Genome Sequence of Brucella melitensis Strain 128, an Isolate of Biovar 3 of Sequence Type 8

Brucella melitensis is the most common Brucella species causing human brucellosis. B. melitensis is divided into 3 biovars. Here, we report the complete genome sequence of B. melitensis strain 128, a strain of biovar 3 of sequence type 8, which is prevalent in China.     

Complete Genome Sequence of Brucella melitensis Biovar 3 Strain NI,Isolated from an Aborted Bovine Fetus

From an aborted bovine fetus in China, a bacterial strain named NI was isolated and identified as Brucella melitensis by a PCR assay. Strain NI was further characterized as B. melitensis biovar 3 using biochemical assays. Here we report the complete genome sequence of strain NI.     

Genome Sequence of Brucella melitensis S66, an Isolate of Sequence Type 8, Prevalent in China

Brucella melitensis is the most-represented Brucella species causing human brucellosis in China. Here we report the complete genome sequence of B. melitensis strain S66, a representative strain of sequence type 8 (ST8), which is prevalent in China, making it possible to compare the genome sequences of isolates from different countries.     

Complete Genome Sequence of Brucella abortus 134, a Biovar 1 Strain Isolated from Human

Brucella abortus is one of the common pathogens causing brucellosis in China. Here, we report the genome sequence of B. abortus strain 134, a strain isolated from a human patient and belonging to biovar 1, the most highly represented biovar among B. abortus strains in China.     

Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32

The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain isolated from a Danish pig, suggests putative adaptation to the porcine host and absence of distinct virulence-associated traits.     

Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2 Isolated from Human

Brucella abortus is divided into eight biovars, of which biovars 1 to 3 are the most frequently represented biovars in strains isolated from humans. Here, we report the genome sequence of B. abortus strain BCB034, a strain isolated from a human patient and that belongs to biovar 2.     

Complete Genome Sequence of Brucella suis Field Strain BCB025 of Sequence Type ST22

Brucella is a genus of relatively conservative pathogenic bacteria. Brucella suis is the most diversified Brucella species. Strains of B. suis belong to different sequence types. Here, we report the genome sequence of B. suis strain BCB025, one isolate of the sequence type 22 epidemic in China.     

Complete Genome Sequence,Phylogenetic Relationships and Molecular Diagnosis of an Indian Isolate of Potato Virus X

The complete genome of a Potato virus X (PVX) isolate from India (ptDel‐9), which occurred symptomlessly in potato but induced ringspots on Nicotiana tabacum cv. Xanthi and necrotic mosaic on Nicotiana benthamiana, was sequenced. The genome was 6435 nucleotides long ( JF430080 ) and contained five open reading frames. The isolate was closely related to those reported from the Eurasian region (95.1–97.1% sequence similarity) and distantly related to those reported from South America (77.2–77.9%). The CP gene was expressed in Escherichia coli as a 76‐kDa fusion protein with maltose‐binding protein and used to generate polyclonal antibodies, which successfully detected PVX in field samples of potato by ELISA. In 20% of field samples, for which ELISA failed, the virus was successfully detected by RT‐PCR. This is the first report of molecular characterization of PVX occurring in India.     

番木瓜环斑病毒海南分离株全基因组序列分析

番木瓜环斑病毒(Papaya ringspot virus,PRSV)是马铃薯Y病毒属(genus Potyvirus)的成员之一.病毒粒体呈线状,长700～900nm,直径为12.5nm.为单分体正链RNA病毒,由多种蚜虫以非持久方式传播.依寄主范围可划分为P型和W型两种.其中P型株系(PRSV-P)是制约生产的重要病原,除了给番木瓜生产带来严重危害,也会危害葫芦科作物.W型株系(PRSV-W)是危害葫芦科作物的主要病原,虽然和PRSV-P型株系血清学反应密切相关,但不侵染番木瓜.     

Complete Genome Sequence of Canine Papillomavirus Type 10

Papillomaviruses are epitheliotropic, nonenveloped, circular, double-stranded DNA viruses within the family Papillomaviridae that are associated with benign and malignant tumors in humans and animals. We report the complete genome sequence of canine papillomavirus type 10 identified from a pigmented plaque located on the head of a mixed-breed bloodhound.     

Complete Genome Sequence of Equine Herpesvirus Type 9

Equine herpesvirus type 9 (EHV-9), which we isolated from a case of epizootic encephalitis in a herd of Thomson''s gazelles (Gazella thomsoni) in 1993, has been known to cause fatal encephalitis in Thomson''s gazelle, giraffe, and polar bear in natural infections. Our previous report indicated that EHV-9 was similar to the equine pathogen equine herpesvirus type 1 (EHV-1), which mainly causes abortion, respiratory infection, and equine herpesvirus myeloencephalopathy. We determined the genome sequence of EHV-9. The genome has a length of 148,371 bp and all 80 of the open reading frames (ORFs) found in the genome of EHV-1. The nucleotide sequences of the ORFs in EHV-9 were 86 to 95% identical to those in EHV-1. The whole genome sequence should help to reveal the neuropathogenicity of EHV-9.     

Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate

The full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.     

Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine

Brucella canis infects several species of animals, and canine is the preferred host. Genome sequences of strains from different hosts are valuable for comparative analysis of host adaptation and microevolution. Here, we report the genome sequence of Brucella canis strain 118, a strain isolated from canine.     

Complete Genome Sequence of an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

The complete sequence of the genome of an aerobic hyper-thermophiliccrenarchaeon, Aeropyrum pernix K1, which optimally grows at95°C, has been determined by the whole genome shotgun methodwith some modifications. The entire length of the genome was1,669,695 bp. The authenticity of the entire sequence was supportedby restriction analysis of long PCR products, which were directlyamplified from the genomic DNA. As the potential protein-codingregions, a total of 2,694 open reading frames (ORFs) were assigned.By similarity search against public databases, 633 (23.5%) ofthe ORFs were related to genes with putative function and 523(19.4%) to the sequences registered but with unknown function.All the genes in the TCA cycle except for that of alpha-ketoglutaratedehydrogenase were included, and instead of the alpha-ketoglutaratedehydrogenase gene, the genes coding for the two subunits of2-oxoacid:ferredoxin oxidoreductase were identified. The remaining1,538 ORFs (57.1%) did not show any significant similarity tothe sequences in the databases. Sequence comparison among theassigned ORFs suggested that a considerable member of ORFs weregenerated by sequence duplication. The RNA genes identifiedwere a single 16S–23S rRNA operon, two 5S rRNA genes and47 tRNA genes including 14 genes with intron structures. Allthe assigned ORFs and RNA coding regions occupied 89.12% ofthe whole genome. The data presented in this paper are availableon the internet homepage (http://www.mild.nite.go.jp).     

1株人乳头瘤病毒6型山东地方株的全基因组序列分析

人乳头瘤病毒6型(Human papillomavirus type 6,HPV6)是引起生殖器疣与复发性喉乳头瘤的主要病原体之一.为明确2019年济南市1例尖锐湿疣患者的病毒基因组序列特征,本研究提取其尖锐湿疣组织标本总DNA,分两段进行HPV6全基因组PCR扩增和步移法Sanger测序,将拼接后的序列与全球36条不同来源的HPV6全基因组序列进行对比分析.结果 显示,1013/19/JN/CHN/HPV6株(以下简称1013/HPV6)基因组全长8031bp,属于变异谱系B1,与全球不同地区HPV6分离株序列的同源性为98.4％～99.9％.1013/HPV6株与B1亚谱系参考株AF092932全基因组序列相比具有19个核苷酸变异位点,分布在7个开放阅读框架(Open Reading Frames,ORFs)和非编码区内.本研究首次分析了分离自中国大陆的HPV6全基因序列特征,研究结果为HPV分子进化的进一步研究和分型诊断试剂的优化提供了数据.     

Complete Genome Sequence of Brucella canis Strain HSK A52141, Isolated from the Blood of an Infected Dog

Brucella canis infection can be clinically inapparent in dogs, and when infection goes unnoticed, there is a chance for dog-to-human transmission. A new strain of B. canis was isolated from the blood of an infected dog in order to analyze the pathogenic mechanism, compare genetic properties, and develop new genetic tools for early diagnosis of canine brucellosis. Herein, we report the complete genome sequence of the strain B. canis HSK A52141. This is the second complete genome sequence and biological annotation available for a member of B. canis.     

Complete Genome Sequence of Lactobacillus plantarum JDM1

Lactobacillus plantarum is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.Lactic acid bacteria (LAB) play a prominent role in the world food supply, performing the main bioconversions in fermented food, and are also used as probiotic supplements in dairy products and other foods. Lactobacillus plantarum is a LAB species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a widely used Chinese commercial LAB with several probiotic functions, using a GS 20 system (454 Life Science Corporation) (11). Two hundred thirty-six thousand, five hundred sixty-three high-quality reads were assembled with the 454 assembly tool, which had an average depth of 18.6-fold coverage of the genome and yielded 367 contigs. Among these, 225 large contigs represented 99.17% of the draft sequence. In the finishing process, the order of the selected large contigs was determined by BLAST analysis with the originally published genome sequence of strain WCFS1 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AL935263","term_id":"342240345","term_text":"AL935263"}}AL935263) (8). Physical gaps were filled through sequencing of PCR products that spanned these regions using ABI 3730 xl DNA sequencers. Sequence assembly was accomplished by using the Phred/Phrap/Consed software package (4, 7). To ensure final accuracy, the errors in homopolymer sites that arose from the pyrosequencing method were solved via comparison with the corresponding sites on WCFS1 and then resequencing of the ambiguous bases using the ABI 3730 xl DNA sequencer.The complete genome of Lactobacillus plantarum JDM1 contains a single, circular chromosome of 3,197,759 bp and two plasmids (pLP2000 [2,062 bp] and pLP9000 [9,254 bp]). The two plasmids have been sequenced and published, with GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"AY096004","term_id":"20853777","term_text":"AY096004"}}AY096004 and {"type":"entrez-nucleotide","attrs":{"text":"AY096005","term_id":"20853804","term_text":"AY096005"}}AY096005 (3). The overall GC content of the chromosome is 44.66%, whereas the plasmids have a GC content slightly lower than that of the chromosome. The entire genome of JDM1 contains 2,948 protein-coding genes, 62 tRNA-encoding genes, and 16 rRNA-encoding genes. Several repeated sequences, designated ISP2, were found in the chromosome which were almost the same as those in WCSF1, identified as a class of transposase-encoding regions representing mobile genetic elements. The other repeated sequence, ISP1 of WCSF1, was absent in JDM1.The entire genomic sequence of L. plantarum JDM1 was a little shorter than that of L. plantarum WCSF1 (3.3 Mb). The two genomes were highly similar (>90% by BLASTN analysis) with respect to genome structure and gene order. Intraspecies diversity may be required for successful adaptation in a complex ecological habitat (2). L. plantarum JDM1 has been grown as a probiotic in rich nutritional medium for so long that the genome may have gradually contracted. As supporting evidence, many sugar transport and metabolism genes in WCFS1 were absent in JDM1.The prophage sequences and locations of JDM1 and WCFS1 are highly variable. L. plantarum JDM1 contains three prophage elements in its genome. R-Pg1, representing a short prophage remnant, is about 14 kb in size, which is similar to R-Lp3 in WCFS1. Pg2 and Pg3 are two ∼39-kb-long prophages that are closely related to Listeria phage B025 (accession no. {"type":"entrez-nucleotide","attrs":{"text":"DQ003639","term_id":"66733223","term_text":"DQ003639"}}DQ003639) and the phage Pediococcus pentosaceus ATCC 25745 (accession no. {"type":"entrez-nucleotide","attrs":{"text":"CP000422","term_id":"116101968","term_text":"CP000422"}}CP000422), respectively.The genomes of LAB evolve actively to adapt to nutritionally rich environments. Even for two strains of the same species, differences obviously exist. The degradation of the genome appears to be an ongoing process not only in all species of Lactobacillus (10) but also in different strains of the same species(2).With the development of better living conditions, the biosafety of food and medicine has received more attention. Lactobacillus bacteria have been supposed to have a “generally accepted as safe” status, but they still have been associated with negative reports (1, 6, 9). More about the functional mechanisms of JDM1 and potential side effects would be explored by complete genome sequencing and data mining. Furthermore, comparative genomics analysis could be carried out with Chinese and European strains. We believe the complete genome of each probiotic strain should be sequenced to ensure safety and stability. At the end of the day, we will get what we pay for in terms of microbial genome sequencing projects (5).     

一株高度变异的中国SV40分离株的全基因组序列分析

对SV40中国云南分离株YNQD38进行了全基因组核苷酸序列测定。覆盖了整个基因组的9个重叠的基因片段被扩增和测序,与其它SV40株进行了序列比对并基于全基因序列建立了遗传进化树。结果显示:基因组全长5125bp,基因组构成与其它SV40毒株相似,均有6个开放读码框架和1个调控区。YNQD38与已被证实高度保守的其它SV40比,全基因组核苷酸同源性仅为91.0%。在SV40的保守区VP1、VP2、VP3、小t抗原(t-ag)和部分大T抗原(不包括大T抗原C末端)区,YNQD38与其它SV40之间核苷酸同源性分别为90.7%~91.1%、91.7%~92.0%、90.2%~90.8%、92.8%~93.3%、88.5%~89.7%。在SV40的可变区大T抗原C末端(T-ag-C)编码区,YNQD38同源性更低,仅为65.7%~74.3%。YNQD38发生在保守区的核苷酸变异多为无义突变,而发生在变异区的核苷酸变异多为有义突变。YNQD38的调控区缺少一个完整的72bp增强子,这种特别的调控区的结构以前未见报道。基于整个基因组构建的进化树显示该株病毒形成了一个独特的组。以上结果表明YNQD38是目前报道的SV40中变异最大的一株,而且也是第一株被完整测序的SV40中国株。这个报道不仅为SV40中国株的基础研究提供了一个完整清楚的分子生物学资料,还对这样一株高度变异的SV40能否成为人类致病因子进行了初步探讨。     

Brucella melitensis Biovar 1 and Brucella abortus S19 Vaccine Strain Infections in Milkers Working at Cattle Farms in the Khartoum Area,Sudan

BackgroundHuman brucellosis is a preventable zoonoses that may become persistent, causing, if left untreated, severe localized disease. Occupational exposure to infected animals or animal products and consumption of fresh contaminated dairy are main risk factors.MethodsOne hundred farmworkers employed at two cattle farms one in Khartoum North and one in Omdurman were screened for the presence of specific antibodies and seropositive workers were invited to donate a blood sample for blood culture. Molecular typing was used to characterize Brucella isolates.ResultsTen percent of farmworkers tested seropositive and while Brucella melitensis biovar 1 was isolated from the blood of three individuals, an isolate identical to the B. abortus S19 vaccine strain was isolated from a fourth person. All four bacteremic individuals were employed as milkers and did not have obvious disease.ConclusionsThe isolation of the highly infectious pathogen B. melitensis from seropositive workers is consistent with the notion that the pathogen may persist in the blood without causing overt disease. While vaccination with strain S19 is essential for the control of bovine brucellosis the vaccine strain may be transmitted to the human population and protective measures remain important to prevent exposure also in view of the presence of B. melitensis. To create awareness for this potentially severe disease more information on the prevalence of the pathogen in different risk groups and in livestock in the Sudan is needed.     

Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage

Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical M. catarrhalis isolates and will facilitate study of M. catarrhalis pathogenesis.