bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contamination of the Hospital Environment with Gastroenteric Viruses: Comparison of Two Pediatric Wards over a Winter Season
Authors: Gallimore Chris I. , Taylor Clive , Gennery Andrew R. , Cant Andrew J. , Galloway Angela , Xerry Jacqueline , Adigwe Juliet , Gray Jim J. 
Published: July 2008

ABSTRACT
The aims of this study were to examine the extent of gastroenteric virus contamination in a pediatric primary immunodeficiency (PPI) ward and a general pediatric ward over a winter season and to determine whether changes to hospital infection control interventions would have an impact on environmental contamination levels within pediatric units. Environmental swabs were collected weekly from 11 sites in both wards from 15 December 2005 to 3 March 2006 and examined for the presence of norovirus (NoV), astrovirus, and rotavirus (RV) by reverse transcriptase PCR. Viruses were detected in 17% and 19% of swabs from both wards. Virus contamination for NoV and RV decreased from 20% to 6% and 15% to 10% of swabs, respectively, in the PPI ward from the 2004 study by Gallimore et al. (C. I. Gallimore, C. Taylor, A. R. Gennery, A. J. Cant, A. Galloway, M. Iturriza-Gomara, and J. J. Gray, J. Clin. Microbiol. 44:395-399, 2006). Overall, changes to cleaning protocols were deemed to have reduced the level of environmental contamination with gastroenteric viruses, but contamination still occurred due to a breakdown in infection control procedures indicated by contamination in areas frequented by parents but used only occasionally by staff.
Utility of New 24-Locus Variable-Number Tandem-Repeat Typing for Discriminating
Mycobacterium tuberculosis
Clinical Isolates Collected in Bulgaria
Authors: Valcheva Violeta , Mokrousov Igor , Narvskaya Olga , Rastogi Nalin , Markova Nadya 
Published: July 2008

ABSTRACT

The present study evaluated new markers for molecular typing of
Mycobacterium tuberculosis
with a collection of strains circulating in Bulgaria. A study sample included 133 strains from epidemiologically unlinked patients from different regions of the country. Spoligotyping was used as a primary typing tool; it subdivided these strains into 37 types, including 15 clusters and 22 singletons. Traditional IS
6110
-restriction fragment length polymorphism (RFLP) typing and novel 24-locus variable number tandem-repeat (VNTR) typing methods were applied to the selection of 73 strains. Discriminatory power (Hunter-Gaston index [HGI]) of these methods was found to be 0.983 and 0.997, respectively. The 73 strains were subdivided into 66 types by a 24-locus mycobacterial interspersed repetitive unit (MIRU)-VNTR scheme, 62 types by a classical 12-locus MIRU-VNTR scheme, 51 types by IS
6110
-RFLP typing, and 31 types by spoligotyping. A combination of the five most polymorphic loci (MIRU40, Mtub04, Mtub21, QUB-11b, and QUB-26) was shown to achieve a high discrimination (HGI = 0.984). To conclude, a complete 24-locus scheme excellently differentiated strains in our study, whereas a reduced 5-locus set provided a sufficiently high differentiation and may be preliminarily suggested for the first-line typing of
M. tuberculosis
isolates in Bulgaria.
Evaluation of Three Real-Time PCR Assays for Detection of
Mycoplasma pneumoniae
in an Outbreak Investigation
Authors: Winchell Jonas M. , Thurman Kathleen A. , Mitchell Stephanie L. , Thacker W. Lanier , Fields Barry S. 
Published: July 2008

ABSTRACT

We compared the performances of three recently optimized real-time PCR assays derived from distinct genomic regions of
Mycoplasma pneumoniae
during an outbreak. Comprehensive evaluation established that a newly described toxin gene represents a superior target for detecting
M. pneumoniae
DNA in clinical specimens, although use of multiple targets may increase testing confidence.
Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible
Staphylococcus aureus
Isolates from Global Clinical Trials
Authors: Goering Richard V. , Shawar Ribhi M. , Scangarella Nicole E. , O'Hara F. Patrick , Amrine-Madsen Heather , West Joshua M. , Dalessandro Marybeth , Becker Julie A. , Walsh Stacey L. , Miller Linda A. , van Horn Stephanie F. , Thomas Elizabeth S. , Twynholm Monique E. 
Published: July 2008

ABSTRACT

Determining the genetic characteristics of
Staphylococcus aureus
is important for better understanding of the global and dynamic epidemiology of this organism as we witness the emergence and spread of virulent and antibiotic-resistant clones. We genotyped 292
S. aureus
isolates (105 methicillin resistant and 187 methicillin susceptible) using a combination of pulsed-field gel electrophoresis, multilocus sequence typing, and SCC
mec
typing. In addition,
S. aureus
isolates were tested for the presence of the Panton-Valentine leukocidin (PVL) genes. Isolates were recovered from patients with uncomplicated skin infections in 10 different countries during five phase III global clinical trials of retapamulin, a new topical antibiotic agent. The most common methicillin-resistant clone had multilocus sequence type 8, pulsed-field type USA300, and SCC
mec
type IV and possessed the PVL genes. This clone was isolated exclusively in the United States. The most common PVL-positive, methicillin-susceptible clone had multilocus sequence type 121 and pulsed-field type USA1200. This clone was found primarily in South Africa and the Russian Federation. Other clones were found at lower frequencies and were limited in their geographic distribution. Overall, considerable genetic diversity was observed within multilocus sequence type clonal complexes and pulsed-field types.
Rapid Detection of
bla
KPC
Carbapenemase Genes by Real-Time PCR
Authors: Hindiyeh Musa , Smollen Gill , Grossman Zehava , Ram Daniela , Davidson Yehudit , Mileguir Fernando , Vax Marina , Ben David Debbie , Tal Ilana , Rahav Galia , Shamiss Ari , Mendelson Ella , Keller Nathan 
Published: July 2008

ABSTRACT

Carbapenem resistance among
Enterobacteriaceae
is an emerging problem worldwide.
Klebsiella pneumoniae
carbapenemase (
bla
KPC
) enzymes are among the most common β-lactamases described. In this study, we report the development and validation of a real-time PCR (q-PCR) assay for the detection of
bla
KPC
genes using TaqMan chemistry. The q-PCR amplification of
bla
KPC
DNA was linear over 7 log dilutions (
r
2
= 0.999; slope, 3.54), and the amplification efficiency was 91.6%. The q-PCR detection limit was 1 CFU, and there was no cross-reaction with DNA extracted from several multidrug-resistant bacteria. Perianal/rectal swabs (
n
= 187) collected in duplicate from 128 patients admitted to Sheba Medical Center surgical intensive care units were evaluated for the presence of carbapenem-resistant bacteria by culturing on MacConkey agar-plus-carbapenem disks and for
bla
KPC
genes by q-PCR. Carbapenem-resistant organisms, all
K. pneumoniae
, were isolated from 47 (25.1%) of the 187 samples collected, while
bla
KPC
genes were detected in 54 (28.9%) of the patient samples extracted by the NucliSENS easyMAG system. Of these, seven samples were positive for
bla
KPC
genes by q-PCR but negative for carbapenem resistance by culture, while all samples in which no carbapenem-resistant bacteria were detected by culture also tested negative by q-PCR. Thus, the sensitivity and specificity of the q-PCR assay after extraction by the NucliSENS easyMAG system were 100% and 95%, respectively. Similar values were obtained after DNA extraction by the Roche MagNA Pure LC instrument: 97.9% sensitivity and 96.4% specificity. Overall, the
bla
KPC
q-PCR assay appears to be highly sensitive and specific. The utilization of q-PCR will shorten the time to bla
KPC
detection from 24 h to 4 h and will help in rapidly isolating colonized or infected patients and assigning them to cohorts.
Changing Patterns in Frequency of Recovery of Five Methicillin-Resistant
Staphylococcus aureus
Clones in Portuguese Hospitals: Surveillance over a 16-Year Period
Authors: Aires-de-Sousa Marta , Correia Bruno , de Lencastre Hermínia 
Published: July 2008

ABSTRACT

A total of 629 nonduplicate methicillin-resistant
Staphylococcus aureus
MRSA isolates were recovered between June and November 2006 from 11 hospitals located in different areas of Portugal. Selected isolates (
n
= 271, 43%) were typed by pulsed-field gel electrophoresis (PFGE), representatives of which were additionally characterized by
spa
typing, multilocus sequence typing, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and the presence of Panton-Valentine leukocidin (PVL). The 271 isolates were classified into 13 different clonal types. Three pandemic clones included the majority (
n
= 241, 88%) of the isolates and were observed in several hospitals: (i) EMRSA-15 (54%)—PFGE type A, ST22,
spa
type t022, SCC
mec
IV—was found in the 11 hospitals studied and was identified as the major clone in seven of them; (ii) the New York/Japan clone (17%)—PFGE B, ST5,
spa
type t067, SCC
mec
II—was identified in nine hospitals and represented the major clone in four; and (iii) the Brazilian MRSA (17%)—PFGE C, ST239,
spa
type t037, SCC
mec
IIIA—was also detected in nine hospitals but never as the main clone. All isolates tested were PVL negative. Clone EMRSA-15 is currently the predominant MRSA clonal type circulating in Portuguese hospitals, but a new wave of MRSA has emerged in the country with the recent introduction and spread of the New York/Japan clone. The Brazilian MRSA that was the leading clone in Portugal in the late 1990s is declining and being progressively replaced by the two former clones. We report the first isolate SCC
mec
type V (ST45) in Portugal.
New
Erwinia
-Like Organism Causing Cervical Lymphadenitis
Authors: Shin Sang Yop , Lee Mi Young , Song Jae-Hoon , Ko Kwan Soo 
Published: July 2008

ABSTRACT

The first case of cervical lymphadenitis due to infection by a new
Erwinia
-like organism is reported. The organism was identified initially as
Pantoea
sp. by a Vitek 2-based assessment but was finally identified as a member of the genus
Erwinia
by 16S rRNA gene sequence analysis. The isolate displayed 98.9% 16S rRNA gene sequence similarity to that of
E. tasmaniensis
and showed phenotypic characteristics that were different from other
Erwinia
species.
Kocuria rhizophilaAdds to the Emerging Spectrum of Micrococcal Species Involved in Human Infections
Authors: Becker Karsten , Rutsch Frank , Uekötter Andreas , Kipp Frank , König Jens , Marquardt Thorsten , Peters Georg , von Eiff Christof 
Published: July 2008

ABSTRACTWe describe the first case of aKocuria rhizophilainfection in a boy with methylmalonic aciduria. A single clone was isolated from blood samples drawn through a port system and from peripheral veins during septic episodes within a 2-year period.K. rhizophilaexpands the emerging number of “micrococci” considered to be etiologically relevant.
Sensitivities of Nasal and Rectal Swabs for Detection of Methicillin-Resistant
Staphylococcus aureus
Colonization in an Active Surveillance Program
Authors: Currie Andrea , Davis Linda , Odrobina Ewa , Waldman Suzanne , White Diane , Tomassi Joanne , Katz Kevin C. 
Published: July 2008

ABSTRACT

All medical and high-risk surgical patients were screened for methicillin-resistant
Staphylococcus aureus
colonization over 3.5 years. The sensitivities of nasal and rectal swabs were 68% and 62%, respectively. Naris and open-skin-site swabs detected 467 (74%) of 627 adult carriers identified. Rectal swabs detected an additional 160 (26%) carriers.
Countrywide Molecular Survey of Methicillin-Resistant
Staphylococcus aureus
Strains in Poland
Authors: Łuczak-Kadłubowska Agnieszka , Sulikowska Agnieszka , Empel Joanna , Piasecka Anna , Orczykowska Monika , Kozinska Aleksandra , Hryniewicz Waleria 
Published: July 2008

ABSTRACT

The present investigation was undertaken to assess the proportion of methicillin-resistant
Staphylococcus aureus
(MRSA) strains among hospital-acquired isolates and to determine the clones of MRSA currently circulating in Poland by using a number of molecular techniques. Between January and May 2005, methicillin resistance was investigated among a total of 915
S. aureus
isolates collected from 39 hospitals. A total of 208 (22.7%) isolates were positive for the
mecA
gene by PCR. The molecular characterization of MRSA isolates was carried out by the multiple-locus variable-number tandem repeat fingerprinting, pulsed-field gel electrophoresis, multilocus sequence typing, and staphylococcal chromosomal cassette
mec
(SCC
mec
) typing methods. The Hungarian (PFGE B; ST239, SCC
mec
type III [ST239-III]), Iberian (ST247-I), and Berlin (ST45-IV) clones were predominant, representing approximately 52.9, 11.5, and 10.0% of the MRSA isolates, respectively. A decline in the proportion of earlier MRSA clones, such as ST5-IV (a Pediatric clone), ST80-IV) (a Mediterranean clone), ST239-III (a Polish and Brazilian clone), and ST30-IV (a southwest Pacific clone) was observed. Additionally, the emergence of an MRSA clone with SCC
mec
type V, possibly representing a community-acquired strain, was observed in two hospitals during this study.
Molecular Diagnosis of Old World Cutaneous Leishmaniasis and Species Identification by Use of a Reverse Line Blot Hybridization Assay
Authors: Nasereddin Abedelmajeed , Bensoussan-Hermano Esther , Schönian Gabriele , Baneth Gad , Jaffe Charles L. 
Published: July 2008

ABSTRACT

Reverse line blot hybridization assays (RLB) have been used for the rapid diagnosis and genotyping of many pathogens. The leishmaniases are caused by a large number of species, and rapid, accurate parasite characterization is important in deciding on appropriate therapy. Fourteen oligonucleotide probes, 2 genus specific and 12 species specific (2 specific for
Leishmania major
, 3 for
L. tropica
, 1 for
L. infantum
, 3 for
L. donovani
, and 3 for
L. aethiopica
), were prepared by using DNA sequences in the internal transcribed spacer 1 (ITS1) region of the rRNA genes. Probe specificity was evaluated by amplifying DNA from 21 reference strains using biotinylated ITS1 PCR primers and the RLB. The genus-specific probes, PP and PP3′, recognized all
Leishmania
species examined, while the species-specific probes were able to distinguish between all the Old World
Leishmania
species. Titrations using purified parasite DNA showed that the RLB is 10- to 100-fold more sensitive than ITS1 PCR and can detect <0.1 pg DNA. The RLB was compared to kinetoplast DNA (kDNA) and ITS1 PCR by using 67 samples from suspected cutaneous leishmaniasis (CL) patients in Israel and the West Bank. The RLB accurately identified 58/59 confirmed positive samples as CL, a result similar to that found by kDNA PCR (59/59) and better than that by ITS1 PCR (50/59). The positive predictive value and negative predictive value of the RLB were 95.1% and 83.3%, respectively.
L. major
or
L. tropica
was identified by the RLB in 55 of the confirmed positive cases, a level of accuracy better than that of ITS1 PCR with restriction fragment length polymorphism (42/59). Thus, RLB can be used to diagnose and characterize Old World CL.
Comparative Study of Nasopharyngeal Aspirate and Nasal Swab Specimens for Diagnosis of Acute Viral Respiratory Infection
Authors: Sung Rita Y. T. , Chan Paul K. S. , Choi Kai C. , Yeung Apple C. M. , Li Albert M. , Tang Julian W. , Ip Margaret , Tsen Tracy , Nelson E. Anthony S. 
Published: July 2008

ABSTRACT
Paired nasopharyngeal aspirate (NPA) and nasal swab (NS) samples from 475 children hospitalized for acute respiratory infection were studied for the detection of influenza virus, parainfluenza virus, respiratory syncytial virus, and adenovirus by immunofluorescence test, viral culture, and multiplex PCR assay. The overall sensitivity of viral detection with NPA specimens was higher than that obtained with NS specimens.
The NY-1 Hantavirus Gn Cytoplasmic Tail Coprecipitates TRAF3 and Inhibits Cellular Interferon Responses by Disrupting TBK1-TRAF3 Complex Formation
Authors: Alff Peter J. , Sen Nandini , Gorbunova Elena , Gavrilovskaya Irina N. , Mackow Erich R. 
Published: July 2008

ABSTRACT
Pathogenic hantaviruses replicate within human endothelial cells and cause two diseases, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. In order to replicate in endothelial cells pathogenic hantaviruses inhibit the early induction of beta interferon (IFN-β). Expression of the cytoplasmic tail of the pathogenic NY-1 hantavirus Gn protein is sufficient to inhibit RIG-I- and TBK1-directed IFN responses. The formation of TBK1-TRAF3 complexes directs IRF-3 phosphorylation, and both IRF-3 and NF-κB activation are required for transcription from the IFN-β promoter. Here we report that the NY-1 virus (NY-1V) Gn tail inhibits both TBK1-directed NF-κB activation and TBK1-directed transcription from promoters containing IFN-stimulated response elements. The NY-1V Gn tail coprecipitated TRAF3 from cellular lysates, and analysis of TRAF3 deletion mutants demonstrated that the TRAF3 N terminus is sufficient for interacting with the NY-1V Gn tail. In contrast, the Gn tail of the nonpathogenic hantavirus Prospect Hill virus (PHV) failed to coprecipitate TRAF3 or inhibit NF-κB or IFN-β transcriptional responses. Further, expression of the NY-1V Gn tail blocked TBK1 coprecipitation of TRAF3 and infection by NY-1V, but not PHV, blocked the formation of TBK1-TRAF3 complexes. These findings indicate that the NY-1V Gn cytoplasmic tail forms a complex with TRAF3 which disrupts the formation of TBK1-TRAF3 complexes and downstream signaling responses required for IFN-β transcription.
Natural Killer Cells Regulate T-Cell Proliferation during Human Parainfluenza Virus Type 3 Infection
Authors: Noone Cariosa M. , Paget Elaine , Lewis Ellen A. , Loetscher Marius R. , Newman Robert W. , Johnson Patricia A. 
Published: July 2008

ABSTRACT
Human parainfluenza virus type 3 (HPIV3) is a major respiratory pathogen in humans. Failure to induce immunological memory associated with HPIV3 infection has been attributed to inhibition of lymphocyte proliferation. We demonstrate that the inability of mixed lymphocytes to respond to virally infected antigen-presenting cells is due to an interleukin-2-dependent, nonapoptotic mechanism involving natural killer (NK) cells and their influence is exerted in a contact-dependent manner. These results suggest a novel regulatory mechanism for NK cells during HPIV3 infection, offering an explanation for viral persistence and poor memory responses.
Heparan Sulfate-Binding Foot-and-Mouth Disease Virus Enters Cells via Caveola-Mediated Endocytosis
Authors: O'Donnell Vivian , LaRocco Michael , Baxt Barry 
Published: July 2008

ABSTRACT

Foot-and-mouth disease virus (FMDV) utilizes different cell surface macromolecules to facilitate infection of cultured cells. Virus, which is virulent for susceptible animals, infects cells via four members of the α
V
subclass of cellular integrins. In contrast, tissue culture adaptation of some FMDV serotypes results in the loss of viral virulence in the animal, accompanied by the loss of virus' ability to use integrins as receptors. These avirulent viral variants acquire positively charged amino acids on surface-exposed structural proteins, resulting in the utilization of cell surface heparan sulfate (HS) molecules as receptors. We have recently shown that FMDV serotypes utilizing integrin receptors enter cells via a clathrin-mediated mechanism into early endosomes. Acidification within the endosome results in a breakdown of the viral capsid, releasing the RNA, which enters the cytoplasm by a still undefined mechanism. Since there is evidence that HS internalizes bound ligands via a caveola-mediated mechanism, it was of interest to analyze the entry of FMDV by cell-surface HS. Using a genetically engineered variant of type O
1
Campos (O
1
C3056R) which can utilize both integrins and HS as receptors and a second variant (O
1
C3056R-KGE) which can utilize only HS as a receptor, we followed viral entry using confocal microscopy. After virus bound to cells at 4°C, followed by a temperature shift to 37°C, type O
1
C3056R-KGE colocalized with caveolin-1, while O
1
C3056R colocalized with both clathrin and caveolin-1. Compounds which either disrupt or inhibit the formation of lipid rafts inhibited the replication of O
1
C3056R-KGE. Furthermore, a caveolin-1 knockdown by RNA interference also considerably reduced the efficiency of O
1
C3056R-KGE infection. These results indicate that HS-binding FMDV enters the cells via the caveola-mediated endocytosis pathway and that caveolae can associate and traffic with endosomes. In addition, these results further suggest that the route of FMDV entry into cells is a function solely of the viral receptor.
Epstein-Barr Virus BART MicroRNAs Are Produced from a Large Intron prior to Splicing
Authors: Edwards Rachel Hood , Marquitz Aron R. , Raab-Traub Nancy 
Published: July 2008

ABSTRACT
Latent Epstein-Barr virus (EBV) infection is associated with several lymphoproliferative disorders, including posttransplant lymphoma, Hodgkin's disease, and Burkitt's lymphoma, as well as nasopharyngeal carcinoma (NPC). Twenty-nine microRNAs (miRNAs) have been identified that are transcribed during latent infection from three clusters in the EBV genome. Two of the three clusters of miRNAs are made from the BamHI A rightward transcripts (BARTs), a set of alternatively spliced transcripts that are highly abundant in NPC but have not been shown to produce a detectable protein. This study indicates that while the BART miRNAs are located in the first four introns of the transcripts, processing of the pre-miRNAs from the primary transcript occurs prior to completion of the splicing reaction. Additionally, production of the BART miRNAs correlates with accumulation of a spliced mRNA in which exon 1 is joined directly to exon 3, suggesting that this form of the transcript may favor production of miRNAs. Sequence variations and processing of pre-miRNAs to the mature form also may account for various differences in miRNA abundance. Importantly, residual intronic pieces that result from processing of the pre-miRNAs were detected in the nucleus. The predicted structures of these pieces suggest there is a bias or temporal pattern to the production of the individual pre-miRNAs. These findings indicate that multiple factors contribute to the production of the BART miRNAs and to the apparent differences in abundance between the individual miRNAs of the cluster.