Review
Microbiology
Xiaobing Hu, Yulong Fan, Chengfeng Mao, Hui Chen, Qiang Wang
Summary: Microalgae, a group of organisms capable of producing various useful substances through photosynthesis, can be genetically modified at the molecular level to serve as Chassis Cells for food, medicine, energy, and environmental protection purposes, thus tapping into the benefits of microalgae resources. This manuscript provides theoretical and technical support for the application of transposons in studying microalgae gene function, by summarizing the sequencing method of transposon insertion sites.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Valentine U. Nlebedim, Roy R. Chaudhuri, Kevin Walters
Summary: The study introduces a novel probabilistic Bayesian approach for classifying bacterial essential genes based on Tn5 transposon insertion density. Through analysis of simulated data and three bacterial datasets, the effectiveness of the method is demonstrated with high classification accuracy.
Review
Multidisciplinary Sciences
Hannah R. Noel, Jessica R. Petrey, Lauren D. Palmer
Summary: Pathogenic Acinetobacter species, especially Acinetobacter baumannii, are a major cause of healthcare-associated infections worldwide. These infections are of great concern due to their high levels of multidrug resistance and extensive drug resistance. Genome sequencing and analysis have revealed that bacterial antibiotic resistance is often acquired and spread through the movement of mobile genetic elements.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2022)
Review
Medicine, General & Internal
Remy A. Bonnin, Agnes B. Jousset, Cecile Emeraud, Saoussen Oueslati, Laurent Dortet, Thierry Naas
Summary: Gram-negative bacteria, especially Enterobacterales, play a significant role in global antimicrobial resistance, with resistance potentially affecting all major classes of anti-gram-negative agents and becoming multidrug resistant or even pan-drug resistant. Beta-lactamase-mediated resistance challenges even the most powerful beta-lactams like carbapenems, with dissemination of carbapenemases-encoding genes among Enterobacterales being a major concern. Different classes of carbapenemases, with varying biochemical properties and detection methods, contribute to the genetic diversity of acquired carbapenemases in Enterobacterales.
FRONTIERS IN MEDICINE
(2021)
Article
Genetics & Heredity
Ezequiel G. Mogro, Nicolas M. Ambrosis, Mauricio J. Lozano
Summary: Bacterial genomes consist of core and accessory genomes, with ISs playing a crucial role in genome evolution and adaptability. ISCompare is a new tool that can analyze differentially located ISs in related bacterial strains, providing a quick and simple approach for researchers.
G3-GENES GENOMES GENETICS
(2021)
Article
Biology
Peijun Ma, Lorrie L. He, Alejandro Pironti, Hannah H. Laibinis, Christoph M. Ernst, Abigail L. Manson, Roby P. Bhattacharyya, Ashlee M. Earl, Jonathan Livny, Deborah T. Hung
Summary: Genetic factors such as high-level transposon insertional mutagenesis and a broader spectrum of resistance-conferring mutations have been identified as facilitators for the evolution of carbapenem resistance in Klebsiella pneumoniae. Loss of systems that restrict horizontal resistance gene uptake, such as the CRISPR-Cas system, also play a role in resistance evolution. Consideration of both current and future efficacy of antibiotics, as well as the genetic background and antibiotic identity of clinical isolates, are important determinants of the propensity for resistance development.
Article
Microbiology
Lakshmi Narayanan, Ozan Ozdemir, Navatha Alugubelly, Reshma Ramachandran, Michelle Banes, Mark Lawrence, Hossam Abdelhamed
Summary: The study used Tn mutagenesis to identify genes and pathways affecting the growth and fitness of Listeria monocytogenes in minimal medium. The findings revealed that biosynthesis of purines, pyrimidines, ATP, and branched-chain fatty acids plays an important role in the pathogenesis of L. monocytogenes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Yanan Wang, Fuyi Li, Manasa Bharathwaj, Natalia C. Rosas, Andre Leier, Tatsuya Akutsu, Geoffrey Webb, Tatiana T. Marquez-Lago, Jian Li, Trevor Lithgow, Jiangning Song
Summary: The study introduces DeepBL, a deep learning-based approach for high-throughput prediction of beta-lactamases in bacterial pathogens. The DeepBL models are trained on datasets with varying sequence redundancy levels and performance is extensively evaluated.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Jincao Hu, Jia Li, Chang Liu, Yan Zhang, Hui Xie, Chuchu Li, Han Shen, Xiaoli Cao
Summary: The characteristics of global beta-lactamase-producing Enterobacter cloacae, including distribution of beta-lactamase, sequence types (STs), and plasmid replicons, were analyzed. Almost all E. cloacae strains carried beta-lactamase encoding genes, with bla(CMH) and bla(ACT) being the most predominant bla(AmpC) genes. Various genotypes of carbapenem-hydrolyzing beta-lactamase (CH β Ls) were identified, with bla(VIM) and bla(KPC) being the most dominant. Diverse STs and plasmid replicons were also identified.
Article
Multidisciplinary Sciences
Fatima Aysha Hussain, Javier Dubert, Joseph Elsherbini, Mikayla Murphy, David VanInsberghe, Philip Arevalo, Kathryn Kauffman, Bruno Kotska Rodino-Janeiro, Hannah Gavin, Annika Gomez, Anna Lopatina, Frederique Le Roux, Martin F. Polz
Summary: In marine Vibrio, phage resistance evolves rapidly and leads to differential susceptibility among bacterial strains. This resistance is cumulative, with each bacterial genome carrying multiple defense elements. The fast evolution of these elements decouples phage resistance from other genomic features.
Article
Microbiology
Jennifer M. Colquhoun, Marjan Farokhyfar, Anna R. Hutcheson, Alexander Anderson, Christopher R. Bethel, Robert A. Bonomo, Anthony J. Clarke, Philip N. Rather
Summary: Beta-lactamase expression is the main resistance mechanism in multidrug-resistant Acinetobacter baumannii, with high-level expression occurring in up to 98.5% of modern isolates. Overexpression of OXA-23 beta-lactamase leads to significant changes in peptidoglycan composition, creating new vulnerabilities and potentially novel antimicrobial targets. This study paves the way for new approaches to treating resistant A. baumannii strains.
Article
Biochemical Research Methods
Anna Abramova, Adriana Osinska, Haveela Kunche, Emil Burman, Johan Bengtsson-Palme
Summary: The software package CAFE-Coefficient can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these coefficients.
Article
Microbiology
Supathep Tansirichaiya, Richard N. Goodman, Xinyu Guo, Issra Bulgasim, Orjan Samuelsen, Mohammed Al-Haroni, Adam P. Roberts
Summary: In this study, the researchers aimed to capture mobile genetic elements (MGEs) in clinical Enterobacteriaceae using the pBACpAK entrapment vector. They successfully captured several insertion sequence (IS) elements and novel transposons. By analyzing the transposition activity within the MGE-free recipient, they gained insights into the interaction and evolution of multidrug resistance-conferring MGEs following conjugation. This study provides a platform for studying the factors affecting intracellular transposition and MGE formation in clinically relevant Enterobacteriaceae.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Ying Zhu, Xinmiao Jia, Peiyao Jia, Xue Li, Qiwen Yang
Summary: NDM-29, a novel carbapenemase that can hydrolyze almost all clinically available beta-lactam antibiotics, was discovered in an Escherichia coli in China. The presence of NDM-29 may pose a threat to antimicrobial resistance control and highlights the importance of monitoring bacterial mutations.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Infectious Diseases
Camille Gonzalez, Herve Volland, Saoussen Oueslati, Lea Niol, Camille Legrand, Laura Francius, Arnaud Chalin, Anais Vogel, Stephanie Simon, Thierry Naas
Summary: A LFIA prototype has been developed and evaluated for the rapid and reliable detection of GES-type beta-lactamases. The method is efficient, rapid, and easy to implement, making it suitable for confirmation of GES-type beta-lactamases in clinical microbiology laboratories.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Letter
Infectious Diseases
Sandrine Bernabeu, Remy A. Bonnin, Laurent Dortet
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Agnes B. Jousset, Sandrine Bernabeu, Cecile Emeraud, Remy A. Bonnin, Alexandra Lomont, Jean Ralph Zahar, Audrey Merens, Christophe Isnard, Nathalie Soismier, Eric Farfour, Vincent Fihman, Nicolas Yin, Olivier Barraud, Herve Jacquier, Anne-Gaelle Ranc, Frederic Laurent, Stephane Corvec, Louise Ruffier d'Epenoux, Emmanuelle Bille, Nicolas Degand, Chloe Plouzeau, Thomas Guillard, Vincent Cattoir, Asaf Mizrahi, Antoine Grillon, Frederic Janvier, Cecile Le Brun, Marlene Amara, Mathilda Bastide, Alban Lemonnier, Laurent Dortet
Summary: This study aimed to provide susceptibility data on a large series of Enterobacterales since the revision of EUCAST categorization break-points in 2020. The results showed that Ceftolozane-tazobactam (C/T) had a susceptibility rate of 88% in Enterobacterales infections, with higher susceptibility in 3GC-resistant strains and lower susceptibility in CRE strains. This prospective study highlights the importance of C/T in the treatment of infections.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Article
Microbiology
Otavio Hallal Ferreira Raro, Patrice Nordmann, Manuel Dominguez Pino, Jacqueline Findlay, Laurent Poirel
Summary: There is an increasing occurrence of multidrug-resistant (MDR) and hypervirulent (hv) Klebsiella pneumoniae (MDR-hvKp) convergent clones. These strains can cause difficult-to-treat infections and have a higher mortality rate in healthy adults. This study in Switzerland identified a rate of 9.0% K. pneumoniae with a virulence genotype, producing carbapenemase and recovered from rectal swabs, urine, and blood. The presence of alarming MDR-hvKp and MDR nonhypervirulent K. pneumoniae (MDR-nhv-Kp) isolates highlights the need for surveillance networks to track and monitor their spread.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Jacqueline Findlay, Laurent Poirel, Maxime Bouvier, Valeria Gaia, Patrice Nordmann
Summary: Carbapenem-resistant Enterobacterales, including KPC-producing Klebsiella pneumoniae, pose a major threat to public health due to their rapid spread. Ceftazidime-avibactam, a beta-lactam/beta-lactamase inhibitor combination, has shown excellent activity against multidrug-resistant KPC-producing Enterobacterales strains. However, there is an increasing occurrence of CAZ-AVI-resistant K. pneumoniae isolates, mainly due to the emergence of KPC variants that confer resistance to CAZ-AVI but retain carbapenem resistance.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Letter
Infectious Diseases
Agnes B. Jousset, Corentin Poignon, Seher Yilmaz, Alexandre Bleibtreu, Cecile Emeraud, Delphine Girlich, Thierry Naas, Jerome Robert, Remy A. Bonnin, Laurent Dortet
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Rita Elias, Anton Spadar, Antoni P. A. Hendrickx, Remy A. Bonnin, Laurent Dortet, Margarida Pinto, Jody E. Phelan, Isabel Portugal, Susana Campino, Gabriela Jorge da Silva, Taane G. Clark, Aida Duarte, Joao Perdigao
Summary: This study characterized the genomic diversity and international dissemination of CRKP strains from tertiary care hospitals in Lisbon, Portugal. Two genomic clusters, ST13/GC1 and ST17/GC2, were identified. Additionally, an emerging OXA-181/ST17-producing strain in Portugal and the ongoing international dissemination of a KPC-3/ST13-producing clone were highlighted.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Maxime Bouvier, Auriane Kerbol, Jacqueline Findlay, Samanta Freire, Laurent Poirel, Patrice Nordmann
Summary: Resist Acineto is a novel immunochromatographic test for detecting the major acquired carbapenemases (OXA-23, OXA-40, OXA-58, and NDM) in Acinetobacter spp. This test is rapid and easy to perform, and it has shown excellent specificity and sensitivity with 100% positive and negative predictive values in both cases.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2023)
Article
Infectious Diseases
Jacqueline Findlay, Patrice Nordmann, Maxime Bouvier, Auriane Kerbol, Laurent Poirel
Summary: This study investigated the spread and emergence of A. baumannii clones co-producing OXA-23 and ArmA in Switzerland. The majority of the isolates were obtained from infections and belonged to the high-risk GC-2 clone. Monitoring and control of these MDR A. baumannii strains are crucial to prevent further spread.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Otavio Hallal Ferreira Raro, Maxime Bouvier, Auriane Kerbol, Jean-Winoc Decousser, Laurent Poirel, Patrice Nordmann
Summary: The study developed a rapid test for the detection of Acinetobacter baumannii susceptibility to the antibiotic cefiderocol. The test showed high sensitivity and specificity and significantly reduced the time required compared to current methods.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Patrice Nordmann, Maxime Bouvier, Laurent Poirel
Summary: Carbapenemase-producing Enterobacterales (CPE) are a major health concern globally, with limited therapeutic options in Switzerland. This study evaluated the susceptibility of CPE isolates recovered in Switzerland from 2018 to 2020 to novel β-lactam/β-lactamase inhibitor combinations, including ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam. The majority of clinical CPE isolates were Klebsiella pneumoniae and Escherichia coli, and the distribution of carbapenemases varied. The study found that meropenem-vaborbactam had the highest susceptibility among the three combinations, followed by ceftazidime-avibactam and imipenem-relebactam. These findings can help optimize first-line therapy for CPE infections.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Christophe Le Terrier, Patrice Nordmann, Chloe Buchs, Doris Yoong Wen Di, Gian Maria Rossolini, Roger Stephan, Mariana Castanheira, Laurent Poirel
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Lydia Galvez-Benitez, Jose Manuel Ortiz de la Rosa, Angel Rodriguez-Villodres, Carlos S. Casimiro-Soriguer, Irene Molina-Panadero, Rocio Alvarez-Marin, Remy A. Bonnin, Thierry Naas, Jeronimo Pachon, Jose Miguel Cisneros, Jose Antonio Lepe, Younes Smani
Summary: This study aimed to identify the mechanisms underlying Piperacillin-tazobactam resistance (P/T-R) in Escherichia coli. The results showed that P/T-R isolates had a higher copy number of the bla(TEM) gene, generated by three different genetic events. In addition, reduced expression of OmpC was observed in two P/T-R strains. This study provides important insights into the acquisition of P/T-R in E. coli, which is crucial for effective treatment and prevention of resistant microorganisms.
JOURNAL OF INFECTION
(2023)
Article
Microbiology
Niklas Kroemer, Lisa F. Amann, Aneeq Farooq, Christoph Pfaffendorf, Miklas Martens, Jean-Winoc Decousser, Nicolas Gregoire, Patrice Nordmann, Sebastian G. Wicha
Summary: Rational combination therapy can increase efficacy and prevent the emergence of resistance. This study found that the combination of ceftazidime/avibactam and fosfomycin showed strong synergy in suppressing bacterial count and preventing resistance. Clinical evaluations are needed to explore dose reductions and the use of this combination for highly resistant strains.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Jacqueline Findlay, Roberto Sierra, Otavio Hallal Ferreira Raro, Marta Aires-de-Sousa, Diego O. Andrey, Patrice Nordmann
Summary: This study analysed a collection of E. coli strains harbouring acquired fosA genes and found high-level resistance to fosfomycin. The strains also carried other antibiotic resistance genes and were capable of transmission through conjugation.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Review
Infectious Diseases
Allison M. Hitchcock, Wesley D. Kufel, Keri A. Mastro Dwyer, Eric F. Sidman
Summary: Lenacapavir is a novel HIV-1 treatment option for patients with multidrug-resistant (MDR) HIV-1 infection. It has a favorable pharmacokinetic profile and has shown good tolerability and efficacy in clinical trials.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2024)
Article
Infectious Diseases
Roberta Gagliardini, Alessandro Tavelli, Stefano Rusconi, Sergio Lo Caputo, Vincenzo Spagnuolo, Maria Mercedes Santoro, Andrea Costantini, Alessandra Vergori, Franco Maggiolo, Andrea Giacomelli, Giulia Burastero, Giordano Madeddu, Eugenia Quiros Roldan, Antonella d'Arminio Monforte, Andrea Antinori, Alessandro Cozzi-Lepri
Summary: This study evaluated multiple treatment failures to modern antiretroviral therapy in HIV-infected individuals and found that approximately 4% of them were difficult to treat. The difficult to treat group, compared to the non-difficult to treat group, was characterized by older age, higher prevalence of AIDS, lower CD4+ cell count, and higher risk of treatment failure.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2024)
