医院相关性ST5型耐甲氧西林金黄色葡萄球菌ZJ5499的全基因测序及序列分析

目的对1例医院获得性耐甲氧西林金黄色葡萄球菌(MRSA)肺炎患者血中分离的1株MRSA(ZJ5499)进行基因组序列信息解析。方法采用Illumina平台高通量测序和Sanger测序相结合对ZJ5499菌株进行全基因组测序,并使用相关软件对序列进行拼接、基因预测、功能注释、直系同源簇注释(COG)及毒力因子和耐药基因分析;并与国内常见流行序列型(ST型)菌株进行进化关系分析、毒力因子和耐药基因比较。结果 ZJ5499菌株基因组大小为2 888 783bp,GC含量32.84%,序列已提交至GenBank数据库,登录号为CP011685。该菌株基因组中含有大量与致病性相关的毒力因子,并含有spc、aadD、mecA、norA和erm(A)五个耐药相关基因,与同一ST型菌株基本一致。进化关系分析显示该菌株与同一ST型菌株关系较近。毒力因子与ST5型菌株没有较大差异,而较其他ST型明显增多。结论本研究报道了临床MRSA菌株ZJ5499的全基因组序列。序列分析发现该菌株的毒力和耐药性与ST5型的菌株相近,而ST5型菌株较其他国内流行ST型菌株携带较多毒力基因。     

Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.Staphylococcus aureus is an important etiologic agent of food-borne diseases due to its ability to produce heat-resistant staphylococcal enterotoxins (SEs) when it grows in foods. In fact some S. aureus strains may produce up to 20 serologically distinct SEs, which could be responsible for food poisoning (30). SEs have been divided initially into serological types SEA through SEE, and recently the existence of new types of SEs has also been reported (5).S. aureus strains harboring enterotoxin genes have been isolated from a variety of foods (38) including dairy products (9, 46, 56). Mastitis caused by this pathogen and poor hygienic processing conditions are the most important sources of dairy product contamination. Growth of enterotoxigenic S. aureus in both raw milk and dairy products poses a potential health hazard to consumers. In this context, new biocontrol strategies to prevent growth of S. aureus, suitable to be applied in the food industry, are being explored.Currently, there is a renewed interest in exploiting the antimicrobial potential of bacterial viruses for bacterial-control applications in agriculture, aquaculture, and the food industry (11, 18, 23, 49). In fact, the use of phages for the treatment of infectious diseases (or phage therapy) has a long successful history in the countries of Eastern Europe (or former Soviet Union) (50). Specifically, S. aureus bacteriophages have been assayed in the treatment of venous leg ulcers and eye infections (22, 42).Prior to any phage application, genome analysis is a prerequisite to examine the safety of the phages, specifically, traits which might enhance the virulence of the infected bacterium. In addition, genome analysis might uncover novel antibacterial targets or agents (33) with promising biotechnological applications (6). For example, various lytic phage proteins (endolysins) have shown great potential in veterinary and human medicine for the treatment and prophylaxis of infections (12) and have been applied as biocontrol agents in dairy products (36). Several technologies employing phages and endolysins for pathogen detection and decontamination have also been patented (7).To date, genomes of over 47 S. aureus phages are available in public databases. The number of known, strictly lytic phages is limited to the close-knit Myoviridae genus of the SPO1-like viruses, containing phages K, Twort, and G1. Apart from this group, a large number of genomes from unclassified Siphoviridae in lysogenic S. aureus strains are available (26, 37). Some temperate bacteriophages may play an important role in the pathogenicity of S. aureus by carrying virulence factors, mediating lateral gene transfer, and even facilitating the adaptation of the pathogen during infection (1, 21, 52).In previous work, we have characterized phiIPLA35 and phiIPLA88 S. aureus phages (17). These two lytic phages, previously named φ35 and φ88, were selected as mutants of the temperate phages φA72 and φH5, respectively, isolated from raw bovine milk. They belong to the Siphoviridae family of double-stranded DNA bacterial viruses in the order Caudovirales. Remarkably, these phages infect S. aureus of bovine and dairy origin while clinical isolates appear to be resistant. Both phiIPLA35 and phiIPLA88 are very well adapted to the dairy environment and effectively inhibit S. aureus growth in milk and curd-manufacturing processes (17, 20).In this study, we have sequenced and annotated the genomes of both bacteriophages, elucidated their physical genome structures, and identified peptidoglycan hydrolytic activities. Comparative genome analysis also allowed us to put phiIPLA35 and phiIPLA88 into a phylogenetic context.     

Mobilization of Genomic Islands of Staphylococcus aureus by Temperate Bacteriophage

The virulence of Staphylococcus aureus, in both human and animal hosts, is largely influenced by the acquisition of mobile genetic elements (MGEs). Most S. aureus strains carry a variety of MGEs, including three genomic islands (νSaα, νSaβ, νSaγ) that are diverse in virulence gene content but conserved within strain lineages. Although the mobilization of pathogenicity islands, phages and plasmids has been well studied, the mobilization of genomic islands is poorly understood. We previously demonstrated the mobilization of νSaβ by the adjacent temperate bacteriophage ϕSaBov from strain RF122. In this study, we demonstrate that ϕSaBov mediates the mobilization of νSaα and νSaγ, which are located remotely from ϕSaBov, mostly to recipient strains belonging to ST151. Phage DNA sequence analysis revealed that chromosomal DNA excision events from RF122 were highly specific to MGEs, suggesting sequence-specific DNA excision and packaging events rather than generalized transduction by a temperate phage. Disruption of the int gene in ϕSaBov did not affect phage DNA excision, packaging, and integration events. However, disruption of the terL gene completely abolished phage DNA packing events, suggesting that the primary function of temperate phage in the transfer of genomic islands is to allow for phage DNA packaging by TerL and that transducing phage particles are the actual vehicle for transfer. These results extend our understanding of the important role of bacteriophage in the horizontal transfer and evolution of genomic islands in S. aureus.     

社区获得性ST59型MRSA HZW450的全基因组测序及分析

目的对1例脓疱疮患者脓液中分离的1株社区获得性耐甲氧西林金黄色葡萄球菌(CA-MRSA)HZW450菌株进行全基因组测序并对序列信息解析。方法使用三代测序PacBio技术对HZW450菌株进行全基因组测序,且使用SMRTanalysis v.R2.3.0对该序列进行序列拼接,上传NCBI进行基因功能注释,用RPSBLAST program进行直系同源簇(COG)注释以及毒力因子相关基因和耐药基因分析。同时比较国内其他地区发现的同一序列型(ST)的菌株毒力因子相关基因及耐药相关基因的差异,并比较HZW450菌株耐药基因型与表型的一致性。结果 HZW450菌株的基因组大小为2 831 958bp,GC占比32.9%,其基因组完成图序列已提交至NCBI GenBank数据库,登录号为CP020741。同时经过分析发现该菌株为ST59型,其基因组中含有许多与致病相关的毒力因子,以及含有耐药基因aph(3′)-III、ant(6)-Ia、mecA、norA、erm(B)和cat(pC233),毒力及耐药基因与ST59型其他菌株比较有差异。该菌株临床药敏结果与耐药基因比较分析发现,耐药表型与基因型存在差异。结论本研究报道了1株CA-MRSA(HZW450)菌株的全基因组序列。基因序列分析显示该菌株携带大量毒力基因,包括lukS-PV、lukF-PV、eta、fnbA、fnbB、sspB、sspC等,编码毒素、粘附、免疫逃逸等相关毒力因子,其毒力较强,致病性较高。     

Genomic and proteomic characterization of Staphylococcus aureus mastitis isolates of bovine origin

Staphylococcus aureus colonizes and infects humans as well as animals. In the present study, 17 S. aureus strains isolated from cows suffering from mastitis were characterized. The well-established multilocus sequence typing (MLST) technique and a diagnostic microarray covering 185 S. aureus virulence and resistance genes were used for genetic and epidemiological analyses. Virulence gene expression studies were performed by analyzing the extracellular protein pattern of each isolate on 2-D gels. By this way, a pronounced heterogeneity of the extracellular proteome between the bovine isolates has been observed which was attributed to genome plasticity and variation of gene expression. Merely 12 proteins were expressed in at least 80% of the isolates, i.e. Atl, Aur, GlpQ, Hla, LtaS, Nuc, PdhB, SAB0846, SAB2176, SAB0566, SspA, and SspB forming the core exoproteome. Fifteen extracellular proteins were highly variably expressed and only present in less than 20% of the isolates. This includes the serine proteases SplB, C, and F, and the superantigens SEC-bov, SEL and TSST-1. Compared to human isolates we identified at least six proteins with significantly different expression frequencies. While SAB0846 was expressed more frequently in bovine isolates, LytM, EbpS, Spa, Geh, and LukL1 were seen less frequently in these isolates.     

Extensive Genomic Diversity among Bovine-Adapted Staphylococcus aureus: Evidence for a Genomic Rearrangement within CC97

Staphylococcus aureus is an important pathogen associated with both human and veterinary disease and is a common cause of bovine mastitis. Genomic heterogeneity exists between S. aureus strains and has been implicated in the adaptation of specific strains to colonise particular mammalian hosts. Knowledge of the factors required for host specificity and virulence is important for understanding the pathogenesis and management of S. aureus mastitis. In this study, a panel of mastitis-associated S. aureus isolates (n = 126) was tested for resistance to antibiotics commonly used to treat mastitis. Over half of the isolates (52%) demonstrated resistance to penicillin and ampicillin but all were susceptible to the other antibiotics tested. S. aureus isolates were further examined for their clonal diversity by Multi-Locus Sequence Typing (MLST). In total, 18 different sequence types (STs) were identified and eBURST analysis demonstrated that the majority of isolates grouped into clonal complexes CC97, CC151 or sequence type (ST) 136. Analysis of the role of recombination events in determining S. aureus population structure determined that ST diversification through nucleotide substitutions were more likely to be due to recombination compared to point mutation, with regions of the genome possibly acting as recombination hotspots. DNA microarray analysis revealed a large number of differences amongst S. aureus STs in their variable genome content, including genes associated with capsule and biofilm formation and adhesion factors. Finally, evidence for a genomic arrangement was observed within isolates from CC97 with the ST71-like subgroup showing evidence of an IS431 insertion element having replaced approximately 30 kb of DNA including the ica operon and histidine biosynthesis genes, resulting in histidine auxotrophy. This genomic rearrangement may be responsible for the diversification of ST71 into an emerging bovine adapted subgroup.     

Determination of phylogenetic relationships among methicillin-resistant Staphylococcus aureus recovered from infected humans and Companion Animals

Companion animals carry different microorganism of severely public health hazard for human; the kindness relation and contact between humans and companion animals may the route in the transmission of most zoonotic bacteria, including Methicillin-Resistant Staphylococcus aureus (MRSA). Therefore, the current study investigate the companion animals mainly dogs and cat as a reservoir for MRSA and the genetic similarity between the recovered strains of MRSA from such companion animals and their owners. One hundred swabs were collected under aseptic condition from companion animals and seventy swabs were collected from nasal and soft tissue of the infected owners in contact. All samples were examined with standard microbiological techniques, antimicrobial sensitivity, molecular typing and genetic finger printing using RAPD-PCR to determine the genetic finger printing of the recovered strains from humans and companion animals. The prevalence of the MRSA was higher in dog’s swabs than human swabs. Dog swabs showed a rate of (44.4%), cat’s revealed (27.3%), while the owner swabs could detect (42.8%). The antibiotics profiles were 69.2% and all MRSA strains were positive for mecA gene (100%), while only 25 strains (38.5%) were positive for Panton Valentine Leukocidin (PVL gene). Phylogenetic tree revealed 4 clusters with complete genetic relatedness and higher identity between the strains recovered from humans and companion animals. Our results revealed that there is great similarity between the recovered strains, indicating that pets play an important role in colonization and transmitting MRSA to humans, and vice versa.     

Genetic Analysis of Lysine Auxotrophs of Staphylococcus aureus

The genetics of lysine biosynthesis in Staphylococcus aureus was examined by a transductional analysis of lysine auxotrophs. These mutants had previously been grouped according to their biochemical characteristics. The mutant sites appeared to be closely linked. Complementation was observed between different groups but not between mutant strains belonging to the same group. A strain was detected which seemed to have a mutant control region. Evidence is presented to support the hypothesis that the lysine biosynthetic region functions as an operon.     

Vancomycin-resistant Staphylococcus aureus

The evolution and molecular mechanisms of vancomycin resistance in Staphylococcus aureus were reviewed. Case reports and research studies on biochemestry, electron microscopy and molecular biology of Staphylococcus aureus were selected from Medline database and summarized in the following review. After almost 40 years of successful treatment of S. aureus with vancomycin, several cases of clinical failures have been reported (since 1997). S. aureus strains have appeared with intermediate susceptibility (MIC 8-16 microg/ml), as well as strains with heterogeneous resistance (global MIC < or =4 microg/ml), but with subpopulations of intermediate susceptibility. In these cases, resistance is mediated by cell wall thickening with reduced cross linking. This traps the antibiotic before it reaches its major target, the murein monomers in the cell membrane. In 2002, a total vancomycin resistant strain (MIC > or =32 microg/ml) was reported with vanA genes from Enterococcus spp. These genes induce the change of D-Ala-D-Ala terminus for D-Ala-D-lactate in the cell wall precursors, leading to loss of affinity for glycopeptides. Vancomycin resistance in S. aureus has appeared; it is mediated by cell wall modifications that trap the antibiotic before it reaches its action site. In strains with total resistance, Enterococcus spp. genes have been acquired that lead to modification of the glycopeptide target.     

金黄色葡萄球菌肠毒素

金黄色葡萄球菌是一种重要的病原体,它产生多种类型的毒素,从而引起各种类型的疾病。金黄色葡萄球菌肠毒素(Staphylococcal enterotoxins,SEs),是一组血清学上互不相同的热稳定肠毒素,有10个血清型。由于食入了被SEs污染的食品而主要引起肠胃炎,此外,SEs还是一种强的超抗原,它可以刺激非特异性T细胞增殖。SEs各型之间有着相似的结构和功能。     

Staphylococcus aureus surface protein SasG contributes to intercellular autoaggregation of Staphylococcus aureus

Staphylococcus aureus surface protein G (SasG) is one of cell surface proteins with cell-wall sorting motif. The sasG mutant showed significantly reduced cell aggregation and biofilm formation. SasG is comprised of variable A domain and multiple tandem repeats of B domain, native-PAGE and in vitro formaldehyde cross-linking experiments revealed that the recombinant protein of the A domain showed homo-oligomerization as an octamer, but B domain did not. This study shows that SasG-A domain contributes to intercellular autoaggregation by homo-oligomerization, and that may facilitate the adherence to host-tissues in the infection of S. aureus.     

Companion Rabbit and Companion Bird Management Practices Among a Representative Sample of Guardians in Victoria,Australia

Although companion animal management practices used by caregivers can influence the welfare of the companion animals, there is little existing information about the ways in which people attempt to meet their companion animals’ needs. A representative sample of rabbit guardians (n = 93, representing 63,000 people) and bird guardians (n = 203, representing 157,000 people) in Victoria, Australia, completed an online survey. Items were related to the environmental, diet/exercise, behavioral, social, and health management practices used by guardians. Guardians sometimes meet their companion animals’ welfare needs, but they do not always engage in best practices. Most (79%) bird guardians reported that they interacted with their birds daily, but only 68% of rabbit guardians did the same. Likewise, 32% of rabbit guardians and 55% of bird guardians never had their companion animals vaccinated. These results may be used for educational campaigns for improving companion animal welfare.     

Genomic diversity in Staphylococcus xylosus

Staphylococcus xylosus is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of S. xylosus intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the S. xylosus C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20 S. xylosus strains of various origins showed that the S. xylosus species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the Staphylococcus genus corresponded in S. xylosus species to a strain-specific region potentially implicated in ecological fitness.     

Genomic Diversity in Staphylococcus xylosus

Staphylococcus xylosus is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of S. xylosus intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the S. xylosus C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20 S. xylosus strains of various origins showed that the S. xylosus species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the Staphylococcus genus corresponded in S. xylosus species to a strain-specific region potentially implicated in ecological fitness.     

金黄色葡萄球菌蛋白质相互作用网络及功能

【目的】金黄色葡萄球菌是一种革兰氏阳性菌,是目前最难以对付的病菌之一。它能引起多种感染,特别是在医院环境中。近年来,抗药性金黄色葡萄球菌传染更加严重,已成为公共卫生威胁。由于以前对于金黄色葡萄球菌的实验性研究大都是基于单个基因或者蛋白进行的,为了更好的研究这个物种,有必要从整体上把握金黄色葡萄球菌的蛋白作用机理。【方法】采用系统发生谱、操纵子法、基因融合法、基因邻近法、同源映射法等五种计算方法预测金黄色葡萄球菌蛋白质相互作用网络。【结果】从蛋白组的角度构建了金黄色葡萄球菌蛋白相互作用网络,并对网络进行功能分析。【结论】网络的分析表明金黄色葡萄球菌的蛋白质相互作用网络也服从scale-free属性,发现了SA0939、SA0868、rplD等重要的蛋白。通过对金黄色葡萄球菌的重要的细胞壁合成和信号转导调控蛋白局部网络分析,发现了一些对这两个系统十分重要的蛋白分子,这些信息将为更好的了解金黄色葡萄球菌的致病机理和开发新的药物靶点提供指导。     

Staphylococcus aureus: Staphylokinase

Staphylokinase is a 136 aa long bacteriophage encoded protein expressed by lysogenic strains of Staphylococcus aureus. Present understanding of the role of staphylokinase during bacterial infection is based on its interaction with the host proteins, alpha-defensins and plasminogen. alpha-Defensins are bactericidal peptides originating from human neutrophils. Binding of staphylokinase to alpha-defensins abolishes their bactericidal properties, which makes staphylokinase a vital tool for staphylococcal resistance to host innate immunity. Complex binding between staphylokinase and plasminogen results in the formation of active plasmin, a broad-spectrum proteolytic enzyme facilitating bacterial penetration into the surrounding tissues. We have recently shown high levels of staphylokinase expression in clinical isolates of skin and mucosal origin and relative low levels in isolates invading internal organs. These findings are supported by sepsis studies using isogenic S. aureus strains demonstrating increased bacterial load in the absence of staphylokinase production. Our observations indicate that staphylokinase favours symbiosis of staphylococci with the host that makes it an important colonization factor.