Dataset Information

Hybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing.

ABSTRACT: Background:The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of K. pneumoniae strain KP58, a pandrug-resistant K. pneumoniae strain that exhibits high levels of resistance to colistin and tigecycline in China. Methods:The K. pneumoniae strain KP58 was recovered from a urine sample of a female patient hospitalized in a tertiary hospital in Hangzhou, China. Antimicrobial susceptibility testing was performed and the minimum inhibitory concentrations (MICs) were determined. Whole-genome sequencing was performed using Illumina and Oxford nanopore sequencing technologies. Genomic features, antimicrobial resistance genes and virulence genes were comprehensively analysed by various bioinformatics approaches. In addition, genomic epidemiological and phylogenetic analyses of K. pneumoniae KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database. Results:K. pneumoniae KP58 was resistant to all antimicrobial agents tested, including tigecycline and colistin. Combining the two sequencing technologies allowed a high-quality complete genome sequence of K. pneumoniae KP58 comprising one circular chromosome and five circular plasmids to be obtained. This strain harbours a variety of acquired antimicrobial resistance and virulence determinants. It also carried an ISKpn26-like insertion in the disrupted mgrB gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of K. pneumoniae KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci. Conclusion:The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant K. pneumoniae in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.

SUBMITTER: Ruan Z

PROVIDER: S-EPMC6982529 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <i>Klebsiella pneumoniae</i> Strain Using Nanopore and Illumina Sequencing.

Ruan Zhi Z Wu Jianyong J Chen Hangfei H Draz Mohamed S MS Xu Juan J He Fang F

Infection and drug resistance 20200121

<h4>Background</h4>The prevalence of multidrug-resistant <i>Klebsiella pneumoniae</i> is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of <i>K. pneumoniae</i> strain KP58, a pandrug-resistant <i>K. pneumoniae</i> strain that exhibits high levels of resistance to colistin and tigecycline in China.<h4>Methods</h4>The <i>K. pneumoniae</i> strain KP58 was recovered from a urine sample of a female patient hospita ...[more]

PMID: 32021334

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Project description:BackgroundSome of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics.ResultsWe generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches.ConclusionsWe present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

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Dataset Information

Hybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing.

Publications

Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <i>Klebsiella pneumoniae</i> Strain Using Nanopore and Illumina Sequencing.

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