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      Glimpse into the genome sequence of a multidrug-resistant Acinetobacter pittii ST950 clinical isolate carrying the bla OXA-72 and bla OXA-533 genes in China

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          Abstract

          The development of carbapenem-resistant Acinetobacter species is of serious concern in the hospital settings and naturally occurring oxacillinase genes ( bla OXA) have been identified in several Acinetobacter species. In this study, we report the genome sequence of A. pittii TCM178 belongs to ST950, a multidrug-resistant isolate that harbored the bla OXA-72 and bla OXA-533 genes simultaneous. The genome size was estimated to be 3,789,564 bp with 3,501 predicted coding regions, and G+C content is 37.60%. Our findings have raised awareness of the possible constitution of a reservoir for peculiar carbapenemase genes in A. pittii that may spread among other Acinetobacter species in China.

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          ISfinder: the reference centre for bacterial insertion sequences

          P. Siguier, J. Perochon, L. Lestrade … (2005)
          ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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            OXA β-lactamases.

            Benjamin Evans, Sebastian Amyes (2014)
            The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.
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              WebMGA: a customizable web server for fast metagenomic sequence analysis

              Sitao Wu, Zhengwei Zhu, Liming Fu … (2011)
              Background The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. Results We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis. Conclusions WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mem Inst Oswaldo Cruz
                Journal ID (iso-abbrev): Mem. Inst. Oswaldo Cruz
                Journal ID (publisher-id): mioc
                Title: Memórias do Instituto Oswaldo Cruz
                Publisher: Instituto Oswaldo Cruz, Ministério da Saúde
                ISSN (Print): 0074-0276
                ISSN (Electronic): 1678-8060
                Publication date (Print and electronic): October 2017
                Publication date (Print): October 2017
                Volume: 112
                Issue: 10
                Pages: 723-727
                Affiliations
                [1 ]Zhejiang University, School of Medicine, Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Hangzhou, Zhejiang, China
                [2 ]The First Affiliated Hospital of Zhejiang Chinese Medical University, Department of General Practice, Hangzhou, Zhejiang, China
                [3 ]The Affiliated Hospital of Hangzhou Normal University, Department of Respiratory Diseases, Hangzhou, Zhejiang, China
                Author notes
                [+ ] Corresponding author: 2001m@ 123456163.com

                AUTHORS’ CONTRIBUTION

                ZR and JFW designed and coordinated all the experiments; YC and JFW performed cultivation, DNA extraction and purification; ZR performed the genome assembly, gene prediction, gene annotation and comparative genomic analysis; ZR and JFW drafted the manuscript. All authors participated in data interpretation and manuscript preparation, provided essential reagents, read and approved the final manuscript.

                Article
                Publisher ID: 0074-02760170019
                DOI: 10.1590/0074-02760170019
                PMC ID: 5607522
                PubMed ID: 28954001
                SO-VID: 5490146b-f6fa-4533-9248-99421fe8a43b
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 19 January 2017
                Date accepted : 11 May 2017
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 21, Pages: 5
                Categories
                Subject: Short Communication

                Keywords: acinetobacter pittii,blaoxa-72,blaoxa-533
                Data availability:
                Keywords: acinetobacter pittii, blaoxa-72, blaoxa-533

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