scholarly journals Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Monica Vogel ◽  
Christian Utpatel ◽  
Caroline Corbett ◽  
Thomas A. Kohl ◽  
Altyn Iskakova ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Successful Implementation ◽  
Whole Genome ◽  
Kyrgyz Republic ◽  
Middle Income ◽  
External Assessment ◽  
Middle Income Countries ◽  
Mdr Tb ◽  
Miseq Platform

AbstractWhole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.

scholarly journals Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

2020 ◽  
Vol 5 ◽  
pp. 3 ◽  
Author(s):  
Kirstyn Brunker ◽  
Gurdeep Jaswant ◽  
S.M. Thumbi ◽  
Kennedy Lushasi ◽  
Ahmed Lugelo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Data ◽  
Genomic Research ◽  
Whole Genome ◽  
Middle Income ◽  
Endemic Disease ◽  
Middle Income Countries ◽  
Virus Genomes ◽  
Low And Middle Income

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

scholarly journals Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

2021 ◽  
Author(s):  
Wasfi Fares ◽  
Kais Ghedira ◽  
Mariem Gdoura ◽  
Anissa Chouikha ◽  
Sondes Haddad-Boubaker ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
High Genetic Diversity ◽  
Middle Income ◽  
Middle Income Countries ◽  
Transmission Period ◽  
Variant Detection ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases.

scholarly journals Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

2020 ◽  
Vol 5 ◽  
pp. 3
Author(s):  
Kirstyn Brunker ◽  
Gurdeep Jaswant ◽  
S.M. Thumbi ◽  
Kennedy Lushasi ◽  
Ahmed Lugelo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Data ◽  
Genomic Research ◽  
Whole Genome ◽  
Middle Income ◽  
Endemic Disease ◽  
Middle Income Countries ◽  
Virus Genomes ◽  
Low And Middle Income

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

scholarly journals Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis

Thorax ◽  
2019 ◽  
Vol 74 (9) ◽  
pp. 882-889 ◽  
Author(s):  
Keira A Cohen ◽  
Abigail L Manson ◽  
Thomas Abeel ◽  
Christopher A Desjardins ◽  
Sinead B Chapman ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Data Sharing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Global Spread ◽  
Mdr Tb ◽  
Global Movement ◽  
Genomic Studies

BackgroundWhile the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed.MethodsIn a global dataset of 5310 M. tuberculosis whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion.ResultsExtensive international dissemination of MDR-TB was observed, with identification of 32 migrant MDR-TB clades with descendants isolated in 17 unique countries. Relatively recent movement of strains from both Beijing and non-Beijing lineages indicated successful global spread of varied genetic backgrounds. Migrant MDR-TB clade members shared relatively recent common ancestry, with a median estimate of divergence of 13–27 years. Migrant extensively drug-resistant (XDR)-TB clades were not observed, although development of XDR-TB within migratory MDR-TB clades was common.ConclusionsApplication of genomic techniques to investigate global MDR migration patterns revealed extensive global spread of MDR clades between countries of varying TB burden. Further expansion of genomic studies to incorporate isolates from diverse global settings into a single analysis, as well as data sharing platforms that facilitate genomic data sharing across country lines, may allow for future epidemiological analyses to monitor for international transmission of MDR-TB. In addition, efforts to perform routine whole-genome sequencing on all newly identified M. tuberculosis, like in England, will serve to better our understanding of the transmission dynamics of MDR-TB globally.

scholarly journals A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt

2017 ◽  
Vol 22 (2) ◽  
Author(s):  
Lena Fiebig ◽  
Thomas A Kohl ◽  
Odette Popovici ◽  
Margarita Mühlenfeld ◽  
Alexander Indra ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Universal Access ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
The European Union ◽  
Cross Border ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Mdr Tb

Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility. Ten isolates from 10 patients shared the same 24-loci MIRU-VNTR pattern. Within this cluster, WGS defined two subgroups of four patients each. The first comprised an MDR-TB patient from Romania who had sought medical care in Austria and two patients from Austria. The second comprised patients, two of them epidemiologically linked, who lived in three different countries but had the same city of provenance in Romania. Our findings strongly suggested that the two cases in Austrian citizens resulted from a newly introduced MDR-TB strain, followed by domestic transmission. For the other cases, transmission probably occurred in the same city of provenance. To prevent further MDR-TB transmission, we need to ensure universal access to early and adequate therapy and collaborate closely in tuberculosis care beyond administrative borders.

scholarly journals Use of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017–2019: an ECDC pilot study

2020 ◽  
Vol 57 (1) ◽  
pp. 2002272
Author(s):  
Elisa Tagliani ◽  
Richard Anthony ◽  
Thomas A. Kohl ◽  
Albert de Neeling ◽  
Vlad Nikolayevskyy ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Pilot Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance System ◽  
European Economic Area ◽  
Whole Genome ◽  
Cross Border ◽  
Lessons Learnt ◽  
Mdr Tb

Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system.WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability.A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 cross-border clusters with increased likelihood of recent transmission (≤5 SNPs distance) comprising 316 RR/MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries.This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGS-based surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters.

Whole-Genome Sequencing of Presumptive MDR-TB Isolates from a Tertiary Healthcare Setting in Mumbai

2021 ◽  
Author(s):  
Amrutraj Zade ◽  
Sanchi Shah ◽  
Nilma Hirani ◽  
Kiran Kondabagil ◽  
Ameeta Joshi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Healthcare Setting ◽  
Whole Genome ◽  
Mdr Tb ◽  
Tertiary Healthcare

scholarly journals Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia

2020 ◽  
Vol 69 (7) ◽  
pp. 1013-1019
Author(s):  
Tryna Tania ◽  
Pratiwi Sudarmono ◽  
R. Lia Kusumawati ◽  
Andriansjah Rukmana ◽  
Wahyu Agung Pratama ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Drug Susceptibility Testing ◽  
Major Public Health Problem ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Mdr Tb

Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia. Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant Mycobacterium tuberculosis in Java, Indonesia. Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared. Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS–MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33–76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population. Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.

scholarly journals Sequencing using a two-steps strategy reveals high genetic diversity in the S gene of SARS-CoV-2 after a high transmission period in Tunis, Tunisia.

2021 ◽  
Author(s):  
Wasfi Fares ◽  
Kais Ghedira ◽  
Mariem Gdoura ◽  
Anissa Chouikha ◽  
Sondos Haddad-Boubaker ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Transmission Rate ◽  
Whole Genome ◽  
High Genetic Diversity ◽  
Middle Income ◽  
High Transmission ◽  
S Gene ◽  
Molecular Tests ◽  
Transmission Period

Recent efforts have reported numerous variants that influence SARS-CoV-2 viral characteristics including pathogenicity, transmission rate and ability of detection by molecular tests. Whole genome sequencing based on NGS technologies is the method of choice to identify all viral variants; however, the resources needed to use these techniques for a representative number of specimens remain limited in many low and middle income countries. To decrease sequencing cost, we developed a couple of primers allowing to generate partial sequences in the viral S gene allowing rapid detection of numerous variants of concern (VOCs) and variants of interest (VOIs); whole genome sequencing is then performed on a selection of viruses based on partial sequencing results. Two hundred and one nasopharyngeal specimens collected during the decreasing phase of a high transmission COVID-19 wave in Tunisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allowed the detection of first introduction in the country of already known VOCs and VOIs as well as others variants that have interesting genomic mutations and need to be kept under surveillance.

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