Abstract
We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical isolate of Acinetobacter nosocomialis called strain M2 (previously known as Acinetobacter baumannii strain M2).
GENOME ANNOUNCEMENT
Acinetobacter nosocomialis is a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, which is composed of A. calcoaceticus, A. baumannii, Acinetobacter pittii (formerly genomic species 3), and A. nosocomialis (formerly genomic species 13 TU) (1). Except for A. calcoaceticus, members of the ACB complex are opportunistic pathogens that pose a significant threat to human health through their ability to cause severe infections. This threat is compounded by both the high incidence of ACB complex infections in critically ill patients and the prevalence of antibiotic resistance exhibited by members of the ACB complex (2).
A. nosocomialis strain M2, isolated in 1996 from a hip infection of a patient at Cleveland MetroHealth Systems (Cleveland, OH), has been studied in several laboratories. An acyl-homoserine lactone autoinducer synthase from strain M2 has been isolated and characterized (3). Nonnative acyl-homoserine lactones have been shown to attenuate strain M2 quorum sensing (4). A novel mechanism of fluoroquinolone resistance has been discovered through the mutagenesis of strain M2 (5). The twitching motility exhibited by strain M2 is mediated by a type IV pilus system, which also mediates the natural transformation phenotype of strain M2 (6). Strain M2 is also motile on the surface of agar plates through an unknown (7) Tfp-independent mechanism (6). In addition, strain M2 is able to outcompete other bacteria using a type VI secretion system (8).
Genomic DNA was prepared using the Qiagen DNA purification kit. Genome sequencing was performed using the Illumina HiSeq and MiSeq platforms maintained at the Research Institute at Nationwide Children’s Hospital Biomedical Genomics Core (http://genomics.nchresearch.org). A total of 4 million paired-end MiSeq reads (300-bp insert size) trimmed to 200 bp and 4 million mate-pair HiSeq reads (3-kb insert size) trimmed to 35 bp were assembled de novo using SeqMan NGen (version 4.1.2; DNAStar, Madison, WI). Postassembly manipulation was performed using SeqMan Pro (DNAStar). This genome assembly yielded 11 contigs comprising a total genome length of 3,782,411 bp and an N50 of 556 kb, with 163-fold average coverage. Genome annotation using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (version 2.0) predicted a total of 3,487 open reading frames.
Previously, strain M2 was classified by multilocus sequence typing (MLST) as belonging to the A. baumannii species (R. A. Bonomo, unpublished data). Two currently available MLST schemes were used to retype strain M2. Four of the seven genes required for MLST using the “Oxford” scheme (see http://pubmlst.org) were identified in the M2 genome. Based upon this analysis, strain M2 is most closely related to an Acinetobacter sp. 13TU isolate from Brazil. Five of the eight genes required for MLST using the “Pasteur” scheme (see http://www.pasteur.fr/mlst) were identified in the strain M2 genome. An analysis of these alleles indicates that strain M2 is most closely related to Acinetobacter sp. 13TU strain RUH 2210. Based on this evidence, we recommend that A. baumannii strain M2 be referred to as A. nosocomialis strain M2.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AWOW00000000. The version described in this paper is version AWOW01000000.
ACKNOWLEDGMENTS
The research reported in this publication was supported by funds and/or facilities provided by the Research Institute at Nationwide Children’s Hospital to R.S.M., the National Institute of Allergy and Infectious Diseases of the National Institutes of Health R01AI072219 and R01AI063517 to R.A.B., the Cleveland Department of Veterans Affairs, the Veterans Affairs Merit Review Program, and the Geriatric Research Education and Clinical Center VISN 10 to R.A.B.
We thank Peter White and members of the Biomedical Genomics Core at Nationwide Children’s Hospital for their outstanding technical assistance. This publication made use of the PubMLST website (http://pubmlst.org/) developed by Keith Jolley (9), which is sited at the University of Oxford and publicly available data on Institute Pasteur MLST website (http://www.pasteur.fr/mlst). The content of this publication is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Footnotes
Citation Carruthers MD, Harding CM, Baker BD, Bonomo RA, Hujer KM, Rather PN, Munson RS, Jr. 2013. Draft genome sequence of the clinical isolate Acinetobacter nosocomialis strain M2. Genome Announc. 1(6):e00906-13. doi:10.1128/genomeA.00906-13.
REFERENCES
- 1. Nemec A, Krizova L, Maixnerova M, van der Reijden TJ, Deschaght P, Passet V, Vaneechoutte M, Brisse S, Dijkshoorn L. 2011. Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). Res. Microbiol. 162:393–404 [DOI] [PubMed] [Google Scholar]
- 2. Peleg AY, Seifert H, Paterson DL. 2008. Acinetobacter baumannii: emergence of a successful pathogen. Clin. Microbiol. Rev. 21:538–582 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Niu C, Clemmer KM, Bonomo RA, Rather PN. 2008. Isolation and characterization of an autoinducer synthase from Acinetobacter baumannii. J. Bacteriol. 190:3386–3392 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Stacy DM, Welsh MA, Rather PN, Blackwell HE. 2012. Attenuation of quorum sensing in the pathogen Acinetobacter baumannii using non-native N-acyl homoserine lactones. ACS Chem. Biol. 7:1719–1728 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Saroj SD, Clemmer KM, Bonomo RA, Rather PN. 2012. Novel mechanism for fluoroquinolone resistance in Acinetobacter baumannii. Antimicrob. Agents Chemother. 56:4955–4957 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Harding CM, Tracy EN, Carruthers MD, Rather PN, Actis LA, Munson RS., Jr 2013. Acinetobacter baumannii strain M2 produces type IV pili which play a role in natural transformation and twitching motility but not surface-associated motility. mBio 4(4):e00360–13. 10.1128/mBio.00360-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Clemmer KM, Bonomo RA, Rather PN. 2011. Genetic analysis of surface motility in Acinetobacter baumannii. Microbiology 157:2534–2544 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Carruthers MD, Nicholson PA, Tracy EN, Munson RS., Jr 2013. Acinetobacter baumannii utilizes a type VI secretion system for bacterial competition. PLoS One 8:e59388. 10.1371/journal.pone.0059388 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Jolley KA, Maiden MCJ. 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. 10.1186/1471-2105-11-595 [DOI] [PMC free article] [PubMed] [Google Scholar]