Article
Biochemistry & Molecular Biology
Celia P. F. Domingues, Joao S. Rebelo, Francisco Dionisio, Teresa Nogueira
Summary: Antimicrobial resistance is a significant threat to public health, as excessive use of antibiotics leads to the emergence of multi-drug resistance. Our large-scale analysis of bacterial genomes revealed that over 95% of the genomes contain genes associated with resistance to various antimicrobial classes. Additionally, we found unexpected co-occurrences of resistance genes in plasmids, increasing the potential for resistance dissemination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Martin Klapper, Alexander Huebner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G. Haensch, Shuaibing Zhang, Walid K. Al-Jammal, Harikumar Suma, James A. Fellows Yates, Jasmin Frangenberg, Irina M. Velsko, Somak Chowdhury, Rosa Herbst, Evgeni Bratovanov, Hans-Martin Dahse, Therese Horch, Christian Hertweck, Manuel Ramon Gonzalez Morales, Lawrence Guy Straus, Ivan Vilotijevic, Christina Warinner, Pierre Stallforth
Summary: Major advances in ancient DNA research have allowed access to paleogenomic diversity, however, the functions and capabilities of this genetic material remain largely unknown. In this study, dental calculus samples from ancient humans were examined, leading to the discovery of a biosynthetic gene cluster that produces previously unknown metabolites called paleofurans. This demonstrates the possibility of obtaining natural products from ancient organisms and opens up new opportunities for exploration in this field.
Article
Biochemical Research Methods
Chrispin Chaguza, Gerry Tonkin-Hill, Stephanie W. Lo, James Hadfield, Nicholas J. Croucher, Simon R. Harris, Stephen D. Bentley
Summary: Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, increasing genomic sequence diversity and aiding in adaptation. RCandy is a platform-independent R package designed for rapid, simple, and flexible visualization of recombination events in bacterial genomes, freely available under the MIT license.
Article
Microbiology
Laura Carrilero, Anastasia Kottara, David Guymer, Ellie Harrison, James P. J. Hall, Michael A. Brockhurst
Summary: Plasmids play a crucial role in bacterial evolution by transferring functional genes between lineages, driving genomic diversification. Plasmid coexistence in bacterial genomes is stably maintained through compensatory evolution to reduce fitness costs, unless positive selection for plasmid-borne gene functions is present. Positive selection leads to unstable plasmid coexistence, discriminating between differential fitness benefits of functionally redundant plasmid replicons. This study helps explain the forces structuring bacterial genomes, highlighting the importance of rare positive selection or nonredundancy of accessory gene functions among coexisting plasmids.
Article
Biochemistry & Molecular Biology
Roberta Genova, Pablo Laborda, Trinidad Cuesta, Jose Luis Martinez, Fernando Sanz-Garcia
Summary: Understanding the consequences of drug resistance in bacterial physiology is crucial for exploiting its weaknesses. Collateral sensitivity, a potentially exploitable phenotype, may not be conserved among different isolates. Identifying robust and conserved collateral sensitivity patterns is important for translating this knowledge into clinical practice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Urszula Lapinska, Margaritis Voliotis, Ka Kiu Lee, Adrian Campey, M. Rhia L. Stone, Brandon Tuck, Wanida Phetsang, Bing Zhang, Krasimira Tsaneva-Atanasova, Mark A. T. Blaskovich, Stefano Pagliara
Summary: Phenotypic variations in microbial cells, driven by differences in drug transport rates, play a crucial role in the resistance of microbial pathogens to pharmacotherapies. This study used microfluidics-based single-cell microscopy and fluorescent antibiotic probes to identify phenotypic variants that avoid antibiotic accumulation. Surprisingly, fast growing variants were found to avoid macrolide accumulation and survive treatment without genetic mutations, contrary to current consensus. These fast growing variants also showed higher expression of ribosomal promoters, facilitating essential cellular processes and reducing macrolide accumulation. This new knowledge can be used to develop strategies to overcome antibiotic treatment failures.
Review
Infectious Diseases
Jinzhou Ye, Xinhai Chen
Summary: Infections caused by antibiotic-resistant bacteria are a major global health challenge. This review compiles the most promising strategies currently under development to tackle antibiotic resistance, including the discovery of novel antibiotics, improvement of existing antibiotics, and the development of alternatives to conventional antibiotics. Clinical or preclinical studies show the great potential of these treatments against antibiotic-resistant bacteria, with some products expected to become commercially available soon.
Article
Multidisciplinary Sciences
Marisa Zenaide Ribeiro Gomes, Elisangela Martins J. de Lima, Caio Augusto Martins Aires, Polyana Silva Pereira, Juwon Yim, Fernando Henrique Silva, Caio Augusto Santos Rodrigues, Thamirys Rachel Tavares e Oliveira, Priscila Pinho da Silva, Cristiane Monteiro Eller, Claudio Marcos Rocha de Souza, Michael Rybak, Rodolpho Mattos Albano, Antonio Basilio de Miranda, Edson Machado, Marcos Catanho
Summary: We report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. A target phenotypic profile was detected in 10% of the tested patients, who had epidemiological links and were involved in intractable infections and death.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Fatemeh Sharifi, Yuzhen Ye
Summary: Reverse transcriptases (RTs) play various roles in different systems in prokaryotes, but there is a lack of computational tools for their identification and characterization. Researchers developed a tool called myRT to identify and classify prokaryotic RTs, providing genomic neighborhood information.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Polymer Science
Yufei Zhang, Anran Li, Ye Zhang, Shihao Hong, Yun Xue, Xianhui Song, Jie Li, Siyuan Huang, Xinge Zhang
Summary: This study presents a promising nanocomposite for the treatment of bacterial keratitis. The nanocomposite effectively binds to bacteria and retains drugs on the ocular surface, leading to rapid bacterial killing and inhibition of bacterial growth. It also exhibits superior drug delivery capabilities and anti-inflammatory effects, suggesting potential clinical applications.
MACROMOLECULAR RAPID COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Juan A. Bonachela, Melinda Choua, Michael R. Heath
Summary: Viruses play critical roles in the dynamics of microbial communities, and their interactions with microbes are influenced by physiological, ecological, and evolutionary responses. This study explores the effects of viral plasticity on host cell size, infection time, and coevolution in a microbe-virus system. The results show that different nutrient conditions can lead to changes in host quality, infection productivity, and viral influence on host evolution. Including viral plasticity in models of host-virus dynamics improves predictability and understanding of eco-evolutionary dynamics.
Article
Multidisciplinary Sciences
Qian Li, Shang Chen, Kui Zhu, Xiaoluo Huang, Yucheng Huang, Zhangqi Shen, Shuangyang Ding, Danxia Gu, Qiwen Yang, Hongli Sun, Fupin Hu, Hui Wang, Jiachang Cai, Bing Ma, Rong Zhang, Jianzhong Shen
Summary: Acquisition of resistance to one antibiotic can sometimes increase susceptibility to a second antibiotic. In this study, it was found that vancomycin-resistant Enterococcus faecium strains showed remarkable increase in susceptibility to pleuromutilin antibiotics (such as lefamulin). The trade-off between vancomycin and pleuromutilins is mediated by epistasis between van gene cluster and msrC, suggesting pleuromutilins may be useful in treating vancomycin-resistant E. faecium infections.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jiao Liu, Xiao Zhang, Pengfei Zou, Jiahui Yao, Lingling Liu, Yun Cai, Tongyi Sun, Yuanyuan Gao, Li-Li Li
Summary: Antibiotic resistance is a serious threat to public health. Researchers have developed nano-antibiotic transformers that enhance the effectiveness of antibiotics and effectively clear bacterial infections.
Article
Environmental Sciences
Han Xu, Zeyou Chen, Xinyan Wu, Lin Zhao, Nan Wang, Daqing Mao, Hongqiang Ren, Yi Luo
Summary: The addition of foreign antibiotic-resistance bacteria increased the diversity and niche breadth of the soil bacterial community, altered its composition and structure. Tetracycline contamination may further enhance these impacts, and the effects of foreign ARB on the soil bacterial community lasted longer than their survival time, potentially challenging the stability of the soil bacterial community.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Chemistry, Multidisciplinary
Haolu Hu, Xiaoxia Kang, Zhenhua Shan, Xiaoxiao Yang, Wei Bing, Li Wu, Haiyan Ge, Haiwei Ji
Summary: The construction of multifunctional nano-enzymes is a feasible strategy for fighting multi-drug resistant bacterial biofilm infections. We have developed a graphene oxide-based nano-enzyme platform that can effectively eradicate drug-resistant bacterial biofilm infections through the triple action of enzyme properties, photothermal therapy, and antimicrobial activity.
Article
Biochemistry & Molecular Biology
Ayari Fuentes-Hernandez, Jessica Plucain, Fabio Gori, Rafael Pena-Miller, Carlos Reding, Gunther Jansen, Hinrich Schulenburg, Ivana Gudelj, Robert Beardmore
Article
Biochemistry & Molecular Biology
Robert Eric Beardmore, Rafael Pena-Miller, Fabio Gori, Jonathan Iredell
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Biochemistry & Molecular Biology
Fabio Gori, Susannah Green Tringe, Boran Kartal, Elena Marchiori, Mike S. M. Jetten
BIOCHEMICAL SOCIETY TRANSACTIONS
(2011)
Article
Biochemical Research Methods
Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, Elena Marchiori
Article
Biotechnology & Applied Microbiology
Fabio Gori, Susannah G. Tringe, Gianluigi Folino, Sacha A. F. T. van Hijum, Huub J. M. Op den Camp, Mike S. M. Jetten, Elena Marchiori
Article
Multidisciplinary Sciences
Rafael Pena-Miller, Ayari Fuentes-Hernandez, Carlos Reding, Ivana Gudelj, Robert Beardmore
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2014)
Article
Biochemistry & Molecular Biology
Carlos Reding, Pablo Catalan, Gunther Jansen, Tobias Bergmiller, Emily Wood, Phillip Rosenstiel, Hinrich Schulenburg, Ivana Gudelj, Robert Beardmore
Summary: The study found that the fastest evolution of erythromycin resistance occurred at a dosage just below the minimal inhibitory concentration. Molecular mechanisms responsible for this phenomenon were identified through whole genome sequencing, revealing a dose-dependent pattern in the resistance mechanisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)