Article
Microbiology
Barbora Trubenova, Dan Roizman, Jens Rolff, Roland R. Regoes
Summary: The resistance of biofilms to antimicrobials is a complex phenomenon involving genetic, physical, and physiological changes as well as increased genetic diversity. A polygenic model has been developed to account for multiple phenotypic mechanisms and can be used to predict the emergence of resistance and its population genetic consequences.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Indorica Sutradhar, Carly Ching, Darash Desai, Mark Suprenant, Emma Briars, Zachary Heins, Ahmad S. Khalil, Muhammad H. Zaman
Summary: A mathematical model was developed to predict the growth of antibiotic-resistant populations in wastewater, showing that low levels of antibiotic residues and horizontal gene transfer are key factors in resistance acquisition. Additionally, synergistic antibiotics at low concentrations were found to lead to increased resistant population growth.
Review
Infectious Diseases
Scott W. Olesen
Summary: This article reviews the strengths and limitations of models of antibiotic resistance and discusses their possible applications in the context of mass drug administration with azithromycin.
INFECTIOUS DISEASES OF POVERTY
(2022)
Article
Biotechnology & Applied Microbiology
Jessica Subirats, Hannah Sharpe, Domenico Santoro, Edward Topp
Summary: It is generally believed that antibiotics provide producing bacteria with a competitive advantage by inhibiting or killing neighboring microorganisms. However, modeling studies have shown that the concentrations of antibiotics near single producing cells are not high enough to have inhibitory effects, while concentrations around aggregates of cells can reach inhibitory levels.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Jessica D. Podoll, Emma Rosen, Wei Wang, Yuefeng Gao, Jing Zhang, Xiang Wang
Summary: Novel antibacterial agents are urgently needed to combat antibiotic resistance. Researchers have discovered a small molecule that can make methicillin-resistant Staphylococcus aureus sensitive to beta-lactam antibiotics again, with low potential for resistance development. This molecule, known as trypyricins, belongs to a new class of broad-spectrum antibacterials and shows promise as an antibiotic adjuvant in fighting resistant bacteria.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Engineering, Biomedical
Zhiyong Chen, Cailing Zhou, Yangfan Xu, Kang Wen, Junfeng Song, Silei Bai, Chenxuan Wu, Wei Huang, Qingyun Cai, Kai Zhou, Hui Wang, Yingjie Wang, Xinxin Feng, Yugang Bai
Summary: The increasing number of infections caused by multi-drug resistance (MDR) bacteria indicates a new global challenge. Antimicrobial peptides (AMPs) and AMP mimics are emerging as effective agents due to their low resistance rate and effectiveness against MDR strains. A novel oligomer with an alternatingly amphiphilic structure and affinity for bacterial DNA demonstrates high therapeutic index and in vivo activity, showing potential as a resistance-resistant and selective antimicrobial agent.
Review
Pharmacology & Pharmacy
Thiago H. da Silva, Timothy Z. Hachigian, Jeunghoon Lee, Matthew D. King
Summary: This article provides an overview of the current use of computational methods, such as machine learning and deep learning, in drug discovery. The development of quantum computing and its limitations in computational drug discovery are also discussed.
DRUG DISCOVERY TODAY
(2022)
Article
Microbiology
Emily E. Whittle, Helen E. McNeil, Eleftheria Trampari, Mark Webber, Tim W. Overton, Jessica M. A. Blair
Summary: Efflux is important for maintaining low intracellular accumulation only in actively growing cells, while envelope permeability is the predominant factor in stationary-phase cells. This study suggests that antibiotics with intracellular targets may be less effective in complex infections with nongrowing or slow-growing bacteria, and efflux inhibitors may potentiate the activity of existing antibiotics in actively growing bacterial infections. The remodeling of the cell envelope prior to stationary phase could provide novel drug targets.
Article
Biochemistry & Molecular Biology
Sandra Cisneros-Mayoral, Lucia Grana-Miraglia, Deyanira Perez-Morales, Rafael Pena-Miller, Ayari Fuentes-Hernandez
Summary: Bacterial adaptation to stressful environments often imposes evolutionary constraints on resistance increases. Exploiting the resistance-cost trade-off is proposed as the basis for antimicrobial treatment strategies to limit the evolution of drug resistance. Recent studies have shown that fluctuating selection can maintain drug efficacy, restore drug susceptibility, but also promote cross-resistance to other antibiotics. This paper combines mathematical modeling, experimental evolution, and whole-genome sequencing to study beta-lactam resistance under fluctuating selective conditions. The results reveal the contingencies of resistance adaptation on the strength of selection and prior drug exposures.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Information Systems
Ignacio Perez-Hurtado, David Orellana-Martin, Miguel A. Martinez-del-Amor, Luis Valencia-Cabrera, Agustin Riscos-Nunez
Summary: This paper presents the challenges of validating and testing P system models in membrane computing and proposes a new design of the P-Lingua language that allows users to define custom variants and derivation modes, among other improvements. It also includes a set of command-line tools for parsing and simulating P-Lingua 5 files.
INFORMATION SCIENCES
(2022)
Review
Multidisciplinary Sciences
Craig R. R. MacNair, Man-Wah Tan
Summary: The survival of bacteria during antibiotic exposure is a complex phenomenon, and bacterial membrane vesicles (MVs) play a significant role as a protective layer. MVs not only reduce the efficacy of antibiotics, but also transmit resistance elements, making them a potential target for unconventional therapy.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Physics, Multidisciplinary
Ulas Hurdoganoglu, Bilgen Kaymakamzade, Nazife Sultanoglu, Emrah Guler, Evren Hincal, Kaya Suer
Summary: Antibiotic resistance poses a threat to global health, with Escherichia coli being a representative bacterium. Using a mathematical model and patient data, this study evaluates the dynamics of ESBL-producing and non-ESBL-producing E. coli infections, and predicts future trends.
Article
Computer Science, Information Systems
Petr Sosik, Max Garzon, Vladimir Smolka, Jan Drastik
Summary: This study explores novel approaches to morphogenetic processes, focusing on geometry and form, with properties such as computational universality, homeostasis, self-reproduction and self-healing. By refining the M systems model and demonstrating its computational universality and capability to solve NP-hard problems, as well as exhibiting macro-properties characteristic of living organisms, this research provides a new theoretical background for modeling complex structures and behaviors. The results obtained using an M system simulator suggest the potential applications of these extended models in various fields of research.
INFORMATION SCIENCES
(2021)
Article
Engineering, Environmental
Yan Wang, Xiaoyu Ni, Xuan Hou, Defang Ma, Bo Zhang, Qian Li, Baoyu Gao
Summary: An electrified carbon nanotube membrane combined with chlorine disinfection was developed to effectively eradicate antibiotic-resistant bacteria and damage antibiotic resistance genes in water samples, providing a potential method for water and sewage treatment plants.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Environmental Sciences
Wilai Chiemchaisri, Chart Chiemchaisri, Chayanid Witthayaphirom, Chitsuphang Saengam, Kanchanarin Mahavee
Summary: The study investigated the resistance alteration of antibiotic-resistant bacteria (ARB) in aging sludge of a membrane bioreactor (MBR) compared to wastewater. The results showed a significant reduction in ARB population in the MBR-aged sludge, possibly due to high dissolved oxygen levels and prolonged sludge age, highlighting the potential of reducing ARB population through appropriate MBR operation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Infectious Diseases
Andrea Garcia-Caballero, Juan de Dios Caballero, Ainhize Maruri, Maria Isabel Serrano-Tomas, Rosa del Campo, Maria Isabel Morosini, Rafael Canton
Summary: FOX DD and MicroScan-WalkAway (R) show high sensitivity and specificity for MRSA detection among CF isolates, with ChromIDTM-MRSA having excellent sensitivity but poorer specificity for CF isolates. The study suggests using FOX DD and MicroScan-WalkAway (R) to confirm ChromIDTM-MRSA positive CF cultures.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2022)
Article
Endocrinology & Metabolism
O. Contreras-Rodriguez, M. Arnoriaga-Rodriguez, R. Miranda-Olivos, G. Blasco, C. Biarnes, J. Puig, J. Rivera-Pinto, M. L. Calle, V Perez-Brocal, A. Moya, C. Coll, L. Ramio-Torrenta, C. Soriano-Mas, J. M. Fernandez-Real
Summary: The study found that obesity and gut dysbiosis can lead to structural changes in hypothalamic networks, further affecting executive function and depressive symptoms.
INTERNATIONAL JOURNAL OF OBESITY
(2022)
Review
Microbiology
Christian G. Giske, John Turnidge, Rafael Canton, Gunnar Kahlmeter
Summary: EUCAST is an international committee focused on susceptibility testing, aiming to harmonize clinical breakpoints in Europe and beyond. Its activities include collecting MIC distribution data, developing software, identifying epidemiological cutoff values, and creating testing methods. EUCAST's decisions are subject to public consultation, except for breakpoints of new antimicrobial agents.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Infectious Diseases
Sergio Garcia-Fernandez, Patricia J. Simner, Gina Thomson, Matthew Faron, Ron Bosboom, Arjanne van Griethuijsen, Maria Garcia-Castillo, Renee Harris, Nathan A. Ledeboer, Rafael Canton, Kenneth S. Thomson
Summary: The new BD MAX Check-Points CPO assay showed good performance in detecting KPC and OXA-48 genes, while data on VIM/IMP and NDM tests were insufficient. This detection method can rapidly and accurately identify the most common CPO infections.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2022)
Article
Immunology
Jose Avendano-Ortiz, Manuel Ponce-Alonso, Emilio Llanos-Gonzalez, Hugo Barragan-Prada, Raquel Barbero-Herranz, Roberto Lozano-Rodriguez, Francesc J. Marquez-Garrido, Jose Maria Hernandez-Perez, Maria-Isabel Morosini, Rafael Canton, Rosa del Campo, Eduardo Lopez-Collazo
Summary: We investigated the effects of different lipopolysaccharide (LPS) modifications on colistin resistance and found that adding Ara4N to LPS increases the survival of Klebsiella pneumoniae in the human body and elicits a stronger inflammatory response.
INFECTION AND IMMUNITY
(2023)
Article
Genetics & Heredity
Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed, Ricardo Futami, Raquel Ceprian, Ricardo Ramos-Ruiz, Genis Martinez, Francisco Jose Roig, Miguel Angel Torres-Font, Fernando Naya-Catala, Josep Alvar Calduch-Giner, Lucia Trilla-Fuertes, Angelo Gamez-Pozo, Vicente Arnau, Jose Maria Sempere-Luna, Jaume Perez-Sanchez, Toni Gabaldon, Carlos Llorens
Summary: The GPRO suite is an ongoing bioinformatic project for the analysis of -omics data. It introduces a client- and server-side solution for comparative transcriptomics and variant analysis. The client-side includes two Java applications, RNASeq and VariantSeq, which manage pipelines and workflows using common command line tools. The server-side, named GPRO Server-Side, hosts all dependencies and requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The solution offers both desktop and web applications, with step-by-step and pipeline modes for execution. It also features an experimental support system called GENIE, with a chatbot assistant and expert system for troubleshooting and recommendations.
Article
Public, Environmental & Occupational Health
Friederike Maechler, Frank Schwab, Sonja Hansen, Michael Behnke, Marc J. Bonten, Rafael Canton, Cristina Diaz Agero, Carolina Fankhauser, Stephan Harbarth, Benedikt D. Huttner, Axel Kola, Petra Gastmeier
Summary: This study aimed to quantify the time delay between screening and initiation of contact isolation for carriers of ESBL-E. The results showed that despite extensive surveillance screening, almost one-third of ESBL-E carriers were not isolated, impeding timely implementation of targeted contact isolation.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Infectious Diseases
Juan Antonio Castillo-Polo, Marta Hernandez-Garcia, Maria Isabel Morosini, Blanca Perez-Viso, Cruz Soriano, Raul De Pablo, Rafael Canton, Patricia Ruiz-Garbajosa
Summary: The study aimed to describe the phenotypic and genotypic characteristics of ceftazidime/avibactam- and cefiderocol-resistant KPC-Klebsiella pneumoniae (KPC-Kp) during an outbreak in a medical ICU. The KPC-Kp isolates involved in the outbreak were found to belong to the high-risk clone ST307 and carried the KPC + CTX-M-15 genes. Cloning experiments showed that specific gene mutations may contribute to resistance to ceftazidime/avibactam and cefiderocol.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Review
Microbiology
Teresa M. Coque, Rafael Canton, Ana Elena Perez-Cobas, Miguel D. Fernandez-de-Bobadilla, Fernando Baquero
Summary: Antimicrobial resistance (AMR) is a global health challenge that has been studied and approached from various perspectives, including patient safety, molecular epidemiology, public health, health economics, community psychology, and history of science. However, there is a lack of dialogue between different stakeholders, hindering the development and implementation of effective strategies to combat AMR.
Review
Biology
Rebeca de la Fuente, Wladimiro Diaz-Villanueva, Vicente Arnau, Andres Moya
Summary: Genomic signature refers to characteristics associated with DNA sequences, which can be used to analyze genotype-phenotype patterns, identify gene expression profiles, or study statistical properties of DNA sequences. This review performs a bibliometric analysis to identify the main genomic signatures and categorizes them according to their conceptual meanings. It highlights the importance of genomic signatures in evolutionary biology.
Article
Infectious Diseases
Rafael Canton, Thomas Gottlieb, Geoffrey W. Coombs, Patrick C. Y. Woo, Tony M. Korman, Maria Garcia-Castillo, Denise Daley, Karri A. Bauer, Michael Wong, Dominik J. Wolf, Fakhar Siddiqui, Mary Motyl
Summary: Antimicrobial resistance (AMR) is a major global public health threat, particularly affecting patients in resource-poor settings. Various surveillance programs exist worldwide, and one of the largest is the SMART program, which has been running for 20 years. The SMART database includes data from nearly 500,000 isolates from over 60 countries, and can help monitor and guide clinical treatment.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2023)
Article
Genetics & Heredity
Beatriz Soriano, Ahmed Ibrahem Hafez, Fernando Naya-Catala, Federico Moroni, Roxana Andreea Moldovan, Socorro Toxqui-Rodriguez, Maria Carla Piazzon, Vicente Arnau, Carlos Llorens, Jaume Perez-Sanchez
Summary: This paper introduces SAMBA, a computational tool that uses a Bayesian network approach to model the network structure and interactions of fish gut microbiomes in aquaculture systems. SAMBA can infer the influence of farming conditions on microbiome diversity and predict changes under different conditions. It is worth noting that SAMBA can be used for modeling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.
Review
Medicine, General & Internal
Francisco Javier Candel, Miguel Salavert, Miren Basaras, Marcio Borges, Rafael Canton, Emilia Cercenado, Catian Cilloniz, Angel Estella, Juan M. Garcia-Lechuz, Jose Garnacho Montero, Federico Gordo, Agustin Julian-Jimenez, Francisco Javier Martin-Sanchez, Emilio Maseda, Mayra Matesanz, Rosario Menendez, Manuel Miron-Rubio, Raul Ortiz de Lejarazu, Eva Polverino, Pilar Retamar-Gentil, Luis Alberto Ruiz-Iturriaga, Susana Sancho, Leyre Serrano
Summary: This paper reviews important issues in the approach to community-acquired pneumonia, including updates in etiology, diagnostic guidance, treatment, management, and prevention.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Health Care Sciences & Services
Miquel Angel Sastre-Femenia, Almudena Fernandez-Munoz, Maria Antonia Gomis-Font, Biel Taltavull, Carla Lopez-Causape, Jorge Arca-Suarez, Luis Martinez-Martinez, Rafael Canton, Nieves Larrosa, Jesus Oteo-Iglesias, Laura Zamorano, Antonio Oliver
Summary: A high-resolution analysis of resistance patterns, genomic epidemiology, and resistome of Pseudomonas aeruginosa in Spain over a five-year period reveals a general decrease in resistance but an increase in the proportion of XDR strains producing carbapenemases, with the high-risk clone ST235 becoming more prevalent.
LANCET REGIONAL HEALTH-EUROPE
(2023)