Abstract
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.
ACKNOWLEDGMENT
This work was supported by Health and Medical Research Fund grant CU09-05-02 from the Food and Health Bureau of the Hong Kong Special Administrative Region.
Footnotes
Citation Yim AK-Y, Kwok JS-L, Yu AC-S, Leung AK-Y, Lau HH-Y, Chan T-F, Ip M, Tsui SK-W. 2015. Draft genome sequence of extensively drug-resistant Acinetobacter baumannii strain CUAB1 from a patient in Hong Kong, China. Genome Announc 3(3):e00442-15. doi:10.1128/genomeA.00442-15.
REFERENCES
- 1.Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM. 2006. Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet 2:e7. doi: 10.1371/journal.pgen.0020007. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595. doi: 10.1093/bioinformatics/btp698. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. Omics 12:137–141. doi: 10.1089/omi.2008.0017. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Tian GB, Adams-Haduch JM, Taracila M, Bonomo RA, Wang HN, Doi Y. 2011. Extended-spectrum AmpC cephalosporinase in Acinetobacter baumannii: ADC-56 confers resistance to cefepime. Antimicrob Agents Chemother 55:4922–4925. doi: 10.1128/AAC.00704-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Opazo A, Sonnevend A, Lopes B, Hamouda A, Ghazawi A, Pal T, Amyes SG. 2012. Plasmid-encoded PER-7 beta-lactamase responsible for ceftazidime resistance in Acinetobacter baumannii isolated in the United Arab Emirates. J Antimicrob Chemother 67:1619–1622. doi: 10.1093/jac/dks087. [DOI] [PubMed] [Google Scholar]
- 7.Rice LB, Carias LL, Hujer AM, Bonafede M, Hutton R, Hoyen C, Bonomo RA. 2000. High-level expression of chromosomally encoded SHV-1 beta-lactamase and an outer membrane protein change confer resistance to ceftazidime and piperacillin-tazobactam in a clinical isolate of Klebsiella pneumoniae. Antimicrob Agents Chemother 44:362–367. doi: 10.1128/AAC.44.2.362-367.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Ardebili A, Lari AR, Talebi M. 2014. Correlation of ciprofloxacin resistance with the AdeABC efflux system in Acinetobacter baumannii clinical isolates. Ann Lab Med 34:433–438. doi: 10.3343/alm.2014.34.6.433. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Chiu CH, Lee HY, Tseng LY, Chen CL, Chia JH, Su LH, Liu SY. 2010. Mechanisms of resistance to ciprofloxacin, ampicillin/sulbactam and imipenem in Acinetobacter baumannii clinical isolates in Taiwan. Int J Antimicrob Agents 35:382–386. doi: 10.1016/j.ijantimicag.2009.12.009. [DOI] [PubMed] [Google Scholar]
- 10.Miyachi H, Miki I, Aoyama N, Shirasaka D, Matsumoto Y, Toyoda M, Mitani T, Morita Y, Tamura T, Kinoshita S, Okano Y, Kumagai S, Kasuga M. 2006. Primary levofloxacin resistance and gyrA/B mutations among Helicobacter pylori in Japan. Helicobacter 11:243–249. doi: 10.1111/j.1523-5378.2006.00415.x. [DOI] [PubMed] [Google Scholar]
- 11.Taba H, Kusano N. 1998. Sparfloxacin resistance in clinical isolates of Streptococcus pneumoniae: involvement of multiple mutations in gyrA and parC genes. Antimicrob Agents Chemother 42:2193–2196. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Hakenbeck R, Martin C, Dowson C, Grebe T. 1994. Penicillin-binding protein 2b of Streptococcus pneumoniae in piperacillin-resistant laboratory mutants. J Bacteriol 176:5574–5577. [DOI] [PMC free article] [PubMed] [Google Scholar]