Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain

Lin, Ann-Chi; Liao, Tsai-Lien; Lin, Yi‐Chun; Lai, Yi‐Chyi; Lu, Min-Chi; Chen, Ying-Tsong

doi:10.1128/jb.01548-12

Cited by 32 publications

(33 citation statements)

References 5 publications

(2 reference statements)

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“…Up to 99% of the reads (13.1 to 36.6 million reads per isolate with a median of 20 million reads; http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13016/suppinfo) could be mapped to a non‐redundant gene list of the K. pneumoniae pan‐genome. This pan‐genome was generated on the basis that the fully sequenced genome of the clinical strain 1084 (sequence type 23) (Lin et al ., ) complemented with publicly available DNA sequence data of 10 K. pneumoniae isolates (see Materials and methods for details) to gain comprehensive and unbiased insights into the transcriptional landscape of this pathogen. To exclude any bias in mapping efficiency due to the choice of the core genome reference strain, we also created a pan‐genome based on a different sequence type (MGH 78578; ST38).…”

Section: Resultsmentioning

confidence: 99%

“…A total of 30 sRNAs were included in the final gene set. To generate a single reference sequence file, sequences of core‐genom genes were selected from the sequence type 23 strain ‘1084’ (Lin et al ., ), and the accessory genes and the singletons were added from each of the remaining 10 genomes considered in this study. The origin of each sequence is indicated by the locus ID in http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13016/suppinfo (see also Table ).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation

Bruchmann

Muthukumarasamy

Pohl

et al. 2015

Environmental Microbiology

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CitationDeep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence typespecific adaptation. 2015, 17 (11) isolates. While the core-transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence.This allowed for the identification of a diminished expression of biofilm-specific genes within the low biofilm producing ST258 isolates as a sequence type-specific trait.2

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation

Bruchmann

Muthukumarasamy

Pohl

et al. 2015

Environmental Microbiology

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“…bla SHV , catB4, macA, macB, and fosA are frequently present on the K. pneumoniae chromosomes (GenBank accession no. CP000647) (25,26).…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

Doi

Hazen

Boitano

et al. 2014

Antimicrob Agents Chemother

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The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of the K. pneumoniae reference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries the bla NDM-1 , armA, and qnrB1 genes, along with tellurium and mercury resistance operons. bla NDM-1 is carried on a unique structure in which Tn125 is further bracketed by IS26 downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, including bla CTX-M-15 and a mercury resistance operon. The ColE-type plasmid pPKPN4 carrying bla OXA-232 is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in the de novo assemblies.

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“…Red (forward) and blue (reverse) shading denotes shared regions of homology, and the black box line illustrates the cps region in each genome. ST258 isolates (NJST258_1 and _2; CP006923 and CP006918) [24], ST11 isolate ATCC BAA-2146 (CP006659) [73], ST38 isolate MGH 78578 (CP000647) and one ST146 isolate (Kp 342) (CP000964) [74] were from United States; ST11 isolates HS11286 (CP003200) [29] and JM45 (CP006656) were from mainland China; two ST23 K1 isolates (NTUH-K2044 and Kp 1084; AP006725 and CP003785) and one ST86 K2 isolate (CP006648) were from were Taiwan [75, 76]; and ST375 isolate (KCTC 2242; CP002910) was from Korea [77], and one ST442 isolate (Kp13; CP003999) is from Brazil [23]. The left panel is the maximum likelihood tree generated using the SNPs extracted by Mauve.…”

Section: Figurementioning

confidence: 99%

Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding

Chen

Mathema

Chavda

et al. 2014

Trends in Microbiology

412

383

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Klebsiella pneumoniae carbapenemases (KPCs) were first identified in 1996 in the USA. Since then, regional outbreaks of KPC-producing K. pneumoniae have occurred in the USA, and have spread internationally. Dissemination of blaKPC involves both horizontal transfer of blaKPC genes and plasmids, and clonal spread. Of epidemiological significance, the international spread of KPC-producing K. pneumoniae is primarily associated with a single multilocus sequence type (ST), ST258, and its related variants. However, the molecular factors contributing to the success of ST258 largely remain unclear. Here, we review the recent progresses in understanding KPC-producing K. pneumoniae that is contributing to our knowledge of plasmid and genome composition and structure among the KPC epidemic clone, and identify possible factors that influence its epidemiological success.

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Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain

Abstract: fWe report the complete genome sequence of Klebsiella pneumoniae 1084, a hypermucoviscosity-negative K1 clinical strain. Sequencing and annotation revealed a 5,386,705-bp circular chromosome (57.4% G؉C content), which contains 4,962 proteincoding genes, 80 tRNA genes, and 25 rRNA genes.

Cited by 32 publications

References 5 publications

Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation

Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation

Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding

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