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Protocols

Whole Genome Sequencing

Please find information related to WGS as well as a protocol for 'Whole Genome Sequencing and Bioinformatic Analysis of Bacterial Isolates Related to the EU Monitoring of Antimicrobial Resistance' in the top menu under Whole Genome Sequencing.

ESBL-, ampC- and carbapenemase-producing E. coli

Quantification of ESBL/AmpC-producing Escherichia coli in caecal content and fresh meat samples - December 2017 (PDF document, 800 KB)

Isolation of ESBL, ampC and carbapenemase-producing E. coli from caecal samples (Version 9, December 2024) (PDF document, 350 KB)

Isolation of ESBL, ampC and carbapenemase-producing E. coli from fresh meat (version 9, December 2024) (PDF document, 350 KB)

Validation of selective macConkey agar plates supplemented with 1 mg/L cefotaxime for monitoring of ESBL and ampC-producing E. coli in meat and animals - November 2017 (PDF document, 80 KB)

Validation of selective and indicative agar plates for monitoring of carbapenemase-producing E. coli (PDF document, 50 KB)

Campylobacter

Protocol for isolation, identification and storage of Campylobacter jejuni and/or C. coli for the EU monitoring of antimicrobial resistance (please access the document via this link to the webpage of the EURL Campylobacter)
The protocol and the work it was based on was presented by Hanna Skarin from the EURL Campylobacter working group at a webinar held on 5 May 2021. See the presentation via this link.

Colistin resistance

PCR for plasmid-mediated colistin resistance genes, mcr-1, mcr-2, mcr-3, mcr-4, mcr-5 and variants (multiplex) - February 2018 (PDF document, 400 KB)

PCR for plasmid-mediated colistin resistance genes, mcr-6, mcr-7, mcr-8, mcr-9, and variants (multiplex) - December 2022 (PDF document, 400 KB)

Enterococcus speciation and Campylobacter species ID

Protocol for PCR amplification of Campylobacter jejuni and C. coli specific genes (PDF document, 100 KB)

Protocol for PCR amplification of E. faecium and E. faecalis specific genes (PDF document, 190 KB)

MRSA

MRSA multiplex PCR-1 protocol; PCR amplification of CC398, mecA, PVL, scn and spa (version 1.1, April 2024) (PDF document, 600 KB)

MRSA multiplex PCR-2 protocol; PCR amplification of mecA, mecC, PVL and spa (version 3.1, April 2024) (PDF document, 400 KB)

Spa-typing protocol; PCR amplification and typing of spa gene (version 2, December 2022) (PDF document, 100 KB)

Isolation of MRSA from food-producing animals and farm environment (version 3, April 2023) (PDF document, 600 KB)

MLST typing (PDF document, 25 KB)