Identification of acquired antimicrobial resistance genes
Ea Zankari,Henrik Hasman,Salvatore Cosentino,Martin Vestergaard,Simon Rasmussen,Ole Lund,Frank Møller Aarestrup,Mette Voldby Larsen +7 more
TLDR
A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.Abstract:
Objectives
Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.read more
Citations
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Journal ArticleDOI
Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.
Patrick Musicha,Patrick Musicha,Nicholas A. Feasey,Nicholas A. Feasey,Amy K. Cain,Amy K. Cain,Teemu Kallonen,Chrispin Chaguza,Chrispin Chaguza,Chikondi Peno,Margaret Khonga,Sarah Thompson,Katherine J. Gray,Alison E. Mather,Robert S. Heyderman,Robert S. Heyderman,Dean Everett,Dean Everett,Nicholas R. Thomson,Nicholas R. Thomson,Chisomo L. Msefula,Chisomo L. Msefula +21 more
TL;DR: A high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi is revealed, highlighting the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
Journal ArticleDOI
Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae From Whole Genome Sequences.
Liu Zhichang,Deng Dun,Huijie Lu,Jian Sun,Luchao Lv,Li Shuhong,Peng Guanghui,Xianyong Ma,Li Jiazhou,Li Zhenming,Ting Rong,Gang Wang +11 more
TL;DR: Results of correlation between the phenotype and the model predictions of the five drugs indicated that both SVM and SCM models could significantly classify the resistant isolates from the sensitive isolates of the bacteria, and would be used as potential tools in antimicrobial resistance surveillance and clinical diagnosis in veterinary medicine.
Journal ArticleDOI
Investigation of novel pmrB and eptA mutations in isogenic Acinetobacter baumannii isolates associated with colistin resistance and increased virulence in vivo
Stefanie Gerson,Jonathan W. Betts,Kai Lucaßen,Carolina Silva Nodari,Carolina Silva Nodari,Julia Wille,Michaele Josten,Stephan Göttig,Jennifer Nowak,Danuta Stefanik,Ignasi Roca,Jordi Vila,José Miguel Cisneros,Roberto M. La Ragione,Harald Seifert,Paul G. Higgins +15 more
TL;DR: Although the mutations in pmrB were associated with colistin resistance, PEtN addition appears not to be the sole factor leading to colist in resistance, indicating that the mechanism of colistsin resistance is far more complex than previously suspected and is potentially strain specific.
Journal ArticleDOI
Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study.
Bailiang Li,Meng Zhan,Smith Etareri Evivie,Smith Etareri Evivie,Da Jin,Li Zhao,Sathi Chowdhury,Shuvan Kumar Sarker,Guicheng Huo,Fei Liu +9 more
TL;DR: The results indicate that E. durans KLDS6.0930 can be safely used as a potential probiotic for human consumption and animal feed and did not induce adverse effects on the organs, hematological and serum biochemical parameters, or cecal bacterial populations in the oral toxicity test.
Journal ArticleDOI
Tetracycline degradation by Klebsiella sp. strain TR5: Proposed degradation pathway and possible genes involved
TL;DR: The findings showed that strain TR5 could be a promising agent for wastewater treatment, and genes involved in TC degradation are worthy of further investigations for enzyme preparations development.
References
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Journal ArticleDOI
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette Voldby Larsen,Salvatore Cosentino,Simon Rasmussen,Carsten Friis,Henrik Hasman,Rasmus L. Marvig,Lars Jelsbak,Thomas Sicheritz-Pontén,David W. Ussery,Frank Møller Aarestrup,Ole Lund +10 more
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.
Journal ArticleDOI
Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes.
TL;DR: A preliminary assessment of the amino acids which may be important in binding aminoglycosides was obtained from data and from the results of mutational analysis of several of the genes encoding am inoglycoside-modifying enzymes.
Journal ArticleDOI
Acquired Antibiotic Resistance Genes: An Overview
Angela H.A.M. van Hoek,Dik Mevius,Dik Mevius,Beatriz Guerra,Peter Mullany,Adam P. Roberts,Henk Aarts +6 more
TL;DR: Attention is paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
Journal ArticleDOI
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
Lance B. Price,Marc Stegger,Henrik Hasman,Maliha Aziz,Jesper Larsen,Paal Skytt Andersen,Talima Pearson,Andrew E. Waters,Jeffrey T. Foster,James M. Schupp,John D. Gillece,Elizabeth M. Driebe,Cindy M. Liu,Cindy M. Liu,Burkhard Springer,Irena Zdovc,Antonio Battisti,Alessia Franco,Jacek Żmudzki,Stefan Schwarz,Patrick Butaye,Eric Jouy,Constança Pomba,M. Concepción Porrero,Raymond Ruimy,Tara C. Smith,D. Ashley Robinson,J. Scott Weese,Carmen Sofia Arriola,Fangyou Yu,Frédéric Laurent,Paul Keim,Paul Keim,Robert Skov,Frank Møller Aarestrup +34 more
TL;DR: The results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA, which appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance.
Journal ArticleDOI
Comparison of antimicrobial resistance phenotypes and resistance genes in Enterococcus faecalis and Enterococcus faecium from humans in the community, broilers, and pigs in Denmark.
TL;DR: Differences in the occurrence of resistance and tetracycline resistance genes were observed among isolates from the different sources, however, similar resistance patterns and resistant genes were detected frequently indicating that transmission of resistant enterococci or resistance genes takes place between humans, broilers, and pigs.
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