January
2021
New member!
The UAntwerp TORCH has a new member: Lena Krauẞer has joined the team and started her PhD under co-supervision of Professor Bouke De Jong (Institute of Tropical Medicine) and Professor Annelies Van Rie! Lena’s research will focus on whole genome sequencing directly from sputum samples towards culture-free whole genome sequencing of Mycobacterium tuberculosis. She will use her wet-lab skills to optimize and adapt laboratory protocols to increase the yield of DNA and avoid contamination from sputum samples for sequencing. Then, using her bioinformatics skills, she will develop and optimize software pipelines to analyse the sequenced DNA for clinical applications.
SEPTEMBER
2020
New member!
The UAntwerp TORCH has a new member: Selien Oostvogels has joined the team and started her PhD at the faculty of Medicine and Health Sciences at the University of Antwerp! Selien has previously joined the consortium for a summer internship at Stellenbosch University, South Africa, in 2018. Selien’s research will focus on identifying compensatory mutations in extensively drug resistant Mycobacterium tuberculosis strains.
July
2020
New member!
The UAntwerp TORCH team has a new full-time member: Dr. Anzaan Dippenaar moved from South Africa, where she was part of the TORCH team at Stellenbosch University under Rob Warren, to the Netherlands. Anzaan and is now full-time part of the UAntwerp TORCH team as a post-doctoral researcher!
JANUARY
2020
sequencing from sputum: soon a reality?
Annelies van Rie and Rob Warren organized a two-day meeting in Cape Town, South Africa, on the 27th and 28th of January 2020, to discuss culture-free whole genome sequencing. Culture-free whole genome sequencing could greatly increase the impact of sequencing in high TB burden countries. To accelerate progress towards this goal, a meeting was organized where experts from different laboratories in Europe and South Africa came together and shared their experience. During the meeting, attendees shared lessons learned from failed and succesful experiments and discussed ideas how to move the field forward.
Back row left to right: Camus Nimmo, Shaheed Valley Omar, Rob Warren, Tanja Niemann, Stefan Niemann, Lizma Streicher, Melanie Grobbelaar, Sander Goossens, Olivia Carulei, Digby Warner, Galo Goig
Front row left to right: Marisa Klopper, Anzaan Dippenaar, Andrea Cabibbe, Annelies Van Rie, Nabila Ismail
OCTOBER
2019
the union
Professor Annelies Van Rie attended the 50th Union World Conference on Lung Health and 2nd TB Science meeting in Hyderabad, India, from October 30th to November 2nd where she gave two oral presentations:
E Riviere, C Meehan, G Abebe, T Heupink, A Van Rie. "Building capacity in Mtb whole genome sequencing and bioinformatics: experience from Ethiopia" - short oral presentation
A Van Rie, S Goossens. Tolerance - invited speaker
July
2019
second VLIR-UOS training
Annelies Van Rie, Conor Meehand, Gemeda Abebe, and Emmanuel Rivière organized the second VLIR-UOS training in South Africa (Stellenbosch University) and Ethiopia (Jimma University). The three-week course was supported by members from the South African TORCH team (Rob Warren, Lizma Streicher, Nabila Ismaïl, Anzaan Dippenaar, Marissa Klopper). A total of nine Ethiopian researchers were given an in-depth course on Whole Genome Sequencing of tuberculosis. Read more
JUNE
2019
ESM Valencia
Multiple TORCH members attended the 40th European Society of Mycobacteriology annual conference in Valencia spain, where we presented several research posters and gave two oral presentations:
Poster presentations
Riviere E, Ismail N, Verboven L, de Vos E, Whitfield MG, Heupink T, Warren RM, Van Rie A. “Exploring Bedaquiline-resistance associated genetic regions in clinical samples from a cohort study of Rifampicin resistant TB patients in South Africa"
Riviere E, Whitfield MG, Nelen J, Heupink T, Van Rie A. “Identifying isoniazid resistance markers for high-dose INH treatment”
Van Rie A, Whitfield MG, de Vos E, Scott L, da Silva P, Hayes C, Heupink T, Sirgel F, Stevens W, Warren RM. “Discordances between molecular assays for detection of rifampicin resistance in Mycobacterium tuberculosis: frequency, mechanisms and clinical impact”
A Dippenaar, M De Vos, FM Marx, SA Adroub, PD van Helden, A Pain, SL Sampson, RM Warren. “Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting”
Oral presentations
Dippenaar A, Derendinger B, Dolby T, Beylis N, van Helden PD, Theron G, Warren RM, de Vos M FluoroType MTBDR VER2.0: “Liquid array technology predicts resistance to rifampicin and isoniazid with high accuracy in clinical specimens”
S Goossens, A Van Rie. “Mechanisms of drug tolerance in Mycobacterium tuberculosis”
March
2019
Visiting professor: Eric juengst
During March, UNC-Chapel Hill professor and bioethics expert Dr. Eric Juengst is visiting the TORCH members in Antwerp, Belgium. Eric Juengst is Director of the UNC Center for Bioethics and Professor in the Department of Social Medicine and the Department of Genetics at the University of North Carolina, Chapel Hill. Dr. Juengst’s research interests and publications have focused on the conceptual and ethical issues raised by new advances in human genetics and biotechnology. Together with Annelies Van Rie, Dr. Juengst will work on the ethical aspects of whole genome sequencing for tuberculosis research and public health.
December
2018
Two grants awarded
The TORCH consortium is happy to anounce that Belgian PhD students Lennert Verboven and Emmanuel Rivière successfully applied for a FWO SB predoctoral mandate! Both PhD candidates were awarded with a 2 year PhD scolarship, once renewable.
Lennert Verboven - A personalized recommendation system for Whole Genome Sequencing based and individualized tuberculosis treatment
Emmanuel Rivière - Development of novel methods to predict the drug resistance phenotype of Mycobacterium tuberculosis variants
Visit to Ethiopia
Annelies Van Rie and Emmanuel Rivière together with Southern partner Gemeda Abebe visited the trainees of the first VLIR training in their home institutions. Mulualem Tadesse was visited at Jimma Univeristy; Shewki Moga, Muluwork Getahun and Solomon Ali were visited at the Ethiopian Public Health Institute in Addis Abeba. All four trainees are actively engaged in whole genome sequencing research on Mycobacterium tuberculosis, the main goal of the TORCH Vlir programme. The Torch consortium is very eager to continue collaborating with these wonderful researchers.
November
2018
TORch joins the CRYPTIC consortium
Annelies Van Rie joined the fourth Annual Committee Meeting in Dubai of the CRyPTIC project. Research proposals utilizing the vast amount of data generated through the CRyPTIC project were presented and discussed. The Torch consortium submitted two research proposals (phylogeny-based GWAS and pDST recommender) which were both approved!
The torch consortium organized a think tank in Stellenbosch, South Africa, for the upcoming TBM trial. Lennert Verboven presented his concept on developing a machine learning model for treatment recommendation based on input from a panel of TB experts.
OCTOBER 2018
TORCH delegation at the 22nd Heremans lecture by Prof. Stefan Kaufmann, titled ‘How to deal with the most successful pathogen on earth: Rational design of immunologic intervention strategies‘
New member!
We have a new member: Sander Goossens has started his PhD at the UAntwerp! He will use whole genome sequencing and RNA sequencing data to investigate the within-host MTB population dynamics and MTB transcriptional responses under drug pressure. Moreover, he is also studying the effect of epigenetic modifications in MTB under drug pressure.
SEPTEMBER 2018
TORCH T-shirts arrived.
JULY
2018
First VLIR-UOS training
The first VLIR-UOS training was organized for six Ethiopian researchers by the Antwerp TORCH team. A three week course was organized focussing on whole genome sequencing of Mycobacterium tuberculosis and subsequent bioinformatic analysis. Additionally, all trainees developed a concept for a research project implementing the material learned during the course. Read more
From left to right: Mebrat Ejo, Muluwork Getahun, Mulualem Tadesse, Shewki Moga, Solomon Ali, Tim Heupink (organizer) and Adane Worku.
DECEMBER 2017
In December Michael Whitfield visited his colleagues in Belgium for collaborative paper writing and Next Generation Sequencing.
The TORCH consortium was awarded a VLIR-UOS grant for capacity building of bioinformatics and whole genome sequencing in Ethiopia, titled: ‘Improved infectious diseases research and surveillance in Ethiopia through capacity building in bioinformatics and sequencing’. This means we will be organizing three courses for young Ethiopian researchers eager to learn more about sequencing!
SEPTEMBER
2017
Margaretha De Vos gave two oral presentations at the ESM congress. The first presentation is titled 'Liquid Array - A new technology for improved anti TB therapy and patient management'. The second presentation is titled 'FluoroType MTB VER2.0 shows excellent sensitivity for the detection of Mycobacterium tuberculosis complex in smear negative specimens'. Lennert Verboven also gave an oral presentation with the title 'Number of effective drugs in the short course MDR-TB regimen according to standard of care drug susceptibility testing and Whole Genome Sequencing'.
June
2017
Dr. Tim Heupink received a one-year postdoctoral fellowship from the University of Antwerp to encourage proposal submission surrounding TB genomics.
February
2017
Tim Heupink participated in the ESOC scientific day to introduce the Center to the scientific comitee at Antwerp University.