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
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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
Co-occurrence of 3 different resistance plasmids in a multi-drug resistant Cronobacter sakazakii isolate causing neonatal infections.
Lining Shi,Quanhui Liang,Zhe Zhan,Jiao Feng,Yachao Zhao,Yong Chen,Mei Huang,Yigang Tong,Weili Wu,Weijun Chen,Xiao-Jun Li,Zhe Yin,Jinglin Wang,Dongsheng Zhou +13 more
TL;DR: This is the first report of fully sequence plasmids in clinical Cronobacter, which provides a deeper insight into plasmid-mediated multi-drug resistance in Cronobacteria from hospital settings.
Journal ArticleDOI
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data.
Tiago F Jesus,Bruno Ribeiro-Gonçalves,Diogo N. Silva,Valeria Bortolaia,Mário Ramirez,João A. Carriço +5 more
TL;DR: By representing the identified hits within the network of relationships between plasmids, allowing the possibility of removing redundant results, and by taking advantage of the browsing capabilities of pATLAS, users can more easily interpret the pipelines’ results.
Journal ArticleDOI
Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics.
TL;DR: Evidence of links linking host-directed therapy with the efflux pump activity to infectious disease is outlined and predictive approaches should be used to determine antimicrobial activities with high pathogen specificity and microbicidal potency.
Journal ArticleDOI
Comparative analysis of KPC-2-encoding chimera plasmids with multi-replicon IncR:Inc pA1763-KPC :IncN1 or IncFII pHN7A8 :Inc pA1763-KPC : IncN1
Daofeng Qu,Yang Shen,Lingfei Hu,Xiaoyuan Jiang,Zhe Yin,Bo Gao,Yuee Zhao,Wenhui Yang,Huiying Yang,Han Jianzhong,Dongsheng Zhou +10 more
TL;DR: It is shown that multiple replicons in coordination with maintenance and conjugation regions of various origins would maintain a broad host range and a stable replication at a steady-state plasmid copy number.
Posted ContentDOI
A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch
Silvia Argimón,Corin A. Yeats,Richard Goater,Khalil Abudahab,Benjamin Taylor,Anthony Underwood,Leonor Sánchez-Busó,Vanessa K. Wong,Zoe A. Dyson,Zoe A. Dyson,Zoe A. Dyson,Satheesh Nair,Se Eun Park,Florian Marks,Andrew J. Page,Jacqueline A. Keane,SD Baker,Kathryn E. Holt,Kathryn E. Holt,Gordon Dougan,David M. Aanensen +20 more
TL;DR: Pathogenwatch democratises genomic epidemiology of S. Typhi by providing an intuitive entry point for the analysis of WGS and linked epidemiological data, enabling international public health monitoring of the emergence and spread of high risk clones.
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.
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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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