Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis

Viedma, Darı́o Garcı́a de

doi:10.1016/j.meegid.2019.01.027

Cited by 4 publications

(2 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Next-generation sequencing-based whole genome sequencing (WGS) of Mycobacterium tuberculosis ( Mtb ) has been shown to accurately detect RR-TB by calling relevant single nucleotide polymorphisms (SNPs) in the rpoB gene (Coll et al, 2018; Miotto et al, 2017). Whole genome sequencing is already being widely implemented in the United Kingdom, the Netherlands, and New York, aimed towards completely replacing phenotypic drug susceptibility testing in the clinic (CRyPTIC Consortium and the 100,000 Genomes Project et al, 2018; de Viedma, 2019). Whole genome sequencing implemented in high burden TB countries was shown to accurately estimate the prevalence of DR-TB (Zignol et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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

Ngabonziza

Lempens

et al. 2019

PeerJ

View full text Add to dashboard Cite

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

show abstract

Section: Introductionmentioning

confidence: 99%

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

Ngabonziza

Lempens

et al. 2019

PeerJ

View full text Add to dashboard Cite

show abstract

“…Next-generation sequencing-based whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) has been shown to accurately detect RR-TB by calling relevant single nucleotide polymorphisms (SNPs) in the rpoB gene (Coll et al, 2018;Miotto et al, 2017). Whole genome sequencing is already being widely implemented in the United Kingdom, the Netherlands, and New York, aimed towards completely replacing phenotypic drug susceptibility testing in the clinic (CRyPTIC Consortium and the 100,000 Genomes Project et al, 2018;de Viedma, 2019). Whole genome sequencing implemented in high burden TB countries was shown to accurately estimate the prevalence of DR-TB (Zignol et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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

Ngabonziza²,

Lempens³

et al. 2019

Preprint

View full text Add to dashboard Cite

38Background. Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed 39 in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. 40 However, as next generation sequencing technologies have become more commonplace in 41 research and surveillance programs, RDTs are being increasingly complemented by whole 42 genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be 43 derived from WGS data. This can facilitate longitudinal analysis of RR-TB burden regardless of 44 the data generation technology employed. By converting WGS to RDT results, we enable 45 comparison of data with different formats and sources particularly for countries that employ 46 different diagnostic algorithms for drug resistance surveys. This allows national TB control 47 programs (NTPs) and epidemiologists to exploit all available data for improved RR-TB 48 surveillance. 49 Methods. We developed the Python-based TB Genome to Test (TBGT) tool that transforms 50 WGS-derived data into laboratory-validated results of the primary RDTs -Xpert MTB/RIF, 51 XpertMTB/RIF Ultra, Genotype MDRTBplus v2.0, and Genoscholar NTM + MDRTB II. The 52 tool was validated through RDT results of RR-TB strains with diverse resistance patterns and 53 geographic origins and applied on routine-derived WGS data.54 Results. The TBGT tool correctly transformed the SNP data into the RDT results and generated 55 tabulated frequencies of the RDT probes as well as rifampicin susceptible cases. The tool 56 supplemented the RDT probe reactions output with the RR-conferring mutation based on 57 identified SNPs. 58 Conclusion. Overall, the TBGT tool allows the NTP to assess whether currently implemented 59 RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT 60 results and enable longitudinal RR-TB data analysis, the TBGT tool may bridge the gap between 61 and among data from periodic surveys, continuous surveillance, research, and routine tests, and 62 may be integrated within the existing national connectivity platform for use by the NTP and 63 epidemiologists to improve setting-specific RR-TB control. The TBGT source code and 64 accompanying documentation is available at https://github.com/KamelaNg/TBGT. 65 66 Introduction 67Resistance to rifampicin (RIF), the most potent anti-tuberculosis (TB) drug, hampers TB control. 68Rifampicin-resistant (RR)-TB persists as an urgent public health crisis as only 29% of estimated 69 RR-TB patients world-wide were detected and notified in 2017. Further, 18% of previously 70 treated TB patients were found to have RR-TB (WorldHealthOrganization 2018). The WHO 71 endorsed the following rapid molecular RR-TB diagnostic test (RDTs) to address this concern: 72 Xpert MTB/RIF (hereinafter called Xpert Classic) and the new version Xpert MTB/RIF Ultra 73 (hereinafter called Ultra) [Cepheid, Sunnyvale, USA] that employ real-time polymerase chain 74 reaction and molecular beacon technology (Blakemore et al. 2010); and the line p...

show abstract

Special Issue on Molecular aspects of mycobacterial infections

Jagielski

Mokrousov

2019

Infection, Genetics and Evolution

View full text Add to dashboard Cite

Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis

Cited by 4 publications

References 44 publications

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

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

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

Special Issue on Molecular aspects of mycobacterial infections

Contact Info

Product

Resources

About