牛支原体中国株的多位点序列分型

为了解中国牛支原体的流行趋势,本试验应用已经建立的牛支原体分型方法,将中国的15株牛支原体进行MLST分型,同时结合数据库中已有的11株中国株的ST型,分析牛支原体中国株的种群结构及进化关系。分型结果显示,15株分离株均获得一样的等位基因号及ST型;共计26株中国株分属于3个ST型,即R-ST10(16/26),RST33(9/26),R-ST34(1/26),而且彼此之间只有1个等位基因的差异,10型和33型之间的差异是rpoD基因,33型和34型之间的差异是danA基因;说明目前牛支原体中国株的种群结构相对单一,流行菌株相对稳定。     

上海市动物源性食品中单增李斯特菌的MLST分析

为了解上海市动物性食品中单增李斯特菌的进化情况和群体遗传学特征，本研究采用MLST法和eBURST软件对33株分离株进行分子分型及进化树分析。结果共分成8个型别，并且33株单增李斯特菌之间遗传相关性不是很大。分为4个进化谱系：ST11和ST196为一个进化谱系，ST9、ST8和ST155为一个进化谱系，ST87和ST277/589为一个进化谱系，所占比例最多的ST121单独一个进化谱系。     

奶牛临床型乳房炎MRSA新疆流行株耐药基因的检测及MLST分型研究

为了解新疆地区奶牛临床型乳房炎MRSA流行株耐药表型、耐药基因分布及分子分型特征,采用纸片扩散法检测了临床分离的71株金黄色葡萄球菌的耐药表型,并对MRSA进行判定;应用多重PCR方法对MRSA流行株进行耐药基因的检测及MLST分型。结果显示,71株金黄色葡萄球菌中共检出13株MRSA,检出率为18.3%。13株MRSA流行株均检出mecA和linA耐药基因,检出率为100.0%;7株检出tetm耐药基因,检出率为53.8%;4株检出msrB耐药基因,检出率为30.8%;4株检出AacA-Da耐药基因,检出率为30.8%;MLST分型结果发现,13株MRSA可分为6种ST型,分别为ST188、ST9、ST63、ST2700、ST968、ST2373,其中ST9型流行较为广泛。本研究为新疆地区奶牛MRSA流行株的耐药特性及分子特征提供了理论基础,为兽医临床合理用药提供了科学依据。     

禽源多杀性巴氏杆菌多位点序列分型研究

为了解国内禽源多杀性巴氏杆菌流行情况,对分离自18省份的84株多杀性巴氏杆菌采用荚膜多重PCR分型和多位点序列分型对其血清型和基因型进行鉴定。结果表明:禽源多杀性巴氏杆菌主要以血清A型为主,占96.4%(81/84);多位点序列分型可将禽源多杀性巴氏杆菌分为5种ST型,其中ST129为主要流行型,占94.0%(79/84)。本研究为我国禽源多杀性巴氏杆菌的流行病学监测和基因多样性提供了数据支持。     

2008—2017年我国部分地区禽源沙门氏菌流行状况及耐药分析

为了解我国禽源沙门氏菌的流行和耐药情况及其血清型、ST型和耐药性之间的关系，对2008—2017年，在我国部分地区分离的90株禽源沙门氏菌，用血清凝集方法鉴定其血清型，用微量肉汤稀释法对部分菌株进行药物敏感性试验；经PCR扩增、测序和比对查询，得到90株菌的ST型，并用BioNumerics 7.6分析MLST分型及其亲缘关系；利用统计学方法，对分离株的血清型、ST型和耐药性进行差异显著性和相关性分析。血清型鉴定结果显示：90株禽源沙门氏菌可分为16种血清型，其中S. Enteritidis为优势血清型。71株菌株的药物敏感性试验结果显示：多重耐药菌株占比90.14%（64/71），对氨苄西林（78.87 %）和磺胺异噁唑（77.46 %）的耐药率较高，仅S. Indiana菌株的ST17型对头孢他啶耐药。其他相关分析结果显示：分离菌株对氨苄西林等7种药物的耐药率显著上升（P＜0.05），而对黏菌素耐药率下降极显著（P＜0.01）；鉴定出14种ST型，其中ST11为优势型；最小生成树显示，仅有一个ST complex，菌株来自7个省市；S. Indiana的耐药率显著高于S. Enteritidis（P＜0.05），且其ST17所耐药物种类多于其他ST型。结果表明：我国禽源沙门氏菌的优势血清型是S. Enteritidis，优势ST型为ST11，其血清型和ST型有一定的相关性，且不同地区分离株之间有一定的亲缘关系；分离株对不同药物的耐药性存在差异，且耐药谱和耐药率与血清型相关，S. Indiana菌株与S. Enteritidis相比更易形成耐药菌株。     

2005年中国新城疫病毒分子流行病学研究

采用2005年从国内不同地区、不同宿主分离到的NDV分离株，选取其中具有代表性的83株，用RT-PCR技术扩增其F基因重要的功能区片段，进一步进行序列测定。序列分析表明所扩增的目的片段长度为535bp，序列测定结果已经登陆到GenBank，登陆号为DQ439866-DQ439948。参照国内外已发表的部分毒株的F基因序列，构建了NDV的遗传进化树，分析毒株间的遗传进化关系。通过遗传进化分析表明83株NDV分离株中有65株属于基因Ⅶ型，9株属于基因Ⅱ型，5株属于基因Ⅰ型，3株属于基因Ⅵ型，1株属于基因Ⅲ型。表明我国目前ND的流行情况比较复杂，其中基因Ⅶ型新城疫病毒所引起的新城疫在国内呈流行趋势，同时也存在其它基因型的散发，从而为我国目前新城疫的防治提供了科学的参考依据。     

乳房链球菌多位点序列分型和遗传进化特征分析

为探究中国不同地区来源的乳房链球菌（Streptococcus uberis，S.uberis）之间的多样性和遗传进化关系，本研究以部分地区分离到的38株乳房链球菌为研究对象，通过对其最小抑菌浓度（minimun inhibitory concentration，MIC）测定和全基因组框架测序，获取38株菌耐药性、耐药基因及毒力基因等相关信息；通过多位点序列分型技术（multilocus sequence typing，MLST）分析了7个管家基因的等位基因谱、序列型（sequence type，ST）和克隆复合体（clonal complexes，CCs），并构建系统进化树。MIC试验共采用15种抗生素，除头孢噻呋和氟苯尼考外，38株乳房链球菌对其中13种抗生素具有不同程度耐药，且江苏地区的耐药性明显强于新疆地区；耐药和毒力基因比对后发现，仅24株菌携带耐药基因，剩余14株则不携带耐药基因且属新疆地区分离株，与MIC试验结果相符；15种毒力基因中，除cfu、hasA/B和lbp外，余下12种毒力基因的携带率均高达100%。MLST结果表明，38株乳房链球菌共属于17个ST型，其中有15个ST型从未报道，仅supan01 1株菌属于ST-5 CCs。进化树结果揭示，38株分离株之间的亲缘性较远，分布呈地区依赖性，且中国部分地区当前流行的乳房链球菌与西方国家流行的菌株差异较大。本研究丰富了乳房链球菌的MLST分型数据库，为了解中国乳房链球菌遗传特性和分布特点提供了参考依据。     

牛源多杀性巴氏杆菌血清分型及毒力相关基因的检测研究

为确定新疆北疆部分地区疑似病例中分离的牛源多杀性巴氏杆菌（Pasteurella multocida,Pm）流行的血清型、ST型及毒力相关基因的分布情况,本研究以分离的17株牛源Pm为研究对象,采用荚膜多重PCR分型法、脂多糖多重PCR分型法（LPS-mPCR）、多位点序列分型法（MLST）及PCR方法检测17株Pm分离株的荚膜型、脂多糖型、MLST型及7类共25个毒力相关基因的分布情况。结果显示,13株Pm的荚膜脂多糖型为A：L3型,ST型均为ST1型,4株Pm荚膜脂多糖型为B：L2型,ST型均为ST44;17株Pm毒力相关基因（exbB、exbD、fimA、fur、hgbA、hsf2、nanB、oma87、ompA、ompH、plpB、psl、ptfA、sodA、sodC、tonB和tbpA）的检出率高达100%,toxA基因的检出率为0。结果表明,从新疆北疆部分地区规模化牛场疑似病例中分离的Pm主要血清型为A：L3：ST1型。     

猪圆环病毒2型山西株全基因组序列分析

为了解山西省猪圆环病毒2型(PCV2)的遗传变异情况,本试验采用PCR方法对山西省分离的4株猪圆环病毒流行株(SXXZ1株、SXXZ2株、SXTY株和SXJZ株)的全基因组进行了扩增、克隆和测序,并将其全基因组序列与国内外34株主要流行毒株进行核苷酸同源性与系统进化树分析。结果显示,4株PCV2山西流行株全基因组核酸序列全长SXJZ株为1 768bp,其余均为1 767bp,分别占25%和75%。4株毒株核苷酸同源性为95.9%~100.0%,与国内外34株参考株同源性为94.5%~99.9%,与国产疫苗株同源性为95.6%~99.8%;PCV2全基因组序列进化分析表明,本研究分离的SXXZ1株、SXXZ2株和SXTY株属于PCV-2b基因型,SXJZ株属于PCV-2e基因型,其中SXXZ1株和SXXZ2株与广东QY株的进化关系最近,SXTY与奥地利AUT5株的进化关系最近,SXJZ与福建FJ株的进化关系最近;而SXXZ1株、SXXZ2株和SXTY株与山西PCV2疫苗DBN-SX07-2株的进化关系较近,SXJZ株与国内PCV2疫苗LG株的进化关系较近。从而证实在山西省流行的PCV2毒株以PCV-2b为主,同时还分离出了PCV-2e亚型,表明山西省存在PCV-2e亚型毒株。本试验结果为山西省PCV2的分子流行病学、遗传变异及防控奠定了基础。     

水禽源沙门菌的分离鉴定与PFGE分子分型

为了明确目前广东省水禽源沙门菌的优势血清型及其分子流行病学动态,采用细菌分离纯化、生化特性鉴定和PCR扩增从316份样品中分离鉴定出188株水禽源沙门菌;采用玻片凝集法将分离株分为4(B、D、C1、E1)个群别8种血清型;采用脉冲场凝胶电泳(PFGE)分型法对分离株进行分子分型,得到PFGE-XbaⅠ带型62种,菌株间相似度为54.1%~100.0%,分为A^I共9个聚类簇与11个单一基因型。结果表明,广东水禽源沙门菌优势血清型为鼠伤寒沙门菌,PFGE-XbaⅠ带型具多样化,其中11种PFGE-XbaⅠ带型在区域和年份小范围集中流行,32种带型跨区域与跨时间交叉分布呈散在"流行暴发",不同血清型分离株的PFGE-XbaⅠ带型差异较大,相同血清型的分离株PFGE-XbaⅠ带型一般具有相同图谱型或聚类在一起。本研究采用PFGE法进行分子分型分析具有流行病学意义,并探明了本地沙门菌分离株血清型与分子分型的关系。     

Differentiation of infectious laryngotracheitis virus isolates by restriction fragment length polymorphic analysis of polymerase chain reaction products amplified from multiple genes

Infectious laryngotracheitis (ILT) has been identified in most countries around the world and remains a threat to the intensive poultry industry. Outbreaks of mild to moderate forms of ILT are common in commercial layer flocks, while sporadic outbreaks of ILT in broiler flocks have also been recognized as an emerging problem in several countries. Examination of viral isolates using restriction fragment length polymorphism of polymerase chain reaction (PCR-RFLP) from individual ILTV genes has suggested that some of these outbreaks were caused by vaccine strains. In this study, PCR-RFLP of a number of ILTV genes/genomic regions including gE, gG, TK, ICP4, ICP18.5, and open reading frame (ORF) B-TK was used to examine a number of historical and contemporary Australian ILTV isolates and vaccine strains. PCR-RFLP of gE using restriction endonuclease EaeI failed to distinguish between any of the isolates including the vaccine strains. PCR-RFLP of gG, TK, and ORFB-TK using restriction endonucleases MspI and FokI, respectively, divided all the isolates into two groups. PCR-RFLP of ICP18.5 and ICP4 using restriction endonuclease HaeIII separated the isolates into three different groups with some field isolates only able to be distinguished from vaccine strains by PCR-RFLP of ICP18.5. A combination of groupings including gG, TK, ICP4, ICP18.5, and ORFB-TK PCR-RFLP classified the ILTV isolates under investigation into five different groups with most isolates distinguishable from vaccine strains. Results from this study reveal that to achieve reliable identification of strains of ILTV, the examination of multiple gene regions will be required, and that most of the recent ILT outbreaks in Australia are not being caused by vaccine strains.     

33株H9N2亚型禽流感病毒分离株分子流行特点的研究

在1998至2007年期间,采集了我国不同地区、不同宿主来源的H9N2亚型禽流感病毒株,应用逆转录聚合酶链反应(RT-PCR)扩增HA基因,获得33株H9N2亚型禽流感病毒的核苷酸序列。结合GenBank中公开发表的其他国内H9亚型禽流感HA基因序列共65株,应用计算机软件绘制进化树,进行H9亚型禽流感病毒谱系全景分析,探索H9亚型禽流感的流行趋势。分析结果表明:这65株的基因进化树主要分为三个系列,每个系列毒株均呈现全国性流行分布;三个系列毒株可在同一时间段内、同一地区发生流行;不同时间的流行毒株虽有变异,但大部分归属于三个系列中。无论从时间的推移上还是地域的转变中,病毒均没有表现出明显的时间演变与地理分布特征,进一步显示了H9亚型禽流感的复杂性和多样性。     

2016-2019年我国部分地区鸡滑液囊支原体分离株vlhA基因遗传进化分析

为了解我国鸡滑液囊支原体(Mycoplasma synoviae,MS)感染的最新流行情况,本研究于2016―2019年从江苏、安徽、山东、河南、河北、宁夏、黑龙江、湖北等8个省份疑似发生MS感染的鸡场采集样品,进行MS菌株的分离鉴定,结果共获得48株MS分离株。对这些分离株的vlhA基因片段测序和分析显示,其中46株均属于K基因型,另外2株分别属于A基因型和E基因型。研究结果表明,当前国内流行的MS优势基因型是K基因型,与其他国家和地区流行的基因型存在显著性差异。本研究结果为制定适合我国鸡群MS控制与净化的策略提供了必要的流行病学依据。     

鸡杆菌中国分离株RAPD分型方法的建立与应用

对9株鸡杆菌进行了血清分型,并应用8条随机引物对该9株鸡杆菌和3个参考菌株(1株巴氏杆菌、1株大肠杆菌和1株链球菌)共12株细菌做随机扩增多态性DNA(RAPD)分型研究。结果显示,9株鸡杆菌分别属于血清Ⅰ型(1/9)、血清Ⅱ型(3/9)和血清Ⅳ型(5/9)。所用8条随机引物中有3条呈现良好的多态性和稳定性,可产生差异显著的指纹图谱。采用SPSS13.0软件分析了不同菌株间的遗传距离,并依此绘制出菌株间的亲缘关系树状图。12株细菌共分为4个聚类群,其中9株鸡杆菌位于同一聚类群中,且又可分为4个聚类亚群。3个参考菌株各自形成一个独立的聚类群。不同血清型的鸡杆菌菌株具有相似的指纹图,同一血清型的菌株指纹图存在差异。结果表明,RAPD基因分型是目前鸡杆菌分子流行病学调查及病原分离鉴定比较理想的方法之一。     

PCR-based typing of Mycobacterium avium isolates in an epidemic among farmed lesser white-fronted geese (Anser erythropus)

Mycobacterium avium is an important veterinary pathogen causing avian tuberculosis in birds. The aim of the study was to evaluate the genetic relatedness in M. avium isolates from deep tissues of farmed lesser white-fronted geese with avian tuberculosis and in samples from the farm environment. The strains were analyzed by two PCR-based typing methods, inverted repeat (IR) typing and random amplified polymorphic DNA (RAPD) analysis. The primers for the inverted repeats of the insertion sequences IS1245 and IS1311 were used in IR typing, and the RAPD analysis was performed with six primers. Seven of the nine avian strains yielded an identical pattern in the IR typing, but they could be divided into two groups in the RAPD analysis. The remaining two bird isolates had an identical IR pattern (IR cluster II) which they shared with two environmental isolates. However, the RAPD analysis revealed that these environmental isolates had a RAPD pattern (RAPD cluster VI) distinct and different from either of the bird isolates (RAPD clusters II and IV). In all, four M. avium strains were verified as being inducers of avian tuberculosis in birds, and all were distinct from the three environmental strains identified. Thus, the results did not confirm the preliminary idea that a single strain had caused the epidemic. The polymorphism among M. avium strains highlighted the great biodiversity among an M. avium population even in a limited environmental setting during a short time span, and indicated the high susceptibility to avian tuberculosis of lesser white-fronted geese.     

Population structure of Mycobacterium bovis isolates from cattle in Mexico

The molecular fingerprints of 878 isolates of Mycobacterium bovis collected from cattle between 2009 and 2010 in different regions of Mexico were used in this study. One hundred and ninety-four spoligotypes were observed in total with a high degree of heterogeneity. Sixty-four percent of the isolates grouped into just nine spoligotypes, and 27% fell into only two spoligotypes: SB0673 and SB0669; 149 were orphan spoligotypes. The two predominant spoligotypes were found in almost all states in Mexico, especially in central Mexico, where there is a high concentration of dairy cattle; however, some spoligotypes were closely associated with restricted geographical areas. The hypothetical evolutionary relationship among spoligotypes was estimated using the spoligoforest program in the spolTools webpage. Four trees with connected components and nine unconnected nodes were found. The biggest tree had SB0140 strain as a root, suggesting this as the oldest strain in the tree. However, the relationship of this spoligotype with SB0673 and SB0669 was weak. The discriminatory power of spoligotyping for this M. bovis sample of isolates was 0.94, and the recent transmission index (RTI) 0.83, suggesting a high rate of recent transmission of some strains of M. bovis in the population. This parameter indicates that new measures are required to stop the dissemination of tuberculosis in cattle.     

1株塞内卡病毒A型的基因组序列与演化分析

旨在分析塞内卡病毒A型（Senecavirus A，SVA） CH-HNCY-2019株的基因组特性和演化，参考SVA毒株SVV-001（GenBank No.NC011349）全基因组序列设计8对引物，通过RT-PCR扩增和测序获得SVA CH-HNCY-2019株全基因序列并进行序列分析。结果显示，SVA分离株CH-HNCY-2019基因组全长为7 294个核苷酸，与中国分离株核苷酸相似性为95.9%~99%，与美国经典株SVV-001核苷酸相似性最低。CH-HNCY-2019与大多数中国2017—2018年分离毒株亲缘关系较近，处于同一分支，而与中国2015—2016年分离株亲缘关系较远。与包括2019年中国广东4个SVA分离株在内的其他国内外分离株相比，CH-HNCY-2019的VP1蛋白的722位氨基酸由L突变为Q；VP3蛋白的499位氨基酸由A突变为V，528位氨基酸由P突变为S，582位氨基酸由E突变为K。本研究成功获得1株SVA CH-HNCY-2019全基因组序列，研究结果提示，SVA中国流行株具有多样性，而且在不断地演变，应加强SVA的分子流行病学调查、生物安全措施和疫苗研发以防止SVA在我国猪群中的广泛传播。     

Phylogenetic analysis of S1 gene of infectious bronchitis virus isolates from China

Between 2006 and 2009, seven strains of infectious bronchitis (IB) virus (IBV) were isolated from vaccinated chicken flocks on different chicken farms in China. The pathogenic characters of seven IBV strains were assessed. Each of the seven strains was infective to the test chickens and could induce an immune response. The results from chicken embryo cross-neutralization assays showed that these strains were antigenically distinct from classic IBV strains of H120, M41, Conn, and Gray. Compared to H120 vaccine strain, point mutation, short insertion, and deletion occurred at many positions in the S1 protein of the seven strains. Five of the seven strains had the motif (HRRRR), which was identical to that of the epidemic IBV strains in China. Two new motifs (HRLRR and RRIRR) emerged in the isolated strains. The homology of the nucleotide and amino acid sequences of the S1 gene among the seven isolates was 81.7%-99.7% and 79.0%-99.4%, respectively. These seven strains were also genetically different from the vaccine strains and non-China IBV strains but closely related to large numbers of Chinese strains. The seven isolates and 36 reference IBV strains were clustered into six distinct groups (I-VI). The seven strains were categorized into groups I, II, and III, forming a big phylogenetic branch, which is closely related to Chinese IBVs, whereas the vaccine strains belonging to group VI are genetically distant from groups I, II, and III. The results from this study indicate that different IBV strains cocirculate in the chicken population in China.     

Isolation and characterization of Clostridium perfringens from apparently healthy animals of the Shandong province of China

In a pilot study the presence and frequency of Clostridium (C.) perfringens was investigated among apparently healthy farm animals in the Shandong province of China. 748 faecal samples were collected from 9 pig-, 4 sheep-, 7 cattle- and 5 rabbit farms. C. perfringens was isolated from 124 samples (16.6%). The isolates were classified into major toxin types by using PCR analysis detecting the genes encoding these toxins. All isolates were identified as C perfringens toxin type A. There are also some reports from different regions in China linking C. perfringens toxin type A strains to gastrointestinal diseases. Therefore further investigations about the epidemiologic role of C perfringens toxin type A strains in the Shandong region are necessary. Currently, cases of enterotoxemia from this region are investigated for the presence of C perfringens.     

川西地区鸡滑液囊支原体分离株的部分生物学特性及其VlhA基因遗传进化分析

为了解鸡滑液囊支原体(MS)在川西地区的感染情况,本研究采集15个肉鸡场疑似MS感染的病鸡咽拭子、跗关节和胸部滑液囊样本共75份,对经PCR检测为阳性的样本进行MS分离,并对分离株的主要生物学特性进行研究,以及对分离株的VlhA基因进行遗传进化分析。结果显示,75份样本MS PCR阳性检出率为41.33%(31/75),11个鸡场感染该病,场阳性率为73.33%(11/15);但仅从其中3个鸡场分离到9株MS,分离株菌落与菌体形态与已知MS培养特性相符,各分离株培养浓度为10~4CCU/mL^10~6CCU/mL,分离株以5×10~5CCU接种7日龄SPF鸡胚,鸡胚于接种后7 d^9 d死亡,且分离回收到接种菌株;9株MS分离株VlhA基因的同源性为86.1%~99.9%,与参考株同源性为86.2%~95.4%,其中分离自同一鸡场的7株MS VlhA基因同源性为96.4%~99.9%;分离株VlhA基因遗传进化分析显示,其中分离自两个不同鸡场的两株MS与国内流行株的亲缘关系最近,而分离自另一鸡场的7株MS与中东地区分离的3株MS亲缘关系较近,表明MS在川西地区肉鸡场呈高感染率,MS VlhA基因变异较大。本研究为川西地区MS的进一步研究提供了基础材料和科学依据。