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      Hypervirulent Klebsiella pneumoniae is emerging as an increasingly prevalent K. pneumoniae pathotype responsible for nosocomial and healthcare-associated infections in Beijing, China

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          ABSTRACT

          Objectives

          Hypervirulent Klebsiella pneumoniae(hvKp) is an increasingly important pathogen. Tracking its epidemiology and evolving antimicrobial resistance will facilitate care.

          Methods

          A retrospective study was conducted in two hospitals. We collected the clinical data. Antimicrobial and virulence-associated phenotype and genotype, sequence type, and whole genome sequencing of selected strains were performed. HvKp was defined by the presence of some combination of  prmpA,  prmpA2, iucA, iroB, and peg-344, genes shown to accurately identify hvKp.

          Results

          Of 158 Kp clinical isolates, 79 (50%) were hvKp. Interestingly, 53/79 (67.1%) of hvKp strains were isolated from patients with nosocomial infection and 19/79 (24.1%) from patients with healthcare-associated infection, but only 7/79 (8.8%) from patients with community-acquired infections. Importantly, 27/53 (50.9%) and 4/19 (21.1%) of hvKp nosocomial and healthcare-associated isolates, respectively, were multi-drug-resistant (MDR); 25/53 (47.2%) and 5/19 (26.3%) expressed ESBLs and 14/53 (26.4%) and 2/19 (10.5%) were carbapenem-resistant. Of the hvKp isolates from community-acquired infection, 0/7 (0%) were MDR and 0/7 (0%) were carbapenem-resistant. Additionally, unique characteristics of nosocomial, healthcare-associated, and community-acquired hvKp infection were identified. In summary, 50% of K. pneumoniae infections were caused by hvKp. A concerning, novel finding from this report is a major shift in hvKp epidemiology. Ninety-one percent of hvKp infections were nosocomial or healthcare-associated, and 43.1% of these isolates were MDR.

          Conclusions

          These data suggest that hvKp may be replacing classical K. pneumoniae as the dominant nosocomial and healthcare-associated pathotype. Ongoing surveillance is needed to determine if this trend is occurring elsewhere.

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          Most cited references43

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

              The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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                Author and article information

                Contributors
                On behalf of : the China Surveillance of Hypervirulent Klebsiella pneumoniae(CS-HVKP) Research Group.
                Journal
                Virulence
                Virulence
                Virulence
                Taylor & Francis
                2150-5594
                2150-5608
                12 September 2020
                2020
                12 September 2020
                : 11
                : 1
                : 1215-1224
                Affiliations
                [a ]Department of Infectious Diseases, Peking University Third Hospital; , Beijing, China
                [b ]Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases; , Beijing, China
                [c ]Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University; , Beijing, China
                [d ]Department of Basic Medical Sciences, School of Medicine, Tsinghua University; , Beijing, China
                [e ]Department of Medicine, University at Buffalo, State University of New York; , Buffalo, NY, USA
                [f ]Veterans Administration Western New York Healthcare System; , Buffalo, New York, USA
                [g ]Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University; , Beijing, China
                Author notes
                [*]

                Chao Liu and Pengcheng Du are co-first authors.

                [#]

                The authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0003-4566-7442
                Article
                1809322
                10.1080/21505594.2020.1809322
                7549996
                32921250
                bbedf7e9-3c69-47d8-b495-99a5b93a75a6
                © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 1, Tables: 4, References: 43, Pages: 10
                Categories
                Research Article
                Research Paper

                Infectious disease & Microbiology
                hypervirulent klebsiella pneumoniae,multi drug resistance,carbapenemase,epidemiology,nosocomial infection,clinical characteristics,risk factor

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