Biology subjects

Chowdhury, F. R.

Publications and source records attributed to Chowdhury, F. R..

5 recordsLinked to original sources

bioRxiv2025

Metabolic and genomic adaptations of Salmonella Typhimurium grown on itaconate

Salmonella enterica ser. Typhimurium (STm) is an enteric pathogen that causes almost 100 million cases of salmonellosis a year. A hallmark of STm is their ability to survive and replicate in the macrophages that phagocytose them. Inside the Salmonella-containing vesicles (SCV) STm is exposed to nutrient limitation and antimicrobial molecules, including itaconate, a dicarboxylate produced at millimolar concentrations by activated macrophages. STm has an itaconate degradation pathway that allows it to detoxify itaconate and convert it into pyruvate and acetyl-CoA. In the SCV, STm undergoes extensive metabolic reprogramming in response to the nutrient limitation and high stress environment, and strict catabolite control is employed at various stages of infection, depending on carbon source availability. The extent to which itaconate is used as a carbon source by STm is not currently well understood. Here, we explore the ability of STm to grow in media containing itaconate as the sole carbon source, identify the genes of the itaconate response operon necessary for itaconate degradation, and confirm their importance during infection of macrophages. Growth on itaconate was substantially slower than in carbon-rich or acetate media, with multiple subcultures allowing for increased growth rates. Genomic analysis suggests that mutations in the RpoS-stress response and increased expression of the DctA transporter improve growth on itaconate. Using metabolomics, it was revealed that growth on itaconate resulted in substantially reduced levels of gluconeogenesis compared to growth on acetate and increased glutathione disulfide levels, indicating a high level of oxidative stress. Overall, our results point towards the STm itaconate degradation pathway having a more important role in detoxifying itaconate, rather than using it as a carbon source inside the macrophage. Additionally, this study establishes media conditions that would enable the high throughput discovery of potential inhibitors of itaconate degradation.

microbiology↗

bioRxiv2025

Large scale laboratory evolution uncovers clinically relevant collateral antibiotic sensitivity

The increasing prevalence of antibiotic resistance is a critical challenge, necessitating the development of strategies to mitigate the evolution of resistance. Collateral sensitivity (CS)-based sequential therapies have been proposed to mitigate resistance evolution. However, the evolutionary repeatability of CS across different experimental conditions and its clinical relevance remain underexplored, hindering its potential for translation into clinical practice. Here, we evolve 20-24 lineages of E. coli against tigecycline (TIG) and piperacillin (PIP), antibiotics suggested to produce CS, through three separate laboratory adaptive evolution (ALE) platforms to test for the robustness of CS interactions and the effect of the choice of ALE on CS evolution. We generate over 130 resistant mutants and 540 resistance and collateral sensitivity measurements to identify a CS relationship between TIG and polymyxin B (POL) that is highly repeatable across all the ALEs tested, suggesting that this CS interaction is preserved across different evolution microenvironments. We determine the mechanism of this novel CS by showing that cells resistant to TIG deactivate the Lon protease and overproduce negatively charged exopolysaccharides, which in turn attracts the polycationic POL and renders cells hypersensitive to the drug. We find that this CS relationship is present in a clinical dataset of over 750 uropathogenic MDR E. coli isolates, and show that the soft agar gradient evolution (SAGE) platform best predicts collateral effects (CS, neutrality or cross resistance) in this dataset. Our study provides a framework for identifying robust CS with clinical implications that can reduce the emergence of resistance to our existing antibiotics.

microbiology↗

bioRxiv2025

Tripartite loops reverse antibiotic resistance

Antibiotic resistance threatens to undo many of the advancements of modern medicine. A slow antibiotic development pipeline makes it impossible to outpace bacterial evolution, making alternative strategies essential to combat resistance. In this study, we introduce cyclic antibiotic regimens composed of three drugs or "tripartite loops" to contain resistance within a closed drug cycle. We show that as bacteria sequentially evolve resistance to the drugs in a loop, they continually trade their past resistance for fitness gains, reverting back to sensitivity. Through fitness and genomic analyses, we find that tripartite loops guide bacterial strains towards evolutionary paths that mitigate fitness costs and reverse resistance to component drugs in the loops and drive levels of resensitization not achievable through previously suggested pairwise regimens. These findings open the door to sequential antibiotic regimens with high resensitization frequencies which will improve the longevity of existing antibiotics even in the face of antibiotic resistance. TOC O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/631305v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1d67a3corg.highwire.dtl.DTLVardef@1f315c7org.highwire.dtl.DTLVardef@1aee0eorg.highwire.dtl.DTLVardef@2e892_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

De novo evolution of antibiotic resistance to Oct-TriA1

The rise of antimicrobial resistance as a global health concern has led to a strong interest in compounds able to inhibit the growth of bacteria without detectable levels of resistance evolution. A number of these compounds have been reported in recent years, including the tridecaptins, a small family of lipopeptides typified by the synthetic analogue octyl-tridecaptin A1. Hypothesizing that prior reports of negligible resistance evolution have been due in part to limitations in the laboratory evolution systems used, we have attempted to select for resistant mutants using a soft agar gradient evolution (SAGE) system developed by our lab. Following optimization of the media conditions by incorporation of the anti-synaeresis agent xanthan gum into the agar matrix, we successfully evolved high-level resistance to both octyl-tridecaptin A1 as well as the challenging lipopeptide antibiotic polymyxin B. Decreased tridecaptin susceptibility was linked to mutations in outer membrane proteins ompC, lptD and mlaA, with the effect of these genes confirmed through a mix of allelic replacement and knockout studies. Overall, this work demonstrates the robust evolutionary potential of bacteria, even in the face of challenging antimicrobial agents.

microbiology↗

bioRxiv2024

Backward collateral sensitivity can restore antibiotic susceptibility

The prevalence of antibiotic resistance continues to rise, rendering many valuable drugs ineffective. Antibiotic cycling regimens that incorporate collateral sensitivity (CS), the phenomenon where resistance to one antibiotic leads to hypersensitivity to another, are hypothesized to slow the evolution of antibiotic resistance. However, the repeatability of CS interactions and their ability to drive bacterial extinction and resensitizations remain unclear. In this study, we thoroughly investigate four drug pairs proposed for cycling regimens with experimental evolution. We find that reported pairwise CS interactions are not always robust, and even when they are, forward CS (where resistance to drug A leads to hypersensitivity to drug B) does not reliably reduce resistance or promote bacterial extinction. Instead, we find that if evolution of resistance to drug B in naive cells is associated with CS to drug A, a phenomenon we term backward CS, drug A-resistant cells can be rendered more sensitive to A again when resistance to B develops. We describe the mechanism of resistance disruption via backward CS in an aminoglycoside-{beta}-lactam pair, where perturbation of the electron transport chain to inhibit aminoglycoside entry impairs {beta}-lactam efflux. Overall, we highlight the importance of applying antibiotics in the correct order in cycling regimens and identify robust CS interactions that may be used to design treatment regimens less likely to lead to resistance evolution. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/622341v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1745531org.highwire.dtl.DTLVardef@85172corg.highwire.dtl.DTLVardef@1b48784org.highwire.dtl.DTLVardef@12d2153_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC GraphicC_FLOATNO C_FIG

evolutionary biology↗