Biology subjects

Danchik, C.

Publications and source records attributed to Danchik, C..

5 recordsLinked to original sources

bioRxiv2025

The Phosphate-Specific Transport System Gene pstA1 Contributes to Rifampin Tolerance in Mycobacterium tuberculosis

Tuberculosis (TB) caused an estimated 10.8 million new cases and 1.25 million deaths in 2023. Antibiotic tolerance, the ability of bacteria to survive exposure to bactericidal antibiotics without genetic resistance mutations, contributes to the need for prolonged treatment. Targeting antibiotic tolerance mechanisms could promote accelerated clearance of Mycobacterium tuberculosis (Mtb), thereby improving medical adherence. Our previous forward genetic screen for rifampin tolerance genes identified pstA1, which is involved in phosphate-specific import. The ABC-type transporter permease PstA1 has previously been implicated in Mtb virulence, as mutants lacking this gene exhibit defective survival during phosphate limitation in vitro, in infected macrophages, and in immunocompetent mice. The minimum inhibitory concentration (MIC) of rifampin was not altered in a pstA1 deletion mutant ({Delta}pstA1), suggesting this difference in susceptibility is not due to antibiotic resistance. Consistent with a role in rifampin tolerance, time-kill assays revealed a shift in the mean duration of killing (2-log reduction) from 1.6 days in wild-type to 1.0 day in {Delta}pstA1, and complementation partially restored this phenotype. We found that pstA1 is specifically required for Mtb survival in the absence of exogenous inorganic phosphate and is important for adaptation to growth in culture without detergent, and within macrophages in an interferon-{gamma}-dependent manner. Differential expression analysis revealed that {Delta}pstA1 exhibited substantial transcriptional reprogramming with 58 differentially expressed genes, including altered expression of metabolic, DNA damage repair, and secretory pathways. PstA1 represents a novel drug target, and inhibitors could serve as adjunctive therapies to shorten treatment times, reducing opportunities for drug resistance emergence. ImportanceTuberculosis remains one of the worlds deadliest infectious diseases, causing over a million deaths annually. Current treatment requires months of antibiotic therapy, and poor adherence to these lengthy regimens contributes to the emergence of drug-resistant strains that are increasingly difficult to treat. A major barrier to shorter treatment is antibiotic tolerance, which allows bacteria to survive drug exposure without genetic resistance mutations. This study identifies the phosphate transport component PstA1 as a critical factor enabling Mycobacterium tuberculosis to tolerate the frontline antibiotic rifampin. Bacteria lacking pstA1 are eliminated more rapidly by rifampin, demonstrating that this transporter actively promotes bacterial survival during treatment. These findings suggest that drugs targeting PstA1 could be combined with standard antibiotics to accelerate bacterial clearance, potentially shortening treatment duration and improving patient adherence. Such adjunctive therapies targeting tolerance mechanisms represent a promising strategy to combat tuberculosis and reduce the global burden of drug-resistant disease.

microbiology↗

bioRxiv2023

Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed. Mtb adapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance in Mtb can serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidate Mtb genes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). Following Mtb adaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation in Mtb mutants lacking the following genes: ercc3, moeA1, rv0049, and rv2179c. These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens. ImportanceTreatment of Mtb infection requires a long course of combination antibiotics, likely due to subpopulations of tolerant bacteria exhibiting decreased susceptibility to antibiotics. Identifying and characterizing the genetic pathways involved in antibiotic tolerance is expected to yield therapeutic targets for the development of novel TB treatment-shortening regimens.

microbiology↗

bioRxiv2022

An intranasal stringent response vaccine targeting dendritic cells as a novel adjunctive therapy against tuberculosis

Lengthy tuberculosis (TB) treatment is required to address the ability of a subpopulation of persistent Mycobacterium tuberculosis (Mtb) to remain in a non-replicating, antibiotic-tolerant state characterized by metabolic remodeling, including induction of the RelMtb-mediated stringent response. We developed a novel therapeutic DNA vaccine construct involving fusion of the relMtb gene with the immature dendritic cell-targeting gene encoding chemokine MIP-3/CCL20. To augment mucosal immune responses, intranasal delivery was also evaluated. We found that the intramuscular MIP-3/relMtb (fusion) vaccine potentiates isoniazid activity more than a similar DNA vaccine expressing relMtb alone in a chronic TB mouse model (absolute reduction of Mtb burden: 0.63 log10 colony-forming units, P=0.0001), inducing pronounced Mtb-protective immune signatures. The intranasal fusion vaccine, an approach combining relMtb fusion to MIP-3 and intranasal delivery, demonstrated the greatest therapeutic effect compared to each approach alone, as evidenced by robust Th1 and Th17 responses systemically and locally and the greatest mycobactericidal activity when combined with isoniazid (absolute reduction of Mtb burden: 1.13 log10, P<0.0001, when compared to the intramuscular vaccine targeting relMtb alone). This DNA vaccination strategy may be a promising adjunctive approach combined with standard therapy to shorten curative TB treatment, and also serve as proof-of-concept for treating other chronic infections.

immunology↗

bioRxiv2021

Genetic determinants of intrinsic antibiotic tolerance in Mycobacterium avium

Mycobacterium avium complex (MAC) is one of the most prevalent causes of nontuberculous mycobacteria pulmonary infection in the United States, yet it remains understudied. Current MAC treatment requires more than a year of intermittent to daily combination antibiotic therapy, depending on disease severity. In order to shorten and simplify curative regimens, it is important to identify the innate bacterial factors contributing to reduced antibiotic susceptibility, namely antibiotic tolerance genes. In this study, we performed a genome-wide transposon screen to elucidate M. avium genes that play a role in the bacteriums tolerance to first- and second-line antibiotics. We identified a total of 193 unique M. avium mutants with significantly altered susceptibility to at least one of the four clinically used antibiotics we tested, including two mutants (in DFS55_00905 and DFS55_12730) with panhypersusceptibility. The products of the antibiotic tolerance genes we have identified may represent novel targets for future drug development studies aimed at shortening the duration of therapy for MAC infections. ImportanceThe prolonged treatment required to eradicate Mycobacterium avium complex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. In this study, we performed a forward genetic screen to identify M. avium antibiotic tolerance genes, whose products may represent attractive targets for the development of novel adjunctive drugs capable of shortening curative treatment for MAC infections.

microbiology↗

bioRxiv2019

Keeping it clean: the cell culture quality control experience at the National Center for Advancing Translational Sciences

Quality control monitoring of cell lines utilized in biomedical research is of critical importance, and is critical for reproducibility of data. Two key pitfalls in tissue culture are 1) cell line authenticity, and 2) mycoplasma contamination. As a collaborative research institute, the National Center for Advancing Translational Sciences receives cell lines from a range of commercial and academic sources, that are adapted for high-throughput screening. Here, we describe the implementation of a routine NCATS-wide mycoplasma testing and short-tandem repeat (STR) testing for cell lines. Initial testing identified a >10% mycoplasma contamination rate, but the implementation of clearly defined protocols that included immediate destruction of contaminated cell lines wherever possible has led to a much-reduced mycoplasma contamination rate, and data for >2,000 cell line samples tested over 3 years, and case studies are provided. STR testing of 170 cell lines with established STR profiles revealed only 5 mis-identified cell lines received from external labs. The data collected over the three years since implementation of this systematic testing demonstrates the importance of continual vigilance for rapid identification of problem cell lines, for ensuring reproducible data in translational science research.

cell biology↗