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      Emergence of Ceftazidime- and Avibactam-Resistant Klebsiella pneumoniae Carbapenemase-Producing Pseudomonas aeruginosa in China

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          ABSTRACT

          Klebsiella pneumoniae carbapenemase (KPC)-producing Pseudomonas aeruginosa (KPC-PA) has been reported sporadically. However, epidemiological and antimicrobial susceptibility data specific for KPC-PA are lacking. We collected 374 carbapenem-resistant P. aeruginosa (CRPA) isolates from seven hospitals in China from June 2016 to February 2019 and identified the bla KPC-2 gene in 40.4% ( n = 151/374) of the isolates. Approximately one-half of all KPC-PA isolates ( n = 76/151; 50.3%) were resistant to ceftazidime-avibactam (CAZ-AVI). Combining Kraken2 taxonomy identification and Nanopore sequencing, we identified eight plasmid types, five of which carried bla KPC-2, and 13 combination patterns of these plasmid types. In addition, we identified IS 26-ΔTn 6296 and Tn 1403-like–ΔTn 6296 as the two mobile genetic elements that mediated bla KPC-2 transmission. bla KPC-2 plasmid curing in 28 strains restored CAZ-AVI susceptibility, suggesting that bla KPC-2 was the mediator of CAZ-AVI resistance. Furthermore, the bla KPC-2 copy number was found to correlate with KPC expression and, therefore, CAZ-AVI resistance. Taken together, our results suggest that KPC-PA is becoming a clinical threat and that using CAZ-AVI to treat this specific pathogen should be done with caution.

          IMPORTANCE Previous research has reported several cases of KPC-PA strains and three KPC-encoding P. aeruginosa plasmid types in China. However, the prevalence and clinical significance of KPC-PA are not available. In addition, the susceptibility of the strains to CAZ-AVI remains unknown. Samples in this study were collected from seven tertiary hospitals prior to CAZ-AVI clinical approval in China. Therefore, our results represent a retrospective study establishing the baseline efficacy of the novel β-lactam/β-lactamase combination agent for treating KPC-PA infections. The observed correlation between the bla KPC copy number and CAZ-AVI resistance suggests that close monitoring of the susceptibility of the strain during treatment is required. It would also be beneficial to screen for the bla KPC gene in CRPA strains for antimicrobial surveillance purposes.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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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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              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                mSystems
                mSystems
                msystems
                mSystems
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2379-5077
                2 November 2021
                Nov-Dec 2021
                2 November 2021
                : 6
                : 6
                : e00787-21
                Affiliations
                [a ] Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang Universitygrid.13402.34, School of Medicine, Hangzhou, China
                [b ] Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
                [c ] Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang Universitygrid.13402.34, School of Medicine, Hangzhou, China
                [d ] Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
                [e ] Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
                [f ] Department of Laboratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
                [g ] Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospitalgrid.413106.1, , Peking Union Medical College, Beijing, China
                [h ] Department of Clinical Laboratory, Quzhou People’s Hospital, Affiliated Quzhou Hospital of Wenzhou Medical University, Quzhou, China
                [i ] Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, China
                [j ] State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang Universitygrid.13402.34, , Hangzhou, China
                [k ] Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang Universitygrid.13402.34, School of Medicine, Hangzhou, China
                University of California, San Francisco
                Author notes
                [*]

                Present address: Jie Chen, Department of Laboratory, Ningbo Medical Center Lihuili Hospital, Ningbo, China.

                Author information
                https://orcid.org/0000-0001-8215-916X
                Article
                mSystems00787-21 msystems.00787-21
                10.1128/mSystems.00787-21
                8562488
                34726488
                c8b84b80-19c1-41a8-a4d6-9872f08efe0f
                Copyright © 2021 Zhu et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 22 June 2021
                : 6 October 2021
                Page count
                supplementary-material: 5, Figures: 4, Tables: 3, Equations: 0, References: 53, Pages: 12, Words: 7146
                Funding
                Funded by: National Natural Science Foundation of China (NSF), FundRef https://doi.org/10.13039/501100001809;
                Award ID: 81830069
                Award Recipient :
                Categories
                Research Article
                open-peer-review, Open Peer Review
                antimicrobial-chemotherapy, Antimicrobial Chemotherapy
                Custom metadata
                November/December 2021

                carbapenem-resistant pseudomonas aeruginosa, bla kpc-2 ,ceftazidime-avibactam,pseudomonas aeruginosa

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