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Pathogen Sequencing service

The Pathogen sequencing service focuses on epidemiological and genomic monitoring at the national level of microbial pathogens of public health interest, including food-borne, AMR (AntiMicrobial Resistance), blood-borne viruses as HIV, Hepatitis and also respiratory viruses as SARS-CoV2 and Influenza.


The service offers its expertise and state-of-the-art technologies of Next-Generation sequencing (NGS), in bioinformatics data analysis pipelines and also in reporting thanks to different experts of scientists, technicians, bioinformaticians and epidemiologists and thanks to an extensive pool of top equipment and various sequencing workflows with Illumina and ONT platforms.

Sequencing can be used to characterize and type these different pathogens. Furthermore, genetic data for these microbial genomes are submitted to various international databases accessible to researchers, epidemiologists and microbiologists worldwide. Tracking these types of pathogens and identifying the strains or variants are crucial because it may help health authorities to respond rapidly in case of clusters. For diagnostic purposes, NGS can also be used to search resistance mutations to detect the presence of resistant variants to HIV antiretrovirals.

Tracking bacteria from food and waterborne diseases, a one health concept

When foodborne pathogens (such as Salmonella and Campylobacter) are detected, medical biology laboratories transmit bacteria isolated from their patients to our laboratory. We determine genomic fingerprints and transfer results to the competent national and international authorities. If several patients are sickened by bacteria with the same genomic fingerprint, there is a suspicion of a common source of infection to be identified, eliminated and prevented. In this situation, national authorities (the Ministry of Health) as well as international ones (the European Centre for Disease Control, ECDC) are informed and the unit supports their investigations. At the same time, we collaborate with veterinary and food laboratories to enrich our pathogen database with non-human isolates from the food chain. These data are also transmitted to the European food database managed by the European Food Safety Authority EFSA. This surveillance under the One Health concept allows us to detect human clusters and make the link with food and animal production.

National Reference Lab for Acute Respiratory Infections

Since several years, we play an essential role in the sentinel surveillance of respiratory viruses.

In 2021, we have been nominated as the National Reference Lab for acute respiratory infections by the Ministry of Health for 7 years.

For Influenza and SARS-Cov2 viruses, LNS is the only laboratory in the country to diagnose and type these viruses by sequencing with Next-generation amplicon sequencing technology. All data on strains or lineages that have circulated in Luxembourg was dispatched to national authorities (the Ministry of Health) and also to European and world authorities (ECDC and WHO) in order to allow them to perform a global epidemiological monitoring and for Flu to perform appropriate strains to include in the vaccine for the next epidemic season.

National Reference Lab for HIV and Hepatitis

At the end of 2022, the LNS, in collaboration with the Centre Hospitalier de Luxembourg (CHL) and the Inspection Sanitaire (INSA), was nominated by the Ministry of Health as a Reference Laboratory for HIV and viral hepatitis.

For HIV, the sequencing of regions of interest of its genome allows us to identify the eventual presence of specific mutations conferring resistance to specific antiretroviral drugs. Thus, we have a crucial mission in the diagnosis and monitoring of HIV infections by alerting clinicians for the presence or not of some resistance to antiretrovirals, giving them the information for next adapting or readapting a specific treatment for an HIV seropositive person with a positive HIV viral load in the blood. In addition, the technology of High-throughput or Deep sequencing allows us to provide more precise results on the presence of these resistant variants, even if they are present in minority in the viral population. For Hepatitis, this sequencing approach will also be used to determine the genotype and search for resistance mutations on the same principle as for HIV.


Ensuring the quality of our services is very important in our activities.

Since March 2023, the service is accredited by OLAS under number 1/047 according to ISO/IEC 15189 – testing. The technical annex is available on the website

For sequencing, these activities accredited are:

  • SARS-CoV2 whole genome sequencing by amplicon NGS sequencing approach with Illumina technology
  • HIV “PROT/RT/INT” genes sequencing by amplicon NGS sequencing approach with Illumina technology

Research, Education and Teaching

The service is involved in several European and national research projects. We contribute regularly to publications in its areas of expertise, with currently several articles, posters and technical reports.

Moreover, the Service is in charge of various courses on molecular techniques at the Medical School of the University of Luxembourg and of theoretical and practical training for sequencing and bioinformatics analyses.

Some key data:

  • More than 9,000 bacterial strains have already been sequenced by Whole Genome Sequencing, mainly Campylobacter, which is the most frequently isolated germ in patients suffering from acute diarrhea.
  • During the pandemic COVID-19 period, “April-2020 to April-2023”, more than 70,000 samples of SARS-Cov-2 have been sequenced by Amplicon Sequencing for tracking and monitoring the variants and for the Ministry of Health.

the team