P11
Results and experiences from four rounds of external quality assessment for Mycobacterium tuberculosis whole genome sequencing in the EU/EEA
E Tagliani(1) R M Anthony(2) V Nikolayevskyy(3) R de Zwaan(2) A Mulder(2) C Ködmön(4) M J van der Werf(4) D M Cirillo(1) D van Soolingen(2)
1:Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy; 2:Tuberculosis reference laboratory, Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), National Institute for Public Health and the Environment (RIVM), Bilthoven; 3:Imperial College London, United Kingdom; 4:European Centre for Disease Prevention and Control, Stockholm, Sweden
The wider availability of whole genome sequencing (WGS) coupled to new developments in bioinformatic tools and databases to interpret Mycobacterium tuberculosis (MTB) WGS data has accelerated the adoption of this method for the routine prediction of antimycobacterial drug resistance and genotyping. This calls for the establishment of a comprehensive external quality control system. Here, we describe the development of the first external quality assessment (EQA) scheme for MTB WGS and report the results of four rounds (2017-2020) implementation within the European tuberculosis (TB) reference laboratories network (ERLTB-Net2).
A panel of 10 genomic DNAs was distributed to ERLTB-Net2 laboratories volunteering to participate. In 2018, five FASTQ files were added to better assess dry WGS processes, and in 2020 three of them were replaced by synthetic files.
Ten National TB reference laboratories participated in all four EQA WGS rounds and seven in at least one round. High confidence resistance mutations were correctly identified by all laboratories, but challenges remained with respect to the identification of mixed loci and interpretation of rare resistance mutations. MTB genotyping and cluster analysis was >90% accurate for pure samples with main challenges being related to the analysis of mixed genotypes and DNA FASTQ files.
The development and implementation of this WGS EQA scheme has contributed to the improved performance of participating laboratories in MTB WGS and data analysis, and to the amelioration of the analytical pipelines. This EQA scheme can serve as a model of comprehensive quality assessment of MTB WGS that can be replicated in different settings worldwide.