Draft Genome Sequence of Extensively Drug-Resistant Acinetobacter baumannii Strain CUAB1 from a Patient in Hong Kong, China.

We report the draft genome sequence of an extensively drug-resistant strain of Acinetobacter baumannii, CUAB1, isolated from a patient in a local Hong Kong hospital. MIC testing was performed, and genes previously associated with drug resistance were located.

GENOME ANNOUNCEMENT

The ubiquitous Gram-negative coccobacillus Acinetobacter baumannii has attracted attention for the past 30 years due to the emergence of multidrug- or even pandrug-resistant strains. This rapidly emerging pathogen causes infections including bacteremia, pneumonia, meningitis, urinary tract infection, and wound infection (1). To further understand the cause of the drug-resistant phenotype of A. baumannii, strain CUAB1 (also known as strain 718532) was isolated from a 70-year-old female patient’s blood in the intensive care unit of a local hospital in Hong Kong, China.

The whole-genome sequence was determined to a depth of 82× using Illumina reads and Velvet 1.1.04 (2) was used for initial de novo assembly. Reads were mapped back to the assembled scaffolds to check for misassemblies and erroneous regions were then locally reassembled. Using the published A. baumannii ACICU for reference mapping by Burrows-Wheeler Aligner 0.6.1 (3), we identified reads that were unassembled but mapped to the reference sequence. Gaps were then filled by adding the corresponding reference sequence regions into the scaffold. Protein prediction was done using the NCBI prokaryotic genome annotation pipeline (4). The 3.6-Mbp genome was assembled into 16 scaffolds with an N50 of 706,416 bp and it has 3,426 predicted genes.

MIC tests using broth microdilution were performed for CUAB1. Tests results showed that CUAB1 exhibited high resistance to carbapenems (imipenem and meropenem) and other β-lactams (piperacillin and piperacillin-tazobactam), although it is less resistant to cefoperazone-sulbactam. It is also resistant to aminoglycosides (amikacin, gentamicin, and tobramicin), as well as cephalosporins (cefepime and ceftazidime). Resistance for the fluoroquinolones vary from being resistant to ciprofloxacin to having intermediate resistance to levofloxacin. However, it is sensitive to tigecycline, a glycylcycline antibiotic. CUAB1 was also determined to be resistant to chloramphenicol.

After bioinformatics analysis, we located coding genes related to resistance of the tested drugs that were previously reported. Six β-lactamases (VM83_01790, VM83_06150, VM83_09370, VM83_11515, VM83_12080, and VM83_16400) and two metallo-β-lactamases (VM83_01900 and VM83_14400) are present in the genome. Their mutations or presence may account for resistance to cefepime (5), ceftazidime (6), and piperacillin-tazobactam (7). Genes that were previously reported to be responsible for resistance for aminoglycoside resistance include a resistance-nodulation-cell division (RND) type efflux pump (adeT with locus tag VM83_17110), two RND transporters (VM83_17120 and VM83_17125), and two adenine deaminases (VM83_05615 and adeC with locus tag VM83_08895) (8). A membrane protein (carO with locus tag VM83_12950) might account for carbapenem resistance (9). Moreover, we located DNA gyrase subunit A (VM83_13220) and subunit B (VM83_00010), whose mutations may account for resistance to fluoroquinolone drugs (10, 11). Last but not least, we located three penicillin-binding proteins (PBPs) (VM83_07595, VM83_11570, and VM83_12445) associated with piperacillin resistance (12). We believe the draft genome of CUAB1 will facilitate future genomic analyses of drug resistance mechanisms in A. baumannii, given its extensively resistant drug profile and whole-genome annotation.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. JZUF00000000. The version described in this paper is the first version, JZUF01000000.