bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Herpesviridae in Whole Blood by Multiplex PCR DNA-Based Microarray Analysis after Hematopoietic Stem Cell Transplantation
Authors: Debaugnies France , Busson Laurent , Ferster Alina , Lewalle Philippe , Azzi Nadira , Aoun Mickael , Verhaegen Godelieve , Mahadeb Bhavna , de Marchin Jérôme , Vandenberg Olivier , Hallin Marie 
Published: May 2014

ABSTRACT

Viral infections are important causes of morbidity and mortality in patients after hematopoietic stem cell transplantation. The monitoring by PCR of
Herpesviridae
loads in blood samples has become a critical part of posttransplant follow-up, representing mounting costs for the laboratory. In this study, we assessed the clinical performance of the multiplex PCR DNA microarray Clart Entherpex kit for detection of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6) as a screening test for virological follow-up. Two hundred fifty-five blood samples from 16 transplanted patients, prospectively tested by routine PCR assays, were analyzed by microarray. Routine PCR detected single or multiple viruses in 42% and 10% of the samples, respectively. Microarray detected single or multiple viruses in 34% and 18% of the samples, respectively. Microarray results correlated well with CMV and EBV detections by routine PCR (kappa tests = 0.79 and 0.78, respectively), whereas a weak correlation was observed with HHV-6 (0.43). HHV-7 was also detected in 48 samples by microarray. In conclusion, the microarray is a reliable screening assay for a posttransplant virological follow-up to detect CMV and EBV infections in blood. However, positive samples must be subsequently confirmed and viral loads must be quantified by PCR assays. Limitations were identified regarding HHV-6 detection. Although it is promising, is easy to use as a first-line test, and allows a reduction in the cost of analysis without undue delay in the reporting of the final quantitative result to the clinician, some characteristics of this microarray should be improved, particularly regarding quality control and the targeted virus panel, such that it could then be used as a routine test.
Diarrhea Burden Due to Natural Infection with Enterotoxigenic Escherichia coli in a Birth Cohort in a Rural Egyptian Community
Authors: Mansour A. , Shaheen H. I. , Amine M. , Hassan K. , Sanders J. W. , Riddle M. S. , Armstrong A. W. , Svennerholm A. M. , Sebeny P. J. , Klena J. D. , Young S. Y. N. , Frenck R. W. 
Published: May 2014

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) is commonly associated with diarrhea in Egyptian children. Children less than 3 years old in Abu Homos, Egypt, had approximately five diarrheal episodes per child every year, and at least one of these episodes was due to ETEC. The epidemiology of ETEC diarrhea among children living in a rural Egyptian community was further evaluated in this study. Between January 2004 and April 2007, 348 neonates were enrolled and followed for 2 years. Children were visited twice weekly, and a stool sample was obtained every 2 weeks regardless of symptomatology. A stool sample was obtained whenever a child had diarrhea. From the routine stool culture, five
E. coli
-like colonies were selected and screened for heat-labile and heat-stable toxins by GM1 enzyme-linked immunosorbent assay (ELISA) and further typed for colonization factor antigens by dot blot assay. Incidence of ETEC infection was estimated among children with diarrhea (symptomatic) and without diarrhea (asymptomatic). Incidence of diarrhea and ETEC-associated diarrhea was 7.8 and 1.48 per child-year, respectively. High risk of repeated ETEC diarrhea was associated with being over 6 months of age, warm season, male gender, and crowded sleeping conditions. Exclusive breast-feeding was protective for repeated ETEC infection. ETEC-associated diarrhea remains common among children living in the Nile Delta. The protective role of breast-feeding demonstrates the importance of promoting exclusive breast-feeding during, at least, the first 6 months of life.
Adoption of Lean Principles in a High-Volume Molecular Diagnostic Microbiology Laboratory
Authors: Mitchell P. Shawn , Mandrekar Jayawant N. , Yao Joseph D. C. 
Published: May 2014

ABSTRACT
Clinical laboratories are constantly facing challenges to do more with less, enhance quality, improve test turnaround time, and reduce operational expenses. Experience with adopting and applying lean concepts and tools used extensively in the manufacturing industry is described for a high-volume clinical molecular microbiology laboratory, illustrating how operational success and benefits can be achieved.
Mycobacterium tuberculosis Strains of the Modern Sublineage of the Beijing Family Are More Likely To Display Increased Virulence than Strains of the Ancient Sublineage
Authors: Ribeiro Simone C. M. , Gomes Lia Lima , Amaral Eduardo P. , Andrade Marcelle R. M. , Almeida Fabricio M. , Rezende Andreza L. , Lanes Verônica R. , Carvalho Eulógio C. Q. , Suffys Philip N. , Mokrousov Igor , Lasunskaia Elena B. 
Published: May 2014

ABSTRACT

Strains of the Beijing genotype family of
Mycobacterium tuberculosis
are a cause of particular concern because of their increasing dissemination in the world and their association with drug resistance. Phylogenetically, this family includes distinct ancient and modern sublineages. The modern strains, contrary to the ancestral counterparts, demonstrated increasing prevalence in many world regions that suggest an enhanced bacterial pathogenicity. We therefore evaluated virulence of modern versus ancient Beijing strains with similar epidemiological and genotype characteristics. For this, we selected six strains that had very similar 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing profiles and belonged to the region of difference 181 (RD181) subgroup but differed using markers (
mutT2
and
mutT4
genes and NTF locus) that discriminate between modern and ancient Beijing sublineages. The strains were isolated from native patients in Brazil and Mozambique, countries with a low prevalence of Beijing strains. The virulence levels of these strains were determined in models of pulmonary infection in mice and
in vitro
macrophage infection and compared with that of a strain from Russia, part of the epidemic and hypervirulent Beijing clone B0/W148, and of the laboratory strain H37Rv. The results showed that two of the three modern Beijing strains were highly pathogenic, exhibiting levels of virulence comparable with that of the epidemic Russian strain. In contrast, all isolates of the ancient sublineage displayed intermediate or low virulence. The data obtained demonstrate that the strains of the modern Beijing sublineage are more likely to exhibit highly virulent phenotypes than ancient strains and suggest that genetic alterations characteristic of the modern Beijing sublineage favor selection of highly virulent bacteria.
Diagnostic Usefulness of Differential Time to Positivity for Catheter-Related Candidemia
Authors: Park Ki-Ho , Lee Mi Suk , Lee Sang-Oh , Choi Sang-Ho , Sung Heungsup , Kim Mi-Na , Kim Yang Soo , Woo Jun Hee , Kim Sung-Han 
Published: May 2014

ABSTRACT

A differential time to positivity (DTP) of ≥120 min is useful for diagnosing catheter-related bacteremia, but data on diagnosing catheter-related candidemia (CRC) in this way are limited. We wished to evaluate the usefulness of the DTP for diagnosing CRC. All adult patients who had the same
Candida
species isolated from blood cultures drawn simultaneously from a central venous catheter (CVC) and a peripheral vein were included at a tertiary care hospital over an 18-month period. A total of 105 patients with candidemia who had positive simultaneous CVC and peripheral vein blood cultures were included in our study. Sixty-one patients (58%) had CRC (47 definite and 14 probable), and 38 (36%) had candidemia from another source (non-CRC). The remaining 6 patients (6%) with indeterminate candidemia were excluded from the final analysis. The overall sensitivity and specificity of a DTP of ≥120 min for diagnosing CRC were 85% (95% confidence interval [CI], 74% to 93%) and 82% (95% CI, 66% to 92%), respectively, and for neutropenic patients, they were 75% (95% CI, 19% to 99%) and 100% (95% CI, 75% to 100%), respectively. For
Candida glabrata
infections, the optimal DTP cutoff was ≥6 h, with a sensitivity of 63% (95% CI, 35% to 85%) and a specificity of 75% (95% CI, 35% to 97%). In summary, DTP is useful for diagnosing CRC, and a DTP of ≥120 min appears to be the optimal cutoff except for CRC caused by
C. glabrata
. For neutropenic patients, DTP may be useful as an adjunct test to rule in CRC and to decide whether a catheter should be removed.
Group A Streptococcus Endometritis following Medical Abortion
Authors: Gendron Nicolas , Joubrel Caroline , Nedellec Sophie , Campagna Jennifer , Agostini Aubert , Doucet-Populaire Florence , Casetta Anne , Raymond Josette , Poyart Claire , Kernéis Solen 
Published: May 2014

ABSTRACT

Medical abortion is not recognized as a high-risk factor for invasive pelvic infection. Here, we report two cases of group A
Streptococcus
(GAS;
Streptococcus pyogenes
) endometritis following medical abortions with a protocol of oral mifepristone and misoprostol.
Multiplex PCR Assay for Identification of Six Different Staphylococcus spp. and Simultaneous Detection of Methicillin and Mupirocin Resistance
Authors: Campos-Peña E. , Martín-Nuñez E. , Pulido-Reyes G. , Martín-Padrón J. , Caro-Carrillo E. , Donate-Correa J. , Lorenzo-Castrillejo I. , Alcoba-Flórez J. , Machín F. , Méndez-Alvarez S. 
Published: May 2014

ABSTRACT

We describe a new, efficient, sensitive, and fast single-tube multiple-PCR protocol for the identification of the most clinically significant
Staphylococcus
spp. and the simultaneous detection of the methicillin and mupirocin resistance loci. The protocol identifies at the species level isolates belonging to
S. aureus
,
S. epidermidis
,
S. haemolyticus
,
S. hominis
,
S. lugdunensis
, and
S. saprophyticus
.
Extraintestinal Microsporidiosis
Authors: Ramanan Poornima , Pritt Bobbi S. 
Published: May 2014

ABSTRACT
Microsporidia are highly specialized obligate intracellular organisms that are closely related to fungi. Although traditionally associated with diarrheal illness in patients with AIDS, extraintestinal infections involving various organs have been reported with increasing frequency in the past decade, particularly in immunocompromised hosts. Diagnosis is usually accomplished by light microscopic identification of spores in body fluids and tissues, using a variety of stains. Transmission electron microscopy, immunofluorescence assays, or molecular methods are necessary for identification to the genus and species level. Early diagnosis is essential for preventing the significant associated morbidity and mortality of extraintestinal microsporidiosis.
Set of Classical PCRs for Detection of Mutations in
Candida glabrata FKS
Genes Linked with Echinocandin Resistance
Authors: Dudiuk Catiana , Gamarra Soledad , Leonardeli Florencia , Jimenez-Ortigosa Cristina , Vitale Roxana G. , Afeltra Javier , Perlin David S. , Garcia-Effron Guillermo 
Published: May 2014

ABSTRACT

Clinical echinocandin resistance among
Candida glabrata
strains is increasing, especially in the United States. Antifungal susceptibility testing is considered mandatory to guide therapeutic decisions. However, these methodologies are not routinely performed in the hospital setting due to their complexity and the time needed to obtain reliable results. Echinocandin failure in
C. glabrata
is linked exclusively to Fks1p and Fks2p amino acid substitutions, and detection of such substitutions would serve as a surrogate marker to identify resistant isolates. In this work, we report an inexpensive, simple, and quick classical PCR set able to objectively detect the most common mechanisms of echinocandin resistance in
C. glabrata
within 4 h. The usefulness of this assay was assessed using a blind collection of 50
C. glabrata
strains, including 16
FKS1
and/or
FKS2
mutants.
Differential Lymphocyte and Antibody Responses in Deer Mice Infected with Sin Nombre Hantavirus or Andes Hantavirus
Authors: Schountz Tony , Quackenbush Sandra , Rovnak Joel , Haddock Elaine , Black William C. , Feldmann Heinz , Prescott Joseph 
Published: May 2014

ABSTRACTHantavirus cardiopulmonary syndrome (HCPS) is a rodent-borne disease with a high case-fatality rate that is caused by several New World hantaviruses. Each pathogenic hantavirus is naturally hosted by a principal rodent species without conspicuous disease and infection is persistent, perhaps for life. Deer mice (Peromyscus maniculatus) are the natural reservoirs of Sin Nombre virus (SNV), the etiologic agent of most HCPS cases in North America. Deer mice remain infected despite a helper T cell response that leads to high-titer neutralizing antibodies. Deer mice are also susceptible to Andes hantavirus (ANDV), which causes most HCPS cases in South America; however, deer mice clear ANDV. We infected deer mice with SNV or ANDV to identify differences in host responses that might account for this differential outcome. SNV RNA levels were higher in the lungs but not different in the heart, spleen, or kidneys. Most ANDV-infected deer mice had seroconverted 14 days after inoculation, but none of the SNV-infected deer mice had. Examination of lymph node cell antigen recall responses identified elevated immune gene expression in deer mice infected with ANDV and suggested maturation toward a Th2 or T follicular helper phenotype in some ANDV-infected deer mice, including activation of the interleukin 4 (IL-4) pathway in T cells and B cells. These data suggest that the rate of maturation of the immune response is substantially higher and of greater magnitude during ANDV infection, and these differences may account for clearance of ANDV and persistence of SNV.IMPORTANCEHantaviruses persistently infect their reservoir rodent hosts without pathology. It is unknown how these viruses evade sterilizing immune responses in the reservoirs. We have determined that infection of the deer mouse with its homologous hantavirus, Sin Nombre virus, results in low levels of immune gene expression in antigen-stimulated lymph node cells and a poor antibody response. However, infection of deer mice with a heterologous hantavirus, Andes virus, results in a robust lymph node cell response, signatures of T and B cell maturation, and production of antibodies. These findings suggest that an early and aggressive immune response to hantaviruses may lead to clearance in a reservoir host and suggest that a modest immune response may be a component of hantavirus ecology.
Continuing Reassortment Leads to the Genetic Diversity of Influenza Virus H7N9 in Guangdong, China
Authors: Lu Jing , Wu Jie , Zeng Xianqiao , Guan Dawei , Zou Lirong , Yi Lina , Liang Lijun , Ni Hanzhong , Kang Min , Zhang Xin , Zhong Haojie , He Xiang , Monagin Corina , Lin Jinyan , Ke Changwen 
Published: May 2014

ABSTRACT
On 30 March 2013, a novel avian influenza A H7N9 virus causing severe human respiratory infections was identified in China. Preliminary sequence analyses have shown that the virus is a reassortant of H7N9 and H9N2 avian influenza viruses. In this study, we conducted enhanced surveillance for H7N9 virus in Guangdong, China, from April to August 2013. We isolated two H7N9 viral strains from environmental samples associated with poultry markets and one from a clinical patient. Sequence analyses showed that the Guangdong H7N9 virus isolated from April to May shared high sequence similarity with other strains from eastern China. The A/Guangdong/1/2013 (H7N9) virus isolated from the Guangdong patient on 10 August 2013 was divergent from previously sequenced H7N9 viruses and more closely related to local circulating H9N2 viruses in the NS and NP genes. Phylogenetic analyses revealed that four internal genes of the A/Guangdong/1/2013 (H7N9) virus—the NS, NP, PB1, and PB2 genes—were in clusters different from those for H7N9 viruses identified previously in other provinces of China. The discovery presented here suggests that continuing reassortment led to the emergence of the A/Guangdong/1/2013 (H7N9) virus as a novel H7N9 virus in Guangdong, China, and that viral adaptation to avian and human hosts must be assessed.

IMPORTANCE
In this study, we isolated and characterized the avian influenza A H7N9 virus in Guangdong, China, from April to August 2013. We show that the viruses isolated from Guangdong environmental samples and chickens from April to May 2013 were highly similar to other H7N9 strains found in eastern China. The H7N9 virus isolated from the clinical patient in Guangdong in August 2013 was divergent from previously identified H7N9 viruses, with the NS and NP genes originating from recent H9N2 viruses circulating in the province. This study provides direct evidence that continuing reassortment occurred and led to the emergence of a novel H7N9 influenza virus in Guangdong, China. These results also shed light on how the H7N9 virus evolved, which is critically important for future monitoring and tracing of viral transmission.
Role of the C Terminus of Lassa Virus L Protein in Viral mRNA Synthesis
Authors: Lehmann Maria , Pahlmann Meike , Jérôme Hanna , Busch Carola , Lelke Michaela , Günther Stephan 
Published: May 2014

ABSTRACT
The N terminus of arenavirus L protein contains an endonuclease presumably involved in “cap snatching.” Here, we employed the Lassa virus replicon system to map other L protein sites that might be involved in this mechanism. Residues Phe-1979, Arg-2018, Phe-2071, Asp-2106, Trp-2173, Tyr-2179, Arg-2200, and Arg-2204 were important for viral mRNA synthesis but dispensable for genome replication. Thus, the C terminus of L protein is involved in the mRNA synthesis process, potentially by mediating cap binding.
CD4
+
T-Cell Help Enhances NK Cell Function following Therapeutic HIV-1 Vaccination
Authors: Jost Stephanie , Tomezsko Phillip John , Rands Keith , Toth Ildiko , Lichterfeld Mathias , Gandhi Rajesh Tim , Altfeld Marcus 
Published: May 2014

ABSTRACT

Increasing data suggest that NK cells can mediate antiviral activity in HIV-1-infected humans, and as such, novel approaches harnessing the anti-HIV-1 function of both T cells and NK cells represent attractive options to improve future HIV-1 immunotherapies. Chronic progressive HIV-1 infection has been associated with a loss of CD4
+
T helper cell function and with the accumulation of anergic NK cells. As several studies have suggested that cytokines produced by CD4
+
T cells are required to enhance NK cell function in various infection models, we hypothesized that reconstitution of HIV-1-specific CD4
+
T-cell responses by therapeutic immunization would restore NK cell activity in infected individuals. Using flow cytometry, we examined the function of CD4
+
T cells and NK cells in response to HIV-1 in subjects with treated chronic HIV-1 infection before and after immunization with an adjuvanted HIV-1 Gp120/NefTat subunit protein vaccine candidate provided by GlaxoSmithKline. Vaccination induced an increased expression of interleukin-2 (IL-2) by Gp120-specific CD4
+
T cells in response to HIV-1 peptides
ex vivo
, which was associated with enhanced production of gamma interferon (IFN-γ) by NK cells. Our data show that reconstitution of HIV-1-specific CD4
+
T-cell function by therapeutic immunization can enhance NK cell activity in HIV-1-infected individuals.

IMPORTANCE
NK cells are effector cells of the innate immune system and are important in the control of viral infection. Recent studies have demonstrated the crucial role played by NK cells in controlling and/or limiting acquisition of HIV-1 infection. However, NK cell function is impaired during progressive HIV-1 infection. We recently showed that therapeutic immunization of treated HIV-1-infected individuals reconstituted strong T-cell responses, measured notably by their production of IL-2, a cytokine that can activate NK cells. The current study suggests that reconstitution of T-cell function by therapeutic vaccination can enhance NK cell activity in individuals with chronic HIV-1 infection. Our findings provide new insights into the interplay between adaptive and innate immune mechanisms involved in HIV-1 immunity and unveil opportunities to harness NK cell function in future therapeutic vaccine strategies to target HIV-1.
Recovery of an HMWP/hmwBP (pUL48/pUL47) Complex from Virions of Human Cytomegalovirus: Subunit Interactions, Oligomer Composition, and Deubiquitylase Activity
Authors: Tullman Jennifer A. , Harmon Mary-Elizabeth , Delannoy Michael , Gibson Wade 
Published: May 2014

ABSTRACT
We report that the human cytomegalovirus (HCMV) high-molecular-weight tegument protein (HMWP, pUL48; 253 kDa) and the HMWP-binding protein (hmwBP, pUL47; 110 kDa) can be recovered as a complex from virions disrupted by treatment with 50 mM Tris (pH 7.5), 0.5 M NaCl, 0.5% NP-40, and 10 mM dithiothreitol [DTT]. The subunit ratio of the complex approximates 1:1, with a shape and structure consistent with an elongated heterodimer. The HMWP/hmwBP complex was corroborated by reciprocal coimmunoprecipitation experiments using antipeptide antibodies and lysates from both infected cells and disrupted virus particles. An interaction of the amino end of pUL48 (amino acids [aa] 322 to 754) with the carboxyl end of pUL47 (aa 693 to 982) was identified by fragment coimmunoprecipitation experiments, and a head-to-tail self-interaction of hmwBP was also observed. The deubiquitylating activity of pUL48 is retained in the isolated complex, which cleaves K11, K48, and K63 ubiquitin isopeptide linkages.

IMPORTANCE
Human cytomegalovirus (HCMV, or human herpesvirus 5 [HHV-5]) is a large DNA-containing virus that belongs to the betaherpesvirus subfamily and is a clinically important pathogen. Defining the constituent elements of its mature form, their organization within the particle, and the assembly process by which it is produced are fundamental to understanding the mechanisms of herpesvirus infection and developing drugs and vaccines against them. In this study, we report isolating a complex of two large proteins encoded by HCMV open reading frames (ORFs) UL47 and UL48 and identifying the binding domains responsible for their interaction with each other and of pUL47 with itself. Our calculations indicate that the complex is a rod-shaped heterodimer. Additionally, we determined that the ubiquitin-specific protease activity of the ORF UL48 protein was functional in the complex, cleaving K11-, K48-, and K63-linked ubiquitin dimers. This information builds on and extends our understanding of the HCMV tegument protein network that is required to interface the HCMV envelope and capsid.