福建省结核分枝杆菌多位点可变数目串联重复序列基因分型研究

目的 了解福建省结核分枝杆菌的多位点可变数目串联重复序列基因分型(MLVA)的特征.方法 选择15个可变数目串联重复位点(VNTR),检测福建省30个耐药监测点临床分离的结核菌株,结果使用BioNumerics (Version 4.5)软件进行聚类分析.结果 313株结核菌被分为9个基因群(Ⅰ～Ⅸ),分别包含220、9、48、2、1、3、10、10、10株菌,以Ⅰ群为主(70.3％,220/313);Ⅰ群菌株异烟肼、链霉素、乙胺丁醇和耐多药的耐药率与其他基因群的差异无统计学意义(P＞0.05),但利福平(RFP)耐药率为33.2％(73/220),明显高于其他群菌株RFP的耐药率20.4％(19/93),差异有统计学意义(P＜0.05).结论 福建省结核分枝杆菌菌株存在明显的基因多态性,以Ⅰ群菌株为主,并与RFP耐药性具有相关性,应加强此类菌株流行的监测.     

初步研究我国土拉菌的亚种及遗传进化关系

目的研究我国土拉弗朗西斯菌（土拉菌）亚种类型及各菌株之间的遗传进化关系。方法对于来源于我国北方地区的10株土拉菌,采用2种型特异引物C1C4和RD1进行PCR,根据扩增产物片段长度来判断所属亚种;同时,使用fopA、tul4和16SrRNA引物,进行3种特异基因的PCR,然后测序;这10株土拉菌及网上已公布基因组序列的3株B型土拉菌、1株subsp.novicida,应用MEGA4软件,进行3种特异基因为基础的系统进化分析。结果采用2种型特异引物C1C4和RD1,鉴定10株土拉菌均为B型亚种;根据MEGA4构建的进化树,我国10株土拉菌可以分为2种基因型,410108、410109和410111为B1型,另外7株土拉菌为B2型;而国外的3株B型土拉菌归为B3型。结论我国北方地区分离的土拉菌可能以B型为主,对于土拉菌B型亚种的起源,我国土拉菌可能早于欧美国家。3种基因为基础的系统进化分析可作为土拉菌基因分型的一种可靠方法。     

内蒙古自治区乌兰察布市羊种布鲁氏菌HOOF基因分型特征

目的 调查2012-2015年内蒙古自治区乌兰察布市83株布鲁氏菌HOOF分型特征。方法 对临床分离的83株布鲁氏菌采用常规方法和AMOS-PCR进行鉴定;利用8个数目可变串联重复序列 位点的HOOF分型方法对菌株进行基因分型,并用Hunter-Gaston 分辨指数评估各VNTR 位点的多态性和对菌株的综合辨别能力,采用BioNumerics 5.0软件聚类分析和构建聚类图。结果 83株试验菌全部为羊种布鲁氏菌,全部8个分型位点具有极高的多态性,多态性指数为0.998;其中6个位点（1、2、4~7）的多态性指数 ≥ 0.678,其分辨力主要来自多态性指数较高的位点。83株羊种布鲁氏菌聚为8大类76个基因型。6个共享基因型包括13株布鲁氏菌,提示感染患者具有流行病学相关性;另70株菌呈现独特的基因型,提示病原分离自无流行病学相关的散发患者。结论 乌兰察布市人布鲁氏菌病流行以散发和局部暴发共存,且散发为主,而交叉感染患者与传染源转移有关。     

全基因组测序技术在结核病流行病学调查中的应用

目的 评估全基因组测序技术在结核病分子流行病学调查中的应用。方法 对2008-2012年在上海市两家结核病定点医院发现9名耐多药患者中分离的结核分枝杆菌具有相同的可变数目串联重复序列,本研究对此进行流行学调查,并对9株结核分枝杆菌进行全基因组测序,分析其传播关系。结果 全基因组序列分析将9株结核分枝杆菌分为两个有传播关系的网络,一个为包括7株结核分枝杆菌（5例和2例患者分别来自不同的医院）的大簇,一个为只有2株结核分枝杆菌的小簇。两个簇之间相差15个单核苷酸多态性（SNP）位点,提示两个簇的遗传距离相对较远,基于菌株SNP差异构建的传播链显示了每个簇内菌株的传播方向和耐药突变积累的过程。结论 基于全基因组测序数据研究耐药结核病的传播网络,能准确判断传播路径和方向,识别传染源和传播缺失环节。     

青海省结核分枝杆菌临床分离株可变数目串联重复序列基因多态性研究

目的 初步了解青海省结核分枝杆菌临床分离株基因多态性和基因分型特征。方法 2009-2012年收集青海省疾病预防控制中心分离的结核分枝杆菌临床分离株,提取DNA,对15个可变数目串联重复序列(VNTR)位点进行PCR扩增和产物电泳分析,使用BioNumerics软件对菌株进行聚类分析。结果 共检测251株结核分枝杆菌临床分离株的15个VNTR位点,显示这些菌株有明显的基因多态性,15个VNTR位点中Hunter-Gaston指数>0.6的VNTR位点有6个,位点分辨能力最高的是MIRU26,经聚类分析,可分为4个基因群,238个基因型。4个基因群分别占4.9%、91.9%、1.6%和1.6%。结论 青海省流行的结核分枝杆菌菌株存在明显的VNTR基因多态性。     

云南省鹤庆县2017年分离鼠疫菌分子溯源

目的 了解2017年云南省鹤庆县新分离的鼠疫菌的基因分型,为该地的鼠疫防控提供科学依据。方法 采用差异片段（DFR）、规律成簇的间隔短回文重复序列（CRISPRs）和多位点可变数目串联重复序列分析（MLVA）3种方法对10株鹤庆县新分离鼠疫菌进行分型,并将10株鼠疫菌及邻近疫源地鼠疫菌株93株纳入聚类分析。结果 鹤庆鼠疫菌株与丽江鼠疫疫源地菌株具有相同的DFR型（Genomovar 05型）及CRISPRs型（Ca7簇,22型）,在MLVA聚类分析中,鹤庆鼠疫菌株与丽江野鼠鼠疫菌株位于同一个簇,两者之间仅有2个位点（N2117,M23）的差异。结论 2017年云南省鹤庆鼠疫菌株与丽江野鼠鼠疫疫源地菌株具有很高的同源性,鹤庆县疫情可能是丽江鼠疫进一步向南扩散的结果。     

类鼻疽伯克霍尔德菌跨洲际流行株的同源性分析及历史溯源

目的 比较不同年代分离自澳大利亚、中国海南地区7株ST562型类鼻疽伯克霍尔德菌（类鼻疽伯克菌）的同源性,并分析其传播来源。方法 利用生物信息学方法提取ST562型类鼻疽伯克菌澳大利亚临床株MSHR5858、中国海南历史菌株350105基因组中Spe Ⅰ限制性酶切片段指纹谱、多位点可变数目串联重复序列多态性指纹（MLVA-4）等遗传特征,并与近年分离的5株海南ST562型临床株的脉冲场凝胶电泳（PFGE,Spe Ⅰ酶切）、MLVA-4分子分型结果相比较。同时分析MSHR5858与350105在基因组水平的共线性及同源性。结果 5株海南ST562型临床株的PFGE带型相同（相似度>97%）且与澳大利亚临床株MSHR5858的Spe Ⅰ限制性带型一致;澳洲临床株（MSHR5858）与海南历史菌株（350105）基因组中Spe Ⅰ限制片段数分别为31和34,其中31个片段的长度一致。5株海南ST562临床株的MLVA-4型别各不相同,但HPPH43（MLVA-4指纹谱：10,8,10,8）与MSHR5858（10,8,8,6）在2341 k、1788 k两个位点重复数相同;HK003（11,8,15,7）、HK061（11,8,17,7）与历史菌株350105（11,8,11,8）在此二位点重复数也相同。此外,350105与MSHR5858在基因组水平具有良好共线性,共有基因占绝大部分,提示来源一致。结论 分离的7株ST562型类鼻疽伯克菌（包括中国海南临床分离株、历史菌株及澳大利亚临床分离株）遗传特征一致,且ST562型近年流行株与历史菌株350105可能具有同源关系。     

MLVA基因分型方法研究世界多地区布鲁氏菌的流行病学特征

目的 通过多位点串联重复序列分析（MLVA）研究世界多国家和地区分离的布鲁氏菌分子流行病学特征。方法 选择11个可变数目串联重复序列位点,使用BioNumerics软件,采用非加权配对算术平均法,对1953－2013年全球48个国家和地区分离的布鲁氏菌VNTR资料进行聚类分析,绘制系统发育树和最小生成树,分析菌株的流行分布特征。结果 布鲁氏菌系统发育树的进化关系与经典的生物分型方法基本上吻合,但猪种生物5型菌株与其他猪种生物1、2、3和4型菌株关系较远;鲸种布鲁氏菌也分为2个部分,并且关系较远。2005－2008年出现了全球布鲁氏菌病（布病）流行,中国是布病多发区,主要流行株为羊种布鲁氏菌,其次是牛种布鲁氏菌,猪种布鲁氏菌主要出现在中国南部省份,犬种布鲁氏菌只在犬中出现,人类没有发现病例。结论 布鲁氏菌具有种的系统发育树特征,并且具有分离的时间、地域和宿主的特异性,这些特征对于布病的防控具有重要意义。     

中国嗜吞噬细胞无形体分离株多间隔序列分型分析

目的 对我国嗜吞噬细胞无形体分离株进行多间隔序列分型（MST）分型。方法 根据GenBank收录的4株无形体全基因组序列，利用Mauve 2.3.1软件行种内基因组比对，选择具有变异间隔区进行引物设计，通过引物特异性及扩增效率等预实验筛选引物，并对实验菌株进行PCR扩增，分析单核苷酸多态性（SNPs）。将每株菌间隔序列拼接后进行分型分析并构建进化树，分析不同地区、不同动物种类来源菌株遗传变异关系。结果 共筛选出22对引物，用于我国11株无形体分离株 MST 分型，SNPs 分析显示，碱基转换发生率最高（60.2%，251/417），其中 A-G 转换居首（18.9%，79/417），颠换占23.0%（96/417），插入及缺失发生率占16.7%（70/417）。11株菌22条间隔序列拼接后（约11 047 bp）均为独立变异型。进化分析发现山东省莱州地区重症患者分离株（LZ-H1、H2、H3、H4、H5）及当地长角血蜱分离株 LZ-T1 与美国 Webster 株及 HZ 株聚为一簇，而北京分离株BJ-H1 与新疆分离株 XJ-H1 和 XJ-H3 聚为一类。莱州地区另一蜱分离株 LZ-T2 与新疆另外一人源分离株聚为一类，与莱州重症患者分离株遗传关系密切。结论 我国无形体分离株间隔序列存在明显的遗传多态性，MST分型技术可用于无形体疫情暴发时的快速诊断和疫情追踪。     

中国北方部分地区北京谱系结核分枝杆菌群体遗传关系的分析

目的 <\b>应用分子遗传学方法探讨234株北京谱系结核分枝杆菌的起源进化及群体间基因流动特征.方法 <\b>对来源于中国北方五省区(黑龙汀、吉林、辽宁、内蒙古和宁夏)234株北京谱系结核分枝杆菌进行24位点可变数目串联重复序列(VNTR)基因分型,计算各VNTR位点的等位基因多态性(h);从个体水平分析其系统发育,即构建NJ树和最小生成树;构建群体水平系统发育树,并在此基础上通过贝叶斯模型计算最近共祖年代;通过分子方差分析了解五省区菌株间的基因流动情况.结果 <\b>24个VNTR位点的等位基因多态性较低(h值:0.000 ～ 0.744).234株北京谱系结核分枝杆菌分散存在NJ树各个进化分支,最小生成树中约62.0％(145/234)的菌株被划分到同一“克隆复合群”.群体水平系统发育树显示234株菌与MIRU-VNTRplus数据库(http://www.miru-vntrplus.org)中的北京谱系结核分枝杆菌的遗传关系最近(Bootstrap值为100);最近共祖年代为5308年(95％CI:4263 ～ 6470年).通过分子方差分析发现吉林与黑龙江、辽宁菌株之间,内蒙古与宁夏菌株之间遗传分化系数的差异无统计学意义(P＞0.05).结论 <\b>中国北方五省区北京谱系结核分枝杆菌的遗传相似性较高,菌株间种系发生关系不明显.推测这些菌株由近期(约5000年前)结核分枝杆菌北京谱系的某一“克隆”进化而来.地理位置接近的区域,菌株间存在基因流动现象.     

Vaccination with a defined Francisella tularensis subsp. novicida pathogenicity island mutant (ΔiglB) induces protective immunity against homotypic and heterotypic challenge

Francisella tularensis, an intracellular Gram-negative bacterium, is the causative agent of tularemia and a potential bioweapon. Currently, there is no licensed vaccine against this organism. We have characterized the efficacy of a defined F. tularensis subsp. novicida mutant (ΔiglB) as a live attenuated vaccine against pneumonic tularemia. Replication of the iglB mutant (KKF235) in murine macrophages was significantly lower than the wild type novicida strain U112, and exhibited an LD₅₀ greater than 10⁶-fold (>10⁷ CFU vs <10 CFU) in an intranasal challenge model. Mice immunized with KKF235 intranasally or orally induced robust antigen-specific splenic IFN-γ recall responses, as well as the production of systemic and mucosal antibodies. Intranasal vaccination with KKF235 protected mice from subsequent homotypic challenge with U112 as well as heterotypic challenge with F. tularensis subsp. holarctica (LVS). Moreover, protected animals also exhibited minimal pathological changes compared with mock-vaccinated and challenged animals. The protection conferred by KKF235 vaccination was shown to be highly dependent on endogenous IFN-γ production. Most significantly, oral immunization with KKF235 protected mice from a highly lethal subsp. tularensis (SCHU S4) pulmonary challenge. Collectively, these results further suggest the feasibility of using defined pathogenicity island mutants as live vaccine candidates against pneumonic tularemia.     

High-resolution melting PCR assay as a powerful tool for the epidemiological surveillance of tularemia in Western Europe

In Europe, tularemia is caused by Francisella tularensis subsp. holarctica and is a sporadic disease affecting mainly wildlife animals and humans. Classification of this species relies on canonical single nucleotide polymorphisms (canSNPs). Four main clades have been described for F. tularensis subsp. holarctica: B.4, B.6, B.12 and B.16. Phylogeographic studies have shown that clade B.6 is predominant in Western Europe and B.12 in Eastern and Central Europe. Based on this global phylogeny, we aimed to design a molecular typing assay for all genetic subclades of subclade B.11, which is the predominant subclade in clade B.6. We designed high-resolution melting (HRM) primers for the screening of 109 canSNPs divided in seven orders of discrimination for the molecular epidemiology analysis and tracking of Francisella tularensis subsp. holarctica in Western Europe.     

Identification of Francisella tularensis Cluster in Central and Western Europe

We conducted a molecular analysis of Francisella tularensis strains isolated in Switzerland and identified a specific subpopulation belonging to a cluster of F. tularensis subsp. holarctica that is widely dispersed in central and western continental Europe. This subpopulation was present before the tularemia epidemics on the Iberian Peninsula.     

Multiple Francisella tularensis Subspecies and Clades, Tularemia Outbreak, Utah

In July 2007, a deer fly–associated outbreak of tularemia occurred in Utah. Human infections were caused by 2 clades (A1 and A2) of Francisella tularensis subsp. tularensis. Lagomorph carcasses from the area yielded evidence of infection with A1 and A2, as well as F. tularensis subsp. holarctica. These findings indicate that multiple subspecies and clades can cause disease in a localized outbreak of tularemia.     

Hare-to-Human Transmission of Francisella tularensis subsp. holarctica,Germany

In November 2012, a group of 7 persons who participated in a hare hunt in North Rhine-Westphalia, Germany, acquired tularemia. Two F. tularensis subsp. holarctica isolates were cultivated from human and hare biopsy material. Both isolates belonged to the FTN002–00 genetic subclade (derived for single nucleotide polymorphisms B.10 and B.18), thus indicating likely hare-to-human transmission.     

Differential ability of novel attenuated targeted deletion mutants of Francisella tularensis subspecies tularensis strain SCHU S4 to protect mice against aerosol challenge with virulent bacteria: Effects of host background and route of immunization

Francisella tularensis subspecies tularensis is a highly virulent facultative intracellular pathogen of humans and a potential biological weapon. A live vaccine strain, F. tularensis LVS, was developed more than 50 years ago by pragmatic attenuation of a strain of the less virulent holarctica subspecies. LVS was demonstrated to be highly effective in human volunteers who were exposed to intradermal challenge with fully virulent subsp. tularensis, but was less effective against aerosol exposure. LVS faces regulatory hurdles that to date have prevented its licensure for general use. Therefore, a better defined and more effective vaccine is being sought. To this end we have created gene deletion mutants in the virulent subsp. tularensis strain and tested them for their ability to elicit a protective immune response against systemic or aerosol challenge with the highly virulent wild-type subsp. tularensis strain, SCHU S4. Both oral and intradermal (ID) primary vaccination routes were assessed in BALB/c and C3H/HeN mice as was oral boosting. One SCHU S4 mutant missing the heat shock gene, clpB, was significantly more attenuated than LVS whereas a double deletion mutant missing genes FTT0918 and capB was as attenuated as LVS. In general mice immunized with SCHU S4ΔclpB were significantly better protected against aerosol challenge than mice immunized with LVS. A single ID immunization of BALB/c mice with SCHU S4ΔclpB was at least as effective as any other regimen examined. Mice immunized with SCHU S4Δ0918ΔcapB were generally protected to a similar degree as mice immunized with LVS. A preliminary examination of immune responses to vaccination with LVS, SCHU S4ΔclpB, or SCHU S4Δ0918ΔcapB provided no obvious correlate to their relative efficacies.     

Cellular and humoral immunity are synergistic in protection against types A and B Francisella tularensis

Herein we report studies with a novel combination vaccine that, when administered to mice, conferred protection against highly virulent strains of Francisella tularensis by stimulating both arms of the immune system. Our earlier studies with Ft.LVS::wbtA, an O-polysaccharide (OPS)-negative mutant derived from the available live vaccine strain of F. tularensis (Ft.LVS), elucidated the role of antibodies to the OPS – a key virulence determinant – in protection against virulent type A organisms. However, when expressed on the organism, the OPS enhances virulence. In contrast, in purified form, the OPS is completely benign. We hypothesized that a novel combination vaccine containing both a component that induces humoral immunity and a component that induces cellular immunity to this intracellular microbe would have an enhanced protective capacity over either component alone and would be much safer than the LVS vaccine. Thus we developed a combination vaccine containing both OPS (supplied in an OPS–tetanus toxoid glycoconjugate) to induce a humoral antibody response and strain Ft.LVS::wbtA (which is markedly attenuated by its lack of OPS) to induce a cell-mediated protective response. This vaccine protected mice against otherwise-lethal intranasal and intradermal challenge with wild-type F. tularensis strains Schu S4 (type A) and FSC 108 (type B). These results represent a significant advance in our understanding of immunity to F. tularensis and provide important insight into the development of a safer vaccine effective against infections caused by clinical type A and B strains of F. tularensis.     

鼠疫耶尔森菌和假结核耶尔森菌基因鉴别方法的建立及评价

目的 建立鼠疫耶尔森菌和假结核耶尔森菌基因鉴别方法。方法 依据鼠疫菌、假结核菌特有的基因组序列["疫岛(PeI)"和"假岛(PsI)"], 与已公布的12株鼠疫菌和4株假结核菌全基因序列进行比对, 设计特异性的引物, 对鼠疫菌、假结核菌和其他肠道细菌进行鉴定。结果 用52株鼠疫菌、57株假结核菌和其他肠道菌株进行验证, 结果显示, 5对鼠疫菌的鉴定引物中, 2对(PeI2和PeI11)仅在52株鼠疫菌中扩出目的条带, 另3对引物(PeI1、PeI3和PeI12)除鼠疫菌外在部分假结核菌株中也扩出目的条带;5对假结核菌鉴定引物中, 1对引物(PsI1)在52株鼠疫菌和57株假结核菌株中扩出目的条带, 4对引物(PsI7、PsI16、PsI18和 PsI19)仅在57株假结核菌株中均扩出目的条带, 在鼠疫菌中未扩出目的条带。结论 用鼠疫菌和假结核菌共有的PsI1序列、鼠疫菌特有的PeI2和PeI11序列及假结核菌特有的PsI7、PsI16、PsI18和 PsI19序列组成的基因鉴别方法, 可以用于鼠疫菌和假结核菌的基因快速鉴别。     

Diversity of Francisella tularensis Subsp. holarctica Lineages,China

We analyzed 10 isolates of Francisella tularensis subspecies holarctica from China and assigned them to known clades by using canonical single-nucleotide polymorphisms. We found 4 diverse subtypes, including 3 from the most basal lineage, biovar japonica. This result indicates unprecedented levels of diversity from a single region and suggests new models for emergence.     

CRISPR1上游侧翼序列用于大肠埃希菌和志贺菌鉴定的效果评价

目的 探讨基于成簇规律间隔的短回文重复序列（CRISPR）1上游侧翼序列对大肠埃希菌和志贺菌鉴定和评价效果。方法 通过BLAST重复序列识别并获得全基因组测序大肠埃希菌和志贺菌的CRISPRs和CRISPR相关基因（CRISPR-associated,cas）,并分析其种系;选取CRISPRs上、下游各500 bp侧翼序列,使用Clustal X进行序列比对;采用PCR方法扩增CRISPR1上游侧翼序列,以确定其对大肠埃希菌和志贺菌鉴定和评价效果。结果 73.4%（149/203）的大肠埃希菌存在I-E型CRISPR/Cas系统,包含了A、B1、D种系;8.4%（17/203）的大肠埃希菌存在I-F型CRISPR/Cas、17.2%（35/203）的大肠埃希菌不存在CRISPR/Cas,这2种大肠埃希菌均属于B2种系;9株志贺菌均存在I-E型CRISPR/Cas。在大肠埃希菌（B2种系外）、志贺菌CRISPR1上游和大肠埃希菌（B2种系）各存在61 bp侧翼序列,序列一致性为99%,且有种属特异性,PCR扩增此区域鉴定大肠埃希菌和志贺菌的灵敏度和特异度均>91%。结论 基于CRISPR1上游序列可用来鉴定大肠埃希菌和志贺菌,且具有很好的效果。