bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral and Airway Microbiota in HIV-Infected Pneumonia Patients
Authors: Iwai Shoko , Fei Matthew , Huang Delphine , Fong Serena , Subramanian Anuradha , Grieco Katherine , Lynch Susan V. , Huang Laurence 
Published: July 2012

ABSTRACT

Despite the increased frequency of recurrent pneumonia in HIV-infected patients and recent studies linking the airway bacterial community (microbiota) to acute and chronic respiratory infection, little is known of the oral and airway microbiota that exist in these individuals and their propensity to harbor pathogens despite antimicrobial treatment for acute pneumonia. This pilot study compared paired samples of the oral and airway microbiota from 15 hospitalized HIV-infected patients receiving antimicrobial treatment for acute pneumonia. Total DNA was extracted, bacterial burden was assessed by quantitative PCR, and amplified 16S rRNA was profiled for microbiome composition using a phylogenetic microarray (16S rRNA PhyloChip). Though the bacterial burden of the airway was significantly lower than that of the oral cavity, microbiota in both niches were comparably diverse. However, oral and airway microbiota exhibited niche specificity. Oral microbiota were characterized by significantly increased relative abundance of multiple species associated with the mouth, including members of the
Bacteroides
,
Firmicutes
, and TM7 phyla, while airway microbiota were primarily characterized by a relative expansion of the
Proteobacteria
. Twenty-two taxa were detected in both niches, including
Streptococcus bovis
and
Chryseobacterium
species, pathogens associated with HIV-infected populations. In addition, we compared the airway microbiota of five of these patients to those of five non-HIV-infected pneumonia patients from a previous study. Compared to the control population, HIV-infected patients exhibited relative increased abundance of a large number of phylogenetically distinct taxa, which included several known or suspected pathogenic organisms, suggesting that recurrent pneumonia in HIV-infected populations may be related to the presence of these species.
Emergence of High-Level Mupirocin Resistance in Coagulase-Negative Staphylococci Associated with Increased Short-Term Mupirocin Use
Authors: Bathoorn Erik , Hetem David J. , Alphenaar Jeriela , Kusters Johannes G. , Bonten Marc J. M. 
Published: July 2012

ABSTRACT

In our hospital, mupirocin has increasingly been used for peri-operative decolonization of
Staphylococcus aureus
. The target for mupirocin is isoleucyl tRNA synthetase (
ileS
). High-level resistance to mupirocin is conferred by acquisition of plasmids expressing a distinct
ileS
gene (
ileS2
). Here we evaluated the longitudinal trends in high-level mupirocin resistance in coagulase-negative staphylococci (CoNS) and linked this to the presence of
ileS2
genes and mupirocin use. We assessed mupirocin resistance in CoNS bloodstream isolates from 2006 to 2011 tested by Phoenix automated testing (PAT). We evaluated the reliability of PAT results using Etest. PAT species determination was confirmed by MALDI-TOF (matrix-assisted laser desorption ionization–time of flight) mass spectrometry. We investigated the presence of
ileS2
in the first 100 consecutive CoNS bloodstream isolates of each year using RT-PCR. Mupirocin use increased from 3.6 kg/year in 2006 to 13.3 kg/year in 2010 and correlated with the increase in the percentage of CoNS isolates carrying
ileS2
(8% in 2006 to 22% in 2011; Spearman's rho, 0.137;
P
= 0.01). The sensitivity and specificity of PAT for detecting high-level mupirocin resistance were 0.97 and 0.97, respectively.
ileS2
was detected in 81 of 82 phenotypically highly mupirocin-resistant strains and associated with resistance to ciprofloxacin, erythromycin, and clindamycin. In conclusion, we found a rapid increase in high-level resistance to mupirocin and resistance to other antibiotics in CoNS associated with an increase in mupirocin use. The associated resistance to other antibiotics may result in a reduction of oral antibiotic options for prolonged treatment of prosthetic infections with CoNS.
Evaluation of Two Novel Rapid rKE16 Antigen-Based Tests for Diagnosis of Visceral Leishmaniasis in India
Authors: Vaish Manisha , Sharma Smriti , Chakravarty Jaya , Sundar Shyam 
Published: July 2012

ABSTRACTWe compared the two formats of rKE16 antigen-based rapid tests, a flowthrough test (KEFT) and a lateral flow test (KELF), with the rK39 rapid test for the diagnosis of visceral leishmaniasis. Sensitivities with KEFT (99%, 198/200) and rK39 (99.5%, 199/200) were comparable and higher than that with KELF (95.5%, 191/200). In the control groups comprising subjects with diseases from areas of nonendemicity or endemicity and subjects with different diseases, the specificities were comparable for all three rapid tests, except that specificity was higher with KELF in the controls from areas of endemicity.
Molecular Typing of Mycobacterium abscessus Based on Tandem-Repeat Polymorphism
Authors: Wong Y. L. , Ong C. S. , Ngeow Y. F. 
Published: July 2012

ABSTRACT

A variable-number tandem-repeat (VNTR) typing assay for the differentiation of
Mycobacterium abscessus
strains was developed. This assay showed complete reproducibility, locus stability, and a discriminatory power (Hunter-Gaston discriminatory index [HGDI] of 0.9563) that is superior to that of multilocus sequencing. It is a promising tool for the investigation of
Mycobacterium abscessus
epidemiology and nosocomial outbreaks.
Multiple Lung Abscesses Caused by Actinomyces graevenitzii Mimicking Acute Pulmonary Coccidioidomycosis
Authors: Nagaoka Kentaro , Izumikawa Koichi , Yamamoto Yoshihiro , Yanagihara Katsunori , Ohkusu Kiyofumi , Kohno Shigeru 
Published: July 2012

ABSTRACT

Actinomyces graevenitzii
is a newly recognized
Actinomyces
species that is seldom isolated from clinical specimens. A case of multiple pulmonary abscesses mimicking acute pulmonary coccidioidomycosis is described in this study, and the findings indicate that this organism is an opportunistic human pathogen.
Streptococcus tigurinus, a Novel Member of the Streptococcus mitis Group, Causes Invasive Infections
Authors: Zbinden Andrea , Mueller Nicolas J. , Tarr Philip E. , Eich Gerhard , Schulthess Bettina , Bahlmann Anna S. , Keller Peter M. , Bloemberg Guido V. 
Published: July 2012

ABSTRACTWe recently described the novel speciesStreptococcus tigurinussp. nov. belonging to theStreptococcus mitisgroup. The type strain AZ_3aTofS. tigurinuswas originally isolated from a patient with infective endocarditis. According to its phenotypic and molecular characteristics,S. tigurinusis most closely related toStreptococcus mitis,Streptococcus pneumoniae,Streptococcus pseudopneumoniae,Streptococcus oralis, andStreptococcus infantis. Accurate identification ofS. tigurinusis facilitated by 16S rRNA gene analysis. We retrospectively analyzed our 16S rRNA gene molecular database, which contains sequences of all clinical samples obtained in our institute since 2003. We detected 17 16S rRNA gene sequences which were assigned toS. tigurinus, including sequences from the 3S. tigurinusstrains described previously.S. tigurinusoriginated from normally sterile body sites, such as blood, cerebrospinal fluid, or heart valves, of 14 patients and was initially detected by culture or broad-range 16S rRNA gene PCR, followed by sequencing. The 14 patients had serious invasive infections, i.e., infective endocarditis (n= 6), spondylodiscitis (n= 3), bacteremia (n= 2), meningitis (n= 1), prosthetic joint infection (n= 1), and thoracic empyema (n= 1). To evaluate the presence ofStreptococcus tigurinusin the endogenous oral microbial flora, we screened saliva specimens of 31 volunteers. After selective growth, alpha-hemolytic growing colonies were analyzed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and subsequent molecular methods.S. tigurinuswas not identified among 608 strains analyzed. These data indicate thatS. tigurinusis not widely distributed in the oral cavity. In conclusion,S. tigurinusis a novel agent of invasive infections, particularly infective endocarditis.
Rapid Detection of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae
Authors: Nordmann Patrice , Dortet Laurent , Poirel Laurent 
Published: July 2012

ABSTRACT

Enterobacterial strains producing clavulanic-acid-inhibited extended-spectrum β-lactamases (ESBLs) are increasingly reported worldwide. Conventional detection of ESBL production remains time-consuming (24 to 48 h). Therefore, the ESBL NDP (Nordmann/Dortet/Poirel) test was developed for a rapid identification of ESBLs in
Enterobacteriaceae
. This biochemical test was based on the
in vitro
detection of a cephalosporin (cefotaxime) hydrolysis that is inhibited by tazobactam addition. The ESBL activity was evidenced by a color change (red to yellow) of a pH indicator (red phenol) due to carboxyl-acid formation resulting from cefotaxime hydrolysis that was reversed by addition of tazobactam (positive test). The ESBL NDP test was applied to cultured strains (215 ESBL producers and 40 ESBL nonproducers). Its sensitivity and specificity were 92.6% and 100%, respectively. Its sensitivity (100%) was excellent for detection of CTX-M producers. A few ESBL producers (
n
= 16) that remained susceptible to cefotaxime were not detected. The test was also evaluated on spiked blood cultures and showed excellent sensitivity and specificity (100% for both). The test was rapid (less than 1 h) and cost-effective. It can be implemented in any health care facility and is well adapted for infection control purposes in particular.
Catheter-Related Bacteremia Caused by Multidrug-Resistant Leclercia adecarboxylata in a Patient with Breast Cancer
Authors: Shin Gee-Wook , You Myung-Jo , Lee Hye-Soo , Lee Chang-Seop 
Published: July 2012

ABSTRACT

We report a multidrug-resistant strain of
Leclercia adecarboxylata
responsible for catheter-related bacteremia in a 47-year-old female with breast cancer. The isolated strain was resistant to several β-lactams, aminoglycosides, and folate pathway inhibitors and harbored

bla
TEM-1

and

bla
CTX-M

group 1 and
intl1
genes (
dfrA12-orfF-aadA2
) as genetic determinants for resistance. Based on a review of the
L. adecarboxylata
literature, there have been only 4 reports of antibiotic-resistant strains. To our knowledge, this is the first report of an
L. adecarboxylata
strain with simultaneous resistance to β-lactams, aminoglycosides, and sulfonamides.
Long-Term Hepatitis B Virus Surface Antigen Decay in HIV-1/Hepatitis B Virus-Coinfected Adults Initiating a Tenofovir-Containing Regimen
Authors: Tuaillon E. , Lozano C. , Kuster N. , Poinso A. , Kania D. , Nagot N. , Mondain A. M. , Pageaux G. P. , Ducos J. , Van de Perre P. , Reynes J. 
Published: July 2012

ABSTRACT

Hepatitis B virus (HBV) surface antigen (HBsAg) decay was explored in HIV-1- and HBV-coinfected patients beginning antiretroviral (ARV) therapy containing tenofovir disoproxil fumarate (TDF). The mean HBsAg decay was 0.38 log
10
IU/ml/year (95% confidence interval [CI], 0.71 to 0.05) in 18 patients with sustained plasma HIV-1 RNA suppression and 0.15 log
10
IU/ml/year (0.21 to 0.09) in 12 patients experiencing HIV-1 virologic failure due to suboptimal adherence to ARV (
P
= 0.17). We estimated that six of these 18 patients will attain HBsAg values below 10 IU/ml after 10 years of treatment.
Formic Acid-Based Direct, On-Plate Testing of Yeast and Corynebacterium Species by Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Theel Elitza S. , Schmitt Bryan H. , Hall Leslie , Cunningham Scott A. , Walchak Robert C. , Patel Robin , Wengenack Nancy L. 
Published: July 2012

ABSTRACT

An on-plate testing method using formic acid was evaluated on the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry system using 90 yeast and 78
Corynebacterium
species isolates, and 95.6 and 81.1% of yeast and 96.1 and 92.3% of
Corynebacterium
isolates were correctly identified to the genus and species levels, respectively. The on-plate method using formic acid yielded identification percentages similar to those for the conventional but more laborious tube-based extraction.
Recurrent Bacteremia Caused by the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex
Authors: Lai Chih-Cheng , Hsu Han-Lin , Tan Che-Kim , Tsai Hsih-Yeh , Cheng Aristine , Liu Chia-Ying , Huang Yu-Tsung , Liao Chun-Hsing , Sheng Wang-Huei , Hsueh Po-Ren 
Published: July 2012

ABSTRACT

This study investigated the clinical and microbiological characteristics of patients with recurrent bacteremia caused by the
Acinetobacter calcoaceticus-Acinetobacter baumannii
(ACB) complex at a medical center. All ACB complex isolates associated with recurrent bacteremia were identified to the genomic species level using a 16S-23S rRNA gene intergenic spacer sequence-based method. Genotypes were determined by the random amplified polymorphic DNA patterns generated by arbitrarily primed PCR and by pulsotypes generated by pulsed-field gel electrophoresis. Relapse of infection was defined as when the genotype of the recurrent isolate was identical to that of the original infecting strain. Reinfection was defined as when the genospecies or genotype of the recurrent isolate differed from that of the original isolate. From 2006 to 2008, 446 patients had ACB complex bacteremia and 25 (5.6%) had recurrent bacteremia caused by the ACB complex. Among the 25 patients, 12 (48%) had relapse of bacteremia caused by
A. nosocomialis
(
n
= 7) or
A. baumannii
(
n
= 5). Among the 13 patients with reinfection, 5 (38.5%) had reinfection caused by different genospecies of the ACB complex. Most of the patients were immunocompromised, and most of the infection foci were catheter-related bloodstream infections. The overall in-hospital mortality rate was 33.3%.
A. baumannii
isolates had lower antimicrobial susceptibility rates than
A. nosocomialis
and
A. pittii
isolates. In conclusion, relapse of ACB complex bacteremia can develop in immunocompromised patients, especially those with central venous catheters. Molecular methods to identify the ACB complex to the genospecies level are essential for differentiating between reinfection and relapse of bacteremia caused by the ACB complex.
Performance of the Abbott RealTime HCV Genotype II RUO Assay
Authors: Shinol Rebecca C. , Gale Howard B. , Kan Virginia L. 
Published: July 2012

ABSTRACT

The Abbott RealTime HCV Genotype II RUO (research use only) assay was evaluated using the automated Abbott RealTime
m
2000 system. Concordance was 98% (81/83 samples) with samples previously typed by the Versant HCV Genotype 2.0 RUO system with manual extraction. The total assay time was reduced from 10.5 to 6.0 h and hands-on time from 13 to 4 min/patient sample.
Evaluation of a New Molecular Test, the BD Max Cdiff, for Detection of Toxigenic Clostridium difficile in Fecal Samples
Authors: Le Guern Rémi , Herwegh Stéphanie , Grandbastien Bruno , Courcol René , Wallet Frédéric 
Published: July 2012

ABSTRACT

A new molecular assay detecting toxigenic
Clostridium difficile
, the BD Max Cdiff (Becton, Dickinson), was evaluated with 360 diarrheal feces samples. It exhibited high sensitivity (97.7%) and specificity (99.7%). The positive (97.7%) and negative (99.7%) predictive values of this test allow an accurate answer within 2 h.
Pleurostomophora ochracea, a Novel Agent of Human Eumycetoma with Yellow Grains
Authors: Mhmoud Najwa A. , Ahmed Sarah Abdalla , Fahal Ahmed H. , de Hoog G. Sybren , Gerrits van den Ende A. H. G. , van de Sande Wendy W. J. 
Published: July 2012

ABSTRACT

The first yellow-grain fungal mycetoma, in a 60-year-old man from Central Sudan, is reported. Morphological and phylogenetic analysis of the ribosomal small subunit (SSU), large subunit (LSU), internal transcribed spacer (ITS), β-tubulin (
BT2
), actin (
ACT1
), and elongation factor (
TEF1
) genes revealed that the isolate deviated from any known agent of mycetoma; it clustered in the genus
Pleurostoma
(anamorph genus,
Pleurostomophora
) in the order
Calosphaeriales
. The novel species, here named
Pleurostomophora ochracea
, is characterized by phenotypic features. The species proved to be highly susceptible to itraconazole, ketoconazole, posaconazole, and voriconazole, but not to fluconazole. The fungus was inhibited by caspofungin at 8 μg/ml, while no inhibition was found with 5-flucytosine (MIC > 64 μg/ml). Compared to other members of the genus
Pleurostomophora
,
P. ochracea
is slow growing, with a relatively high optimum growth temperature (36 to 37°C). This is the first case of a yellow-grain fungal mycetoma; yellow grains are otherwise of bacterial nature. Our case emphasizes that identification of mycetoma agents by the color of the grain only is not sufficient and may lead to inappropriate therapy.
Comparison of Four Chromogenic Culture Media for Carbapenemase-Producing Enterobacteriaceae
Authors: Wilkinson Kathryn M. , Winstanley Trevor G. , Lanyon Clare , Cummings Stephen P. , Raza Muhammad W. , Perry John D. 
Published: July 2012

ABSTRACT

Four chromogenic media for carbapenemase-producing
Enterobacteriaceae
(CPE) and two selective broths were challenged with a collection of
Enterobacteriaceae
with well-defined β-lactamases and 100 stool samples. With low inocula of 130 isolates of CPE, the sensitivities of the four chromogenic media were as follows: Brilliance CRE, 78%; chromID Carba, 91%; chromID ESBL, 96%; and Colorex KPC, 56%. The corresponding sensitivities of Trypticase soy broth plus ertapenem or meropenem were 78% and 47%, respectively.
Pangaea and the Out-of-Africa Model of Varicella-Zoster Virus Evolution and Phylogeography
Authors: Grose Charles 
Published: July 2012

ABSTRACTThe goal of this minireview is to provide an overview of varicella-zoster virus (VZV) phylogenetics and phylogeography when placed in the broad context of geologic time. Planet Earth was formed over 4 billion years ago, and the supercontinent Pangaea coalesced around 400 million years ago (mya). Based on detailed tree-building models, the base of the phylogenetic tree of theHerpesviridaefamily has been estimated at 400 mya. Subsequently, Pangaea split into Laurasia and Gondwanaland; in turn, Africa rifted from Gondwanaland. Based on available data, the hypothesis of this minireview is that the ancestral alphaherpesvirus VZV coevolved in simians, apes, and hominins in Africa. When anatomically modern humans first crossed over the Red Sea 60,000 years ago, VZV was carried along in their dorsal root ganglia. Currently, there are five VZV clades, distinguishable by single nucleotide polymorphisms. These clades likely represent continued VZV coevolution, as humans with latent VZV infection left Arabia and dispersed into Asia (clades 2 and 5) and Europe (clades 1, 3, and 4). The prototype VZV sequence contains nearly 125,000 bp, divided into 70 open reading frames. Generally, isolates within a clade display >99.9% identity to one another, while members of one clade compared to a second clade show 99.8% identity to one another. Recently, four different VZV genotypes that do not segregate into the previously defined five clades have been identified, a result indicating a wider than anticipated diversity among newly collected VZV strains around the world.
Biological Roles and Functional Mechanisms of Arenavirus Z Protein in Viral Replication
Authors: Wang Jialong , Danzy Shamika , Kumar Naveen , Ly Hinh , Liang Yuying 
Published: July 2012

ABSTRACT

Arenaviruses can cause severe hemorrhagic fever diseases in humans, with limited prophylactic or therapeutic measures. A small RING-domain viral protein Z has been shown to mediate the formation of virus-like particles and to inhibit viral RNA synthesis, although its biological roles in an infectious viral life cycle have not been directly addressed. By taking advantage of the available reverse genetics system for a model arenavirus, Pichinde virus (PICV), we provide the direct evidence for the essential biological roles of the Z protein's conserved residues, including the G2 myristylation site, the conserved C and H residues of RING domain, and the poorly characterized C-terminal L79 and P80 residues. Dicodon substitutions within the late (L) domain (
PS
A
PP
Y
EP
) of the PICV Z protein, although producing viable mutant viruses, have significantly reduced virus growth, a finding suggestive of an important role for the intact L domain in viral replication. Further structure-function analyses of both PICV and Lassa fever virus Z proteins suggest that arenavirus Z proteins have similar molecular mechanisms in mediating their multiple functions, with some interesting variations, such as the role of the G2 residue in blocking viral RNA synthesis. In summary, our studies have characterized the biological roles of the Z protein in an infectious arenavirus system and have shed important light on the distinct functions of its domains in virus budding and viral RNA regulation, the knowledge of which may lead to the development of novel antiviral drugs.
Measles Virus Transmission from Dendritic Cells to T Cells: Formation of Synapse-Like Interfaces Concentrating Viral and Cellular Components
Authors: Koethe Susanne , Avota Elita , Schneider-Schaulies Sibylle 
Published: July 2012

ABSTRACT

Transmission of measles virus (MV) to T cells by its early CD150
+
target cells is considered to be crucial for viral dissemination within the hematopoietic compartment. Using cocultures involving monocyte-derived dendritic cells (DCs) and T cells, we now show that T cells acquire MV most efficiently from
cis
-infected DCs rather than DCs having trapped MV (
trans
-infection). Transmission involves interactions of the viral glycoprotein H with its receptor CD150 and is therefore more efficient to preactivated T cells. In addition to rare association with actin-rich filopodial structures, the formation of contact interfaces consistent with that of virological synapses (VS) was observed where viral proteins accumulated and CD150 was redistributed in an actin-dependent manner. In addition to these molecules, activated LFA-1, DC-SIGN, CD81, and phosphorylated ezrin-radixin-moesin proteins, which also mark the HIV VS, redistributed toward the MV VS. Most interestingly, moesin and substance P receptor, both implicated earlier in assisting MV entry or cell-to-cell transmission, also partitioned to the transmission structure. Altogether, the MV VS shares important similarities to the HIV VS in concentrating cellular components potentially regulating actin dynamics, conjugate stability, and membrane fusion as required for efficient entry of MV into target T cells.
Histone H3 Lysine 4 Methylation Marks Postreplicative Human Cytomegalovirus Chromatin
Authors: Nitzsche Alexandra , Steinhäußer Charlotte , Mücke Katrin , Paulus Christina , Nevels Michael 
Published: July 2012

ABSTRACT
In the nuclei of permissive cells, human cytomegalovirus genomes form nucleosomal structures initially resembling heterochromatin but gradually switching to a euchromatin-like state. This switch is characterized by a decrease in histone H3 K9 methylation and a marked increase in H3 tail acetylation and H3 K4 methylation across the viral genome. We used ganciclovir and a mutant virus encoding a reversibly destabilized DNA polymerase to examine the impact of DNA replication on histone modification dynamics at the viral chromatin. The changes in H3 tail acetylation and H3 K9 methylation proceeded in a DNA replication-independent fashion. In contrast, the increase in H3 K4 methylation proved to depend widely on viral DNA synthesis. Consistently, labeling of nascent DNA using “click chemistry” revealed preferential incorporation of methylated H3 K4 into viral (but not cellular) chromatin during or following DNA replication. This study demonstrates largely selective epigenetic tagging of postreplicative human cytomegalovirus chromatin.