Abstract
We report the annotated genome sequence of multidrug-resistant Pseudomonas aeruginosa strain NCGM1179, which is highly resistant to carbapenems, aminoglycosides, and fluoroquinolones and is emerging at medical facilities in Japan.
GENOME ANNOUNCEMENT
Pseudomonas aeruginosa is a Gram-negative rod bacterium of the Pseudomonadaceae family of bacteria. It is an opportunistic pathogen, causing urinary tract infections, respiratory system infections, dermatitis, bacteremia, and a variety of systemic infections, particularly in immunosuppressed patients (11). P. aeruginosa is intrinsically resistant to many antibiotics and has a remarkable capacity for acquiring new resistance mechanisms under selective pressure of antibiotics; therefore, the emergence of multidrug-resistant (MDR) P. aeruginosa with resistance to aminoglycosides, beta-lactams, and fluoroquinolones poses serious problems for medical facilities in various countries (2, 3, 6, 7, 12), including Japan (4, 9, 10).
MDR P. aeruginosa NCGM1179 was isolated from the respiratory tract of an inpatient in Japan in 2010. A further 16 isolates with identical patterns of pulsed-field gel electrophoresis were obtained from respiratory tracts of hospitalized patients among 10 prefectures in the same year, indicating that the NCGM1179 strain was emerging at medical facilities throughout Japan. The strain was highly resistant to carbapenems, aminoglycosides, and fluoroquinolones, with MIC90s of more than 64 μg/ml, and produced IMP-type metallo-β-lactamase and aminoglycoside 6′-N-acetyltransferase [AAC(6′)]-Iae (5, 8).
The genome of strain NCGM1179 was sequenced using a GS FLX Titanium sequencer using Pyrosequencing technology. We obtained a total of 863,079 reads, covering a total of 232,282,665 bp. The number of contigs (over 100 bp) was 290, and the number of bases was 6,735,052 bp. The number of contigs (over 500 bp) was 258, and the number of bases was 6,727,128 bp. The number of scaffolds was 25, and that of bases was 7,014,004. The largest scaffold size was 6,910,294 bp. The genome of strain NCGM1179 has a G+C content of 66.0%, and the draft assemblies contained 6,213 potential protein-coding sequences, 61 tRNA and 1 transfer messenger RNA (tmRNA). Primary coding sequence extraction and initial functional assignment were performed by the RAST (Rapid Annotation using Subsystem Technology) automated annotation servers (1). Their results were compared to verify the annotation and were corrected manually by in silico molecular cloning (In Silico Biology, Inc., Kanagawa, Japan).
Nucleotide sequence accession numbers.
Nucleotide sequences of the chromosome of P. aeruginosa NCGM1179 have been deposited in the DNA Database of Japan under accession no. DF126593 to DF126613.
Acknowledgments
This study was supported by grants (H21-Shinko-ippan-008) from the Ministry of Health, Labor, and Welfare of Japan. Tohru Miyoshi-Akiyama was supported by a Grant for International Health Research (23A-301) from the Ministry of Health, Labor, and Welfare.
REFERENCES
- 1. Aziz R. K., et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Hocquet D., Bertrand X., Kohler T., Talon D., Plesiat P. 2003. Genetic and phenotypic variations of a resistant Pseudomonas aeruginosa epidemic clone. Antimicrob. Agents Chemother. 47:1887–1894 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Karlowsky J., et al. 2003. Surveillance for antimicrobial susceptibility among clinical isolates of Pseudomonas aeruginosa and Acinetobacter baumannii from hospitalized patients in the United States, 1998 to 2001. Antimicrob. Agents. Chemother. 47:1681–1688 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Kirikae T., Mizuguchi Y., Arakawa Y. 2008. Investigation of isolation rates of Pseudomonas aeruginosa with and without multidrug resistance in medical facilities and clinical laboratories in Japan. J. Antimicrob. Chemother. 61:612–615 [DOI] [PubMed] [Google Scholar]
- 5. Kitao T., et al. 2010. Development of an immunochromatographic assay for the rapid detection of AAC(6′)-Iae-producing multidrug-resistant Pseudomonas aeruginosa. J. Antimicrob. Chemother. 65:1382–1386 [DOI] [PubMed] [Google Scholar]
- 6. Lee K., et al. 2002. Bla(VIM-2) cassette-containing novel integrons in metallo-beta-lactamase-producing Pseudomonas aeruginosa and Pseudomonas putida isolates disseminated in a Korean hospital. Antimicrob. Agents Chemother. 46:1053–1058 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Pournaras S., et al. 2005. Spread of efflux pump-overexpressing, non-metallo-beta-lactamase-producing, meropenem-resistant but ceftazidime-susceptible Pseudomonas aeruginosa in a region with blaVIM endemicity. J. Antimicrob. Chemother. 56:761–764 [DOI] [PubMed] [Google Scholar]
- 8. Sekiguchi J., et al. 2005. Multidrug-resistant Pseudomonas aeruginosa strain that caused an outbreak in a neurosurgery ward and its aac(6′)-Iae gene cassette encoding a novel aminoglycoside acetyltransferase. Antimicrob. Agents Chemother. 49:3734–3742 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Sekiguchi J., et al. 2007. Molecular epidemiology of outbreaks and containment of drug-resistant Pseudomonas aeruginosa in a Tokyo hospital. J. Infect. Chemother. 13:418–422 [DOI] [PubMed] [Google Scholar]
- 10. Sekiguchi J., et al. 2007. Outbreaks of multidrug-resistant Pseudomonas aeruginosa in community hospitals in Japan. J. Clin. Microbiol. 45:979–989 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Silby M., Winstanley W. C., Godfrey S. A., Levy S. B., Jackson R. W. 2011. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. Rev. 35:652–680 [DOI] [PubMed] [Google Scholar]
- 12. Tassios P., Gennimata T. V., Maniatis A. N., Fock C., Legakis N. J., and the Greek Pseudomonas aeruginosa Study Group 1998. Emergence of multidrug resistance in ubiquitous and dominant Pseudomonas aeruginosa serogroup O:11. J. Clin. Microbiol. 36:897–901 [DOI] [PMC free article] [PubMed] [Google Scholar]