Genotyping via whole genome sequencing

Test description

Description:

• Extraction of genomic DNA from the pure strain, using magnetic beads
• ISO-accredited sequencing (short-reads)
• Analysis with in-house bioinformatic tools

Result:

Complete characterisation of the strain, including cgMLST profile and antibiotic resistance genes. 

Purpose of the test

Molecular subspecies and/or cgMLST profile 

Criteria for performing this test in the context of reference activities

Fine-typing, or phylogenetic clustering of strains in the context of outbreak investigations

Instructions for samples

• Type: The applicant sends an isolated and purified strain in a tube transport medium. Alternatively, a culture in liquid or solid medium or, exceptionally, a DNA extract of the sample should be sent. 
• Minimum quantity: Not applicable.

Instructions for transport

Samples should be packed in a double container and stored at room temperature. The container should be hermetically sealed.

Unacceptable applications

Not applicable.

Turn around time (and frequency of analysis)

• Turnaround time: 25 working days 
• Days of analysis: Any weekday ( except public holidays, extended weekends and the period between Christmas and New Year).

Reporting of test results

This analysis is carried out as part of surveillance. If the applicant requires a report of this analysis, it is best to contact the NRC by telephone or electronically . The analysis report will then be sent in the manner desired by the applicant.