bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mannose-Binding Lectin Deficiency Facilitates AbdominalCandidaInfections in Patients with Secondary Peritonitis
Authors: van Till J. W. Olivier , Modderman Piet W. , de Boer Martin , Hart Margreet H. L. , Beld Marcel G. H. M. , Boermeester Marja A. 
Published: November 2007

ABSTRACTMannose-binding lectin (MBL) deficiency due to variations in the MBL gene is associated with increased susceptibility to infections. In this study, the association between MBL deficiency and the occurrence of abdominal yeast infection (AYI) in peritonitis patients was examined. Eighty-eight patients with secondary peritonitis requiring emergency laparotomy were included. MBL genotype (wild type [WT] versus patients with variant genotypes), MBL plasma concentrations, andCandidarisk factors were examined in patients with and those without AYI (positive abdominal yeast cultures during [re]laparotomy). A variant MBL genotype was found in 53% of patients with AYI and 38% of those without AYI (P= 0.18). A significantly higher proportion of variant patients had an AYI during early peritonitis (during first laparotomy) than WT patients (39% versus 16%, respectively;P= 0.012). Patients with AYI had lower MBL levels than did patients without AYI (0.16 μg/ml [0.0 to 0.65 μg/ml] versus 0.65 μg/ml (0.19 to 1.95 μg/ml);P= 0.007). Intensity of colonization (odds ratio [OR], 1.1; 95% confidence interval [CI], 1.0 to 1.1), MBL plasma concentrations of <0.5 μg/ml (OR, 4.5; 95% CI, 1.2 to 16.3), and numbers of relaparotomies (OR, 1.7; 95% CI, 1.0 to 2.8) were independently associated with AYI. In summary, deficient MBL plasma levels were independently associated with the development of AYI in patients with secondary peritonitis and seemed to facilitate early infection.
Overlapping Population Structures of Nasal Isolates of
Staphylococcus aureus
from Healthy Dutch and American Individuals
Authors: Melles Damian C. , Tenover Fred C. , Kuehnert Matthew J. , Witsenboer Hanneke , Peeters Justine K. , Verbrugh Henri A. , van Belkum Alex 
Published: November 2007

ABSTRACT

To understand
Staphylococcus aureus
nasal carriage and its relationship with subsequent disease, insight into the natural (nonclinical) bacterial population structure is essential. This study investigated whether the distributions of
S. aureus
genotypes that cause colonization differ by geographic locales. High-throughput amplified fragment length polymorphism (AFLP) analysis was performed on nasal isolates of
S. aureus
from healthy American (
n
= 391) and Dutch (
n
= 829) volunteers. In total, 164,970 binary outcomes, covering 135 different markers per isolate, were scored. Methicillin resistance was defined for all strains; pulsed-field gel electrophoresis typing was performed for the American isolates. The overall population structures of the American and Dutch
S. aureus
isolates were comparable. The same four major AFLP clusters (I to IV) and subclusters were identified for both collections. However, the Dutch methicillin-susceptible
S. aureus
(MSSA) isolates were overrepresented in AFLP cluster III (
P
= 0.0016). Furthermore, the majority of the American methicillin-resistant
S. aureus
isolates (90.5%) were located in AFLP cluster I (
P
< 0.0001). This result identifies differences in the local prevalence of certain
S. aureus
genotypes. AFLP clusters II and III, which represent multilocus sequence typing clonal complexes 30 and 45, respectively, account for 46.4% of all MSSA isolates in the study, suggesting that these two lineages have evolved as extremely successful pandemic colonizers of humans. In conclusion, the overall population structures of American and Dutch nasal carriage isolates of
S. aureus
are surprisingly similar, despite subtle geographic differences in the prevalence of certain
S. aureus
genotypes.
fimA
Genotypes and Multilocus Sequence Types of
Porphyromonas gingivalis
from Patients with Periodontitis
Authors: Enersen Morten , Olsen Ingar , Kvalheim Øyvind , Caugant Dominique A. 
Published: November 2007

ABSTRACT

Fimbriae are important virulence factors of pathogenic bacteria, facilitating their attachment to host and bacterial cells. In the periodontal pathogen
Porphyromonas gingivalis
, the
fimA
gene is classified into six types (genotypes I, Ib, II, III, IV, and V) on the basis of different nucleotide sequences, with
fimA
genotypes II and IV being prevalent in isolates from patients with periodontitis. The aims of this study were to examine the distribution of
fimA
genotypes in a collection of 82
P. gingivalis
isolates from adult periodontitis patients of worldwide origin and to investigate the relationship between the
fimA
genotypes and the sequence types (STs), as determined by multilocus sequence typing (MLST), of the isolates. The
fimA
gene was amplified by PCR with primer sets specific for each genotype. The STs of all strains were assigned according to the MLST database for
P. gingivalis
(
www.pubmlst.org/pgingivalis
). The 82 strains showed extensive genetic diversity and were assigned to 69 STs. Only isolates with closely related STs harbored the same
fimA
genotype. Twenty-eight (34.1%) strains harbored
fimA
genotype II, while only the reference strain for
fimA
genotype V reacted with the primers specific for this genotype. Twenty-one isolates (25.6%) were positive by more than one of the
fimA
PCR assays; the most frequent combinations were genotypes I, Ib, and II (eight isolates) and genotypes I and II (four isolates). Sequencing of the
fimA
gene from selected isolates did not support the observed specific
fimA
genotype combinations, suggesting that the genotyping method used for the major fimbriae in
P. gingivalis
should be reevaluated.
Prospective Identification of Enteroviruses Involved in Meningitis in 2006 through Direct Genotyping in Cerebrospinal Fluid
Authors: Mirand Audrey , Henquell Cécile , Archimbaud Christine , Chambon Martine , Charbonne Françoise , Peigue-Lafeuille Hélène , Bailly Jean-Luc 
Published: November 2007

ABSTRACT

Enterovirus infections were investigated with special emphasis on performing rapid molecular identification of enterovirus serotypes responsible for aseptic meningitis directly in cerebrospinal fluid (CSF). Enterovirus genotyping was carried out directly with specimens tested for the diagnostic procedure, using two seminested PCR assays designed to amplify the complete and partial gene sequences encoding the VP1 and VP4/VP2 capsid proteins, respectively. The method was used for identifying the enterovirus serotypes involved in meningitis in 45 patients admitted in 2005. Enterovirus genotyping was achieved in 98% of the patients studied, and we obtained evidence of 10 of the most frequent serotypes identified earlier by genotyping of virus isolates. The method was applied for the prospective investigation of 54 patients with meningitis admitted consecutively in 2006. The enterovirus serotypes involved were identified with the cerebrospinal fluid (CSF) of 52 patients (96%) and comprised 13 serotypes within the human enterovirus B species and 1 within the human enterovirus A species. The three most common serotypes were echovirus 13 (E13; 24%), E6 (23%), and coxsackievirus B5 (11.5%), a pattern different from that observed in 2005. Genotyping of virus isolates was also performed in 35 patients in 2006 (meningitis,
n
= 31; other diseases,
n
= 4). By comparison, direct genotyping in CSF yielded a more complete pattern of enterovirus serotypes, thereby allowing the detection of rare serotypes: three less common serotypes (CB2, E21, and E27) were not detected by indirect genotyping alone. The study shows the feasibility of prospective enterovirus genotyping within 1 week in a laboratory setting.
Comparison of the Human Immunodeficiency Virus (HIV) Type 1-Specific Immunoglobulin G Capture Enzyme-Linked Immunosorbent Assay and the Avidity Index Method for Identification of Recent HIV Infections
Authors: Loschen Stephan , Bätzing-Feigenbaum Jörg , Poggensee Gabriele , Cordes Christiane , Hintsche Bettina , Rausch Michael , Dupke Stephan , Gohlke-Micknis Silvia , Rödig Jana , Hamouda Osamah , Kücherer Claudia 
Published: November 2007

ABSTRACT

The sensitivity and specificity of the human immunodeficiency virus (HIV) type 1-specific immunoglobulin G capture enzyme-linked immunosorbent assay (BED-CEIA) were compared with those of the avidity index method to identify recent HIV infection using a panel of 148 samples (81 patients) representing durations of infection ranging from 0 to 222 weeks. The results from the two tests were similar (sensitivity of 80% versus 74% [
P
= 0.53]; specificity of 86% versus 82% [
P
= 0.67]).
Evidence from Multiplex Molecular Assays for Complex Multipathogen Interactions in Acute Respiratory Infections
Authors: Brunstein John D. , Cline Christy L. , McKinney Steven , Thomas Eva 
Published: November 2007

ABSTRACTWhile most diagnostic processes cease with the detection of the first relevant infectious agent, newer multiplexed molecular methods which provide simultaneous analysis of multiple agents may give a more accurate representation of the true pathogen spectrum in these samples. To examine this in the context of respiratory infections, acute-phase respiratory specimens submitted to our clinical diagnostic microbiology/virology laboratory for our routine VIRAP diagnosis protocol during the spring 2006 peak respiratory infection season were processed in parallel by analysis with Genaco (QiaPlex) ResPlex I and ResPlex II molecular diagnostic panels. A total of 1,742 specimens were examined for 21 relevant targets each. The resulting data reveal that multiple infections are frequent and provide evidence for complex interactions between different infectious agents. Statistically relevant association patterns (both positive and negative) were observed between particular pathogens. While some interactions we observed are substantiated by prior reports in the literature, several specific patterns do not appear to have been reported previously. In addition, we report preliminary clinical evidence which supports a hypothesis that these coinfections are medically relevant and that effective treatment for severe respiratory tract infections will increasingly require diagnosis of all involved pathogens, as opposed to single-pathogen reporting.
Evaluation of a Commercialized In Situ Hybridization Assay for Detecting Human Papillomavirus DNA in Tissue Specimens from Patients with Cervical Intraepithelial Neoplasia and Cervical Carcinoma
Authors: Guo Ming , Gong Yun , Deavers Michael , Silva Elvio G. , Jan Yee Jee , Cogdell David E. , Luthra Rajyalashmi , Lin E. , Lai Hung Cheng , Zhang Wei , Sneige Nour 
Published: November 2007

ABSTRACT

To evaluate a commercialized in situ hybridization (ISH) assay for detecting human papillomavirus (HPV) DNA, we compared the ability of a new ISH probe, Inform HPV III (Ventana Medical Systems, Tucson, AZ), to that of PCR assays to detect HPV DNA in cervical tissue specimens with normal cervix (20 cases), cervical intraepithelial neoplasia (CIN; CIN 1, 27 cases; CIN 2, 28 cases; and CIN 3, 33 cases), and cervical carcinoma (29 cases). General HPV DNA was detected using consensus primer-mediated PCR assays. HPV genotyping was performed by using EasyChip HPV blot (King Car Yuan Shan Institute, I-Lan, Taiwan). HPV16 integration status (E2/E6 ratio) was determined by using quantitative real-time PCR. Our findings showed that the ISH and PCR had fair to good agreements in detecting HPV DNA across all CIN categories without significant differences (Kappa coefficient, 0.34 to 0.63;
P
= 0.13 to 1.0). However, ISH detected significantly fewer HPV-positive cases in carcinoma than PCR did (Kappa coefficient, 0.2;
P
= 0.03). Eleven cases with ISH
−
PCR
+
results had HPV types that can be detected by Inform HPV III. Five carcinoma cases with ISH
−
PCR
+
results showed a significantly higher level of integrated HPV16 (
P
= 0.008) than did the ISH
+
cases. As a consequence, lower copy numbers of episomal HPV16 in carcinoma might be the cause for the false-negative ISH results. Although the punctate signal pattern of HPV significantly increased with the severity of disease (
P
trend = 0.01), no significant difference in the HPV16 integration status was observed between the cases with a punctate signal only and the cases with mixed punctate and diffuse signals (
P
= 0.4). In conclusion, ISH using the Inform HPV III probe seems comparable to PCR for detecting HPV DNA in cervical tissue with CINs. False-negative ISH results appear to be associated with the lower copy numbers of the episomal HPV16 but not with the ability of the Inform HPV III probe to detect specific HPV types. In addition, signal patterns, especially a mixed punctate and diffuse pattern of HPV, cannot be reliably used to predict viral integration status.
Rapid Diagnosis of Human Brucellosis by Quantitative Real-Time PCR: a Case Report of Brucellar Spondylitis
Authors: Navarro-Martínez Amalia , Navarro Elena , Castaño Maria Jesús , Solera Javier 
Published: November 2007

ABSTRACTBlood samples and a bone biopsy specimen from one patient diagnosed with spondylodiscitis of unknown etiology were analyzed by quantitative real-time PCR to detectBrucella melitensis. The high sensitivity and specificity of this assay allowed the diagnosis of brucellar spondylitis within 24 h, a result that we were unable to obtain through the use of conventional methods.
Specimen Dilution Improves Sensitivity of the Amplified
Mycobacterium tuberculosis
Direct Test for Smear Microscopy-Positive Respiratory Specimens
Authors: Guerra Renata L. , Baker James F. , Alborz Roya , Armstrong Derek T. , Kiehlbauch Julia A. , Conde Marcus B. , Dorman Susan E. , Hooper Nancy M. 
Published: November 2007

ABSTRACT

Specimen dilution has been proposed as a strategy to minimize amplified
Mycobacterium tuberculosis
direct (MTD) test inhibition (N. Pollock, J. Westerling, and A. Sloutsky, Am. J. Clin. Pathol. 126:142-147, 2006; A. Sloutsky, L. L. Han, and B. G. Werner, J. Clin. Microbiol. 42:1547-1551, 2004). We evaluated the impact of respiratory specimen dilution on MTD test accuracy in a public health laboratory. The difference in MTD test sensitivity between the dilution and conventional methods was 15.9% (
P
= 0.001) for smear microscopy-positive specimens and −3.6% (
P
= 0.38) for smear microscopy-negative specimens.
Multicenter Evaluation of the
Candida albicans
/
Candida glabrata
Peptide Nucleic Acid Fluorescent In Situ Hybridization Method for Simultaneous Dual-Color Identification of
C. albicans
and
C. glabrata
Directly from Blood Culture Bottles
Authors: Shepard Janeen R. , Addison Rachel M. , Alexander Barbara D. , Della-Latta Phyllis , Gherna Michael , Haase Gerhard , Hall Gerri , Johnson Jennifer K. , Merz William G. , Peltroche-Llacsahuanga Heidrun , Stender Henrik , Venezia Richard A. , Wilson Deborah , Procop Gary W. , Wu Fann , Fiandaca Mark J. 
Published: November 2007

ABSTRACT

We evaluated the performance of the
Candida albicans
/
Candida glabrata
peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method, a rapid two-color assay for detection of
C. albicans
and
C. glabrata
, in a multicenter study. The assay is designed for use directly from positive blood culture bottles in a FISH format. Intact, fixed cells are labeled fluorescent green (
C. albicans
) or fluorescent red (
C. glabrata
) by rRNA hybridization of fluorophore-labeled PNA probes. Results are available <3 h after cultures signal positive. An evaluation of 197 routine blood culture bottles newly positive for yeast by Gram staining was performed at five hospitals. The sensitivities of detection for
C. albicans
, and
C. glabrata
were 98.7% (78/79) and 100% (37/37), respectively, and the specificity for both components of the assay was 100% (82/82). The assay was also evaluated with 70 fungal reference strains and was challenged in the BacT/ALERT microbiological detection system with spiked blood culture bottles. These results support the use of the assay for rapid, simultaneous identification of
C. albicans
and
C. glabrata
in positive blood culture bottles. This rapid assay may aid in the selection of initial antifungal drugs, leading to improved patient outcomes.
Emergence of Fluoroquinolone-Resistant
Haemophilus influenzae
Strains among Elderly Patients but Not among Children
Authors: Yokota Shin-ichi , Ohkoshi Yasuo , Sato Kiyoshi , Fujii Nobuhiro 
Published: November 2007

ABSTRACT

We screened 457
Haemophilus influenzae
strains isolated in Japan during 2002 to 2004 and identified 12 fluoroquinolone-resistant strains (2.6%). The resistant strains were divided into three genotypes (eight, three, and one of each type). These were isolated from patients over 58 years of age. Several fluoroquinolone-resistant clones appeared to have invaded the population of elderly patients in a particular area, Sapporo city.
High Rate of Human Bocavirus and Adenovirus Coinfection in Hospitalized Israeli Children
Authors: Hindiyeh Musa Y. , Keller Nathan , Mandelboim Michal , Ram Daniela , Rubinov Jana , Regev Liora , Levy Virginia , Orzitzer Sara , Shaharabani Hilda , Azar Roberto , Mendelson Ella , Grossman Zehava 
Published: November 2007

ABSTRACT
We investigated coinfection of human bocavirus (HBoV) and other respiratory viruses in hospitalized children by real-time PCR. A high rate (69.2%) of adenovirus infection was found among children infected with HBoV. Such high rates of HboV-adenovirus coinfection have not been previously reported, underscoring the need to investigate the contribution of HBoV in patient clinical presentations.
Human Immunodeficiency Virus Type 1 Vif Functionally Interacts with Diverse APOBEC3 Cytidine Deaminases and Moves with Them between Cytoplasmic Sites of mRNA Metabolism
Authors: Marin Mariana , Golem Sheetal , Rose Kristine M. , Kozak Susan L. , Kabat David 
Published: November 2007

ABSTRACT

Vif
IIIB
, which has been a standard model for the viral infectivity factor of human immunodeficiency virus type 1 (HIV-1), binds the cytidine deaminase APOBEC3G (A3G) and induces its degradation, thereby precluding its lethal incorporation into assembling virions. Additionally, Vif
IIIB
less efficiently degrades A3F, another potent anti-HIV-1 cytidine deaminase. Although the APOBEC3 paralogs A3A, A3B, and A3C have weaker anti-HIV-1 activities and are only partially degraded by Vif
IIIB
, we found that Vif
IIIB
induces their emigration from the nucleus to the cytosol and thereby causes net increases in the cytosolic concentrations and anti-HIV-1 activities of A3A and A3B. In contrast, some other Vifs, exemplified by Vif
HXB2
and Vif
ELI-1
, much more efficiently degrade and thereby neutralize all APOBEC3s. Studies focused mainly on A3F imply that it occurs associated with mRNA-PABP1 in translationally active polysomes and to a lesser extent in mRNA processing bodies (P-bodies). A3F appears to stabilize the P-bodies with which it is associated. A correspondingly small proportion of Vif
IIIB
also localizes in P-bodies in an A3F-dependent manner. Stress causes A3A, A3B, A3C, and A3F to colocalize efficiently with Vif
IIIB
and mRNA-PABP1 complexes in stress granules in a manner that is prevented by cycloheximide, an inhibitor of translational elongation. Coimmunoprecipitation studies suggest that Vifs from different HIV-1 isolates associate with all tested APOBEC3s. Thus, Vifs interact closely with structurally diverse APOBEC3s, with effects on their subcellular localization, degradation rates, and antiviral activities. Cytosolic APOBEC3-Vif complexes are predominantly bound to mRNAs that dynamically move between translationally active and storage or processing pools.
Establishment and Maintenance of the Innate Antiviral Response to West Nile Virus Involves both RIG-I and MDA5 Signaling through IPS-1
Authors: Fredericksen Brenda L. , Keller Brian C. , Fornek Jamie , Katze Michael G. , Gale Michael 
Published: November 2007

ABSTRACTRIG-I and MDA5, two related pathogen recognition receptors (PRRs), are known to be required for sensing various RNA viruses. Here we investigated the roles that RIG-I and MDA5 play in eliciting the antiviral response to West Nile virus (WNV). Functional genomics analysis of WNV-infected fibroblasts from wild-type mice and RIG-I null mice revealed that the normal antiviral response to this virus occurs in two distinct waves. The initial response to WNV resulted in the expression of interferon (IFN) regulatory factor 3 target genes and IFN-stimulated genes, including several subtypes of alpha IFN. Subsequently, a second phase of IFN-dependent antiviral gene expression occurred very late in infection. In cells lacking RIG-I, both the initial and the secondary responses to WNV were delayed, indicating that RIG-I plays a critical role in initiating innate immunity against WNV. However, another PRR(s) was able to trigger a response to WNV in the absence of RIG-I. Disruption of both MDA5 and RIG-I pathways abrogated activation of the antiviral response to WNV, suggesting that MDA5 is involved in the host's defense against WNV infection. In addition, ablation of the function of IPS-1, an essential RIG-I and MDA5 adaptor molecule, completely disabled the innate antiviral response to WNV. Our data indicate that RIG-I and MDA5 are responsible for triggering downstream gene expression in response to WNV infection by signaling through IPS-1. We propose a model in which RIG-I and MDA5 operate cooperatively to establish an antiviral state and mediate an IFN amplification loop that supports immune effector gene expression during WNV infection.
Broad Antiretroviral Activity and Resistance Profile of the Novel Human Immunodeficiency Virus Integrase Inhibitor Elvitegravir (JTK-303/GS-9137)
Authors: Shimura Kazuya , Kodama Eiichi , Sakagami Yasuko , Matsuzaki Yuji , Watanabe Wataru , Yamataka Kazunobu , Watanabe Yasuo , Ohata Yoshitsugu , Doi Satoki , Sato Motohide , Kano Mitsuki , Ikeda Satoru , Matsuoka Masao 
Published: November 2007

ABSTRACTIntegrase (IN), an essential enzyme of human immunodeficiency virus (HIV), is an attractive antiretroviral drug target. The antiviral activity and resistance profile in vitro of a novel IN inhibitor, elvitegravir (EVG) (also known as JTK-303/GS-9137), currently being developed for the treatment of HIV-1 infection are described. EVG blocked the integration of HIV-1 cDNA through the inhibition of DNA strand transfer. EVG inhibited the replication of HIV-1, including various subtypes and multiple-drug-resistant clinical isolates, and HIV-2 strains with a 50% effective concentration in the subnanomolar to nanomolar range. EVG-resistant variants were selected in two independent inductions, and a total of 8 amino acid substitutions in the catalytic core domain of IN were observed. Among the observed IN mutations, T66I and E92Q substitutions mainly contributed to EVG resistance. These two primary resistance mutations are located in the active site, and other secondary mutations identified are proximal to these primary mutations. The EVG-selected IN mutations, some of which represent novel IN inhibitor resistance mutations, conferred reduced susceptibility to other IN inhibitors, suggesting that a common mechanism is involved in resistance and potential cross-resistance. The replication capacity of EVG-resistant variants was significantly reduced relative to both wild-type virus and other IN inhibitor-resistant variants selected by L-870,810. EVG and L-870,810 both inhibited the replication of murine leukemia virus and simian immunodeficiency virus, suggesting that IN inhibitors bind to a conformationally conserved region of various retroviral IN enzymes and are an ideal drug for a range of retroviral infections.