Characterization of a CTX-M-15 Producing Klebsiella Pneumoniae Outbreak Strain Assigned to a Novel Sequence Type (1427)

Alcántar-Curiel, 2013, Multi-functional analysis of Klebsiella pneumoniae fimbrial types in adherence and biofilm formation, Virulence, 4, 129, 10.4161/viru.22974

Assefa, 2009, ABACAS: algorithm-based automatic contiguation of assembled sequences, Bioinformatics, 25, 1968, 10.1093/bioinformatics/btp347

Aziz, 2008, The RAST Server: rapid annotations using subsystems technology, BMC Genomics, 9, 75, 10.1186/1471-2164-9-75

Baraniak, 2013, Comparative population analysis of Klebsiella pneumoniae strains with extended-spectrum β-lactamases colonizing patients in rehabilitation centers in four countries, Antimicrob. Agents Chemother., 57, 1992, 10.1128/AAC.02571-12

Bialek-Davenet, 2014, Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups, Emerging Infect. Dis., 20, 1812, 10.3201/eid2011.140206

Bialek-Davenet, 2011, In vitro selection of ramR and soxR mutants overexpressing efflux systems by fluoroquinolones as well as cefoxitin in Klebsiella pneumoniae, Antimicrob. Agents Chemother., 55, 2795, 10.1128/AAC.00156-11

Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683

Boetzer, 2012, Toward almost closed genomes with GapFiller, Genome Biol., 13, R56, 10.1186/gb-2012-13-6-r56

Bonemann, 2010, Tubules and donuts: a type VI secretion story, Mol. Microbiol., 76, 815, 10.1111/j.1365-2958.2010.07171.x

Brisse, 2013, wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains, J. Clin. Microbiol., 51, 4073, 10.1128/JCM.01924-13

Carattoli, 2009, Resistance plasmid families in Enterobacteriaceae, Antimicrob. Agents Chemother., 53, 2227, 10.1128/AAC.01707-08

Chen, 2014, The role of pgaC in Klebsiella pneumoniae virulence and biofilm formation, Microb. Pathog., 77, 89, 10.1016/j.micpath.2014.11.005

D'Andrea, 2013, CTX-M-type β-lactamases: a successful story of antibiotic resistance, Int. J. Med. Microbiol., 303, 305, 10.1016/j.ijmm.2013.02.008

Darch, 2015, Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection, Sci. Rep., 5, 7649, 10.1038/srep07649

Darling, 2010, ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement, PLoS ONE, 5, e11147, 10.1371/journal.pone.0011147

Dolejska, 2013, Plasmid content of a clinically relevant Klebsiella pneumoniae clone from the Czech Republic producing CTX-M-15 and QnrB1, Antimicrob. Agents Chemother., 57, 1073, 10.1128/AAC.01886-12

Filippa, 2013, Outbreak of multidrug-resistant Klebsiella pneumoniae carrying qnrB1 and blaCTX−M15 in a French intensive care unit, Ann. Intensive Care, 3, 18, 10.1186/2110-5820-3-18

Hirai, 2013, Detection of chromosomal blaCTX−M−15 in Escherichia coli O25b-B2-ST131 isolates from the Kinki region of Japan, Int. J. Antimicrob. Agents, 42, 500, 10.1016/j.ijantimicag.2013.08.005

Huang, 2013, Copy number change of the NDM-1 sequence in a multidrug-resistant Klebsiella pneumoniae clinical isolate, PLoS ONE, 8, e62774, 10.1371/journal.pone.0062774

Lawley, 2003, F factor conjugation is a true type IV secretion system, FEMS Microbiol. Lett., 224, 1, 10.1016/S0378-1097(03)00430-0

Lee, 2011, High prevalence of CTX-M-15-producing Klebsiella pneumoniae isolates in Asian countries: diverse clones and clonal dissemination, Int. J. Antimicrob. Agents, 38, 160, 10.1016/j.ijantimicag.2011.03.020

Li, 2014, Molecular pathogenesis of Klebsiella pneumoniae, Future Microbiol., 9, 1071, 10.2217/fmb.14.48

Livermore, 2007, CTX-M: changing the face of ESBLs in Europe, J. Antimicrob. Chemother., 59, 165, 10.1093/jac/dkl483

Machado, 2006, Dissemination in Portugal of CTX-M-15-, OXA-1-, and TEM-1-producing Enterobacteriaceae strains containing the aac(6′)-Ib-cr gene, which encodes an aminoglycoside- and fluoroquinolone-modifying enzyme, Antimicrob. Agents Chemother., 50, 3220, 10.1128/AAC.00473-06

Mathers, 2015, The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae, Clin. Microbiol. Rev., 28, 565, 10.1128/CMR.00116-14

Ogawa, 2012, Functional study of the novel multidrug efflux pump KexD from Klebsiella pneumoniae, Gene, 498, 177, 10.1016/j.gene.2012.02.008

Paterson, 2005, Extended-spectrum β-lactamases: a clinical update, Clin. Microbiol. Rev., 18, 657, 10.1128/CMR.18.4.657-686.2005

Peirano, 2010, Molecular epidemiology of Escherichia coli producing CTX-M β-lactamases: the worldwide emergence of clone ST131 O25:H4, Int. J. Antimicrob. Agents, 35, 316, 10.1016/j.ijantimicag.2009.11.003

Pitout, 2008, Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public-health concern, Lancet Infect. Dis., 8, 159, 10.1016/S1473-3099(08)70041-0

Rodrigues, 2014, Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: a successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFIIK), Int. J. Med. Microbiol., 304, 1100, 10.1016/j.ijmm.2014.08.003

Russell, 2014, Type VI secretion system effectors: poisons with a purpose, Nat. Rev. Microbiol., 12, 137, 10.1038/nrmicro3185

Shon, 2013, Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed, Virulence, 4, 107, 10.4161/viru.22718

Shu, 2009, Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates, Microbiology, 155, 4170, 10.1099/mic.0.029017-0

Snitkin, 2012, Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing, Sci. Transl. Med., 4, 148ra116, 10.1126/scitranslmed.3004129

Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446

Tal Jasper, 2015, The complex epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae, Future Microbiol., 10, 819, 10.2217/fmb.15.16

Tielen, 2013, Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions, PLoS ONE, 8, e71845, 10.1371/journal.pone.0071845

Weigel, 1998, gyrA Mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae, Antimicrob. Agents Chemother., 42, 2661, 10.1128/AAC.42.10.2661

Wyres, 2015, Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258, Genome Biol. Evol., 7, 1267, 10.1093/gbe/evv062

Yang, 2011, Evolutionary dynamics of bacteria in a human host environment, Proc. Natl. Acad. Sci. U.S.A., 108, 7481, 10.1073/pnas.1018249108

Zhou, 2015, The mosaic genome structure and phylogeny of Shiga toxin-producing Escherichia coli O104:H4 is driven by short-term adaptation, Clin. Microbiol. Infect., 21, 468, 10.1016/j.cmi.2014.12.009