bluuebunny/crossref_metadata_2025_split huggingface dataset:
European Multicenter Evaluation of High-Density DNA Probe Arrays for Detection of Hepatitis B Virus Resistance Mutations and Identification of Genotypes
Authors: Tran N. , Berne R. , Chann R. , Gauthier M. , Martin D. , Armand M.-A. , Ollivet A. , Teo C. G. , Ijaz S. , Flichman D. , Brunetto M. , Bielawski K. P. , Pichoud C. , Zoulim F. , Vernet G. 
Published: August 2006

ABSTRACTPolymorphisms along the hepatitis B virus (HBV) genome have an impact on disease outcome, sensitivity to antiviral treatment, escape from vaccination, and laboratory diagnosis. We have designed a diagnostic tool based on duplex amplification of the whole HBV genome and a high-density DNA chip designed to detect 245 mutations, 20 deletions, and 2 insertions at 151 positions and to determine the genotype of the virus in serum. Assay performances were evaluated with 170 samples, characterized by determination of viral load and sequencing of the Pol, S, and precore genes and the basal core promoter. One hundred fifty-three samples (90%) could be amplified and analyzed by the chip. Only two samples with more than 103genome copies/ml could not be analyzed. Genotype had no impact on analytical sensitivity. Reproducibility studies showed no difference between repeats for codon and genotype determination. Genotype determination by sequencing and the chip were concordant in 148 of 151 samples. Twelve thousand one hundred sixty-one codons were analyzed by both techniques. Only 89.4% could be determined by sequencing, and among the remaining 11,335 codons, 92.8% were identical by sequencing and the chip. Failures to identify an amino acid by the chip were mainly due to reduced hybridization efficiency attributed to unexpected polymorphisms. Optimization of the chip-based reagent for the analysis of the HBV genome is ongoing. This first evaluation showed that DNA chip technology can provide important information in relation to the clinical management of chronic hepatitis B.
Characterization of
Shigella
Strains in Iran by Plasmid Profile Analysis and PCR Amplification of
ipa
Genes
Authors: Farshad Shohreh , Sheikhi Raheleh , Japoni Aziz , Basiri Ezzatollah , Alborzi Abdolvahab 
Published: August 2006

ABSTRACT

To characterize
Shigella
clinical strains, we studied 82
Shigella
strains recovered from 719 stool samples of patients with bloody diarrhea in Shiraz, Iran, over the period from April to October 2003. Serological assay classified the
Shigella
isolates as follows: 61 (74.39%)
Shigella sonnei
isolates, 16 (19.51%)
Shigella flexneri
isolates, 3 (3.65%)
Shigella boydii
isolates, and 2 (2.43%)
Shigella dysenteriae
isolates. In an antibiogram test, all
Shigella
strains were susceptible to ceftazidime, ciprofloxacin, and ceftriaxone. They showed high degrees of sensitivity to nalidixic acid, gentamicin, cephalothin, and amikacin. Approximately 90.24% of the
Shigella
isolates were resistant to co-trimoxazole. The plasmid profile patterns of all strains were determined by a modified alkaline lysis method. The average number of plasmid bands for each strain was 9.5. By plasmid profile analysis we identified 56 genotypes among all isolates and 42, 14, 3, and 2 genotypes among the
S. sonnei
,
S. flexneri
,
S. boydii
, and
S. dysenteriae
strains, respectively. PCR assays showed that all isolates were positive for two virulence genes,
ipaBCD
and
ipaH
. In conclusion, these data mandate local monitoring of drug resistance and its consideration in the empirical therapy of
Shigella
infections. These results also demonstrate that plasmid profile analysis is more reliable than antibiotic susceptibility pattern analysis for the identification of
Shigella
epidemic strains isolated in Iran.
Comparison of the LCx Human Immunodeficiency Virus (HIV) RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan Assays for Quantitation of HIV Type 1 RNA in Plasma
Authors: Foulongne Vincent , Montes Brigitte , Didelot-Rousseau Marie-Noelle , Segondy Michel 
Published: August 2006

ABSTRACT
The LCx human immunodeficiency virus (HIV) RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan assays for HIV type 1 (HIV-1) were compared for their abilities to quantitate HIV-1 RNA in plasma. High degrees of correlation and agreement were observed between the assays. Differences in HIV-1 RNA levels according to HIV-1 subtypes did not reach statistical significance.
New
Staphylococcus aureus
Genotyping Method Based on Exotoxin (
set
) Genes
Authors: Aguiar-Alves Fábio , Medeiros Fred , Fernandes Octavio , Gudziki Pereira Rossiane Maria , Perdreau-Remington Françoise , Riley Lee W. 
Published: August 2006

ABSTRACT

A variety of methods for genotyping
Staphylococcus aureus
isolates exists: the two most widely used methods are pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Here, we describe a sequence-based genotyping method based on genes encoding
S. aureus
superantigen-like proteins, which belong to a family of exotoxins called staphylococcal exotoxins. The sequences of PCR-amplified internal fragments of three different
set
genes (
set2
,
set5
, and
set7
) of 61 well-characterized clinical methicillin-resistant
S. aureus
(MRSA) and methicillin-susceptible
S. aureus
(MSSA) isolates and reference strains were compared. Phylogenetic analysis was performed based on single-nucleotide polymorphisms (SNP). The SNP dendrograms of the
set
gene sequences differentiated the 61 isolates into 22 distinct subgroups, designated exotoxin sequence types (ETST), while the standard seven-gene MLST profiles differentiated the same 61 isolates into 19 subgroups. Of the 19 different MLST subgroups, 16 corresponded to 16 distinct ETST groups. However, three MLST subgroups, ST1, ST30, and ST36, were each further separated into more than one ETST subgroup. The exotoxin-based genotyping method was able to discriminate MRSA and MSSA isolates according to their specific epidemiological characteristics. This SNP analysis of the three
set
genes is thus equally or more discriminatory than the seven-gene MLST method, providing a good alternative typing tool for a laboratory that has sequencing capability.
Enhanced Reverse Transcription-PCR Assay for Detection of Norovirus Genogroup I
Authors: Dreier Jens , Störmer Melanie , Mäde Dietrich , Burkhardt Sabine , Kleesiek Knut 
Published: August 2006

ABSTRACT
We have developed a one-tube reverse transcription (RT)-PCR method using the real-time TaqMan PCR system for the detection of norovirus genogroup I (NV GGI). By introduction of a novel probe based on locked nucleic acid technology, we enhanced the sensitivity of the assay compared to those of conventional TaqMan probes. The sensitivity of the NV GGI RT-PCR was determined by probit analysis with defined RNA standards and quantified norovirus isolates to 711 copies/ml (95% detection limit). In order to detect PCR inhibition, we included a heterologous internal control (IC) system based on phage MS2. This internally controlled RT-PCR was tested on different real-time PCR platforms, LightCycler, Rotorgene, Mastercycler EP realplex, and ABI Prism. Compared to the assay without an IC, the duplex RT-PCR exhibited no reduction in sensitivity in clinical samples. In combination with an established NV GGII real-time RT-PCR, we used the novel assay in a routine assay for diagnosis of clinical and food-borne norovirus infection. We applied this novel assay to analyze outbreaks of nonbacterial acute gastroenteritis. Norovirus of GGI was detected in these outbreaks. Sequence and similarity plot analysis of open reading frame 1 (ORF1) and ORF2 showed two genotypes, GGI/2 and GGI/4, in semiclosed communities.
Molecular Identification of
Leuconostoc mesenteroides
as a Cause of Brain Abscess in an Immunocompromised Patient
Authors: Albanese Alessio , Spanu Teresa , Sali Michela , Novegno Federica , D'Inzeo Tiziana , Santangelo Rosaria , Mangiola Annunziato , Anile Carmelo , Fadda Giovanni 
Published: August 2006

ABSTRACT

Leuconostoc
species are emerging pathogens that can cause severe infections, particularly in immunocompromised patients. Using molecular methods, we identified
Leuconostoc mesenteroides
as the cause of a brain abscess which was successfully treated by surgery and antimicrobial treatment. This is the first report of brain abscess caused by this species.
Therapeutic Failures of Antibiotics Used To Treat Macrolide-Susceptible
Streptococcus pyogenes
Infections May Be Due to Biofilm Formation
Authors: Baldassarri Lucilla , Creti Roberta , Recchia Simona , Imperi Monica , Facinelli Bruna , Giovanetti Eleonora , Pataracchia Marco , Alfarone Giovanna , Orefici Graziella 
Published: August 2006

ABSTRACT

Streptococcus pyogenes
infections often fail to respond to antibiotic therapy, leading to persistent throat carriage and recurrent infections. Such failures cannot always be explained by the occurrence of antibiotic resistance determinants, and it has been suggested that
S. pyogenes
may enter epithelial cells to escape antibiotic treatment. We investigated 289
S. pyogenes
strains isolated from different clinical sources to evaluate their ability to form biofilm as an alternative method to escape antibiotic treatment and host defenses. Up to 90% of
S. pyogenes
isolates, from both invasive and noninvasive infections, were able to form biofilm. Specific
emm
types, such as
emm
6, appeared to be more likely to produce biofilm, although variations within strains belonging to the same type might suggest biofilm formation to be a trait of individual strains rather than a general attribute of a serotype. Interestingly, erythromycin-susceptible isolates formed a significantly thicker biofilm than resistant isolates (
P
< 0.05). Among resistant strains, those carrying the
erm
class determinants formed a less organized biofilm than the
mef
(A)-positive strains. Also,
prtF1
appeared to be negatively associated with the ability to form biofilm (
P
< 0.01). Preliminary data on a selection of strains indicated that biofilm-forming isolates entered epithelial cells with significantly lower efficiency than biofilm-negative strains. We suggest that
prtF1
-negative macrolide-susceptible or
mef
(A)-carrying isolates, which are poorly equipped to enter cells, may use biofilm to escape antimicrobial treatments and survive within the host. In this view, biofilm formation by
S. pyogenes
could be responsible for unexplained treatment failures and recurrences due to susceptible microorganisms.
First Report of Bacteremia by
Asaia bogorensis
, in a Patient with a History of Intravenous-Drug Abuse
Authors: Tuuminen Tamara , Heinäsmäki Terhi , Kerttula Tuija 
Published: August 2006

ABSTRACT

We report the first documented case of bacteremia caused by
Asaia bogorensis
in a young patient with a history of intravenous-drug abuse.
A. bogorensis
was identified by sequencing the 16S rRNA gene. The isolate was exceptionally resistant to almost all antibiotics that are routinely tested for gram-negative rods but was susceptible to netilmicin, gentamicin, and doxycycline.
Azole Resistance of
Candida glabrata
in a Case of Recurrent Fungemia
Authors: Posteraro Brunella , Tumbarello Mario , La Sorda Marilena , Spanu Teresa , Trecarichi Enrico Maria , De Bernardis Flavia , Scoppettuolo Giancarlo , Sanguinetti Maurizio , Fadda Giovanni 
Published: August 2006

ABSTRACT

We describe a case of recurrent
Candida glabrata
fungemia that became unresponsive to fluconazole treatment. Posttreatment isolates from blood and vaginal cultures of the immunocompetent patient were azole resistant and exhibited upregulated expression of
CgCDR1
/
CgCDR2
efflux pumps compared to the original isolates. Amphotericin B therapy eradicated the infection.
Use of an Immunochromatographic Dipstick Test for Rapid Detection of
Trypanosoma cruzi
in Sera from Animal Reservoir Hosts
Authors: Cardinal Marta V. , Reithinger Richard , Gürtler Ricardo E. 
Published: August 2006

ABSTRACT

We evaluated an immunochromatographic dipstick test to detect
Trypanosoma cruzi
in canine serum samples from areas of endemicity (
n
= 141) and nonendemicity (
n
= 28) for Chagas' disease with known serological and xenodiagnostic test results. The dipstick test had a specificity of at least 94% and a sensitivity of at least 96%. The dipstick tested could become the first choice for screening purposes in disease surveillance or intervention programs.
Synergistes
Group Organisms of Human Origin
Authors: Horz Hans-Peter , Citron Diane M. , Warren Yumi A. , Goldstein Ellie J. C. , Conrads Georg 
Published: August 2006

ABSTRACT

The bacterial division
Synergistes
represents a poorly characterized phylotype of which only a few isolates have been cultured, primarily from natural environments. Recent detection of
Synergistes
-like sequence types in periodontal pockets and caries lesions of humans prompted us to search the R. M. Alden culture collection (Santa Monica, Calif.) for biochemically unidentifiable, slow-growing, obligately anaerobic gram-negative bacilli. Here we report on five clinical isolates cultured from peritoneal fluid and two isolates from soft-tissue infections that together constitute three separate evolutionary lineages within the phylogenetic radiation of the division
Synergistes
. One of these clusters was formed by the peritoneal isolates and had an 85% similarity to
Synergistes jonesii
, the first described
Synergistes
species, which was isolated from the rumen of a goat. The isolates from soft-tissue infections, on the other hand, formed two distinct lineages moderately related to each other with a similarity of approximately 78%. In addition, by using a newly designed 16S rRNA gene-based PCR assay with intended target specificity for
Synergistes
, we found that the dominant phylotype from a fecal sample was nearly identical to that of the strains obtained from peritonitis. Conversely, sequence types detected in periodontal pockets formed a separate cluster that shared a similarity of only 80% with the soft-tissue isolates. These findings suggest a high diversity of medically important
Synergistes
clades that apparently are unique to individual ecological niches in the human body. In conclusion, we now have available the first characterized human isolates of the division
Synergistes
which are colonizing, and probably infecting, several sites in the human body.
Short-Sequence-Repeat Analysis ofMycobacterium aviumsubsp.paratuberculosisandMycobacterium aviumsubsp.aviumIsolates Collected from Animals Throughout the United States Reveals Both Stability of Loci and Extensive Diversity
Authors: Harris N. Beth , Payeur Janet B. , Kapur Vivek , Sreevatsan Srinand 
Published: August 2006

ABSTRACTWe analyzed the multilocus short sequence repeats (SSRs) of 211 and 56 isolates ofMycobacterium aviumsubsp.paratuberculosisandM. aviumsubsp.avium, respectively. TheM. aviumsubsp.paratuberculosisisolates could be differentiated into 61 genotypes. TheM. aviumsubsp.aviumisolates showed limited diversity. These SSRs are stable and suitable for studying the molecular epidemiology ofM. aviumsubsp.paratuberculosis.
Evaluation of In Situ Methods Used To Detect
Mycobacterium avium
subsp.
paratuberculosis
in Samples from Patients with Crohn's Disease
Authors: Jeyanathan Mangalakumari , Alexander David C. , Turenne Christine Y. , Girard Christiane , Behr Marcel A. 
Published: August 2006

ABSTRACT

In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for
Mycobacterium avium
subsp.
paratuberculosis
in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL/6 mice were artificially infected with
Mycobacterium avium
subsp.
paratuberculosis
strain K10 and
M. tuberculosis
H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods,
Mycobacterium avium
subsp.
paratuberculosis
bacilli were observed to be shorter, smaller, and less rod shaped than
M. tuberculosis
bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS
900
element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification ×1,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of
Mycobacterium avium
subsp.
paratuberculosis
bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for
Mycobacterium avium
subsp.
paratuberculosis
in tissue is governed more by bacterial burden than by staining method.
Invasive Meningococcal Disease in Québec, Canada, Due to an Emerging Clone of ST-269 Serogroup B Meningococci with Serotype Antigen 17 and Serosubtype Antigen P1.19 (B:17:P1.19)
Authors: Law Dennis K. S. , Lorange Manon , Ringuette Louise , Dion Réjean , Giguère Michel , Henderson Averil M. , Stoltz Jan , Zollinger Wendell D. , De Wals Philippe , Tsang Raymond S. W. 
Published: August 2006

ABSTRACT

During periods of endemic meningococcal disease, serogroup B
Neisseria meningitidis
is responsible for a significant percentage of invasive diseases, and no particular clone or strain predominates (F. E. Ashton and D. A. Caugant, Can. J. Microbiol. 47: 293-289, 2001), However, in the winter of 2004 to 2005, a cluster of serogroup B meningococcal disease occurred in one region in the province of Québec, Canada. The
N. meningitidis
strain responsible for this cluster of cases was identified as sequence type ST-269 with the antigenic formula B:17:P1.19. Retrospective analysis of isolates from 2000 onwards showed that this clone first emerged in the province of Québec in 2003. The emergence of this clone of serogroup B meningococci occurred after a mass vaccination against serogroup C
N. meningitidis
, suggesting possible capsule replacement.
Identification of
Acinetobacter
Species and Genotyping of
Acinetobacter baumannii
by Multilocus PCR and Mass Spectrometry
Authors: Ecker Joseph A. , Massire Christian , Hall Thomas A. , Ranken Raymond , Pennella Thuy-Trang D. , Agasino Ivy Cristina , Blyn Lawrence B. , Hofstadler Steven A. , Endy Timothy P. , Scott Paul T. , Lindler Luther , Hamilton Tacita , Gaddy Charla , Snow Kerry , Pe Marie , Fishbain Joel , Craft David , Deye Gregory , Riddell Scott , Milstrey Eric , Petruccelli Bruno , Brisse Sylvain , Harpin Vanessa , Schink Amy , Ecker David J. , Sampath Rangarajan , Eshoo Mark W. 
Published: August 2006

ABSTRACT

Members of the genus
Acinetobacter
are ubiquitous in soil and water and are an important cause of nosocomial infections. A rapid method is needed to genotype
Acinetobacter
isolates to determine epidemiology and clonality during infectious outbreaks. Multilocus PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) is a method that uses the amplicon base compositions to genotype bacterial species. In order to identify regions of the
Acinetobacter
genome useful for this method, we sequenced regions of six housekeeping genes (
trpE
,
adk
,
efp
,
mutY
,
fumC
, and
ppa
) from 267 isolates of
Acinetobacter
. Isolates were collected from infected and colonized soldiers and civilians involved in an outbreak in the military health care system associated with the conflict in Iraq, from previously characterized outbreaks in European hospitals, and from culture collections. Most of the isolates from the Iraqi conflict were
Acinetobacter baumannii
(189 of 216 isolates). Among these, 111 isolates had genotypes identical or very similar to those associated with well-characterized
A. baumannii
isolates from European hospitals. Twenty-seven isolates from the conflict were found to have genotypes representing different
Acinetobacter
species, including 8 representatives of
Acinetobacter
genomospecies 13TU and 13 representatives of
Acinetobacter
genomospecies 3. Analysis by the PCR/ESI-MS method using nine primer pairs targeting the most information-rich regions of the
trpE
,
adk
,
mutY
,
fumC
, and
ppa
genes distinguished 47 of the 48
A. baumannii
genotypes identified by sequencing and identified at the species level at least 18
Acinetobacter
species. Results obtained with our genotyping method were essentially in agreement with those obtained by pulse-field gel electrophoresis analysis. The PCR/ESI-MS genotyping method required 4 h of analysis time to first answer with additional samples subsequently analyzed every 10 min. This rapid analysis allows tracking of transmission for the implementation of appropriate infection control measures on a time scale previously not achievable.
Catheter-Related Fungemia Due toCandida thermophila
Authors: Bar-Meir Maskit , Sutton Deanna A. , Wickes Brian , Kurtzman Cletus P. , Goldman Stewart , Zheng Xiaotian 
Published: August 2006

ABSTRACTWe report a case of bloodstream infection caused byCandida thermophila, a yeast not previously associated with human disease. The infection occurred in a 13-year-old boy with medulloblastoma who presented with 1 day of fever. Multiple blood cultures were positive for yeast. Removal of the catheter resulted in prompt resolution of the fever and sterilization of the blood cultures. The species was identified by sequencing domains 1 and 2 of the large subunit rRNA gene. Antifungal susceptibility testing was also performed.
Comparison of Dalbavancin MIC Values Determined by Etest (AB BIODISK) and Reference Dilution Methods Using Gram-Positive Organisms
Authors: Fritsche Thomas R. , Rennie Robert P. , Goldstein Beth P. , Jones Ronald N. 
Published: August 2006

ABSTRACT

While standardized microdilution testing methodologies and quality control ranges exist for the novel glycolipopeptide dalbavancin, no testing methods have been described that are immediately available for routine use in clinical laboratories. In this study, we found that the dalbavancin Etest (AB BIODISK, Solna, Sweden) procedure demonstrated a high degree of agreement (100% within ±2 log
2
dilution steps) with the standardized broth microdilution method, validating the use of the Etest as an alternative test for investigational or clinical purposes following regulatory approval.