integrative conjugative elements

整合共轭元素
  • 文章类型: Journal Article
    猪链球菌是猪感染的主要原因,造成广泛的经济损失。此外,它也可以感染野生动物,并可能导致人类严重感染。在全世界的猪链球菌中已经描述了增加的抗微生物抗性(AMR),并且大多数AMR基因由移动遗传元件(MGEs)携带。这有助于它们通过水平基因转移传播。从人类中分离出的102个菌株的集合,法国的猪和野猪进行了全基因组测序,以便:(i)研究其遗传多样性,(ii)评估其在毒力相关基因中的含量,(iii)破译负责其AMR及其与MGE的关联的机制,和(iv)研究它们通过自然转化获得胞外DNA的能力。通过对主成分的分层聚类分析确定了一些毒力相关因子,可将侵袭性CC1菌株与其他菌株区分开。在基因组中发现了过多的AMR基因(n=217)。除了经常报道的erm(B)和tet(O)基因,最近描述的AMR基因被鉴定[vga(F)/sprA,增值税(D)]。在青霉素和氟喹诺酮耐药分离株中分别检测到PBP/MraY和GyrA/ParC的修饰。检测到新的AMR基因-MGE关联。大多数菌株具有能力所需的全套基因,即通过自然转化获得细胞外DNA(可能携带AMR基因)。因此,不应忽视这些AMR基因的传播风险。
    Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.
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  • 文章类型: Journal Article
    耐万古霉素肠球菌(VRE)是一种日益明确的人类疾病,大多数感染是由vanA和vanB基因型引起的;对其他临床相关基因型的了解较少。在这里,我们报告了一个vanDVRE屎(VREfm)的基因组探索,在一次感染发作中从头出现。对万古霉素敏感的屎肠球菌(VSEfm)受体的基因组和所得的VREfm进行长读数测序并关闭,全基因组比对,交叉映射和直向聚类用于识别基因组变异。确定了三个关键差异。(i)VREfm染色体获得了包含vanD基因座的142.6kb整合共轭元件(ICE)。(ii)通过ISEfml插入破坏天然连接酶(ddl)。(iii)发生了未知结果的大的1.74Mb染色体倒位。VREfm与全球vanD基因组集合的比对和基于系统发育的比较确定了vanD周围120-160kb基因组区域的强烈相似性,暗示了一个通用的移动元素和集成站点,不管不同的分类学,分离株的地理和宿主起源。这种分离的多样性表明,这种推定的ICE(及其来源)在全球范围内传播,并且能够被不同的属获得。虽然vanDVREfm的发生率很低,了解其出现和传播的潜力对于减少抗菌素耐药性的持续努力至关重要.
    Vancomycin-resistant Enterococcus (VRE) is an increasingly identified cause of human disease, with most infections resulting from the vanA and vanB genotypes; less is known about other clinically relevant genotypes. Here we report a genomic exploration of a vanD VRE faecium (VREfm), which arose de novo during a single infectious episode. The genomes of the vancomycin-susceptible E. faecium (VSEfm) recipient and resulting VREfm were subjected to long-read sequencing and closed, with whole-genome alignments, cross-mapping and orthologue clustering used to identify genomic variation. Three key differences were identified. (i) The VREfm chromosome gained a 142.6 kb integrative conjugative element (ICE) harbouring the vanD locus. (ii) The native ligase (ddl) was disrupted by an ISEfm1 insertion. (iii) A large 1.74 Mb chromosomal inversion of unknown consequence occurred. Alignment and phylogenetic-based comparisons of the VREfm with a global collection of vanD-harbouring genomes identified strong similarities in the 120-160 kb genomic region surrounding vanD, suggestive of a common mobile element and integration site, irrespective of the diverse taxonomic, geographical and host origins of the isolates. This isolate diversity revealed that this putative ICE (and its source) is globally disseminated and is capable of being acquired by different genera. Although the incidence of vanD VREfm is low, understanding its emergence and potential for spread is crucial for the ongoing efforts to reduce antimicrobial resistance.
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  • 文章类型: Journal Article
    目的:本研究的目的是表征ICEAplChn2,一种携带19种耐药基因的新型SXT/R391相关整合和缀合元件(ICE),在猪胸膜肺炎放线杆菌的临床分离中。方法:使用第三代PacBio和第二代Illumina的组合完成胸膜肺炎杆菌CP063424菌株的全基因组测序(WGS)。推定的ICE由在线工具ICEfinder预测。ICEAplChn2通过PCR分析,共轭实验,和生物信息学工具。结果:胸膜肺炎杆菌CP063424菌株对克林霉素的最低抑菌浓度(1,024mg/L)较高。WGS数据显示,ICEAplChn2长度为167,870bp,编码151个基因,包括多个抗生素抗性基因,如erm(42),Vane,LpxC,dfrA1,gls,aadA3,EreA,dfrA32,tetR(C),tet(C),sul2,aph(3)″-lb,aph(6)-l,floR,dfra,ANT(3″)-IIa,catB11和VanRE,发现与胸膜肺炎杆菌CP063424染色体上的SXT/R391家族相关。通过PCR检测ICEAplChn2的环状中间体,但是共轭实验表明它不是自我传播的。结论:据我们所知,ICEAplChn2是SXT/R391家族中具有最年夜抗性基因的最长成员。同时,发现ATP结合盒超家族被插入到ICEAplChn2中并具有新的插入区,这是SXT/R391系列中的第一个描述。
    Objective: The objective of this study was to characterize ICEAplChn2, a novel SXT/R391-related integration and conjugation element (ICE) carrying 19 drug resistance genes, in a clinical isolate of Actinobacillus pleuropneumoniae from swine. Methods: Whole genome sequencing (WGS) of A. pleuropneumoniae CP063424 strain was completed using a combination of third-generation PacBio and second-generation Illumina. The putative ICE was predicted by the online tool ICEfinder. ICEAplChn2 was analyzed by PCR, conjugation experiments, and bioinformatics tools. Results: A. pleuropneumoniae CP063424 strain exhibited high minimum inhibitory concentrations of clindamycin (1,024 mg/L). The WGS data revealed that ICEAplChn2, with a length of 167,870 bp and encoding 151 genes, including multiple antibiotic resistance genes such as erm(42), VanE, LpxC, dfrA1, golS, aadA3, EreA, dfrA32, tetR(C), tet(C), sul2, aph(3)″-lb, aph(6)-l, floR, dfrA, ANT(3″)-IIa, catB11, and VanRE, was found to be related to the SXT/R391 family on the chromosome of A. pleuronipneumoniae CP063424. The circular intermediate of ICEAplChn2 was detected by PCR, but conjugation experiments showed that it was not self-transmissible. Conclusions: To our knowledge, ICEAplChn2 is the longest member with the most resistance genes in the SXT/R391 family. Meanwhile, ATP-binding cassette superfamily was found to be inserted in the ICEAplChn2 and possessed a new insertion region, which is the first description in the SXT/R391 family.
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  • 文章类型: Journal Article
    移动遗传元件可以创新具有新特征的细菌。在植物致病性链霉菌中,频繁和最近获得的整合和共轭或可移动的遗传元件预计会导致新的谱系的出现,获得了合成Thaxtomin的能力,在块茎和块根作物上诱导常见结痂病的植物毒素必需库。这里,我们确定了与毒力有关的链霉菌-马铃薯病理系统的组成部分,并将其作为嵌套和相互作用的系统进行了研究,以重新评估进化模型.我们对166个菌株的基因组进行了测序和分析,这些菌株是从主要来自田间种植的马铃薯的六十年的采样中分离出来的。毒力基因与遗传元件的多种亚型相关,遗传元件的传播机制和进化史不同。证据与很少的古代采集事件一致,随后反复丢失或交换携带ThaxtominA相关基因的元素。与毒力有关的另一种遗传元件的亚型更多分布在链霉菌中。然而,含有毒力基因的遗传元件的亚型分类和分类学身份都不能预测马铃薯的致病性。最后,研究结果表明,植物病原菌株通常是马铃薯田特有的,一些谱系是通过历史传播建立的,并通过最近的传播事件进一步分散。通过揭示基因和细菌分散对农业环境中革兰氏阳性病原体进化的多种机制,分层和全系统表征的结果完善了我们的理解。
    Mobile genetic elements can innovate bacteria with new traits. In plant pathogenic Streptomyces, frequent and recent acquisition of integrative and conjugative or mobilizable genetic elements is predicted to lead to the emergence of new lineages that gained the capacity to synthesize Thaxtomin, a phytotoxin neccesary for induction of common scab disease on tuber and root crops. Here, we identified components of the Streptomyces-potato pathosystem implicated in virulence and investigated them as a nested and interacting system to reevaluate evolutionary models. We sequenced and analysed genomes of 166 strains isolated from over six decades of sampling primarily from field-grown potatoes. Virulence genes were associated to multiple subtypes of genetic elements differing in mechanisms of transmission and evolutionary histories. Evidence is consistent with few ancient acquisition events followed by recurrent loss or swaps of elements carrying Thaxtomin A-associated genes. Subtypes of another genetic element implicated in virulence are more distributed across Streptomyces. However, neither the subtype classification of genetic elements containing virulence genes nor taxonomic identity was predictive of pathogenicity on potato. Last, findings suggested that phytopathogenic strains are generally endemic to potato fields and some lineages were established by historical spread and further dispersed by few recent transmission events. Results from a hierarchical and system-wide characterization refine our understanding by revealing multiple mechanisms that gene and bacterial dispersion have had on shaping the evolution of a Gram-positive pathogen in agricultural settings.
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  • 文章类型: Journal Article
    多杀性巴氏杆菌在世界各地的许多宿主物种中引起一系列疾病,包括牛呼吸道疾病(BRD),主要见于饲养场牛。这项研究评估了从澳大利亚四个州的BRD受影响的饲养场牛的死后肺拭子中获得的139个多杀性疟原虫分离株的遗传多样性:新南威尔士州,昆士兰,南澳大利亚,和维多利亚在2014-2019年。全基因组测序(WGS)用于确定荚膜血清群,脂多糖基因型,多位点序列类型和系统发育关系。两种囊膜类型(A和D),与大多数分离株(132/139;95%)属于A型;和三个脂多糖(LPS)基因型鉴定(L1[6/139;4.3%],L3[124/139;89.2%]和L6[9/139;6.4%)])。鉴定了多位点序列类型(ST)ST9、ST13、ST17、ST20、ST36、ST50、ST58、ST79、ST124、ST125、ST132、ST167、ST185、ST327、ST394和三个新的ST[ST396、ST397和ST398]。ST394(59/139;42.4%)和ST79(44/139;32%)在所有四个州中最普遍。表现出对单一的表型抗性的分离株,双重或多种抗生素(大环内酯,四环素和氨基青霉素)主要是ST394(23/139;17%)。在抗性ST394分离株中鉴定的横向移动元件包括小质粒,编码大环内酯和/或四环素抗性,分布在所有州;以及来自同一昆士兰州饲养场的位于染色体上的整合共轭元件(ICE)(4ST394和1ST125)。这项研究强调了基因组的多样性,来自澳大利亚的牛多杀性疟原虫分离株的流行病学关系和AMR关联,并提供了与其他主要牛肉生产国相比独特的ST患病率的见解。
    Pasteurella multocida causes a range of diseases in many host species throughout the world, including bovine respiratory disease (BRD) which is predominantly seen in feedlot cattle. This study assessed genetic diversity among 139 P. multocida isolates obtained from post-mortem lung swabs of BRD-affected feedlot cattle in four Australian states: New South Wales, Queensland, South Australia, and Victoria during 2014-2019. Whole-genome sequencing (WGS) was used to determine capsular serogroup, lipopolysaccharide genotypes, multi-locus sequence types and phylogenetic relationships. Two capsular types (A and D), with most isolates (132/139; 95%) belonging to type A; and three lipopolysaccharide (LPS) genotypes were identified (L1 [6/139; 4.3%], L3 [124/139; 89.2%] and L6 [9/139; 6.4%)]). Multi-locus sequence types (STs) ST9, ST13, ST17, ST20, ST36, ST50, ST58, ST79, ST124, ST125, ST132, ST167, ST185, ST327, ST394, and three novel STs [ST396, ST397, and ST398] were identified, with ST394 (59/139; 42.4%) and ST79 (44/139; 32%) the most prevalent in all four states. Isolates displaying phenotypic resistance to single, dual or multiple antibiotics (macrolide, tetracycline and aminopenicillins) were predominantly ST394 (23/139; 17%). Laterally mobile elements identified in the resistant ST394 isolates included small plasmids, encoding macrolide and/or tetracycline resistance, distributed in all states; and chromosomally located integrative conjugative elements (ICEs) (4 ST394 and 1 ST125) from the same Queensland feedlot. This study highlights the genomic diversity, epidemiological relationships and AMR associations in bovine P. multocida isolates from Australia and provides insight into the unique ST prevalence compared to other major beef-producing countries.
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  • 文章类型: Journal Article
    在本期《细菌学杂志》上,J.-S.Bourassa,G.Jeannotte,S.Lebel-Beaucage,和P.B.Beauregard(JBacteriol204:e00181-22,2022,https://doi.org/10.1128/jb.00181-22)表明,ICEBs1在枯草芽孢杆菌生物膜中的繁殖几乎完全依赖于跨缀合物。它似乎仅限于初始供体细胞附近的细菌簇,它们不均匀地分布在生物膜中,并向气液界面垂直扩展。
    In this issue of the Journal of Bacteriology, J.-S. Bourassa, G. Jeannotte, S. Lebel-Beaucage, and P. B. Beauregard (J Bacteriol 204:e00181-22, 2022, https://doi.org/10.1128/jb.00181-22) showed that ICEBs1 propagation in Bacillus subtilis biofilm relies almost exclusively on transconjugants. It appears restricted to clusters of bacteria in a close neighborhood of initial donor cells, which are heterogeneously distributed in the biofilm and expand vertically toward the air-liquid interface.
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  • 文章类型: Journal Article
    通过水平基因转移(HGT)获得抗生素抗性(ABR)基因是细菌病原体多药耐药性上升的关键驱动因素。根据定义,细菌防御系统限制了外来遗传物质的流入,因此可能会限制ABR的获取。CRISPR-Cas适应性免疫系统是细菌中最普遍的防御系统之一,在大约一半的细菌基因组中发现,但目前尚不清楚它们是否以及在多大程度上有助于限制ABR的传播.我们分析了大约4万个全基因组,包括完整的RefSeq数据集,包括11种临床上重要的人类病原体属,包括肠球菌,葡萄球菌,不动杆菌和假单胞菌。我们对CRISPR-Cas和HGT指标之间的关联进行了建模,发现具有CRISPR-Cas系统的病原体携带ABR基因的可能性比缺乏这种防御系统的病原体低。对CRISPR-Cas靶向的可移动遗传元件(MGEs)的分析支持了该宿主防御系统阻断ABR重要载体的模型。这些结果表明,多重耐药菌株的潜在“免疫受损”状态可能会被用于依赖于MGE的定制干预措施中,如噬菌体或噬菌粒,治疗由细菌病原体引起的感染。本文是“微生物可移动遗传元件的秘密生命”主题的一部分。
    The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential \'immunocompromised\' state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue \'The secret lives of microbial mobile genetic elements\'.
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  • 文章类型: Journal Article
    集成可移动元件(IME)很普遍,但对集成元件的研究却很少,这些集成元件可以切除和劫持共同居住的共轭元件的转移装置以促进其自身的传播。64个推定的IME,拥有密切相关的动员和重组模块,在14种链球菌和金黄色葡萄球菌中发现。五十三整合到宿主整合共轭元件(ICE)的转移起源(oriT)中,编码MobT松弛酶,属于三个遥远的家族:ICESt3,Tn916和ICE6013。其他整合到不相关的IME或染色体位点中。用抗生素抗性基因标记后,测量了这些IME之一(称为IME_oriTs)及其宿主ICE的共轭转移。尽管IME集成在ICE中,它不作为主机ICE的一部分转移(没有顺式动员)。IME切除和转移分别从ICE(不影响其转移速率)使用其自己的松弛酶,与所有已知的MobT松弛酶密切相关,并在转移后集成在ICE的ORET中。总的来说,IME_oriTs使用MobT编码的ICE既作为宿主又作为共轭转移的助手。由于其中一半携带lsa(C),他们积极参与Firmicutes中lincosamide-streptograminA-胸膜肌动蛋白抗性的传播。
    Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide-streptogramin A-pleuromutilin resistance among Firmicutes.
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  • 文章类型: Journal Article
    猪链球菌是一种人畜共患病原体,怀疑是抗生素耐药性(AMR)基因的储库。对214株27种血清型的基因组进行了AMR基因和染色体移动遗传元件(MGEs)的筛选,特别是整合共轭要素(ICEs)和整合可移动性要素(IME)。通过切除测试和缀合实验研究了宿主携带AMR基因的IME的两个ICE的功能。计算机搜索显示了416个与ICE相关的元素和457个与IME相关的元素。这些MGE表现出令人印象深刻的多样性和可塑性,ICE或IME在ICE内部的整合以及元件之间的重组。所有检测到的393个AMR基因均由MGE携带。如前所述,ICE是猪链球菌AMR基因的主要载体。与Tn5252相关的ICE似乎也携带细菌素簇。此外,而IME-AMR基因的关联从未在猪链球菌中描述过,我们发现大多数AMR基因实际上是由IME携带的。获得了ICE向另一种细菌物种(嗜热链球菌)的自主转移-导致携带tet(O)的IME的顺式动员。这些结果表明,除了ICE,IME可能在猪链球菌AMR基因的传播中起主要作用。
    Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)-leading to the cis-mobilization of an IME carrying tet(O)-was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.
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  • 文章类型: Journal Article
    In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.
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