Volume 23, Number 11—November 2017
Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan
- Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A. 2015;112:E3574–81.
- Lee CR, Lee JH, Park KS, Kim YB, Jeong BC, Lee SH. Global dissemination of carbapenemase-producing Klebsiella pneumoniae: epidemiology, genetic context, treatment options, and detection methods. Front Microbiol. 2016;7:895.
- Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, et al. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Mol Med. 2015;7:227–39.
- World Health Organization. Antimicrobial resistance: global report on surveillance 2014. Geneva: The Organization; 2014.
- Centers for Disease Control and Prevention. New carbapenem-resistant Enterobacteriaceae warrant additional action by healthcare providers [cited 2017 Jan 5]. https://emergency.cdc.gov/han/han00341.asp
- Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing; twentieth informational supplement. M100-S20. Wayne (PA): The Institute; 2010.
- Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom. 2016;2:e000083.
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
- Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132.
- Brisse S, Passet V, Grimont PA. Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol. 2014;64:3146–52.
- Pérez-Vázquez M, Oteo J, García-Cobos S, Aracil B, Harris SR, Ortega A, et al. Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain. J Antimicrob Chemother. 2016;71:887–96.
- Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.
- Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom. 2016;2:e000056.
- Stamatakis A. Using RAxML to infer phylogenies. Curr Protoc Bioinformatics. 2015;51:6.14.1-14.
- Arena F, Henrici De Angelis L, Pieralli F, Di Pilato V, Giani T, Torricelli F, et al. Draft genome sequence of the first hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae isolate from a bloodstream infection. Genome Announc. 2015;3:e00952–15.
1These authors contributed equally to this article.
2Current affiliation: CAMS, Aljouf University, Aljouf, Saudi Arabia.
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