In Vitro Synergistic Activity of Rifampicin Combined with Minimal Effective Antibiotic Concentration (MEAC) of Polymyxin B Against Extensively Drug-Resistant, Carbapenem-, and Polymyxin B-Resistant Klebsiella pneumoniae Clinical Isolates.
Current microbiology
We investigated the in vitro antibacterial activity of the combination rifampicin (RIF) + polymyxin B (PB) against extensively drug-resistant (XDR) Klebsiella pneumoniae isolates. We evaluated clinical isolates co-resistant to PB (non-mcr carriers; eptB, mgrB, pmr operon, and ramA mutations) and to carbapenems (KPC, CTX-M, and SHV producers; including KPC + NDM co-producer), belonging to sequence types (ST) ST16, ST11, ST258, ST340, and ST437. We used the standard broth microdilution method to determine RIF and PB minimum inhibitory concentration (MIC) and the checkerboard assay to evaluate the fractional inhibitory concentration index (FICI) of RIF + PB as well as to investigate the lowest concentrations of RIF and PB that combined (RIF + PB) had antibacterial activity. Time-kill assays were performed to evaluate the synergistic effect of the combination against selected isolates. PB MIC (32-256 µg/mL) and RIF MIC (32-1024 µg/mL) were determined. FICI (<0.5) indicated a synergistic effect for all isolates evaluated for the combination RIF + PB. Our results showed that low concentrations of PB (PB minimal effective antibiotic concentration [MEAC], ≤0.25-1 µg/mL) favor RIF (≤0.03-0.125 µg/mL) to reach the bacterial target and exert antibacterial activity against PB-resistant isolates, and the synergistic effect was also observed in time-kill results. The combination of RIF + PB showed in vitro antibacterial activity against XDR, carbapenem-, and PB-resistant K. pneumoniae and could be further studied as a potential combination therapy, with cost-effectiveness and promising efficacy.
10.1007/s00284-024-03897-1
Antibacterial and antibiofilm activities of bacteriocin produced by a new strain of Enterococcus faecalis BDR22.
Naunyn-Schmiedeberg's archives of pharmacology
A large number of recalcitrant bacterial pathogens cannot be easily treated by antibiotics due to the existence of biofilm. Hence, an alternative strategy needs to be adopted to remove the biofilm without the development of antibiotic resistance. Bacteriocins, ribosome-mediated proteinaceous toxins, having potential to inhibit the growth of closely or distantly related bacteria. In the present study, after screening a number of sources, a bacteriocin-producing strain, Enterococcus faecalis BDR22, was isolated that showed a significant reduction in the growth of planktonic cells of Gram-positive Staphylococcus aureus, Bacillus subtilis, and Gram-negative Pseudomonas aeruginosa, Escherichia coli, Serratia marcescens, Enterobacter cloacae, and Klebsiella pneumoniae compared to the conventional antibiotic tetracycline. The considerable reduction of the biofilm-forming sessile cells of the test organisms S. aureus (ATCC 23235) and P. aeruginosa (ATCC 10145), with no significant cell revival even after withdrawal of the treatment, was also observed. The extracellular polymeric substance (EPS) content of the biofilm was also reduced, with around 84% total carbohydrate reduction found for both microorganisms. The antibiofilm activities of the strain against test organisms were clearly visible from scanning electron micrographs and confirmed by the changes in functional groups (C-H, -OH, C = C, C-N etc.) of biofilm matrices by Fourier transform infrared spectroscopy (FTIR) analysis. The molecular docking interactions with docking energies ∆G of - 54.40 kcal/mol and - 66.2373 kcal/mol validate the affinity of the bacteriocin towards the biofilm-forming protein, which confirms the competence of the bacteriocin-producing strain to act as an effective antimicrobial and antibiofilm agent, replacing antibiotics.
10.1007/s00210-024-03458-0
Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling.
PLoS pathogens
With the emergence of multidrug-resistant bacteria, the World Health Organization published a catalog of microorganisms urgently needing new antibiotics, with the carbapenem-resistant Acinetobacter baumannii designated as "critical". Such isolates, frequently detected in healthcare settings, pose a global pandemic threat. One way to facilitate a systemic view of bacterial metabolism and allow the development of new therapeutics is to apply constraint-based modeling. Here, we developed a versatile workflow to build high-quality and simulation-ready genome-scale metabolic models. We applied our workflow to create a metabolic model for A. baumannii and validated its predictive capabilities using experimental nutrient utilization and gene essentiality data. Our analysis showed that our model iACB23LX could recapitulate cellular metabolic phenotypes observed during in vitro experiments, while positive biomass production rates were observed and experimentally validated in various growth media. We further defined a minimal set of compounds that increase A. baumannii's cellular biomass and identified putative essential genes with no human counterparts, offering new candidates for future antimicrobial development. Finally, we assembled and curated the first collection of metabolic reconstructions for distinct A. baumannii strains and analyzed their growth characteristics. The presented models are in a standardized and well-curated format, enhancing their usability for multi-strain network reconstruction.
10.1371/journal.ppat.1012528
Investigating the Efficacy of Various Natural Products in Raw Form against Multidrug-Resistant Bacteria.
Infectious disorders drug targets
BACKGROUND:The alarming increase in antibiotic resistance urges alternative and efficacious antimicrobial solutions. Historically, medicinal plants have been used for therapeutic purposes, such as relieving pain and healing wounds. However, the evaluation of the natural therapeutic effects of medicinal plants in a manner that resembles how humans typically consume them is lacking. Therefore, in this study, many medicinal plants known to have some antimicrobial effects, including Frankincense, Garlic, Myrrh, and Ginger, were evaluated for their direct antibacterial activity in raw form. MATERIALS AND METHODS:The direct antimicrobial activity of medicinal plants was evaluated against a variety of Gram-positive and Gram-negative bacterial strains, such as Staphylococcus aureus (S. Aureus), Acinetobacter baumannii and Klebsiella pneumoniae using agar well diffusion method and turbidity measurements in suspension culture. RESULTS:Out of all the tested medicinal plants, only raw garlic (Allium sativum) powder, when dissolved in water or vinegar, offered a straightforward antibacterial activity. A combination of garlic extract and vinegar increased antibacterial activity. Aqueous garlic extracts displayed robust antimicrobial activity against many resistant bacteria. Other medicinal plants used in this study had absent or minimal antibacterial effects. CONCLUSION:Only garlic in its raw form was effective against antibiotic-resistant bacteria. The increase in the antibacterial activity of garlic when combined with vinegar suggests the synergistic activity of garlic. The straightforward antibacterial action of raw garlic may be strategically harnessed to combat the continuous challenge of increasing antibiotic resistance. This work promotes additional testing of more natural products (in raw form) and assesses their therapeutic effects clinically.
10.2174/0118715265320631240826073359
Transmission of dominant strains of Campylobacter jejuni and Campylobacter coli between farms and retail stores in Ecuador: Genetic diversity and antimicrobial resistance.
PloS one
Thermotolerant Campylobacter is an important zoonotic pathogen known for causing gastroenteritis in humans, with poultry as its primary reservoir. A total of 468 samples were collected, of which 335 were chicken carcass samples (representing the food component), and 133 were chicken caeca samples (representing the animal component). These samples underwent culture, with colonies examined under a microscope. Species identification was achieved through multiplex PCR. Additionally, antimicrobial susceptibility profiles were determined using the Kirby-Bauer method, testing for sensitivity to gentamicin, ciprofloxacin, tetracycline, and erythromycin. Additionally, 55 C. jejuni (62.5%) and 33 C. coli (37.5%) isolates were selected for whole genome sequencing (WGS). A High prevalence of Campylobacter was observed, with rates of 95.5% (n = 127, CI95%: 92.5% - 98.5%) in the animal component and 72.5% (n = 243, CI95%: 69.9% - 75.1%) in the food component. Specifically, C. jejuni was detected in 33.1% (n = 42) of poultry farms and 38.3% (n = 93) of chicken carcasses, while C. coli was found in 64.6% (n = 82) of poultry farms and 60.5% (n = 147) of chicken carcasses. Antimicrobials with the highest rates of resistance (67%-100%) were ciprofloxacin and tetracycline, in both animal and food component isolates. Erythromycin resistance was notable, ranging from 22% to 33%, with only two C. jejuni isolates from retail were resistant to gentamicin. Furthermore, multidrug resistance was identified in 23% (20 isolates) of the Campylobacter isolates. Genetic analysis revealed the presence of fourteen resistance genes in both C. jejuni and C. coli isolates, including tet(O), blaOXA-460, blaOXA-184, blaOXA-489, blaOXA-193, blaOXA-784, blaOXA-603, aph(3')-IIIa, aad9, aph(2'')-If, aadE-Cc, sat4, and ant(6)-Ia. Additionally, twenty-five plasmids were detected in the 88 Campylobacter isolates examined. Interestingly, most isolates also harbored genes encoding putative virulence factors associated with pathogenicity, invasion, adherence, and production of cytolethal distending toxin (cdt): cheV, cheA, cheW, cheY, flaA, flgR, flaC, flaD, flgB, flgC, ciaB, ciaC. The WGS analysis showed the presence of several cgSTs in both animal and food components, with nine of them widely disseminated between components. Moreover, C. coli and C. jejuni isolates from different sources presented less than 11 single nucleotide polymorphisms (SNPs), suggesting clonality (16 isolates). Further analysis using SNP tree demonstrated widespread distribution of certain C. jejuni and C. coli clones across multiple farms and retail stores. This study presents, for the first-time, insights into the clonality, plasmid diversity, virulence, and antimicrobial resistance (AMR) of thermotolerant Campylobacter strains originating from the Ecuadorian poultry industry. The identification of AMR genes associated with the main antibiotics used in the treatment of campylobacteriosis in humans, highlights the importance of the prudent use of antimicrobials in the poultry industry. Additionally, this research remarks the need for regional studies to understand the epidemiology of this pathogen.
10.1371/journal.pone.0308030
Prediction of Antibiotic Susceptibility in E. coli Isolates Using Machine Learning.
Studies in health technology and informatics
Antimicrobial resistance (AMR) poses a significant global health threat, resulting in 4.96 million deaths in 2019, with projections reaching 10 million by 2050. This resistance, primarily due to the overuse of antibiotics, complicates the treatment of infections caused by various microorganisms, including the gram-negative bacterium Escherichia coli. Traditional culture-based methods for detecting AMR are slow and imprecise, hindering timely clinical decision-making. In contrast, whole genome sequencing offers a faster, more accurate alternative for AMR detection. A novel machine learning study leveraging whole genomic sequencing data to predict the phenotypic susceptibility of Escherichia coli to ciprofloxacin is presented. Using a novel dataset of 256 bacterial genomes and related susceptibility data, features were generated based on AMRFinderPlus findings and k-mer frequencies. The machine learning models, Random Forest and XGBoost, were evaluated using a five-fold cross-validation approach. Results showed that combining AMRFinderPlus and k-mer frequency features could achieve more than 90% accuracy using the XGBoost gradient boosting model. These findings suggest that the best results may be achieved using reference-free features combined with known gene markers.
10.3233/SHTI240907
New antibacterial candidates against Acinetobacter baumannii discovered by in silico-driven chemogenomics repurposing.
PloS one
Acinetobacter baumannii is a worldwide Gram-negative bacterium with a high resistance rate, responsible for a broad spectrum of hospital-acquired infections. A computational chemogenomics framework was applied to investigate the repurposing of approved drugs to target A. baumannii. This comprehensive approach involved compiling and preparing proteomic data, identifying homologous proteins in drug-target databases, evaluating the evolutionary conservation of targets, and conducting molecular docking studies and in vitro assays. Seven drugs were selected for experimental assays. Among them, tavaborole exhibited the most promising antimicrobial activity with a minimum inhibitory concentration (MIC) value of 2 μg/ml, potent activity against several clinically relevant strains, and robust efficacy against biofilms from multidrug-resistant strains at a concentration of 16 μg/ml. Molecular docking studies elucidated the binding modes of tavaborole in the editing and active domains of leucyl-tRNA synthetase, providing insights into its structural basis for antimicrobial activity. Tavaborole shows promise as an antimicrobial agent for combating A. baumannii infections and warrants further investigation in preclinical studies.
10.1371/journal.pone.0307913
Current challenges in antibiotic resistance.
Hand W L
Adolescent medicine (Philadelphia, Pa.)
The striking, widespread increase in bacterial resistance to antibiotics is an issue of great concern. Worldwide emergence of antibiotic resistances in our common gram-positive coccal pathogens is probably the most serious problem we have in the realm of bacterial infections. The most important of these organisms are penicillin-resistant Streptococcus pneumoniae, vancomycin-resistant Enterococcus, and methicillin- (and now vancomycin-) resistant Staphylococcus aureus. Although known by the above names, all of these organisms are multidrug-resistant. Beta-lactam and vancomycin resistances in gram-positive cocci are caused by altered cell wallñbinding sites with decreased affinity for the drug. Another serious problem is that of resistance in certain gram-negative bacilli due to extended-spectrum beta-lactamase production. These antibiotic resistances in common pathogens have made antimicrobial therapy of many infections extremely difficult or virtually impossible in some instances. The extensive, and often inappropriate, use of antibiotics in the U.S. and worldwide is the major factor in the emergence and spread of antimicrobial resistance. Microbial mechanisms, epidemiology, clinical importance, treatment, and prevention of these antibiotic resistance problems are discussed.