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Whole-genome sequencing and characterization of an antibiotic resistant Neisseria meningitidis B isolate from a military unit in Vietnam.
Annals of Clinical Microbiology and Antimicrobials ( IF 5.7 ) Pub Date : 2019-05-06 , DOI: 10.1186/s12941-019-0315-z
Thach Xuan Tran 1 , Trang Thu Le 1 , Long Phi Trieu 2 , Christopher M Austin 3 , Dong Van Quyen 1, 4 , Huong Minh Nguyen 1
Affiliation  

BACKGROUND Invasive meningococcal disease (IMD) persists in military units in Vietnam despite the availability of antibiotics and vaccines. A hindrance to reducing the incidence of IMD in Vietnam is a lack of molecular data from isolates of the causative agent, Neisseria meningitidis from this country. Here, we characterized key genetic and epidemiological features of an invasive N. meningitidis isolate from a military unit in Vietnam using whole-genome sequencing. METHODS Neisseria meningitidis was isolated from a conscript admitted for meningitis and tested against seven antibiotics. DNA from the isolate was extracted and sequenced using the Illumina HiSeq platform. Denovo assembly and scaffolding were performed to construct a draft genome assembly, from which genes were predicted and functionally annotated. Genome analysis included epidemiological characterization, genomic composition and identification of antibiotic resistance genes. RESULTS Susceptibility testing of the isolate showed high levels of resistance to chloramphenicol and diminished susceptibility to ampicillin and rifampicin. A draft genome of ~ 2.1 Mb was assembled, containing 2451 protein coding sequences, 49 tRNAs and 3 rRNAs. Fifteen coding sequences sharing ≥ 84% identity with known antibiotic resistance genes were identified. Genome analysis revealed abundant repetitive DNAs and two prophages. Epidemiological typing revealed newly described sequence type, antigenic finetype and Bexsero® Antigen Sequence Typing (BAST). The BAST profile showed no coverage by either Bexsero® or Trumenba®. CONCLUSIONS Our results present the first genome assembly of an invasive N. meningitidis isolate from a military unit in Vietnam. This study illustrates the usefulness of whole genome sequencing (WGS) analysis for epidemiological and antibiotic resistance studies and surveillance of IMD in Vietnam.

中文翻译:

来自越南某军事单位的抗生素抗性脑膜炎奈瑟氏球菌B分离株的全基因组测序和表征。

背景技术尽管可获得抗生素和疫苗,但在越南的军事单位中仍持续存在侵袭性脑膜炎球菌病(IMD)。越南降低IMD发病率的一个障碍是缺乏来自该国的致病菌脑膜炎奈瑟氏菌分离株的分子数据。在这里,我们使用全基因组测序对越南某军事单位侵袭性脑膜炎奈瑟氏球菌的关键遗传和流行病学特征进行了表征。方法从入院的脑膜炎应征者中分离出脑膜炎奈瑟氏球菌,并针对7种抗生素进行了测试。提取分离物中的DNA,并使用Illumina HiSeq平台进行测序。进行了Denovo组装和脚手架构建了基因组组装草图,从中预测了基因并对其进行了功能注释。基因组分析包括流行病学表征,基因组组成和抗生素抗性基因的鉴定。结果对分离株的药敏试验表明,其对氯霉素的抗药性高,对氨苄西林和利福平的敏感性降低。组装了约2.1 Mb的基因组草图,其中包含2451个蛋白质编码序列,49个tRNA和3个rRNA。鉴定出与已知抗生素抗性基因具有≥84%同一性的十五个编码序列。基因组分析揭示了丰富的重复DNA和两个提议。流行病学分型揭示了新描述的序列类型,抗原精细型和Bexsero®抗原序列分型(BAST)。BAST配置文件显示Bexsero®或Trumenba®均未覆盖。结论我们的结果提出了侵袭性N的第一个基因组组装。脑膜炎从越南的一个军事单位中分离出来。这项研究说明了全基因组测序(WGS)分析在越南流行病学和抗生素耐药性研究以及IMD监测中的有用性。
更新日期:2020-04-22
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