V Nikolayevskyy1, S Niemann2, R Anthony3, D van Soolingen3, E Tagliani4, C Ködmön5, M J van der Werf5, D M Cirillo4. 1. Public Health England, London, UK; Imperial College, London, UK. Electronic address: vlad.nikolayevskyy@phe.gov.uk. 2. Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany. 3. Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands. 4. Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy. 5. European Centre for Disease Prevention and Control, Stockholm, Sweden.
Abstract
BACKGROUND: Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES: To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES: A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT: Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS: WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached. Crown
BACKGROUND:Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES: To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES: A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT: Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS: WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached. Crown
Authors: Roland Diel; Thomas A Kohl; Florian P Maurer; Matthias Merker; Karen Meywald Walter; Jörg Hannemann; Albert Nienhaus; Philip Supply; Stefan Niemann Journal: Eur Respir J Date: 2019-11-28 Impact factor: 16.671
Authors: Kathryn Winglee; Clinton J McDaniel; Lauren Linde; Steve Kammerer; Martin Cilnis; Kala M Raz; Wendy Noboa; Jillian Knorr; Lauren Cowan; Sue Reynolds; James Posey; Jeanne Sullivan Meissner; Shameer Poonja; Tambi Shaw; Sarah Talarico; Benjamin J Silk Journal: Front Public Health Date: 2021-06-21
Authors: Katharine S Walter; Caroline Colijn; Ted Cohen; Barun Mathema; Qingyun Liu; Jolene Bowers; David M Engelthaler; Apurva Narechania; Darrin Lemmer; Julio Croda; Jason R Andrews Journal: Microb Genom Date: 2020-07-31
Authors: Elisa Tagliani; Richard Anthony; Thomas A Kohl; Albert de Neeling; Vlad Nikolayevskyy; Csaba Ködmön; Florian P Maurer; Stefan Niemann; Dick van Soolingen; Marieke J van der Werf; Daniela Maria Cirillo Journal: Eur Respir J Date: 2021-01-05 Impact factor: 16.671