Molecular typing of Staphylococcus aureus isolated from cows, goats and sheep with intramammary infections on the basis of gene polymorphisms and toxins genes

We investigated 116 Staphylococcus aureus isolates from cows, goats and sheep with intramammary infections (IMI) in Italy to provide information about the spread of enterotoxigenic strains and to compare strains isolated from different ruminant species. The isolates were typed by restriction fragment length polymorphism (RFLP) analysis of the coagulase (coa) gene, by analysis of polymorphisms of the X region of protein A (spa) gene and by detection of genes encoding enterotoxins (sea, seb, sec, sed, see, seg, seh, sei, sej and sel). Seven different coa types and 12 different spa types were distinguished. On the basis of polymerase chain reaction-RFLP, 29 different coa subtypes were identified. Two different coa subtypes accounted for 49% and 67% of bovine and ovine isolates respectively. Only seven coa subtypes were observed in isolates from more than one host species and no coa subtype was present in isolates from all three ruminant species. Furthermore, 85 of the isolates (73%) harboured at least one enterotoxin gene (se) with a predominance of sea, sed and sej among isolates from bovine IMI, and sec and sel among isolates from caprine and ovine IMI. Comparing the S. aureus isolates on the basis of gene polymorphisms and presence of se genes, significant differences were found in distributions of genotypes among isolates from cows, goats and sheep.     

Genotyping of Staphylococcus aureus isolated from bovine mastitis.

The present study was designed to comparatively investigate 25 Staphylococcus aureus strains isolated from bovine subclinical mastitis. The S. aureus strains, obtained from six different farms at five locations in one region of Germany, were characterized by phenotypic and genotypic methods. The S. aureus could be identified and further characterized by their cultural, biochemical and hemolytic properties. To analyze the epidemiological relationship the isolates were subjected to DNA fingerprinting by macrorestriction analysis of their chromosomal DNA, by PCR amplification of the gene encoding the 16S-23S rRNA intergenic spacer, by PCR amplification of the gene encoding the IgG binding region and the X region of protein A and by amplifying, and subsequent, digestion of the gene encoding staphylococcal coagulase. The macrorestriction analysis revealed five DNA restriction patterns with DNA patterns I, III and IV occurring in three, four, and three different farms, respectively. In addition, clones with different DNA patterns could be found within one herd. The PCR products for the spacer DNA, the spa gene encoding the X region of protein A and the coa gene encoding coagulase corresponded mostly to the pattern observed by DNA fingerprinting. Amplification of the gene encoding the IgG binding region revealed sizes of 620 bp for 20 of the isolates and 280 bp for four isolates indicating, for the latter, a deletion of segments in this region. These findings show, that single, widely distributed clones seemed to be responsible for cases of bovine subclinical mastitis found in one region of Germany.     

猪瘟病毒E2基因部分核苷酸序列的遗传进化关系的研究

本研究利用RT-PCR及测序获得了16株猪瘟病毒E2基因部分核苷酸序列。利用DNAStar软件对其6株已发表的猪瘟病毒毒株序列进行了比较和分析，构建了猪瘟病毒遗传发生树。结果可以看出所绘制的遗传发生树分为2个组群，每个组群分为3个亚组群。13株猪瘟流行毒在2个组群中均有分布，猪瘟石门系强毒和C株属于同一组群、同一亚组群。70～80年代分离的4株猪瘟病毒755和Alfort株（法国）在同一组群，25%和Brescia株（意大利）是同一组群，90年代分离的9株猪瘟病毒33.3%和Alfort株（法国）在同一组群，66.7%和Brescia株（意大利）是同一组群。13株猪瘟流行毒株中7株和C株在同一组群，其中70～80年代的1株，90年代的6株。其余的6株猪瘟流行毒株均在另一组群。不同地区及不同材料C-株疫苗的E2基因的核苷酸序列有一定的差异，GPE株与中国的C株有较近的遗传进化关系，而法国的Thiverval株则与中国C株的遗传进化关系较远。本研究的结果对了解我国猪瘟分子流行病学的特点具有重要的意义。     

新城疫病毒山东分离株ShD-5-06 F和HN基因序列分析

从山东济南某非典型新城疫发病鸡群中分离到一株新城疫病毒株（ShD-5—06）,研究其生物学特性表明,该病毒具有新城疫强毒株的一些特征。从该分离株扩增出其F和HN基因,并与标准株进行同源性比较,为探讨NDV是否发生变异提供理论依据。本试验通过RT—PCR法特异性地扩增出F和HN基因全基因序列,并对其与已经发表的序列进行核苷酸序列测定和分析。结果表明,ShD-5—06株的F和HN基因开放性阅读框架（ORF）为1662bp和1716bp,分别编码489个和571个氨基酸。与国外发表的部分新城疫病毒强毒株和弱毒株之间相应序列进行比较,F基因核苷酸序列的同源性在84．1％～88．7％之间,氨基酸同源性在88．1％～93．3％之间;HN基因核苷酸序列的同源性在82．19,5～87．4％之间,氨基酸同源性在88．6％～90．9%之间;F蛋白裂解位点区（112～117）氨基酸组成与强毒株一致,说明NDV山东分离株（ShD-5—06）为新城疫强毒株。     

Characterization of enterotoxigenic Staphylococcus aureus strains isolated from bovine mastitis in north-east Switzerland

Thirty-four strains of enterotoxin-producing Staphylococcus aureus obtained from milk samples of 34 dairy cows suffering from mastitis from 34 different farms in north-east Switzerland were identified and further characterized by pheno- and genotypic methods. This included the identification of staphylococcal enterotoxin (SE) types, an antibiotic resistance testing, the appraisal of hemolysis, the egg yolk reaction, the detection of the clumping factor and protein A by means of a latex agglutination, the PCR amplification of a S. aureus specific part of the gene encoding the 16S-23S rRNA "intergenic spacer" region and a species specific part of the 23S rRNA-gene, the PCR amplification of the clumping factor (clfA) gene, the X region and the IgG-binding region of the protein A (spa) gene, the coagulase (coa) gene and additionally a macrorestriction analysis of the chromosomal DNA. Within the 26 cultures which formed a single SE, there were 23 SEC- and three SED-formers. Eight cultures were SEAD formers. It was remarkable that 22 SEC formers were also positive for TSST-1. Eighteen of the 23 SEC-formers could be classified as being of the same phenotype. Most of the cultures of one enterotoxin type also showed a great uniformity in the size and number of repeats of the X region as well as in the size of the IgG-binding region of protein A gene and in the size of the coagulase gene. Macrorestriction analysis revealed 11 PFGE patterns. These were in part only different from each other in a few fragments and thus displayed close clonal relations. The results of the present investigation show that a broad distribution of identical or closely related enterotoxin-producing S. aureus clones seem to contribute to the bovine mastitis problem in north-east Switzerland.     

Cloning and Sequence Analysis of Complete Genomes of Porcine Circovirus Type 2 (PCV-2) Jiangxi Strains

In order to understand the epidemiology and evolution of PCV-2 in Jiangxi province, a pair of primers was designed according to the PCV-2 gene sequence published in GenBank. After PCR amplification, we got the whole genome sequence of 9 strains PCV-2 isolates, and the nucleotide and protein sequences were analyzed, the genetic evolutionary tree was constructed. The results showed that the complete genome of 8 out of the 9 strains were 1 767 bp in length and one strain was 1 768 bp. By analyzing the whole genome sequences of the nucleotide,the homology of nucleotide sequences of the 9 strains was 94.7% to 99.9%.Compared with other whole genome sequences of PCV-2 in GenBank, the homology was 94.3% to 99.8%. The homology of nucleotide sequences of the ORF1 of the 9 strain was 96.9% to 100.0%. ORF2 and ORF3 encoding protein amino acid sequence had some locus mutation. Phylogenetic tree analysis showed that the 9 strains could be divided into 3 genotypes,5 strains belonged to PCV-2b, 3 strains belonged to PCV-2d, and 1 strain belonged to PCV-2a. This study was helpful to monitor and control of PCV-2 in Jiangxi province.     

猪圆环病毒2型江西株的全基因组克隆和序列分析

为了解江西地区猪圆环病毒2型（PCV-2）的流行和进化情况,根据GenBank上已发表的PCV-2全基因序列设计1对引物,PCR扩增后得到9条PCV-2全基因序列,并对其全基因序列核苷酸和蛋白序列进行分析,绘制遗传进化树。结果表明,江西地区流行的9株PCV-2中,基因组序列全长分为8株1 767 bp和1株1 768 bp,9株PCV-2的核苷酸同源性为94.7%~99.9%,与GenBank己发表的PCV-2分离株全基因组同源性介于94.3%~99.8%之间,而9株PCV-2的ORF1核苷酸序列同源性为96.9%~100.0%。ORF2和ORF3编码的蛋白氨基酸序列存在部分位点突变。遗传进化树显示为3种基因型：5株PCV-2b、3株PCV-2d、1株PCV-2a。本研究有助于江西地区PCV-2的监测和防制。     

1株基因Ⅶ型新城疫病毒的生物学特性研究及全基因组序列分析

为研究当前流行的新城疫病毒（Newcastle disease virus,NDV）基因型、致病性及其与传统新城疫病毒疫苗株（La Sota等）的核苷酸差异,试验从某发病鸡场病死鸡体内分离到1株疑似NDV毒株,经红细胞凝集试验（HA）和红细胞凝集抑制试验（HI）初步确定为鸡源NDV。参照GenBank公布的NDV F基因部分片段（登录号：JF950510.1）设计1对引物,通过RT-PCR技术扩增分离株的F基因并克隆、测序,测序结果与NCBI中NDV F基因序列进行比对,构建系统进化树并分析其基因型;通过测定鸡胚平均致死时间（MDT）、1日龄鸡脑内致病指数（ICPI）和6周龄鸡静脉致病指数（IVPI）判断病毒致病性;参照GenBank公布的NDV全基因组序列（登录号：JF950510.1）设计9对引物对分离株进行全基因组序列测定,并分析其基因组结构。结果表明,RT-PCR扩增得到F基因长约500 bp,基于F基因构建的系统进化树显示分离株为基因Ⅶ型NDV;MDT、ICPI和IVPI分别为52.8 h、1.675和2.46,表明分离株属于强毒株。全基因组序列分析显示,分离株全基因组全长15 192 bp,与传统La Sota株基因组相比,序列多出6个碱基,核苷酸序列同源性82.8%。本研究成功分离到1株基因Ⅶ型NDV强毒株,且与传统疫苗毒株La Sota的核苷酸序列同源性差异较大。     

Prevalence of coagulase gene polymorphism in Staphylococcus aureus isolates causing bovine mastitis.

This study was conducted to investigate polymorphism of the coagulase gene of Staphylococcus aureus causing bovine mastitis. One hundred eighty-seven strains of S. aureus were isolated from bovine mastitic milk samples obtained from 187 different Danish dairy farms. The isolates were characterised for restriction fragment length polymorphism (RFLP) of the coagulase gene. A variable region of the coagulase gene was amplified using the polymerase chain reaction (PCR) followed by AluI restriction enzyme digestion. A total of 15 different RFLP patterns were observed. The predominant pattern was found in 35% of the isolates. The ease of analysing coagulase gene polymorphisms among a large number of strains, and the multiple distinct polymorphic patterns generated, supports the use of this technique in epidemiological investigations of bovine mastitis. The predominating variants may have predelection for causing intramammary infections.     

我国部分地区1996-2008年传染性支气管炎病毒分离株膜蛋白基因的遗传变异与系统进化分析

1996-2008年从我国不同地区分离30株传染性支气管炎病毒（Infectious Bronchitis Viruses,IBV）野毒株的M基因,采用RT-PCR方法克隆测定所分离的野毒株和澳大利亚T株的M基因序列,利用生物信息学软件与GenBank中公布的部分国内外IBV毒株的M基因序列进行比较分析,研究我国IBV的分子流行学特点和分子遗传变异规律。结果发现所测毒株M基因具有4种不同长度的开放阅读框：669bp、672bp、678bp和681bp,分别编码222、223、225和226个氨基酸的多肽,这些长度的差异是由5′端的核苷酸插入或缺失造成的。30个IBV分离株间的同源性在89．5％～100％之间。以疫苗株H120氨基酸位置为参照,在被比较的73株IBVM蛋白中发现62个位点存在变异,其中以2～5、10～16、44～46、217～222等4个区域氨基酸取代率较高。系统进化分析显示,被比较的73个IBV毒株分为5个进化群,我国的IBV分属于其中的4个群,其中第一群和第四群与我国所使用的疫苗病毒株相距较远。同时发现部分近年的分离株与10多年前分离株具有很近遗传进化关系。从M基因看,在我国出现了多种基因型IBV共存的现象,分离株与疫苗株的遗传差异提示我们需要对疫苗的选用做出重新评估。     

新城疫病毒ShD-5-04株F基因和HN基因序列分析

从山东潍坊某非典型新城疫发病鸡群中分离到一株新城疫病毒(暂命名:ShD-5-04),其生物学特性表明该病毒具有新城疫强毒株的一些特征。通过RT-PCR特异性地扩增出F和HN基因序列,并对其进行核苷酸序列测定和分析,结果表明ShD-5-04株的F和HN基因开放性阅读框架(ORF)为1662bp和1716bp,分别编码489个和571个氨基酸,与国外发表的部分新城疫病毒强毒株和弱毒株之间相应序列进行比较,F基因核苷酸序列的同源性在84.1%～88.7%之间,氨基酸同源性在88.1%～93.3%之间;HN基因核苷酸序列的同源性在82.1%～87.4%之间,氨基酸同源性在88.6%～90.9%之间;F蛋白裂解位点区(112-117)氨基酸组成与强毒株一致,说明NDV山东分离株(ShD-5-04)为新城疫强毒株。     

Identification of genotypes of Giardia intestinalis isolates from dogs in Japan by direct sequencing of the PCR amplified glutamate dehydrogenase gene

Giardia has been detected in domestic dogs in Japan, but the genotype of isolates has remained unclear because identification has relied on conventional microscopy. Here we tried to identify the genotypes of four isolates from dogs in Japan by direct sequencing of the PCR amplified Giardia glutamate dehydrogenase (GDH) gene. The primer pair GDHF3 and GDHB5, targeting the GDH gene, was designed to prime a region of the GDH gene sequence conserved in the strains found to have the dog-specific genotype. The specific PCR product (approximately 220 bp), amplified with this primer pair, was only observed when Giardia DNA was used as the template. The sequences of the diagnostic fragments were identical among the isolates from dogs, and were differed by 15 bp or 1 bp from the strains, which were found to be the dog-specific genotypes, Assemblage C or D respectively. To verify the identity of the amplified DNA, a phylogenetic analysis was performed. Consequently, the sequence of the isolates from dogs clearly clustered with the strain found to be Assemblage D with neighbor-joining analyses. Therefore, all the isolates from dogs examined were identified as the dog-specific genotype, Assemblage D. In the present study, we revealed the genotype of Giardia isolates in Japan, and showed that direct sequencing of the PCR product amplified with the primer pair GDHF3 and GDHB5 was a useful tool for distinguishing between the zoonotic and dog-specific genotypes.     

Molecular heterogeneity in clinical isolates of Malassezia pachydermatis from dogs

Molecular investigation of 16 strains, conventionally identified to be Malassezia pachydermatis, isolated from dogs in Japan was carried out by random amplification of polymorphic DNA (RAPD) and chitin synthase 2 (CHS2) gene sequence analyses. The RAPD band patterns of 13 clinical isolates were identical to that of standard strain of M. pachydermatis (CBS-1879). The other three clinical isolates were different from the standard strain of M. pachydermatis in RAPD patterns, and two of the three isolates were identical. About 620 bp genomic DNA fragments of the CHS2 gene were amplified from the same 16 clinical isolates of M. pachydermatis by polymerase chain reaction (PCR) and sequenced. The phylogenetic analysis of the nucleotide sequences of CHS2 gene fragments of the 16 clinical isolates revealed that the 13 strains were genetically very close to the standard strain of M. pachydermatis and the other two isolates were genetically close to the standard strain of M. furfur rather than M. pachydermatis. The remaining one isolate was phylogenetically distinct from all the seven Malassezia species reported so far.     

Genotyping of Haemophilus parasuis isolated from northwest China using PCR-RFLP based on the ompA gene

Outer membrane proteins (OMPs) are the major virulent factors of Haemophilus parasuis. PCR-RFLP targeting the ompA gene was conducted to investigate the possibility of genotyping H. parasuis in this study. Fifteen reference strains and 49 isolates from pig farms in northwest China were genotyped by PCR-RFLP with a pair of specific primers. The results indicated that both the 15 reference strains and 49 isolates could be classified into 8 different genotypes by PCR-RFLP, respectively. Seven genotypes including AA, BB, BA, CA, BC, BD and CD existed simultaneously in the reference strains and isolates, but genotype CB only existed in the isolated strains. Interestingly, genotypes BA, CD and CA were only found in diseased pigs and accounted for 38.8%, 22.4% and 18.4% of the isolates, respectively. On the other hand, strains isolated from apparently healthy pigs were classified into genotypes AA, BB, BC and CB. However, the virulent reference serovar 1 strain has an AA genotype, and the fact that nearly all strains from the healthy pigs belonged to serovars classed as virulent suggests that these genotypes might also include virulent strains; therefore, further validation with more field strains is needed. The capability of the RFLP-PCR method based on the ompA gene for genotyping H. parasuis isolates indicates that this method may be a useful tool for epidemiological study.     

Genetic Variation Analysis of S Gene of Porcine Epidemic Diarrhea Virus Isolated in Shanxi Provine

In order to investigate the variation in S gene of porcine epidemic diarrhea virus (PEDV), the 4 strains of PEDV S gene nucleotide sequences were obtained, through RT-PCR amplification of tissue samples from Shanxi province. The obtained sequences and the deduced amino acid were analyzed and compared with the other published PEDV strains. Sequence analysis showed that compared with CV777 vaccine, there were 12 nucleotides insertions between 170 to 171 bp, 3 nucleotides insertions between 401 to 402 and 454 to 455 bp, 6 nucleotides deletion between 461 to 468 bp. The nucleotide and amino acid homologies were 99.2% to 99.8% and 98.6% to 99.7% respectively among 4 strains of PEDV S gene; Comparing with the strains isolated from China in 2011 to 2015, CV777 vaccine, attenuated DR13 and CV777, the nucleotide homologies were 95.0% to 98.5%,93.2% to 93.6%,92.1% to 92.9%,93.7% to 94.4%,respectively.The amino acid homology were 96.2% to 98.9%,91.9% to 92.9%,91.9% to 92.6%,92.9% to 94.0%, respectively. Phylogenetic analysis revealed that 4 strains of PEDV S gene belonged to the first group and had high correlative genetic relationship with the PEDV strains which isolated after 2010 in China, and had far correlative genetic relationship with the PEDV strains which isolated before 2010 in China, 2 strains of Japanese, 7 strains of South Korea, 2 vaccine strains. The results suggested that the prevalence of PEDV in Shanxi province had a more obvious variation. Therefore, it was necessary to develop a new vaccine to control the outbreak of PEDV.     

猪流行性腹泻病毒山西分离株S基因遗传变异分析

为分析山西地区猪流行性腹泻病毒（PEDV）的遗传变异情况,试验利用RT-PCR方法对2014-2015年山西省疑似猪流行性腹泻的阳性病料进行克隆和测序,获得4个S基因片段,并对其基因序列和推导的氨基酸序列与国内外毒株进行比对分析。序列分析结果显示,4株PEDV山西分离株的S基因与CV777 vaccine相比,在170~171 bp之间插入12个核苷酸,在401~402、454~455 bp之间均插入3个核苷酸,在461~468 bp之间缺失6个核苷酸。4株PEDV山西分离株S基因之间核苷酸和氨基酸同源性分别为99.2%~99.8%和98.6%~99.7%,与2011-2015年中国流行毒株、CV777 vaccine、attenuated DR13、CV777的核苷酸同源性分别95.0%~98.5%、93.2%~93.6%、93.2%~93.7%、93.7%~94.4%,氨基酸同源性分别为96.2%~98.9%、91.9%~92.6%、92.1%~92.9%、92.9%~94.0%。遗传进化树分析结果表明,PEDV S基因分为3个群,4株PEDV山西分离株属于第一群,与2010年以后国内流行毒株（除AH-M、SQ2014）的亲缘关系较近,与2010年以前中国流行毒株、2个日本株、7个韩国株、2个疫苗株的亲缘关系较远。研究结果提示山西省流行的PEDV发生较明显的变异,需研发新的疫苗来控制PEDV的暴发。     

Genotypic characterization of Staphylococcus aureus strains isolated from rabbit lesions

Since staphylococcal infections are the main pathological problem in rabbit does, the objective of this study was to characterize epidemiologically Staphylococcus aureus isolates from different lesion types in rabbits. Using 3 genetic markers (coagulase, staphylococcal protein A and clumping factor B genes), 22 different genotypes were identified among 301 isolates recovered from 259 rabbit does with 10 different kinds of chronic purulent lesions. These infected rabbits were obtained from 30 herds located in the Valencia province on the Spanish Mediterranean coast. The most frequent genotype was designated A1/II1/delta (coa/spa/clfB combination genotype) and represented 70.76% of the isolates. Although most genotypes were previously identified in other countries, novel types were also documented. No specificity between genotypes and nature of the pathologic process could be identified. After genetic comparison between strains from different origins, the results may suggest that rabbit, bovine and human S. aureus isolates are not clonally related, suggesting that specific host-dependent pathogenic factors may have evolved independently in these species. These differences indicate that a rational and effective strategy to control infections caused by rabbit-specific isolates may be advantageous.     

Heteroduplex mobility assay for genotyping infectious bursal disease virus

A heteroduplex mobility assay (HMA) was developed to genotype infectious bursal disease virus (IBDV). This method analyzed 390-base pair (bp) polymerase chain reaction (PCR) products, encompassing the hypervariable region of the VP2 gene. IBDV strains from the United States and other countries were analyzed. The HMA was able to differentiate standard, antigenic variants and very virulent strains of IBDV. Minor differences between different strains from the same subtype were also detected. Close relationships between field IBDV with vaccines prepared with Delaware E strain were determined by HMA. The results obtained by HMA were confirmed by restriction fragment length polymorphism (RFLP) and phylogenetic analysis of nucleotide sequences. The HMA proved to be a useful technique to rapidly genotype different field strains of IBDV and should prove to be a useful tool in epidemiologic studies.     

几株鸡新城疫病毒的分离鉴定及其基因型分析

从几个发生禽病的地区分离到6株病毒,经过血凝试验、血凝抑制试验、中和试验、分子生物学试验等确定为鸡新城疫病毒;根据GenBank公布的新城疫F基因强弱毒株相关基因序列设计合成1对特异性引物,扩增出的F基因片段长度约为610 bp,测序后进行序列比对,并分析其核苷酸序列和氨基酸序列,结果显示,有3株具有新城疫强毒株特性,同时还具备新城疫Ⅶ基因型特征,另外根据平均死亡时间(MDT)、脑内致病指数(ICPI)和静脉致病指数(IVPI)指标测定结果,最终判定这3株是新城疫强毒株且属于基因Ⅶ型,其余3株病毒分离株与La Sota的核酸序列同源性与氨基酸序列同源性均为99%。     

鸭圆环病毒ORF3基因的克隆及序列分析

为了解鸭圆环病毒(DuCV)不同分离株ORF3基因变异情况及分析其同源性,本研究从临床病料中分离10株DuCV,扩增ORF3基因并测定其序列.通过与已知序列比对分析发现,DuCV ORF3基因分为两种基因型,大小分别为237 bp和297bp.ORF3基因同一基因型之间的核苷酸同源性为95.8％～100％,氨基酸同源性为88.6％～100％,而不同基因型之间的核苷酸同源性仅为87.8％～91.6％,氨基酸同源性仅为72.2％～81.0％.