bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and Clinical Impact of
Acinetobacter baumannii
Colonization and Infection at a Military Medical Center
Authors: Petersen Kyle , Cannegieter Suzanne C. , van der Reijden Tanny J. , van Strijen Beppie , You David M. , Babel Britta S. , Philip Andrew I. , Dijkshoorn Lenie 
Published: November 2010

ABSTRACT

The epidemiology of
Acinetobacter baumannii
emerging in combat casualties is poorly understood. We analyzed 65 (54 nonreplicate)
Acinetobacter
isolates from 48 patients (46 hospitalized and 2 outpatient trainees entering the military) from October 2004 to October 2005 for genotypic similarities, time-space relatedness, and antibiotic susceptibility. Clinical and surveillance cultures were compared by amplified fragment length polymorphism (AFLP) genomic fingerprinting to each other and to strains of a reference database. Antibiotic susceptibility was determined, and multiplex PCR was performed for OXA-23-like, -24-like, -51-like, and -58-like carbapenemases. Records were reviewed for overlapping hospital stays of the most frequent genotypes, and risk ratios were calculated for any association of genotype with severity of Acute Physiology and Chronic Health Evaluation II (APACHE II) score or injury severity score (ISS) and previous antibiotic use. Nineteen genotypes were identified; two predominated, one consistent with an emerging novel international clone and the other unique to our database. Both predominant genotypes were carbapenem resistant, were present at another hospital before patients' admission to our facility, and were associated with higher APACHE II scores, higher ISSs, and previous carbapenem antibiotics in comparison with other genotypes. One predominated in wound and respiratory isolates, and the other predominated in wound and skin surveillance samples. Several other genotypes were identified as European clones I to III.
Acinetobacter
genotypes from recruits upon entry to the military, unlike those in hospitalized patients, did not include carbapenem-resistant genotypes.
Acinetobacter
species isolated from battlefield casualties are diverse, including genotypes belonging to European clones I to III. Two carbapenem-resistant genotypes were epidemic, one of which appeared to belong to a novel international clone.
“
Mycobacterium avium
subsp.
hominissuis
” in Neck Lymph Nodes of Children and their Environment Examined by Culture and Triplex Quantitative Real-Time PCR
Authors: Kaevska Marija , Slana Iva , Kralik Petr , Reischl Udo , Orosova Jaroslava , Holcikova Alena , Pavlik Ivo 
Published: November 2010

ABSTRACT

“
Mycobacterium avium
subsp.
hominissuis
” often causes cervical lymphadenitis in children; its prompt and accurate identification enables adequate therapy, tracing, and prevention. The aims of this study were to determine the causative agent of lymphadenitis using culture, PCR, and triplex quantitative real-time PCR (qPCR) methods with DNA directly isolated from tissue, as well as to identify possible sources of infection from the environment. We confirmed the diagnoses by detecting
M. avium
subsp.
hominissuis
using qPCR with DNA directly isolated from lymph node biopsy specimens of two patients. In order to trace the source of infection from the environment, a method of DNA isolation from soil and other environmental samples, such as dust, cobwebs, and compost, was developed. The triplex qPCR examination revealed the presence of
M. avium
subsp.
hominissuis
in a high proportion of the environmental samples (42.8% in the first patient's house and 47.6% in the second patient's house). Both patients were also exposed to
M. avium
subsp.
avium
, which was present due to the breeding of infected domestic hens. The high infectious dose of
M. avium
subsp.
hominissuis
or the increased susceptibility of humans to
M. avium
subsp.
hominissuis
compared to
M. avium
subsp.
avium
could be the reason why the children were infected with
M. avium
subsp.
hominissuis.
Human Papillomavirus (HPV) DNA Triage of Women with Atypical Squamous Cells of Undetermined Significance with Amplicor HPV and Hybrid Capture 2 Assays for Detection of High-Grade Lesions of the Uterine Cervix
Authors: Dufresne Simon , Sauthier Philippe , Mayrand Marie-Hélène , Petignat Patrick , Provencher Diane , Drouin Pierre , Gauthier Philippe , Dupuis Marie-Josée , Michon Bertrand , Ouellet Stéphan , Hadjeres Rachid , Ferenczy Alex , Franco Eduardo L. , Coutlée François 
Published: November 2010

ABSTRACT

Up to 20% of women having a cytology smear showing atypical squamous cells of undetermined significance (ASC-US) and infected with high-risk human papillomavirus (HR HPV) have high-grade cervical intraepithelial neoplasia (CIN 2/3). Results obtained with the Amplicor HPV and Hybrid Capture 2 (HC-2) assays for HR HPV DNA detection in women referred to colposcopy for an ASC-US smear were compared. Cervical samples in PreservCyt were tested for the presence of 13 HR HPV types with HC-2, with Amplicor at three cutoffs for positivity (0.2, 1.0, and 1.5 optical density units), and for 36 genotypes with the Linear Array (LA). Of 396 eligible women, 316 did not have CIN, 47 had CIN 1, 29 had CIN 2/3, and 4 had CIN of unknown grade. HR HPV was detected in 129 (32.6%) and 164 (41.4%) samples with HC-2 and Amplicor HPV (cutoff, 0.2), respectively (
P
= 0.01). Overall, 112 specimens were positive and 215 were negative with the HC-2 and Amplicor HPV assays (agreement of 82.6%; 95% confidence interval [CI], 78.5 to 86.0). The clinical sensitivity and specificity of Amplicor HPV at cutoffs of 0.2, 1.0 and 1.5 and of HC-2 for detection of CIN 2/3 were 89.7% (95% CI, 72.8 to 97.2) and 62.5% (95% CI, 57.5 to 52.4), 89.7% (95% CI, 72.8 to 97.2) and 64.5% (95% CI, 59.4 to 69.2), 89.7% (95% CI, 72.8 to 97.2) and 64.7% (95% CI, 59.7 to 69.5), and 93.1% (95% CI, 77.0 to 99.2) and 72.2% (95% CI, 67.4 to 76.5), respectively. Both HR HPV detection tests identified women with ASC-US who would benefit the most from colposcopy. Women with persistent HR HPV infection need further investigation despite a first normal colposcopy.
Distinguishing Acute from Chronic Hepatitis C Virus (HCV) Infection Based on Antibody Reactivities to Specific HCV Structural and Nonstructural Proteins
Authors: Araujo Aufra C. , Astrakhantseva Irina V. , Fields Howard A. , Kamili Saleem 
Published: November 2010

ABSTRACT
Currently available serological assays for detection of antibodies to hepatitis C virus (HCV) cannot reliably discriminate acute from chronic HCV infection. We developed a multiplexed, flow-cytometric microsphere immunoassay to measure anti-HCV-IgG reactivities to the core, NS3, NS4, and NS5 HCV recombinant proteins and applied it to 99 serum samples from 24 anti-HCV seroconverters and 141 anti-HCV-IgG and HCV RNA-positive plasma specimens from chronically infected people. Differences in the geometric means or means of signal/cutoff ratios between the two sample sets were statistically significant for all the antigens tested. A multivariate logistic regression model correctly classified the samples in two groups, with a cross-validation accuracy of 90.8% for the acute group and 97.2% for the chronic group. The immunoassay described has the potential to distinguish acute from chronic HCV infection.
Is Infection by
Dermatophilus congolensis
Underdiagnosed?
Authors: Amor Aranzazu , Enríquez Ana , Corcuera Maria Teresa , Toro Carlos , Herrero Dolores , Baquero Margarita 
Published: November 2010

ABSTRACT

Dermatophilus congolensis
, which affects animal species, is an uncommon human infection. Few cases, mainly in tropical areas, have been reported. We describe the first human infection in Spain in a traveler returning from Central America. Diagnosis of human infection may be underestimated in people in contact with animals.
Development and Characterization of a Highly Specific and Sensitive SYBR Green Reverse Transcriptase PCR Assay for Detection of the 2009 Pandemic H1N1 Influenza Virus on the Basis of Sequence Signatures
Authors: Medina Rafael A. , Rojas Mark , Tuin Astrid , Huff Stephen , Ferres Marcela , Martinez-Valdebenito Constanza , Godoy Paula , García-Sastre Adolfo , Fofanov Yuriy , SantaLucia John 
Published: November 2010

ABSTRACT
The emergence and rapid spread of the 2009 H1N1 pandemic influenza virus showed that many diagnostic tests were unsuitable for detecting the novel virus isolates. In most countries the probe-based TaqMan assay developed by the U.S. Centers for Disease Control and Prevention was used for diagnostic purposes. The substantial sequence data that became available during the course of the pandemic created the opportunity to utilize bioinformatics tools to evaluate the unique sequence properties of this virus for the development of diagnostic tests. We used a comprehensive computational approach to examine conserved 2009 H1N1 sequence signatures that are at least 20 nucleotides long and contain at least two mismatches compared to any other known H1N1 genome. We found that the hemagglutinin (HA) and neuraminidase (NA) genes contained sequence signatures that are highly conserved among 2009 H1N1 isolates. Based on the NA gene signatures, we used Visual-OMP to design primers with optimal hybridization affinity and we used ThermoBLAST to minimize amplification artifacts. This procedure resulted in a highly sensitive and discriminatory 2009 H1N1 detection assay. Importantly, we found that the primer set can be used reliably in both a conventional TaqMan and a SYBR green reverse transcriptase (RT)-PCR assay with no loss of specificity or sensitivity. We validated the diagnostic accuracy of the NA SYBR green assay with 125 clinical specimens obtained between May and August 2009 in Chile, and we showed diagnostic efficacy comparable to the CDC assay. Our approach highlights the use of systematic computational approaches to develop robust diagnostic tests during a viral pandemic.
Molecular Detection, Epidemiology, and Genetic Characterization of Novel European Field Isolates of Equine Infectious Anemia Virus
Authors: Cappelli Katia , Capomaccio Stefano , Cook Frank R. , Felicetti Michela , Marenzoni Maria Luisa , Coppola Giacomo , Verini-Supplizi Andrea , Coletti Mauro , Passamonti Fabrizio 
Published: November 2010

ABSTRACT

The application of molecular diagnostic techniques along with nucleotide sequence determination to permit contemporary phylogenetic analysis of European field isolates of equine infectious anemia virus (EIAV) has not been widely reported. As a result, of extensive testing instigated following the 2006 outbreak of equine infectious anemia in Italy, 24 farms with a history of exposure to this disease were included in this study. New PCR-based methods were developed, which, especially in the case of DNA preparations from peripheral blood cells, showed excellent correlation with OIE-approved agar gel immunodiffusion (AGID) tests for identifying EIAV-infected animals. In contrast, the OIE-recommended oligonucleotide primers for EIAV failed to react with any of the Italian isolates. Similar results were also obtained with samples from four Romanian farms. In addition, for the first time complete characterization of
gag
genes from five Italian isolates and one Romanian isolate has been achieved, along with acquisition of extensive sequence information (86% of the total
gag
gene) from four additional EIAV isolates (one Italian and three Romanian). Furthermore, in another 23 cases we accomplished partial characterization of
gag
gene sequences in the region encoding the viral matrix protein. Analysis of this information suggested that most Italian isolates were geographically restricted, somewhat reminiscent of the “clades” described for human immunodeficiency virus type 1 (HIV-1). Collectively this represents the most comprehensive genetic study of European EIAV isolates conducted to date.
Identification of Oseltamivir Resistance among Pandemic and Seasonal Influenza A (H1N1) Viruses by an His275Tyr Genotyping Assay Using the Cycling Probe Method
Authors: Suzuki Yasushi , Saito Reiko , Sato Isamu , Zaraket Hassan , Nishikawa Makoto , Tamura Tsutomu , Dapat Clyde , Caperig-Dapat Isolde , Baranovich Tatiana , Suzuki Takako , Suzuki Hiroshi 
Published: November 2010

ABSTRACTNeuraminidase inhibitors are agents used against influenza viruses; however, the emergence of drug-resistant strains is a major concern. Recently, the prevalence of oseltamivir-resistant seasonal influenza A (H1N1) virus increased globally and the emergence of oseltamivir-resistant pandemic influenza A (H1N1) 2009 viruses was reported. In this study, we developed a cycling probe real-time PCR method for the detection of oseltamivir-resistant seasonal influenza A (H1N1) and pandemic influenza A (H1N1) 2009 viruses. We designed two sets of primers and probes that were labeled with 6-carboxyfluorescein or 6-carboxy-X-rhodamine to identify single nucleotide polymorphisms (SNPs) that correspond to a histidine and a tyrosine at position 275 in the neuraminidase protein, respectively. These SNPs confer susceptibility and resistance to oseltamivir, respectively. In the 2007-2008 season, the prevalence of oseltamivir-resistant H1N1 viruses was 0% (0/72), but in the 2008-2009 season, it increased to 100% (282/282). In the 2009-2010 season, all of the pandemic influenza A (H1N1) 2009 viruses were susceptible to oseltamivir (0/73, 0%). This method is sensitive and specific for the screening of oseltamivir-resistant influenza A (H1N1) viruses. This method is applicable to routine laboratory-based monitoring of drug resistance and patient management during antiviral therapy.
Diversity of Pulsed-Field Gel Electrophoresis Patterns of
Mycobacterium abscessus
Type 2 Clinical Isolates
Authors: Matsumoto Cristianne Kayoko , Chimara Erica , Bombarda Sidney , Duarte Rafael Silva , Leão Sylvia Cardoso 
Published: November 2010

ABSTRACT

An epidemic of infections by rapidly growing mycobacteria related to surgical procedures between 2004 and 2008 in Brazil was caused by a unique strain showing the
Mycobacterium abscessus
type 2 pattern when it was analyzed by the molecular method of PCR-restriction enzyme analysis of the
hsp65
gene (PRA-
hsp65
). In order to investigate the diversity of
M. abscessus
type 2 clinical isolates and to assess whether this epidemic strain was present in specimens from nonsurgical patients, we studied 52 isolates from 38 patients showing this characteristic PRA-
hsp65
pattern obtained between 2005 and 2009. All isolates were identified by sequencing of region V of the
rpoB
gene and typed by pulsed-field gel electrophoresis (PFGE) using two restriction enzymes, DraI and AseI. Seven isolates obtained from sputum, bronchoalveolar lavage fluid, and urine in three different Brazilian states showed
rpoB
sequences 100% similar to the
rpoB
sequence of epidemic strain INCQS 594 and PFGE patterns highly related to the patterns of isolates, evidencing the presence of the epidemic strain in isolates from patients not associated with the surgical epidemic. The remaining isolates showed diverse
rpoB
sequences, with the highest similarities being to the corresponding sequences of
M. massiliense
T
CIP 108297 (21 isolates),
M. bolletii
T
CIP 108541 (19 isolates), or
M. abscessus
T
ATCC 19977 (5 isolates). Two additional clusters could be detected by PFGE. PFGE showed 100% typeability and reproducibility and discriminatory powers, calculated by Simpson's index of diversity, of 0.978 (DraI) and 0.986 (AseI), confirming its suitability for the discrimination of
M. abscessus
type 2 isolates.
Multiplexed Typing of
Mycobacterium avium
subsp.
paratuberculosis
Types I, II, and III by Luminex xMAP Suspension Array
Authors: Gastaldelli Michele , Stefani Elisabetta , Lettini Antonia Anna , Pozzato Nicola 
Published: November 2010

ABSTRACT

Differentiation among types I, II, and III is the primary step in typing
Mycobacterium avium
subsp.
paratuberculosis.
We propose an innovative approach based on detection of gyrase B (
gyrB
) gene polymorphisms by suspension array technology, with high discriminatory power and high-throughput potential.
Factors Associated with Nasal Colonization of Methicillin-Resistant
Staphylococcus aureus
among Healthy Children in Taiwan
Authors: Chen Chih-Jung , Hsu Kuang-Hung , Lin Tzou-Yien , Hwang Kao-Pin , Chen Po-Yen , Huang Yhu-Chering 
Published: November 2010

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) has been identified as a major cause of community-associated (CA)
S. aureus
infections in the past decade. The main reservoir in the community for MRSA and the factors contributing to its worldwide spread remain poorly defined. Between July 2005 and June 2008, a total of 6,057 healthy children 2 to 60 months of age were screened for carriage of
S. aureus
and
Streptococcus pneumoniae
in Taiwan. The prevalence and epidemiological factors influencing MRSA carriage were determined. MRSA strains were tested for antimicrobial susceptibility and underwent molecular characterization. The overall prevalences of MRSA and
S. aureus
carriage were 7.8% and 23.2%, respectively. A majority (88%) of MRSA isolates belonged to a common Asian-Pacific CA-MRSA lineage, multilocus sequence type 59, and were resistant to multiple non-beta-lactam antibiotics. The carriage rate of MRSA was higher among subjects 2 to 6 months old (
P
< 0.0001), residing in northern Taiwan (
P
= 0.0003), and enrolled later in the study (
P
< 0.0001). MRSA colonization was associated with the number of children in the family (adjusted odds ratio [aOR], 1.114; 95% confidence interval [CI], 1.002 to 1.240;
P
= 0.0463) and day care attendance (aOR, 1.530; 95% CI, 1.201 to 1.949;
P
= 0.0006). Breast feeding (
P
< 0.0001) and colonization with
S. pneumoniae
(
P
= 0.0170) were protective against MRSA colonization. We concluded that epidemic CA-MRSA strains increasingly colonized Taiwanese children between 2005 and 2008. The carriage rate varied significantly across different demographical features. Crowding was an independent environmental risk factor that might accelerate CA-MRSA transmission in the community.
Polymorphisms in the Intermediate Region of VacA Impact
Helicobacter pylori
-Induced Disease Development
Authors: Jones Kathleen R. , Jang Sungil , Chang Jennifer Y. , Kim Jinmoon , Chung In-Sik , Olsen Cara H. , Merrell D. Scott , Cha Jeong-Heon 
Published: November 2010

ABSTRACT

Helicobacter pylori
is the etiological agent of diseases such as gastritis, gastric and duodenal ulcers, and two types of gastric cancers. While some insight has been gained into the etiology of these diverse manifestations, by and large, the reason that some individuals develop more severe disease remains elusive. Recent studies have focused on the roles of
H. pylori
toxins CagA and VacA on the disease process and have suggested that both toxins are intimately involved. Moreover, CagA and VacA are polymorphic within different
H. pylori
strains, and particular polymorphisms seem to show a correlation with the development of particular disease states. Among VacA polymorphisms, the intermediate region has recently been proposed to play a major role in disease outcome. In this article, we describe a detailed sequence analysis of the polymorphic intermediate region of
vacA
from strains obtained from a large South Korean population. We show that polymorphisms found at amino acid position 196 are associated with more severe disease manifestations. Additionally, polymorphisms found at amino acid position 231 are linked to disease in strains that carry the non-EPIYA-ABD allele of CagA. Collectively, these data help explain the impact of the VacA intermediate region on disease and lead to the hypothesis that there are allele-driven interactions between VacA and CagA.
Novel Multiplex Oligonucleotide-Conjugated Bead Suspension Array for Rapid Identification of Enterovirus 71 Subgenogroups
Authors: Wu Y. , Tan E. L. , Yeo A. , Chan K. P. , Nishimura H. , Cardosa M. J. , Poh C. L. , Quak S. H. , Chow Vincent T. 
Published: November 2010

ABSTRACT
A high-throughput multiplex bead suspension array was developed for the rapid subgenogrouping of EV71 strains, based on single nucleotide polymorphisms observed within the VP1 region with a high sensitivity as low as 1 PFU. Of 33 viral isolates and 55 clinical samples, all EV71 strains were successfully detected and correctly subgenogrouped.
Predominance of Porcine P[23] Genotype Rotaviruses in Piglets with Diarrhea in Northern Thailand
Authors: Okitsu Shoko , Khamrin Pattara , Thongprachum Aksara , Maneekarn Niwat , Mizuguchi Masashi , Ushijima Hiroshi 
Published: November 2010

ABSTRACT
Of 131 stool samples collected from piglets with diarrhea in northern Thailand between July 2006 and August 2008, 14 (10.7%) were positive for group A rotavirus. Sequence analysis showed that 13 strains (92.9%) belonged to the rare P[23] genotype combination with G9 or G3 genotypes.
Identification of Novel Endogenous Betaretroviruses Which Are Transcribed in the Bovine Placenta
Authors: Baba Kenji , Nakaya Yuki , Shojima Takayuki , Muroi Yoshikage , Kizaki Keiichiro , Hashizume Kazuyoshi , Imakawa Kazuhiko , Miyazawa Takayuki 
Published: November 2010

ABSTRACTSequences of retroviral origin occupy approximately 10% of mammalian genomes. Various infectious endogenous retroviruses (ERVs) and functional retroviral elements have been reported for several mammals but not cattle. Here, we identified two proviruses, designated bovine endogenous retrovirus K1 (BERV-K1) and BERV-K2, containing full-length envelope (env) genes in the bovine genome. Phylogenetic analysis revealed that they belong to the genusBetaretrovirus. By reverse transcription (RT)-PCR, both BERV-K1 and -K2envmRNAs were detected in the placenta and cultured bovine trophoblast cells. Real-time RT-PCR analysis using RNAs isolated from various bovine tissues revealed that BERV-K1envmRNA was preferentially expressed in the placenta. Moreover, we also found the expression of doubly spliced transcripts, named theREBK1andREBK2genes. Both the REBK1 and REBK2 proteins have motifs for a putative nuclear localization signal and a nuclear export signal. REBK1 and REBK2 fused with green fluorescent proteins were localized mainly in the nuclei when they were expressed in bovine and porcine cells. In theenvand 3′ long terminal repeats of BERV-K1 and -K2, we found regulatory elements responsible for the splicing and transport of viral RNAs and/or translation of theenvgenes. Although we have not identified the expressed Env proteins in bovine tissues, these data suggest that both BERV-K1 and BERV-K2 express Env proteins and that these proteins may have physiological functionsin vivo.
Viral Serine/Threonine Protein Kinases
Authors: Jacob Thary , Van den Broeke Céline , Favoreel Herman W. 
Published: November 2010

ABSTRACT
Phosphorylation represents one the most abundant and important posttranslational modifications of proteins, including viral proteins. Virus-encoded serine/threonine protein kinases appear to be a feature that is unique to large DNA viruses. Although the importance of these kinases for virus replication in cell culture is variable, they invariably play important roles in virus virulence. The current review provides an overview of the different viral serine/threonine protein kinases of several large DNA viruses and discusses their function, importance, and potential as antiviral drug targets.