bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predominance and Emergence of Clones of Hospital-Acquired Methicillin-Resistant
Staphylococcus aureus
in Malaysia
Authors: Ghaznavi-Rad Ehsanollah , Shamsudin Mariana Nor , Sekawi Zamberi , Khoon Liew Yun , Aziz Mohammad Nazri , Hamat Rukman Awang , Othman Norlijah , Chong Pei Pei , van Belkum Alex , Ghasemzadeh-Moghaddam Hamed , Neela Vasanthakumari 
Published: January 2010

ABSTRACT

We define the epidemiology of predominant and sporadic methicillin-resistant
Staphylococcus aureus
(MRSA) strains in a central teaching and referral hospital in Kuala Lumpur, Malaysia. This is done on the basis of
spa
sequencing, multilocus sequence typing (MLST), staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and virulence gene profiling. During the period of study, the MRSA prevalence was 44.1%, and 389 MRSA strains were included. The prevalence of MRSA was found to be significantly higher in the patients of Indian ethnicity (
P
< 0.001). The majority (92.5%) of the isolates belonged to ST-239,
spa
type t037, and possessed the type III or IIIA SCC
mec
. The arginine catabolic mobile element (ACME)
arcA
gene was detected in three (1.05%) ST-239 isolates. We report the first identification of ACME
arcA
gene-positive ST-239. Apart from this predominant clone, six (1.5%) isolates of ST-22, with two related
spa
types (t032 and t4184) and a singleton (t3213), carrying type IVh SCC
mec
, were detected for the first time in Asia. A limited number of community-acquired (CA) MRSA strains were also detected. These included ST-188/t189 (2.1%), ST-1/t127 (2.3%), and ST-7/t091 (1%). Panton-Valentin leukocidin (PVL) was detected in all ST-1 and ST-188 strains and in 0.7% of the ST-239 isolates. The majority of the isolates carried
agr
I, except that ST-1 strains were
agr
III positive. Virulence genes
seg
and
sei
were seen only among ST-22 isolates. In conclusion, current results revealed the predominance of ST-239-SCC
mec
III/IIIA and the penetration of ST-22 with different virulence gene profiles. The emergence in Malaysia of novel clones of known epidemic and pathogenic potential should be taken seriously.
Molecular Changes Associated with Altered Patterns of Norovirus Outbreak Epidemics in Victoria, Australia, in 2006 to 2007
Authors: Bruggink Leesa D. , Marshall John A. 
Published: January 2010

ABSTRACT
Noroviruses (NoVs) are now considered the most common cause of outbreaks of nonbacterial gastroenteritis, but the factors which control the incidence of NoVs are poorly understood. In 2006, the pattern of NoV outbreak epidemics in Victoria, Australia, changed compared to the pattern for 2002 to 2005 and 2007. This study examined molecular correlates of the changed NoV periodicity. For the period of 2002 to 2007, 8,507 fecal specimens from 1,495 gastroenteritis outbreaks were tested for NoV by reverse transcription-PCR, and 1,018 NoV outbreaks were identified. Nucleotide sequence analysis was used to define genotypes and GII.4 variants. For 2002 to 2007, GII.4 was the predominant genotype. For the period of 2002 to 2005 and 2007, a single NoV outbreak epidemic occurred in warmer months of each year, but in 2006 two epidemics occurred in 1 year, one in colder months and one in warmer months of the year. For 2002 to 2007, four major GII.4 variants, “2002 Oxford/Farmington Hills,” “2004 Hunter,” “2006a,” and “2006b,” were identified. Each NoV outbreak epidemic was linked principally to one of these four variants, and there was a time link, a delay of 2 to 6 months, between the first detection of a GII.4 variant and the first outbreak epidemic in which it was the principal variant. The unusual 2006 pattern of outbreak epidemics can then be correlated with the appearance of two GII.4 variants within a short space of time, resulting in two outbreak epidemics in a short space of time, i.e., in the 1 year. This study provides a potentially greater ability to predict the characteristics of NoV epidemics.
Human Papillomavirus DNA Detection in Menstrual Blood from Patients with Cervical Intraepithelial Neoplasia and Condyloma Acuminatum
Authors: Wong Sze Chuen Cesar , Au Thomas Chi Chuen , Chan Sammy Chung Sum , Chan Charles Ming Lok , Lam Money Yan Yee , Zee Benny Chung Ying , Pong Wei Mei , Chan Anthony Tak Cheung 
Published: January 2010

ABSTRACT

The Papanicolaou test generates pain and embarrassment, and cytology screening has limited sensitivity for detection of cervical neoplasia. These factors urge the use of another screening test that can overcome these limitations. We explore a completely noninvasive method using detection of human papillomavirus (HPV) DNA in women's menstrual blood (MB). The participants were divided into 3 cohorts: (i) 235 patients with cervical intraepithelial neoplasia 3 (CIN 3) (
n
= 48), CIN 2 (
n
= 60), CIN 1 (
n
= 58), or condyloma acuminatum (CAC) (
n
= 69) before treatment or remission; (ii) from the first cohort of patients, 108 CIN 3 or CIN 2 patients after treatment and 62 CIN 1 or CAC patients after remission; and (iii) 323 apparently normal subjects (ANS) without any cervical disease. The HPV genotypes of the infected patients were confirmed by direct sequencing. Quantitative real-time PCR (QRT-PCR) was used to measure the MB HPV16 load for 15 infected patients. Results showed that the sensitivity, specificity, and positive and negative predictive values for detection of MB HPV DNA in samples from patients with CIN or CAC were 82.8%, 93.1%, 90.0%, and 87.9%, respectively. Moreover, MB HPV DNA was found in samples from 22.2% of CIN 3 or CIN 2 patients after treatment, 0.0% of CIN 1 or CAC patients after remission, and 8.1% of ANS, 4 of whom were found to have CIN 1 or CAC. Furthermore, QRT-PCR showed that the normalized MB HPV16 DNA copy numbers in samples from patients with CIN 1 to CIN 3 were significantly increased. These preliminary results suggested that MB HPV DNA is a potential noninvasive marker for these premalignant cervical diseases.
Influenza Virus Inactivation for Studies of Antigenicity and Phenotypic Neuraminidase Inhibitor Resistance Profiling
Authors: Jonges Marcel , Liu Wai Ming , van der Vries Erhard , Jacobi Ronald , Pronk Inge , Boog Claire , Koopmans Marion , Meijer Adam , Soethout Ernst 
Published: January 2010

ABSTRACTIntroduction of a new influenza virus in humans urges quick analysis of its virological and immunological characteristics to determine the impact on public health and to develop protective measures for the human population. At present, however, the necessity of executing pandemic influenza virus research under biosafety level 3 (BSL-3) high-containment conditions severely hampers timely characterization of such viruses. We tested heat, formalin, Triton X-100, and β-propiolactone treatments for their potencies in inactivating human influenza A(H3N2) and avian A(H7N3) viruses, as well as seasonal and pandemic A(H1N1) virus isolates, while allowing the specimens to retain their virological and immunological properties. Successful heat inactivation coincided with the loss of hemagglutinin (HA) and neuraminidase (NA) characteristics, and β-propiolactone inactivation reduced the hemagglutination titer and NA activity of the human influenza virus 10-fold or more. Although Triton X-100 treatment resulted in inconsistent HA activity, the NA activities in culture supernatants were enhanced consistently. Nonetheless, formalin treatment permitted the best retention of HA and NA properties. Triton X-100 treatment proved to be the easiest-to-use influenza virus inactivation protocol for application in combination with phenotypic NA inhibitor susceptibility assays, while formalin treatment preserved B-cell and T-cell epitope antigenicity, allowing the detection of both humoral and cellular immune responses. In conclusion, we demonstrated successful influenza virus characterization using formalin- and Triton X-100-inactivated virus samples. Application of these inactivation protocols limits work under BSL-3 conditions to virus culture, thus enabling more timely determination of public health impact and development of protective measures when a new influenza virus, e.g., pandemic A(H1N1)v virus, is introduced in humans.
Novel Screening Agar for Detection of Vancomycin-Nonsusceptible
Staphylococcus aureus
Authors: Carey-Ann Burnham D. , Weber Carol J. , Dunne W. Michael 
Published: January 2010

ABSTRACT

In January 2006, the Clinical and Laboratory Standards Institute (CLSI) updated breakpoints for vancomycin susceptibility testing for
Staphylococcus aureus
such that an MIC greater than 2 mg/liter was considered to represent nonsusceptibility to vancomycin. Previously, an MIC of 4 mg/liter had been considered to represent susceptibility. Additionally, in 2009, the CLSI altered the guidelines for staphylococci such that disk diffusion was no longer an acceptable means for testing vancomycin susceptibility in these organisms. To accommodate the change in breakpoints and methodological updates, we designed a medium consisting of brain heart infusion agar with 3 mg/liter vancomycin (BHI-V3) to screen for isolates of
S. aureus
with reduced susceptibility to vancomycin. We challenged this medium using a previously characterized collection of 100 isolates of
S. aureus
, including 55 vancomycin-susceptible isolates and 45 isolates representing vancomycin-intermediate strains of
S. aureus
(VISA) (with vancomycin MICs of 4 mg/liter or greater). All of the VISA isolates grew on the agar, for 100% sensitivity. Nineteen vancomycin-susceptible isolates also grew on the agar, for 65% specificity. We then incorporated BHI-V3 into clinical practice. In the first 60 days postimplementation, we identified 17 potential VISA isolates out of 421
S. aureus
isolates tested. Thirteen out of the 17 were confirmed to represent VISA isolates. In light of the excellent sensitivity of this medium, we recommend that clinical laboratories incorporate BHI-V3 to screen for vancomycin-nonsusceptible isolates of
S. aureus
.
Toll-Like Receptor Agonists Synergistically Increase Proliferation and Activation of B Cells by Epstein-Barr Virus
Authors: Iskra Stefanie , Kalla Markus , Delecluse Henri-Jacques , Hammerschmidt Wolfgang , Moosmann Andreas 
Published: January 2010

ABSTRACTEpstein-Barr virus (EBV) efficiently drives proliferation of human primary B cellsin vitro, a process relevant for human diseases such as infectious mononucleosis and posttransplant lymphoproliferative disease. Human B-cell proliferation is also driven by ligands of Toll-like receptors (TLRs), notably viral or bacterial DNA containing unmethylated CpG dinucleotides, which triggers TLR9. Here we quantitatively investigated how TLR stimuli influence EBV-driven B-cell proliferation and expression of effector molecules. CpG DNA synergistically increased EBV-driven proliferation and transformation, T-cell costimulatory molecules, and early production of interleukin-6. CpG DNA alone activated only memory B cells, but CpG DNA enhanced EBV-mediated transformation of both memory and naive B cells. Ligands for TLR2 or TLR7/8 or whole bacteria had a weaker but still superadditive effect on B-cell transformation. Additionally, CpG DNA facilitated the release of transforming virus by established EBV-infected lymphoblastoid cell lines. These results suggest that the proliferation of EBV-infected B cells and their capability to interact with immune effector cells may be directly influenced by components of bacteria or other microbes present at the site of infection.
New, Closely Related Haloarchaeal Viral Elements with Different Nucleic Acid Types
Authors: Roine Elina , Kukkaro Petra , Paulin Lars , Laurinavičius Simonas , Domanska Aušra , Somerharju Pentti , Bamford Dennis H. 
Published: January 2010

ABSTRACT

During the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus,
Haloarcula hispanica
pleomorphic virus 1 (HHPV-1), that infects the halophilic archaeon
Haloarcula hispanica
. The virus contains a circular double-stranded DNA genome of 8,082 bp in size. The organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus HRPV-1, a pleomorphic single-stranded DNA virus that infects a halophilic archaeon
Halorubrum
sp. Analysis of the two halovirus sequences, as well as the entire nucleotide sequence of the 10.8-kb pHK2-plasmid and a 12.6-kb chromosomal region in
Haloferax volcanii
, allows us to suggest a new group of closely related viruses with genomes of either single-stranded or double-stranded DNA. Currently, closely related viruses are considered to have the same genome type. Our observation clearly contradicts this categorization and indicates that we should reconsider the way we classify viruses. Our results also provide a new example of related viruses where the viral structural proteins have not diverged as much as the proteins associated with genome replication. This result further strengthens the proposal for higher-order classification to be based on virion architecture rather than on genome type or replication mechanism.
Virus Shedding and Potential for Interspecies Waterborne Transmission of Highly Pathogenic H5N1 Influenza Virus in Sparrows and Chickens
Authors: Forrest Heather L. , Kim Jeong-Ki , Webster Robert G. 
Published: January 2010

ABSTRACT
To elucidate the role of sparrows as intermediate hosts of highly pathogenic avian influenza H5N1 viruses, we assessed shedding and interspecies waterborne transmission of A/duck/Laos/25/06 in sparrows and chickens. Inoculated birds shed virus at high titers from the oropharynx and cloaca, and infection was fatal. Waterborne transmission from inoculated sparrows to contact chickens was absent, while 25% of sparrows were infected via waterborne transmission from chickens. The viral shedding and susceptibility to infection we observed in sparrows, coupled with their presence in poultry houses, could facilitate virus spread among poultry and wild birds in the face of an H5N1 influenza virus outbreak.
Extralymphoid CD8
+
T Cells Resident in Tissue from Simian Immunodeficiency Virus SIVmac239Δnef-Vaccinated Macaques Suppress SIVmac239 Replication
Ex Vivo
Authors: Greene Justin M. , Lhost Jennifer J. , Burwitz Benjamin J. , Budde Melisa L. , Macnair Caitlin E. , Weiker Madelyn K. , Gostick Emma , Friedrich Thomas C. , Broman Karl W. , Price David A. , O'Connor Shelby L. , O'Connor David H. 
Published: January 2010

ABSTRACT

Live-attenuated vaccination with simian immunodeficiency virus (SIV) SIVmac239Δnef is the most successful vaccine product tested to date in macaques. However, the mechanisms that explain the efficacy of this vaccine remain largely unknown. We utilized an
ex vivo
viral suppression assay to assess the quality of the immune response in SIVmac239Δnef-immunized animals. Using major histocompatibility complex-matched Mauritian cynomolgus macaques, we did not detect SIV-specific functional immune responses in the blood by gamma interferon (IFN-γ) enzyme-linked immunospot assay at select time points; however, we found that lung CD8
+
T cells, unlike blood CD8
+
T cells, effectively suppress virus replication by up to 80%. These results suggest that SIVmac239Δnef may be an effective vaccine because it elicits functional immunity at mucosal sites. Moreover, these results underscore the limitations of relying on immunological measurements from peripheral blood lymphocytes in studies of protective immunity to HIV/SIV.
E1A Interacts with Two Opposing Transcriptional Pathways To Induce Quiescent Cells into S Phase
Authors: Sha Jingfeng , Ghosh Mrinal K. , Zhang Keman , Harter Marian L. 
Published: January 2010

ABSTRACT
Despite data suggesting that the adenovirus E1A protein of 243 amino acids creates an S-phase environment in quiescent cells by overcoming the nucleosomal repression of E2F-regulated genes, the precise mechanisms underlying E1A's ability in this process have not yet been defined at the biochemical level. In this study, we show by kinetic analysis that E1A, as opposed to an E1A mutant failing to bind p130, can temporally eliminate corepressor complexes consisting of p130-E2F4 and HDAC1/2-mSin3B from the promoters of E2F-regulated genes in quiescent cells. Once the complexes are removed, the di-methylation of H3K9 at these promoters becomes dramatically diminished, and this in turn allows for the acetylation of H3K9/14 and the recruitment of activating E2F family members, which is then followed by the transcriptional activity of the E2F-regulated genes. Remarkably, although an E1A mutant that can no longer bind to a histone acetyltransferase (PCAF) is as capable as wild-type E1A in eliminating corepressor complexes and methyl groups from the promoters of these genes, it cannot mediate the acetylation of H3K9/14 or induce their transcription. These findings suggest that corepressors as well as coactivators are acted upon by E1A to derepress E2F-regulated genes in quiescent cells. Thus, our results highlight for the first time a functional relationship between E1A and two transcriptional pathways of differing functions for transitioning cells out of quiescence and into S phase.
Directional Spread of Surface-Associated Retroviruses Regulated by Differential Virus-Cell Interactions
Authors: Sherer Nathan M. , Jin Jing , Mothes Walther 
Published: January 2010

ABSTRACT
The spread of viral infections involves the directional progression of virus particles from infected cells to uninfected target cells. Prior to entry, the binding of virus particles to specific cell surface receptors can trigger virus surfing, an actin-dependent lateral transport of viruses toward the cell body (M. J. Lehmann et al., J. Cell Biol. 170:317-325, 2005; M. Schelhaas, et al., PLoS Pathog. 4:e1000148, 2008; J. L. Smith, D. S. Lidke, and M. A. Ozbun, Virology 381:16-21, 2008). Here, we have used live-cell imaging to demonstrate that for cells chronically infected with the gammaretrovirus murine leukemia virus in which receptor has been downregulated, a significant portion of completely assembled virus particles are not immediately released into the supernatant but retain long-term association with the cell surface. Retention can be attributed, at least in part, to nonspecific particle attachment to cell surface glycosylaminoglycans. In contrast to virus surfing, viruses retained at the surface of infected cells undergo a lateral motility that is random and actin independent. This diffusive motility can be abruptly halted and converted into inward surfing after treatment with Polybrene, a soluble cation that increases virus-cell adsorption. In the absence of Polybrene, particle diffusion allows for an outward flow of viruses to the infected cell periphery. Peripheral particles are readily captured by and transmitted to neighboring uninfected target cells in a directional fashion. These data demonstrate a surface-based mechanism for the directional spread of viruses regulated by differential virus-cell interactions.
Distinct Hepatitis B Virus Dynamics in the Immunotolerant and Early Immunoclearance Phases
Authors: Wang Hurng-Yi , Chien Ming-Hung , Huang Hsiang-Po , Chang Hsiao-Chi , Wu Chung-Che , Chen Pei-Jer , Chang Mei-Hwei , Chen Ding-Shinn 
Published: January 2010

ABSTRACTLittle is known about hepatitis B virus (HBV) diversity changes within a host during the immunotolerant phase of chronic HBV infection. Such knowledge, nevertheless, may help in understanding how host immunity and HBV interact at the early stage of infection. In this study, serial serum samples were collected from a long-term (>17 years) follow-up cohort of seven patients, and multiple copies of the full-length viral genome from serially sampled sera were recovered and analyzed. Viral genetic diversity was positively correlated with host immunity, represented by levels of alanine aminotransferase (ALT), but was negatively correlated with the viral copy number. During the immunotolerant phase, when the host immunity was feeble (ALT < 20 U/liter), viral nucleotide diversity decreased while copy numbers increased. Rates of evolutionary change derived for different patients were in a very narrow range (1.6 × 10−5to 5.4 × 10−5/site/year). As the disease progressed toward the immunoclearance phase (ALT > 20 U/liter), viral diversity increased but copy numbers decreased. Evolutionary rates varied among patients in accordance with their levels of ALT, ranging from 9.6 × 10−6to 3.2 × 10−4/site/year. More than half (19/32 sites) of positively selected sites resided in immune epitopes, suggesting their possible role in host immunity. Our results demonstrate that host immunity is a dominant factor in HBV evolution. Different selective forces, including immune-mediated positive selection and virus-mediated negative selection, operate in tandem in shaping viral population dynamics within a host.
Recombinant Yellow Fever Vaccine Virus 17D Expressing Simian Immunodeficiency Virus SIVmac239 Gag Induces SIV-Specific CD8
+
T-Cell Responses in Rhesus Macaques
Authors: Bonaldo Myrna C. , Martins Mauricio A. , Rudersdorf Richard , Mudd Philip A. , Sacha Jonah B. , Piaskowski Shari M. , Costa Neves Patrícia C. , Veloso de Santana Marlon G. , Vojnov Lara , Capuano Saverio , Rakasz Eva G. , Wilson Nancy A. , Fulkerson John , Sadoff Jerald C. , Watkins David I. , Galler Ricardo 
Published: January 2010

ABSTRACT

Here we describe a novel vaccine vector for expressing human immunodeficiency virus (HIV) antigens. We show that recombinant attenuated yellow fever vaccine virus 17D expressing simian immunodeficiency virus SIVmac239 Gag sequences can be used as a vector to generate SIV-specific CD8
+
T-cell responses in the rhesus macaque. Priming with recombinant BCG expressing SIV antigens increased the frequency of these SIV-specific CD8
+
T-cell responses after recombinant YF17D boosting. These recombinant YF17D-induced SIV-specific CD8
+
T cells secreted several cytokines, were largely effector memory T cells, and suppressed viral replication in CD4
+
T cells.
Host Range, Prevalence, and Genetic Diversity of Adenoviruses in Bats
Authors: Li Yan , Ge Xingyi , Zhang Huajun , Zhou Peng , Zhu Yan , Zhang Yunzhi , Yuan Junfa , Wang Lin-Fa , Shi Zhengli 
Published: January 2010

ABSTRACT

Bats are the second largest group of mammals on earth and act as reservoirs of many emerging viruses. In this study, a novel bat adenovirus (AdV) (BtAdV-TJM) was isolated from bat fecal samples by using a bat primary kidney cell line. Infection studies indicated that most animal and human cell lines are susceptible to BtAdV-TJM, suggesting a possible wide host range. Genome analysis revealed 30 putative genes encoding proteins homologous to their counterparts in most known AdVs. Phylogenetic analysis placed BtAdV-TJM within the genus
Mastadenovirus
, most closely related to tree shrew and canine AdVs. PCR analysis of 350 bat fecal samples, collected from 19 species in five Chinese provinces during 2007 and 2008, indicated that 28 (or 8%) samples were positive for AdVs. The samples were from five bat species,
Hipposideros armiger
,
Myotis horsfieldii
,
M. ricketti
,
M
yotis
spp., and
Scotophilus kuhlii
. The prevalence ranged from 6.25% (
H. armiger
in 2007) to 40% (
M. ricketti
in 2007). Comparison studies based on available partial sequences of the
pol
gene demonstrated a great genetic diversity among bat AdVs infecting different bat species as well as those infecting the same bat species. This is the first report of a genetically diverse group of DNA viruses in bats. Our results support the notion, derived from previous studies based on RNA viruses (especially coronaviruses and astroviruses), that bats seem to have the unusual ability to harbor a large number of genetically diverse viruses within a geographic location and/or within a taxonomic group.