bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Analysis of an Echovirus 3 Strain Isolated from an Individual Concurrently with Appearance of Islet Cell and IA-2 Autoantibodies
Authors: Williams Çiğdem H. , Oikarinen Sami , Tauriainen Sisko , Salminen Kimmo , Hyöty Heikki , Stanway Glyn 
Published: February 2006

ABSTRACT

Growing evidence has implicated members of the genus
Enterovirus
of the family
Picornaviridae
in the etiology of some cases of type 1 diabetes (T1D). To contribute to an understanding of the molecular determinants underlying this association, we determined the complete nucleotide sequence of a strain of echovirus 3 (E3),
Human enterovirus B
(HEV-B) species, isolated from an individual who soon after virus isolation developed autoantibodies characteristic of T1D. The individual has remained positive for over 6 years for tyrosine phosphatase-related IA-2 protein autoantibodies and islet cell autoantibodies, indicating an ongoing autoimmune process, although he has not yet developed clinical T1D. The sequence obtained adds weight to the observation that recent enterovirus isolates differ significantly from prototype strains and provides further evidence of a role for recombination in enterovirus evolution. In common with most HEV-B species members, the isolate exhibits 2C and VP1 sequences suggested as triggers of autoimmunity through molecular mimicry. However, comparisons with the E3 prototype strain and previously reported diabetogenic and nondiabetogenic HEV-B strains do not reveal clear candidates for sequence features of PicoBank/DM1/E3 that could be associated with autoantibody appearance. This is the first time a virus strain isolated at the time of commencement of beta-cell damage has been analyzed and is an invaluable addition to enterovirus strains isolated previously at the onset of T1D in the search for specific molecular features which could be associated with diabetes induction.
Use of the
espZ
Gene Encoded in the Locus of Enterocyte Effacement for Molecular Typing of Shiga Toxin-Producing
Escherichia coli
Authors: Gilmour Matthew W. , Tracz Dobryan M. , Andrysiak Ashleigh K. , Clark Clifford G. , Tyson Shari , Severini Alberto , Ng Lai-King 
Published: February 2006

ABSTRACT

Infections with Shiga toxin-producing
Escherichia coli
(STEC) result in frequent cases of sporadic and outbreak-associated enteric bacterial disease in humans. Classification of STEC is by
stx
genotype (encoding the Shiga toxins), O and H antigen serotype, and seropathotype (subgroupings based upon the clinical relevance and virulence-related genotypes of individual serotypes). The
espZ
gene is encoded in the locus of enterocyte effacement (LEE) pathogenicity island responsible for the attaching and effacing (A/E) lesions caused by various
E. coli
pathogens (but not limited to STEC), and this individual gene (∼300 bp) has previously been identified as hypervariable among these A/E pathogens. Sequence analysis of the
espZ
locus encoded by additional STEC serotypes and strains (including O26:H11, O121:H19, O111:NM, O145:NM, O165:H25, O121:NM, O157:NM, O157:H7, and O5:NM) indicated that distinct sequence variants exist which correlate to subgroups among these serotypes. Allelic discrimination at the
espZ
locus was achieved using Light Upon eXtension real-time PCR and by liquid microsphere suspension arrays. The allele subtype of
espZ
did not correlate with STEC seropathotype classification; however, a correlation with the allele type of the LEE-encoded intimin (
eae
) gene was supported, and these sequence variations were conserved among individual serotypes. The study focused on the characterization of three clinically significant seropathotypes of LEE-positive STEC, and we have used the observed genetic variation at a pathogen-specific locus for detection and subtyping of STEC.
Use of PCR-Restriction Fragment Length Polymorphism Analysis To Identify the Main New WorldLeishmaniaSpecies and Analyze Their Taxonomic Properties and Polymorphism by Application of the Assay to Clinical Samples
Authors: Rotureau Brice , Ravel Christophe , Couppié Pierre , Pratlong Francine , Nacher Mathieu , Dedet Jean-Pierre , Carme Bernard 
Published: February 2006

ABSTRACTAt least 13 characterizedLeishmaniaspecies are known to infect humans in South America. Five of these parasites are transmitted in the sylvatic ecotopes of the whole French Guianan territory and responsible for cutaneous leishmaniasis. For the diagnosis of cutaneous leishmaniasis, restriction fragment length polymorphism (RFLP) analyses have shown promising results. Thus, the end of the small subunit and internal transcribed spacer 1 of the rRNA genes were sequenced and targeted by PCR-RFLP analysis in the 10 main New World (NW)Leishmaniaspecies from the two subgenera. Then, the procedure was tested on 40 samples from patients with cutaneous leishmaniasis, and its results were compared with those of conventional methods. (i) The results of this simple genus-specific method were in agreement with those of previous isoenzyme analyses. (ii) This method distinguished the most medically relevantLeishmaniaspecies with only one enzyme (RsaI). (iii) This method could be performed directly on human biopsy specimens (sensitivity of 85.7%). Performing NWLeishmaniaspecies typing rapidly and easily in the field constitutes a very valuable improvement for detection ofLeishmaniaspp. Revealing great diversity with several enzymes, this method could also be useful for taxonomic, ecological, and epidemiological studies in space and time.
Molecular Epidemiology of
Leishmania
(
Viannia
)
guyanensis
in French Guiana
Authors: Rotureau Brice , Ravel Christophe , Nacher Mathieu , Couppié Pierre , Curtet Isabelle , Dedet Jean-Pierre , Carme Bernard 
Published: February 2006

ABSTRACT

Little information is available about the genetic variability of
Leishmania
populations and the possible correlations with ecoepidemiological features of leishmaniases. The present study was carried out in French Guiana, a country where cutaneous leishmaniases (CL) are endemic over the whole territory. The genetic polymorphism of a nuclear sequence encompassing the end of the ribosomal small subunit and the internal transcribed spacer 1 of 265 isolates from patients with CL was examined by restriction fragment length polymorphism analysis. Genotypes based on the fingerprinting phenetic integration were compared to epidemiological, clinical, and geographical data. In agreement with previous reports, five different
Leishmania
species were identified, but
Leishmania
(
Viannia
)
guyanensis
represented 95.8% of the samples. Two distinct
L
. (
V
.)
guyanensis
populations were found to originate in two ecologically characterized regions. Higher lesional parasite densities and the need for additional treatments were significantly linked to genotype group I. Parasites of genotype group II were more likely to cause chronic and disseminated cutaneous forms in patients.
L
. (
V
.)
guyanensis
was previously said not to be very polymorphic; however, the present analysis resulted in a significant degree of discrimination among
L
. (
V
.)
guyanensis
isolates from diverse ecological areas and with different clinical implications.
Sequence Variation of the SeM Gene ofStreptococcus equiAllows Discrimination of the Source of Strangles Outbreaks
Authors: Kelly Charlotte , Bugg Maxine , Robinson Carl , Mitchell Zoe , Davis-Poynter Nick , Newton J. Richard , Jolley Keith A. , Maiden Martin C. J. , Waller Andrew S. 
Published: February 2006

ABSTRACTImproved understanding of the epidemiology ofStreptococcus equitransmission requires sensitive and portable subtyping methods that can rationally discriminate between strains.S. equiis highly homogeneous and cannot be distinguished by multilocus enzyme electrophoretic or multilocus sequence-typing methods that utilize housekeeping genes. However, on sequence analysis of the N-terminal region of the SeM genes of 60S. equiisolates from 27 strangles outbreaks, we identified 21 DNA codon changes. These resulted in the nonsynonymous substitution of 18 amino acids and allowed the assignment ofS. equistrains to 15 distinct subtypes. Our data suggest the presence of multiple epitopes across this region that are subjected to selective immune pressure (nonsynonymous-synonymous substitution rate [dN/dS] ratio = 3.054), particularly during the establishment of long-termS. equiinfection. We further report the application of SeM gene subtyping as a method to investigate potential cases of disease related to administration of a live attenuatedS. equivaccine. SeM gene subtyping successfully differentiated between the vaccine strain and field strains ofS. equiresponsible for concurrent disease. These results were confirmed by the development and application of a PCR diagnostic test, which identifies thearoApartial gene deletion present in the Equilis StrepE vaccine strain. Although the vaccine strain was found to be responsible for injection site lesions, all seven outbreaks of strangles investigated in recently vaccinated horses were found to be due to concurrent infection with wild-typeS. equiand not due to reversion of the vaccine strain.
Comparison of Physician- and Self-Collected Genital Specimens for Detection of Human Papillomavirus in Men
Authors: Hernandez Brenda Y. , McDuffie K. , Goodman M. T. , Wilkens L. R. , Thompson P. , Zhu X. , Wong W. , Ning L. 
Published: February 2006

ABSTRACT

There is currently no consensus regarding the most appropriate methods of sampling for the detection of genital human papillomavirus (HPV) in men. We employed a recently developed collection method involving abrasion and moistened swabbing of the genital skin surface for the detection of HPV in a cohort of 136 university-affiliated males in Hawaii. Genital specimens collected by physicians using this method were compared with self-collected specimens from the same individuals obtained 24 h later. Self-collected specimens yielded a greater proportion of sufficient specimens than physician-collected specimens. HPV detection was comparable in physician- and self-collected specimens; detection was highest in the penile shaft (51.2% and 51.5%, respectively,
P
= 0.96), followed by the scrotum (41.2% and 46.2%,
P
= 0.43), the glans/coronal sulcus (31.9% and 33.1%,
P
= 0.84), and the foreskin (33.3% and 28.6%,
P
= 0.74). Site-specific agreement in HPV detection between paired physician- and self-collected samples ranged from 67.2% (kappa = 0.34) for the penile shaft to 95.0% (kappa = 0.89) for the foreskin. There was a high degree of concordance in HPV genotypes in HPV-positive pairs. The most common type was HPV type 84, which comprised approximately 15% of the specimens. The emery paper-swab method offers an efficient sampling method for genital HPV DNA detection in men that could be used both within and outside of the clinical setting.
Extensive Hospital-Wide Spread of a Multidrug-Resistant
Enterobacter cloacae
Clone, with Late Detection Due to a Variable Antibiogram and Frequent Patient Transfer
Authors: Leverstein-van Hall Maurine A. , Blok Hetty E. M. , Paauw Armand , Fluit Ad C. , Troelstra Annet , Mascini Ellen M. , Bonten Marc J. M. , Verhoef Jan 
Published: February 2006

ABSTRACT

A hospital-wide increase in the number of patients with aminoglycoside-resistant
Enterobacter cloacae
(AREC) isolated from clinical cultures was detected in December 2002 using a classical surveillance system (CSS). CSS refers to a strategy based on the recognition of an increased incidence of a species with a particular antibiogram at certain wards in a limited period. Since clonal spread was suspected, hospital records were reviewed for
E. cloacae
culture-positive patients. Based upon genotyping of 139 clinical
E. cloacae
isolates from 80 patients, it was concluded that 53 patients had had clinical cultures with a single AREC clone since April 2001. Determinants for unnoticed spread were investigated retrospectively, as was the possibility that a computer-assisted surveillance method would have detected this outbreak at an earlier stage. Determinants associated with late detection of clonal spread were the following: (i) the absence of a hospital-wide increase in incidence of
E. cloacae
cases for 1.5 years, (ii) the long time interval between cases, (iii) the hospital-wide occurrence of new cases, due to a high number of patient transfers between wards, (iv) the large variety of clinical sites, and (v) the high variability of antibiograms (
n
= 33). Retrospective application of a recently described computer-assisted surveillance method as well as an “in-house”-developed algorithm resulted in earlier detection of the outbreak of 6 and 12 months, respectively. These findings suggest that computerized tools for surveillance may recognize resistance trends that are too complex to be detected by manual review and indicate the need for prospective evaluation of such algorithms.
Nasopharyngeal versus Oropharyngeal Sampling for Isolation of Potential Respiratory Pathogens in Adults
Authors: Lieberman David , Shleyfer Elena , Castel Hana , Terry Andrei , Harman-Boehm Ilana , Delgado Jorge , Peled Nechama , Lieberman Devora 
Published: February 2006

ABSTRACT

The optimal methodology for the identification of colonization by potential respiratory pathogens (PRP) in adults is not well established. The objectives of the present study were to compare the sensitivities of sampling the nasopharynx and the oropharynx for identification of PRP colonization and to compare the sensitivities of samples from the nasopharynx by swab and by washing for the same purpose. The study included 500 participants with a mean age of 65.1 ± 17.8 years. Of these, 300 patients were hospitalized for acute febrile lower respiratory tract infection and 200 were controls. Each participant was sampled by oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasopharyngeal washing (NPW). The samples were tested by conventional bacteriological methods to identify
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
. OPS detected colonization by
S. pneumoniae
in 30% of the subjects compared with 89% by NPS and NPW (
P
< 0.000001). The corresponding rates for
H. influenzae
were 49% and 64%, respectively (no significant difference [NS]), and for
M. catarrhalis
were 72% and 46%, respectively (
P
< 0.0004). NPS identified 61% of the cases of colonization with
S. pneumoniae
, compared with 76% by NPW (NS). The corresponding rates for
H. influenzae
were 31% and 56%, respectively (
P
< 0.04), and for
M. catarrhalis
were 39% and 33%, respectively (NS). We conclude that the sensitivities of nasopharyngeal and oropharyngeal sampling for identification of PRP colonization in adults are different for each of the three bacteria in this category. The combined results of sampling from both sites are necessary to obtain a true picture of the rate of colonization. NPW is superior to NPS.
Triazole Cross-Resistance among
Candida
spp.: Case Report, Occurrence among Bloodstream Isolates, and Implications for Antifungal Therapy
Authors: Magill Shelley S. , Shields Christine , Sears Cynthia L. , Choti Michael , Merz William G. 
Published: February 2006

ABSTRACT

Candida
spp. are common causes of bloodstream infections among hospitalized patients. Fluconazole (FLC) remains a first-line therapy for candidemia; and voriconazole (VRC), an expanded-spectrum triazole, was recently approved for the treatment of candidemia in nonneutropenic patients. In vitro studies have suggested that VRC has potent activity against
Candida
spp. with reduced susceptibilities to FLC. We present a case report of invasive candidiasis and candidemia due to a
Candida glabrata
isolate that developed resistance to all currently available triazole antifungals after a course of FLC treatment. This case prompted us to determine the frequency of cross-resistance among bloodstream
Candida
isolates collected during a recent 12-month period at a large, academic medical center. FLC MICs were determined for 125 of 153 isolates (81.7%). Thirty of 125 isolates (24%) were resistant or showed reduced susceptibilites to FLC (MICs ≥ 16 μg/ml). When 28 of these 30 isolates were tested for their VRC susceptibilities, 9 (32%) had MICs that were ≥2 μg/ml. Five of these nine isolates were
C. glabrata
, two isolates were
Candida tropicalis
, one isolate was
Candida albicans
, and one isolate was
Candida parapsilosis
. All five
Candida krusei
isolates tested had VRC MICs ≤0.5 μg/ml. These data have prompted the introduction of reflexive FLC susceptibility testing of first bloodstream
Candida
isolates at our institution. The case report and our data also suggest that VRC should be avoided as initial therapy in unstable patients with invasive candidiasis, particularly in the setting of prior azole exposure. Studies are needed to define the clinical significance of in vitro resistance to the newer antifungal agents.
Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for
hsp65
Gene-Based Identification of
Nocardia
Species
Authors: Rodríguez-Nava Verónica , Couble Andrée , Devulder Gregory , Flandrois Jean-Pierre , Boiron Patrick , Laurent Frédéric 
Published: February 2006

ABSTRACT

Nocardia
identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the
hsp65
gene to differentiate
Nocardia
species, including 36 new species. Our results confirm that
hsp65
PRA must no longer be used for
Nocardia
species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an
hsp65
database and a 16S rRNA database and found that the
hsp65
region contained sufficient polymorphisms for comprehensive
Nocardia
species identification.
Recovering Streptococci from the Throat, a Practical Alternative to Direct Plating in Remote Tropical Communities
Authors: McDonald Malcolm , Towers Rebecca , Fagan Peter , McKinnon Melita , Benger Norma , Andrews Ross , Currie Bart J. , Carapetis Jonathan 
Published: February 2006

ABSTRACT

Throat swabs are regarded as the “gold standard” for diagnosing streptococcal pharyngitis and for surveillance research. Culturing throats in remote tropical settings is logistically difficult, and these settings are commonly burdened by high rates of streptococcal disease. The survival of streptococci on swabs may depend on whether they are of “throat” or “skin” type, as determined by
emm
pattern typing. The aims of this study were to compare the recovery rates of beta-hemolytic streptococci (BHS) using three different transport methods and to determine whether the recovery rates correlated with the
emm
pattern type. Monthly duplicate throat swabs were taken from occupants of selected households in three remote Aboriginal communities. Paired swabs were separated and handled in one of three ways: (i) direct inoculation onto culture media with cold-box transport (plated), (ii) sealed in a bag with a silica gel desiccant and cold-box transport (desiccant), and (iii) transport at ambient temperature and humidity (ambient).
emm
pattern typing was done by standard methods. Over 23 months, 4,842 throat swabs were taken, and 4,122 were paired. BHS were recovered on 11.5% of the 4,842 occasions (group A, 4.5%; group C, 1.7%; group G, 5.4%). Results from paired swabs showed the plated method was superior to desiccant and desiccant was better than ambient. Pooled data indicated that plated and desiccant were equivalent, and both were significantly better than ambient. There was no correlation between the
emm
pattern type and recovery of group A streptococci by different methods. In tropical and remote settings, cold-box transport with desiccant and subsequent inoculation of culture plates in the laboratory is a practical alternative to direct plating.
Rapid Susceptibility Testing of Medically Important Zygomycetes by XTT Assay
Authors: Antachopoulos Charalampos , Meletiadis Joseph , Roilides Emmanuel , Sein Tin , Walsh Thomas J. 
Published: February 2006

ABSTRACT

The XTT colorimetric assay quantifies fungal growth by measuring fungal metabolism and has been used successfully for susceptibility testing of
Aspergillus
species after 24 and 48 h of incubation. In the present study using 14 clinical isolates of Zygomycetes (
Rhizopus oryzae
[5 isolates],
Cunninghamella
spp. [3 isolates],
Mucor
spp. [3 isolates], and
Absidia corymbifera
[3 isolates]), significant metabolic activity was demonstrated before visual or spectrophotometric detection of fungal growth by performing the XTT assay as early as 6 h after inoculation. Testing of susceptibility to amphotericin B, posaconazole, and voriconazole was subsequently performed using the XTT method (100 μg/ml XTT, 25 μM menadione) at 6, 8, or 12 h after inoculation and the CLSI (formerly NCCLS) M38-A method with visual and spectrophotometric MIC determinations at 24 h after inoculation. Concentration-effect curves obtained with the use of the
E
max
model (a sigmoid curve with variable slope) were comparable between the early XTT and spectrophotometric readings at 24 h. Complete inhibition of early metabolic activity with the azoles was delayed in comparison to that with amphotericin B. Using appropriate cutoff levels, agreement was demonstrated between the early XTT and 24-h spectrophotometric or visual readings. In particular, for MIC-0 (the lowest drug concentration showing absence of visual growth) of amphotericin B, overall agreement levels were 90 to 93% for the 6-h XTT assay and 100% for the 8- and 12-h time points. For MIC-0 of posaconazole, agreement levels were 86% for the 6-h XTT and 93 to 100% for the 8- and 12-h time points. The overall agreement levels for MIC-0 and MIC-2 (the lowest drug concentration showing prominent reduction of growth compared with the control well) of voriconazole (compared with 24-h spectrophotometric readings) were 93 to 98% for the 8- and 12-h XTT assays. These results support the use of the XTT method for rapid MIC determination for Zygomycetes.