Deciphering the Structural Diversity and Classification of the Mobile Tigecycline Resistance Gene tet(X)-Bearing Plasmidome among Bacteria
Deciphering the Structural Diversity and Classification of the Mobile Tigecycline Resistance Gene tet(X)-Bearing Plasmidome among Bacteria
复制标题
破译细菌中携带替加环素抗性基因 tet(X) 的质粒组的结构多样性和分类
DOI：
10.1128/msystems.00134-20
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发表时间：
2020-03-01
期刊：
影响因子：
6.4
通讯作者：
Wang, Zhiqiang
中科院分区：
文献类型：
--
作者：
Li, Ruichao;Lu, Xiaoyu;Wang, Zhiqiang
替格环素是一种广谱四环素，作为最后的抗菌剂用于治疗由超级细菌引起的感染，如产生碳青霉烯酶或粘菌素耐药的病原体。质粒介导的替吉环素耐药基因tet(X4)的出现引起了公众的极大关注。然而，携带tet(X4)的质粒和细菌的多样性在很大程度上仍未得到调查。为了弥补这一知识空白，我们首次利用先进的测序技术对不同来源的携带tet(X)的质粒体进行了全面的鉴定和鉴定。携带tet(X4)的移动元件的巨大多样性表明tet(X4)基因在细菌中具有高度的传播性。在全球范围内加强对动物和人类病原体中tet(X)基因的严格监测至关重要。摘要新的质粒介导的抗性基因的出现引起了公众的极大关注。最近，在不同来源的不同病原体中发现了移动性tet(X)变异。然而，携带tet(X)的质粒的多样性在很大程度上仍不清楚。本研究采用药敏试验、接合试验、S1核酸酶脉冲场凝胶电泳法和聚合酶链式反应对中国屠宰场分离的所有tet(X)阳性替格环素耐药菌株进行了表型和基因分型。通过全基因组测序和单质粒分子分析，研究了携带tet(X)基因的菌株和质粒染色体的多样性和多态性。共鉴定出74株携带tet(X4)的大肠埃希菌和1株携带tet(X6)的普罗维登西亚雷氏原虫。27株含tet(X4)基因的菌株可通过质粒转移到受体菌株。对本研究中分离到的所有含tet(X4)的质粒和网上报道的15个含tet(X4)的质粒进行了分析。含Tet(X4)的质粒大小在9~294 kb之间，可分为类ColE_2、IncQ、IncX_1、IncA/C2、IncF_2、IncFIB和具有不同复制子的杂交质粒。携带核心TET(X4)的遗传背景被分为四个主要组：ISCR2-TET(X4)-ABH、ISCR2-ABH-TET(X4)-ISCR2-ABH-TET(X4)-ISCR2-VirD2-Flor和abh-tet(X4)-ISCR2-yheS-cat-zitR-ISCR2-virD2-floR.TET(X4)的串联重复序列普遍由ISCR2介导。同一微生物区系中存在不同的Tet(X)菌株。携带tet(X4)的多药耐药质粒的重组是由IS26和其他同源区域介导的。最后，单质粒-分子分析捕获了携带tet(X4)的质粒的异质性状态。这些发现极大地扩展了我们对微生物中携带tet(X)的质体组的了解，为研究人类、动物和环境中替环素耐药组的结构和多样性奠定了基础。对不同微生物群的tet(X)基因进行系统的研究，以了解其进化和生态。重要性替格环素是一种广谱四环素，作为最后的抗菌剂用于治疗由超级细菌引起的感染，如产生碳青霉烯酶或粘菌素耐药的病原体。质粒介导的替吉环素耐药基因tet(X4)的出现引起了公众的极大关注。然而，携带tet(X4)的质粒和细菌的多样性在很大程度上仍未得到调查。为了弥补这一知识空白，我们首次利用先进的测序技术对不同来源的携带tet(X)的质粒体进行了全面的鉴定和鉴定。携带tet(X4)的移动元件的巨大多样性表明tet(X4)基因在细菌中具有高度的传播性。在全球范围内加强对动物和人类病原体中tet(X)基因的严格监测至关重要。
Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally. ABSTRACT The emergence of novel plasmid-mediated resistance genes constitutes a great public concern. Recently, mobile tet(X) variants were reported in diverse pathogens from different sources. However, the diversity of tet(X)-bearing plasmids remains largely unknown. In this study, the phenotypes and genotypes of all the tet(X)-positive tigecycline-resistant strains isolated from a slaughterhouse in China were characterized by antimicrobial susceptibility testing, conjugation, pulsed-field gel electrophoresis with S1 nuclease (S1-PFGE), and PCR. The diversity and polymorphism of tet(X)-harboring strains and plasmidomes were investigated by whole-genome sequencing (WGS) and single-plasmid-molecule analysis. Seventy-four tet(X4)-harboring Escherichia coli strains and one tet(X6)-bearing Providencia rettgeri strain were identified. The tet(X4)-bearing elements in 27 strains could be transferred to the recipient strain via plasmids. All tet(X4)-bearing plasmids isolated in this study and 15 tet(X4)-bearing plasmids reported online were analyzed. tet(X4)-bearing plasmids ranged from 9 to 294 kb and were categorized as ColE2-like, IncQ, IncX1, IncA/C2, IncFII, IncFIB, and hybrid plasmids with different replicons. The core tet(X4)-bearing genetic contexts were divided into four major groups: ISCR2-tet(X4)-abh, △ISCR2-abh-tet(X4)-ISCR2, ISCR2-abh-tet(X4)-ISCR2-virD2-floR, and abh-tet(X4)-ISCR2-yheS-cat-zitR-ISCR2-virD2-floR. Tandem repeats of tet(X4) were universally mediated by ISCR2. Different tet(X)-bearing strains existed in the same microbiota. Reorganization of tet(X4)-bearing multidrug resistance plasmids was found to be mediated by IS26 and other homologous regions. Finally, single-plasmid-molecule analysis captured the heterogenous state of tet(X4)-bearing plasmids. These findings significantly expand our knowledge of the tet(X)-bearing plasmidome among microbiotas, which establishes a baseline for investigating the structure and diversity of human, animal, and environmental tigecycline resistomes. Characterization of tet(X) genes among different microbiotas should be performed systematically to understand the evolution and ecology. IMPORTANCE Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally.