Abstract
We report here the 4.1-Mb draft genome sequence of Acinetobacter baumannii strain 5021_13, a cerebrospinal fluid isolate from northern India. This genome information will help studies toward understanding the epidemiology and pathogenicity of this important nosocomial pathogen.
GENOME ANNOUNCEMENT
Acinetobacter baumannii has emerged as one of the most successful pathogens in the health care setting globally, causing a variety of infections that include bacteremia, pneumonia, meningitis, urinary tract infection, and wound infection (1, 2). In India, there are many reports on the emergence of multidrug-resistant strains of A. baumannii (3, 4). Infection of the central nervous system by multidrug-resistant A. baumannii is difficult to treat and results in a high mortality rate (5). In this study, we report the genome sequence of strain 5021_13, isolated from a cerebrospinal fluid specimen from a patient admitted to the neurosurgery ward of the Postgraduate Institute for Medical Education and Research (PGIMER), Chandigarh, a tertiary-care hospital located in the northern part of India.
High-molecular-weight genomic DNA was isolated using the ZR Fungal/Bacterial DNA MiniPrep kit (Zymo Research) and quantified using a Qubit 2.0 fluorometer (Life Technologies). Illumina sequencing libraries were prepared by using the Nextera XT sample preparation kit (Illumina, Inc., San Diego, CA, USA) with dual indexing adapters from Illumina, as per the manufacturer guidelines. Sequencing libraries were normalized and sequenced by using a 2 × 250-bp paired-end configuration on the in-house Illumina MiSeq (Illumina, Inc.) platform. A total of 2,837,504 reads were generated, amounting to 398,925,392 bp, and were de novo assembled using CLC Genomics Workbench version 7.5 (CLC bio, Aarhus, Denmark) into 187 contigs, with a total length of 4,120,995 bp and mean coverage of 96.8×. The assembly has an N50 of 46,149 bp and average contig length of 22,037 bp, with a mean G+C content of 38.8%. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/), and a total of 3,932 coding sequences (CDSs), 2 rRNAs, and 59 tRNAs were predicted.
BLAST analysis of the complete 16S rRNA gene sequence extracted from the genome by RNAmmer version 1.2 (6) revealed 99.87% similarity to type strain A. baumannii ATCC 19696T. Further average nucleotide identity (ANI) was calculated using JSpecies version 1.2.1 (7). The ANI value between this isolate with the genome of type strain A. baumannii ATCC 19696T. (8) is 97.4%. For ANI, a 95 to 96% cutoff is used for species delineation, showing that this isolate belongs to A. baumannii.
This genome will aid in the whole genome-based phylogenetic and comparative analyses of this important opportunistic pathogen isolated from diverse clinical samples from India and the rest of the world.
Nucleotide sequence accession numbers.
The draft genome sequence of A. baumannii 5021_13 is available in DDBJ/EMBL/GenBank under the accession no. LGYV00000000. The version described in this paper is the first version, LGYV01000000.
ACKNOWLEDGMENTS
S.K. is working as senior research fellow supported by the Department of Biotechnology (DBT). P.P.P. and S.M. are supported by a fellowship from the University Grant Commission (UGC) and Council of Scientific and Industrial Research (CSIR), respectively.
Footnotes
Citation Kumar S, Patil PP, Midha S, Ray P, Patil PB, Gautam V. 2015. Genome sequence of Acinetobacter baumannii strain 5021_13, isolated from cerebrospinal fluid. Genome Announc 3(5):e01213-15. doi:10.1128/genomeA.01213-15.
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