Biology subjects

Coscolla, M.

Publications and source records attributed to Coscolla, M..

14 recordsLinked to original sources

bioRxiv2026

Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance

BACKGROUNDRapid, interoperable whole-genome tools for Mycobacterium tuberculosis complex (MTBC) surveillance remain limited for harmonised lineage assignment across recognised lineages and simultaneous resistance-associated variant detection. AIMTo develop and validate Pathotypr, an alignment-free tool for harmonised MTBC lineage assignment and resistance genotyping from assemblies and raw reads. METHODSWe reconstructed an MTBC phylogeny from 26,813 genomes using 609,003 polymorphic sites, derived an updated lineage marker backbone, and implemented a k-mer/Random Forest framework with marker-based lineage and WHO catalogue-based resistance calling. Performance was evaluated on 498 RefSeq assemblies, 88,071 UShER-TB typed sequencing samples, 162 clinical read sets for closest-reference matching, and 7,148 CRyPTIC isolates with phenotypic drug susceptibility data. RESULTSPathotypr supported all 14 currently recognised MTBC lineages (L1-L10, A1-A4). On 498 complete genomes, marker-based and alignment-free lineage calls were 100% concordant, and prediction accuracy remained 100% on 254 independent assemblies. In 88,071 non-ambiguous UShER-TB samples, root-lineage concordance with TB-Profiler was 100%, while Pathotypr additionally identified lineage 10, A1 and A2. Resistance predictions showed 85.0% genotype-phenotype concordance overall, with high performance for rifampicin (95.8% sensitivity, 95.0% specificity) and isoniazid (93.0%, 97.9%). Runtime was about 1 second per sample, enabling analysis of 88,071 samples in approximately 24 hours on four threads. In the MDR-enriched CRyPTIC collection, Pathotypr supported reconstruction of 135 probable introduction events into Germany, Italy and Ukraine; 33.7% of introduction-associated isolates carried MDR/pre-XDR genotypes. CONCLUSIONPathotypr enables rapid, harmonised MTBC lineage assignment and high-confidence resistance screening, supporting near real-time and cross-border tuberculosis surveillance.

genomics↗

bioRxiv2024

Host-strain compatibility influences transcriptional responses in Mycobacterium tuberculosis infections

Tuberculosis, caused by Mycobacterium tuberculosis, is a leading cause of infectious mortality and affects humans and other mammals. Understanding the drivers of its host-specificity shapes the landscape of infectivity, which could potentially inform strategies for tuberculosis management. We hypothesise that host-strain compatibility influences infection outcome and we aim to reveal bacteria and host specific transcriptional responses during in vitro infections. We infected human and bovine cell lines with two human-associated M. tuberculosis strains from lineages 5 and 6, as well as two animal-associated strains (Mycobacterium bovis and the Chimpanzee bacillus), and quantified infection ratios, cell death, and transcriptional responses. By integrating those data from different compatibility combinations, we identified global transcription profiles associated with strain-host compatibility. Our results show that the most compatible host-strain combinations had higher infection rates, and different transcriptional patterns than low-compatibility infections. Both hosts had similar transcriptional responses to their most compatible strains, upregulating pathways related with increased cell proliferation. Host proliferation could potentially favour bacterial growth, explaining the success of the strain in its corresponding host. Conversely, both hosts responded to non-associated strains with defence related transcriptional patterns, among other pathways, supporting their lower success in the non-associated host. Finally, we revealed bacteria and host-specific expression patterns in molecules implicated in immune response and inflammation through the eicosanoid pathway. In conclusion, we confirmed that bacteria-host compatibility determines common transcriptional responses, but also specific responses that depend on the infecting strain. This study enhances the understanding of host-specific adaptation mechanisms in M. tuberculosis.

microbiology↗

bioRxiv2024

Adaptive advantage of deletion repair in the N terminal domain of the SARS-CoV-2 spike protein in variants of concern

Mutations within the N-terminal domain (NTD) of the spike (S) protein are critical for the emergence of successful SARS-CoV-2 viral lineages. The NTD has been repeatedly impacted by deletions, often exhibiting complex and dynamic patterns, such as the recurrent emergence and disappearance of deletions in dominant variants. This study investigates the influence of repair of NTD lineage-defining deletions found in the BA.1 lineage (Omicron variant) on viral success. We performed comparative genomic analyses of more than 10 million SARS-CoV-2 genomes from GISAID to decipher the transmission success of viruses lacking S:{Delta}H69/V70, S:{Delta}V143/Y145, or both. These findings were contrasted against a screening of publicly available raw sequencing data, revealing substantial discrepancies between data repositories, suggesting that spurious deletion repair observations in GISAID may result from systematic artifacts. Specifically, deletion repair events were approximately an order of magnitude less frequent in the read-run survey. Our results suggest that deletion repair events are rare, isolated events with limited direct influence on SARS-CoV-2 evolution or transmission. Nevertheless, such events could facilitate the emergence of fitness-enhancing mutations. To explore potential drivers of NTD deletion repair patterns, we characterized the viral phenotype of such markers in a surrogate in vitro system. Repair of the S:{Delta}H69/V70 deletion reduced viral infectivity, while simultaneous repair with S:{Delta}V143/Y145 led to lower fusogenicity. In contrast, individual S:{Delta}V143/Y145 repair enhanced both fusogenicity and susceptibility to neutralization by sera from vaccinated individuals. This work underscores the complex genotype-phenotype landscape of the spike NTD in SARS-CoV-2, which impacts viral biology, transmission efficiency, and immune escape potential, offering insights with direct relevance to public health, viral surveillance, and the adaptive mechanisms driving emerging variants.

evolutionary biology↗

bioRxiv2023

VIPERA: Viral Intra-Patient Evolution Reporting and Analysis

Viral mutations within patients nurture the adaptive potential of SARS-CoV-2 during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein we describe VIPERA (Viral Intra-Patient Evolution Reporting and Analysis), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, thus enabling an easy and automatic analysis of intra-patient SARS-CoV-2 sequences.

bioinformatics↗

bioRxiv2022

Genomic analysis of Mycobacterium brumae sustains its nonpathogenic and immunogenic phenotype

M. brumae is a rapid-growing, non-pathogenic Mycobacterium species, originally isolated from environmental and human samples in Barcelona, Spain. M. brumae is not pathogenic and its in vitro phenotype and immunogenic properties have been well characterized. However, the knowledge of its underlying genetic composition is still incomplete. In this study, we first describe the 4 Mb genome of the M. brumae type strain ATCC 51384T assembling PacBio reads, and second, we assess the low intraspecies variability by comparing the type strain with Illumina reads from three additional strains. M. brumae genome is composed of a circular chromosome with a high GC content of 69.2 % and containing 3,791 CDSs, 97 pseudogenes, one prophage and no CRISPR loci. M. brumae has shown no pathogenic potential in in vivo experiments, and our genomic analysis confirms its phylogenetic position with other non-pathogenic and rapid growing mycobacteria. Accordingly, we determined the absence of virulence related genes, such as ESX-1 locus and most PE/PPE genes, among others. Although immunogenic potential of M. brumae was proved to be as high as Mycobacterium bovis BCG, the only mycobacteria licensed to treat cancer, the genomic content of M. tuberculosis T cell and B cell antigens in M. brumae is considerably lower than those of M. bovis BCG. Overall, this work provides relevant genomic data on one of the species of the mycobacterial genus with high therapeutic potential.

genetics↗

bioRxiv2021

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has now reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

molecular biology↗

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↗

bioRxiv2020

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity

Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum), from each other. However, genome variability and gene content especially of L5 and L6 strains have not been fully explored and may be potentially important for pathobiology and current approaches for genomic analysis of MTBC isolates, including transmission studies. We compared the genomes of 358 L5 clinical isolates (including 3 completed genomes and 355 Illumina WGS (whole genome sequenced) isolates) to the L5 complete genomes and H37Rv, and identified multiple genes differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sublineage into L5.3.1 and L5.3.2. These gene content differences had a small knock on effect on transmission cluster estimation, with clustering rates influenced by the selection of reference genome, and with potential over-estimation of recent transmission when using H37Rv as the reference genome. Our data show that the use of H37Rv as reference genome results in missing SNPs in genes unique for L5 strains. This potentially leads to an underestimation of the diversity present in the genome of L5 strains and in turn affects the transmission clustering rates. As such, a full capture of the gene diversity, especially for high resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most WGS data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions. Data summarySequence data for the Illumina dataset are available at European Genome-phenome Archive (EGA; https://www.ebi.ac.uk/ega/) under the study accession numbers PRJEB38317 and PRJEB38656. Individual runs accession numbers are indicated in Table S8. PacBio raw reads for the L5 Benin genome are available on the ENA accession SAME3170744. The assembled L5 Benin genome is available on NCBI with accession PRJNA641267. To ensure naming conventions of the genes in the three L5 genomes can be followed, we have uploaded these annotated GFF files to figshare at https://doi.org/10.6084/m9.figshare.12911849.v1. Custom python scripts used in this analysis can be found at https://github.com/conmeehan/pathophy.

genetics↗

bioRxiv2018

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

BackgroundBovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen.\n\nMethodsMycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes.\n\nResultsMycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR=2.7,p=0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001,OR=124.4,95% CI=30.1-508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana.\n\nConclusionOur data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups.

microbiology↗

bioRxiv2018

Reference Set of Mycobacterium tuberculosis Clinical Strains: A tool for research and product development

The Mycobacterium tuberculosis complex (MTBC) causes tuberculosis (TB) in humans and various other mammals. The human-adapted members of the MTBC comprise seven phylogenetic lineages that differ in their geographical distribution. There is growing evidence that this phylogenetic diversity modulates the outcome of TB infection and disease. For decades, TB research and development has focused on the two canonical MTBC reference strains H37Rv and Erdman, both of which belong to Lineage 4. Relying on only a few laboratory-adapted strains can be misleading as study results might not be directly transferrable to clinical settings where patients are infected with a diverse array of strains, including drug-resistant variants. Here, we argue for the need to expand TB research and development by incorporating the phylogenetic diversity of the MTBC. To facilitate such work, we have assembled a group of 20 genetically well-characterized clinical strains representing the seven known human-adapted MTBC lineages. With the \"MTBC clinical strains reference set\" we aim to provide a standardized resource for the TB community. We hope it will enable more direct comparisons between studies that explore the physiology of MTBC beyond the lab strains used thus far. We anticipate that detailed phenotypic analyses of this reference strain set will increase our understanding of TB biology and assist in the development of new control tools that are universally effective.

microbiology↗

bioRxiv2018

A New Phylogenetic Framework for the Animal-adapted Mycobacterium tuberculosis Complex

Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are proposed to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven more by contact rates and demographic aspects of the host population rather than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host specificity.

evolutionary biology↗

bioRxiv2018

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

Large sequence datasets are difficult to visualize and handle. Additionally, they are often not an adequate representation of the natural diversity, but the result of uncoordinated and convenience sampling. Consequently, they can suffer from redundancy and sampling biases. Here we present Treemmer, a simple tool to evaluate the redundancy of phylogenetic trees and reduce their complexity by eliminating leaves that contribute the least to the tree diversity.\n\nTreemmer can reduce the size of datasets with different phylogenetic structures and levels of redundancy while maintaining a sub-sample that is representative of the original diversity.

bioinformatics↗

bioRxiv2017

Tuberculosis outbreak investigation using phylodynamic analysis

The fast evolution of pathogenic viruses has allowed for the development of phylodynamic approaches that extract information about the epidemiological characteristics of viral genomes. Thanks to advances in whole genome sequencing, they can be applied to slowly evolving bacterial pathogens like Mycobacterium tuberculosis.\n\nIn this study, we investigate the epidemiological dynamics underlying two M. tuberculosis outbreaks using phylodynamic methods. The first outbreak occurred in the Swiss city of Bern (1993-2012) and was caused by a drug-susceptible strain belonging to the phylogenetic M. tuberculosis Lineage 4. The second outbreak was caused by a multidrug-resistant (MDR) strain of Lineage 2, imported from the Wat Tham Krabok (WTK) refugee camp in Thailand into California.\n\nThere is little temporal signal in the Bern data set and moderate temporal signal in the WTK data set. We estimate an evolutionary rate of 0.0039 per single nucleotide polymorphism (SNP) per year for Bern and 0.0024 per SNP per year for WTK. Nevertheless, due to its high sampling proportion (90%) the Bern outbreak allows robust estimation of epidemiological parameters despite the poor temporal signal. Conversely, theres much uncertainty in the epidemiological estimates concerning the WTK outbreak, which has a small sampling proportion (9%). Our results suggest that both outbreaks peaked around 1990, although the Bernese outbreak was only detected in 1993, and the WTK outbreak around 2004. Furthermore, individuals were infected for a significantly longer period (around 9 years) in the WTK outbreak than in the Bern outbreak (4-5 years).\n\nOur work highlights both the limitations and opportunities of phylodynamic analysis of outbreaks involving slowly evolving pathogens: (i) estimation of the evolutionary rate is difficult on outbreak time scales and (ii) a high sampling proportion allows quantification of the age of the outbreak based on the sampling times, and thus allows for robust estimation of epidemiological parameters.

epidemiology↗

bioRxiv2017

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

Mycobacterium africanum (Maf) causes up to half of human tuberculosis in West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including both L5 and L6. We found that the genomic diversity of L6 was higher than in L5, and the selection pressures differed between both groups. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Conversely, human T cell epitopes were under purifying selection in L5, but under positive selection in L6. Although only 10% of the T cell epitopes were variable, mutations were mostly lineage-specific. Our findings indicate that Maf L5 and L6 are genomically distinct, possibly reflecting different ecological niches.

genomics↗