bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly Resistant Microorganisms in a Teaching Hospital: The Role of Horizontal Spread in a Setting of Endemicity
Authors: Willemsen Ina , Mooij Marlies , van der Wiel Marsha , Bogaers Diana , van der Bijl Madelon , Savelkoul Paul , Kluytmans Jan 
Published: October 2008

Objective.To determine the incidence density of highly resistant organisms (HROs) and the relative contribution of horizontal spread in a setting of endemicity.Methods.Prospective surveillance was performed among hospitalized patients during an 18-month period. Enterobacteriaceae, non-fermentative gram-negative bacilli,Staphylococcus aureus, Streptococcus pneumoniae,andEnterococcus faecium—all considered highly resistant, according to Dutch guidelines—were included. Epidemiological linkage and nosocomial transmission were determined on the basis of molecular typing and hospital admission data.Results.From 119 patients, we recovered a total of 170 unique HRO isolates, as follows:Escherichia coli,96 isolates;Klebsiellaspecies, 11 isolates;Enterobacterspecies, 8 isolates;Proteusspecies, 9 isolates;Citrobacterspecies, 5 isolates;Pseudomonasspecies, 5 isolates;Aci-netobacterspecies, 3 isolates;Morganellaspecies, 2 isolates;Salmonellaspecies, 1 isolate;Serratiaspecies, 1 isolate;S. pneumoniae,20 isolates; andS. aureus,9 isolates. No vancomycin-resistantE. faeciumwas found. The incidence density was 4.3 HRO isolates per 10,000 patient-days. The majority of HRO isolates were unique, and nosocomial transmission was observed 4 times for highly resistant gram-negative bacilli (case reproduction rate, 0.05) and 4 times for penicillin-nonsusceptibleS. pneumoniae(case reproduction rate, 0.29). A stay on the intensive care unit was the main determinant for the recovery of an HRO.Conclusion.Nosocomial transmission of HROs was observed 8 times during the 18-month period. The intensive care unit was identified as the main reservoir of horizontal spread of HROs. This study shows that nosocomial transmission of HROs is largely preventable using transmission precautions.
Outcomes of Carbapenem-Resistant Klebsiella pneumoniae Infection and the Impact of Antimicrobial and Adjunctive Therapies
Authors: Patel Gopi , Huprikar Shirish , Factor Stephanie H. , Jenkins Stephen G. , Calfee David P. 
Published: October 2008

Background.Carbapenem-resistant Klebsiella pneumoniae is an emerging healthcare-associated pathogen.Objective.To describe the epidemiology of and clinical outcomes associated with carbapenem-resistant K. pneumoniae infection and to identify risk factors associated with mortality among patients with this type of infection.Setting.Mount Sinai Hospital, a 1,171-bed tertiary care teaching hospital in New York City.Design.Two matched case-control studies.Methods.In the first matched case-control study, case patients with carbapenem-resistant K. pneumoniae infection were compared with control patients with carbapenem-susceptible K. pneumoniae infection. In the second case-control study, patients who survived carbapenem-resistant K. pneumoniae infection were compared with those who did not survive, to identify risk factors associated with mortality among patients with carbapenem-resistant K. pneumoniae infection.Results.There were 99 case patients and 99 control patients identified. Carbapenem-resistant K. pneumoniae infection was independently associated with recent organ or stem-cell transplantation (P = .008), receipt of mechanical ventilation (P = .04), longer length of stay before infection (P = .01), and exposure to cephalosporins (P = .02) and carbapenems (P < .001). Case patients were more likely than control patients to die during hospitalization (48% vs 20%; P < .001) and to die from infection (38% vs 12%; P < .001). Removal of the focus of infection (ie, debridement) was independently associated with patient survival (P = .002). The timely administration of antibiotics with in vitro activity against carbapenem-resistant K. pneumoniae was not associated with patient survival.Conclusions.Carbapenem-resistant K. pneumoniae infection is associated with numerous healthcare-related risk factors and with high mortality. The mortality rate associated with carbapenem-resistant K. pneumoniae infection and the limited antimicrobial options for treatment of carbapenem-resistant K. pneumoniae infection highlight the need for improved detection of carbapenem-resistant K. pneumoniae infection, identification of effective preventive measures, and development of novel agents with reliable clinical efficacy against carbapenem-resistant K. pneumoniae.
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots
Authors: Demey J. R. , Vicente-Villardón J. L. , Galindo-Villardón M. P. , Zambrano A. Y. 
Published: October 2008

Abstract
For characterization of genetic diversity in genotypes several molecular techniques, usually resulting in a binary data matrix, have been used. Despite the fact that in Cluster Analysis (CA) and Principal Coordinates Analysis (PCoA) the interpretation of the variables responsible for grouping is not straightforward, these methods are commonly used to classify genotypes using DNA molecular markers. In this article, we present a novel algorithm that uses a combination of PCoA, CA and Logistic Regression (LR), as a better way to interpret the variables (alleles or bands) associated to the classification of genotypes. The combination of three standard techniques with some new ideas about the geometry of the procedures, allows constructing an External Logistic Biplot (ELB) that helps in the interpretation of the variables responsible for the classification or ordination. An application of the method to study the genetic diversity of four populations from Africa, Asia and Europe, using the HapMap data is included.
Availability: The Matlab code for implementing the methods may be obtained from the web site: http://biplot.usal.es.
Contact: jhonny.demey@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Small RNA gene identification and mRNA target predictions in bacteria
Authors: Pichon Christophe , Felden Brice 
Published: October 2008

Abstract
Motivation: Bacterial small ribonucleic acids (sRNAs) that are not ribosomal and transfer or messenger RNAs were initially identified in the sixties, whereas their molecular functions are still under active investigation today. It is now widely accepted that most play central roles in gene expression regulation in response to environmental changes. Interestingly, some are also implicated in bacterial virulence. Functional studies revealed that a large subset of these sRNAs act by an antisense mechanism thanks to pairing interactions with dedicated mRNA targets, usually around their translation start sites, to modulate gene expression at the posttranscriptional level. Some sRNAs modulate protein activity or mimic the structure of other macromolecules. In the last few years, in silico methods have been developed to detect more bacterial sRNAs. Among these, computational analyses of the bacterial genomes by comparative genomics have predicted the existence of a plethora of sRNAs, some that were confirmed to be expressed in vivo. The prediction accuracy of these computational tools is highly variable and can be perfectible. Here we review the computational studies that have contributed to detecting the sRNA gene and mRNA targets in bacteria and the methods for their experimental testing. In addition, the remaining challenges are discussed.
Contact: bfelden@univ-rennes1.fr
Suppression of 4-Coumarate-CoA Ligase in the Coniferous GymnospermPinus radiata
Authors: Wagner Armin , Donaldson Lloyd , Kim Hoon , Phillips Lorelle , Flint Heather , Steward Diane , Torr Kirk , Koch Gerald , Schmitt Uwe , Ralph John 
Published: October 2008

AbstractSevere suppression of 4-coumarate-coenzyme A ligase (4CL) in the coniferous gymnosperm Pinus radiata substantially affected plant phenotype and resulted in dwarfed plants with a “bonsai tree-like” appearance. Microscopic analyses of stem sections from 2-year-old plants revealed substantial morphological changes in both wood and bark tissues. This included the formation of weakly lignified tracheids that displayed signs of collapse and the development of circumferential bands of axial parenchyma. Acetyl bromide-soluble lignin assays and proton nuclear magnetic resonance studies revealed lignin reductions of 36% to 50% in the most severely affected transgenic plants. Two-dimensional nuclear magnetic resonance and pyrolysis-gas chromatography-mass spectrometry studies indicated that lignin reductions were mainly due to depletion of guaiacyl but not p-hydroxyphenyl lignin. 4CL silencing also caused modifications in the lignin interunit linkage distribution, including elevated β-aryl ether (β-O-4 unit) and spirodienone (β-1) levels, accompanied by lower phenylcoumaran (β-5), resinol (β-β), and dibenzodioxocin (5-5/β-O-4) levels. A sharp depletion in the level of saturated (dihydroconiferyl alcohol) end groups was also observed. Severe suppression of 4CL also affected carbohydrate metabolism. Most obvious was an up to approximately 2-fold increase in galactose content in wood from transgenic plants due to increased compression wood formation. The molecular, anatomical, and analytical data verified that the isolated 4CL clone is associated with lignin biosynthesis and illustrated that 4CL silencing leads to complex, often surprising, physiological and morphological changes in P. radiata.
Antibodies against Glucan, Chitin, and
Saccharomyces cerevisiae
Mannan as New Biomarkers of
Candida albicans
Infection That Complement Tests Based on
C. albicans
Mannan
Authors: Sendid B. , Dotan N. , Nseir S. , Savaux C. , Vandewalle P. , Standaert A. , Zerimech F. , Guery B. P. , Dukler A. , Colombel J. F. , Poulain D. 
Published: October 2008

ABSTRACT

Antibodies against
Saccharomyces cerevisiae
mannan (ASCA) and antibodies against synthetic disaccharide fragments of glucans (ALCA) and chitin (ACCA) are biomarkers of Crohn's disease (CD). We previously showed that
Candida albicans
infection generates ASCA. Here, we explored ALCA and ACCA as possible biomarkers of invasive
C. albicans
infection (ICI). ASCA, ALCA, ACCA, and
Candida
mannan antigen and antibody detection tests were performed on 69 sera obtained sequentially from 18 patients with ICIs proven by blood culture, 59 sera from CD patients, 47 sera from hospitalized subjects colonized by
Candida
species (CZ), and 131 sera from healthy controls (HC). ASCA, ALCA, and ACCA levels in CD and ICI patients were significantly different from those in CZ and HC subjects (
P
< 0.0001). In ICI patients, these levels increased as infection developed. Using ASCA, ALCA, ACCA, and Platelia
Candida
tests, 100% of ICIs were detected, with the kinetics of the antibody response depending on the patient during the time course of infection. A large number of sera presented with more than three positive tests. This is the first evidence that the detection of antibodies against chitin and glucans has diagnostic value in fungal infections and that these tests can complement more specific tests. Future trials are necessary to assess the value of these tests in multiparametric analysis, as well as their pathophysiological relevance.
Influence of Interleukin 1α (IL-1α), IL-4, and IL-6 Polymorphisms on Genetic Susceptibility to Chronic Osteomyelitis
Authors: Tsezou Aspasia , Poultsides Lazaros , Kostopoulou Fotini , Zintzaras Elias , Satra Maria , Kitsiou-Tzeli Sofia , Malizos Konstantinos N. 
Published: October 2008

ABSTRACTThe association between cytokine gene polymorphisms and chronic osteomyelitis was investigated in order to determine whether genetic variability in cytokine genes predisposes to osteomyelitis susceptibility. Significant genotypic and allelic associations were observed between interleukin 1α (IL-1α) −889-C/T, IL-4 −1098-G/T and −590-C/T, and IL-6 −174-G/C polymorphisms and osteomyelitis in the Greek population, pointing towards their potential involvement in osteomyelitis pathogenesis.
Role of Dendritic Cells in Enhancement of Herpes Simplex Virus Type 1 Latency and Reactivation in Vaccinated Mice
Authors: Mott Kevin R. , Ghiasi Homayon 
Published: October 2008

ABSTRACTOcular infection with herpes simplex virus type 1 (HSV-1) frequently leads to recurrent infection, which is a major cause of corneal scarring. Thus, the prevention of the establishment of latency should be a primary goal of vaccination against HSV-1. To this end, we have examined the contribution of dendritic cells (DCs) to the efficacy of a vaccine against ocular HSV-1 infection. Transgenic mice (expressing a CD11c-diphtheria toxin receptor-green fluorescent protein construct) with a BALB/c background were immunized with a vaccine consisting of DNA that encodes five HSV-1 glycoproteins or were immunized with vector control DNA. The vaccinated mice were then depleted of their DCs through the injection of diphtheria toxin before and after ocular challenge with HSV-1. Analyses of HSV-1 replication in the eye, blepharitis, corneal scarring, and the survival of the infected mice upon primary infection indicated that DC depletion neither promoted nor compromised the efficacy of the vaccine. In contrast, DC depletion was associated with an approximately fivefold reduction in the level of latent virus in the trigeminal ganglia (TGs) of latently infected mice, as well as a significant reduction in the reactivation rate of latent virus. The possibility that DCs enhance the latency of HSV-1 in the TGs of ocularly infected mice suggests for the first time that DCs, rather than acting as “immune saviors,” can exacerbate disease and compromise vaccine efficacy by enhancing viral latency and reactivation.
Design of Multiplexed Detection Assays for Identification of Avian Influenza A Virus Subtypes Pathogenic to Humans by SmartCycler Real-Time Reverse Transcription-PCR
Authors: Wang Wei , Ren Peijun , Mardi Sek , Hou Lili , Tsai Cheguo , Chan Kwok Hung , Cheng Peter , Sheng Jun , Buchy Philippe , Sun Bing , Toyoda Tetsuya , Lim Wilina , Peiris J. S. Malik , Zhou Paul , Deubel Vincent 
Published: October 2008

ABSTRACT
Influenza A virus (IAV) epidemics are the result of human-to-human or poultry-to-human transmission. Tracking seasonal outbreaks of IAV and other avian influenza virus (AIV) subtypes that can infect humans, aquatic and migratory birds, poultry, and pigs is essential for epidemiological surveillance and outbreak alerts. In this study, we performed four real-time reverse transcription-PCR (rRT-PCR) assays for identification of the IAV M and hemagglutinin (HA) genes from six known AIVs infecting pigs, birds, and humans. IAV M1 gene-positive samples tested by single-step rRT-PCR and a fluorogenic Sybr green I detection system were further processed for H5 subtype identification by using two-primer-set multiplex and Sybr green I rRT-PCR assays. H5 subtype-negative samples were then tested with either a TaqMan assay for subtypes H1 and H3 or a TaqMan assay for subtypes H2, H7, and H9 and a beacon multiplex rRT-PCR identification assay. The four-tube strategy was able to detect 10 RNA copies of the HA genes of subtypes H1, H2, H3, H5, and H7 and 100 RNA copies of the HA gene of subtype H9. At least six H5 clades of H5N1 viruses isolated in Southeast Asia and China were detected by that test. Using rRT-PCR assays for the M1 and HA genes in 202 nasopharyngeal swab specimens from children with acute respiratory infections, we identified a total of 39 samples positive for the IAV M1 gene and subtypes H1 and H3. When performed with a portable SmartCycler instrument, the assays offer an efficient, flexible, and reliable platform for investigations of IAV and AIV in remote hospitals and in the field.
Ciprofloxacin-Resistant
Salmonella enterica
Serovar Typhi from Kuwait with Novel Mutations in
gyrA
and
parC
Genes
Authors: Dimitrov Tzonyo , Dashti Ali A. , Albaksami Ossama , Udo Edet E. , Jadaon Mehrez M. , Albert M. John 
Published: October 2008

ABSTRACT

Blood isolates of
Salmonella enterica
serovar Typhi from two recently returned Bangladeshi patients in Kuwait were ciprofloxacin resistant, with ciprofloxacin MICs of 12 mg/liter for both isolates. Both isolates had three novel
gyrA
mutations (55-Leu→Trp, 87-Asp→Ala, and 106-Gln→Arg) and three novel
parC
mutations (84-Glu→Lys, 106-Trp→Gly, and 128-Tyr→Asp).
Uncultivated Bacteria as Etiologic Agents of Intra-Amniotic Inflammation Leading to Preterm Birth
Authors: Han Yiping W. , Shen Tao , Chung Peter , Buhimschi Irina A. , Buhimschi Catalin S. 
Published: October 2008

ABSTRACT

Intra-amniotic infection and inflammation are major causes of preterm birth (PTB). However, intra-amniotic inflammation is often detected in the absence of infection. This may partly be due to the culturing methods employed in hospital laboratories, which are unable to detect the uncultivated species. In this study, intra-amniotic microbial infections associated with PTB were examined by both culture and 16S rRNA-based culture-independent methods and were corroborated by the presence of intra-amniotic inflammation. Amniotic fluid (AF) specimens from 46 pregnancies complicated by PTB and 16 asymptomatic women were analyzed. No bacterial DNA was amplified in AF collected from the asymptomatic women. Among the 46 samples associated with PTB, bacterial DNA was amplified from all (16/16) of the culture-positive samples and 17% (5/30) of the culture-negative samples. In the culture-positive group, additional species were detected in more than half (9/16) of the cases by PCR and clone analysis. Altogether, approximately two- thirds of the species detected by the culture-independent methods were not isolated by culture. They included both uncultivated and difficult-to-cultivate species, such as
Fusobacterium nucleatum
,
Leptotrichia
(
Sneathia
) spp., a
Bergeyella
sp., a
Peptostreptococcus
sp.,
Bacteroides
spp., and a species of the order
Clostridiales
. To examine intra-amniotic inflammation, an AF proteomic fingerprint (mass-restricted score) was determined by surface-enhanced laser desorption ionization-time-of-flight mass spectrometry. Inflammation was detected in all five samples which were culture negative but PCR positive. Women who were PCR positive more often had elevated interleukin-6 levels in their AF, histological chorioamnionitis, and funisitis and delivered neonates with early-onset neonatal sepsis. Previously unrecognized, uncultivated, or difficult-to-cultivate species may play a key role in the initiation of PTB.
Phenotypic and Genotypic Analysis of Enterotoxigenic
Escherichia coli
in Samples Obtained from Egyptian Children Presenting to Referral Hospitals
Authors: Shaheen H. I. , Abdel Messih I. A. , Klena J. D. , Mansour A. , El-Wakkeel Z. , Wierzba T. F. , Sanders J. W. , Khalil S. B. , Rockabrand D. M. , Monteville M. R. , Rozmajzl P. J. , Svennerholm A. M. , Frenck R. W. 
Published: October 2008

ABSTRACT

Hospital surveillance was established in the Nile River Delta to increase the understanding of the epidemiology of diarrheal disease among Egyptian children. Between September 2000 and August 2003, samples obtained from children less than 5 years of age who had diarrhea and who were seeking hospital care were cultured for enteric bacteria. Colonies from each culture with a morphology typical of that of
Escherichia coli
were tested for the heat-labile (LT) and heat-stable (ST) toxins by a GM-1-specific enzyme-linked immunosorbent assay and colonization factor (CF) antigens by an immunodot blot assay. Enterotoxigenic
E. coli
(ETEC) isolates were recovered from 320/1,540 (20.7%) children, and ETEC isolates expressing a known CF were identified in 151/320 (47%) samples. ST CFA/I, ST CS6, ST CS14, and LT and ST CS5 plus CS6 represented 75% of the CFs expressed by ETEC isolates expressing a detectable CF. Year-to-year variability in the proportion of ETEC isolates that expressed a detectable CF was observed (e.g., the proportion that expressed CFA/I ranged from 10% in year 1 to 21% in year 3); however, the relative proportions of ETEC isolates expressing a CF were similar over the reporting period. The proportion of CF-positive ETEC isolates was higher among isolates that expressed ST. ETEC isolates expressing CS6 were isolated significantly less often (
P
< 0.001) than isolates expressing CFA/I in children less than 1 year of age. Macrorestriction profiling of CFA/I-expressing ETEC isolates by using the restriction enzyme XbaI and pulsed-field gel electrophoresis demonstrated a wide genetic diversity among the isolates that did not directly correlate with the virulence of the pathogen. The genome plasticity demonstrated in the ETEC isolates collected in this work suggests an additional challenge to the development of a globally effective vaccine for ETEC.
Concurrent Genotyping and Quantitation of Cytomegalovirus gB Genotypes in Solid-Organ-Transplant Recipients by Use of a Real-Time PCR Assay
Authors: Pang Xiaoli , Humar Atul , Preiksaitis Jutta K. 
Published: October 2008

ABSTRACT

We have developed a real-time genotyping and quantitative PCR (RT-GQ-PCR) assay to genotype cytomegalovirus (CMV) and quantify viral loads simultaneously in solid organ transplant (SOT) recipients. Special minor-groove DNA-binding probes were designed based on sequence polymorphism in the gB gene to increase genotyping specificity for gB1 to gB4. For validation, 28 samples with known genotypes determined by restriction fragment analysis (RFA) and 121 with unknown genotypes were tested. All samples were from SOT patients with CMV viremia. A 100% concordance for genotyping was achieved by using the RT-GQ-PCR with known genotypes determined by RFA. The RT-GQ-PCR identified more cases of CMV infections with mixed genotypes than RFA did. No cross-reaction between genotypes was observed. All four gB genotypes were detected in the 121 samples of unknown genotype. gB1 was the predominant single genotype (
n
= 61, 50.4%), followed by gB2 (
n
= 26, 21.0%), gB3, (
n
= 11, 9.1%), and gB4 (
n
= 3, 2.5%). Mixed-genotype infections were detected in 17% (20/121) of the samples. Patients with mixed-genotype infections had significantly higher CMV viral loads than those with single-genotype infections (
P
= 0.019). The RT-GQ-PCR assay was found to be highly sensitive and specific, with a wide dynamic range (2.7 to 10.7 log
10
copies/ml) and very good precision (coefficient of variation, ∼1.78%). With the prominent feature of concurrent CMV gB genotyping and quantitation in a single reaction, the new assay provides a rapid and cost-effective method for monitoring CMV infection in SOT recipients.