Draft Genome Sequence of an Acinetobacter Genomic Species 3 Strain Harboring a bla_NDM-1 Gene

Abstract

Here we report the draft genome sequence of one Acinetobacter genomic species 3 strain, D499, which harbors the bla_NDM-1 gene. The total length of the assembled genome is 4,103,824 bp, and 3,896 coding sequences (CDSs) were predicted within the genome. A previously unreported bla_NDM-1-bearing plasmid was identified in this strain.

GENOME ANNOUNCEMENT

The past years have witnessed the dramatic uprising and spreading of pathogenic bacteria bearing antibiotic resistance and even multidrug resistances. NDM-1 (New Delhi metallo-β-lactamase), a newly reported carbapenem resistance-encoding gene, has been identified worldwide from diverse pathogens, like Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Acinetobacter baumannii, etc. (1, 6, 9, 15). The bacteria bearing the NDM-1 gene are known as “superbugs” and have attracted intensive public health attention. The NDM-1 gene has been detected on plasmids and chromosomes as well (5, 17).

A group including Acinetobacter genomic species 3, together with A. baumannii, Acinetobacter genomic species 13TU, and A. calcoaceticus, has been proposed as the A. calcoaceticus-A. baumannii complex (ACB complex), as it is difficult to distinguish them from each other by phenotypic properties (4, 12). Like A. baumannii, Acinetobacter genomic species 3 is responsible for both community-acquired and nosocomial infections (2, 10). Intensive phylogenetic analysis has led recently to the proposal of Acinetobacter genomic species 3 as a novel species (Acinetobacter pittii) (11). Here we report the draft genome of a bla_NDM-1-bearing strain, D499, which is the second genome available from Acinetobacter genomic species 3 other than strain SH024 (ADCH00000000) according to the Genomes Online Database (http://www.genomesonline.org).

Whole-genome sequencing was performed using Illumina HiSeq 2000 (Illumina Inc.) by generating paired-end libraries with an average insert size of 500 bp and 6 kb following the manufacturer's instructions. Ultimately, 400 Mb and 210 Mb of high-quality data were generated from each library, with read lengths of 90 bp and 49 bp, respectively. The paired-end reads were first de novo assembled using SOAPdenovo v1.06 according to the method described previously (13), and then contigs were manually connected according to their 6-kb paired-end relationships. The coding sequences (CDSs) were predicted using Glimmer v3.02 (3), and homologous comparison to a nonredundant public database was performed by BLAST for function annotation. The rRNA and tRNA were identified using RNAmmer (7) and tRNAscan-SE 1.21 (14), the antibiotic resistance genes were annotated using Antibiotic Resistance Genes Database (8), and the insertion sequence (IS) elements were annotated by ISsaga (16).

Finally, we obtained 30 contigs with a total length of 4,103,824 bp, including one 47.1-kb circular contig identified as a bla_NDM-1-bearing plasmid. Fifty-two and 3,844 CDSs were predicted on the plasmid and the other 29 contigs, respectively. The average nucleotide identity (ANI) between strains D499 and SH024 is 98.8%. The bla_NDM-1-encoding plasmid is different from the previously reported one in E. coli (5). The bla_NDM-1 region in the plasmid harbored a high-GC% island (61.98%; the average GC% of the strain is 38.85%) flanked by two insertion sequence elements (ISAba125 and ISAba11), implying that this island might be transferred by recombination. Besides the bla_NDM-1 gene, 19 other antibiotic resistance-related genes were predicted on the assembled genome (8).

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AGFH00000000. The version described in this paper is the first version, AGFH01000000.