Biology subjects

Mendoza-Losana, A.

Publications and source records attributed to Mendoza-Losana, A..

5 recordsLinked to original sources

bioRxiv2026

OPTIKA, a new high content kill-kinetic assay to longitudinally assess in vitro drug combinations against Mycobacterium tuberculosis

In vitro methods to characterize drug combinations typically involve phenotypic screenings using checkerboard assays (CBA) or, more recently, DiaMOND. Such approaches rely on the Fractional Inhibitory Concentration Index (FICI), a fixed-time measurement of growth inhibition that, nonetheless, necessitates secondary validation by time-kill assays (TKA). Longitudinal time-kinetics of bacterial killing are considered the gold standard in vitro proxy for antimicrobial activity, but they required increased assay complexity, particularly against the slow growing Mycobacterium tuberculosis. Here, we developed a new methodology named OPTIKA (Optimized Time Kill Assays) that enhances the capacity of traditional TKA by over 1000-fold. This allows for easy and dynamic examination of n-way drug interactions by simultaneously monitoring bactericidal and sterilizing capacities in a longitudinal manner. We then replicated previous DiaMOND studies and performed comparisons using CBA and OPTIKA methodologies. We demonstrate that selection of the efficacy parameters (either routed on bacteriostatic, bactericidal or sterilizing properties) affects the interpretation of in vitro drug interactions and, consequently, its potential translational value. The increased assay throughput provided by OPTIKA offers a novel framework for developing tuberculosis treatment regimens. TeaserOPTIKA is a new methodology that increases time-kill assay performance against Mycobacterium tuberculosis by over 1,000-fold

microbiology↗

bioRxiv2025

Exploring Mycobacterium tuberculosis rRNA Transcriptomic Signatures asResponse to Anti-TB Treatment in Whole Blood RNA-seq Data

Current clinical tools for monitoring tuberculosis (TB) treatment response rely mostly on sputum culture and chest X-ray, which are unreliable in patients with low bacterial loads and lack the desirable promptness. There is a need for biomarkers able to provide earlier and more accurate insights into pathogen viability and response to therapy. We analyzed publicly available whole-blood RNA-seq data from 79 TB patients sampled at diagnosis, and weeks 1, 4, and 24 of standard anti-TB treatment. After aligning human reads and filtering, remaining reads were mapped to the Mycobacterium tuberculosis H37Rv genome to quantify rRNA subunit transcripts (16S, 23S, 5S, ITS1, ITS2). Microbiome profiles were assessed using Kraken2/Bracken, with alpha/beta diversity analyses and differential abundance (ANCOM-BC2). 16S and 23S rRNA transcripts were consistently detected across all treatment times, with 23S reads dominating in diagnosis and early stages of treatment shifting toward a significant predominance of 16S reads at week 24. 5S and ITS1 were inconsistently detected, whereas ITS2 was undetectable. Alpha diversity (Shannon index) increased during treatment (significant at weeks 1 and 4), while beta diversity showed significant shifts over time despite no significant differences in total M. tuberculosis abundance. Our findings suggest that it may be feasible to detect M. tuberculosis rRNA signatures in blood RNA-seq and suggest dynamic transcriptomic changes during treatment. The 16S/23S ratio and minor rRNA units may serve as complementary biomarkers for treatment monitoring and other transcriptomic-based biomarkers. Future work should validate these findings in larger cohorts using optimized RNA-seq protocols focusing on the pathogen.

bioinformatics↗

bioRxiv2024

Sanfetrinem, an oral beta-lactam antibiotic repurposed for the treatment of tuberculosis

Tuberculosis (TB) is historically the worlds deadliest infectious disease. New TB drugs that can avoid pre-existing resistance are desperately needed. The {beta}-lactams are the oldest and most widely used class of antibiotics to treat bacterial infections but, for a variety of reasons, they were largely ignored until recently as a potential treatment option for TB. Recently, a growing body of evidence indicates that later-generation carbapenems in the presence of {beta}-lactamase inhibitors could play a role in TB treatment. However, most of these drugs can only be administered intravenously in the clinic. We performed a screening of {beta}-lactams against intracellular Mycobacterium tuberculosis (Mtb) and identified sanfetrinem cilexetil as a promising oral {beta}-lactam candidate. Preclinical in vitro and in vivo studies demonstrated that: (i) media composition impacts the activity of sanfetrinem against Mtb, being more potent in the presence of physiologically relevant cholesterol as the only carbon source, compared to the standard broth media; (ii) sanfetrinem shows broad spectrum activity against Mtb clinical isolates, including MDR/XDR strains; (iii) sanfetrinem is rapidly bactericidal in vitro against Mtb despite being poorly stable in the assay media; (iv) there are strong in vitro synergistic interactions with amoxicillin, ethambutol, rifampicin and rifapentine and, (v) sanfetrinem cilexetil is active in an in vivo model of infection. These data, together with robust pre-clinical and clinical studies of broad-spectrum carbapenem antibiotics carried out in the 1990s by GSK, identified sanfetrinem as having potential for treating TB and catalyzed a repurposing proof-of-concept Phase 2a clinical study (NCT05388448) currently underway in South Africa.

microbiology↗

bioRxiv2024

Direct inhibitors of InhA with efficacy similar or superior to isoniazid in novel drug regimens for tuberculosis

Isoniazid is an important first-line medicine to treat tuberculosis (TB). Isoniazid resistance increases the risk of poor treatment outcomes and development of multidrug resistance, and is driven primarily by mutations involving katG, encoding the pro-drug activating enzyme, rather than its validated target, InhA. The chemical tractability of InhA has fostered efforts to discover direct inhibitors of InhA (DIIs). During the past five years, successful target engagement and in vivo efficacy have been demonstrated by diverse DIIs. In this study, we bridge the gap in understanding the potential contribution of DIIs to novel combination regimens and demonstrate a clear distinction of DIIs, like GSK693 and the newly described GSK138, from isoniazid, based on activity against clinical isolates and contribution to novel drug regimens. The results presented increase the understanding of DII mechanism of action and provide further impetus to continue exploiting InhA as a promising target for TB drug development.

pharmacology and toxicology↗

bioRxiv2018

Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening

The potential use of clinically approved beta-lactams for Buruli ulcer (BU) treatment was investigated with representative classes analyzed in vitro for activity against Mycobacterium ulcerans. Beta-lactams tested were effective alone and displayed a strong synergistic profile in combination with antibiotics currently used to treat BU, i.e. rifampicin and clarithromycin; this activity was further potentiated in the presence of the beta-lactamase inhibitor clavulanate. In addition, quadruple combinations of rifampicin, clarithromycin, clavulanate and beta-lactams resulted in multiplicative reductions in their minimal inhibitory concentration (MIC) values. The MIC of amoxicillin against a panel of clinical isolates decreased more than 200-fold within this quadruple combination. Amoxicillin/clavulanate formulations are readily available with clinical pedigree, low toxicity, and orally and pediatric available; thus, supporting its potential inclusion as a new anti-BU drug in current combination therapies.

microbiology↗