Acinetobacter baumannii is an emerging human pathogen causing nosocomial and  community-acquired infections. Here, we present the complete genome sequence of the  clinical A. baumannii strain R2090 carrying the metallo-β-lactamase gene blaNDM-1 in its  chromosome within the transposon Tn125

Krahn, Thomas

Maus, Irena

Nordmann, Patrice

Poirel, Laurent

Pühler, Alfred

Schlüter, Andreas

Wibberg, Daniel

Winkler, Anika

PubMed

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Complete Genome Sequence of the Clinical Strain Acinetobacterbaumannii R2090 Carrying the Chromosomally Encoded Metallo--Lactamase Gene blaNDM-1Thomas Krahn,a Daniel Wibberg,a Irena Maus,a Anika Winkler,a Patrice Nordmann,b Alfred Pühler,a Laurent Poirel,b Andreas SchlüteraCenter for Biotechnology, Bielefeld University, Bielefeld, Germanya; Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University ofFribourg, Fribourg, SwitzerlandbAcinetobacter baumannii is an emerging human pathogen causing nosocomial and community-acquired infections. Here, wepresent the complete genome sequence of the clinical A. baumannii strain R2090 carrying the metallo--lactamase geneblaNDM-1 in its chromosome within the transposon Tn125.Received 23 July 2015 Accepted 25 July 2015 Published 10 September 2015Citation Krahn T, Wibberg D, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A. 2015. Complete genome sequence of the clinical strain Acinetobacter baumanniiR2090 carrying the chromosomally encoded metallo--lactamase gene blaNDM-1. Genome Announc 3(5):e01008-15. doi:10.1128/genomeA.01008-15.Copyright © 2015 Krahn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Andreas Schlüter, aschluet@cebitec.uni-bielefeld.de.Acinetobacter baumannii is a widespread serious pathogen (1)causing nosocomial infections (2). Also, community-acquired infections initiated by this pathogen feature high mor-tality rates (3). In this study, we present the complete genomesequence of the strain R2090, representing a community-acquiredA. baumannii sequence type.The strain R2090 was recovered from a rectal swab from apatient hospitalized in an Egyptian hospital. It was classified asbelonging to the species A. baumannii, since its 16S rRNA genesequence is identical to the corresponding sequence of theA. bau-mannii type strain ATCC 19606 (4).For the establishment of the A. baumannii R2090 genome se-quence, purified chromosomal DNA was used to construct an8-kb mate pair sequencing library (Nextera mate pair samplepreparation kit, Illumina, Inc.). The sequencing approach on anIlluminaMiSeq system yielded 3,108,361 sequence reads account-ing for 699,271,346 bases sequence information. Thus, a 183-foldcoverage was achieved for the 3.8-Mb A. baumannii genome. Theobtained sequence reads were assembled using the GS De NovoAssembler software (version 2.8, Roche) (5, 6), which resulted inone scaffold composed of 57 contigs. Subsequently, an in silico gapclosure approach followed by a PCR-based finishing strategy(7–9) was applied to complete the circular chromosome. Annota-tion of the 3,819,158-bp genome featuring a GC content of39.04% was performed within the GenDB 2.0 system (10) andresulted in the prediction of 3,601 coding sequences, 73 tRNAgenes, and 6 rrn operons.The genome of A. baumannii R2090 is highly related to thecommunity-acquiredA. baumannii strain D1279779 that was iso-lated from an indigenous Australian patient who suffered from abacteremic infection (11). Both strains belong to sequence type267. Calculation of the average nucleotide identity (ANI calcula-tor [http://enve-omics.ce.gatech.edu/ani/]) confirmed close relat-edness of both strains with an ANI value of 99.92%.Comparative analyses of strains R2090 andD1279779 revealeddifferences in putative virulence determinants. In strainD1279779, genes encoding a type VI secretion system are missing(11). In contrast, strain R2090 carries at least 13 of 17 genes of thetype VI secretion system cluster. Moreover, strain D1279779 har-bors three type I pili systems putatively involved in adherence andbiofilm formation (12), whereas two of these clusters featuredinsertions of transposable elements in strain R2090.An ARG-ANNOT analysis (13) indicated presence of themetallo--lactamase (MBL) gene blaNDM-1 exclusively in theR2090 chromosome in addition to other putative resistance deter-minants present in both genomes. The gene blaNDM-1 encodes abroad-spectrum carbapenemase with the capability to inactivateall -lactam antibiotics except aztreonam (14). As previously de-scribed, this gene is located on the transposon Tn125 (15, 16).Occurrence of blaNDM-1 in strain R2090 is important with regardsto the dissemination of this serious antibiotic resistance determi-nant among A. baumannii strains (11, 17).Comparison of the R2090 genome to the genomes of otherclinical A. baumannii isolates is expected to provide deeper in-sights into the development of multiresistant derivatives of thisemerging human pathogen.Nucleotide sequence accession number. The Acinetobacterbaumannii R2090 genome sequence has been deposited in theEMBL/GenBank database (EBI, NCBI) under the accession num-ber LN868200.ACKNOWLEDGMENTSThe bioinformatics support of the BMBF-funded project “Bielefeld-Gießen Center for Microbial Bioinformatics”—BiGi (grant 031A533)within the German Network for Bioinformatics Infrastructure (de. NBI)is gratefully acknowledged. I.M. and D.W. acknowledge the receipt of ascholarship from the CLIB Graduate Cluster “Industrial Biotechnology,”cofinanced by the Ministry of Innovation of North Rhine-Westphalia.REFERENCES1. Gootz TD, Marra A. 2008. Acinetobacter baumannii: an emergingmultidrug-resistant threat. Expert Rev Anti Infect Ther 6:309–325. http://dx.doi.org/10.1586/14787210.6.3.309.crossmarkGenome AnnouncementsSeptember/October 2015 Volume 3 Issue 5 e01008-15 genomea.asm.org 12. Bergogne-Bérézin E, Towner KJ. 1996. Acinetobacter spp. as nosocomialpathogens: microbiological, clinical, and epidemiological features. ClinMicrobiol Rev 9:148–165.3. Falagas ME, Karveli EA, Kelesidis I, Kelesidis T. 2007. Community-acquired Acinetobacter infections. Eur J Clin Microbiol Infect Dis 26:857–868. http://dx.doi.org/10.1007/s10096-007-0365-6.4. Davenport KW, Daligault HE, Minogue TD, Bruce DC, Chain PS,Coyne SR, Jaissle JG, Koroleva GI, Ladner JT, Li PE, Palacios GF,Scholz MB, Teshima H, Johnson SL. 2014. 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Theepidemiology of multidrug-resistant Acinetobacter baumannii: does thecommunity represent a reservoir? Infect Control Hosp Epidemiol 24:275–279. http://dx.doi.org/10.1086/502209.Krahn et al.Genome Announcements2 genomea.asm.org September/October 2015 Volume 3 Issue 5 e01008-15

Complete genome sequence of the clinical strain Acinetobacter baumannii R2090 Carrying the chromosomally encoded Metallo-β-Lactamase Gene blaNDM-1

http://dx.doi.org/10.1128/genomeA.01008-15

Complete genome sequence of the clinical strain Acinetobacter baumannii R2090 Carrying the chromosomally encoded Metallo-β-Lactamase Gene blaNDM-1

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