PROKARYOTES
crossm Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen Cheng-Yen Kao,a Jing-Jou Yan,b Yu-Chun Lin,c Po-Xing Zheng,c Jiunn-Jong Wua Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwana; Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwanb; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwanc
Carbapenem-resistant Klebsiella pneumoniae strain 1756 was isolated from a pus specimen from a Taiwanese patient. Here, the complete genome sequence of strain 1756 is presented.
ABSTRACT
K
lebsiella pneumoniae is a Gram-negative opportunistic bacillus in the family Enterobacteriaceae with worldwide distribution that causes pneumonia, liver abscess, septicemia, and urinary tract infection in humans. Carbapenems are considered to be the most effective broad-spectrum -lactam antimicrobial agents for the defense of multidrug resistant Gram-negative organisms, including K. pneumoniae. However, over the past decade the carbapenem resistances of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii have emerged as significant public health threats (1, 2). Here, we report the complete genome sequence of K. pneumoniae strain 1756, isolated from a pus specimen from a 63-year-old Taiwanese women. K. pneumoniae strain 1756 was sequenced using the PacBio RS II platform (Pacific Biosciences, USA), generating a library containing 76,075 single reads with an average length of 14,567 bp and a 173-fold average coverage. Reads were assembled using HGAP version 3.0, which returned three contigs. One short contig (30,002 bp) without a plasmid replicon was discarded because the assembly was problematic. For the remaining two contigs, the head segment was almost identical to the tail segment, indicating the circular nature of the contigs. The 1756 genome has a size of 5,195,816 bp and a G⫹C content of 57.6%. Sequences were annotated at NCBI (http://www.ncbi.nlm.nih.gov/genome/annotation _prok) or with the RAST prokaryotic genome annotation server (http://rast.nmpdr.org/) (3). RAST annotation results showed that the genome contained 4,856 coding sequences and 111 RNA genes. The MLST, ResFinder, and PlasmidFinder (http:// www.genomicepidemiology.org/) databases were used to find the sequence type, antibiotic resistance genes, and the plasmid types present in the isolates (4, 5). The MLST scheme of strain 1756, based on the sequences of seven housekeeping genes (gapA2, infB1, mdh37, pgi1, phoE3, rpoB1, tonB56), indicated that this strain belongs to a new ST type (ST2549). Antimicrobial resistance genes against -lactams (blaSHV-11), fluoroquinolones (oxqAB), and fosfomycin (fosA) were identified on its chromosome sequence. Strain 1756 harbored a IncI1-type plasmid (pKP1756, 73,952 bp) with antimicrobial resistance genes aph(3=)-Ia, aadA22, aac(3)-IId, blaCMY-2, and blaTEM-1B conferring resistance to aminoglycosides and -lactams. IncI1 plasmids are highly prevalent in Enterobacteriaceae and associated with the spread of several resistance genes (6). An insertion mutation in the porin OmpK36 of strain 1756 was identified, which is likely to be associated with resistance to carbapenems in the absence of carbapenemase genes Volume 5 Issue 13 e00066-17
Received 20 January 2017 Accepted 24 January 2017 Published 30 March 2017 Citation Kao C-Y, Yan J-J, Lin Y-C, Zheng P-X, Wu J-J. 2017. Complete genome sequence of carbapenem-resistant Klebsiella pneumoniae strain 1756, isolated from a pus specimen. Genome Announc 5:e00066-17. https:// doi.org/10.1128/genomeA.00066-17. Copyright © 2017 Kao et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jiunn-Jong Wu, [email protected].
genomea.asm.org 1
Kao et al.
(7). This genome will facilitate exploration of the pathogenesis and antibiotic resistance of K. pneumoniae. Accession number(s). The complete genome sequence of K. pneumoniae strain 1756 has been deposited in GenBank under the accession numbers CP019219 (chromosome) and CP019220 (plasmid). ACKNOWLEDGMENTS We thank Robert Jonas for helpful comments on this manuscript. We also thank the team of curators of the Institut Pasteur MLST and whole-genome MLST databases for curating the data and making them publicly available at http://bigsdb.web.pasteur.fr/. This study was supported by grant MOST 104-2320-B-006-018-MY3 from the Ministry of Science and Technology, Taiwan and by grant NCKUH-10301002 from the National Cheng Kung University Hospital, Tainan, Taiwan.
REFERENCES 1. Gniadek TJ, Carroll KC, Simner PJ. 2016. Carbapenem-resistant nonglucose-fermenting gram-negative Bacilli: the missing piece to the puzzle. J Clin Microbiol 54:1700 –1710. https://doi.org/10.1128/JCM.03264-15. 2. Potter RF, D’Souza AW, Dantas G. 2016. The rapid spread of carbapenemresistant Enterobacteriaceae. Drug Resist Updat 29:30 – 46. https://doi.org/ 10.1016/j.drup.2016.09.002. 3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 4. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012.
Volume 5 Issue 13 e00066-17
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. https://doi.org/10.1128/JCM.06094-11. 5. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640 –2644. https://doi.org/ 10.1093/jac/dks261. 6. Carattoli A. 2009. Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother 53:2227–2238. https://doi.org/10.1128/ AAC.01707-08. 7. Tsai YK, Fung CP, Lin JC, Chen JH, Chang FY, Chen TL, Siu LK. 2011. Klebsiella pneumoniae outer membrane porins OmpK35 and OmpK36 play roles in both antimicrobial resistance and virulence. Antimicrob Agents Chemother 55:1485–1493. https://doi.org/10.1128/AAC .01275-10.
genomea.asm.org 2
crossm Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen Cheng-Yen Kao,a Jing-Jou Yan,b Yu-Chun Lin,c Po-Xing Zheng,c Jiunn-Jong Wua Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwana; Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwanb; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwanc
Carbapenem-resistant Klebsiella pneumoniae strain 1756 was isolated from a pus specimen from a Taiwanese patient. Here, the complete genome sequence of strain 1756 is presented.
ABSTRACT
K
lebsiella pneumoniae is a Gram-negative opportunistic bacillus in the family Enterobacteriaceae with worldwide distribution that causes pneumonia, liver abscess, septicemia, and urinary tract infection in humans. Carbapenems are considered to be the most effective broad-spectrum -lactam antimicrobial agents for the defense of multidrug resistant Gram-negative organisms, including K. pneumoniae. However, over the past decade the carbapenem resistances of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii have emerged as significant public health threats (1, 2). Here, we report the complete genome sequence of K. pneumoniae strain 1756, isolated from a pus specimen from a 63-year-old Taiwanese women. K. pneumoniae strain 1756 was sequenced using the PacBio RS II platform (Pacific Biosciences, USA), generating a library containing 76,075 single reads with an average length of 14,567 bp and a 173-fold average coverage. Reads were assembled using HGAP version 3.0, which returned three contigs. One short contig (30,002 bp) without a plasmid replicon was discarded because the assembly was problematic. For the remaining two contigs, the head segment was almost identical to the tail segment, indicating the circular nature of the contigs. The 1756 genome has a size of 5,195,816 bp and a G⫹C content of 57.6%. Sequences were annotated at NCBI (http://www.ncbi.nlm.nih.gov/genome/annotation _prok) or with the RAST prokaryotic genome annotation server (http://rast.nmpdr.org/) (3). RAST annotation results showed that the genome contained 4,856 coding sequences and 111 RNA genes. The MLST, ResFinder, and PlasmidFinder (http:// www.genomicepidemiology.org/) databases were used to find the sequence type, antibiotic resistance genes, and the plasmid types present in the isolates (4, 5). The MLST scheme of strain 1756, based on the sequences of seven housekeeping genes (gapA2, infB1, mdh37, pgi1, phoE3, rpoB1, tonB56), indicated that this strain belongs to a new ST type (ST2549). Antimicrobial resistance genes against -lactams (blaSHV-11), fluoroquinolones (oxqAB), and fosfomycin (fosA) were identified on its chromosome sequence. Strain 1756 harbored a IncI1-type plasmid (pKP1756, 73,952 bp) with antimicrobial resistance genes aph(3=)-Ia, aadA22, aac(3)-IId, blaCMY-2, and blaTEM-1B conferring resistance to aminoglycosides and -lactams. IncI1 plasmids are highly prevalent in Enterobacteriaceae and associated with the spread of several resistance genes (6). An insertion mutation in the porin OmpK36 of strain 1756 was identified, which is likely to be associated with resistance to carbapenems in the absence of carbapenemase genes Volume 5 Issue 13 e00066-17
Received 20 January 2017 Accepted 24 January 2017 Published 30 March 2017 Citation Kao C-Y, Yan J-J, Lin Y-C, Zheng P-X, Wu J-J. 2017. Complete genome sequence of carbapenem-resistant Klebsiella pneumoniae strain 1756, isolated from a pus specimen. Genome Announc 5:e00066-17. https:// doi.org/10.1128/genomeA.00066-17. Copyright © 2017 Kao et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jiunn-Jong Wu, [email protected].
genomea.asm.org 1
Kao et al.
(7). This genome will facilitate exploration of the pathogenesis and antibiotic resistance of K. pneumoniae. Accession number(s). The complete genome sequence of K. pneumoniae strain 1756 has been deposited in GenBank under the accession numbers CP019219 (chromosome) and CP019220 (plasmid). ACKNOWLEDGMENTS We thank Robert Jonas for helpful comments on this manuscript. We also thank the team of curators of the Institut Pasteur MLST and whole-genome MLST databases for curating the data and making them publicly available at http://bigsdb.web.pasteur.fr/. This study was supported by grant MOST 104-2320-B-006-018-MY3 from the Ministry of Science and Technology, Taiwan and by grant NCKUH-10301002 from the National Cheng Kung University Hospital, Tainan, Taiwan.
REFERENCES 1. Gniadek TJ, Carroll KC, Simner PJ. 2016. Carbapenem-resistant nonglucose-fermenting gram-negative Bacilli: the missing piece to the puzzle. J Clin Microbiol 54:1700 –1710. https://doi.org/10.1128/JCM.03264-15. 2. Potter RF, D’Souza AW, Dantas G. 2016. The rapid spread of carbapenemresistant Enterobacteriaceae. Drug Resist Updat 29:30 – 46. https://doi.org/ 10.1016/j.drup.2016.09.002. 3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 4. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012.
Volume 5 Issue 13 e00066-17
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. https://doi.org/10.1128/JCM.06094-11. 5. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640 –2644. https://doi.org/ 10.1093/jac/dks261. 6. Carattoli A. 2009. Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother 53:2227–2238. https://doi.org/10.1128/ AAC.01707-08. 7. Tsai YK, Fung CP, Lin JC, Chen JH, Chang FY, Chen TL, Siu LK. 2011. Klebsiella pneumoniae outer membrane porins OmpK35 and OmpK36 play roles in both antimicrobial resistance and virulence. Antimicrob Agents Chemother 55:1485–1493. https://doi.org/10.1128/AAC .01275-10.
genomea.asm.org 2
