For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
14
views
104
references
 Top references
cited by
13
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      227
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Graphical abstract

          Abstract

          The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the bla OXA-23 gene, while certain isolates harbored the bla NDM-1 or bla IMP-14 genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., armA, aph(6)-Id, and aph(3″)-Ib), fosfomycin resistance gene ( abaF), and tetracycline resistance genes ( tet(B) and tet(39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the ompA, adeF, pgaA, lpxA, and bfmR genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections.

          Related collections

          Most cited references104

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
          Article 0 comments Cited 7804 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

            Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
            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.
            Article 0 comments Cited 6728 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              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.
              Article 0 comments Cited 4957 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Kamonnut Singkhamanan
                Virasakdi Chongsuvivatwong
                Prasit Palittapongarnpim
                Rattanaruji Pomwised
                Mingkwan Yingkajorn
                Sarunyou Chusri
                Komwit Surachat
                Journal
                Journal ID (nlm-ta): Comput Struct Biotechnol J
                Journal ID (iso-abbrev): Comput Struct Biotechnol J
                Title: Computational and Structural Biotechnology Journal
                Publisher: Research Network of Computational and Structural Biotechnology
                ISSN (Electronic): 2001-0370
                Publication date PMC-release: 06 January 2022
                Publication date Collection: 2022
                Publication date (Electronic): 06 January 2022
                Volume: 20
                Pages: 545-558
                Affiliations
                [a ]Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
                [b ]Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
                [c ]Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
                [d ]Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
                [e ]Department of Microbiology, Fujita Health University, Aichi, Japan
                [f ]Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
                [g ]Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
                [h ]Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
                [i ]Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
                [j ]Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
                Author notes
                [* ]Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand. sarunyouchusri@ 123456hotmail.com komwit.s@ 123456psu.ac.th
                Article
                Publisher Item ID: S2001-0370(22)00001-0
                DOI: 10.1016/j.csbj.2021.12.038
                PMC ID: 9582705
                PubMed ID: 36284706
                SO-VID: c530497a-b9c6-4722-be6c-11bfb1d73cb1
                Copyright © © 2022 The Author(s)
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 16 September 2021
                Date revision received : 25 December 2021
                Date accepted : 30 December 2021
                Categories
                Subject: Research Article

                Keywords: carbapenem-resistant acinetobacter baumannii (crab),whole-genome sequencing (wgs),bioinformatics tool,sequence type (st),antimicrobial resistance (amr) gene,mobile genetic element (mge)
                Data availability:
                Keywords: carbapenem-resistant acinetobacter baumannii (crab), whole-genome sequencing (wgs), bioinformatics tool, sequence type (st), antimicrobial resistance (amr) gene, mobile genetic element (mge)

                Comments

                Comment on this article

                scite_

                Similar content227

                See all similar

                Cited by13

                See all cited by

                Most referenced authors6,208

                See all reference authors