Genotyping via whole genome sequencing

Test description

Description:

• Extraction of genomic DNA, sequencing via ISO accredited methodology (both wet and dry lab)
• From this NGS, identification of the ‘sequencing type’ (ST) and the ‘clonal complex’ (CC) of Neisseria meningitidis strains. is performed according to the nomenclature available on the Neisseria MLST website (http://pubmlst.org/neisseria/(external link)(external link)). 
• cgMLST (core genome MLST): the sequence of a set of ‘core genome’ genes is obtained via Whole genome sequencing and compared with an online database (http://pubmlst.org/neisseria/(external link)(external link)).
• Characterisation of the alleles of genes porA (hypervariable regions 1 and 2 (VR1 and VR2)) and of gene fetA from Neisseria meningitidis. The numbers of the alleles are assigned according to the nomenclature available on the Neisseria.org website (http://neisseria.org/nm/typing/(external link)(external link)).

Results:
This molecular subtyping of Neisseria meningitidis allows comparison of strains to detect geographical clusters and epidemics in this way.

Purpose of the test

Molecular subtyping by NGS, identifying the (cg)MLST type and sequence of genes fetA and porA of Neisseria meningitidis strains.

Criteria for performing this test in the context of reference activities

This test is performed on all confirmed Neisseria meningitidis strains isolated from a normal sterile body fluid (lumbar fluid, blood, peritoneal fluid) from patients presenting with symptoms of acute Neisseria meningitidis infection (meningitis, sepsis, …). In case the strain was not confirmed by culture, the sample may be sent to the NRC for molecular characterisation.

Instructions for samples

• Type: The applicant sends an isolated and purified Neisseria meningitidis strain inoculated on a tube of transport medium or petri plate for analysis. The applicant may also provide a sample of blood, serum or cerebrospinal fluid in the absence of culture.
• Minimum amount: Not applicable

Instructions for transport

For safety reasons, bottoms should be packed in a double protective container and stored at room temperature. Refrigerated transport should absolutely be avoided. The container must be hermetically sealed.

Unacceptable applications

Not applicable. 

Turnaround time (and frequency of analysis)

• Turnaround time: 20 working days
• Days of analysis: Any weekday (excluding: 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, the NRC is best contacted by telephone or electronically . The analysis report will then be sent in the manner desired by the applicant.