Different IncI1 plasmids from Escherichia coli carry ISEcp1-blaCTX-M-15 associated with different Tn2-derived elements

Plasmid - Tập 80 - Trang 118-126 - 2015
Zhiyong Zong1,2, Andrew N. Ginn1, Hana Dobiasova1,3,4, Jonathan R. Iredell1, Sally R. Partridge1
1Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia
2Department of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
3Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
4CEITEC VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic

Tài liệu tham khảo

Ahmed, 2012, Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including Shiga toxin encoding phage stx2, PLoS ONE, 7, e48228, 10.1371/journal.pone.0048228 Amos, 2014, Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment, J. Antimicrob. Chemother, 69, 1785, 10.1093/jac/dku079 Arvand, 2015, Extended-spectrum beta-lactamase-producing Shiga toxin gene (stx1)-positive Escherichia coli O91:H14 carrying blaCTX-M-15 on an IncI1-ST31 plasmid isolated from a human patient in Germany, Int. J. Med. Microbiol, 305, 404, 10.1016/j.ijmm.2015.03.003 Bailey, 2011, Distribution of the blaTEM gene and blaTEM-containing transposons in commensal Escherichia coli, J. Antimicrob. Chemother, 66, 745, 10.1093/jac/dkq529 Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, 19, 455, 10.1089/cmb.2012.0021 Barton, 1995, A general method for detecting and sizing large plasmids, Anal. Biochem, 226, 235, 10.1006/abio.1995.1220 Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683 Boyd, 2004, Complete nucleotide sequence of a 92-kilobase plasmid harboring the CTX-M-15 extended-spectrum beta-lactamase involved in an outbreak in long-term-care facilities in Toronto, Canada, Antimicrob. Agents Chemother, 48, 3758, 10.1128/AAC.48.10.3758-3764.2004 Brolund, 2014, Epidemiology of extended-spectrum β-lactamase-producing Escherichia coli in Sweden 2007–2011, Clin. Microbiol. Infect, 20, O344, 10.1111/1469-0691.12413 Brouwer, 2014, Complete genome sequences of IncI1 plasmids carrying extended-spectrum β-lactamase genes, Genome Announc, 2, 10.1128/genomeA.00859-14 Brouwer, 2015, IncI shufflons: assembly issues in the next-generation sequencing era, Plasmid, 10.1016/j.plasmid.2015.04.009 Chen, 2014, Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli sequence type 131 strain in China, Antimicrob. Agents Chemother, 58, 2422, 10.1128/AAC.02587-13 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 Foster, 1981, Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats, Cell, 23, 215, 10.1016/0092-8674(81)90286-5 Galimand, 2005, Worldwide disseminated armA aminoglycoside resistance methylase gene is borne by composite transposon Tn1548, Antimicrob. Agents Chemother, 49, 2949, 10.1128/AAC.49.7.2949-2953.2005 Garcia-Fernandez, 2008, Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum β-lactamases in Escherichia coli and Salmonella of human and animal origin, J. Antimicrob. Chemother, 61, 1229, 10.1093/jac/dkn131 Gerdes, 2000, Plasmid and chromosome partitioning: surprises from phylogeny, Mol. Microbiol, 37, 455, 10.1046/j.1365-2958.2000.01975.x Golub, 1985, Conjugative plasmids of enteric bacteria from many different incompatibility groups have similar genes for single-stranded DNA-binding proteins, J. Bacteriol, 162, 235, 10.1128/JB.162.1.235-241.1985 Gołębiewski, 2007, Complete nucleotide sequence of the pCTX-M3 plasmid and its involvement in spread of the extended-spectrum β-lactamase gene blaCTX-M-3, Antimicrob. Agents Chemother, 51, 3789, 10.1128/AAC.00457-07 Harmer, 2014, Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26, MBio, 5, e1801, 10.1128/mBio.01801-14 Hopkins, 2006, Replicon typing of plasmids carrying CTX-M or CMY β-lactamases circulating among Salmonella and Escherichia coli isolates, Antimicrob. Agents Chemother, 50, 3203, 10.1128/AAC.00149-06 Howland, 1989, The ssb gene of plasmid ColIb-P9, J. Bacteriol, 171, 2466, 10.1128/jb.171.5.2466-2473.1989 Johnson, 2011, Comparative genomics and phylogeny of the IncI1 plasmids: a common plasmid type among porcine enterotoxigenic Escherichia coli, Plasmid, 66, 144, 10.1016/j.plasmid.2011.07.003 Koonin, 1993, A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif, J. Mol. Biol, 229, 1165, 10.1006/jmbi.1993.1115 Magoc, 2011, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, 27, 2957, 10.1093/bioinformatics/btr507 Manges, 2001, Widespread distribution of urinary tract infections caused by a multidrug-resistant Escherichia coli clonal group, N. Engl. J. Med, 345, 1007, 10.1056/NEJMoa011265 Mellmann, 2011, Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology, PLoS ONE, 6, e22751, 10.1371/journal.pone.0022751 Naseer, 2011, The CTX-M conundrum: dissemination of plasmids and Escherichia coli clones, Microb. Drug Resist, 17, 83, 10.1089/mdr.2010.0132 O'Brien, 2002, Emergence, spread, and environmental effect of antimicrobial resistance: how use of an antimicrobial anywhere can increase resistance to any antimicrobial anywhere else, Clin. Infect. Dis, 34, S78, 10.1086/340244 Overbeek, 2014, The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Res, 42, D206, 10.1093/nar/gkt1226 Partridge, 2011, Analysis of antibiotic resistance regions in Gram-negative bacteria, FEMS Microbiol. Rev, 35, 820, 10.1111/j.1574-6976.2011.00277.x Partridge, 2005, Evolution of transposons containing blaTEM genes, Antimicrob. Agents Chemother, 49, 1267, 10.1128/AAC.49.3.1267-1268.2005 Partridge, 2011, Complete sequence of pJIE143, a pir-type plasmid carrying ISEcp1-blaCTX-M-15 from an Escherichia coli ST131 isolate, Antimicrob. Agents Chemother, 55, 5933, 10.1128/AAC.00639-11 Partridge, 2011, Recombination in IS26 and Tn2 in the evolution of multi-resistance regions carrying blaCTX-M-15 on conjugative IncF plasmids from Escherichia coli, Antimicrob. Agents Chemother, 55, 4971, 10.1128/AAC.00025-11 Platell, 2010, Clonal group distribution of fluoroquinolone-resistant Escherichia coli among humans and companion animals in Australia, J. Antimicrob. Chemother, 65, 1936, 10.1093/jac/dkq236 Poirel, 2003, Insertion sequence ISEcp1B is involved in expression and mobilization of a blaCTX-M β-lactamase gene, Antimicrob. Agents Chemother, 47, 2938, 10.1128/AAC.47.9.2938-2945.2003 Poirel, 2005, ISEcp1B-mediated transposition of blaCTX-M in Escherichia coli, Antimicrob. Agents Chemother, 49, 447, 10.1128/AAC.49.1.447-450.2005 Rodríguez, 2004, Chromosome-encoded CTX-M-3 from Kluyvera ascorbata: a possible origin of plasmid-borne CTX-M-1-derived cefotaximases, Antimicrob. Agents Chemother, 48, 4895, 10.1128/AAC.48.12.4895-4897.2004 Rohde, 2011, Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4, N. Engl. J. Med, 365, 718, 10.1056/NEJMoa1107643 Sakuma, 2013, ExcA proteins of IncI1 plasmid R64 and IncIγ plasmid R621a recognize different segments of their cognate TraY proteins in entry exclusion, Plasmid, 69, 138, 10.1016/j.plasmid.2012.11.004 Sampei, 2010, Complete genome sequence of the incompatibility group I1 plasmid R64, Plasmid, 64, 92, 10.1016/j.plasmid.2010.05.005 Seral, 2012, [Characterisation of a CTX-M-15-producing Shigella sonnei in a Spanish patient who had not travelled abroad], Enferm. Infecc. Microbiol. Clin, 30, 469, 10.1016/j.eimc.2011.11.015 Smet, 2010, Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences, PLoS ONE, 5, e11202, 10.1371/journal.pone.0011202 Tagg, 2014, Complete sequencing of IncI1 sequence type 2 plasmid pJIE512b indicates mobilization of blaCMY-2 from an IncA/C plasmid, Antimicrob. Agents Chemother, 58, 4949, 10.1128/AAC.02773-14 Takahashi, 2011, The genome sequence of the incompatibility group Iγ plasmid R621a: evolution of IncI plasmids, Plasmid, 66, 112, 10.1016/j.plasmid.2011.06.004 Tietze, 2015, Comparative genomic analysis of two novel sporadic Shiga toxin-producing Escherichia coli O104:H4 strains isolated 2011 in Germany, PLoS ONE, 10, e0122074, 10.1371/journal.pone.0122074 Timofte, 2014, Detection and molecular characterization of Escherichia coli CTX-M-15 and Klebsiella pneumoniae SHV-12 β-lactamases from bovine mastitis isolates in the United Kingdom, Antimicrob. Agents Chemother, 58, 789, 10.1128/AAC.00752-13 Wirth, 2006, Sex and virulence in Escherichia coli: an evolutionary perspective, Mol. Microbiol, 60, 1136, 10.1111/j.1365-2958.2006.05172.x Woodford, 2009, Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone, Antimicrob. Agents Chemother, 53, 4472, 10.1128/AAC.00688-09 Yamaichi, 2015, High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4, Nucleic Acids Res, 43, 348, 10.1093/nar/gku1262 Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, 18, 821, 10.1101/gr.074492.107 Zhu, 2009, Complete nucleotide sequence of pCTX-M360, an intermediate plasmid between pEL60 and pCTX-M3, from a multidrug-resistant Klebsiella pneumoniae strain isolated in China, Antimicrob. Agents Chemother, 53, 5291, 10.1128/AAC.00032-09 Zong, 2008, Dominance of blaCTX-M within an Australian extended-spectrum β-lactamase gene pool, Antimicrob. Agents Chemother, 52, 4198, 10.1128/AAC.00107-08