Whole genome sequencing for the molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains isolated at the Italian ASST Fatebenefratelli Sacco Hospital, 2012-2014.
Whole genome sequencing for the molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains isolated at the Italian ASST Fatebenefratelli Sacco Hospital, 2012-2014.
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DOI：
10.1186/s12879-017-2760-7
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发表时间：
2017-10-10
影响因子：
3.7
通讯作者：
Lista F
中科院分区：
文献类型：
--
作者：
Rimoldi SG;Gentile B;Pagani C;Di Gregorio A;Anselmo A;Palozzi AM;Fortunato A;Pittiglio V;Ridolfo AL;Gismondo MR;Rizzardini G;Lista F
碳青霉烯类耐药肺炎克雷伯菌菌株的出现威胁着抗菌治疗。68株产碳青霉烯酶K.对2012年至2014年期间在Luigi Sestival大学医院-ASST Fatebenefratelli Sestival（米兰，意大利）分离的肺炎菌株进行微生物学和分子学表征。对他们进行药物敏感性和碳青霉烯酶表型检测，通过重复基因外回文聚合酶链反应（REP-PCR）进行研究，并通过下一代测序进行全测序，以进行多位点序列分型（MLST）、耐药基因组、基因组和质粒含量及其核心单核苷酸多态性（SNP）基因型的计算机分析。所有样本均对碳青霉烯类、其他β-内酰胺类和环丙沙星耐药;许多对氨基糖苷类和替加环素耐药; 7例对粘菌素耐药。耐药基因组分析显示存在blaKPC基因，以及与碳青霉烯类和其他β-内酰胺类耐药相关的较低频率的blaSHV、blaTEM、blaCTX-M和blaOXA。其他基因赋予耐药性的氨基糖苷类，氟喹诺酮类，苯酚，磺胺类，四环素，甲氧苄啶和大环内酯-林可酰胺-链阳性。研究了与AcrAB-TolC外排泵依赖性和泵非依赖性替加环素耐药机制相关的基因，但由于敏感、中间和耐药菌株中存在共同突变，因此不可能将基因组特征与替加环素耐药明确关联。关于粘菌素耐药性，mgrB基因被IS 5样元件破坏，在2例病例中未检测到移动的mcr-1和mcr-2基因。该基因组图谱揭示了3型菌毛和铁摄取系统基因，这在哺乳动物宿主环境中的定殖阶段是重要的。计算机检测的质粒复制子被分类为IncFIB（pQil）、IncFIB（K）、ColRNAi、IncX 1、IncX 3、IncFII（K）、IncN、IncL/M（pMU 407）和IncFIA（HI 1）。REP-PCR显示了5个主要的簇，MLST显示了6种不同的序列类型：512，258，307，1519，745和101。核心SNP基因分型，导致四个集群，与MLST数据相关。相同测序类型的分离株通常具有共同的遗传性状，但SNP分析比REP-PCR或MLST分析允许更大的菌株跟踪和区分。我们的研究结果支持在临床医学中实施细菌基因组学的重要性，以补充传统方法并克服其有限的分辨率。本文的在线版本（10.1186/s12879-017-2760-7）包含补充材料，可供授权用户使用。
The emergence of carbapenem-resistant Klebsiella pneumoniae strains is threatening antimicrobial treatment. Sixty-eight carbapenemase-producing K. pneumoniae strains isolated at Luigi Sacco University Hospital-ASST Fatebenefratelli Sacco (Milan, Italy) between 2012 and 2014 were characterised microbiologically and molecularly. They were tested for drug susceptibility and carbapenemase phenotypes, investigated by means of repetitive extra-genic palindromic polymerase chain reaction (REP-PCR), and fully sequenced by means of next-generation sequencing for the in silico analysis of multi-locus sequence typing (MLST), their resistome, virulome and plasmid content, and their core single nucleotide polymorphism (SNP) genotypes. All of the samples were resistant to carbapenems, other β-lactams and ciprofloxacin; many were resistant to aminoglycosides and tigecycline; and seven were resistant to colistin. Resistome analysis revealed the presence of blaKPC genes and, less frequently blaSHV, blaTEM, blaCTX-M and blaOXA, which are related to resistance to carbapenem and other β-lactams. Other genes conferring resistance to aminoglycoside, fluoroquinolone, phenicol, sulphonamide, tetracycline, trimethoprim and macrolide-lincosamide-streptogramin were also detected. Genes related to AcrAB-TolC efflux pump-dependent and pump-independent tigecycline resistance mechanisms were investigated, but it was not possible to clearly correlate the genomic features with tigecycline resistance because of the presence of a common mutation in susceptible, intermediate and resistant strains. Concerning colistin resistance, the mgrB gene was disrupted by an IS5-like element, and the mobile mcr-1 and mcr-2 genes were not detected in two cases. The virulome profile revealed type-3 fimbriae and iron uptake system genes, which are important during the colonisation stage in the mammalian host environment. The in silico detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX1, IncX3, IncFII(K), IncN, IncL/M(pMU407) and IncFIA(HI1). REP-PCR showed five major clusters, and MLST revealed six different sequence types: 512, 258, 307, 1519, 745 and 101. Core SNP genotyping, which led to four clusters, correlated with the MLST data. Isolates of the same sequencing type often had common genetic traits, but the SNP analysis allowed greater strain tracking and discrimination than either the REP-PCR or MLST analysis. Our findings support the importance of implementing bacterial genomics in clinical medicine in order to complement traditional methods and overcome their limited resolution. The online version of this article (10.1186/s12879-017-2760-7) contains supplementary material, which is available to authorized users.
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DOI：
10.1016/j.tig.2014.07.003
发表时间：
2014-09
期刊：
Trends in genetics : TIG
影响因子：
--
作者：
Köser CU;Ellington MJ;Peacock SJ
通讯作者：
Peacock SJ
影响因子：
19
作者：
Monaco, M.;Giani, T.;Rossolini, G. M.
通讯作者：
Rossolini, G. M.
影响因子：
5.2
作者：
Conte, Viola;Monaco, Monica;Pantosti, Annalisa
通讯作者：
Pantosti, Annalisa
过度抗呼吸和多药的肺炎克隆基团的基因组定义。
影响因子：
11.8
作者：
Bialek-Davenet S;Criscuolo A;Ailloud F;Passet V;Jones L;Delannoy-Vieillard AS;Garin B;Le Hello S;Arlet G;Nicolas-Chanoine MH;Decré D;Brisse S
通讯作者：
Brisse S
DOI：
10.3390/ph6111335
发表时间：
2013-11-01
期刊：
Pharmaceuticals (Basel, Switzerland)
影响因子：
--
作者：
Morrissey I;Hackel M;Badal R;Bouchillon S;Hawser S;Biedenbach D
通讯作者：
Biedenbach D