BioF is a novel B2 metallo-β-lactamase from Pseudomonas sp. isolated from an on-farm biopurification system.
TL;DR: In this article, a new subclass B2 MBL was identified in a new environmental Pseudomonas sp. strain isolated from an on-farm biopurification system (BPS).
Abstract: Antimicrobial resistance represents a major global health concern and environmental bacteria are considered a source of resistance genes. Carbapenems are often used as the last antibiotic option to treat multidrug-resistant bacteria. Metallo-β-lactamases (MBLs) are able to render resistance to almost all β-lactam antibiotics, including carbapenems. Unfortunately, there are no inhibitors against MBLs for clinical use. Subclass B2 MBLs are the only enzymes working as strict carbapenemases, under-represented, encoded in chromosome genes and only functional as mono-zinc enzymes. Despite current efforts in MBLs inhibitor development, B2 carbapenemase activity is especially difficult to suppress, even in vitro. In this study we characterized BioF, a novel subclass B2 MBL identified in a new environmental Pseudomonas sp. strain isolated from an on-farm biopurification system (BPS). Although blaBioF is most likely a chromosomal gene, it is found in a genomic island and may represent a step previous to the horizontal transmission of B2 genes. The new B2 MBL is active as a mono-zinc enzyme and is a potent carbapenemase with incipient activity against some cephalosporins. BioF activity is not affected by excess zinc and is only inhibited at high metal chelator concentrations. The discovery and characterization of B2 MBL BioF as a potent carbapenemase in a BPS bacterial isolate emphasizes the importance of exploring antibiotic resistances existing in the environmental microbiota under the influence of human activities before they could emerge clinically.
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TL;DR: The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine and has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses.
Abstract: The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
21,952 citations
TL;DR: Recommendations of the National Committee for Clinical Laboratory Standards continue to be based on this publication; the “Kirby-Bauer” method is, among the many disk methods used in other countries, still the one that has been researched most thoroughly and updated continuously.
Abstract: In the words of the authors, the paper by A. W. Bauer et al., from the University of Washington in Seattle, on a standardized single-disk method for antibiotic susceptibility testing “. . . consolidate(s) and update(s) previous descriptions of the method and provide(s) a concise outline for its performance and interpretation.” Clinical microbiologists were relieved that finally a disk diffusion method had been standardized, could be used with ease, and provided reliable results as compared with minimum inhibitory concentration tests. The pivotal role of Hans Ericsson’s theoretical and practical studies (H. Ericsson and G. Svartz-Malmberg, Antibiot. Chemother. 6:41–74, 1959), as well as earlier reports by some of the authors of the publications cited, must be mentioned as a matter of fairness. Most of the recommendations given are still valid today even though some of the antimicrobial agents are obsolete, new ones have been added, some zone sizes had to be modified, and new media were designed for Haemophilus influenzae and Neisseria gonorrhoeae. Recommendations of the National Committee for Clinical Laboratory Standards continue to be based on this publication; the “Kirby-Bauer” method is, among the many disk methods used in other countries, still the one that has been researched most thoroughly and updated continuously. ALEXANDER VON GRAEVENITZ
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TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.
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TL;DR: A comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures, which is automated and illustrated by the modelling of trypsin from two other serine proteinases.
12,386 citations
TL;DR: Zdobnov et al. as discussed by the authors proposed a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, and implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs.
Abstract: Motivation Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. Results We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. Availability and implementation Software implemented in Python and datasets available for download from http://busco.ezlab.org. Contact evgeny.zdobnov@unige.ch Supplementary information Supplementary data are available at Bioinformatics online.
7,747 citations