Multidrug-resistant Pathogens Research Articles

Exploring the Antibacterial Properties and Chemical Profiles of Essential Oils from Syzygium aromaticum and Nigella sativa Against MDR Bacteria

For centuries, plants have been studied for their healing properties. Recently, the rise of antibiotic resistance in bacteria has prompted scientists to explore herbal remedies. Syzygium aromaticum, from the Myrtaceae family, has been utilized as a histological clearing agent. In contrast, Nigella sativa (black cumin), a member of the Ranunculaceae family, has long been utilized in traditional medicine dating back to ancient times. The current study investigates the chemical composition and antibacterial activity of essential oils from Syzygium aromaticum (clove) and Nigella sativa (black cumin) against multidrug-resistant (MDR) bacteria. Using the agar well diffusion method, Syzygium aromaticum exhibited significant antibacterial activity, particularly against Salmonella typhi (30.66 mm inhibition zone), while Nigella sativa was effective only against Staphylococcus aureus (19 mm). The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values for Syzygium aromaticum ranged from 3.53 to 7.06 mg/mL, indicating stronger antibacterial properties than Nigella sativa (MIC: 12.7 mg/mL, MBC: 22.5 mg/mL). GC-MS analysis revealed that Syzygium aromaticum contained bioactive compounds like Diglycolic acid (76.59%) and Eugenol (2.06%), while Nigella sativa was dominated by Heptasiloxane (80.83%) and Thymoquinone (2.66%). These findings suggest that Syzygium aromaticum essential oil could serve as a potent natural antimicrobial agent against MDR pathogens.

Metal-phenolic nanoparticles enhance low temperature photothermal therapy for bacterial biofilm in superficial infections.

Bacterial infections, especially induced by multidrug-resistant pathogens, have become a significant global health concern. In the infected tissues, biofilms not only serve as a source of nutrients but also act as protective barriers that impede antibiotic penetration. Herein, we developed tea polyphenols epigallocatechin gallate (EGCG) Au nanoparticles (E-Au NPs) through direct one-step self-assembly methods by EGCG chelating with Au ions to eradicate antibiotic-resistant bacteria methicillin-resistant Staphylococcus aureus (MRSA) and prevent the formation of biofilm under near-infrared (NIR) irradiation. The outstanding antibacterial effect involved in mild photothermal therapy, reactive oxygen species production, pathogenicity-related genes regulation, and quinoprotein formation that were specific to the polyphenol-based NPs. The excellent antibacterial and anti-inflammatory therapeutic efficacy of E-Au NPs was validated and topically applied in murine MRSA-infected skin wounds and keratitis model in vivo to kill bacteria, reduce the inflammation response and promote wound healing. Furthermore, the ophthalmic and systemic biosafety profiles were thoroughly evaluated while no significant side effects were revealed achieving a balance between high-efficiency antibacterial properties and biocompatibility. This study provides an effective therapeutic agent of metal-phenolic materials for superficial tissue infection with favorable prognosis and potential in clinical translation.

New emerging materials with potential antibacterial activities.

The increasing prevalence of multidrug-resistant pathogens is a critical public health issue, necessitating the development of alternative antibacterial agents. Examples of these pathogens are methicillin-resistant Staphylococcus aureus (MRSA) and the emergence of "pan-resistant" Gram-negative strains, such as Pseudomonas aeruginosa and Acinetobacter baumannii, which occurred more recently. This review examines various emerging materials with significant antibacterial activities. Among these are nanomaterials such as quantum dots, carbon quantum dots, metal-organic frameworks (MOFs), covalent organic frameworks (COFs), and layered double hydroxides, all of which demonstrate excellent antibacterial properties. Interestingly, including antibacterial agents within the structure of these materials can help avoid bacterial resistance and improve the long-term efficacy of the materials. Additionally, the antibacterial potential of liquid solvents, including ionic liquids and both deep eutectic solvents and natural deep eutectic solvents, is explored. The review discusses the synthesis methods, advantages, and antibacterial efficacy of these new materials. By providing a comprehensive overview of these innovative materials, this review aims to contribute to the ongoing search for effective solutions to combat antibiotic resistance. Key studies demonstrating antibacterial effects against pathogens like Escherichia coli, Staphylococcus aureus, and multidrug-resistant strains are summarized. MOFs have exhibited antibacterial properties through controlled ion release and surface interactions. COFs have enhanced the efficacy of encapsulated antibiotics and displayed intrinsic antibacterial activity. Other nanomaterials, such as quantum dots, have generated reactive oxygen species, leading to microbial inactivation. This review aims to provide insights into these new classes of antibacterial materials and highlight them for addressing the global crisis of antibiotic resistance. KEY POINTS: • Nanomaterials show strong antibacterial effects against drug-resistant bacteria • Emerging solvents like ionic liquids offer novel solutions for bacterial resistance • MOFs and COFs enhance antibiotic efficacy, showing promise in combating resistance.

Uncovering the arsenal of class II bacteriocins in salivarius streptococci.

Facing the antibiotic resistance crisis, bacteriocins are considered as a promising alternative to treat bacterial infections. In the human commensal Streptococcus salivarius, the production of unmodified bacteriocins (or salivaricins) is directly controlled at the transcriptional level by quorum-sensing. To discover hidden bacteriocins, we harnessed here the unique molecular signatures of salivaricins not yet used in available computational pipelines and performed genome mining followed by orthogonal reconstitution and expression. From 100 genomes of S. salivarius, we identified more than 50 bacteriocin candidates clustered into 21 groups. Strain-based analysis of bacteriocin combinations revealed significant diversity, reflecting the plasticity of seven independent loci. Activity tests showed both narrow and broad-spectrum bacteriocins with overlapping activities against a wide panel of Gram-positive bacteria, including notorious multidrug-resistant pathogens. Overall, this work provides a search-to-test generic pipeline for bacteriocin discovery with high impact for bacterial ecology and broad applications in the food and biomedical fields.

Burden and Risk Factors for Coinfections in Patients with a Viral Respiratory Tract Infection

Which patients should be monitored for coinfections or should receive empirical antibiotic treatment, in patients with an acute viral respiratory infection, is largely unknown. We evaluated the prevalence, characteristics, outcomes of coinfected patients, and risk factors associated with a coinfection among patients with an acute viral infection. A retrospective, single-center study recruited consecutive patients from October 2022 to March 2023 presenting to the emergency department with signs of a respiratory tract infection. Patients were screened for respiratory viruses and bacterial/fungal secondary infections according to local standard procedures. Outcomes included severe disease, in-hospital complications, all-cause in-hospital and ICU-related mortality, time to death, time to discharge, and time to coinfection. The analysis included 652 patients. A viral infection and a secondary bacterial/fungal infection were detected in 39.1% and 40% of cases. Compared with the rest of the cohort, coinfected patients had more frequently severe disease (88.3%, p < 0.001; 51% in patients with SARS-CoV-2) and higher in-hospital mortality (16.5%, p = 0.010). Nephropathy (OR 3.649, p = 0.007), absence of COVID-19 vaccination (OR 0.160, p < 0.001), SARS-CoV-2 infection (OR 2.390, p = 0.017), and lower blood pressure at admission (OR 0.980, p = 0.007) were independent risk factors for coinfection. Multidrug-resistant pathogens were detected in 30.8% of all coinfections. Patients with a viral infection are at high risk of bacterial coinfections, which carry a significant morbidity and mortality burden.

Single-cell transcriptomics unveils skin cell specific antifungal immune responses and IL-1Ra- IL-1R immune evasion strategies of emerging fungal pathogen Candida auris.

Candida auris is an emerging multidrug-resistant fungal pathogen that preferentially colonizes and persists in skin tissue, yet the host immune factors that regulate the skin colonization of C. auris in vivo are unknown. In this study, we employed unbiased single-cell transcriptomics of murine skin infected with C. auris to understand the cell type-specific immune response to C. auris. C. auris skin infection results in the accumulation of immune cells such as neutrophils, inflammatory monocytes, macrophages, dendritic cells, T cells, and NK cells at the site of infection. We identified fibroblasts as a major non-immune cell accumulated in the C. auris infected skin tissue. The comprehensive single-cell profiling revealed the transcriptomic signatures in cytokines, chemokines, host receptors (TLRs, C-type lectin receptors, NOD receptors), antimicrobial peptides, and immune signaling pathways in individual immune and non-immune cells during C. auris skin infection. Our analysis revealed that C. auris infection upregulates the expression of the IL-1RN gene (encoding IL-1R antagonist protein) in different cell types. We found IL-1Ra produced by macrophages during C. auris skin infection decreases the killing activity of neutrophils. Furthermore, C. auris uses a unique cell wall mannan outer layer to evade IL-1R-signaling mediated host defense. Collectively, our single-cell RNA seq profiling identified the transcriptomic signatures in immune and non-immune cells during C. auris skin infection. Our results demonstrate the IL-1Ra and IL-1R-mediated immune evasion mechanisms employed by C. auris to persist in the skin. These results enhance our understanding of host defense and immune evasion mechanisms during C. auris skin infection and identify potential targets for novel antifungal therapeutics.

Identifying how drug efflux mechanisms impact Acinetobacter baumannii evolutionary paths to ciprofloxacin resistance

Acinetobacter baumannii is a multi-drug resistant pathogen commonly found in clinical settings. This pathogen frequently uses efflux pumps to mitigate antibiotic treatment stress and eliminate the drug. When A. baumannii is exposed to antibiotics, it often develops mutations in the efflux pump regulator genes, causing an increase in efflux pump production. We hypothesize that efflux is a key pathway that leads to treatment failure in A. baumannii infections. The extent to which increasing drug efflux impacts other cellular functions remains unknown. To identify how efflux pump mutations impact growth, resistance, and evolvability, wildtype A. baumannii laboratory strain 17978UN, along with four mutants of this strain, each with a single nucleotide polymorphism (SNP) in an efflux pump regulator (adeL L341R, adeN I49N, adeR D23Y, and adeS R152S), were propagated in the presence of antibiotic and an efflux pump inhibitor to place selective pressure on the isolates. SNPs increase the production of efflux pumps; inhibiting efflux ability will determine if the effect of each SNP is nullified. All evolved populations demonstrated differences in fitness and antibiotic resistance in comparison to their respective ancestors; the extent of adaptation affecting each phenotype was highly dependent on the regulator that was mutated. Counterintuitively, efflux inhibitors also placed stress on wild-type A. baumannii which leads to antibiotic resistance. These results demonstrate that efflux regulator mutations can influence population adaptability and cause treatment failure. Understanding the role that different efflux systems play in treatment failure and drug resistance evolution will be instrumental in developing treatment strategies that hinder the development of antibiotic resistance.

Culture-Independent Quantitative PCR Detected Mobilized Colistin Resistance Genes (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5) in Chicken Gut Contents in Bangladesh

Inappropriate antimicrobial use in food animal farming propels antimicrobial resistance (AMR) that affects all health domains. Colistin is a ‘Reserve’ antibiotic for human treatment to be conserved for multidrug-resistant pathogens; however, it is being used as an animal growth promoter in many developing countries. The evolution of mobilized colistin resistance (mcr) gene-mediated colistin resistance has been reported to be associated with rampant colistin use. This study investigated the current variants of the mcr gene in chicken gut contents in Bangladesh. A cross-sectional study was designed to assess the mcr-1 to mcr-5 genes in 80 fresh poultry droppings from commercial poultry farms and 40 poultry droppings from household farms. DNA was extracted from each poultry dropping using commercial kits (Qiagen GmbH, Hilden, Germany). Real-time quantitative polymerase chain reaction (RT-qPCR) was employed using the qTOWER3 thermal cycler (Analytik Jena GmbH, Jena, Germany) to analyze the mcr gene variants in the extracted DNA. This study observed that 47.5% (57/120) of the samples exhibited the presence of at least one mcr gene out of the five variants investigated. The individual detection rates of the mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes were 42.5% (51/120), 2.5% (3/120), 1.7% (2/120), 5% (6/120), and 9.2% (11/120), respectively. The co-carriage of two or more genes was found in over 10% (10/57) of the samples. The triple occurrence of mcr genes was identified in three samples with the combination of mcr-1+mcr-2+mcr-4, mcr-1+mcr-3+mcr-5, and mcr-1+mcr-4+mcr-5. Overall, a significantly higher number of mcr genes were identified in the commercial farm chicken droppings compared to the household chicken droppings (p = 0.007). The existence of mcr genes in poultry feces in Bangladesh emphasizes the importance of proper poultry waste disposal and good hygiene practices in poultry livestock and its value chain. The potential impact of environmental ARGs should be considered in national and global policy documents. An integrated and combined approach to the One Health concept should be applied in all domains to understand and control the environment’s role in the evolution and transmission of AMR.

CapD deletion in the Elizabethkingia miricola capsular locus leads to capsule production deficiency and reduced virulence.

Elizabethkingia miricola is a multidrug-resistant pathogen that can cause life-threatening infections in immunocompromised humans and outbreaks in amphibians. However, the specific virulence factors of this microorganism have not been described. In this study, we identified the polysaccharide biosynthesis protein-encoding gene capD, which is located in the conserved region of the Wzy-dependent capsule synthesis gene cluster in the E. miricola strain FL160902, and investigated its role in the pathogenesis of E. miricola. Our results revealed that the capD deletion strain (ΔcapD) lost its typical encapsulated structure, with a 45% reduction in cell wall thickness. CapD affects wza expression in the capsule polysaccharide synthesis pathway. Furthermore, the survival rates were significantly reduced in ΔcapD in response to complement-mediated killing, desiccation stress, and macrophage phagocytosis, whereas biofilm formation, surface hydrophobicity, and adherence to both endothelial and epithelial cells were increased. Additionally, the deletion of capD sharply attenuated the virulence of E. miricola in a frog infection model. Complementation of the capD gene restored the biological properties and virulence to wild-type levels. Overall, these findings suggest that CapD contributes to polysaccharide synthesis and plays a crucial role in the pathogenesis of E. miricola.

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

Features of the pathogen and efficacy of drug-resistant tuberculosis treatment

According to the World Health Organization (WHO), nearly 10.6 million new cases of tuberculosis were detected in 2022, indicating an increase of 3.5 % from the reported 10.3 million in 2021. After the COVID-19 pandemic, the incidence of tuberculosis increased by 3.9 % from 2020 to 2022. According to the latest regulatory documents, multidrug-resistant pathogen is diagnosed when any bacteriologic or molecular genetic methods reveal drug resistance of M. Tuberculosis complex at least to isoniazid and rifampicin regardless of resistance to other antituberculosis drugs.With a wide range of virulence genes, the tuberculosis pathogen expresses genes in different phases of infection. Some genes are “switched on” in the early phases and are important for overcoming immune defenses and spreading the pathogen in the host, while others are important for survival in the latent phase. These characteristics of Mycobacterium tuberculosis determine the need for correct and adequate selection of therapy. The problem of diagnostics and treatment of drug-resistant tuberculosis remains extremely urgent. Despite the introduction of new tests for rapid determination of drug susceptibility spectrum of Mycobacterium tuberculosis, the problem of timely and adequate prescription of chemotherapy regimen remains. When selecting therapy, the problem of prescribing a combination of antituberculosis drugs with proven efficacy against M. tuberculosis remains. The need to assess the patient’s comorbid status, which affects the effectiveness of treatment and the occurrence of relapses, remains relevant.Despite the introduction of new tests for rapid determination of the drug susceptibility spectrum of Mycobacterium tuberculosis, the problem of timely and adequate prescription of chemotherapy remains relevant. The problem of prescribing a combination of antituberculosis drugs with proven efficacy against M. tuberculosis remains in the selection of therapy. Currently, the introduction of bedaquiline in therapy regimens is important for improving the effectiveness of tuberculosis treatment. In addition, studies are underway to shorten the duration of therapy for MDR-TB and XDR-TB, which is particularly important for maintaining patient adherence to treatment.

Microbial profile of diabetic foot osteomyelitis from the northwest of England

BackgroundOsteomyelitis of the diabetic foot is a common and challenging complication affecting patients with diabetic foot ulcers and infections. The complexity of these infections lies in their polymicrobial nature, high rates of persistence and recurrence. This study examined the microbiological profile of diabetic foot osteomyelitis from a teaching hospital in Northwest England and their resistance patterns to understand its impact on infection persistence and to direct effective treatment.MethodsA retrospective review of 105 patients who underwent surgical management for diabetic foot osteomyelitis between 2019 and 2024. We analysed three consecutive culture samples for each patient to assess for the microbiological profile and resistance patterns of these infections and to monitor infection recurrence and persistence rates.ResultsA total of 105 patients were identified. Infection eradication was noted in 42% of the cohort, infection persistence in 18%, and late infection recurrence in 40%. Polymicrobial growth was evident in 72% of our study sample. Gram-positive bacteria made up the majority of the bacterial isolates in all 3 culture samples, 74.81% in sample 1, 69.31% in sample 2, and 55.1% in sample 3. Staphylococcus aureus was the most prevalent gram-positive bacteria, at 52.38% in sample 1, 36.19% in sample 2, and 18.09% in sample 3, followed by Haemolytic Streptococcus, Enterococcus and Corynebacterium. The frequently identified gram-negative bacteria were Pseudomonas in sample 1 (7.61%), E. coli and Proteus in sample 2 (5,71%), Pseudomonas and Proteus in sample 3 (2.85%). Gram-positive bacteria were resistant to penicillin and macrolides with resistance of staphylococcus aureus to clarithromycin identified among all 3 culture samples. Gram-negative bacteria were most resistant to amoxicillin. Staphylococcus aureus was responsible for infection persistence in most of our cohort (12/19) 63.15%. Among those patients, Staphylococcus was resistant to clarithromycin in 6 of the cases. The 5-year mortality rate for our study sample was 32.38%.ConclusionThis study highlights the prevalence of polymicrobial growth and multi-drug resistant pathogens in the scope of diabetic foot osteomyelitis. It highlights the predominance of Staphylococcus aureus and its resistant strains among patients affected by diabetic foot osteomyelitis in Greater Manchester.

CRISPR-Cas9-Mediated Targeting of Multidrug Resistance Genes in Methicillin-Resistant Staphylococcus aureus.

Antibiotic resistance poses a global health crisis limiting the efficacy of available therapeutic agents. We explored CRISPR-Cas-based antimicrobials to combat multidrug resistance in methicillin-resistant Staphylococcus aureus (MRSA), targeting methicillin (mecA), gentamicin (aacA), and ciprofloxacin (grlA, grlB) resistance genes. Engineered CRISPR plasmids with specific single-guide RNAs were electroporated into MRSA strains. Real-time polymerase chain reaction assessed gene expression changes, while antibiotic susceptibility tests (ASTs) evaluated resistance status. Results showed a 1.5-fold decrease in mecA, a 5.5-fold decrease in grlA, a 6-fold decrease in grlB, and a 4-fold decrease in aacA expression. ASTs demonstrated the reversal of resistance to beta-lactam, quinolone, and aminoglycoside antibiotics. Western blot analysis revealed a 70% decrease in penicillin-binding protein 2a expression. Sanger sequencing confirmed point mutations in the grlB and aacA genes. Our findings highlight the potential of CRISPR-Cas9 technology to restore antibiotic efficacy against multidrug-resistant pathogens.

Characterization and Differentiation of Candida auris on Dixon’s Agar Using Raman Spectroscopy

Candida auris, an emerging multidrug-resistant fungal pathogen, poses significant challenges in healthcare settings due to its high misidentification rate and resilience to treatments. Despite advancements in diagnostic tools, a gap remains in rapid, cost-effective identification methods that can differentiate C. auris from other Candida species, particularly on non-standard culture media. We used Raman spectroscopy to characterize C. auris grown on modified Dixon’s agar (mDixon) and differentiated it from Candida albicans and Candida parapsilosis. Key Raman spectral markers at 1171 cm−1 and 1452 cm−1, linked to mannan and β-glucan composition, differentiated C. auris into two subgroups, A and B. Despite the spectral similarities of groups A and B with C. albicans and C. parapsilosis, respectively, all Candida species were distinguishable through principal component analysis (PCA). Additionally, this study is the first to demonstrate the distinct spectral signature of mDixon agar, achieved through spatially offset Raman spectroscopy (SORS), which enables accurate discrimination between the culture medium and fungal samples. The observed inter-individual variability within C. auris, coupled with the spectral overlap between C. auris subgroups and other Candida species, highlights a major challenge in differentiating closely related fungi due to their similar molecular composition. Enhancements in spectral resolution and further fluorescence minimization from the culture medium are needed to reliably detect the subtle biochemical differences within these species. Despite these challenges, the results underscore the potential of Raman spectroscopy as a real-time, non-destructive, and complementary tool for fungal pathogen identification.

Comprehensive Approaches to Combatting Acinetobacter baumannii Biofilms: From Biofilm Structure to Phage-Based Therapies

Acinetobacter baumannii—a multidrug-resistant (MDR) pathogen that causes, for example, skin and soft tissue wounds; urinary tract infections; pneumonia; bacteremia; and endocarditis, particularly due to its ability to form robust biofilms—poses a significant challenge in clinical settings. This structure protects the bacteria from immune responses and antibiotic treatments, making infections difficult to eradicate. Given the rise in antibiotic resistance, alternative therapeutic approaches are urgently needed. Bacteriophage-based strategies have emerged as a promising solution for combating A. baumannii biofilms. Phages, which are viruses that specifically infect bacteria, offer a targeted and effective means of disrupting biofilm and lysing bacterial cells. This review explores the current advancements in bacteriophage therapy, focusing on its potential for treating A. baumannii biofilm-related infections. We described the mechanisms by which phages interact with biofilms, the challenges in phage therapy implementation, and the strategies being developed to enhance its efficacy (phage cocktails, engineered phages, combination therapies with antibiotics). Understanding the role of bacteriophages in both biofilm disruption and in inhibition of its forming could pave the way for innovative treatments in combating MDR A. baumannii infections as well as the prevention of their development.

Pioneering Klebsiella Pneumoniae Antibiotic Resistance Prediction With Artificial Intelligence-Clinical Decision Support System-Enhanced Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry: Retrospective Study.

The rising prevalence and swift spread of multidrug-resistant gram-negative bacteria (MDR-GNB), especially Klebsiella pneumoniae (KP), present a critical global health threat highlighted by the World Health Organization, with mortality rates soaring approximately 50% with inappropriate antimicrobial treatment. This study aims to advance a novel strategy to develop an artificial intelligence-clinical decision support system (AI-CDSS) that combines machine learning (ML) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), aiming to significantly improve the accuracy and speed of diagnosing antibiotic resistance, directly addressing the grave health risks posed by the widespread dissemination of pan drug-resistant gram-negative bacteria across numerous countries. A comprehensive dataset comprising 165,299 bacterial specimens and 11,996 KP isolates was meticulously analyzed using MALDI-TOF MS technology. Advanced ML algorithms were harnessed to sculpt predictive models that ascertain resistance to quintessential antibiotics, particularly levofloxacin and ciprofloxacin, by using the amassed spectral data. Our ML models revealed remarkable proficiency in forecasting antibiotic resistance, with the random forest classifier emerging as particularly effective in predicting resistance to both levofloxacin and ciprofloxacin, achieving the highest area under the curve of 0.95. Performance metrics across different models, including accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1-score, were detailed, underlining the potential of these algorithms in aiding the development of precision treatment strategies. This investigation highlights the synergy between MALDI-TOF MS and ML as a beacon of hope against the escalating threat of antibiotic resistance. The advent of AI-CDSS heralds a new era in clinical diagnostics, promising a future in which rapid and accurate resistance prediction becomes a cornerstone in combating infectious diseases. Through this innovative approach, we answered the challenge posed by KP and other multidrug-resistant pathogens, marking a significant milestone in our journey toward global health security.

Discovery of a family of menaquinone-targeting cyclic lipodepsipeptides for multidrug-resistant Gram-positive pathogens

Menaquinone (MK) in bacterial membrane is an attractive target for the development of novel therapeutic agents. Mining the untapped chemical diversity encoded by Gram-negative bacteria presents an opportunity to identify additional MK-binding antibiotics (MBAs). By MK-binding motif searching of bioinformatically predicted linear non-ribosomal peptides from 14,298 sequenced genomes of 45 underexplored Gram-negative bacterial genera, here we identify a novel MBA structural family, including silvmeb and pseudomeb, using structure prediction-guided chemical synthesis. Both MBAs show rapid bacteriolysis by MK-dependent membrane depolarization to achieve their potent activities against a panel of Gram-positive pathogens. Furthermore, both MBAs are proven to be effective against methicillin-resistant Staphylococcus aureus in a murine peritonitis-sepsis model. Our findings suggest that MBAs are a kind of structurally diverse and still underexplored antibacterial lipodepsipeptide class. The interrogation of underexplored bacterial taxa using synthetic bioinformatic natural product methods is an appealing strategy for discovering novel biomedically relevant agents to confront the crisis of antimicrobial resistance.

Cefiderocol in Combating Carbapenem-Resistant Acinetobacter baumannii: Action and Resistance

Acinetobacter baumannii (A. baumannii) has emerged as a prominent multidrug-resistant (MDR) pathogen, significantly complicating treatment strategies due to its formidable resistance mechanisms, particularly against carbapenems. Reduced membrane permeability, active antibiotic efflux, and enzymatic hydrolysis via different β-lactamases are the main resistance mechanisms displayed by A. baumannii, and they are all effective against successful treatment approaches. This means that alternate treatment approaches, such as combination therapy that incorporates beta-lactams, β-lactamase inhibitors, and novel antibiotics like cefiderocol, must be investigated immediately. Cefiderocol, a new catechol-substituted siderophore cephalosporin, improves antibacterial activity by allowing for better bacterial membrane penetration. Due to its unique structure, cefiderocol can more efficiently target and destroy resistant bacteria by using iron transport systems. Through its inhibition of peptidoglycan formation through binding to penicillin-binding proteins (PBPs), cefiderocol avoids conventional resistance pathways and induces bacterial cell lysis. The possibility of resistance development due to β-lactamase synthesis and mutations in PBPs, however, emphasizes the need for continued investigation into cefiderocol’s efficacy in combination treatment regimes. Cefiderocol’s siderophore mimic mechanism is especially important in iron-limited conditions because it can use ferric-siderophore transporters to enter cells. Additionally, its passive diffusion through bacterial porins increases its intracellular concentrations, making it a good option for treating carbapenem-resistant A. baumannii, especially in cases of severe infections and ventilator-associated diseases (IVACs). Cefiderocol may reduce MDR infection morbidity and mortality when combined with customized antimicrobial treatments, but further investigation is needed to improve patient outcomes and address A. baumannii resistance issues.

Correction: Khan et al. Molecular Profiling, Characterization and Antimicrobial Efficacy of Silver Nanoparticles Synthesized from Calvatia gigantea and Mycena leaiana Against Multidrug-Resistant Pathogens. Molecules 2023, 28, 6291

“Iqbal Ahmad Alvi” and “Muhammad Ikram” were not included as authors in the original publication [...]

Highly Effective Modulator Therapy: Implications for the Microbial Landscape in Cystic Fibrosis

Cystic fibrosis (CF) is an autosomal recessive multisystem disorder caused by mutations in the cystic fibrosis conductance regulator (CFTR) anion channel. In the lungs specifically, CFTR mutations lead to changes in mucus viscosity and defective mucociliary clearance. Moreover, people with CF (pwCF) mount an insufficient immune response to invading pathogens, which predisposes individuals to chronic airway disease associated with chronic inflammation, colonization, and recurrent infections by mainly opportunistic pathogens. These chronic infections in the CF lung are typically polymicrobial and frequently harbour multidrug-resistant pathogens, making both treatment and eradication very challenging. During the last decade, the development of highly effective CFTR modulator therapy (HEMT) has led to a breakthrough in treatment options for pwCF. While the majority of pwCF now live longer and have fewer CF exacerbations, colonisation with common respiratory pathogens persists, thereby contributing to chronic inflammation and infection. Interestingly, there are limited reports examining the lung microbiome in the post-modulator era. Since ETI treatment is still quite novel and has only been used for about five years by now, this review will be one of the first discussing the current literature on the effect of ETI on CF pathogens. In addition, we will identify unanswered questions that remain from the effect of HEMT on the CF microbiome.