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Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data University of Antwerp

Sergio Buenestado-Serrano, Miguel Martinez-Lirola, Anzaan Dippenaar, Amadeo Sanz-Perez, Jose Antonio Garrido-Cardenas, Ana Belen Esteban-Garcia, Adriana Justine Garcia-Toledo, Cristina Rodriguez-Grande, Marta Herranz-Martin, Sheri M. Saleeb, et al.
The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the large amount of information stored in historical databases. Long-read sequencing could bridge this knowledge gap by allowing analysis of repetitive ...

Collaborative learning in the digital age: empowering tuberculosis researchers through virtual training University of Antwerp

Anzaan Dippenaar, Taime Sylvester, Christopher Ealand, Nabila Ismail, Niaina Rakotosamimanana, Michele Miller, Bavesh D. Kana, Rob M. Warren
Integrating whole genome sequencing (WGS) of the Mycobacterium tuberculosis complex into routine care, surveillance, and research in high tuberculosis burden settings remains challenging due to limited resources and skills. While technological platforms for scaling WGS are emerging, scaling wet lab and analytic components often depends on partnerships where such skills have been established. To address this, a virtual training program was ...

A genome-focused investigation reveals the emergence of a Mycobacterium tuberculosis strain related to multidrug-resistant tuberculosis in the Amazon Region of Brazil University of Antwerp

Emilyn Costa Conceicao, Johannes Loubser, Arthur Emil Santos dos Guimaraes, Abhinav Sharma, Liliana Kokusanilwa Rutaihwa, Anzaan Dippenaar, Richard Steiner Salvato, Ricardo Jose Paula de Souza e Guimaraes, Maria Cristina da Silva Lourenco, Wandyra Araujo Barros, et al.
A previous study in Par & aacute;, Northern Brazil, described a strain of Mycobacterium tuberculosis with a unique genotype (SIT2517/T1) associated with multidrug-resistant tuberculosis (MDR-TB). To improve our understanding of MDR-TB transmission dynamics of these strains within this region, we performed phenotypic and genotypic drug susceptibility testing (pDST/gDST), 24-loci mycobacterial interspersed repetitive units (MIRU-VNTR) ...

Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA University of Antwerp

Anzaan Dippenaar, Nabila Ismail, Tim Heupink, Melanie Grobbelaar, Johannes Loubser, Annelies Van Rie, Robin M. Warren
Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix ...

Exploring the potential of Oxford Nanopore Technologies sequencing for Mycobacterium tuberculosis sequencing: an assessment of R10 flowcells and V14 chemistry University of Antwerp

Anzaan Dippenaar, Emilyn Costa Conceicao, Felicia Wells, Johannes Loubser, Brendon Mann, Miguel de Diego Fuertes, Robin Mark Warren, Annelies Van Rie
Oxford Nanopore Technologies (ONT) sequencing is a promising technology. We assessed the performance of the new ONT R10 flowcells and V14 rapid sequencing chemistry for Mtb whole genome sequencing of Mycobacterium tuberculosis (Mtb) DNA extracted from clinical primary liquid cultures (CPLCs). Using the recommended protocols for MinION Mk1C, R10.4.1 MinION flowcells, and the ONT Rapid Sequencing Kit V14 on six CPLC samples, we obtained a pooled ...

Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations University of Antwerp

Julian L. Coetzee, Nastassja L. Kriel, Johannes Loubser, Anzaan Dippenaar, Samantha L. Sampson, Stephanus T. Malherbe, Jacoba M. Mouton
Current tuberculosis (TB) treatment is typically effective against drug-susceptible Mycobacterium tuberculosis, but can fail due to acquired drug resistance or phenotypic resistance. M. tuberculosis persisters, a subpopulation of viable but non-replicating (VBNR) antibiotic-tolerant bacteria, are thought to contribute to poor TB treatment outcomes. In this exploratory study, we investigated treatment-na & iuml;ve drug-susceptible clinical ...

The impact of genotype on the phenotype of Mycobacterium tuberculosis ΔsufR mutants University of Antwerp

Danicke Willemse, Lucinda Baatjies, Anzaan Dippenaar, Robin M. Warren, Monique J. Williams
Iron-sulphur (FeS) cluster biogenesis is a tightly regulated process in vivo. In Mycobacterium tuberculosis (Mtb), SufR functions as a transcriptional repressor of the operon encoding the primary FeS cluster biogenesis system. Previously, three independently isolated mutants (ARv1460stop_1.19, ARv1460stop _5.19 and ARv1460stop _5.20) harbouring the same deletion in sufR, displayed different growth kinetics in OADC supplemented 7H9 media. To ...

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation University of Antwerp

Michael B. Hall, Marie Sylvianne Rabodoarivelo, Anastasia Koch, Anzaan Dippenaar, Sophie George, Melanie Grobbelaar, Robin Warren, Timothy M. Walker, Helen Cox, Sebastien Gagneux, et al.
Background Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. The aim of this study was to determine whether Nanopore sequencing data can provide ...

New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing University of Antwerp

Livia Maria Pala Anselmo, Juliana Failde Gallo, Juliana Maira Watanabe Pinhata, Kamila Chagas Peronni, Wilson Araujo da Silva Junior, Patricia Cassia de Ruy, Emilyn Costa Conceicao, Anzaan Dippenaar, Robin Mark Warren, Aline Aparecida Monroe, et al.
Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. Objective: To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS). Methods: This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between ...

Emergence of canonical and noncanonical genomic variants following in vitro exposure of clinical Mycobacterium tuberculosis strains to bedaquiline or clofazimine University of Antwerp

N. Ismail, Anzaan Dippenaar, R.M. Warren, R.P.H. Peters, S.V. Omar
In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of ...