Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data

• DOI: 10.7717/peerj.7564
• Publication Date: 2019-08-26T03:23:32Z
• Authors: Kamela C. S. Ng; Jean Claude S. Ng...; Pauline Lempens; Bouke C. de Jong; Frank van Leth; Conor J. Meehan
• Keywords: GenoType MDRTBplus v2.0; 0303 health sciences; QH301-705.5; Bioinformatics; Xpert MTB/RIF; R; XpertMTB/RIF Ultra; Mycobacterium tuberculosis; Single nucleotide polymorphism; 3. Good health; Whole genome sequences; 03 medical and health sciences; Rifampicin-resistant tuberculosis; Next generation sequencing; Medicine; Biology (General); Python; GenoscholarNTM+MDRTB II

Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace research surveillance programs, RDTs being increasingly complemented by whole genome (WGS). While comparison between is difficult, all RDT results can be derived from WGS data. This facilitate continuous analysis RR-TB burden regardless the data generation technology employed. By converting to results, we enable with different formats sources particularly low- middle-income high TB-burden countries that employ algorithms drug resistance surveys. allows TB control programs (NTPs) epidemiologists utilize available setting improved surveillance.We developed Python-based MycTB Genome Test (MTBGT) tool transforms WGS-derived into laboratory-validated primary RDTs-Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, GenoscholarNTM+MDRTB II. The was validated through strains diverse patterns geographic origins applied on routine-derived data.The MTBGT correctly transformed single nucleotide polymorphism (SNP) generated tabulated frequencies probes well rifampicin-susceptible cases. supplemented probe reactions output RR-conferring mutation based identified SNPs. facilitated Xpert platforms collection periods Rwanda.Overall, make sense light readily assess whether currently implemented adequately detect their setting. With its feature transform analysis, may bridge gap among periodic surveys, surveillance, research, tests, integrated within information system use NTP improve setting-specific control. source code accompanying documentation at https://github.com/KamelaNg/MTBGT.