Genome Sequence of an OXA23-Producing, Carbapenem-Resistant Acinetobacter baumannii Strain of Sequence Type ST75

Abstract

The increase of Acinetobacter baumannii resistance to carbapenems is of great concern. OXA23 is one of the most prevalent carbapenemases of A. baumannii that causes outbreaks. Here, we announce the genome sequence of an OXA23-producing A. baumannii strain assigned ST75, a newly emerged sequence type harboring carbapenemase.

GENOME ANNOUNCEMENT

Acinetobacter baumannii has emerged as one of the most troublesome pathogens for its remarkable capability to acquire antibiotic resistance and is the leading cause of hospital-acquired infections (9). Due to the extensive use of broad-spectrum antibiotics, A. baumannii could rapidly generate resistance to the antibiotics. To date, isolates of A. baumannii have been found to be resistant to all the known antibiotics. Carbapenems represent reserved antibiotics. The increasing trend of carbapenem resistance in A. baumannii worldwide becomes a great concern since it limits drastically the range of therapeutic alternatives. Outbreaks caused by carbapenem-resistant clonal A. baumannii have been reported on a national and even worldwide scale (3, 11).

Several types of carbapenemase have been reported in A. baumannii. The most widespread β-lactamases with carbapenemase activity in A. baumannii are carbapenem-hydrolyzing class D β-lactamases (CHDLs) (10). These enzymes belong to three unrelated groups of clavulanic acid-resistant β-lactamases, represented by OXA23, OXA24, and OXA58. Genetically related OXA23-producing clones of outbreaks have been reported in several Asian countries, especially in China (2, 5). Multilocus sequence typing of the strains showed that OXA23-producing clones belonged to limited sequence types, of which ST22 is the most represented sequence type (4, 5). This reflects that certain resistant strains might have advantages in survival in hospital environments and causing outbreaks (6). In our etiological and resistance survey, we detected OXA23-producing outbreak A. baumannii strains of a new sequence type, ST75, which was emerged from other sequence types. Here, we announce the genome sequence of an A. baumannii isolate, BZICU-2, a representative strains of ST75, making it possible for genome comparison and further investigation of outbreaks caused by A. baumannii.

The genomic DNA of BZICU-2 was sequenced with a HighSeq 2000 sequencer with paired-end protocol. The low-quality reads were filtered, and the remaining reads were assembled with Clcbio genomics workbench version 3.6.5 by the de novo assembly method. About 1 Gb of clear data was obtained. After the reads were filtered, about 5.5 million reads meeting the criteria were assembled. A total of 184 contigs covering a total of 3,880,475 bp was generated. All the contigs were >200 bp in length; 8 contigs were >100 kb, and 74 contigs were >10 kb. The average length of contigs was 21 kb. The final approximate coverage for these contigs was about 120×.

Then, the genome sequence was annotated with different tools. Open reading frames (ORFs) were predicted by the RAST (1). The rRNA was predicted by using RNAmmer (7), and tRNAs were identified with tRNAscan-SE 1.21 (8). The total genome has a G+C content of 57.28%. A total of 3,630 coding sequences were predicted, including 3,607 protein coding sequences, 21 tRNAs, one copy of large-subunit rRNA, and one copy of small-subunit rRNA. The initial functional assignment of the potential protein coding sequences was also performed by RAST. Further detailed analyses, including functional annotations, comparative genomics, and environment adaptation, are in process and will be included in our future publication.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ALOH00000000. The version described in this paper is the first version, ALOH01000000.