Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones
Tài liệu tham khảo
Bagley, 1985, Habitat association of Klebsiella species, Infect. Contr., 6, 52, 10.1017/S0195941700062603
Podschun, 1998, Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors, Clin. Microbiol. Rev., 11, 589, 10.1128/CMR.11.4.589
Jones, 2010, Microbial etiologies of hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia, Clin. Infect. Dis., 51, S81, 10.1086/653053
Pendleton, 2013, Clinical relevance of the ESKAPE pathogens, Exp. Rev. Anti Infect. Ther., 11, 297, 10.1586/eri.13.12
2014
Chaves, 2001, SHV-1 β-lactamase is mainly a chromosomally encoded species-specific enzyme in Klebsiella pneumoniae, Antimicrob. Agents Chemother., 45, 2856, 10.1128/AAC.45.10.2856-2861.2001
Sirot, 1988, Klebsiella pneumoniae and other Enterobacteriaceae producing novel plasmid-mediated beta-lactamases markedly active against third-generation cephalosporins: epidemiologic studies, Clin. Infect. Dis., 10, 850, 10.1093/clinids/10.4.850
Nordmann, 2009, The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria, Lancet Infect. Dis., 9, 228, 10.1016/S1473-3099(09)70054-4
Nordmann, 2011, The emerging NDM carbapenemases, Trends Microbiol., 19, 588, 10.1016/j.tim.2011.09.005
Liu, 2016, Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study, Lancet Infect. Dis., 16, 161, 10.1016/S1473-3099(15)00424-7
Diancourt, 2005, Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates, J. Clin. Microbiol., 43, 4178, 10.1128/JCM.43.8.4178-4182.2005
Brisse, 2009, Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization, PLoS One, 4, e4982, 10.1371/journal.pone.0004982
Maiden, 2006, Multilocus sequence typing of bacteria, Annu. Rev. Microbiol., 60, 561, 10.1146/annurev.micro.59.030804.121325
Bialek-Davenet, 2014, Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups, Emerg. Infect. Dis., 20, 1812, 10.3201/eid2011.140206
Jolley, 2010, BIGSdb: scalable analysis of bacterial genome variation at the population level, BMC Bioinformatics., 10, 595, 10.1186/1471-2105-11-595
Holt, 2015, 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., 112, E3574, 10.1073/pnas.1501049112
Snitkin, 2012, Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing, Sci. Transl. Med., 4, 148ra116, 10.1126/scitranslmed.3004129
The, 2015, A high-resolution genomic analysis of multidrug- resistant hospital outbreaks of Klebsiella pneumoniae, EMBO Molec. Med., 7, 227, 10.15252/emmm.201404767
Bowers, 2015, Genomic analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella pneumoniae pandemic, PLoS One, 10, e0133727, 10.1371/journal.pone.0133727
Zhou, 2016, Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae, Sci. Rep., 6, 20840, 10.1038/srep20840
Stoesser, 2014, Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting, Antimicrob. Agents Chemother., 58, 7347, 10.1128/AAC.03900-14
Marsh, 2015, Genomic epidemiology of an endoscope-associated outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae, PLoS One, 10, e0144310, 10.1371/journal.pone.0144310
Deleo, 2014, Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae, Proc. Natl. Acad. Sci. U. S. A., 111, 4988, 10.1073/pnas.1321364111
Struve, 2015, Mapping the evolution of hypervirulent Klebsiella pneumoniae, mBio, 6, 1, 10.1128/mBio.00630-15
Brisse, 2014, Int. J. Syst. Evol. Microbiol., 64, 3146, 10.1099/ijs.0.062737-0
Rosenblueth, 2004, Klebsiella variicola, a novel species with clinical and plant-associated isolates, Syst. Appl. Microbiol., 27, 27, 10.1078/0723-2020-00261
Chen, 2014, Epidemic Klebsiella pneumoniae ST258 is a hybrid strain, mBio, 5, e01355, 10.1128/mBio.01355-14
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
Vos, 2009, A comparison of homologous recombination rates in bacteria and archaea, ISME J., 3, 199, 10.1038/ismej.2008.93
Follador, 2016, The diversity of Klebsiella pneumoniae surface polysaccharides, MGen, 2
Edwards, 1952, Capsule types of Klebsiella, J. Infect. Dis., 91, 92, 10.1093/infdis/91.1.92
Edmunds, 1954, Further Klebsiella capsule types, J. Infect. Dis., 94, 65, 10.1093/infdis/94.1.65
Ørskov, 1977, New Klebsiella capsular antigen, K82, and the deletion of five of those previously assigned, Int. J. Syst. Bacteriol., 27, 386, 10.1099/00207713-27-4-386
Pan, 2015, Genetic analysis of capsular polysaccharide synthesis gene clusters in 79 capsular types of Klebsiella spp, Nat. Sci. Rep., 5, 15573, 10.1038/srep15573
Medini, 2005, The microbial pan-genome, Curr. Opin. Genet. Dev., 15, 589, 10.1016/j.gde.2005.09.006
Ramirez, 2014, Plasmid-mediated antibiotic resistance and virulence in Gram-negatives: the Klebsiella pneumoniae paradigm, Microbiol. Spectr., 2, 1, 10.1128/microbiolspec.PLAS-0016-2013
Bojer, 2013, ClpP-dependent and -independent activities encoded by the polycistronic ClpK-encoding locus contribute to heat shock survival in Klebsiella pneumoniae, Res. Microbiol., 164, 205, 10.1016/j.resmic.2012.11.005
Löhr, 2015, Persistence of a pKPN3-like CTX-M-15-encoding IncFIIK plasmid in a Klebsiella pneumoniae ST17 host during two years of intestinal colonization, PLoS One, 10, e0116516, 10.1371/journal.pone.0116516
Paczosa, 2016, Klebsiella pneumoniae: going on the offense with a strong defense, Microbiol. Mol. Biol. Rev., 80, 629, 10.1128/MMBR.00078-15
Iredell, 2016, Antibiotic resistance in Enterobacteriaceae: mechanisms and clinical implications, BMJ, 352, h6420, 10.1136/bmj.h6420
Conlan, 2014, Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae, Sci. Transl. Med., 6, 254ra126, 10.1126/scitranslmed.3009845
Mathers, 2015, Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing, Antimicrob. Agents Chemother., 59, 1656, 10.1128/AAC.04292-14
Mathers, 2011, Molecular dissection of an outbreak of carbapenem-resistant Enterobacteriaceae reveals intergenus KPC carbapenemase transmission through a promiscuous plasmid, mBio, 2, e00204, 10.1128/mBio.00204-11
Sheppard, 2016, Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC, Antimicrob. Agents Chemother., 60, 3767, 10.1128/AAC.00464-16
Mshana, 2015, Molecular epidemiology and characterization of an outbreak causing Klebsiella pneumoniae clone carrying chromosomally located blaCTX-M-15 at a German University-Hospital, BMC Microbiol., 15, 122, 10.1186/s12866-015-0460-2
Zowawi, 2015, Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae, Sci. Rep., 5, 15082, 10.1038/srep15082
Chen, 2014, Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding, Trends Microbiol., 22, 686, 10.1016/j.tim.2014.09.003
Lee, 2016, Global dissemination of carbapenemase-producing Klebsiella pneumoniae: epidemiology, genetic context, treatment options, and detection methods, Front. Microbiol., 7, 1, 10.3389/fmicb.2016.00895
Conlan, 2016, Plasmid dynamics in KPC-positive Klebsiella pneumoniae during long-term patient colonization, mBio, 7, e00742, 10.1128/mBio.00742-16
Adler, 2016, Dissemination of the blaKPC gene by clonal spread and horizontal gene transfer: comparative study of incidence and molecular mechanisms, J. Antimicrob. Chemother., 71, 2143, 10.1093/jac/dkw106
Poirel, 2012, Genetic features of the widespread plasmid coding for the carbapenemase OXA-48, Antimicrob. Agents Chemother., 56, 559, 10.1128/AAC.05289-11
Potron, 2013, Intercontinental spread of OXA-48 beta-lactamase-producing Enterobacteriaceae over a 11-year period, 2001 to 2011, Eur. Surveill., 18, 20549, 10.2807/1560-7917.ES2013.18.31.20549
Czobor, 2016, Efficient transmission of IncFIIY and IncL plasmids and Klebsiella pneumoniae ST101 clone producing OXA-48, NDM-1 or OXA-181 in Bucharest hospitals, Int. J. Antimicrob. Agents, 48, 223, 10.1016/j.ijantimicag.2016.05.004
Pérez-Vázquez, 2016, Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain, J. Antimicrob. Chemother., 71, 887, 10.1093/jac/dkv458
Doi, 2014, Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing, Antimicrob. Agents Chemother., 58, 5947, 10.1128/AAC.03180-14
Chen, 2014, Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan, PLoS One, 9, 1
Coelho, 2010, Characterisation of the CTX-M-15-encoding gene in Klebsiella pneumoniae strains from the Barcelona metropolitan area: plasmid diversity and chromosomal integration, Int. J. Antimicrob. Agents, 36, 73, 10.1016/j.ijantimicag.2010.03.005
Markovska, 2014, Predominance of IncL/M and IncF plasmid types among CTX-M-ESBL-producing Escherichia coli and Klebsiella pneumoniae in Bulgarian hospitals, Apmis, 122, 608, 10.1111/apm.12204
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
Padilla, 2010, Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence, Antimicrob. Agents Chemother., 54, 177, 10.1128/AAC.00715-09
Bialek-Davenet, 2015, Differential contribution of AcrAB and OqxAB efflux pumps to multidrug resistance and virulence in Klebsiella pneumoniae, J. Antimicrob. Chemother., 70, 81, 10.1093/jac/dku340
Martinez-Martinez, 2008, Extended-spectrum beta-lactamases and the permeability barrier, Clin. Microbiol. Infect., 14, 82, 10.1111/j.1469-0691.2007.01860.x
Weigel, 1998, gyrA mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae, Antimicrob. Agents Chemother., 42, 2661, 10.1128/AAC.42.10.2661
Chen, 2003, The roles of mutations in gyrA, parC, and ompK35 in fluoroquinolone resistance in Klebsiella pneumoniae, Microb. Drug Res., 9, 265, 10.1089/107662903322286472
Tsai, 2011, Klebsiella pneumoniae outer membrane porins OmpK35 and OmpK36 play roles in both antimicrobial resistance and virulence, Antimicrob. Agents Chemother., 55, 1485, 10.1128/AAC.01275-10
Tóth, 2014, Fitness cost associated with resistance to fluoroquinolones is diverse across clones of Klebsiella pneumoniae and may select for CTX-M-15 type extended-spectrum β-lactamase, Eur. J. Clin. Microbiol. Infect. Dis., 33, 837, 10.1007/s10096-013-2022-6
Doi, 2015, Carbapenemase-producing Enterobacteriaceae, Semin. Respir. Crit. Care Med., 36, 74, 10.1055/s-0035-1544208
Cannatelli, 2013, In vivo emergence of colistin resistance in Klebsiella pneumoniae producing KPC-type carbapenemases mediated by insertional inactivation of the PhoQ/PhoP mgrB regulator, Antimicrob. Agents Chemother., 57, 5521, 10.1128/AAC.01480-13
Jayol, 2014, Resistance to colistin associated with a single amino acid change in protein PmrB among Klebsiella pneumoniae isolates of worldwide origin, Antimicrob. Agents Chemother., 58, 4762, 10.1128/AAC.00084-14
Poirel, 2015, The mgrB gene as a key target for acquired resistance to colistin in Klebsiella pneumoniae, J. Antimicrob. Chemother., 70, 75, 10.1093/jac/dku323
Cheng, 2016, Amino acid substitutions of CrrB responsible for resistance to colistin through CrrC in Klebsiella pneumoniae, Antimicrob. Agents Chemother., 60, 3709, 10.1128/AAC.00009-16
Di Pilato, 2016, MCR-1.2: a new MCR variant encoded by a transferable plasmid from a colistin-resistant KPC carbapenemase-producing Klebsiella pneumoniae of sequence type 512, Antimicrob. Agents Chemother., 60, 5612, 10.1128/AAC.01075-16
Cannatelli, 2015, Polymyxin resistance caused by mgrB inactivation is not associated with significant biological cost in Klebsiella pneumoniae, Antimicrob. Agents Chemother., 59, 2898, 10.1128/AAC.04998-14
Arena, 2016, Colistin resistance caused by inactivation of the MgrB regulator is not associated with decreased virulence of sequence type 258 KPC carbapenemase-producing Klebsiella pneumoniae, Antimicrob. Agents Chemother., 60, 2509, 10.1128/AAC.02981-15
Giani, 2015, Large nosocomial outbreak of colistin-resistant, carbapenemase-producing Klebsiella pneumoniae traced to clonal expansion of an mgrB deletion mutant, J. Clin. Microbiol., 53, 3341, 10.1128/JCM.01017-15
Hentschke, 2010, ramR mutations in clinical isolates of Klebsiella pneumoniae with reduced susceptibility to tigecycline, Antimicrob. Agents Chemother., 54, 2720, 10.1128/AAC.00085-10
Roy, 2013, Tigecycline susceptibility in Klebsiella pneumoniae and Escherichia coli causing neonatal septicaemia (2007-10) and role of an efflux pump in tigecycline non-susceptibility, J. Antimicrob. Chemother., 68, 1036, 10.1093/jac/dks535
Ruzin, 2005, Influence of transcriptional activator RamA on expression of multidrug efflux pump AcrAB and tigecycline susceptibility in Klebsiella pneumoniae, Antimicrob. Agents Chemother., 49, 1017, 10.1128/AAC.49.3.1017-1022.2005
Villa, 2014, Genomics of KPC-producing Klebsiella pneumoniae sequence type 512 clone highlights the role of RamR and ribosomal S10 protein mutations in conferring tigecycline resistance, Antimicrob. Agents Chemother., 58, 1707, 10.1128/AAC.01803-13
Gaiarsa, 2015, Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics, Antimicrob. Agents Chemother., 59, 389, 10.1128/AAC.04224-14
Munoz-Price, 2013, Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases, Lancet Infect. Dis., 13, 785, 10.1016/S1473-3099(13)70190-7
Pitout, 2015, Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance, Antimicrob. Agents Chemother., 59, 5873, 10.1128/AAC.01019-15
Lian-Hui, 2016, Diversity of the genetic environment of the blaKPC-2 gene among Klebsiella pneumoniae clinical isolates in a Chinese hospital, Microb. Drug Res., 22, 15, 10.1089/mdr.2014.0281
Pereira, 2013, Update of the molecular epidemiology of KPC-2-producing Klebsiella pneumoniae in Brazil: spread of clonal complex 11 (ST11, ST437 and ST340), J. Antimicrob. Chemother., 68, 312, 10.1093/jac/dks396
Baraniak, 2016, NDM-producing Enterobacteriaceae in Poland, 2012-14: inter-regional outbreak of Klebsiella pneumoniae ST11 and sporadic cases, J. Antimicrob. Chemother., 71, 85, 10.1093/jac/dkv282
Wright, 2014, Population Structure of KPC-producing Klebsiella pneumoniae from Midwestern US hospitals, Antimicrob. Agents Chemother, 58, 4961, 10.1128/AAC.00125-14
Kitchel, 2009, Molecular epidemiology of KPC-producing Klebsiella pneumoniae isolates in the United States: clonal expansion of multilocus sequence type 258, Antimicrob. Agents Chemother., 53, 3365, 10.1128/AAC.00126-09
Deshpande, 2006, Occurrence and characterization of carbapenemase-producing Enterobacteriaceae: report from the SENTRY Antimicrobial Surveillance Program (2000-2004), Microb. Drug Res., 12, 223, 10.1089/mdr.2006.12.223
Adler, 2012, A swordless knight: epidemiology and molecular characteristics of the blaKPC-negative sequence type 258 Klebsiella pneumoniae clone, J. Clin. Microbiol., 50, 3180, 10.1128/JCM.00987-12
Thomas, 2013, Early (2008-2010) hospital outbreak of Klebsiella pneumoniae producing OXA-48 carbapenemase in the UK, Int. J. Antimicrob. Agents, 42, 531, 10.1016/j.ijantimicag.2013.08.020
Sánchez-Romero, 2012, Nosocomial outbreak of VIM-1-producing Klebsiella pneumoniae isolates of multilocus sequence type 15: molecular basis, clinical risk factors, and outcome, Antimicrob. Agents Chemother., 56, 420, 10.1128/AAC.05036-11
Balm, 2013, OXA-181-producing Klebsiella pneumoniae establishing in Singapore, BMC Infect. Dis., 13, 58, 10.1186/1471-2334-13-58
Novais, 2012, Spread of an OmpK36-modified ST15 Klebsiella pneumoniae variant during an outbreak involving multiple carbapenem-resistant Enterobacteriaceae species and clones, Eur. J. Clin. Microbiol. Infect. Dis., 31, 3057, 10.1007/s10096-012-1665-z
Stillwell, 2015, Outbreak of KPC-3 producing carbapenem-resistant Klebsiella pneumoniae in a US pediatric hospital, J. Pediatr. Infect. Dis., 4, 330, 10.1093/jpids/piu080
Mammina, 2012, Ongoing spread of colistin-resistant Klebsiella pneumoniae in different wards of an acute general hospital, Italy, June to December 2011, Eur. Surveill., 17, 1, 10.2807/ese.17.33.20248-en
Cubero, 2015, Carbapenem-resistant and carbapenem-susceptible isogenic isolates of Klebsiella pneumoniae ST101 causing infection in a tertiary hospital, BMC Microbiol., 15, 177, 10.1186/s12866-015-0510-9
Hrabák, 2009, International clones of Klebsiella pneumoniae and Escherichia coli with extended-spectrum β-lactamases in a Czech hospital, J. Clin. Microbiol., 47, 3353, 10.1128/JCM.00901-09
Österblad, 2012, Carbapenemase-producing enterobacteriaceae in Finland: the first years (2008-11), J. Antimicrob. Chemother., 67, 2860, 10.1093/jac/dks299
Marcade, 2012, The emergence of multidrug-resistant Klebsiella pneumoniae of international clones ST13, ST16, ST35, ST48 and ST101 in a teaching hospital in the Paris region, Epidemiol. Infect., 141, 1705, 10.1017/S0950268812002099
Bachman, 2015, Genome-wide identification of Klebsiella pneumoniae fitness genes during lung infection, mBio, 6, e00775, 10.1128/mBio.00775-15
Bruchmann, 2015, Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation, Env. Microbiol., 17, 4690, 10.1111/1462-2920.13016
Larsen, 2012, Multilocus sequence typing of total-genome-sequenced bacteria, J. Clin. Microbiol., 50, 1355, 10.1128/JCM.06094-11
Joensen, 2014, Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli, J. Clin. Microbiol., 52, 1501, 10.1128/JCM.03617-13
Zankari, 2012, Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 67, 2640, 10.1093/jac/dks261
Carattoli, 2014, PlasmidFinder and pMLST: in silico detection and typing of plasmids, Antimicrob. Agents Chemother., 58, 3895, 10.1128/AAC.02412-14
Inouye, 2014, SRST2: rapid genomic surveillance for public health and hospital microbiology labs, Genome Med., 6, 90, 10.1186/s13073-014-0090-6
Hawkey, 2015, ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data, BMC Genomics, 16, 667, 10.1186/s12864-015-1860-2