Biology subjects

Morales, Y.

Publications and source records attributed to Morales, Y..

3 recordsLinked to original sources

bioRxiv2024

Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens

Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide problem. Combination antimicrobial therapies may be an important strategy to overcome resistance and broaden the spectrum of existing antibiotics. However, this strategy is limited by the ability to efficiently screen large combinatorial chemical spaces. Here, we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique strain-antibiotic-compound combinations. In this dataset, compounds more frequently exhibited synergy with known antibiotics than single-agent activity. We identified a compound, P2-56, and developed a more potent analog, P2-56-3, which potentiated rifampin (RIF) activity against Acinetobacter baumannii and Klebsiella pneumoniae. Using phenotypic assays, we showed P2-56-3 disrupts the outer membrane of A. baumannii. To identify pathways involved in the mechanism of synergy between P2-56-3 and RIF, we performed genetic screens in A. baumannii. CRISPRi-induced partial depletion of lipooligosaccharide transport genes (lptA-D, lptFG) resulted in hypersensitivity to P2-56-3/RIF treatment, demonstrating the genetic dependency of P2-56-3 activity and RIF sensitization on lpt genes in A. baumannii. Consistent with outer membrane homeostasis being an important determinant of P2-56-3/RIF tolerance, knockout of maintenance of lipid asymmetry complex genes and overexpression of certain resistance-nodulation-division efflux pumps - a phenotype associated with multidrug-resistance - resulted in hypersensitivity to P2-56-3. These findings demonstrate the immense scale of phenotypic antibiotic combination screens using DropArray and the potential for such approaches to discover new small molecule synergies against multidrug-resistant ESKAPE strains. Significance StatementThere is an unmet need for new antibiotic therapies effective against the multidrug-resistant, Gram-negative ESKAPE pathogens. Combination therapies have the potential to overcome resistance and broaden the spectrum of existing antibiotics. In this study, we use DropArray, a massively parallel combinatorial screening tool, to assay more than 1.3 million combinations of small molecules against the Gram-negative ESKAPE pathogens, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. We discovered a synthetic small molecule potentiator, P2-56, of the antibiotic rifampin effective in A. baumannii and K. pneumoniae. We generated P2-56-3, a more potent derivative of P2-56, and found that it likely potentiates rifampin by compromising the outer membrane integrity. Our study demonstrates a high-throughput strategy for identifying antibiotic potentiators against multidrug-resistant bacteria.

microbiology↗

bioRxiv2024

NLRP3 and AIM2 inflammasomes exacerbate the pathogenic Th17 cell response to eggs of the helminth Schistosoma mansoni

Infection with the helminth Schistosoma mansoni can cause exacerbated morbidity and mortality via a pathogenic host CD4 T cell-mediated immune response directed against parasite egg antigens, with T helper (Th) 17 cells playing a major role in the development of severe granulomatous hepatic immunopathology. The role of inflammasomes in intensifying disease has been reported; however, neither the types of caspases and inflammasomes involved, nor their impact on the Th17 response are known. Here we show that enhanced egg-induced IL-1{beta} secretion and pyroptotic cell death required both caspase-1 and caspase-8 as well as NLRP3 and AIM2 inflammasome activation. Schistosome genomic DNA activated AIM2, whereas reactive oxygen species, potassium efflux and cathepsin B, were the major activators of NLRP3. NLRP3 and AIM2 deficiency led to a significant reduction in pathogenic Th17 responses, suggesting their crucial and non-redundant role in promoting inflammation. Additionally, we show that NLRP3- and AIM2-induced IL-1{beta} suppressed IL-4 and protective Type I IFN (IFN-I) production, which further enhanced inflammation. IFN-I signaling also curbed inflammasome-mediated IL-1{beta} production suggesting that these two antagonistic pathways shape the severity of disease. Lastly, Gasdermin D (Gsdmd) deficiency resulted in a marked decrease in egg-induced granulomatous inflammation. Our findings establish NLRP3/AIM2-Gsdmd axis as a central inducer of pathogenic Th17 responses which is counteracted by IFN-I pathway in schistosomiasis. SummarySchistosomiasis is a major tropical parasitic disease caused by trematode worms of the genus Schistosoma. Morbidity and mortality in infection with the species Schistosoma mansoni are due to a pathogenic CD4 T cell-mediated immune response directed against parasite eggs, resulting in granulomatous inflammation. In severe cases of schistosomiasis, there is liver fibrosis, hepatosplenomegaly, portal hypertension, gastro-intestinal hemorrhage and death. Here we describe the role of two proteins, the NLRP3 and AIM2 inflammasomes, in intensifying disease. We found that upstream proteins which activate these inflammasomes are caspase-1 and caspase 8; these in turn lead to the activation of another protein, Gasdermin D (Gsdmd), which facilitates the release of the proinflammatory cytokine IL-1{beta}. Importantly, we observed that mice deficient in Gsdmd exhibit diminished pathology. Finally, we discovered that the protective Type I Interferon (IFN-I) pathway counteracts the caspase/inflammasome/Gsdmd axis thereby controlling egg mediated inflammation. These results give us a deeper understanding of the functional features of the crosstalk between inflammasome and IFN-I pathway, which may lead to the identification of novel targets for therapeutic intervention.

immunology↗

bioRxiv2022

Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model in vivo responses

The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Antibiotic susceptibility is affected in part by the growth state of bacteria within various tissues. Here we tested the hypothesis that drug-drug interactions vary in different media, and hence, using a medium that reflects tissue environments will better predict in vivo outcomes. We systematically studied pair-wise antibiotic interactions in three different media (CAMHB, a urine mimetic, and a lung mimetic) using three Gram-negative ESKAPE pathogens, Acinetobacter baumannii (Ab), Klebsiella pneumoniae (Kp), and Pseudomonas aeruginosa (Pa). There were pronounced differences in responses to antibiotic combinations between the three bacterial species grown in the same medium. However, within species, Pa responded to drug combinations similarly when grown in all three different media, whereas Ab responded similarly when grown in CAMHB and a lung mimetic medium. By contrast, drug interactions in Kp were poorly correlated across three different media. To assess whether distinct media were predictive of antibiotic interactions in Kp in the lungs of mice, we developed a treatment strategy and tested three antibiotic combination pairs. Measurements obtained in vitro from lung mimetic medium, but not rich medium, predicted in vivo outcomes. This work demonstrates that antibiotic interactions are highly variable when comparing across three gram-negative pathogens and highlights the importance of growth medium by showing a superior correlation between in vitro interactions in a growth medium that resembles the tissue environment and in vivo outcomes.

microbiology↗