bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translational benefits from research on rare genodermatoses
Authors: McGrath John A 
Published: April 2004

SUMMARYSignificant new discoveries about many of the genodermatoses have been made recently through an improved knowledge of the human genome, advances in molecular screening strategies and also through more comprehensive Internet DNA databases. By 2003, over 350 single gene skin disorders had been characterized at a molecular level. These new data provide more detailed information for patients, allow for more accurate diagnoses, and help improve genetic counselling. Other benefits include the feasibility of carrier screening and DNA‐based prenatal testing, as well as a platform for devising new treatments, including somatic gene therapy. Research on rare single gene disorders also provides new insight into more common skin conditions. For example, new ideas about photosensitivity are emerging from discoveries of mutations in a novel component of the actin cytoskeleton (kindlin‐1) in the rare inherited poikiloderma disorder, Kindler syndrome. Likewise, new clues to understanding disease pathology in lichen sclerosus have been gleaned from the discovery of pathogenic mutations in the skin protein, extracellular matrix protein 1, in the rare sclerosing inherited skin disorder, lipoid proteinosis. Finally, new insight into what can cause exuberant granulation tissue in chronic wounds has been provided by the discovery of specific mutations in the basement membrane protein, laminin 5, in the rare inherited condition, laryngo‐onychocutaneous syndrome. It is clear that a precise research focus on the rare genodermatoses is providing practical benefits for sufferers of these disorders, as well as new lessons and ideas about more common acquired skin conditions.
Possible role of Mycobacterium tuberculosis complex in Melkersson–Rosenthal syndrome demonstrated with Gen‐Probe amplified Mycobacterium tuberculosis direct test
Authors: Apaydin Rebiay , Bahadir Sevgi , Kakklikkaya Neşe , Bilen Nilgün , Bayramgürler Dilek 
Published: April 2004

SUMMARYMelkersson–Rosenthal (MRS) syndrome is characterized by a classical triad of recurrent or persistent orofacial swelling, peripheral facial nerve paralysis and lingua plicata. Granulomatous cheilitis (GC) is regarded as a monosymptomatic form of MRS. The exact aetiologies of MRS and GC are unknown. In this study we investigated the possible role of mycobacteria in these two conditions. A ribosomal RNA amplification‐based Gen‐Probe amplified Mycobacterium tuberculosis direct test was used to investigate the presence of M. tuberculosis complex in paraffin‐embedded skin biopsy specimens from five patients with MRS and one patient with GC. Three of the six specimens were shown to be positive using this system; one of the positive specimens also showed positive Ziehl–Neelsen staining. These results suggest a possible mycobacterial aetiology for MRS and GC.
Grover's disease: 34 years on
Authors: Quirk Christopher J , Heenan Peter J 
Published: April 2004

SUMMARYGrover's disease is an entity reported worldwide and recognized as a common disease since Grover first described it in 1970. Its cause remains obscure, but hospitalized, febrile and sun‐damaged patients are particularly prone. It is frequently associated with some other skin diseases, including eczemas, psoriasis and solar keratoses. Acantholysis is the universal histological finding in all the varying clinical presentations. Treatment in the past has been ad hoc, but topical therapy, acitretin and phototherapy can suppress symptoms.
Diversity of Noroviruses Cocirculating in the North of England from 1998 to 2001
Authors: Gallimore Chris I. , Green Jonathan , Lewis David , Richards Alison F. , Lopman Benjamin A. , Hale Antony D. , Eglin Roger , Gray Jim J. , Brown David W. G. 
Published: April 2004

ABSTRACT

A study was undertaken to investigate the diversity of noroviruses (NVs) in fecal samples from patients from 529 outbreaks and 141 sporadic cases of gastroenteritis in the North of England from September 1998 to August 2001. NV strains were detected by electron microscopy and characterized by a combination of the Grimsby virus antigen enzyme-linked immunosorbent assay, reverse transcriptase PCR, the heteroduplex mobility assay, and DNA sequencing. Twenty-one distinct NV strains, including several novel or variant strains not seen previously, were found circulating in the population studied. Genogroup II NVs were responsible for 83% of the outbreaks. Several strains cocirculated at any one time. The Bristol (Grimsby/Lordsdale) and Hawaii (Girlington) genotypes were the most prevalent among the NVs identified, detected in 49 and 20% of the outbreaks, respectively. A limited number of other genogroup II and I strains were cocirculating. The virus populations detected in hospitals and nursing homes were distinct from those found in community-based outbreaks. Outbreaks in hospitals and nursing homes were more likely to be caused by genogroup II strain Grimsby or Girlington (
P
< 0.0001) than by other genogroup II or I strains.
Detection and Genotyping of Varicella-Zoster Virus by TaqMan Allelic Discrimination Real-Time PCR
Authors: Campsall Paul A. , Au Nicholas H. C. , Prendiville Julie S. , Speert David P. , Tan Rusung , Thomas Eva E. 
Published: April 2004

ABSTRACT
A proportion of individuals vaccinated with live attenuated Oka varicella-zoster virus (VZV) vaccine subsequently develop attenuated chicken pox and/or herpes zoster. To determine whether postvaccination varicella infections are caused by vaccine or wild-type virus, a simple method for distinguishing the vaccine strain from wild-type virus is required. We have developed a TaqMan real-time PCR assay to detect and differentiate wild-type virus from Oka vaccine strains of VZV. The assay utilized two fluorogenic, minor groove binding probes targeted to a single nucleotide polymorphism in open reading frame 62 that distinguishes the Oka vaccine from wild-type strains. VZV DNA could be genotyped and quantified within minutes of thermocycling completion due to real-time monitoring of PCR product formation and allelic discrimination analysis. The allelic discrimination assay was performed in parallel with two standard PCR-restriction fragment length polymorphism (RFLP) methods on 136 clinical and laboratory VZV strains from Canada, Australia, and Japan. The TaqMan assay exhibited a genotyping accuracy of 100% and, when compared to both PCR-RFLP methods, was 100 times more sensitive. In addition, the method was technically simpler and more rapid. The TaqMan assay also allows for high-throughput genotyping, making it ideal for epidemiologic study of the live attenuated varicella vaccine.
Development, Evaluation, and Validation of an Oligonucleotide Probe Hybridization Assay To Subtype Human Immunodeficiency Virus Type 1 Circulating Recombinant Form CRF02_AG
Authors: Njai Harr F. , Van der Auwera Gert , Ngong Chiambah A. , Heyndrickx Leo , Sawadago Souleymane , Whittle Hilton , Nyambi Phillipe , Colebunders Robert , van der Groen Guido , Janssens Wouter 
Published: April 2004

ABSTRACT

We have developed and validated an oligonucleotide probe hybridization assay for human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) CRF02_AG. In the p17 coding region of the
gag
gene, a CRF02_AG-specific signature pattern was observed. Five working probes were designed to discriminate CRF02_AG infections from infections by all other documented subtypes and CRFs in an enzyme-linked immunosorbent assay-based oligonucleotide probe hybridization assay. Nucleic acids were extracted from a panel of HIV-1-positive plasma samples from Cameroon, Bénin, Côte d'Ivoire, Kenya, Zambia, and Belgium and from blood spots from The Gambia. CRF02_AG (
n
= 147) and non-CRF02 (
n
= 100) samples were analyzed to evaluate and validate the oligonucleotide probe hybridization assay. The CRF02_AG-specific oligonucleotide probe hybridization assay has a high sensitivity and specificity, with good positive and negative predictive values in regions of high and low prevalence. A validation of the assay with West and West Central African samples indicated a sensitivity of 98.4% and a specificity of 96.7%. The oligonucleotide probe hybridization assay as a diagnostic tool will allow for rapid screening for CRF02_AG. This could be used to track the HIV epidemic in terms of documenting the real prevalence of CRF02_AG strains and will complement efforts in vaccine development. Moreover, this technology can easily be applied in laboratories in developing countries.
Evaluation of Automated Sample Preparation and Quantitative PCR LCx Assay for Determination of Human Immunodeficiency Virus Type 1 RNA
Authors: Muller Zsofia , Stelzl Evelyn , Bozic Michael , Haas Josef , Marth Egon , Kessler Harald H. 
Published: April 2004

ABSTRACT
Efforts have been made to achieve full automation of molecular assays for quantitative detection of human immunodeficiency virus type 1 (HIV-1). In the present study, the Abbott LCx HIV RNA Quantitative assay was evaluated in conjunction with automated HIV-1 RNA extraction on the MagNA Pure LC instrument and compared to the conventional LCx HIV RNA Quantitative assay, which uses a manual nucleic acid extraction protocol. Accuracy, linearity, and interassay and intra-assay variations were determined. The performance of the assay in a routine clinical laboratory was tested with a total of 105 clinical specimens. When the accuracy of the LCx HIV RNA Quantitative assay with the automated sample preparation protocol was tested, all results were found to be within ±0.5 log unit of the expected results. Determination of linearity resulted in a quasilinear curve over 3.5 log units. For determination of interassay variation, coefficients of variation were found to be between 21 and 66% for the LCx HIV RNA Quantitative assay with the automated sample preparation protocol and between 10 and 69% for the LCx HIV RNA Quantitative assay with manual sample preparation. For determination of intra-assay variation, coefficients of variation were found to be between 7 and 25% for the LCx HIV RNA Quantitative assay with the automated sample preparation protocol and between 7 and 19% for the LCx HIV RNA Quantitative assay with manual sample preparation. When clinical samples were tested by the LCx HIV RNA Quantitative assay with the automated sample preparation protocol and the results were compared with those of the LCx HIV RNA Quantitative assay with manual sample preparation, 95% of all positive results were found to be within ±0.5 log unit. In conclusion, the assay with automated sample preparation proved to be suitable for use in the routine diagnostic laboratory and required significantly less hands-on time.
Identification of Three Clinically Relevant
Borrelia burgdorferi
Sensu Lato Genospecies by PCR-Restriction Fragment Length Polymorphism Analysis of 16S-23S Ribosomal DNA Spacer Amplicons
Authors: Ranka Renate , Bormane Antra , Salmina Kristine , Baumanis Viesturs 
Published: April 2004

ABSTRACT

We report the results of a study of the prevalences of three clinically relevant
Borrelia burgdorferi
sensu lato genospecies (
Borrelia burgdorferi
sensu stricto,
Borrelia afzelii
, and
Borrelia garinii
) in 1,040 questing
Ixodes
ticks from all regions of Latvia, where Lyme borreliosis is endemic. The prevalences of
Borrelia
in
Ixodes ricinus
and
Ixodes persulcatus
were 22.6 and 27.9%, respectively. Molecular typing of
B. burgdorferi
from infected ticks was performed by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified fragments of the 16S-23S (
rrs-rrlA
) rRNA intergenic spacer by using species-specific primers and subsequent sequencing. The dominant
Borrelia
species in both
Ixodes
species was
B. afzelii.
In addition, different restriction patterns of
B. garinii
and
B. afzelii
were also identified. This study demonstrates that the 16S-23S rRNA PCR-RFLP typing method is simple, sensitive, and fast and that it allows one to differentiate among
B. burgdorferi
species and subspecies with various degrees of pathogenic potential directly in ticks. These features are important in monitoring Lyme disease.
Dynamics of Long-Term Colonization of Respiratory Tract byHaemophilus influenzaein Cystic Fibrosis Patients Shows a Marked Increase in Hypermutable Strains
Authors: Román Federico , Cantón Rafael , Pérez-Vázquez María , Baquero Fernando , Campos José 
Published: April 2004

ABSTRACTThe persistence and variability of 188Haemophilus influenzaeisolates in respiratory tract of 30 cystic fibrosis (CF) patients over the course of 7 years was studied. Antibiotic susceptibility testing, DNA fingerprinting, and analysis of outer membrane protein profiles were performed on all isolates. A total of 115 distinct pulsed-field gel electrophoresis profiles were identified. Ninety percent of patients were cocolonized with two or more clones over the studied period. A third of the patients were cross-colonized with one or twoH. influenzaestrains; 11% of the clones persisted for 3 or more months. Biotype, outer membrane protein profiles, and resistance profiles showed variation along the studied period, even in persisting clones. Four isolates (2.1%) recovered from 3 patients were type f capsulate, with three of them belonging to the same clone. β-Lactamase production was detected in 23.9% of isolates while 7% of the β-lactamase-negative isolates presented diminished susceptibility to ampicillin (β-lactamase-negative ampicillin resistance phenotype). Remarkably, 21.3% of theH. influenzaeisolates presented decreased susceptibility to ciprofloxacin, which was mainly observed in persisting clones. Of theH. influenzaeisolates from CF patients, 18 (14.5%) were found to be hypermutable in comparison with 1 (1.4%) from non-CF patients (P< 0.0001). Ten patients (33.3%) were colonized by hypermutable strains over the study period. A multiresistance phenotype and long-term clonal persistence were significantly associated in some cases for up to 7 years. These results suggest thatH. influenzaebronchial colonization in CF patients is a dynamic process, but better-adapted clones can persist for long periods of time.
Phenotypic and Genetic Characterization of a Unique Variant of Serogroup C ET-15 Meningococci (with the Antigenic Formula C:2a:P1.7,1) Causing Invasive Meningococcal Disease in Quebec, Canada
Authors: Tsang Raymond S. W. , Tsai Chao Ming , Zhu Peixuan , Ringuette Louise , Lorange Manon , Law Dennis K. S. 
Published: April 2004

ABSTRACT

Serogroup C
Neisseria meningitidis
belonging to the electrophoretic type (ET) ET-15, a variant of ET-37, is endemic in Canada. Like other serogroup C ET-37 meningococci, the endemic ET-15 strains are usually found to carry the serotype and serosubtype antigens of 2a:P1.5,2. In 2001, a sudden increase in the number of cases of serogroup C meningococcal disease in Quebec, Canada, was caused by an antigenic variant of the ET-15 strain. This antigenic variant carries the unique serosubtype marker of P1.7,1. Strains of C:2a:P1.7,1 meningococci were not isolated in Canada in large numbers prior to 2001, and the characteristics of these meningococcal strains linked to an outbreak in Quebec, Canada, are described in the present study.
Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya
Authors: Kariuki Samuel , Revathi Gunturu , Muyodi Jane , Mwituria Joyce , Munyalo Agnes , Mirza Sajjad , Hart C. Anthony 
Published: April 2004

ABSTRACT

We characterized by antibiotic susceptibility, plasmid analysis, incompatibility grouping, and pulsed-field gel electrophoresis (PFGE) of XbaI- and SpeI-digested DNA 102
Salmonella enterica
serovar Typhi (serovar Typhi) isolated from recent outbreaks of typhoid in three different parts of Kenya. Only 13.7% were fully susceptible, whereas another 82.4% were resistant to each of the five commonly available drugs: ampicillin, chloramphenicol, and tetracycline (MICs of >256 μg/ml); streptomycin (MIC, >1,024 μg/ml); and cotrimoxazole (MIC of >32 μg/ml). Resistance to these antibiotics was encoded on a 110-kb self-transferable plasmid of IncHI1 incompatibility group. The MICs of nalidixic acid (MIC, 8 to 16 μg/ml) and ciprofloxacin (MIC of 0.25 to 0.38 μg/ml) for 41.7% of the 102 serovar Typhi isolates were 5- and 10-fold higher, respectively, than for sensitive strains. Amplification by PCR and sequencing of the genes coding for gyrase (
gyrA
and
gyrB
) and topoisomerase IV (
parE
and
parC
) within the quinolone resistance-determining region revealed that the increase in the MICs of the quinolones had not resulted from any significant mutation. Analysis of genomic DNA from both antimicrobial agent-sensitive and multidrug-resistant serovar Typhi by PFGE identified two distinct subtypes that were in circulation in the three different parts of Kenya. As the prevalence of multidrug-resistant serovar Typhi increases, newer, more expensive, and less readily available antimicrobial agents will be required for the treatment of typhoid in Kenya.
Genotyping and Coalescent Phylogenetic Analysis of
Pneumocystis jiroveci
from South Africa
Authors: Robberts Frans J. L. , Liebowitz Lynne D. , Chalkley Lynda J. 
Published: April 2004

ABSTRACT

Sequence analysis of
Pneumocystis jiroveci
internal transcribed spacer (ITS) regions has become an important epidemiological tool. The objectives of the present study were to investigate sequence variations in the ITS1-5.8S ribosomal DNA (rDNA)-ITS2 regions; determine the
P. jiroveci
genotypes present in Cape Town, South Africa; and resolve the lineage evolution of the types by use of the coalescent theory. ITS regions were amplified from samples collected from 19 patients. PCR products were cloned, and four to five clones were sequenced from each specimen. Statistical parsimony was applied for coalescence-based network genotype analysis. The most prevalent type was Eg (14 of 19 patients, 33 of 83 clones), followed by Gg (4 of 19 patients, 7 of 83 clones), Eu (3 of 19 patients, 5 of 83 clones), and Gh (2 of 19 patients, 2 of 83 clones). Four new combinations (Eo, Je, Ge, and No), 11 new ITS1 sequences, and 13 new ITS2 sequences were identified. A new ITS2 type was detected in three patients and was designated type u. Coinfection appeared to be common, with 15 of 19 patients harboring more than one type and with up to six types per specimen. The resultant parsimony network identified Eg as the most probable ancestral haplotype and supported the occurrence of recombinational events within the population studied. Although the 5.8S rDNA region revealed only 13 clones containing one to two nucleotide polymorphisms, it may assist in defining types. Coalescent theory proposed that Eg is an ancestral type from which microevolutionary subtypes radiate.
Evaluation of the Automated Phoenix System for Potential Routine Use in the Clinical Microbiology Laboratory
Authors: Donay J.-L. , Mathieu D. , Fernandes P. , Prégermain C. , Bruel P. , Wargnier A. , Casin I. , Weill F. X. , Lagrange P. H. , Herrmann J. L. 
Published: April 2004

ABSTRACT

A comparative study was designed to evaluate the identification (ID) and antimicrobial susceptibility testing (AST) performances of the BD Phoenix Automated Microbiology System (Becton Dickinson Diagnostic Systems [BD], Pont de Claix, France). A total of 305 single clinical isolates were collected, and comparisons were made with routine manual methods in use in our microbiology laboratories. The percentages of correct IDs were 93.3, 89.4, 91.8, and 85.7% for enterobacteria, nonfermenting gram-negative bacilli, staphylococci, and streptococci-enterococci, respectively. The median ID time was 3 h, and the median time for AST was 10 h 30 min. AST results showed variable percentages of errors for the different antibiotics. None of the enterobacteria and 0.3% of
Pseudomonas aeruginosa
isolates showed a very major error (VME). Only one strain of
Staphylococcus aureus
showed a VME with oxacillin. We demonstrate here the efficiency of the Phoenix system, which can be used for the majority of strains encountered in a university-based laboratory, for ID and AST.
Practical Strategies for Performance Optimization of the Enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test
Authors: Sloutsky A. , Han L. L. , Werner B. G. 
Published: April 2004

ABSTRACT

The enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test was evaluated using a combined set of 338 acid-fast smear-positive and smear-negative, respiratory and nonrespiratory clinical specimens received by the Massachusetts State Tuberculosis Laboratory from September 1999 through March 2002. Microbiological culture was used as the reference method; therefore, the sensitivity and specificity of the MTD test were calculated for culture-positive specimens only. The initial assessment indicated that the overall sensitivity, specificity, and positive and negative predictive values of the MTD test for all specimens grouped together were 62, 98, 99, and 68%, respectively. A detailed discrepancy analysis revealed that two major factors causing negative MTD results in specimens that were culture positive for
M. tuberculosis
complex were patient treatment with antituberculosis drugs prior to testing and the presence of inhibitory substances in the specimen. Based on these findings, a protocol for optimizing MTD test performance in this setting is proposed in which (i) specimens from patients taking antituberculosis medications are excluded from testing and (ii) all initially MTD-negative or MTD-equivocal specimens are subjected to testing for inhibitors. If this strategy was followed, the MTD test sensitivity would be at least 91%, a significant improvement over the initial sensitivity of 62%. Accordingly, the negative predictive value would increase from 68 to 91%.
Multiplex PCR Genotyping Assay That Distinguishes between Isolates ofClostridium perfringensType A Carrying a Chromosomal Enterotoxin Gene (cpe) Locus, a PlasmidcpeLocus with an IS1470-Like Sequence, or a PlasmidcpeLocus with an IS1151Sequence
Authors: Miyamoto Kazuaki , Wen Qiyi , McClane Bruce A. 
Published: April 2004

ABSTRACTClostridium perfringenstype A isolates carrying the enterotoxin (cpe) gene are important causes of both food poisoning and non-food-borne diarrheas in humans. In North America and Europe, food poisoning isolates were previously shown to carry a chromosomalcpegene, while non-food-borne gastrointestinal (GI) disease isolates from those two geographic locations were found to have a plasmidcpegene. In this report, we describe the development of an economical multiplex PCRcpegenotyping assay that works with culture lysates to distinguish among type A isolates carrying a chromosomalcpegene, a plasmidcpegene with a downstream IS1470-like sequence, or a plasmidcpegene with a downstream IS1151sequence. When this multiplex PCR assay was applied in molecular epidemiologic studies, it was found that (i) all 57 examined type A isolates with a plasmidcpegene have either IS1470-like or IS1151sequences downstream of the plasmidcpegene; (ii) an IS1470-like sequence, rather than an IS1151sequence, is more commonly present downstream of the plasmidcpegene (particularly in North American non-food-borne human GI disease isolates); and (iii) as previously shown in the United States and Europe, isolates carrying the chromosomalcpegene also appear to be the major cause ofC. perfringensfood poisoning in Japan. The superiority of this new multiplex PCR assay over existingcpegenotyping approaches should facilitate further molecular epidemiologic investigations ofC. perfringensenterotoxin-associated GI illnesses and their associatedcpe-positive type A isolates.