Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area
ABSTRACT Here, we report the development and key features of the first external quality assessment (EQA) scheme for Mycobacterium tuberculosis whole-genome sequencing (WGS). The results of four rounds (2017 to 2020) of implementation within the European tuberculosis reference laboratories network (E...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-02-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02244-22 |
| _version_ | 1811164395078680576 |
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| author | R. M. Anthony E. Tagliani V. Nikolayevskyy R. de Zwaan A. Mulder M. Kamst C. Ködmön M. J. van der Werf D. Cirillo D. van Soolingen |
| author_facet | R. M. Anthony E. Tagliani V. Nikolayevskyy R. de Zwaan A. Mulder M. Kamst C. Ködmön M. J. van der Werf D. Cirillo D. van Soolingen |
| author_sort | R. M. Anthony |
| collection | DOAJ |
| description | ABSTRACT Here, we report the development and key features of the first external quality assessment (EQA) scheme for Mycobacterium tuberculosis whole-genome sequencing (WGS). The results of four rounds (2017 to 2020) of implementation within the European tuberculosis reference laboratories network (ERLTB-Net-2) are presented and discussed. EQA panels comprising 10 genomic DNAs were distributed to ERLTB-Net 2 laboratories volunteering to participate in this exercise. Since 2018, five FASTQ files were added to better assess the dry WGS processes, and in 2020, three of the five files were replaced by synthetic files (providing additional flexibility for the mutations included in the panels). Ten National tuberculosis reference laboratories participated in all four EQA rounds, and seven participated in at least one. 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 mutations. M. tuberculosis genotyping and clustering analysis was >90% accurate for pure samples with the 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 continuous improvement in performance of participating laboratories in M. tuberculosis WGS and data analysis. This scheme can serve as a model of comprehensive quality assessment for M. tuberculosis WGS that can be replicated in different settings worldwide. IMPORTANCE The wider availability of whole-genome sequencing (WGS) coupled to new developments in bioinformatic tools and databases to interpret Mycobacterium tuberculosis complex WGS data has accelerated the adoption of this method for the routine prediction of antimycobacterial drug resistance and genotyping, thus necessitating the establishment of a comprehensive external quality control system. Here, we report 4 years of development and results from such a panel. |
| first_indexed | 2024-04-10T15:21:55Z |
| format | Article |
| id | doaj.art-beef0a0ed8c8474b9b585ce5ab47b5e7 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-10T15:21:55Z |
| publishDate | 2023-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-beef0a0ed8c8474b9b585ce5ab47b5e72023-02-14T14:15:49ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-02-0111110.1128/spectrum.02244-22Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic AreaR. M. Anthony0E. Tagliani1V. Nikolayevskyy2R. de Zwaan3A. Mulder4M. Kamst5C. Ködmön6M. J. van der Werf7D. Cirillo8D. van Soolingen9National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The NetherlandsEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, ItalyDepartment of Infectious Diseases, Imperial College London, London, United KingdomNational Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The NetherlandsNational Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The NetherlandsNational Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The NetherlandsEuropean Centre for Disease Prevention and Control, Stockholm, SwedenEuropean Centre for Disease Prevention and Control, Stockholm, SwedenEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, ItalyNational Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The NetherlandsABSTRACT Here, we report the development and key features of the first external quality assessment (EQA) scheme for Mycobacterium tuberculosis whole-genome sequencing (WGS). The results of four rounds (2017 to 2020) of implementation within the European tuberculosis reference laboratories network (ERLTB-Net-2) are presented and discussed. EQA panels comprising 10 genomic DNAs were distributed to ERLTB-Net 2 laboratories volunteering to participate in this exercise. Since 2018, five FASTQ files were added to better assess the dry WGS processes, and in 2020, three of the five files were replaced by synthetic files (providing additional flexibility for the mutations included in the panels). Ten National tuberculosis reference laboratories participated in all four EQA rounds, and seven participated in at least one. 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 mutations. M. tuberculosis genotyping and clustering analysis was >90% accurate for pure samples with the 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 continuous improvement in performance of participating laboratories in M. tuberculosis WGS and data analysis. This scheme can serve as a model of comprehensive quality assessment for M. tuberculosis WGS that can be replicated in different settings worldwide. IMPORTANCE The wider availability of whole-genome sequencing (WGS) coupled to new developments in bioinformatic tools and databases to interpret Mycobacterium tuberculosis complex WGS data has accelerated the adoption of this method for the routine prediction of antimycobacterial drug resistance and genotyping, thus necessitating the establishment of a comprehensive external quality control system. Here, we report 4 years of development and results from such a panel.https://journals.asm.org/doi/10.1128/spectrum.02244-22Mycobacterium tuberculosisMycobacteriumgenome analysisquality assurance |
| spellingShingle | R. M. Anthony E. Tagliani V. Nikolayevskyy R. de Zwaan A. Mulder M. Kamst C. Ködmön M. J. van der Werf D. Cirillo D. van Soolingen Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area Microbiology Spectrum Mycobacterium tuberculosis Mycobacterium genome analysis quality assurance |
| title | Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area |
| title_full | Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area |
| title_fullStr | Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area |
| title_full_unstemmed | Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area |
| title_short | Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area |
| title_sort | experiences from 4 years of organization of an external quality assessment for mycobacterium tuberculosis whole genome sequencing in the european union european economic area |
| topic | Mycobacterium tuberculosis Mycobacterium genome analysis quality assurance |
| url | https://journals.asm.org/doi/10.1128/spectrum.02244-22 |
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