Biology subjects

Borrell Farnov, S.

Publications and source records attributed to Borrell Farnov, S..

6 recordsLinked to original sources

bioRxiv2026

Proteogenomic discovery of novel small proteins in clinical Mycobacterium tuberculosis strains

Even though our meta-analysis ranks Mycobacterium tuberculosis genomes among the bacterial pathogens that are most straightforward to assemble, most available assemblies relied on short-read sequencing and contain genomic blind spots that miss functionally important genes. Complete genomes are essential for functional genomics, particularly for identifying small ORF-encoded proteins (SEPs; [≤]100 amino acids), which can play critical biological roles yet are frequently missed by standard annotations. Here, we generated complete long-read assemblies for six clinical reference strains representing lineage 1 and the more pathogenic lineage 2, followed by comparative genomic and proteogenomic analyses. We additionally provide software to predict comprehensive sets of mycobacteria-specific proline-glutamic acid (PE) and PPE family genes, including lineage-specific variants. Using parallel accumulation-serial fragmentation mass spectrometry, we detected approximately two-thirds of each strains annotated proteome from unfractionated cell extracts. Extending our proteogenomic framework across related strains, and adding rigorous control of proteogenomic discovery rates using entrapment strategies, we revealed 12-24 previously unannotated proteins per strain, predominantly SEPs, 56-60 alternative translation start sites, and 9-17 expressed pseudogenes. Newly identified proteins included conserved and lineage-specific SEPs, an antitoxin, candidate antimicrobial peptides and novel proteins under purifying selection. Overall, applying this improved proteogenomics method to phylogenomically selected clinical reference strains provides a valuable approach for discovering candidate diagnostics or therapeutics, as illustrated here for a WHO-listed critical bacterial pathogen.

microbiology↗

bioRxiv2025

Epistasis between drug resistance-conferring mutations in Mycobacterium tuberculosis

Studies in model organisms show that mutations conferring resistance to different antibiotics can interact epistatically, but the biological and epidemiological consequences of such interactions are unknown. Here we show that in Mycobacterium tuberculosis (Mtb), positive sign epistasis between RpoB and GyrA mutations causing resistance to rifampicin and fluoroquinolone, respectively, can lead to double-resistant strains with high in vitro fitness. Two of these RpoB-GyrA mutation combinations account for 53% in a global collection of highly drug-resistant Mtb clinical isolates, compared to <0.7% for RpoB-GyrA combinations with low in vitro fitness. Moreover, the two high-fitness RpoB-GyrA combinations are associated with a more benign and idiosyncratic proteome perturbation compared to low-fitness combinations. Our findings highlight the relevance of epistasis for the emergence and spread of antimicrobial resistance.

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

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↗

bioRxiv2020

Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis

The Mycobacterium tuberculosis (Mtb) complex includes ten phylogenetically distinct human-adapted lineages with varying geographical distributions and pathogenicity. Lineage 1 (L1) is associated with low virulence, while Lineage 2 (L2) is linked to hyper-virulence, increased transmission, and drug resistance. We performed multi-layer comparative analyses integrating whole-genome sequencing with quantitative transcriptomic and proteomic profiling of a panel of L1 and L2 clinical strains, each grown under two in vitro conditions. Our data revealed variable correlations between transcript and protein levels across strains and gene categories, indicating lineage-specific post-translational regulation. Transcriptional and translational differences scaled with phylogenetic distance, with one in three SNPs on average leading to gene expression changes. A newly developed genome-scale transcriptional regulatory model identified master transcription factors--closely linked to the sigma factor network--whose targets were differentially expressed between L1 and L2. Notably, DosR proteins showed higher basal levels and a stronger nitric oxide (NO) response in L2. Time-course validation using an Rv1985c induction and wild-type H37Rv under hypoxia and reaeration confirmed the role of Rv1985c in the differentially expressed genes between L1 and L2. These findings suggest that limited genetic variation can translate into significant phenotypic differences via differential regulation of key transcriptional networks. HighlightsO_LIProteomic and transcriptomic characterization of fully sequenced diverse L1 and L2 clinical strains of Mtb. C_LIO_LIPost translational control mechanisms for regulatory and virulence genes are mitigated in Mtb L2. C_LIO_LIA genome-scale transcriptional framework identifies DosR, Rv1985c, Lsr2 and Rv0691c as master transcription factors responsible for differential target gene expression in L2 compared to L1 strains. C_LIO_LIL1 and L2 DosR proteins respond differently to nitric oxide stress, thus determining a relevant phenotype. C_LIO_LITime-course phenotypic and transcriptomic data under hypoxia and reaeration validate Rv1985c as a key transcription factor differentiating L2 and L1 strains. C_LI

systems biology↗

bioRxiv2018

Multiple Introductions of the Mycobacterium tuberculosis Lineage 2 Beijing into Africa over centuries

The Lineage 2-Beijing (L2-Beijing) sub-lineage of Mycobacterium tuberculosis has received much attention due to its high virulence, fast disease progression, and association with antibiotic resistance. Despite several reports of the recent emergence of L2-Beijing in Africa, no study has investigated the evolutionary history of this sub-lineage on the continent. In this study, we used whole genome sequences of 817 L2 clinical strains from 14 geographical regions globally distributed to investigate the origins and onward spread of this lineage in Africa. Our results reveal multiple introductions of L2-Beijing into Africa linked to independent bacterial populations from East-and Southeast Asia. Bayesian analyses further indicate that these introductions occurred during the past 300 years, with most of these events pre-dating the antibiotic era. Hence, the success of L2-Beijing in Africa is most likely due to its hypervirulence and high transmissibility rather than drug resistance.

evolutionary biology↗