RT Journal Article
SR Electronic
T1 Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 834150
DO 10.1101/834150
A1 Andrea Sanchini
A1 Christine Jandrasits
A1 Julius Tembrockhaus
A1 Thomas Andreas Kohl
A1 Christian Utpatel
A1 Florian P. Maurer
A1 Stefan Niemann
A1 Walter Haas
A1 Bernhard Y. Renard
A1 Stefan Kröger
YR 2019
UL http://biorxiv.org/content/early/2019/11/08/834150.abstract
AB Introduction Improving 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 analysis at a large scale.Aim We investigated to what extent we could use globally available WGS raw data of MDR/XDR-TB isolates available from the public sequence repositories to improve TB surveillance.Methods We extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.Results We aggregated a dataset that includes 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, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and 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.Conclusion We demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and 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.