Biology subjects

Lobo-Vega, R.

Publications and source records attributed to Lobo-Vega, R..

3 recordsLinked to original sources

bioRxiv2025

Establishing thresholds for azole tolerance and persistence in Aspergillus fumigatus to study their impact on voriconazole treatment in vivo

Antimicrobial tolerance and persistence are phenomena that enable pathogenic microbes to survive for extended periods in the presence of high concentrations of cidal drugs. Current evidence suggests that these phenomena may contribute to treatment failure and could even lead to the development of resistance. However, our understanding of antifungal tolerance and persistence in Aspergillus fumigatus, as well as their potential role in therapeutic failure, remains limited. In this study, we present an optimized, easy-to-perform method for detecting A. fumigatus tolerance and persistence to azole antifungals, based on a single colony-forming unit (CFU) measurement. Additionally, we developed a microscopic approach to investigate the dynamics of conidial killing in medium-throughput assays. Using these methods, we established epidemiological threshold values to classify strains as tolerant or persister and applied them to screen and categorize a collection of clinical isolates. Furthermore, we demonstrate that tolerance--but not persistence--negatively impacts the efficacy of voriconazole treatment in a Galleria mellonella infection model. Based on these findings, we propose that tolerance and persistence should be monitored in clinical isolates and potentially considered when determining therapeutic strategies.

microbiology↗

bioRxiv2022

SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome

Mutant spectra of RNA viruses are important to understand viral pathogenesis, and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultra-deep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of thirty nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCEThe study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity, and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.

microbiology↗

bioRxiv2020

Amino acid substitutions associated with treatment failure of hepatitis C virus infection

Despite the high virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. Identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultra-deep sequencing (UDS) methods for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV from 220 patients who failed therapy, which are not bona fide resistance-associated substitutions (RAS). They were present frequently in basal and post-treatment virus of patients who failed therapy to different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Coherently, their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. Also, they have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value of treatment response are discussed.

microbiology↗