Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.
Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.
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DOI：
10.1186/s12866-018-1325-2
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发表时间：
2018-11-23
期刊：
影响因子：
4.2
通讯作者：
Venkateswaran K
中科院分区：
文献类型：
--
作者：
Singh NK;Bezdan D;Checinska Sielaff A;Wheeler K;Mason CE;Venkateswaran K
对从国际空间站（ISS）分离的5株布甘肠杆菌（Enterobacter bugandensis）进行了抗微生物药物耐药性（AMR）表型特征、多重耐药（MDR）基因谱以及潜在毒力和致病性相关基因的分析，并与3株临床菌株的基因组进行了比较。利用纳米孔和Illumina reads的杂交从头组装对ISS菌株的全基因组序列进行了表征。除了传统的微生物分类方法外，采用多位点序列分型（MLST）分析对系统发育谱系进行分类。采用琼脂扩散片法检测抗生素药敏。利用子系统技术和RNAmmer服务器对组装和搭建后的基因组草图进行快速注释，用于下游分析。ISS菌株与所有公开的肠杆菌基因组的分子系统发育和全基因组分析显示，ISS菌株为布甘杆菌，与EB-247T型菌株和2个临床分离株（153_ECLO和MBRL 1077）相似。8个菌株的基因组分析结果显示，与碳水化合物代谢（635个）、氨基酸及其衍生物（496个）、蛋白质代谢（291个）、辅助因子、维生素、假体基、色素（275个）、膜转运（247个）和RNA代谢（239个）相关的基因共4733个。此外，在ISS菌株中发现的112个基因与毒力、疾病和防御有关。在ISS菌株中还发现了与抗生素和有毒化合物耐药相关的基因，包括耐多药三方系统。在ISS菌株中也观察到编码MarA、MarB、MarC和MarR的多重抗生素耐药位点或MAR操纵子，它们调节60多个基因，包括在大肠杆菌K12中报道的药物外排系统的上调。考虑到这些ISS肠杆菌基因组的多药耐药结果和致病性增加的机会（pathgenfinder算法的概率为bb0.79%），这些物种对未来的任务提出了重要的健康考虑。对从国际空间站分离的菌株进行全面的基因组鉴定有助于了解致病潜力，并为未来的任务提供信息，但需要在体内系统中分析它们，以确定微重力对其致病性的影响。本文的在线版本（10.1186/s12866-018-1325-2）包含补充材料，授权用户可以使用。
The antimicrobial resistance (AMR) phenotypic properties, multiple drug resistance (MDR) gene profiles, and genes related to potential virulence and pathogenic properties of five Enterobacter bugandensis strains isolated from the International Space Station (ISS) were carried out and compared with genomes of three clinical strains. Whole genome sequences of ISS strains were characterized using the hybrid de novo assembly of Nanopore and Illumina reads. In addition to traditional microbial taxonomic approaches, multilocus sequence typing (MLST) analysis was performed to classify the phylogenetic lineage. Agar diffusion discs assay was performed to test antibiotics susceptibility. The draft genomes after assembly and scaffolding were annotated with the Rapid Annotations using Subsystems Technology and RNAmmer servers for downstream analysis. Molecular phylogeny and whole genome analysis of the ISS strains with all publicly available Enterobacter genomes revealed that ISS strains were E. bugandensis and similar to the type strain EB-247T and two clinical isolates (153_ECLO and MBRL 1077). Comparative genomic analyses of all eight E. bungandensis strains showed, a total of 4733 genes were associated with carbohydrate metabolism (635 genes), amino acid and derivatives (496 genes), protein metabolism (291 genes), cofactors, vitamins, prosthetic groups, pigments (275 genes), membrane transport (247 genes), and RNA metabolism (239 genes). In addition, 112 genes identified in the ISS strains were involved in virulence, disease, and defense. Genes associated with resistance to antibiotics and toxic compounds, including the MDR tripartite system were also identified in the ISS strains. A multiple antibiotic resistance (MAR) locus or MAR operon encoding MarA, MarB, MarC, and MarR, which regulate more than 60 genes, including upregulation of drug efflux systems that have been reported in Escherichia coli K12, was also observed in the ISS strains. Given the MDR results for these ISS Enterobacter genomes and increased chance of pathogenicity (PathogenFinder algorithm with > 79% probability), these species pose important health considerations for future missions. Thorough genomic characterization of the strains isolated from ISS can help to understand the pathogenic potential, and inform future missions, but analyzing them in in-vivo systems is required to discern the influence of microgravity on their pathogenicity. The online version of this article (10.1186/s12866-018-1325-2) contains supplementary material, which is available to authorized users.
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