基于PacBio测序的对叶百部叶绿体基因组结构及系统发育分析

目的：获得对叶百部Stemona tuberosa高质量叶绿体基因组信息,明确其结构、序列特征,同时确定对叶百部的系统发育地位。方法：采用Illumina NovaSeq 6000和PacBio RSⅡ平台对对叶百部分别进行建库测序,利用生物信息软件将2个测序平台的数据进行混合组装和碱基校正,最终获得高质量叶绿体基因组,随后对其序列特征、重复序列、基因多样性和系统发育进行分析。结果：对叶百部叶绿体基因组大小为154 379 bp,叶绿体基因组结构为典型环状四段式,1对27 074 bp的反向重复区（IR）,1个大小为17 924 bp的小单拷贝区（SSC）和1个82 307 bp的大单拷贝区（LSC）,平均鸟嘌呤和肥嘧啶所占的比率（GC）含量为37.86%;共注释得到121个基因,包括30个tRNA基因,4个rRNA基因和87蛋白编码基因,其中6个tRNA基因和12个蛋白质编码基因中存在内含子;对叶百部叶绿体基因组中共发现49个长重复序列和59个单核苷酸简单重复序列（SSR）;4个百部属的叶绿体基因组比较分析表明ycf1和ndhF基因具有高度多样性;基于叶绿体基因组构建的系统发育树与对...     

Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020

Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARS-CoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARS-CoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22^nd, 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25^th, 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.     

基于高通量测序的鼠类肠道细菌群落多样性分析

目的探明鼠类肠道细菌群落组成和多样性。方法分离鼠类完整肠道并提取总DNA,利用Oxford Nanopore Technologies公司(MK1C)的纳米孔单分子测序技术对其肠道细菌16S rRNA的全区序列进行测序,统计肠道细菌的操作分类单元(operational taxonomic unit,OTU)数量,分析其物种组成、丰度及Alpha、Beta多样性。结果获得鼠类肠道细菌16S rRNA优质序列1161377条,根据序列相似性进行聚类分析获得1484个OTUs。共注释到24个门,48个纲,113个目,241个科和534个属;在门分类水平上,以厚壁菌门Firmicutes和变形菌门Proteobacteria为优势门类;在属分类水平上,优势属为肠球菌Enterococcus、乳酸杆菌Lactobacillus和葡萄球菌Staphylococcus,其丰度分别为38.7%,17.65%和7.48%。Alpha多样性分析结果显示,鼠类肠道细菌的观测物种数、Chao1指数、Shannon指数和Simpson指数分别为1484、1825.77、3.91和0.058。Beta多样性分析结果显示臭鼬和小家鼠肠道菌群组成最接近,而黄胸鼠和小家鼠肠道菌群组成相差最大。结论鼠类肠道细菌菌群整体多样性比较丰富,可为有效评估鼠传疾病传播风险提供依据。     

ABCB4基因突变合并巨细胞病毒感染致婴儿胆汁淤积症的诊治分析并文献复习

目的探讨ABCB4基因突变合并巨细胞病毒(CMV)感染致婴儿胆汁淤积症(IC)患儿的临床特征、基因检测结果和诊治方案。 方法选择2019年8月3日,于中山大学附属第七医院就诊并确诊为ABCB4基因突变合并CMV感染致IC的1例婴儿(女性,生后9个月)为研究对象。回顾性分析其临床病例资料,包括临床特征、实验室检查结果及基因检测结果。同时,检索国内外数据库中ABCB4基因突变所致IC患儿的相关文献,并进行文献复习。本研究遵循的程序符合2013年新修订的《世界医学协会赫尔辛基宣言》要求。 结果本例IC患儿在本院诊治结果如下。①病史采集：系G₂P₂,足月顺产,外观无异常,否认新生儿黄疸病史,生后2个月龄时出现皮肤及巩膜呈暗绿色,伴反复呕奶,当地医院治疗并诊断为胆汁淤积性肝病、CMV感染和泌尿系统感染,抗病毒治疗2周后好转出院。出院时,其血清总胆汁酸(sTBA)为152.8 μmol/L,CMV-DNA<4×10² copies/mL,口服熊去氧胆酸胶囊10 mg/(kg·d)治疗后,皮肤暗绿色逐渐消退,大、小便正常。出院后定期监测肝功能,sTBA、γ-谷氨酰转肽酶(GGT)仍然较正常值增高。②实验室检查：血清CMV免疫球蛋白(Ig)G抗体呈阳性、CMV IgM抗体呈阴性,CMV-DNA<55×10² copies/mL。基因检测结果：患儿及其父亲均携带ABCB4基因杂合变异。治疗结果：经口服熊去氧胆酸胶囊10 mg/(kg·d)及谷胱甘肽片0.1 g/次× 3次/d治疗后,对患儿定期复查sTBA、GGT。随访到18个月龄时,其各项指标逐渐恢复正常范围。③文献复习结果：共计检索到8篇国内外报道的因ABCB4基因突变引起IC相关文献,纳入14例IC患儿,均被诊断为进行性家族性肝内胆汁淤积3型(PFIC3),伴肝大,sTBA、GGT水平升高等。14例IC患儿中,共检测到ABCB4基因突变位点20个。其中,9例IC患儿接受熊去氧胆酸治疗,7例随访结果显示临床症状及实验室检查指标有所好转。 结论携带ABCB4基因突变,可引起IC。对于sTBA升高、肝酶异常的病因不明确、治疗效果不佳IC患儿,建议完善基因检测进一步排查ABCB4基因突变所致胆汁淤积症。     

Territorywide Study of Early Coronavirus Disease Outbreak,Hong Kong,China

Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10⁻³ substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.     

Genomic Characterization of hlyF-positive Shiga Toxin–Producing Escherichia coli,Italy and the Netherlands, 2000–2019

Shiga toxin–producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000–2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx₂ subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance–encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.     

Genomic and Pathologic Findings for Prototheca cutis Infection in Cat

Severe nasal Prototheca cutis infection was diagnosed postmortem for an immunocompetent cat with respiratory signs. Pathologic examination and whole-genome sequencing identified this species of algae, and susceptibility testing determined antimicrobial resistance patterns. P. cutis infection should be a differential diagnosis for soft tissue infections of mammals.     

mNGS协助诊断无焦痂型丛林斑疹伤寒1例

 丛林斑疹伤寒是由恙虫病东方体感染引起的一种急性人畜共患传染病。临床表现为发热、皮疹、淋巴结肿大,被叮咬部位出现特异性焦痂和溃疡是该病诊断的最主要依据,没有焦痂和溃疡的患者往往很难识别。本文报告1例54岁男性患者,以发热、淋巴结肿大及全身多个脏器损伤为主要临床表现,因无特征性焦痂,且经验性使用抗菌药物效果不佳,给诊疗带来困难。病例标本送宏基因组二代测序(mNGS)明确病原体为恙虫病东方体。换用左氧氟沙星及阿奇霉素治疗后患者症状很快好转,最终痊愈出院。mNGS已被证明比传统培养方法更敏感,在早期诊断恙虫病方面优于传统临床方法,尤其是对于没有典型焦痂的患者。     

鹦鹉热衣原体肺炎患者临床特点分析

 目的 探讨分析鹦鹉热衣原体肺炎患者的临床表现及辅助检查结果特征,以提高对该病的认识。方法 回顾性分析某医院2019年6月- 2021年8月经宏基因组二代测序（mNGS）诊断鹦鹉热衣原体肺炎的9例患者临床资料。结果 9例患者中男性7例,女性2 例,包含1例妊娠36⁺²周孕妇;年龄25~70岁,中位年龄63岁;临床主要表现为高热（9例）、咳嗽（9例）、咳痰（7例）。白细胞计数正常8例,淋巴细胞计数降低9例,CRP升高9例,ESR升高9例,PCT正常4例,门冬氨酸氨基转移酶和丙氨酸氨基转移酶升高6例。9例患者胸部 CT均表现为斑片或斑片实变影。经血及肺泡灌洗液mNGS确诊后使用多西环素、莫西沙星、左氧氟沙星、阿奇霉素单药治疗方案,疗程14~21 d,均好转出院。结论 鹦鹉热衣原体肺炎临床表现多样、诊断困难,mNGS检测可以快速明确病原学诊断,有助于及时启动特异性抗感染治疗,可减少抗菌药物的使用,改善预后。     

PCR在猴B病毒鉴定中的应用研究

目的为鉴定新分离毒株是否为B病毒.方法根据ScinicarielloF报道的引物,用PCR方法扩增BV147、HSV-1、HSV-2,对扩增产物进行SacⅡ内切酶消化.结果这一对引物可同时对这3种病毒进行扩增,但只有BV147的扩增产物可被SacⅡ内切酶切开.对BV147扩增片段克隆测序的结果证实,其与美国B病毒E2490株部分基因(UL27)相对应位置的核苷酸同源性为100%.结论初步建立了检测B病毒DNA的PCR方法并测定了新分离病毒毒株的部分基因序列,证明新分离的病毒为B病毒.