Biology Department, New Mexico State University, Las Cruces, New Mexico, USA
Biology Department, New Mexico State University, Las Cruces, New Mexico, USA.
mSphere. 2019 Apr 3;4(2):e00040-19. doi: 10.1128/mSphere.00040-19.
is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large outbreak in Wisconsin in the United States; this ICE has integrated into the gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
是一种新兴的全球多药耐药机会性病原体。我们评估了来自世界各地不同地理区域的各种环境和人类感染中 13 个完整基因组和 23 个草图基因组菌株的多样性。在研究中，31/36（86.1%）菌株中发现了推定的整合和共轭元件（ICEs）。总共鉴定出 52 个推定的 ICE（包括 8 个缺少整合酶的退化元件），并根据共轭模块的结构和松弛酶、偶联蛋白、TraG 和 TraJ 蛋白序列的系统发育将它们分为三种类型。发现 II 型和 III 型 ICE 整合到 tRNA 基因附近，而 I 型 ICE 整合到基因间区或基因中。ICE 携带各种货物基因，包括转录调节基因和赋予抗生素抗性的基因。适应性免疫 CRISPR-Cas 系统在 9 个菌株中发现，其中包括 5 个菌株中 CRISPR-Cas 机制和 ICE 存在于同一染色体的不同位置。一个来自 ICE 的间隔子存在于一个菌株的 CRISPR 基因座中。菌株中 ICE 的分布没有表现出地理或时间模式。与在 spp 中广泛研究的 CTnDOT 相比， 中的 ICE 在结构和序列上有所不同。ICE 的分类将有助于进一步研究 ICE 对毒力、基因组流行病学和 的适应性基因组学的影响。 是一种机会性病原体，随着更多基因组被测序，来自世界各地的菌株之间的遗传多样性变得明显。基因组比较确定了 36 个菌株中有 31 个具有三种类型的推定 ICE。ICE 的多样性表明它们有不同的起源。其中一个 ICE 先前从美国威斯康星州的一次大型疫情中发现，该 ICE 已整合到疫情株的 基因中，产生了突变体表型。与许多细菌物种中的 ICE 一样， 中的 ICE 携带各种货物基因，使受体能够抵抗抗生素并适应各种生态位。在 36 个菌株中有 9 个具有适应性免疫 CRISPR-Cas 系统。在一个没有 ICE 的菌株的 CRISPR 基因座中发现了一个 ICE 衍生的间隔子，表明过去曾遭遇过 ICE 并对其进行了有效防御。
