PDF(Pubmed)
Abstract：
BACKGROUND: Increasing incidence of Enterococcus faecium resistant to key antimicrobials used in therapy of hospitalized patients is a worrisome phenomenon observed worldwide. Our aim was to characterize a tigecycline-, linezolid- and vancomycin-resistant E. faecium isolate with the vanA and vanB genes, originating from a hematoma of a patient hospitalized in an intensive care unit in Poland.
METHODS: Antimicrobial susceptibility (a broad panel) was tested using gradient tests with predefined antibiotic concentrations. The complete genome sequence was obtained from a mixed assembly of Illumina MiSeq and Oxford Nanopore\'s MinION reads. The genome was analyzed with appropriate tools available at the Center for Genomic Epidemiology, PubMLST and GenBank. Transferability of oxazolidinone, tigecycline and vancomycin resistance genes was investigated by conjugation, followed by PCR screen of transconjugants for antimicrobial resistance genes and plasmid rep genes characteristic for the donor and genomic sequencing of selected transconjugants.
RESULTS: The isolate was resistant to most antimicrobials tested; susceptibility to daptomycin, erythromycin and chloramphenicol was significantly reduced, and only oritavancin retained the full activity. The isolate represented sequence type 18 (ST18) and carried vanA, vanB, poxtA, fexB, tet(L), tet(M), aac(6\')-aph(2\'\'), ant(6)-Ia and ant(6\')-Ii. The vanA, poxtA and tet(M) genes located on ~ 40-kb plasmids were transferable by conjugation yielding transconjugants resistant to vancomycin, linezolid and tigecycline. The substitutions in LiaS, putative histidine kinase, SulP, putative sulfate transporter, RpoB and RpoC were potential determinants of an elevated daptomycin MIC. Comparative analyses of the studied isolate with E. faecium isolates from other countries revealed its similarity to ST18 isolates from Ireland and Uganda from human infections.
CONCLUSIONS: We provide the detailed characteristics of the genomic determinants of antimicrobial resistance of a clinical E. faecium demonstrating the concomitant presence of both vanA and vanB and resistance to vancomycin, linezolid, tigecycline and several other compounds and decreased daptomycin susceptibility. This isolate is a striking example of an accumulation of resistance determinants involving various mechanisms by a single hospital strain.
METHODS: Antimicrobial susceptibility (a broad panel) was tested using gradient tests with predefined antibiotic concentrations. The complete genome sequence was obtained from a mixed assembly of Illumina MiSeq and Oxford Nanopore\'s MinION reads. The genome was analyzed with appropriate tools available at the Center for Genomic Epidemiology, PubMLST and GenBank. Transferability of oxazolidinone, tigecycline and vancomycin resistance genes was investigated by conjugation, followed by PCR screen of transconjugants for antimicrobial resistance genes and plasmid rep genes characteristic for the donor and genomic sequencing of selected transconjugants.
RESULTS: The isolate was resistant to most antimicrobials tested; susceptibility to daptomycin, erythromycin and chloramphenicol was significantly reduced, and only oritavancin retained the full activity. The isolate represented sequence type 18 (ST18) and carried vanA, vanB, poxtA, fexB, tet(L), tet(M), aac(6\')-aph(2\'\'), ant(6)-Ia and ant(6\')-Ii. The vanA, poxtA and tet(M) genes located on ~ 40-kb plasmids were transferable by conjugation yielding transconjugants resistant to vancomycin, linezolid and tigecycline. The substitutions in LiaS, putative histidine kinase, SulP, putative sulfate transporter, RpoB and RpoC were potential determinants of an elevated daptomycin MIC. Comparative analyses of the studied isolate with E. faecium isolates from other countries revealed its similarity to ST18 isolates from Ireland and Uganda from human infections.
CONCLUSIONS: We provide the detailed characteristics of the genomic determinants of antimicrobial resistance of a clinical E. faecium demonstrating the concomitant presence of both vanA and vanB and resistance to vancomycin, linezolid, tigecycline and several other compounds and decreased daptomycin susceptibility. This isolate is a striking example of an accumulation of resistance determinants involving various mechanisms by a single hospital strain.
摘要：
背景：对住院患者治疗中使用的关键抗菌药物耐药的屎肠球菌发病率增加是一个令人担忧的现象。我们的目的是表征替加环素-，具有vanA和vanB基因的利奈唑胺和万古霉素抗性屎肠球菌分离株，源自波兰重症监护病房住院患者的血肿。
方法：使用预定义的抗生素浓度的梯度测试来测试抗微生物药物敏感性（广泛的小组）。完整的基因组序列是从IlluminaMiSeq和OxfordNanopore的MinION读数的混合组装获得的。使用基因组流行病学中心可用的适当工具分析基因组，PubMLST和GenBank。恶唑烷酮的可转移性，通过结合研究替加环素和万古霉素抗性基因，然后通过PCR筛选转接头的抗菌素抗性基因和供体特征性质粒rep基因，并对选定的转接头进行基因组测序。
结果：该分离株对大多数测试的抗菌药物具有抗性；对达托霉素的敏感性，红霉素和氯霉素明显减少，只有oritavancin保留了全部活动。分离株代表序列类型18(ST18)并携带vanA，vanB,poxtA,fexB,tet(L),tet(M),aac(6\')-aph(2\'\'),蚂蚁(6)-Ia和蚂蚁(6')-Ii。VNA,位于〜40-kb质粒上的poxtA和tet（M）基因可通过缀合转移，产生抗万古霉素的偶联物，利奈唑胺和替加环素。LiaS中的替补,推定组氨酸激酶，SulP,推定的硫酸盐转运蛋白，RpoB和RpoC是达托霉素MIC升高的潜在决定因素。与来自其他国家的屎肠球菌分离株进行研究的分离株的比较分析显示，它与来自爱尔兰和乌干达的人类感染的ST18分离株相似。
结论：我们提供了临床屎肠球菌抗菌素耐药性基因组决定因素的详细特征，表明同时存在vanA和vanB以及对万古霉素的耐药性，利奈唑胺,替加环素和其他几种化合物，并降低了达托霉素的敏感性。该分离株是单个医院菌株涉及各种机制的抗性决定因子积累的一个突出例子。
方法：使用预定义的抗生素浓度的梯度测试来测试抗微生物药物敏感性（广泛的小组）。完整的基因组序列是从IlluminaMiSeq和OxfordNanopore的MinION读数的混合组装获得的。使用基因组流行病学中心可用的适当工具分析基因组，PubMLST和GenBank。恶唑烷酮的可转移性，通过结合研究替加环素和万古霉素抗性基因，然后通过PCR筛选转接头的抗菌素抗性基因和供体特征性质粒rep基因，并对选定的转接头进行基因组测序。
结果：该分离株对大多数测试的抗菌药物具有抗性；对达托霉素的敏感性，红霉素和氯霉素明显减少，只有oritavancin保留了全部活动。分离株代表序列类型18(ST18)并携带vanA，vanB,poxtA,fexB,tet(L),tet(M),aac(6\')-aph(2\'\'),蚂蚁(6)-Ia和蚂蚁(6')-Ii。VNA,位于〜40-kb质粒上的poxtA和tet（M）基因可通过缀合转移，产生抗万古霉素的偶联物，利奈唑胺和替加环素。LiaS中的替补,推定组氨酸激酶，SulP,推定的硫酸盐转运蛋白，RpoB和RpoC是达托霉素MIC升高的潜在决定因素。与来自其他国家的屎肠球菌分离株进行研究的分离株的比较分析显示，它与来自爱尔兰和乌干达的人类感染的ST18分离株相似。
结论：我们提供了临床屎肠球菌抗菌素耐药性基因组决定因素的详细特征，表明同时存在vanA和vanB以及对万古霉素的耐药性，利奈唑胺,替加环素和其他几种化合物，并降低了达托霉素的敏感性。该分离株是单个医院菌株涉及各种机制的抗性决定因子积累的一个突出例子。
