Carbapenem-resistant Enterobacteriaceae: Reference material database
Data files
Jul 28, 2026 version files 100.81 KB
-
CRE_carbapenemase_reference_material_database_CORRECTIONS.csv
97.18 KB
-
README.md
3.63 KB
Abstract
Carbapenem beta-lactam antibiotics are used in the medical field to treat severe late-stage bacterial infections. This has led to an increase in carbapenem resistant-bacteria due to their ability to produce carbapenemases and to transfer carbapenemase genes both vertically and horizontally. It has become imperative to be able to detect and manage the presence of carbapenemases in human infection and the environment. The use of a comprehensive set of reference materials containing carbapenemases in quality control, validation, diagnostics, and standardisation will aid in addressing the challenges of carbapenemase detection. We have collated a list of microbial and DNA reference materials, as well as internal and external quality control materials. Each entry in our list includes a reference name, description, availability, storage requirements, biosafety level, type of carbapenemase produced, and more. Due to the location of our working group, and the local abundance of certain carbapenem-resistant bacteria, this database focuses on carbapenemases derived from carbapenem-resistant Enterobacteriaceae (CRE). Reference materials identified that are relevant to other carbapenem-resistant organisms (CRO) were excluded.
Dataset DOI: 10.5061/dryad.zw3r228nt
Description of the data and file structure
Our submission is a single datasheet (CRE_carbapenemase_reference_material_database_CORRECTIONS.csv). Each row in the datasheet corresponds to a reference material standard, and each column corresponds to a specific descriptor for that standard. Cells list "unknown" or “not stated” it was not possible to find the needed information from publicly available provider descriptions. Cells list “NA” when this data is not applicable to this entry. Information for spreadsheet v1.1 was collated in late 2025 and checked throughout early 2026.
Columns names are listed below, with clarifying explanations in italics:
-
Name (short)
-
Name (extended)
-
Description
-
Host organism name: the organism from which pathogenic material was gathered from
-
Host site: the site on the host where this material was gathered from, e.g., blood, sputum
-
Material Type: i.e., Cells or DNA
-
Availability: whether this material is currently available to order. If availability if limited, refer to other information and links for clarification.
-
Reference type: i.e. reference material, internal quality control or external quality control
-
Source: where this material is/was available to order from
-
Format/state: how the material will arrive - e.g., Frozen, Freeze-Dried, etc.
-
Biosafety Level: indicates safety of the material, ranging from 1 (lowest) to 4 (highest)
-
Storage conditions: requirements for sample storage
-
blaIMP: yes/no on whether this sample contains the blaIMP gene, including the gene variant number in brackets if known
-
blaVIM: yes/no on whether this sample contains the blaVIM gene, including the gene variant number in brackets if known
-
blaKPC: yes/no on whether this sample contains the blaKPC gene, including the gene variant number in brackets if known
-
blaNDM: yes/no on whether this sample contains the blaNDM gene, including the gene variant number in brackets if known
-
blaOXA: yes/no on whether this sample contains the blaOXA gene, including the gene variant number in brackets if known
-
Other carbapenemases: yes/no on whether this sample contains carbapenemase genes other than the main 5 as stated in other columns, including the gene in brackets
-
Other information: e.g. whether this sample is only available as a panel, or available from other sources under a different name, etc.
-
Sources: references used to populate the row
Comments on finished database as of April 2026
There are 245 materials listed in this database. Of these materials, it has been assessed by their respective suppliers that:
-
14 contain blaIMP
-
23 contain blaVIM
-
95 contain blaKPC
-
67 contain blaNDM
-
110 contain blaOXA
-
2 contain other notable carbapenemase genes
This database consists of 14 external quality control materials, 6 internal quality control materials and 221 reference materials.
This database excludes materials derived from carbapenem resistant organisms (CROs) that are not in the family Enterobacteriaceae where possible.
Thank you to IFCC Committee Molecular Diagnostics in Infectious Diseases (C-MDID) for their contribution to the development of this database.
To contribute an addition or a correction, please reach out to Dr. Louise O’Hara (Louise.OHara@LGCgroup.com) or Dr Denise O’Sullivan (Denise.OSullivan@LGCgroup.com).
Reference materials
We interpret the term "reference materials" as any physical material that can be used for quality control, validation, diagnostics, and standardization in microbiology workflows.
Reference materials were identified by accessing known reference material websites, such as the National Collection of Type Cultures (NCTC) and the American Type Culture Collection (ATCC), and typing ‘carbapenemase’ into the search bar. All search results were added to the database, excluding materials containing or derived from CROs (carbapenem-resistant organisms that are not in the family Enterobacteriaceae).
When investigating potential internal quality control resources, some suggested use of external specific reference materials from ATCC or NCTC – however it was noted that some of these recommended reference materials were not listed in website search engines under the key word ‘carbapenemase’.
To ensure inclusion of all accessible reference materials, further searches were done on the reference material websites by typing specific carbapenemase names into the search bar. IMP, VIM, NDM, KPC and OXA (all referring to presence of the genes blaIMP, blaVIM, etc) were searched and any search results not already in the database were added.
Internal quality controls
Internal quality controls are samples of the target that are typically supplied in existing testing kits as a positive control. This ensures continued validation and quality control of the product. Some companies will manufacture their own positive controls rather than recommending existing reference materials.
These were identified by researching existing nucleic acid amplification-based carbapenemase testing kits. Some previously used testing kits were referenced in these searches but further information could not be found on them due to company closure/product discontinuation; sufficient data was not available to add any internal quality controls from these kits to the database.
External quality controls
External quality controls are materials provided to institutions by External Quality Assessment (EQA) / Proficiency Testing (PT) organisations in order to gather data on and assess the quality of sample testing in the broader community. Institutions that have developed methods to detect carbapenemases can opt to take part in external quality control and receive these externally generated reference materials.
External quality controls for CREs were found by researching and identifying External Quality Assessment (EQA) / Proficiency Testing (PT) organisations and typing ‘carbapenemase’ into their search bar. Alternatively, the key word ‘carbapenemase’ was found in past project reports or a catalogue of ongoing quality control schemes.