bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probe Hybridization Array Typing: a Binary Typing Method for
Escherichia coli
Authors: Srinivasan U. , Zhang L. , France A. M. , Ghosh D. , Shalaby W. , Xie J. , Marrs C. F. , Foxman B. 
Published: December 2006

ABSTRACT

The ability to distinguish between
Escherichia coli
strains is critical for outbreak investigations. Binary typing, based on the presence or absence of genetic material, provides a high-throughput alternative to gel- and PCR-based typing techniques that generate complex banding patterns and lack uniform interpretation criteria. We developed, validated, and determined the discriminatory power of an
E. coli
binary typing method, probe hybridization array typing (PHAT). In PHAT, the absence or presence of genetic material is identified by using DNA hybridization to produce a reproducible and portable fingerprint for each genome. PHAT probes were generated from genome subtractive hybridization experiments. We PHAT typed the ECOR collection of strains from a variety of geographical locations, and 33 rectal
E. coli
strains selected from college-aged women with urinary tract infection. In the set of 33 human rectal strains, the discriminatory power of PHAT (98%) equaled that of multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. However, for ECOR strains, which include nonhuman strains, the current set of PHAT probes was less discriminating than MLST, ribotyping, and enterobacterial repetitive intergenic consensus sequence PCR (80% versus 97, 92, and 97%, respectively). When we limited the analysis to ECOR strains of B2 and D lineage, which are associated with human infection, current PHAT probes were highly discriminatory (94%). PHAT can be applied in a high-throughput format (i.e., “library on a slide”), the discriminatory ability can be varied based on the probe set, and PHAT is readily adapted to other bacterial species with high variation in genetic content.
Use of Fluconazole as a Surrogate Marker To Predict Susceptibility and Resistance to Voriconazole among 13,338 Clinical Isolates of
Candida
spp. Tested by Clinical and Laboratory Standards Institute-Recommended Broth Microdilution Methods
Authors: Pfaller M. A. , Messer S. A. , Boyken L. , Rice C. , Tendolkar S. , Hollis R. J. , Diekema D. J. 
Published: December 2006

ABSTRACT

Clinical laboratories frequently face the problem of delayed availability of commercially prepared approved reagents for performing susceptibility testing of new antimicrobials. Although this problem is encountered more often with antibacterial agents, it is also an issue with antifungal agents. A current example is voriconazole, a new triazole antifungal with an expanded spectrum and potency against
Candida
spp.,
Aspergillus
spp., and other opportunistic fungal pathogens. The present study addresses the use of fluconazole as a surrogate marker to predict the susceptibility of
Candida
spp. to voriconazole. Reference broth microdilution MIC results for 13,338 strains of
Candida
spp. isolated from more than 200 medical centers worldwide were used. Voriconazole MICs and interpretive categories (susceptible, ≤1 μg/ml; susceptible dose dependent, 2 μg/ml; resistant, ≥4 μg/ml) were compared with those of fluconazole by regression statistics and error rate bounding analyses. For all 13,338 isolates, the absolute categorical agreement was 91.6% (false susceptible or very major error [VME], 0.0%). Since voriconazole is 16- to 32-fold more potent than fluconazole, the performance of fluconazole as a surrogate marker for voriconazole susceptibility was improved by designating those isolates with fluconazole MICs of ≤32 μg/ml as being susceptible to voriconazole, resulting in a categorical agreement of 97% with 0.1% VME. Clinical laboratories performing antifungal susceptibility testing of fluconazole against
Candida
spp. can reliably use these results as surrogate markers until commercial FDA-approved voriconazole susceptibility tests become available.
Development of a Real-Time PCR Assay To Detect
Treponema pallidum
in Clinical Specimens and Assessment of the Assay's Performance by Comparison with Serological Testing
Authors: Leslie David E. , Azzato Franca , Karapanagiotidis Theo , Leydon Jennie , Fyfe Janet 
Published: December 2006

ABSTRACT

The incidence of infectious syphilis in men who have sex with men and human immunodeficiency virus-infected patients has increased steadily in Victoria, Australia, since 2002. A TaqMan real-time PCR assay targeting the
polA
gene of
Treponema pallidum
(TpPCR) was developed. The analytical sensitivity of the assay was estimated to be 1.75 target copies per reaction. Initially, the assay was used to test a variety of specimens (excluding blood) from 598 patients. Of the 660 tests performed, positive PCR results were obtained for 55 patients. TpPCR results were compared with serology results for 301 patients being investigated for early syphilis. Of these patients, 41 were positive by both TpPCR and serology, 246 were negative by both TpPCR and serology, 4 were TpPCR positive but negative by serology, and 10 were TpPCR negative but showed evidence of recent or active infection by serology. Directly compared with serology, TpPCR showed 95% agreement, with a sensitivity of 80.39% and a specificity of 98.40%. Potential factors leading to the discrepant results are discussed. Concurrent serology on 21 patients with TpPCR-positive primary syphilitic lesions demonstrated that a panel of current syphilis serological tests has high sensitivity for the detection of early syphilis. We found that TpPCR is a useful addition to serology for the diagnosis of infectious syphilis. Direct comparison with other
T. pallidum
PCR assays will be required to fully assess the limitations of the assay.
Propionibacterium acnes
as a Cause of Prosthetic Valve Aortic Root Abscess
Authors: Hinestrosa Federico , Djurkovic Svetolik , Bourbeau Paul P. , Foltzer Michael A. 
Published: December 2006

ABSTRACT

Propionibacterium acnes
isolates usually have relatively low virulence and are often classified as contaminants when isolated from blood and tissue cultures. We report a patient with
Propionibacterium acnes
bacteremia and late prosthetic valve endocarditis, complicated by an aortic root abscess.
Genetic Profiling of the Oral Microbiota Associated with Severe Early-Childhood Caries
Authors: Li Y. , Ge Y. , Saxena D. , Caufield P. W. 
Published: December 2006

ABSTRACT

The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (
n
= 12) (42 ± 3.7) than in the S-ECC children (
n
= 8) (35 ± 4.3); the difference was statistically significant (
P
= 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (
P
= 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.
Serological Cross-Reactivity between Different
Chlamydia
-Like Organisms
Authors: Casson Nicola , Entenza José M. , Greub Gilbert 
Published: December 2006

ABSTRACT

The serological cross-reactivity between different recently described
Chlamydia
-related organisms was determined. Mouse sera exhibited a strong reactivity against autologous antigen and closely related heterologous antigen but no cross-reactivity with distantly related species. These results are important to better interpret serological studies and assess the pathogenic role of these obligate intracellular bacteria.
Rapid Molecular Strategy for Filovirus Detection and Characterization
Authors: Zhai Junhui , Palacios Gustavo , Towner Jonathan S. , Jabado Omar , Kapoor Vishal , Venter Marietjie , Grolla Allen , Briese Thomas , Paweska Janusz , Swanepoel Robert , Feldmann Heinz , Nichol Stuart T. , Lipkin W. Ian 
Published: December 2006

ABSTRACT
Filoviruses have the capacity to cause lethal outbreaks of hemorrhagic fever in primates. Here we present a simple consensus reverse transcription-PCR method for filovirus recognition and characterization and demonstrate its utility with all known filovirus strains. Phylogenetic assignment is achieved by automated web-based sequence analysis of amplification products.
Role of Large Sequence Polymorphisms (LSPs) in Generating Genomic Diversity among Clinical Isolates of
Mycobacterium tuberculosis
and the Utility of LSPs in Phylogenetic Analysis
Authors: Alland David , Lacher David W. , Hazbón Manzour Hernando , Motiwala Alifiya S. , Qi Weihong , Fleischmann Robert D. , Whittam Thomas S. 
Published: December 2006

ABSTRACT

Mycobacterium tuberculosis
strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur repeatedly in a genomic region may provide insights into the biological roles of LSPs and identify useful phylogenetic markers. We analyzed 163 clinical
M. tuberculosis
isolates for 17 LSPs identified in a genomic comparison of
M. tuberculosis
strains H37Rv and CDC1551. LSPs were mapped onto a single-nucleotide polymorphism (SNP)-based phylogenetic tree created using nine novel SNP markers that were found to reproduce a 212-SNP-based phylogeny. Four LSPs (group A) mapped to a single SNP tree segment. Two LSPs (group B) and 11 LSPs (group C) were inferred to have arisen independently in the same genomic region either two or more than two times, respectively. None of the group A LSPs but one group B LSP and five group C LSPs were flanked by IS
6110
sequences in the references strains. Genes encoding members of the proline-glutamic acid or proline-proline-glutamic acid protein families were present only in group B or C LSPs. SNP- versus LSP-based phylogenies were also compared. We classified each isolate into 58 LSP types by using a separate LSP-based phylogenetic analysis and mapped the LSP types onto the SNP tree. LSPs often assigned isolates to the correct phylogenetic lineage; however, significant mistakes occurred for 6/58 (10%) of the LSP types. In conclusion, most LSPs occur in genomic regions that are prone to repeated insertion/deletion events and were responsible for an unexpectedly high degree of genomic variation in clinical
M. tuberculosis.
Group B and C LSPs may represent polymorphisms that occur due to selective pressure and affect the phenotype of the organism, while group A LSPs are preferable phylogenetic markers.
A-to-G Hypermutation in the Genome of Lymphocytic Choriomeningitis Virus
Authors: Zahn Roland C. , Schelp Ina , Utermöhlen Olaf , von Laer Dorothee 
Published: December 2006

ABSTRACT
The interferon-inducible adenosine deaminase that acts on double-stranded RNA (ADAR1-L) has been proposed to be one of the antiviral effector proteins within the complex innate immune response. Here, the potential role of ADAR1-L in the innate immune response to lymphocytic choriomeningitis virus (LCMV), a widely used virus model, was studied. Infection with LCMV clearly upregulated ADAR1-L expression and activity. The editing activity of ADAR1-L on an RNA substrate was not inhibited by LCMV replication. Accordingly, an adenosine-to-guanosine (A-to-G) and uracil-to-cytidine (U-to-C) hypermutation pattern was found in the LCMV genomic RNA in infected cell lines and in mice. In addition, two hypermutated clones with a high level of A-to-G or U-to-C mutations within a short stretch of the viral genome were isolated. Analysis of the functionality of viral glycoprotein revealed that A-to-G- and U-to-C-mutated LCMV genomes coded for nonfunctional glycoprotein at a surprisingly high frequency. Approximately half the GP clones with an amino acid mutation lacked functionality. These results suggest that ADAR1-L-induced mutations in the viral RNA lead to a loss of viral protein function and reduced viral infectivity. This study therefore provides strong support for the contribution of ADAR1-L to the innate antiviral immune response.
Attenuation of Herpes Simplex Virus Neurovirulence with Picornavirus
cis
-Acting Genetic Elements
Authors: Campbell Stephanie A. , Mulvey Matthew , Mohr Ian , Gromeier Matthias 
Published: December 2006

ABSTRACT

Viral pathogenesis depends on a suitable milieu in target host cells permitting viral gene expression, propagation, and spread. In many instances, viral genomes can be manipulated to select for propagation in certain tissues or cell types. This has been achieved for the neurotropic poliovirus (PV) by exchange of the internal ribosomal entry site (IRES), which is responsible for translation of the uncapped plus-strand RNA genome. The IRES of human rhinovirus type 2 (HRV2) confers neuron-specific replication deficits to PV but has no effect on viral propagation in malignant glioma cells. We report here that placing the critical

γ
1

34.5
virulence genes of herpes simplex virus type 1 (HSV) under translation control of the HRV2 IRES results in neuroattenuation in mice. In contrast, IRES insertion permits HSV propagation in malignant glioma cell lines that do not support replication of HSV recombinants carrying

γ
1

34.5
deletions. Our observations indicate that the conditions for alternative translation initiation at the HRV2 IRES in malignant glioma cells differ from those in normal central nervous system (CNS) cells. Picornavirus regulatory sequences mediating cell type-specific gene expression in the CNS can be utilized to target cancerous cells at the level of translation regulation outside their natural context.
Vaccination of Cats with Attenuated Feline Immunodeficiency Virus Proviral DNA Vaccine Expressing Gamma Interferon
Authors: Gupta Soumi , Leutenegger Christian M. , Dean Gregg A. , Steckbeck Jonathan D. , Cole Kelly Stefano , Sparger Ellen E. 
Published: December 2006

ABSTRACT

A feline immunodeficiency virus (FIV) provirus with a
vif
gene deletion (FIVΔvifATGγ) that coexpresses feline gamma interferon (IFN-γ) was tested as a proviral DNA vaccine to extend previous studies showing efficacy with an FIV-pPPRΔvif DNA vaccine. Cats were vaccinated with either FIVΔvifATGγ or FIV-pPPRΔvif proviral plasmid DNA or with both FIV-pPPRΔvif DNA and a feline IFN-γ expression plasmid (pCDNA-IFNγ). A higher frequency of FIV-specific T-cell proliferation responses was observed in cats immunized with either FIVΔvifATGγ or FIV-pPPRΔvif plus pCDNA-IFNγ, while virus-specific cytotoxic-T-lymphocyte responses were comparable between vaccine groups. Antiviral antibodies were not observed postvaccination. Virus-specific cellular and humoral responses were similar between vaccine groups after challenge with a biological FIV isolate (FIV-PPR) at 13 weeks postimmunization. All vaccinated and unvaccinated cats were infected after FIV-PPR challenge and exhibited similar plasma virus loads. Accordingly, inclusion of plasmids containing IFN-γ did not enhance the efficacy of FIV-pPPRΔvif DNA immunization. Interestingly, the lack of protection associated with FIV-pPPRΔvif DNA immunization contrasted with findings from a previous study and suggested that multiple factors, including timing of FIV-pPPRΔvif inoculations and challenge, as well as route of challenge virus delivery, may significantly impact vaccine efficacy.
The S Segment of Punta Toro Virus (
Bunyaviridae
,
Phlebovirus
) Is a Major Determinant of Lethality in the Syrian Hamster and Codes for a Type I Interferon Antagonist
Authors: Perrone Lucy A. , Narayanan Krishna , Worthy Melissa , Peters C. J. 
Published: December 2006

ABSTRACT

Two
strains of Punta Toro virus (PTV), isolated from febrile humans in
Panama, cause a differential pathogenesis in Syrian hamsters, which
could be a useful model for understanding the virulence characteristics
and differential outcomes in other phleboviral infections such as Rift
Valley fever virus. Genetic reassortants produced between the lethal
Adames (A/A/A) and nonlethal Balliet (B/B/B) strains were used in this
study to investigate viral genetic determinants for pathogenesis and
lethality in the hamster model. The S segment was revealed to be a
critical genome segment, determining lethality with log
10
50% lethal doses for each PTV genotype as follows (L/M/S convention):
A/A/A, <0.7; B/A/A, <0.7; A/B/A, 1.5; B/B/A, 2.2;
B/A/B, 4.7; A/B/B, >4.7; A/A/B, >4.7; B/B/B,>
4.7. In addition, the Adames strain inhibits the induction of
alpha/beta interferon (IFN-α/β) in vivo and in vitro
and inhibits the activation of the IFN-β promoter. Expression
of the PTV Adames NSs protein, encoded by the S RNA segment, inhibited
the virus-mediated induction of an IFN-β promoter-driven
reporter gene, suggesting that PTV NSs functions as a type I IFN
antagonist. Taken together, these data indicate a mechanism of
pathogenesis in which the suppression of the type I IFN response early
during PTV infection leads to early and uncontrolled viral replication
and, ultimately, hamster death. This study contributes to our
understanding of
Phlebovirus
pathogenesis and identifies
potential targets for immune modulation to increase host
survival.
Inhibition of Retinoic Acid-Inducible Gene I-Mediated Induction of Beta Interferon by the NS1 Protein of Influenza A Virus
Authors: Mibayashi Masaki , Martínez-Sobrido Luis , Loo Yueh-Ming , Cárdenas Washington B. , Gale Michael , García-Sastre Adolfo 
Published: December 2006

ABSTRACT
The retinoic acid-inducible gene I product (RIG-I) has been identified as a cellular sensor of RNA virus infection resulting in beta interferon (IFN-β) induction. However, many viruses are known to encode viral products that inhibit IFN-β production. In the case of influenza A virus, the viral nonstructural protein 1 (NS1) prevents the induction of the IFN-β promoter by inhibiting the activation of transcription factors, including IRF-3, involved in IFN-β transcriptional activation. The inhibitory properties of NS1 appear to be due at least in part to its binding to double-stranded RNA (dsRNA), resulting in the sequestration of this viral mediator of RIG-I activation. However, the precise effects of NS1 on the RIG-I-mediated induction of IFN-β have not been characterized. We now report that the NS1 of influenza A virus interacts with RIG-I and inhibits the RIG-I-mediated induction of IFN-β. This inhibition was apparent even when a mutant RIG-I that is constitutively activated (in the absence of dsRNA) was used to trigger IFN-β production. Coexpression of RIG-I, its downstream signaling partner, IPS-1, and NS1 resulted in increased levels of RIG-I and NS1 within an IPS-1-rich, solubilization-resistant fraction after cell lysis. These results suggest that RIG-I, IPS-1, and NS1 become part of the same complex. Consistent with this idea, NS1 was also found to inhibit IFN-β promoter activation by IPS-1 overexpression. Our results indicate that, in addition to sequestering dsRNA, the NS1 of influenza A virus binds to RIG-I and inhibits downstream activation of IRF-3, preventing the transcriptional induction of IFN-β.
The Varicella-Zoster Virus (VZV) ORF9 Protein Interacts with the IE62 Major VZV Transactivator
Authors: Cilloniz Cristian , Jackson Wallen , Grose Charles , Czechowski Donna , Hay John , Ruyechan William T. 
Published: December 2006

ABSTRACT
The varicella-zoster virus (VZV) ORF9 protein is a member of the herpesvirus UL49 gene family but shares limited identity and similarity with the UL49 prototype, herpes simplex virus type 1 VP22. ORF9 mRNA is the most abundantly expressed message during VZV infection; however, little is known concerning the functions of the ORF9 protein. We have found that the VZV major transactivator IE62 and the ORF9 protein can be coprecipitated from infected cells. Yeast two-hybrid analysis localized the region of the ORF9 protein required for interaction with IE62 to the middle third of the protein encompassing amino acids 117 to 186. Protein pull-down assays with GST-IE62 fusion proteins containing N-terminal IE62 sequences showed that amino acids 1 to 43 of the acidic transcriptional activation domain of IE62 can bind recombinant ORF9 protein. Confocal microscopy of transiently transfected cells showed that in the absence of other viral proteins, the ORF9 protein was localized in the cytoplasm while IE62 was localized in the nucleus. In VZV-infected cells, the ORF9 protein was localized to the cytoplasm whereas IE62 exhibited both nuclear and cytoplasmic localization. Cotransfection of plasmids expressing ORF9, IE62, and the viral ORF66 kinase resulted in significant colocalization of ORF9 and IE62 in the cytoplasm. Coimmunoprecipitation experiments with antitubulin antibodies indicate the presence of ORF9-IE62-tubulin complexes in infected cells. Colocalization of ORF9 and tubulin in transfected cells was visualized by confocal microscopy. These data suggest a model for ORF9 protein function involving complex formation with IE62 and possibly other tegument proteins in the cytoplasm at late times in infection.
Protection against Vaccinia Virus Challenge by CD8 Memory T Cells Resolved by Molecular Mimicry
Authors: Cornberg Markus , Sheridan Brian S. , Saccoccio Frances M. , Brehm Michael A. , Selin Liisa K. 
Published: December 2006

ABSTRACT

Live vaccinia virus (VV) vaccination has been highly successful in eradicating smallpox. However, the mechanisms of immunity involved in mediating this protective effect are still poorly understood, and the roles of CD8 T-cell responses in primary and secondary VV infections are not clearly identified. By applying the concept of molecular mimicry to identify potential CD8 T-cell epitopes that stimulate cross-reactive T cells specific to lymphocytic choriomeningitis virus (LCMV) and VV, we identified after screening only 115 peptides two VV-specific immunogenic epitopes that mediated protective immunity against VV. An immunodominant epitope, VV-e7r
130
, did not generate cross-reactive T-cell responses to LCMV, and a subdominant epitope, VV-a11r
198
, did generate cross-reactive responses to LCMV. Infection with VV induced strong epitope-specific responses which were stable into long-term memory and peaked at the time virus was cleared, consistent with CD8 T cells assisting in the control of VV. Two different approaches, direct adoptive transfer of VV-e7r-specific CD8 T cells and prior immunization with a VV-e7r-expressing ubiquitinated minigene, demonstrated that memory CD8 T cells alone could play a significant role in protective immunity against VV. These studies suggest that exploiting cross-reactive responses between viruses may be a useful tool to complement existing technology in predicting immunogenic epitopes to large viruses, such as VV, leading to a better understanding of the role CD8 T cells play during these viral infections.