Biology subjects

Goig, G. A.

Publications and source records attributed to Goig, G. A..

9 recordsLinked to original sources

bioRxiv2025

Within-host evolution of drug tolerance in Mycobacterium tuberculosis.

SynopsisO_ST_ABSBackgroundC_ST_ABSMycobacterium tuberculosis (Mtb) causes tuberculosis (TB) in humans. Poor treatment responses are a threat to global TB control, as such, understanding contributing factors to poor responses is important. We hypothesized that antibiotic tolerance could contribute to delayed culture conversion (recalcitrant TB), and resistance amplification in patients during TB treatment. ObjectivesTo investigate the role of drug tolerance in delayed culture conversion and resistance amplification in TB patients. MethodsWe collected serial Mtb isolates from i) patients with drug-susceptible TB who remained culture positive for up to 6 years (i.e. recalcitrant TB), and ii) patients with multidrug-resistant TB (MDR-TB) where resistance amplified during treatment. We measured tolerance to rifampicin (RIF) in drug-susceptible TB strains and tolerance to moxifloxacin (MFX) in MDR-TB strains using a real-time time-kill assay. ResultsRIF tolerance evolved within-host, increasing up to and ~1.5-fold, however, there was no apparent contribution of RIF tolerance to delayed culture conversion. Tolerance to Mfx in MDR-TB patients appeared negatively associated with resistance amplification and consistently decreased over time in patients. ConclusionOur findings confirm that antibiotic tolerance evolves in Mtb within patients over time during treatment. However, there was no evidence that this tolerance influences treatment responses, calling for further investigation of contributors to adverse treatment responses and their mitigation.

microbiology↗

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

Drug-induced differential culturability in diverse strains of Mycobacterium tuberculosis.

Differential culturable bacteria grow in liquid culture medium but are unable to form colonies on solid medium. Differentially culturable Mycobacterium tuberculosis (Mtb) bacteria, have been found in tuberculosis (TB) patient sputa. We hypothesized that antibiotic treatment can induce differential culturability in Mtb. We investigated the effect of exposure to TB drugs on Mtb culturability using clinical samples from an ongoing TB patient cohort and by conducting several in vitro experiments with a diverse set of Mtb strains. In patients, serial sputa were more likely to generate Mtb-positive cultures in liquid as opposed to solid medium, with this liquid culture bias extending up to 5 months post diagnosis. Experimentally, there was a disparity between bacterial time to positivity (TTP) and colony forming units (CFUs) when Mtb was exposed to isoniazid (INH) and rifampicin (RIF) alone or in combination. Cultures recovered from RIF treatment yielded more CFUs on agar plates, but INH-treated cultures had a faster TTP in liquid. Follow up experiments using a fluorescently labelled laboratory strain of Mtb revealed that CFUs overestimated killing by INH treatment. Here we provide evidence in Mtb that drug exposure affects culturability on solid medium, which has implications for treatment monitoring and drug-pathogen interaction studies.

microbiology↗

bioRxiv2024

Large contribution of repeats to genetic variation in a transmission cluster of Mycobacterium tuberculosis

Repeats are the most diverse and dynamic, but also the least well understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions, and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias they have received much less attention. Long-read sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen Mycobacterium tuberculosis from PacBio HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We find that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which can be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. While recombination events are less frequent than point mutations, they can affect large regions and introduce multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involve ppe18 and ppe57, two genes possibly involved in immune subversion. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this "monomorphic" bacterial pathogen awaits investigation.

genomics↗

bioRxiv2024

Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis

Culturing Mycobacterium tuberculosis (MTB) from tuberculosis cases is the basis for many research and clinical applications. Paradoxically, it is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. The alternative, culture-free sequencing from diagnostic samples, is a promising but challenging approach both to obtain and analyse the MTB genome from the complex sample. This study obtains high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics pipeline. Our approach reveals that 88% of variants called in culture-free sequencing analysis are false positives due to supplementary alignments, mostly in enriched-sputa samples. Overall, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants frequency (0.98). Our findings extrapolate to all publicly available data, thus demonstrating that in most cases culture accurately mirrors clinical samples.

genomics↗

bioRxiv2023

HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa

Persons living with HIV are known to be at increased risk of developing tuberculosis (TB) disease upon infection with Mycobacterium tuberculosis (Mtb). However, it has remained unclear how HIV co-infection affects subsequent Mtb transmission from these patients. Here, we customized a Bayesian phylodynamic framework to estimate the effects of HIV co-infection on the Mtb transmission dynamics from sequence data. We applied our model to four Mtb genomic datasets collected in sub-Saharan African countries with a generalized HIV epidemic. Our results confirm that HIV co-infection is a strong risk factor for developing active TB. Additionally, we demonstrate that HIV co-infection is associated with a reduced effective reproductive number for TB. Stratifying the population by CD4+ T-cell count yielded similar results, suggesting that, in this context, CD4+ T-cell count is not a better predictor of Mtb transmissibility than HIV infection status. Together, our genome-based analyses complement observational household studies, and firmly establish the negative association between HIV co-infection and Mtb transmissibility. Author summaryMany sub-Saharan African countries have seen a considerable rise in TB incidence since the introduction of HIV, suggesting a strong interaction between HIV and TB epidemics. HIV infection is recognized as an important risk factor for developing TB, but the contribution of HIV-infected TB patients to further Mtb transmission is poorly understood. In this study, we analyzed four sets of Mtb genomic sequences collected in different countries, including sequences from HIV-negative and HIV-positive TB patients. We applied a phylodynamic model to these sequences, aimed at inferring transmission dynamics within and between different host populations. While our findings support that HIV is a strong risk factor for TB, we show that HIV-positive TB patients generate a significantly lower number of secondary TB cases than HIV-negative patients. This suggests that HIV-positive patients often act as sinks in Mtb transmission chains, while HIV-negative patients are a major source of transmission.

microbiology↗

bioRxiv2019

Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

Tuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that are unique to the MTBC. Some of these genes could be targeted to assess the physiological status of the bacilli. Remarkably, none of the conventional MTBC markers is in our catalog. In addition, we develop a qPCR assay to accurately quantify MTBC DNA in clinical samples.

microbiology↗

bioRxiv2018

Pervasive contaminations in sequencing experiments are a major source of false genetic variability: a Mycobacterium tuberculosis meta-analysis

Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data usually neglect the errors introduced by potential contaminations. We performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS by analyzing more than 4,000 bacterial samples from 20 different studies. We found that contaminations are pervasive and can introduce large biases in variant analysis. We showed that these biases can translate in hundreds of false positive and negative SNPs, even for samples with slight contaminations. Studies investigating complex biological traits from sequencing data can be completely biased if contaminations are neglected during the bioinformatic analysis. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Our results urge for the implementation of such pipelines as sequencing technologies consolidate as a precision tool in the research and clinical context.

genomics↗