Klebsiella pneumoniae of capsular type K1 is the most common causative agent of both health care-associated and community-acquired infections. Here, we report the draft genome sequences of 10 K1-type K. pneumoniae strains isolated from patients in an infectious disease hospital and neurosurgical intensive care unit in Russia.
ABSTRACT
Klebsiella pneumoniae of capsular type K1 is the most common causative agent of both health care-associated and community-acquired infections. Here, we report the draft genome sequences of 10 K1-type K. pneumoniae strains isolated from patients in an infectious disease hospital and neurosurgical intensive care unit in Russia.
ANNOUNCEMENT
Klebsiella pneumoniae is a well-known opportunistic pathogen that causes community-acquired and health care-associated infections (1, 2). A capsular polysaccharide is the major virulence factor of K. pneumoniae (1, 3). Of the number of documented capsular types, strains of the K1 type, along with those of the K2 type, are the most virulent human pathogens (4, 5). We previously reported genome sequences of 10 strains of the K. pneumoniae K2 type, isolated from patients in an infectious disease hospital and neurosurgical intensive care unit (6). In this study, we report the genome sequences of K1-type K. pneumoniae strains isolated in the same hospitals (7).
Bacteria were grown at 37°C on nutrient medium no. 1 (Obolensk, Russia). Genomic DNA was isolated using the phenol-chloroform extraction and ethanol precipitation methods (https://fdocuments.in/download/phenol-chloroform-isoamyl-alcohol-pci-dna-isoamyl-alcohol-pci-dna-extraction). Draft genome sequencing was performed using Nextera XT DNA sample preparation kits, a MiSeq reagent kit v.3 (300 cycles), and the MiSeq platform (Illumina). For each genome, the paired reads without filtering were de novo assembled with Unicycler v.0.4.7 (8). Default parameters were used for all software. The resulting draft genome sizes ranged from 5.52 to 5.81 Mb, with GC contents ranging from 56.9 to 57.2%. The final assemblies were annotated with the NCBI Prokaryotic Genome Annotation Pipeline (9), resulting in the identification of total numbers of genes ranging from 6,147 to 5,453 (Table 1). Raw reads were used for multilocus sequence type (MLST) analysis with MLST v.2.0 (https://cge.cbs.dtu.dk/services/MLST/). All strains were assigned to sequence type 23.
TABLE 1.
Strain-identifying information and basic statistics on assemblies and annotations
| Strain name | Raw data SRA accession no. | GenBank accession no. | No. of reads | N50 (bp) | No. of contigs | Genome size (bp) | Total no. of genes | GC content (%) | Genome coverage (×) | Plasmid replicon type(s) | Drug resistance phenotype and predicted resistance gene(s)b
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BLA | AMI | FQN | FOS | PHE | SUL | TRI | TET | MLS | |||||||||||
| KPS73a | SRR9208895 | VKCS00000000 | 807,366 | 220,354 | 74 | 5,558,879 | 5,451 | 57.2 | 17 | IncHI1B | blaSHV-190 | oqxA, oqxB | fosA | ||||||
| KPB1802a | SRR9208897 | VKCV00000000 | 729,262 | 157,398 | 74 | 5,620,879 | 5,519 | 57.0 | 25 | IncHI1B | blaSHV-190 | oqxA, oqxB | fosA | ||||||
| KPi1683a | SRR9208901 | VKCX00000000 | 751,372 | 180,119 | 78 | 5,580,912 | 5,452 | 57.2 | 35 | IncHI1B | blaSHV-190 | oqxA, oqxB | fosA | ||||||
| KPi3695 | SRR9208904 | VTRP00000000 | 592,094 | 154,881 | 77 | 5,573,189 | 5,453 | 57.1 | 27 | IncHI1B | blaSHV-190 | oqxA, oqxB | fosA | ||||||
| KPB1493a | SRR9208896 | VKCT00000000 | 501,624 | 56,694 | 300 | 5,521,123 | 5,669 | 57.0 | 22 | IncHI1B, IncFII(K) | blaSHV-190, blaCTXM15, blaTEM-1B, blaOXA-1 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib | aac(6')-Ib-cr, qnrB1 | fosA | catB3 | sul2 | dfrA14 | tetA | |
| KPB3188 | SRR9208900 | VKCU00000000 | 717,240 | 105,254 | 202 | 5,614,863 | 5,675 | 57.0 | 31 | IncHI1B, IncFII(K), IncL/M | blaSHV-190, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-48 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib | aac(6')-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | dfrA14 | tetA | |
| KPB1103a | SRR9208898 | VKCW00000000 | 660,384 | 97,397 | 151 | 5,594,258 | 5,644 | 57.2 | 29 | IncHI1B, IncFII(K), IncL/M | blaSHV-190, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-48 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib | aac(6')-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | dfrA14 | tetA | |
| KPB475a | SRR9208903 | VTRO00000000 | 980,374 | 151,126 | 143 | 5,661,349 | 5,714 | 56.9 | 42 | IncHI1B, IncFII(K), IncL/M | blaSHV-190, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-48 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib | aac(6')-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | dfrA14 | tetA | |
| KPB470 | SRR9208899 | VTRN00000000 | 762,324 | 86,243 | 223 | 5,490,022 | 5,582 | 57.2 | 31 | IncHI1B, IncFII(K), IncL/M | blaSHV-190, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-48 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib | aac(6')-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | dfrA14 | tetA | |
| KPB463-13 | SRR9208902 | VTRQ00000000 | 688,138 | 99,224 | 245 | 5,811,379 | 5,966 | 56.9 | 29 | IncHI1B, IncFII(K), IncL/M, Col440I, IncFIA(HI1) | blaSHV-190, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-48 | aac(6')-Ib-cr, aph(6)-Id, aph(3'')-Ib, armA | aac(6')-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul1, sul2 | dfrA14 | tetA | msr(E), mph(E) |
Additional information on strain characterization is provided in a previous publication (7).
BLA, beta-lactams; AMI, aminoglycoside; FQN, fluoroquinolone; FOS, fosfomycin; PHE, phenicol; SUL, sulphonamide; TRI, trimethoprim; TET, tetracycline; MLS, macrolide, lincosamide, and streptogramin B. Resistance phenotype was determined using a Vitek 2 Compact instrument (bioMérieux, France). ResFinder v.2.1 (14) was used to determine the presence of resistance genes.
Five types of plasmid replicons were determined in the assembled genomes using PlasmidFinder v.2.1 (10) (Table 1). All of the strains harbored a pLVPK-like virulence plasmid (11) containing an IncHI1B replicon, genes rpmA and/or rmpA2 encoding regulators of the mucoid phenotype specific to hypervirulent K. pneumoniae, and siderophore gene clusters iucABCD, iutA, and iroBCDN. Important differences in antibiotic resistance phenotype and resistance genes between strains with different plasmid profiles were revealed (Table 1). The strains harboring only a pLVPK-like plasmid were resistant to ampicillin, fluoroquinolone, and fosfomycin due to the presence of the chromosomal genes blaSHV-190, oqxA and/or oqxB, and fosA, respectively. Strain KPB1493 acquired the IncFII(K) plasmid, which additionally carried genes providing resistance to aminoglycosides, phenicols, sulfonamides, trimethoprim, and tetracyclines. Strains KPB3188, KPB1103, KPB475, KPB470, and KPB463-13 harbored the IncL/M plasmid carrying the carbapenemase gene blaOXA-48 and demonstrate resistance to carbapenems. The extrachromosomal genome of strain KPB463-13 and its resistance phenotype are even more complicated because of the presence of two more plasmids, namely a cryptic plasmid, Col440I, that was detected in many extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae strains (12), and an IncFIA(HI1) plasmid that is possibly associated with armA, sul1, msr(E), and mph(E) genes. It is important to emphasize the identification of epidemiologically significant genes encoding the blaOXA-48 carbapenemase and the bifunctional enzyme aac(6′)-Ib-cr.
The presented diversity of the genomes in the K. pneumoniae strains reflects the important role of plasmids in the horizontal transfer of resistance genes, which is the prevalent mechanism of originating antimicrobial resistance acquisition in bacterial pathogens (13).
Data availability.
Genome sequences were deposited in the GenBank/ENA/DDBJ databases under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
We are grateful to Vladimir E. Malikov (Moscow Infectious Disease Hospital No. 1) and Olga N. Ershova (Burdenko Neurosurgery Institute, Moscow) for providing Klebsiella pneumoniae isolates for the research.
This work was funded by the Russian Science Foundation (grant 15-15-00058).
REFERENCES
- 1.Podschun R, Ullmann U. 1998. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11:589–603. doi: 10.1128/CMR.11.4.589. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Shon AS, Bajwa RP, Russo TA. 2013. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 4:107–118. doi: 10.4161/viru.22718. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Cortes G, Borrell N, de Astorza B, Gómez C, Sauleda J, Albertí S. 2002. Molecular analysis of the contribution of the capsular polysaccharide and the lipopolysaccharide O side chain to the virulence of Klebsiella pneumoniae in a murine model of pneumonia. Infect Immun 70:2583–2590. doi: 10.1128/iai.70.5.2583-2590.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Yu WL, Ko WC, Cheng KC, Lee CC, Lai CC, Chuang YC. 2008. Comparison of prevalence of virulence factors for Klebsiella pneumoniae liver abscesses between isolates with capsular K1/K2 and non-K1/K2 serotypes. Diagn Microbiol Infect Dis 62:1–6. doi: 10.1016/j.diagmicrobio.2008.04.007. [DOI] [PubMed] [Google Scholar]
- 5.Liu YM, Li BB, Zhang YY, Zhang W, Shen H, Li H, Cao B. 2014. Clinical and molecular characteristics of emerging hypervirulent Klebsiella pneumoniae bloodstream infections in mainland China. Antimicrob Agents Chemother 58:5379–5385. doi: 10.1128/AAC.02523-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Volozhantsev NV, Kislichkina AA, Lev AI, Solovieva EV, Myakinina VP, Mukhina TN, Bogun AG, Fursova NK. 2018. Draft genome sequences of 10 clinical K2-type Klebsiella pneumoniae strains isolated in Russia. Microbiol Resour Announc 7:e01023-18. doi: 10.1128/MRA.01023-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Lev AI, Astashkin EI, Kislichkina AA, Solovieva EV, Kombarova TI, Korobova OV, Ershova ON, Alexandrova IA, Malikov VE, Bogun AG, Borzilov AI, Volozhantsev NV, Svetoch EA, Fursova NK. 2018. Comparative analysis of Klebsiella pneumoniae strains isolated in 2012–2016 that differ by antibiotic resistance genes and virulence genes profiles. Pathog Glob Health 112:142–151. doi: 10.1080/20477724.2018.1460949. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. doi: 10.1371/journal.pcbi.1005595. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi: 10.1128/AAC.02412-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Chen YT, Chang HY, Lai YC, Pan CC, Tsai SF, Peng HL. 2004. Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene 337:189–198. doi: 10.1016/j.gene.2004.05.008. [DOI] [PubMed] [Google Scholar]
- 12.Lepuschitz S, Schill S, Stoeger A, Pekard-Amenitsch S, Huhulescu S, Inreiter N, Hartl R, Kerschner H, Sorschag S, Springer B, Brisse S, Allerberger F, Mach RL, Ruppitsch W. 2019. Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals. Sci Total Environ 662:227–235. doi: 10.1016/j.scitotenv.2019.01.179. [DOI] [PubMed] [Google Scholar]
- 13.Carattoli A. 2013. Plasmids and the spread of resistance. Int J Med Microbiol 303:298–304. doi: 10.1016/j.ijmm.2013.02.001. [DOI] [PubMed] [Google Scholar]
- 14.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. doi: 10.1093/jac/dks261. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Genome sequences were deposited in the GenBank/ENA/DDBJ databases under the accession numbers listed in Table 1.