-
Molecular Ecology May 2024Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in the evolution of organisms. Metabolic models with different levels...
Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in the evolution of organisms. Metabolic models with different levels of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) the kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) the rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into the mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relationship of metabolic trade-offs to the classical black box Y-model that provides a conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.
Topics: Biological Evolution; Kinetics; Metabolic Networks and Pathways; Models, Biological
PubMed: 36773330
DOI: 10.1111/mec.16879 -
International Journal of Molecular... Apr 2024Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods... (Review)
Review
Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.
Topics: Fungi; Aerosols; Bacteria; Air Microbiology; Humans; Health Facilities
PubMed: 38673740
DOI: 10.3390/ijms25084154 -
Clinical Epigenetics Jun 2024Gastrointestinal malignancies encompass a diverse group of cancers that pose significant challenges to global health. The major histocompatibility complex (MHC) plays a... (Review)
Review
BACKGROUND
Gastrointestinal malignancies encompass a diverse group of cancers that pose significant challenges to global health. The major histocompatibility complex (MHC) plays a pivotal role in immune surveillance, orchestrating the recognition and elimination of tumor cells by the immune system. However, the intricate regulation of MHC gene expression is susceptible to dynamic epigenetic modification, which can influence functionality and pathological outcomes.
MAIN BODY
By understanding the epigenetic alterations that drive MHC downregulation, insights are gained into the molecular mechanisms underlying immune escape, tumor progression, and immunotherapy resistance. This systematic review examines the current literature on epigenetic mechanisms that contribute to MHC deregulation in esophageal, gastric, pancreatic, hepatic and colorectal malignancies. Potential clinical implications are discussed of targeting aberrant epigenetic modifications to restore MHC expression and 0 the effectiveness of immunotherapeutic interventions.
CONCLUSION
The integration of epigenetic-targeted therapies with immunotherapies holds great potential for improving clinical outcomes in patients with gastrointestinal malignancies and represents a compelling avenue for future research and therapeutic development.
Topics: Humans; Gastrointestinal Neoplasms; Epigenesis, Genetic; Major Histocompatibility Complex; Gene Expression Regulation, Neoplastic; Immunotherapy; DNA Methylation; Tumor Escape
PubMed: 38915093
DOI: 10.1186/s13148-024-01698-8 -
The Science of the Total Environment Mar 2024Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions,... (Review)
Review
Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.
Topics: Humans; Drug Resistance, Microbial; Bacteria; Genes, Bacterial; Anti-Bacterial Agents; Metal Nanoparticles
PubMed: 38220012
DOI: 10.1016/j.scitotenv.2024.170080 -
The Science of the Total Environment Jun 2024Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through... (Review)
Review
A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.
Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.
Topics: Wastewater; Anti-Bacterial Agents; Drug Resistance, Microbial; Microalgae; Waste Disposal, Fluid; Bacteria; Metagenomics; Aquaculture; Water Pollutants, Chemical; Symbiosis; Genes, Bacterial
PubMed: 38657817
DOI: 10.1016/j.scitotenv.2024.172601 -
BMC Oral Health Jan 2024Gene sequencing (GS) has numerous applications in combatting oral-cavity related disorders, including identifying genetic risk factors for diseases, developing targeted... (Meta-Analysis)
Meta-Analysis
Gene sequencing (GS) has numerous applications in combatting oral-cavity related disorders, including identifying genetic risk factors for diseases, developing targeted therapies, and improving diagnostic methods. It can help identify specific genetic mutations or variations that increase the risk of developing oral-cavity related disorders, such as oral cancer, periodontal disease, and cleft lip and palate. By the means of the following investigation, our primary objective was to assess the impact of GS technique in diagnosing and potentially treating diseases of the oral cavity by the means of a systematic review and meta-analysis. We commenced by defining the terms "gene sequencing," "oral cavity," and "disorders" as the important elements in our investigation's subject. Next, relevant databases like PubMed, Scopus, Embase, Web of Science, and Google Scholar were searched using keywords and synonyms for each concept, such as "genomic sequencing," "DNA sequencing," "oral health," "oral diseases," "dental caries," "periodontal disease," "oral cancer," and "salivary gland disorders." We combined several search terms, such as "gene sequencing AND oral disorders AND periodontal disease" or "oral cancer OR genomic sequencing," to further hone your search results using Boolean operators like "AND" and "OR." The oral cavity analysis obtained by CS in the selected articles revealed that most of the disorders were, in fact, a direct causal event influenced by the oral microbiome. Moreover, each sampled oral cavity evidenced a different microbial community, which predicted the precipitation of benign as well as malignant conditions, though not on a definitive basis. In the last ten years, genomic sequencing had advanced remarkably as majority of our selected studies observed, making it possible to diagnose and treat a variety of oral and maxillofacial disorders, including cancer. It was also used to ascertain a person's genetic make-up as well as to spot numerous genetic abnormalities that can predispose individuals to diseases. Understanding the different sequencing techniques and the resulting genetic anomalies may help with their clinical application and lead to an improvement in illness diagnosis and prognosis as a whole in the field of dentistry.
Topics: Humans; Dental Caries; Cleft Lip; Cleft Palate; Mouth Diseases; Mouth Neoplasms; Periodontal Diseases
PubMed: 38233799
DOI: 10.1186/s12903-023-03541-7 -
Mycopathologia May 2024The global spread of Trichophyton indotineae presents a pressing challenge in dermatophytosis management. This systematic review explores the current landscape of T.... (Review)
Review
INTRODUCTION
The global spread of Trichophyton indotineae presents a pressing challenge in dermatophytosis management. This systematic review explores the current landscape of T. indotineae infections, emphasizing resistance patterns, susceptibility testing, mutational analysis, and management strategies.
METHODS
A literature search was conducted in November 2023 using Embase, PubMed, Scopus, and Web of Science databases. Inclusion criteria covered clinical trials, observational studies, case series, or case reports with T. indotineae diagnosis through molecular methods. Reports on resistance mechanisms, antifungal susceptibility testing, and management were used for data extraction.
RESULTS AND DISCUSSION
A total of 1148 articles were identified through the systematic search process, with 45 meeting the inclusion criteria. The global spread of T. indotineae is evident, with cases reported in numerous new countries in 2023. Tentative epidemiological cut-off values (ECOFFs) suggested by several groups provide insights into the likelihood of clinical resistance. The presence of specific mutations, particularly Phe397Leu, correlate with higher minimum inhibitory concentrations (MICs), indicating potential clinical resistance. Azole resistance has also been reported and investigated in T. indotineae, and is a growing concern. Nevertheless, itraconazole continues to be an alternative therapy. Recommendations for management include oral or combination therapies and individualized approaches based on mutational analysis and susceptibility testing.
CONCLUSION
Trichophyton indotineae poses a complex clinical scenario, necessitating enhanced surveillance, improved diagnostics, and cautious antifungal use. The absence of established clinical breakpoints for dermatophytes underscores the need for further research in this challenging field.
Topics: Antifungal Agents; Humans; Drug Resistance, Fungal; Mutation; Microbial Sensitivity Tests; Tinea; Trichophyton; Global Health
PubMed: 38734753
DOI: 10.1007/s11046-024-00856-z -
Chemosphere Jun 2024Antibiotic resistance (AR) is considered one of the greatest global threats in the current century, which can only be overcome if all interconnected areas of humans,...
Antibiotic resistance (AR) is considered one of the greatest global threats in the current century, which can only be overcome if all interconnected areas of humans, animals and the environment are taken into account as part of the One Health concept proposed by the World Health Organization (WHO). Water and wastewater are among the most important environmental media of AR sources, where the phenomena are generally non-linear. Therefore, the aim of this study was to investigate the application of machine learning-based methods (MLMs) to solve AR-induced problems in water and wastewater. For this purpose, most relevant databases were searched in the period between 1987 and 2023 to systematically analyze and categorize the applications. Accordingly, the results showed that out of 12 applications, 11 (91.6%) were for shallow learning and 1 (8.3%) for deep learning. In shallow learning category, n = 6, 50% of the applications were regression and n = 4, 33.3% were classification, mainly using artificial neural networks, decision trees and Bayesian methods for the following objectives: Predicting the survival of antibiotic-resistant bacteria (ARB), determining the order of influencing parameters on AR-based scores, and identifying the major sources of antibiotic resistance genes (ARGs). In addition, only one study (8.3%) was found for clustering and no study for association. Surprisingly, deep learning had been used in only one study (8.3%) to predict ARGs sequences. Therefore, working on the knowledge gaps of AR, especially using clustering, association and deep learning methods, would be a promising option to analyze more aspects of the related problems. However, there is still a long way to go to consider and apply MLMs as unique approaches to study different aspects of AR in water and wastewater.
Topics: Wastewater; Machine Learning; Drug Resistance, Microbial; Anti-Bacterial Agents; Bacteria; Bayes Theorem; Neural Networks, Computer; Drug Resistance, Bacterial
PubMed: 38704045
DOI: 10.1016/j.chemosphere.2024.142223 -
Applied Microbiology and Biotechnology May 2024A more optimized culture medium used in vitro to mimic the bacterial composition of original oral flora as similar as possible remains difficult at present, and the goal...
A more optimized culture medium used in vitro to mimic the bacterial composition of original oral flora as similar as possible remains difficult at present, and the goal of this study is to develop a novel oral biofilm medium to restore the original oral microbiome. Firstly, we conducted a systematic literature review by searching PubMed and summarized the current reported culture media in vitro. Seven culture media were found. We used mixed saliva as the origin of oral species to compare the effects of the above media in culturing oral multispecies biofilms. Results indicated that among the seven media brain heart infusion containing 1% sucrose (BHIs) medium, PG medium, artificial saliva (AS) medium, and SHI medium could obviously gain large oral biofilm in vitro. The nutrients contained in different culture media may be suitable for the growth of different oral bacteria; therefore, we optimized several novel media accordingly. Notably, results of crystal violet staining showed that the biofilm cultured in our modified artificial saliva (MAS) medium had the highest amount of biofilm biomass. 16S rRNA gene sequencing showed that the operational taxonomic units (OTUs) and Shannon index of biofilm cultured in MAS medium were also the highest among all the tested media. More importantly, the 16S rRNA gene sequencing analysis indicated that the biofilm cultured in MAS medium was closer to the original saliva species. Besides, biofilm cultured by MAS was denser and produced more exopolysaccharides. MAS supported stable biofilm formation on different substrata. In conclusion, this study demonstrated a novel MAS medium that could culture oral biofilm in vitro closer to the original oral microbiome, showing a good application prospect. KEY POINTS: • We compare the effects of different media in culturing oral biofilms • A novel modified artificial saliva (MAS) medium was obtained in our study • The MAS medium could culture biofilm that was closer to oral microbiome.
Topics: Biofilms; Culture Media; Microbiota; Mouth; Humans; RNA, Ribosomal, 16S; Saliva; Bacteria; Saliva, Artificial
PubMed: 38730049
DOI: 10.1007/s00253-024-13149-8 -
Journal of Global Antimicrobial... Jun 2024Heterogeneous vancomycin-intermediate Staphylococcus aureus is considered one of the main causes in treatment failure of vancomycin, which leads to poor clinical... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Heterogeneous vancomycin-intermediate Staphylococcus aureus is considered one of the main causes in treatment failure of vancomycin, which leads to poor clinical outcomes. Herein, we comprehensively evaluated characteristics such as global prevalence, trend, and genetic backgrounds of these strains.
METHODS
In this study, we conducted a meta-analysis based on PRISMA checklist 2020. In the beginning, global databases were searched to achieve the studies related to the prevalence of hVISA in clinical isolates of methicillin-resistant Staphylococcus aureus. After retrieving the eligible English studies, the prevalence of hVISA isolates and their trend changes were assessed using event rate with 95% confidence intervals.
RESULTS
In the present study, the prevalence of 114 801 MRSA isolates (of 124 studies) was 64%. According to our results, although the frequency of infection with hVISA is increasing in recent years, there is not a significant difference between Asian countries and Europe/America (6.1% vs. 6.8%). In addition, infection with hVISA bacteria was higher in bacteraemic patients than other infections (9.4% vs. 5.5%), which increases hospitalization, treatment costs, and mortality in these patients. Isolates harbouring SCCmec types II and III are most common genotypes in hVISA strains.
CONCLUSIONS
The prevalence of hVISA is increasing, which will reduce the effectiveness of vancomycin treatment in the coming years. The presence of hVISA stains in blood samples was higher than the other samples, which is threatening for bacteraemic patients. The results of the current study indicate a universal program to identify and control the spread of such strains in nosocomial infections.
Topics: Humans; Staphylococcal Infections; Methicillin-Resistant Staphylococcus aureus; Anti-Bacterial Agents; Vancomycin; Prevalence; Vancomycin-Resistant Staphylococcus aureus; Microbial Sensitivity Tests; Vancomycin Resistance; Global Health; Genotype
PubMed: 38336227
DOI: 10.1016/j.jgar.2024.02.002