Biology subjects

Ruiz-Rodriguez, P.

Publications and source records attributed to Ruiz-Rodriguez, P..

7 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

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

Human tuberculosis is caused by members of the Mycobacterium tuberculosis Complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto as well as two lineages (L5 and L6) traditionally referred to as M. africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known on their genomic diversity, phylogeography and evolution. Here, we analyzed the genomes of 365 L5 and 326 L6 strains, plus five related genomes that had not been classified into any of the known MTBC lineages, isolated from patients from 21 African countries. Our population genomic and phylogeographical analyses show that the unclassified genomes belonged to a new group that we propose to name MTBC Lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure, genetic diversity and association with drug resistance. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of tuberculosis in Africa and globally.

genomics↗