Biology subjects

Zwyer, M.

Publications and source records attributed to Zwyer, M..

6 recordsLinked to original sources

bioRxiv2025

Assessment of different techniques and markers to distinguish recrudescence from new infection in an antimalarial therapeutic efficacy study conducted in Rwanda

IntroductionAccurate estimation of antimalarial drug efficacy against P. falciparum requires PCR correction to distinguish recrudescence from new infection in recurrent infections. Genotyping length polymorphic or SNP-rich markers, and various decision algorithms based on match counting or probabilistic approaches may be used for this purpose. In this study, we compared several markers and decision algorithms using samples collected in a therapeutic efficacy study conducted in Rwanda to identify the most suitable and robust approaches for PCR correction. MethodsWe optimized nested PCR assays to genotype four microsatellites and assessed their sensitivity in detecting minority clones with laboratory parasite strain mixtures. We analyzed patient samples by capillary electrophoresis and amplicon deep sequencing and assessed the diversity and allelic frequency of msp1, msp2, glurp, microsatellites (Poly-, PfPK2, TA40, TA81), and SNP-rich markers (ama1-D2, ama1-D3, cpmp, cpp, csp). We then classified the samples into recrudescence or new infection based on different marker combinations (msp1/msp2/glurp, msp1/msp2/microsatellite, and SNP-rich markers) and three decision algorithms (WHO algorithm, 2/3 algorithm, and a Bayesian approach), and compared our results with previously published findings. ResultsAmong microsatellites, TA40 and PfPK2 had the highest sensitivity in detecting minority clones; however, their intra-assay reproducibility was found to be limited. The 3D7 allelic family of the msp2 gene, glurp and SNP-rich markers had the highest genetic diversity. In distinguishing recrudescence from new infection, the WHO algorithm identified the fewest recrudescences across all marker combinations. Conversely, the 2/3 algorithm identified the highest number of recrudescences, and the algorithm based on Bayesian statistics yielded intermediate results. We observed the least variability in classification results among the different algorithms for the SNP-rich markers ama1-D2/ama1-D3/cpmp combination. In our study, replacing glurp with one of the four analyzed microsatellites or using SNP-rich markers did not significantly alter the final number of recrudescent infections. InterpretationOur findings emphasize the importance of using assays with high sensitivity in detecting minority clones, and markers with high diversity and low allelic frequency for accurate PCR correction. The SNP-rich markers method yielded the most consistent results in detecting recrudescences, regardless of the decision algorithm used. Therefore, it holds great potential for performing reliable PCR correction. Further evaluation of decision algorithms based on probabilistic approaches, compared to match-counting methods, is essential to ensure the accuracy and consistency of PCR-corrected drug efficacy estimations.

molecular biology↗

bioRxiv2025

Variability in intrinsic drug tolerance in Mycobacterium tuberculosis corresponds with phylogenetic lineage

Drug tolerance allows bacteria to survive extended exposure to bactericidal drugs and is thought to play a role in drug resistance evolution. In Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), multidrug resistant TB (MDR-TB) outbreaks are frequently caused by strains belonging to two phylogenetic lineages of the human-adapted strains of the Mtb Complex, namely lineages (L) 2 and L4. We hypothesized that members of L2 and L4 are more intrinsically drug tolerant, and as such, more readily evolve drug resistance. To explore this, we devised a high throughput in vitro assay to measure drug tolerance in Mtb. We selected a cohort of strains representative of the globally most frequent lineages L1 - L4. We measured tolerance to rifampicin and bedaquiline and found L3 and L4 strains to have higher tolerance compared to L1 and L2 strains. In addition, phylogenetically closely related strains exhibited similar levels of tolerance, suggesting that tolerance is heritable. Finally, we explored genes previously reported to be associated with tolerance in Mtb and found significant enrichment in mutations in genes involved in cell wall and cell processes, intermediary metabolism and respiration, as well as lipid metabolism in high-tolerance strains.

microbiology↗

bioRxiv2024

Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages

Mycobacterium tuberculosis complex (MTBC) lineages show substantial variability in virulence, but the epidemiological consequences of this variability have not been studied in detail. Here, we aimed for a lineage-specific epidemiological characterization by applying phylodynamic models to genomic data from different countries, representing the most abundant MTBC lineages. Our results show that all lineages are associated with similar durations and levels of infectiousness, resulting in similar reproductive numbers. However, L1 and L6 are associated with a delayed onset of infectiousness, leading to longer periods between subsequent transmission events. Together, our findings highlight the role of MTBC phylogenetic diversity in tuberculosis disease progression and transmission.

genomics↗

bioRxiv2024

Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

Infectious diseases have affected humanity for millennia and are among the strongest selective forces. Tuberculosis (TB) is an ancient disease, caused by the human-adapted members of the Mycobacterium tuberculosis complex (MTBC). The outcome of TB infection and disease is highly variable, and co-evolution between human populations and MTBC strains may account for some of this variability. Particular human genetic ancestries have been associated with higher susceptibility to TB, but socio-demographic aspects of the disease can confound such associations. Here, we studied 1,000 TB patients from Dar es Salaam, Tanzania, together with their respective MTBC isolates, by combining human and bacterial genomics with clinical data. We found that the genetic background of the TB patient population was strongly influenced by migrationsof Bantu-speaking populations from West Africa, which is in contrast to the corresponding MTBC genotypes that were mainly introduced from outside Africa. These findings suggest a recent evolutionary history of co-existence between the human and MTBC populations in Dar es Salaam. We detected no evidence of an effect of human genetic ancestry, or MTBC phylogenetic diversity alone, nor their interaction, on TB disease severity. There was also no evidence of an association between human variation genome-wide and TB disease severity.Treatment-seeking, social and environmental factors are likely to be the main determinants of disease severity at the point of care in this patient population. Author SummaryTuberculosis (TB) is an ancient infectious disease that continues to challenge global health efforts. Here, we explored the interplay between human and bacterial genetics on TB in Dar es Salaam, Tanzania. We found that neither the genetic ancestry of the patient, nor the bacterial genotype alone, nor their interaction, influenced the severity of TB. Our finding indicate that in this patient population, social and environmental factors may be the main determinants of TB disease severity.

evolutionary biology↗

bioRxiv2021

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels and array designs, since the selected single nucleotide polymorphisms (SNPs) may fail to capture population-specific haplotype structures, hence the full extent of common genetic variation. Here, we propose to sequence the full genome of a small subset of an underrepresented study cohort to inform the selection of population-specific add-on SNPs, such that the remaining array-genotyped cohort could be more accurately imputed. Using a Tanzania-based cohort as a proof-of-concept, we demonstrate the validity of our approach by showing improvements in imputation accuracy after the addition of our designed addon SNPs to the base H3Africa array.

genetics↗

bioRxiv2020

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the worlds new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We show that South Asia played a central role in the dispersion of these two lineages to neighboring regions. Moreover, we found that L1 exhibits signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

genomics↗