Prevalence and genomic characterization of Group A Streptococcus dysgalactiae subsp. equisimilis isolated from patients with invasive infections in Toyama prefecture,Japan

Streptococcus dysgalactiae subsp. equisimilis (SDSE) causes severe invasive streptococcal infections, especially in elderly people. Between 2013 and 2018, 88 streptococci were isolated from clinical blood culture in a hospital in Toyama prefecture, Japan. The collection included six Group A SDSE (ASD) strains, which are rarely isolated. Multilocus sequence typing categorized five of the six strains into ST128 and the remaining strain into a new type. Maximum-likelihood phylogenetic analysis revealed that the six ASD strains had highly similar genome sequences. Bayesian analysis indicated that the most recent common ancestor of the strains appeared 39 years ago. The ASD strains possessed carbohydrate synthase genes that are conserved in Streptococcus pyogenes strains, whereas one strain featured a different arrangement of the gene cluster. The carbohydrate synthase genes varied by Lancefield type (A, C, and G).     

Identification of lactoferrin-binding proteins in Streptococcus dysgalactiae subsp. dysgalactiae and Streptococcus agalactiae isolated from cows with mastitis

Three strains of Streptococcus dysgalactiae subsp. dysgalactiae (S. dysgalactiae) and five strains of Streptococcus agalactiae were used to identify lactoferrin-binding proteins (LBPs). LBPs from extracted surface proteins were detected by polyacrylamide gel electrophoresis and Western blotting. All strains of S. dysgalactiae evaluated had 52- and 74-kDa protein bands. All strains of S. agalactiae evaluated had 52-, 70- and 110-kDa protein bands. In addition, a 45-kDa band was detected in two of five S. agalactiae strains evaluated. This study demonstrated that S. dysgalactiae and S. agalactiae of bovine origin contain two and three major LBPs, respectively.     

Prevalence of emm1 Streptococcus pyogenes having a novel type of genomic composition

Streptococcus pyogenes is a causative agent of streptococcal toxic shock syndrome (STSS). The complete genome sequence of a S. pyogenes strain 10–85 isolated from a STSS patient was recently announced. In this study, the genome sequence was dissected and it was found that the genomic region around 200 kbp (region A) and the genomic region around 1600 kbp (region B) were replaced by each other in strain 10–85, when compared with those in reference strains SF370 and A20. In order to address whether this replacement is unique to 10–85, we further analyzed 163 emm1‐type strains. The results indicated that none of the strains isolated before 1990 had the replacement. In contrast, most of the strains isolated at least after 2000 appeared to have the 10–85‐type replacement.     

Superantigen-like gene(s) in human pathogenic Streptococcus dysgalactiae,subsp equisimilis: genomic localisation of the gene encoding streptococcal pyrogenic exotoxin G (speG(dys))

Streptococcus pyogenes (GAS) causes about 90% of streptococcal human infections while group C (GCS) and G (GGS) streptococci can be pathogenic for different mammalians. Especially the human pathogenic GCS and GGS, Streptococcus dysgalactiae, subsp. equisimilis, account for 5-8% of the human streptococcal diseases like wound infections, otitis media, purulent pharyngitis and also streptococcal toxic shock syndrome. A defined superantigen so far was not identified in GCS and GGS strains. In the present investigation we screened DNA of GCS and GGS human isolates for the presence of genes for streptococcal pyrogenic exotoxins (spe) by hybridisation with probes that stand for the GAS genes speA, speC, speZ (smeZ), speH, speG, speI, speJ and ssa. In many GCS and GGS strains we found positive reactions with the probes speG, speJ and ssa, but not with the probes for the remaining genes under investigation. PCR amplification with subsequent sequence analysis of the PCR fragments revealed only the presence of the gene speG in GCS and GGS strains, while no DNA fragments specific for speJ and ssa could be amplified. Additionally, the upstream and downstream regions flanking speG in GGS strain 39072 were sequenced. Remarkable differences were found in the neighbourhood of speG between GAS and GGS sequences. Downstream of speG we identified in strain GGS 39072 two new open reading frames encoding proteins with no similarity to protein sequences accessible in the databases so far. In the compared GAS strains SF370 and MGAS8232, this segment, apart from some small fragments, had been deleted. Our analysis suggests that a gene transfer from GGS to GAS has preceded following deletion of the two genes orf1 and orf2 in GAS.     

Differentiation of human and animal strains of Streptococcus dysgalactiae by pulsed-field gel electrophoresis

The genetic diversity among 54 human isolates and 33 animal isolates belonging to the species Streptococcus dysgalactiae (20 α-haemolytic Streptococcus dysgalactiae, 23 Streptococcus equisimilis, 43 group G streptococci and one group L streptococcus) was evaluated by macrorestriction analysis of chromosomal DNA with SmaI and resolution by pulsed-field gel electrophoresis. This technique revealed a high degree of intraspecies polymorphism, leading to the differentiation of 80 distinct banding patterns, and identified the presence of two major clusters, one containing isolates of human origin and the other isolates of animal origin. These results suggest that human and animal isolates of S. dysgalactiae are genetically distinct, and support the recent proposal of the subspecies S. dysgalactiae subsp. equisimilis for human isolates. The heterogeneity revealed within isolates from the same host type indicates that pulsed-field gel electrophoresis is a powerful epidemiological tool for studying S. dysgalactiae infections.     

Complete genome sequence and characterization of virulence genes in Lancefield group C Streptococcus dysgalactiae isolated from farmed amberjack (Seriola dumerili)

Lancefield group C Streptococcus dysgalactiae causes infections in farmed fish. Here, the genome of S. dysgalactiae strain kdys0611, isolated from farmed amberjack (Seriola dumerili) was sequenced. The complete genome sequence of kdys0611 consists of a single chromosome and five plasmids. The chromosome is 2,142,780 bp long and has a GC content of 40%. It possesses 2061 coding sequences and 67 tRNA and 6 rRNA operons. One clustered regularly interspaced short palindromic repeat, 125 insertion sequences, and four predicted prophage elements were identified. Phylogenetic analysis based on 126 core genes suggested that the kdys0611 strain is more closely related to S. dysgalactiae subsp. dysgalactiae than to S. dysgalactiae subsp. equisimilis. The genome of kdys0611 harbors 87 genes with sequence similarity to putative virulence‐associated genes identified in other bacteria, of which 57 exhibit amino acid identity (>52%) to genes of the S. dysgalactiae subsp. equisimilis GGS124 human clinical isolate. Four putative virulence genes, emm5 (FGCSD_0256), spg_2 (FGCSD_1961), skc (FGCSD_1012), and cna (FGCSD_0159), in kdys0611 did not show significant homology with any deposited S. dysgalactiae genes. The chromosomal sequence of kdys0611 has been deposited in GenBank under Accession No. AP018726. This is the first report of the complete genome sequence of S. dysgalactiae isolated from fish.     

Partial sequencing of sodA gene and its application to identification of Streptococcus dysgalactiae subsp. dysgalactiae isolated from farmed fish

AIMS: To investigate the difference between Lancefield group C Streptococcus dysgalactiae (GCSD) strains isolated from diseased fish and animals by sequencing and phylogenetic analysis of the sodA gene. METHODS AND RESULTS: The sodA gene of Strep. dysgalactiae strains isolated from fish and animals were amplified and its nucleotide sequences were determined. Although 100% sequence identity was observed among fish GCSD strains, the determined sequences from animal isolates showed variations against fish isolate sequences. Thus, all fish GCSD strains were clearly separated from the GCSD strains of other origin by using phylogenetic tree analysis. In addition, the original primer set was designed based on the determined sequences for specifically amplify the sodA gene of fish GCSD strains. The primer set yield amplification products from only fish GCSD strains. CONCLUSIONS: By sequencing analysis of the sodA gene, the genetic divergence between Strep. dysgalactiae strains isolated from fish and mammals was demonstrated. Moreover, an original oligonucletide primer set, which could simply detect the genotype of fish GCSD strains was designed. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that Strep. dysgalactiae isolated from diseased fish could be distinguished from conventional GCSD strains by the difference in the sequence of the sodA gene.     

Delayed onset of systemic bacterial dissemination and subsequent death in mice injected intramuscularly with Streptococcus pyogenes strains.

Streptococcus pyogenes causes severe invasive diseases in humans, including necrotizing fasciitis, sepsis, and streptococcal toxic shock syndrome (STSS). We found that mice infected intramuscularly (i.m.) with S. pyogenes strains developed bacteremia and subsequent sudden death after at least 10 days of a convalescent period. Mostly, it occurred more than 21 days after muscle infection. We provisionally designate this phenomenon as "delayed death." Just after muscle infection, all the mice lost weight and activity, but recovered completely within 3 days. They had kept good activity and a fine coat of fur till one or two days before their death. Some of the dead mice were found to have soft-tissue necrosis. There was no correlation between the virulence leading to the delayed death and the severity of diseases from which strains were isolated. It was also found that the production of neither streptococcal pyrogenic exotoxin (SPE) A nor B correlated to the virulence leading to delayed death. The bacteria obtained from the organs of the mice with delayed death expressed capsule. We suggest that the mice with delayed onset of systemic bacterial dissemination and subsequent death after muscle infection with S. pyogenes are the animal models of STSS, because the pathophysiology is extremely similar to that of human STSS.     

Neither the A- nor B-repeat regions of the fibrinogen-binding protein of Streptococcus equi subsp. equi are essential for fibrinogen binding

The major cell wall-associated protein (FgBP) of Streptococcus equi subsp. equi possesses two internal blocks of repeated sequence (A and B) and binds horse fibrinogen (Fg) avidly through residues located in the N-terminal half of the molecule. In the present study, we investigated the roles of the two repeats blocks in Fg binding through construction of recombinant FgBP proteins containing defined internal deletions of sequence. Ligand binding experiments clearly showed that neither repeat is essential for Fg binding. However, residues within the B repeats seem to play a major role in the aberrant mobility observed for FgBP following sodium dodecyl sulfate polyacrylamide gel electrophoresis.     

丝状支原体山羊亚种PG3株的全基因组序列测定与分析

【目的】全面了解丝状支原体山羊亚种PG3株的全基因组序列信息,寻找该病原体的主要保护性抗原基因。【方法】利用高通量Illumina Hi Seq 2000测序技术对丝状支原体山羊亚种PG3株的全基因组进行测序与拼接,借助软件和数据库对全基因组序列所承载的遗传信息进行注释和分析。【结果】丝状支原体山羊亚种PG3株基因组大小为1 025 065 bp,G+C%为23.6%,预测含有846个编码基因。根据COG分类和KEGG代谢通路分类,基因组中绝大多数基因主要与蛋白翻译、核糖体结构与合成、DNA复制与修复、糖代谢和环境信号传递与转换方面有关。该菌株具有丝状支原体山羊亚种特有的麦芽糊精/麦芽糖代谢途径。与Mmc str.95010的基因组的比对结果显示二者具有良好的共线性关系。在基因组中发现3个串联排列的可变表面脂蛋白基因,即GL000459、GL000461和GL000462。【结论】获得丝状支原体山羊亚种PG3株的全基因组序列,分析基因组基本特征,初步解析3个串联排列的可变表面脂蛋白基因,为进一步研究支原体可变表面脂蛋白的功能和研制生物工程疫苗奠定基础。     

Exopolysaccharide production by Lactobacillus delbruckii subsp. bulgaricus and Streptococcus thermophilus strains under different growth conditions

Summary The optimal temperature, pH and incubation time for production of exopolysaccharide (EPS) by Lactobacillus delbruckii subsp. bulgaricus and Streptococcus thermophilus strains in MRS and M17 media, respectively, were determined. In all strains, the temperature and incubation time for EPS production were 45 °C and 18 h, respectively. At 45 °C, L. delbruckiisubsp. bulgaricus B3 and G12 and S. thermophilus W22 strains produced 263, 238 and 127 mg/l, respectively. At 18 h, B3, G12 and W22 strains produced 220, 152 and 120 mg/l, respectively. While the pH for highest EPS production by L. delbruckii subsp. bulgaricus strains was 6.2 (in B3 strain: 211 mg/l, in G12 strain: 175 mg/l), for highest EPS production byS. thermophilus strain it was 6.8 (114 mg/l).     

辽东丁香完整叶绿体基因组的结构与特征

为获得辽东丁香（Syringa villosa subsp. wolfii）叶绿体全基因组的基本特征,采用高通量测序技术分析了其叶绿体基因组序列信息,并讨论其系统演化位置。结果表明：（1）辽东丁香叶绿体基因组全长156 517 bp,具有典型的四分体结构;具有131个功能基因,包括36个tRNA基因、8个rRNA基因和87个蛋白质编码基因。（2）该叶绿体基因组蛋白编码区的总密码子偏好性（RSCU）分析显示,RSCU值>1的密码子有31个,其中以A/U碱基结尾的有21个;RSCU值<1的密码子有34个,其中以G/C碱基结尾的密码子有22个。（3）在辽东丁香的叶绿体基因组中,检测出334个散在重复序列,包括170个正向重复序列和164个回文重复序列;检测到227个SSR位点,其中226个位点成功设计出PCR引物。（4）最大似然法构建系统进化树分析显示,辽东丁香与云南丁香（S. yunnanensis）亲缘关系最近。本研究通过对辽东丁香叶绿体基因组重复序列、IR边界、系统发育等进行分析,为辽东丁香后续的分子标记开发、系统发育分析、物种资源鉴定评价、DNA条形码开发等提供参考。     

Erythrogenic toxins A, B and C: Occurrence of the genes and exotoxin formation from clinical Streptococcus pyogenes strains associated with streptococcal toxic shock-like syndrome

We report the study of 53 clinical isolates of group A streptococci, all from patients with streptococcal toxic shock-like syndrome. The strains were analysed for the occurrence of the genes of erythrogenic toxins (pyrogenic exotoxins) types A, B and C and in vitro production of these toxins. In contrast to reports indicating that 85% of the toxic shock-like syndrome-associated isolates contained the erythrogenic toxin A gene, only 58.5% of our strains harboured this gene. The erythrogenic toxin C gene was detected in 22.6% of the isolates. Erythrogenic toxin A and erythrogenic toxin B were produced by 68.7% and 58.3% of the strains containing either gene. For all group A streptococci, irrespective of clinical association, the erythrogenic toxin B gene was detected in all the isolates tested. Thus, it is difficult to define a specific role for erythrogenic toxin B in toxic shock-like syndrome as there was no clear correlation between this disease and the presence of toxin genes. Our results suggest the existence of other pathogenic factor(s) produced by group A streptococci which may stimulate human peripheral T lymphocytes in a manner similar to that of erythrogenic toxins, thus explaining different observations in previous epidemiological genetic studies.     

马链球菌兽疫亚种类M蛋白的基因克隆、序列分析及其在猪源链球菌的检测

根据已发表的马链球菌兽疫亚种 (Streptococcusequisubsp .zooepidemicus)马源株的类M蛋白基因序列 ,设计和合成一对引物 ,以兽疫亚种猪源ATCC35 2 4 6株的基因组DNA为模板 ,通过PCR技术 ,扩增出类M蛋白基因并定向克隆至表达载体pET_32a( )中 ,测定其序列 ,GenBank接收号为AY2 6 3781。类M蛋白基因含一个完整的开放阅读框 ,全长为 1137bp ,编码 379个氨基酸残基。经DNAStar软件分析 ,ATCC35 2 4 6株类M蛋白基因与兽疫亚种马源W6 0株、马亚种的类M蛋白基因及A群化脓链球菌的M蛋白基因的同源性分别为 86 9%、30 8%、2 9 4 % ;推导的氨基酸序列的同源性分别为 84 3%、2 1 9%、2 3 4 %。但ATCC35 2 4 6株类M蛋白的C末端细胞膜锚定区与M蛋白、马亚种类M蛋白高度同源。用上述设计的引物进行PCR试验 ,检测 34株猪源链球菌类M蛋白基因 ,发现所有 16株C群猪源链球菌均能检测出类M蛋白基因 ,而所有猪链球菌 (Streptococcussuis) 1型和 2型菌株及S群、B群、D群链球菌共 13株均不能检出类M蛋白基因 ,而 5株未鉴定的猪源链球菌中 3株能检测出类M基因。     

A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp.bulgaricus and Streptococcus thermophilus

Aims: We have developed a direct viable count (DVC)‐FISH procedure for quickly and easily discriminating between viable and nonviable cells of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains, the traditional yogurt bacteria. Methods and Results: direct viable count method has been modified and adapted for Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus analysis by testing different times of incubation and concentrations of DNA‐gyrase inhibitors. DVC procedure has been combined with fluorescent in situ hybridization (FISH) for the specific detection of viable cells of both bacteria with specific rRNA oligonucleotide probes (DVC‐FISH). Of the four antibiotics tested (novobiocin, nalidixic acid, pipemidic acid and ciprofloxacin), novobiocin was the most effective for DVC method and the optimum incubation time was 7 h for both bacteria. The number of viable cells was obtained by the enumeration of specific hybridized cells that were elongated at least twice their original length for Lactobacillus and twice their original size for Streptococcus. Conclusions: This technique was successfully applied to detect viable cells in inoculated faeces. Significance and Impact of the Study: Results showed that this DVC‐FISH procedure is a quick and culture‐independent useful method to specifically detect viable Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus in different samples, being applied for the first time to lactic acid bacteria.     

Comparative analysis reveals changes in transcriptomes of sugarcane upon infection by Leifsoniaxyli subsp. xyli

Ratoon stunting disease (RSD) caused by bacterium Leifsoniaxyli subsp. xyli (Lxx) is a devastating disease of sugarcane over a large part of the world. Genetic improvement for RSD‐resistant varieties is considered the most effective method to control the disease. However, genetic improvement of sugarcane is hindered by the limited information about the molecular mechanisms underlying Lxx pathogenicity and defence responses in sugarcane. In this study, genome‐wide gene expression profiling was used to compare RSD‐resistant (CP72‐2086) and RSD‐susceptible (GT11) genotypes at different infection time points in order to identify the candidate regulators for RSD resistance. A total of 14,494 differentially expressed genes (DEGs) were identified, indicating that dramatic changes had occurred in gene expression upon Lxx infection, especially in the susceptible genotype. Enrichment analysis showed that a large number of genes related to plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis and starch and sucrose metabolism was responsible for sugarcane response to Lxx infection. Plant hormone signalling pathway genes were significantly differentially expressed at the early infection stage between the two genotypes. The resistant genotype chose the jasmonic acid‐ and ethylene‐dependent host‐defence pathways to resist Lxx infection, whereas the susceptible genotype preferred the salicylic acid‐dependent host‐defence pathways. These findings help unravel the molecular mechanisms of sugarcane plant–Lxx interactions and may pave the way for sugarcane breeding for disease resistance.     

Crystal structure of the streptococcal superantigen SpeI and functional role of a novel loop domain in T cell activation by group V superantigens

Superantigens (SAgs) are potent microbial toxins that bind simultaneously to T cell receptors (TCRs) and class II major histocompatibility complex molecules, resulting in the activation and expansion of large T cell subsets and the onset of numerous human diseases. Within the bacterial SAg family, streptococcal pyrogenic exotoxin I (SpeI) has been classified as belonging to the group V SAg subclass, which are characterized by a unique, relatively conserved ∼15 amino acid extension (amino acid residues 154 to 170 in SpeI; herein referred to as the α3-β8 loop), absent in SAg groups I through IV. Here, we report the crystal structure of SpeI at 1.56 Å resolution. Although the α3-β8 loop in SpeI is several residues shorter than that of another group V SAg, staphylococcal enterotoxin serotype I, the C-terminal portions of these loops, which are located adjacent to the putative TCR binding site, are structurally similar. Mutagenesis and subsequent functional analysis of SpeI indicates that TCR β-chains are likely engaged in a similar general orientation as other characterized SAgs. We show, however, that the α3-β8 loop length, and the presence of key glycine residues, are necessary for optimal activation of T cells. Based on Vβ-skewing analysis of human T cells activated with SpeI and structural models, we propose that the α3-β8 loop is positioned to form productive intermolecular contacts with the TCR β-chain, likely in framework region 3, and that these contacts are required for optimal TCR recognition by SpeI, and likely all other group V SAgs.     

马源马链球菌兽疫亚种3株新疆分离株基因型的鉴定及MLST分析

【背景】马链球菌兽疫亚种(Streptococcus equi subsp. zooepidemicus,SeZ)是引起马腺疫的主要病原,还可引起猪链球菌病,加强该菌的地方株分子流行病学监测对有效防控相关疫病十分必要。【目的】对新疆地区2个马场SeZ分离株进行鉴定和药敏特性分析,并分析3株新疆分离株的分子流行与菌株的遗传进化特征。【方法】对分离纯化的3株病原菌(ZHZ113、ZHZ211和ZHZ523)进行染色观察、生化及药敏特性检测,对16S rRNA和SeM基因进行遗传进化分析,以链球菌7个管家基因arcC、nrdE、proS、spi、tdk、tpi和yqiL为目的基因对3株分离菌进行多位点序列分型(Multilocus Sequence Typing,MLST)研究。【结果】3株SeZ的药敏结果显示这3株分离菌对不同抗生素的耐药程度不同,但均对头孢西丁、庆大霉素、链霉素、红霉素、左氧氟沙星、环丙沙星、土霉素等11种药物敏感。16SrRNA基因序列分析显示这3株分离菌均属于Ⅱ群(兽疫链球菌)。3株菌的MLST分型结果分别为ST39、ST419、ST421型,其中ST419和ST42...