you wish to contribute with translations, check the project site on Transifex.

License

SENAITE.AST Copyright (C) 2020-2024 RIDING BYTES & NARALABS

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Changelog

1.1.0 (2024-01-04)

• #31 Support lower than, greater than and fractions for MIC values

• #30 Fix sizes for numeric fields are too small

• #26 Fix Sensitivity result is not updated when selective reporting is missing

• #25 Do not allow to “submit” AST analyses with no result save

• #23 Fix AST calculation does not work when extrapolated antibiotics

• #22 Hide Unit and display Submitter before Captured in AST entry

• #21 Fix AST entry is empty when analyses categorization for sample is checked

• #20 Compatibility with senaite.app.listing#87

1.0.0 (2022-06-18)

• #17 Selective reporting for extrapolated antibiotics

• #15 Support for extrapolated antibiotics

• #13 Allow addition of new antibiotics to submitted/verified AST analyses

• #12 Negative values for diameter and zone size tests not permitted

• #12 Do not allow to submit AST analyses with empties

• #11 Better styling of AST Panel selector in Sample view

• #10 Allow to remove retracted AST analyses retests

• Initial Release