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Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China Xue-Jing Yang,a Sai Wang,b Jun-Min Cao,a,c Jia-Hui Houa Department of Clinical Laboratory, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of Chinaa; Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of Chinab; Department of Hospital Infection Control, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of Chinac
Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. Here we present draft genome assemblies of Klebsiella pneumoniae AS, which was isolated in China. The genomic information will provide a better understanding of the physiology, adaptation, and evolution of K. pneumoniae.
Received 12 July 2016 Accepted 18 July 2016 Published 22 September 2016 Citation Yang X-J, Wang S, Cao J-M, Hou J-H. 2016. Draft genome sequence of Klebsiella pneumoniae strain AS isolated from Zhejiang Provincial Hospital of TCM, China. Genome Announc 4(5):e00930-16. doi:10.1128/genomeA.00930-16. Copyright © 2016 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jun-Min Cao, [email protected].
K
lebsiella pneumoniae is a type of Gram-negative bacterium that can cause different types of health care-associated infections, including pneumonia, bloodstream infections, wound or surgical site infections, and meningitis. K. pneumoniae has become an important pathogen in nosocomial infections (1). The threat of K. pneumoniae has increased with the emergence of strains resistant to carbapenem antibiotics (2). Here we present the draft genome sequence of one K. pneumoniae strain AS that was isolated from a patient in Zhejiang Provincial Hospital of TCM. The genome of K. pneumoniae strain AS was sequenced using Illumina MiSeq technology at the Hangzhou Guhe Information Technology Co Ltd. (Hangzhou, China), with paired-end reads of 2 ⫻ 250 bp and an insert fragment of 450 bp. The 3,635,263 paired reads were trimmed and assembled using CLC NGS Cell v6.5. The draft genome sequence was submitted to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) for annotation (3). The annotation method was best-placed reference protein set, GeneMarkS⫹. Genes encoding tRNAs were determined using the tRNAscan-SE (4) and structural RNAs (5S, 16S, and 23S rRNAs) were used in a BLASTn search against the reference set. 5S hits were further refined using Cmsearch. Functional annotation was achieved using the Web CD search tool (5) and BLAST against the ARDB (Antibiotic Resistance Genes Database) (6). The genome from K. pneumoniae strain AS is 5,555,747 bp long with 57.11% G⫹C content. After assembly, the draft genome consists of 129 contigs of ⬎200 bp and a N50 of 95,480 bp. Overall, the AS genome has a total of 5,580 predicted features, including 5,509 coding sequences (CDS) (5,408 proteincoding genes and 101 pseudogenes), 71 RNAs (5 rRNAs, 54 tRNAs, and 12 noncoding RNAs [ncRNAs]). The top three numbers of proteins assigned to clusters of orthologous groups (COGs) are 586 (general function prediction only), 549 (amino acid transport and metabolism), 527 (carbohydrate transport
September/October 2016 Volume 4 Issue 5 e00930-16
and metabolism). One remarkable feature is the huge number of genes (349 genes) that are devoted to 99 kinds of antibiotic resistance types. Of these, 96 genes are annotated as MacAMacB efflux system, which is attributed to macrolides resistance (7). The draft genome sequence of K. pneumoniae strain AS determined in this study is essential for the identification of specific genetic features of this strain and for understanding the mechanisms of its antibiotic resistance activity. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. LZCT00000000. The version described in this paper is version LZCT01000000. ACKNOWLEDGMENTS We thank Bo-Zhu and Wei-Jie Song for their critical discussion and editing of the manuscript. This work was funded by the Science and Technology Program of Zhejiang province (No. 2013C33181) and the Zhejiang Provincial Medical and Health Science and Technology Project (No. 2016KYB216).
REFERENCES 1. Lockhart SR, Abramson MA, Beekmann SE, Gallagher G, Riedel S, Diekema DJ, Quinn JP, Doern GV. 2007. Antimicrobial resistance among gram-negative bacilli causing infections in intensive care unit patients in the United States between 1993 and 2004. J Clin Microbiol 45:3352–3359. http://dx.doi.org/10.1128/JCM.01284-07. 2. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, Alberti S, Bush K, Tenover FC. 2001. Novel carbapenem-hydrolyzing beta-lactamase, KPC-1, from a carbapenemresistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother 45:1151–1161. http://dx.doi.org/10.1128/AAC.45.4.1151 -1161.2001. 3. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2015. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 43: D599 –D605. 4. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-
Genome Announcements
genomea.asm.org 1
Yang et al.
tion of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964. http://dx.doi.org/10.1093/nar/25.5.0955. 5. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.
2 genomea.asm.org
6. Liu B, Pop M. 2009. ARDB—antibiotic resistance genes database. Nucleic Acids Res 37:D443–D447. http://dx.doi.org/10.1093/nar/gkn656. 7. Villa L, Feudi C, Fortini D, García-Fernández A, Carattoli A. 2014. Genomics of KPC-producing Klebsiella pneumoniae sequence type 512 clone highlights the role of RamR and ribosomal S10 protein mutations in conferring tigecycline resistance. Antimicrob Agents Chemother 58: 1707–1712. http://dx.doi.org/10.1128/AAC.01803-13.
Genome Announcements
September/October 2016 Volume 4 Issue 5 e00930-16
Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China Xue-Jing Yang,a Sai Wang,b Jun-Min Cao,a,c Jia-Hui Houa Department of Clinical Laboratory, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of Chinaa; Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of Chinab; Department of Hospital Infection Control, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of Chinac
Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. Here we present draft genome assemblies of Klebsiella pneumoniae AS, which was isolated in China. The genomic information will provide a better understanding of the physiology, adaptation, and evolution of K. pneumoniae.
Received 12 July 2016 Accepted 18 July 2016 Published 22 September 2016 Citation Yang X-J, Wang S, Cao J-M, Hou J-H. 2016. Draft genome sequence of Klebsiella pneumoniae strain AS isolated from Zhejiang Provincial Hospital of TCM, China. Genome Announc 4(5):e00930-16. doi:10.1128/genomeA.00930-16. Copyright © 2016 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jun-Min Cao, [email protected].
K
lebsiella pneumoniae is a type of Gram-negative bacterium that can cause different types of health care-associated infections, including pneumonia, bloodstream infections, wound or surgical site infections, and meningitis. K. pneumoniae has become an important pathogen in nosocomial infections (1). The threat of K. pneumoniae has increased with the emergence of strains resistant to carbapenem antibiotics (2). Here we present the draft genome sequence of one K. pneumoniae strain AS that was isolated from a patient in Zhejiang Provincial Hospital of TCM. The genome of K. pneumoniae strain AS was sequenced using Illumina MiSeq technology at the Hangzhou Guhe Information Technology Co Ltd. (Hangzhou, China), with paired-end reads of 2 ⫻ 250 bp and an insert fragment of 450 bp. The 3,635,263 paired reads were trimmed and assembled using CLC NGS Cell v6.5. The draft genome sequence was submitted to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) for annotation (3). The annotation method was best-placed reference protein set, GeneMarkS⫹. Genes encoding tRNAs were determined using the tRNAscan-SE (4) and structural RNAs (5S, 16S, and 23S rRNAs) were used in a BLASTn search against the reference set. 5S hits were further refined using Cmsearch. Functional annotation was achieved using the Web CD search tool (5) and BLAST against the ARDB (Antibiotic Resistance Genes Database) (6). The genome from K. pneumoniae strain AS is 5,555,747 bp long with 57.11% G⫹C content. After assembly, the draft genome consists of 129 contigs of ⬎200 bp and a N50 of 95,480 bp. Overall, the AS genome has a total of 5,580 predicted features, including 5,509 coding sequences (CDS) (5,408 proteincoding genes and 101 pseudogenes), 71 RNAs (5 rRNAs, 54 tRNAs, and 12 noncoding RNAs [ncRNAs]). The top three numbers of proteins assigned to clusters of orthologous groups (COGs) are 586 (general function prediction only), 549 (amino acid transport and metabolism), 527 (carbohydrate transport
September/October 2016 Volume 4 Issue 5 e00930-16
and metabolism). One remarkable feature is the huge number of genes (349 genes) that are devoted to 99 kinds of antibiotic resistance types. Of these, 96 genes are annotated as MacAMacB efflux system, which is attributed to macrolides resistance (7). The draft genome sequence of K. pneumoniae strain AS determined in this study is essential for the identification of specific genetic features of this strain and for understanding the mechanisms of its antibiotic resistance activity. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. LZCT00000000. The version described in this paper is version LZCT01000000. ACKNOWLEDGMENTS We thank Bo-Zhu and Wei-Jie Song for their critical discussion and editing of the manuscript. This work was funded by the Science and Technology Program of Zhejiang province (No. 2013C33181) and the Zhejiang Provincial Medical and Health Science and Technology Project (No. 2016KYB216).
REFERENCES 1. Lockhart SR, Abramson MA, Beekmann SE, Gallagher G, Riedel S, Diekema DJ, Quinn JP, Doern GV. 2007. Antimicrobial resistance among gram-negative bacilli causing infections in intensive care unit patients in the United States between 1993 and 2004. J Clin Microbiol 45:3352–3359. http://dx.doi.org/10.1128/JCM.01284-07. 2. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, Alberti S, Bush K, Tenover FC. 2001. Novel carbapenem-hydrolyzing beta-lactamase, KPC-1, from a carbapenemresistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother 45:1151–1161. http://dx.doi.org/10.1128/AAC.45.4.1151 -1161.2001. 3. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2015. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 43: D599 –D605. 4. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-
Genome Announcements
genomea.asm.org 1
Yang et al.
tion of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964. http://dx.doi.org/10.1093/nar/25.5.0955. 5. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:D222–D226. http://dx.doi.org/10.1093/nar/gku1221.
2 genomea.asm.org
6. Liu B, Pop M. 2009. ARDB—antibiotic resistance genes database. Nucleic Acids Res 37:D443–D447. http://dx.doi.org/10.1093/nar/gkn656. 7. Villa L, Feudi C, Fortini D, García-Fernández A, Carattoli A. 2014. Genomics of KPC-producing Klebsiella pneumoniae sequence type 512 clone highlights the role of RamR and ribosomal S10 protein mutations in conferring tigecycline resistance. Antimicrob Agents Chemother 58: 1707–1712. http://dx.doi.org/10.1128/AAC.01803-13.
Genome Announcements
September/October 2016 Volume 4 Issue 5 e00930-16
