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      Identification of a novel aminoglycoside O-nucleotidyltransferase AadA33 in Providencia vermicola

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          Abstract

          A novel chromosome-encoded aminoglycoside O-nucleotidyltransferase AadA33 was identified in Providencia vermicola strain P13. The AadA33 shares the highest amino acid identity of 51.28% with the function characterized AadA31. Antibiotic susceptibility testing and enzyme kinetics analysis revealed that the function of AadA33 is to mediate spectinomycin and streptomycin resistance. The recombinant strain harboring aadA33 (pUCP20- aadA33/ Escherichia coli DH5α) displayed >256- and 128-fold increases in the minimum inhibitory concentration levels to spectinomycin and streptomycin, respectively, compared with the control strains pUCP20/DH5α. Enzyme kinetic parameters manifested the substrate of AadA33 including spectinomycin and streptomycin, with k cat/ K m of 3.28 × 10 4 (M −1 s −1) and 3.37 × 10 4 (M −1 s −1), respectively. Bioinformatics analysis revealed its structural mechanism of antimicrobial resistance, genetic context, and phylogenetic relationship with other aminoglycoside O-nucleotidyltransferases. This study of AadA33 contributed to understanding the function and resistance mechanism of aminoglycoside O-nucleotidyltransferase.

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          Most cited references39

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Prokka: rapid prokaryotic genome annotation.

            T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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              Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

              Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                13 September 2022
                2022
                : 13
                Affiliations
                [1] 1The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University , Wenzhou, China
                [2] 2Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University , Wenzhou, China
                [3] 3Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic , Jinhua, China
                Author notes

                Edited by: Chang-Wei Lei, Sichuan University, China

                Reviewed by: Yingshun Zhou, Southwest Medical University, China; Shangshang Qin, Zhengzhou University, China

                *Correspondence: Qiyu Bao, baoqy@ 123456genomics.cn

                This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2022.990739
                9513248
                7ce8acb7-de1b-4ce7-9b7e-e9f0fa54cd97
                Copyright © 2022 Feng, Gao, Jiang, Shi, Li, Liu, Zhang, Zhang, Li, Lin, Lu, Li, Zhang, Hu, Bao and Lin.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 5, Tables: 6, Equations: 0, References: 40, Pages: 11, Words: 5489
                Funding
                Funded by: Science & Technology Project of Wenzhou City, China
                Award ID: N20210001
                Award ID: Y2020112
                Funded by: Zhejiang Provincial Natural Science Foundation of China
                Award ID: LY19C060002
                Award ID: LQ17H190001
                Funded by: Natural Science Foundation of China , doi 10.13039/501100001809;
                Award ID: 81973382
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                aminoglycoside o-nucleotidyltransferase,aada33,providencia vermicola,enzyme kinetics,novel antimicrobial resistance gene

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