Article
Microbiology
Mingxing Yang, Dong Liu, Xiaoquan Li, Chuting Xiao, Yingge Mao, Jiaqi He, Jiao Feng, Li Wang
Summary: Gram-negative bacteria producing extended-spectrum beta-lactamase (ESBL) are common and pose a significant threat in both community and hospital settings. This study examined a strain of Escherichia coli isolated from a 7-day-old infant's blood in China, which carried multiple ESBL genes and drug resistance plasmids. The findings suggest that these bacteria are highly resistant to antibiotics and capable of maintaining resistance through chromosomal location of the ESBL genes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
S. Harbaoui, S. Ferjani, M. S. Abbassi, M. Saidani, T. Gargueh, M. Ferjani, Y. Hammi, I Boutiba-Ben Boubaker
Summary: This study aimed to characterize cefotaxime-resistant Enterobacteriaceae (CTX-R-En) isolated from hospitalized children in a Tunisian paediatric ward.
LETTERS IN APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Eva A. Edward, Nelly M. Mohamed, Azza S. Zakaria
Summary: Egypt has recently experienced the emergence of multidrug-resistant Klebsiella pneumoniae, presenting a significant challenge to healthcare. The rapid dissemination of bla(CTX-M) genes, particularly bla(CTX-M-14) and bla(CTX-M-15), among these multidrug-resistant K. pneumoniae has been observed. This study investigates the occurrence of bla(CTX-M-IV) among K. pneumoniae isolates from a major hospital in Alexandria, Egypt. Approximately 22% of the tested isolates were found to carry the bla(CTX-M-IV) gene. Whole genome sequencing revealed the presence of high-risk clone ST383 in one of the isolates, which carried bla(CTX-M-14) on an IncL/M plasmid and bla(CTX-M-15) on a hybrid IncHI1B/IncFIB plasmid. These plasmids showed similarities to those found in other countries such as the UK, Germany, and China. The presence of plasmids with enhanced genetic plasticity poses a significant threat as it allows the evolution of K. pneumoniae isolates causing untreatable infections. Nationwide surveillance is urgently needed to monitor the prevalence of these superbugs with limited treatment options.
Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Martin J. Field
Summary: This paper explores the effectiveness of extending the technique of density fitting to treat interactions with external electrostatic potentials. The study finds that fitted densities can accurately reproduce the energies, forces, and properties obtained using unfitted densities, as long as a suitable operator is employed for the fitting. The precision is expected to improve with the development of basis sets specifically designed for these types of interactions, and the approximation could lead to substantial speed-ups in large hybrid potential simulations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Biochemistry & Molecular Biology
Kevin Clark, Natalia B. Pigni, Kithmini Wijesiri, Jose A. Gascon
Summary: Increased interest in sequencing cyanobacterial genomes has led to the discovery of new homologs to both the N-terminal and C-terminal domains of the Orange Carotenoid Protein (OCP). One of these homologs (HCP2) exclusively binds canthaxanthin and shows a significantly red-shifted absorption spectrum.
Article
Microbiology
Eun-Jeong Yoon, You Jeong Choi, Dokyun Kim, Dongju Won, Jong Rak Choi, Seok Hoon Jeong
Summary: The increasing prevalence of E. coli producing CTX-M ESBL in clinical settings is a major concern due to its significant impact on treatment options. This study investigates the molecular mechanisms of resistance and dissemination of this resistant strain. The unique chromosomal location of the bla(CTX-M) gene and its impact on resistance and fitness cost were evaluated.
MICROBIOLOGY SPECTRUM
(2022)
Review
Biochemistry & Molecular Biology
Brigitta Elsaesser, Peter Goettig
Summary: Experimental evidence for enzymatic mechanisms is often limited and biased by the methods used. Despite apparent contradictions, opposing views often turn out to be special cases of a more comprehensive and superior concept.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Hanshu Fang, Chung-Ho Lee, Huiluo Cao, Shuo Jiang, Simon Yung-Chun So, Cindy Wing-Sze Tse, Vincent Chi-Chung Cheng, Pak-Leung Ho
Summary: The study evaluated the NG-Test(R) CTX-M MULTI lateral flow assay (CTX-M LFA) for rapid detection of CTX-M producers in spiked and clinical blood cultures. The results showed that the CTX-M LFA could accurately detect all CTX-M producers in spiked blood cultures, but false-positive results were observed in clinical blood cultures. Therefore, the CTX-M LFA can provide a reliable and rapid detection method for CTX-M producers in blood cultures.
Article
Infectious Diseases
Elizabeth Liedhegner, Brandon Bojar, Rachelle E. Beattie, Caitlin Cahak, Krassimira R. Hristova, Troy Skwor
Summary: The study highlights the similarity in antibiotic resistance patterns and pathogenic potential between clinical strains and treated effluent E. coli populations, indicating that effluents could serve as a reservoir for future multi-drug resistant E. coli clinical infections.
Article
Infectious Diseases
Mohamed Belmahdi, Nadia Safia Chenouf, Abdelkrim Ait Belkacem, Sandra Martinez-Alvarez, Mario Sergio Pino-Hurtado, Zahra Benkhechiba, Samiha Lahrech, Ahcene Hakem, Carmen Torres
Summary: This study investigates the antimicrobial resistance and virulence threats of Escherichia coli isolates recovered from intestinal and fecal samples of chickens, turkeys, and sparrows. The study finds that sparrows could be a vector in the dissemination of ESBL-producing E. coli isolates to other environments. Additionally, this study reports the first detection of the bla(CTX-M-14) gene from sparrows at a global level and in turkeys in Algeria.
Article
Chemistry, Physical
Sergio Marti, Kemel Arafet, Alessio Lodola, Adrian J. Mulholland, Katarzyna Swiderek, Vicent Moliner
Summary: A simulation study explored the inhibition mechanism of the SARS-CoV-2 main protease, revealing a two-step process strongly influenced by the functional groups in the inhibitors' warheads. The results and methods used in the study can guide the design of efficient inhibitors for the SARS-CoV-2 main protease.
Article
Chemistry, Physical
Sergio Marti, Kemel Arafet, Alessio Lodola, Adrian J. Mulholland, Katarzyna Swiderek, Vicent Moliner
Summary: This study simulated the inhibition mechanism of the main protease of the novel coronavirus, revealing a two-step mechanism for two proposed peptidyl covalent inhibitors.
Article
Nanoscience & Nanotechnology
Nawras Abidi, Stephan N. Steinmann
Summary: Atomistic modeling of electrified interfaces is important in electrocatalysis, corrosion, electrodeposition, batteries, and related devices. The use of grand-canonical density functional theory (GCDFT) with implicit solvation models has become popular. However, the accuracy of these models for solvation effects at interfaces is not well known. Hybrid quantum mechanical/molecular mechanics (QM/MM) models have been proposed as a promising alternative. In this study, we demonstrate the implementation of electrostatic embedding in the VASP code and its application in GCDFT for studying the hydrogen evolution reaction (HER) on MoS2. Our results show that electrostatic embedding has a significant effect on polar sites, while having almost indistinguishable results compared to the implicit solvent for apolar systems.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Physical
Germano Giuliani, Federico Melaccio, Samer Gozem, Andrea Cappelli, Massimo Olivucci
Summary: In this study, replica-exchange molecular dynamics and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics approach were used to model the absorption and fluorescence properties of bacterial luciferin-luciferase. The effect of the protein environment on the fluorophore's excited-state potential energy surface was discussed, as well as the role of the protein in enhancing the fluorescence quantum yield in bacterial bioluminescence.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Medicinal
Ignacio Lizana, Gonzalo A. Jana, Eduardo J. Delgado
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2015)
Article
Chemistry, Multidisciplinary
Ignacio Lizana, Eduardo J. Delgado
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2018)
Article
Biophysics
Ignacio Lizana, Eduardo J. Delgado
BIOPHYSICAL JOURNAL
(2019)
Article
Chemistry, Multidisciplinary
Ignacio Lizana, Diego Ortiz-Lopez, Aleksei Delgado-Hurtado, Eduardo J. Delgado
Article
Chemistry, Physical
Felipe Toledo, Ignacio Lizana, Antonio Buljan, Ximena Zarate, Gina Pecchi, Eduardo J. Delgado
Summary: The adsorption of furfural on SrTiO3 and SrCoxTi1-xO3 perovskites varies depending on the type of isomer present, with cis isomer adsorbing through the interaction of both oxygen atoms and trans isomer interacting only through the carbonyl oxygen. The substitution of titanium by cobalt also significantly affects the adsorption modes, with cis isomer adsorbing through simultaneous interaction with cobalt and titanium atoms and trans isomer adsorbing solely through interaction with cobalt and titanium atoms.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Ignacio Lizana, Elena A. Uribe, Eduardo J. Delgado
Summary: The study addresses the issue of high-level resistance to antibiotics by using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The results show that avibactam inhibits KPC-2 through the formation of a tetrahedral intermediate in acylation and deacylation stages. The calculated activation barriers and rate constants are in good agreement with experimental values, allowing for an accurate estimation of the inhibition constant.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Multidisciplinary Sciences
Ignacio Lizana, Julio Colmenares-Zerpa, Gina Pecchi, R. J. Chimentao, Eduardo J. Delgado
Summary: This theoretical study investigates the dehydration of glycerol over SrTiO3-type perovskite, revealing a four-stage mechanism with the rate-limiting step of 2,3-enol formation. The research provides important theoretical insights for the conversion of glycerol.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Ignacio Lizana, Gina Pecchi, Elena A. Uribe, Eduardo J. Delgado
Summary: This article theoretically studied the inhibitory mechanisms of ETX2514 and avibactam against OXA-24. The results showed that both inhibitors share similar steps and intermediates in the inhibition process, but have different activation barriers. The endocyclic double bond and methyl substituent in the piperidine ring of ETX2514 contribute to its stronger inhibitory ability. Additionally, Lys218 and carboxylated Lys84 of ETX2514 play a crucial role in the mechanism by coordinating their protonation states.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Physical
Omar Alvarado, Ignacio Lizana, Gonzalo Jana, Inaki Tunon, Eduardo Delgado
CHEMICAL PHYSICS LETTERS
(2017)