Molecular diagnosis of polymicrobial brain abscesses with 16S-rDNA-based next-generation sequencing.

OBJECTIVES: Brain abscesses lead to high mortality despite antibiotic and surgical treatment. Identification of causative bacteria is important to guide antibiotic therapy, but culture-based methods and molecular diagnostics by Sanger sequencing of 16S PCR products are hampered by antibiotic treatment and the often polymicrobial nature of brain abscesses. We have applied 16S-rRNA-based next-generation sequencing (NGS) for metagenomic analysis of intracranial abscess (brain and epidural) and meningitis samples. METHODS: Seventy-nine samples from 54 patients with intracranial abscesses or meningitis were included. DNA was subjected to 16S PCR. Amplicons were analysed with the Illumina MiSeq system, sequence reads were blasted versus the NCBI 16S bacterial database and analysed using MEGAN software. Results were compared to those of gram-staining, culture and Sanger sequencing. RESULTS: The NGS workflow was successful for 51 intracranial abscesses (46 brain and five epidural) and nine meningitis samples. Inclusion of (mono)bacterial meningitis samples allowed us to establish a cut-off criterion for the exclusion of contaminating sequences. In total 86 bacterial taxa were identified in brain abscesses by NGS, with Streptococcus intermedius and Fusobacterium nucleatum as most prevalent species; Propionibacterium and Staphylococcus spp. were associated with epidural abscesses. NGS identified two or more bacterial taxa in 31/51 intracranial abscesses, revealing the polymicrobial nature of these infections and allowing the discrimination of up to 16 bacterial taxa per sample. CONCLUSION: These results extend earlier studies showing that NGS methods expand the spectrum of bacteria detected in brain abscesses and demonstrate that the MiSeq platform is suitable for metagenomic diagnostics of this severe infection.

No evidence of XMRV infection in immunocompromised patients and HIV-positive individuals from Germany.

BACKGROUND: Xenotropic murine leukaemia virus-related virus (XMRV) has been detected in patients with prostate cancer and chronic fatigue syndrome (CFS). The detection of XMRV in healthy individuals has raised concern about a possible virus transmission by blood products. However, recent studies challenge the association between XMRV and human disease. This study investigated whether or not XMRV is present in patients with altered immune function and individuals at increased risk of blood-borne viral infections in Germany. METHODS: We investigated 503 peripheral blood mononuclear cell (PBMC) samples from 240 patients with iatrogenic immune suppression (71 haematopoietic stem cell recipients, 132 solid organ transplant recipients, 37 others) and 311 PBMC samples from 302 patients with HIV-1 infection for the presence of proviral XMRV by real-time polymerase chain reaction (PCR). RESULTS: All 814 PBMC samples from 542 patients tested negative for XMRV DNA and positive for an internal herpesvirus saimiri (HVS) control. Human genomic DNA was detected in all samples, and 90% of the samples contained >10,000 cell equivalents per XMRV PCR reaction. CONCLUSIONS: Our failure to detect proviral XMRV provides evidence against the presence of XMRV in patients at increased risk of viral infections in Germany.

Rhadinovirus vector-derived human telomerase reverse transcriptase expression in primary T cells.

The rhadinovirus herpesvirus saimiri (HVS) as a gene delivery vector allows large DNA insertions and long-termed gene expression. In the case of T-cell transduction, such vectors use the viral transformation-associated genes of HVS C488 for T-cell amplification. In this report, we investigated whether the gene for the catalytic telomerase subunit human telomerase reverse transcriptase (hTERT) can substitute for the transformation-associated genes in rhadinoviral T-cell transduction and amplification. By using virus mutants generated by en passant mutagenesis from bacterial artificial chromosomes, we observed a very early and functional transgene expression even by virus mutants without transformation-associated genes. The markers of T-cell transformation by HVS, namely CD2 hyperreactivity, overexpression of interleukin-26, and of the tyrosine kinase Lyn could neither be induced nor enhanced by ectopic hTERT expression. When the viral transformation-associated genes were replaced by the hTERT gene, it was not sufficient for growth transformation, although hTERT was efficiently transduced and functionally expressed by the rhadinovirus vector. Thus, the transformation-associated proteins StpC and Tip are responsible for the T-cell phenotype after transduction by HVS and, additionally, modulate telomerase activity independently of hTERT expression.

Regulated and constitutive expression of anti-inflammatory cytokines by nontransforming herpesvirus saimiri vectors.

Herpesviral saimiri-(HVS) mediated expression of bovine growth hormone was one of the first applications of an episomal viral vector for gene therapy. Meanwhile, the long-term persistence of HVS vectors has been confirmed in a broad spectrum of infectable target cells in vitro and in vivo. Regulated gene expression is useful for many applications of gene therapy. Therefore, we inserted the Mifepristone-antiprogestin-inducible expression system (GeneSwitchtrade mark) into HVS viral vectors to regulate the combined expression of anti-inflammatory cytokines, IL-10 and IL-1RA. Constitutive CMV-promoter/enhancer-driven and Mifepristone-inducible cytokine expression was compared in the viral context in transduced primary human fibroblasts and rheumatoid arthritis (RA) fibroblast-like cells (RASF). Long-term persistence of vector genomes was shown for both construct types. Constitutive expression was efficient and more rapid in onset than in the inducible system, in which the selective induction of interleukin expression along with low background levels was obtained by Mifepristone concentrations that were more than 1000-fold below those required for endogenous Progesterone antagonism. Furthermore, transgene expression corresponded to vector doses. Global patterns of cytokine secretion were not significantly changed due to viral transduction, indicating a rather inert behavior of the viral vector itself. In an attempt to emulate the inflammatory cytokine-enriched environment in rheumatoid arthritic joints, the function of the vectors could be demonstrated in vitro by the successful blockade of IL-1beta-stimulated matrix-metalloproteinase (MMP)-3 expression from RASF cells. Evaluation of this system in future studies, in suitable long-term SCID models of RA or in non-human primate models, will exploit the possible in vivo benefits of nontransforming HVS vectors in gene therapy.

Marker gene transfer into human haemopoietic cells using a herpesvirus saimiri-based vector.

Herpesvirus-based gene therapy vectors offer an attractive alternative to retroviral vectors because of their episomal nature and ability to accommodate large transgenes. Saimiriine herpesvirus 2 (HVS) is a prototypical gamma-2 herpesvirus that can latently infect numerous different cell types. A cosmid-generated HVS vector in which transforming genes have been deleted and the marker gene encoding enhanced green fluorescent protein (HVS-GFP) has been incorporated was evaluated for its potential to transduce CD34+ haemopoietic progenitors selected from cord blood. Expression of GFP could subsequently be readily detected in cells of the erythroid lineage in both CFU-GEMM assays and liquid differentiation cultures. These results confirm the potential of HVS as a candidate vector for gene therapy applications using primitive haemopoietic cells and suggest that it may be applicable to disorders affecting cells of the erythroid lineage.

Cell surface heparan sulfate is a receptor for human herpesvirus 8 and interacts with envelope glycoprotein K8.1.

An immunodominant envelope glycoprotein is encoded by the human herpesvirus 8 (HHV-8) (also termed Kaposi's sarcoma-associated herpesvirus) K8.1 gene. The functional role of glycoprotein K8.1 is unknown, and recognizable sequence homology to K8.1 is not detectable in the genomes of most other closely related gammaherpesviruses, such as herpesvirus saimiri or Epstein-Barr virus. In search for a possible function for K8.1, we expressed the ectodomain of K8.1 fused to the Fc part of human immunoglobulin G1 (K8.1DeltaTMFc). K8.1DeltaTMFc specifically bound to the surface of cells expressing glycosaminoglycans but not to mutant cell lines negative for the expression of heparan sulfate proteoglycans. Binding of K8.1DeltaTMFc to mammalian cells could be blocked by heparin. Interestingly, the infection of primary human endothelial cells by HHV-8 could also be blocked by similar concentrations of heparin. The specificity and affinity of these interactions were then determined by surface plasmon resonance measurements using immobilized heparin and soluble K8.1. This revealed that K8.1 binds to heparin with an affinity comparable to that of glycoproteins B and C of herpes simplex virus, which are known to be involved in target cell recognition by binding to cell surface proteoglycans, especially heparan sulfate. We conclude that cell surface glycosaminoglycans play a crucial role in HHV-8 target cell recognition and that HHV-8 envelope protein K8.1 is at least one of the proteins involved.

Interleukin-12 receptor beta1 deficiency in a patient with abdominal tuberculosis.

Two siblings with interleukin-12 receptor beta1 (IL-12Rbeta1) deficiency but different clinical phenotypes were studied. Both are homozygous for an IL12RB1 missense mutation that prevents receptor expression and abolishes cellular responses to IL-12. Transfection of the patients' T cells with wild-type IL12RB1 restored IL-12Rbeta1 expression and function. One patient had the expected phenotype of disseminated bacille Calmette-Guérin (BCG) infection in early childhood, whereas the other did not develop BCG infection, despite 3 inoculations with live BCG. Abdominal tuberculosis was diagnosed in this second patient at age 18 years. To date, neither of them has had clinical disease caused by environmental mycobacteria. These observations show unexpected interfamilial and intrafamilial heterogeneity of the clinical phenotype associated with IL-12Rbeta1 deficiency. The patients may be resistant to BCG but remain vulnerable to Mycobacterium tuberculosis. A diagnosis of IL-12Rbeta1 deficiency should therefore be considered in selected patients with severe tuberculosis, despite their resistance to BCG and a lack of atypical mycobacteriosis.

Independence of herpesvirus-induced T cell lymphoma from viral cyclin D homologue.

Cyclin D family members are cellular protooncogenes, and their viral homologues in the Kaposi's sarcoma-associated herpesvirus (KSHV, human herpesvirus type 8 [HHV-8]) and the closely related Herpesvirus saimiri have been implicated as putative cofactors of viral transformation and pathogenesis. KSHV is regularly found in Kaposi's sarcoma and in the primary effusion B cell lymphoma and Castleman's disease associated with immunosuppression and AIDS. H. saimiri strain C488 transforms human and marmoset T cells in vitro and causes polyclonal T cell lymphoma in New World monkeys. The viral cyclins stimulate cell cycle progression of quiescent fibroblasts, and they form active cyclin-dependent kinase (CDK)6 complexes of broad substrate specificity that can resist and downregulate cellular CDK inhibitors. This study shows that the viral cyclin of H. saimiri strain C488 is not required for viral replication, T cell transformation, and pathogenicity in New World primates.

Herpesvirus saimiri vFLIP provides an antiapoptotic function but is not essential for viral replication, transformation, or pathogenicity.

Apoptosis of infected cells is an important host defense mechanism, and many viruses have exploited antiapoptotic proteins that interfere with crucial cellular pathways. Viral FLICE inhibitory proteins (vFLIPs) are encoded by rhadinoviruses like herpesvirus saimiri, the related Kaposi's sarcoma-associated herpesvirus-human herpesvirus 8 (KSHV/HHV8), and the poxvirus responsible for molluscum contagiosum. The vFLIPs can block the interaction of the death receptor-adapter complex with the cellular effector FLICE (caspase-8), and this prevents the initiation of the downstream caspase cascade. KSHV/HHV8 vFLIP overexpression can confer resistance to T-cell-mediated apoptosis and acts as a tumor progression factor in a murine B-cell lymphoma model. To analyze the function of herpesvirus vFLIPs in the genetic background of the virus and in a model for viral pathogenesis, we deleted the vFLIP gene (open reading frame 71) from the genome of herpesvirus saimiri strain C488. The viral deletion mutant was viable and replicated like the wild-type virus. An antiapoptotic effect could be attributed to the vFLIP gene, but we also show that the vFLIP gene of herpesvirus saimiri is dispensable for viral transformation of T cells in vitro and for pathogenicity in cottontop tamarins in vivo.

Stable marker gene transfer into human bone marrow stromal cells and their progenitors using novel herpesvirus saimiri-based vectors.

We have evaluated the ability of new herpesvirus saimiri (HVS)-based vectors to deliver a marker gene green fluorescent protein (GFP) into human bone marrow (BM) stromal cells and their progenitors. Stromal cells expanded from adherent layers of long-term BM cultures (LTC) were susceptible to HVS-based infection in a dose-dependent manner, and the efficiency of 94.8 +/- 2.0% was achieved using single exposure with HVS/EGFP vector at multiplicity of infection (moi) of approximately 50. Colony-forming unit-fibroblast (CFU-F) assay established the ability of HVS-based vectors to infect progenitors for bone marrow stroma fibroblasts and transfer the marker gene over multiple cell divisions in the absence of selective pressure. HVS was not toxic for stromal cells and progenitors and no viral replication was detected upon growth of modified stroma. On the basis these data, we believe that HVS-based constructs can offer a new opportunity for selective gene delivery into bone marrow stromal cells and progenitors. The ability of HVS to infect nondividing cells can be considered advantageous in the development of both ex vivo and in vivo strategies.

The URNA genes of herpesvirus saimiri (strain C488) are dispensable for transformation of human T cells in vitro.

The herpesvirus saimiri strain C488 genome contains five genes for small nuclear RNAs, termed herpesvirus saimiri URNAs (or HSURs). Using a cosmid-based approach, all HSURs were precisely deleted from the genome. The mutant virus replicated at levels that were similar to those of wild-type viruses in OMK cells. Although the HSURs are expressed in wild-type virus-transformed human T-cell lines, the deletion does not affect viral transformation in cell culture.

Herpesvirus saimiri as a model for gammaherpesvirus oncogenesis.

Herpesvirus saimiri (HVS) causes T-lymphoproliferative dis-$borders in several New World and Old World primate species and in certain rabbits.In vitro infection leads to permanent growth of primary T cells of primate and human origins. The transformation-relevant proteins of HVS interact with cellular proto-oncoproteins which results in cell growth transformation. In addition, virus-encoded cellular homologues may contribute to transformation or persistence of HVS by altering cellular signal transduction and deregulating cell growth control. Because of the presence of a permissive cell culture system and in vitro Land in vivo transformation assays, HVS provides a unique opportunity to investigate the mechanisms of cancer induction by oncogenic herpesviruses.

New eukaryotic semaphorins with close homology to semaphorins of DNA viruses.

Semaphorins were initially described as a family of repulsive guidance molecules in embryonal development. Their basic structure consists of an N-terminal signal sequence, the defining semaphorin domain ofapproximately 500 amino acids, an Ig-like domain,and a variable carboxy-terminus. We recently described a viral semaphorin homologue encoded by the alcelaphine herpesvirus type 1. Less conserved, truncated homologues were also identified in poxviruses. Here we describe new human and murine semaphorin homologues. The respective genes were cloned and sequenced, and they were termed H-Sema-L and M-Sema-L (HGMW-approved symbols SEMAL and Semal, respectively). A multiply spliced mRNA of 3.2 kb is expressed in human placenta, spleen, thymus, and gonadal tissue. H-Sema-L maps to chromosome 15q22.3-q23 and M-Sema-L to the homologous locus 9A3.3-B in the mouse genome. The expression patterns and the presence of related genes in large DNA viruses suggest that this new semaphorin has a relevant function in the immune system.

Primary structure of the alcelaphine herpesvirus 1 genome.

Alcelaphine herpesvirus 1 (AHV-1) causes wildebeest-associated malignant catarrhal fever, a lymphoproliferative syndrome in ungulate species other than the natural host. Based on biological properties and limited structural data, it has been classified as a member of the genus Rhadinovirus of the subfamily Gammaherpes-virinae. Here, we report on cloning and structural analysis of the complete genome of AHV-1 C500. The low GC content DNA (L-DNA) region of the genome consists of 130,608 bp with low (46.17%) GC content and marked suppression of CpG dinucleotide frequency. Like in herpesvirus saimiri, the prototype of the rhadinoviruses, the L-DNA is flanked by approximately 20 to 25 GC-rich (71.83%) high GC content DNA (H-DNA) repeats of 1,113 to 1,118 nucleotides. The analysis of the L-DNA sequence revealed 70 open reading frames (ORFs), 61 of which showed homology to other herpesviruses. The conserved ORFs are arranged in four blocks collinear to other Rhadinovirus genomes. These gene blocks are flanked by nonconserved regions containing ORFs without similarities to known herpesvirus genes. Notably, a spliced reading frame with a coding capacity for a 199-amino-acid protein is located in a position homologous to the transforming genes of herpesvirus saimiri at the left end of the L-DNA. A gene with homology to the semaphorin family is located adjacent to this. Despite common biological and epidemiological properties, AHV-1 differs significantly from herpesvirus saimiri with regard to cell homologous genes, probably using a different set of effector proteins to achieve a similar T-lymphocyte-transforming phenotype.

Human herpesvirus 8 encodes a homolog of interleukin-6.

Kaposi's sarcoma is a multifocal lesion that is reported to be greatly influenced by cytokines such as interleukin-6 (IL-6) and oncostatin M. DNA sequences of a novel human gammaherpesvirus, termed human herpesvirus 8 (HHV-8) or Kaposi sarcoma-associated herpesvirus, have been identified in all epidemiological forms of Kaposi's sarcoma with high frequency. The presence of HHV-8 DNA is also clearly associated with certain B-cell lymphomas (body cavity-based lymphomas) and multicentric Castleman's disease. Sequence analysis of a 17-kb fragment revealed that adjacent to a block of conserved herpesvirus genes (major DNA-binding protein, glycoprotein B, and DNA polymerase), the genome of HHV-8 encodes structural homolog of IL-6. This cytokine is involved not only in the pathogenesis of Kaposi's sarcoma but also in certain B-cell lymphomas and multicentric Castleman's disease. The viral counterpart of IL-6 (vIL-6) has conserved important features such as cysteine residues involved in disulfide bridging or an amino-terminal signal peptide. Most notably, the region known to be involved in receptor binding is highly conserved in vIL-6. This conservation of essential features and the remarkable overlap between diseases associated with HHV-8 and diseases associated with IL-6 disregulation clearly suggest that vIL-6 is involved in HHV-8 pathogenesis.

Alcelaphine herpesvirus type 1 has a semaphorin-like gene.

Alcelaphine herpesvirus type 1, a rhadinovirus causing malignant catarrhal fever of ruminants, has an 1959 nucleotide open reading frame with significant homologies to semaphorin genes. While truncated genes of similar structure have been found in poxviruses, this is the first known example of a semaphorin-like gene in a herpesvirus.

Epidermodysplasia verruciformis associated human papillomaviruses present a subgenus-specific organization of the regulatory genome region.

The regulatory regions of the human papillomaviruses (HPVs) 9, 17, 20, and 36 were mapped, sequenced, and aligned. They revealed an arrangement of putative protein binding sites specific for the epidermodysplasia verruciformis associated HPVs. Three subgroups could be differentiated.