Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data.
IntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. The large amount of publicly available whole genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analyses at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR Mycobacterium tuberculosis isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of M. tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR M. tuberculosis isolates from Germany in 2012 and 2013.ResultsWe aggregated a dataset that included 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, Cluster 2 included 56 MDR/XDR isolates from Moldova, Georgia and Germany. When comparing the WGS data from Germany with the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. Comparing the German with the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.
['Sanchini|Andrea|A|', 'Jandrasits|Christine|C|', 'Tembrockhaus|Julius|J|', 'Kohl|Thomas Andreas|TA|', 'Utpatel|Christian|C|', 'Maurer|Florian P|FP|', 'Niemann|Stefan|S|', 'Haas|Walter|W|', 'Renard|Bernhard Y|BY|', 'Kröger|Stefan|S|']
D000995:Antitubercular Agents D024901:Drug Resistance, Multiple, Bacterial D005845:Georgia D005858:Germany D006801:Humans D009169:Mycobacterium tuberculosis D018088:Tuberculosis, Multidrug-Resistant D000073336:Whole Genome Sequencing
genomic sequencing data mycobacterium tuberculosis public repositories molecular cluster molecular surveillance multidrug-resistant tuberculosis