bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Multiplex PCR Assay for Detection of the Staphylococcal Virulence Marker Panton-Valentine Leukocidin Genes and Simultaneous Discrimination of Methicillin-Susceptible from -Resistant Staphylococci
Authors: McClure Jo-Ann , Conly John M. , Lau Vicky , Elsayed Sameer , Louie Thomas , Hutchins Wendy , Zhang Kunyan 
Published: March 2006

ABSTRACT

We developed a new multiplex PCR assay for detection of Panton-Valentine leukocidin virulence genes and simultaneous discrimination of methicillin-susceptible from -resistant staphylococci. This assay is simple, rapid, and accurate and offers the potential for prompt detection of newly emerging community-associated methicillin-resistant
Staphylococcus aureus
.
Effective Detection of Toxigenic
Clostridium difficile
by a Two-Step Algorithm Including Tests for Antigen and Cytotoxin
Authors: Ticehurst John R. , Aird Deborah Z. , Dam Lisa M. , Borek Anita P. , Hargrove John T. , Carroll Karen C. 
Published: March 2006

ABSTRACT

We evaluated a two-step algorithm for detecting toxigenic
Clostridium difficile
: an enzyme immunoassay for glutamate dehydrogenase antigen (Ag-EIA) and then, for antigen-positive specimens, a concurrent cell culture cytotoxicity neutralization assay (CCNA). Antigen-negative results were ≥99% predictive of CCNA negativity. Because the Ag-EIA reduced cell culture workload by ≈75 to 80% and two-step testing was complete in ≤3 days, we decided that this algorithm would be effective. Over 6 months, our laboratories' expenses were US$143,000 less than if CCNA alone had been performed on all 5,887 specimens.
Comparative Prevalence of Virulence Factors in
Escherichia coli
Causing Urinary Tract Infection in Male Infants with and without Bacteremia
Authors: Bonacorsi Stéphane , Houdouin Véronique , Mariani-Kurkdjian Patricia , Mahjoub-Messai Farah , Bingen Edouard 
Published: March 2006

ABSTRACT

Escherichia coli
isolates causing urinary tract infection in 83 male infants younger than 90 days with and without bacteremia were compared for phylogenetic groups and the presence of 10 virulence factors. Our result suggest that the absence of both hemolysin and antigen K1 may be used as a negative predictive factor for bacteremia.
Molecular Identification of
Tritrichomonas foetus
-Like Organisms as Coinfecting Agents of Human
Pneumocystis
Pneumonia
Authors: Duboucher Christophe , Caby Stéphanie , Dufernez Fabienne , Chabé Magali , Gantois Nausicaa , Delgado-Viscogliosi Pilar , Billy Christophe , Barré Eric , Torabi Edith , Capron Monique , Pierce Raymond J. , Dei-Cas Eduardo , Viscogliosi Eric 
Published: March 2006

ABSTRACT

Trichomonads closely related to the bovid parasite
Tritrichomonas foetus
were identified in the bronchoalveolar lavage sample from a patient with AIDS in association with
Pneumocystis
pneumonia. This human case of
T. foetus
-like infection emphasizes the zoonotic potential of trichomonads, although the existence of a human-host-adapted
T. foetus
strain cannot be excluded.
Usefulness of Eschar PCR for Diagnosis of Scrub Typhus
Authors: Lee Seung-Hyun , Kim Dong-Min , Cho Young Shin , Yoon Sung Ho , Shim Soo Kyoung 
Published: March 2006

ABSTRACT
We report here on the case of a child who was infected with scrub typhus, and we made the diagnosis according to the serology and by performing PCRs on the child's eschar. The patient was treated with azithromycin, and he did not experience any complications. Performing nested PCR on the eschar might be both a rapid diagnostic test for scrub typhus in the early acute stage and a differential test as to whether or not a scab is a scrub typhus eschar.
Treatment Failure Due to Emergence of Resistance to Carbapenem during Therapy for
Shewanella algae
Bacteremia
Authors: Kim Dong-Min , Kang Cheol-In , Lee Chang Seop , Kim Hong-Bin , Kim Eui-Chong , Kim Nam Joong , Oh Myoung-don , Choe Kang-Won 
Published: March 2006

ABSTRACT

We describe a case of bacteremia due to imipenem-susceptible
Shewanella algae
. Despite treatment with imipenem, the patient developed a spinal epidural abscess, from which imipenem-resistant
S. algae
was isolated. The development of resistance should be monitored when
S. algae
infection is treated with imipenem, even though the strain is initially susceptible to imipenem.
Use of DNA Sequencing Analysis To Confirm Fungemia Due to
Trichosporon dermatis
in a Pediatric Patient
Authors: Gunn Shelly R. , Reveles Xavier T. , Hamlington Jeanette D. , Sadkowski Lee C. , Johnson-Pais Teresa L. , Jorgensen James H. 
Published: March 2006

ABSTRACT

This is the first reported case of human disease caused by
Tricosporon dermatis
, an organism recently transferred to the genus
Trichosporon
from
Cryptococcus
and now confirmed to be a human pathogen.
Post-Kala-Azar Dermal Leishmaniasis Due to
Leishmania infantum
in a Human Immunodeficiency Virus Type 1-Infected Patient
Authors: Stark D. , Pett S. , Marriott D. , Harkness J. 
Published: March 2006

ABSTRACT

We report the first case of post-kala-azar dermal leishmaniasis due to
Leishmania infantum
in a human immunodeficiency virus type 1-infected patient in Australia. Molecular characterization of the isolate was performed using PCR restriction fragment length polymorphism targeting both repetitive sequences from
Leishmania
nuclear DNA and repetitive kinetoplast DNA minicircles for species differentiation.
Use of Enzyme-Linked Immunospot Assay with
Mycobacterium tuberculosis
- Specific Peptides for Diagnosis of Recent Infection with
M. tuberculosis
after Accidental Laboratory Exposure
Authors: Leyten Eliane M. S. , Mulder Bert , Prins Corine , Weldingh Karin , Andersen Peter , Ottenhoff Tom H. M. , van Dissel Jaap T. , Arend Sandra M. 
Published: March 2006

ABSTRACT

This report of an accidental exposure to
Mycobacterium tuberculosis
in a microbiological laboratory illustrates the value of gamma interferon enzyme-linked immunospot assay using peptides of ESAT-6, CFP-10, TB37.6, and TB7.7 for the diagnosis of latent infection. In particular, positive responses to peptides 2 to 6 of TB37.6 were observed exclusively in recently infected persons.
Phylogenetic, Virological, and Clinical Characteristics of Genotype C Hepatitis B Virus with TCC at Codon 15 of the Precore Region
Authors: Chan Henry Lik-Yuen , Tse Chi-Hang , Ng Eddie Yuen-Tok , Leung Kwong-Sak , Lee Kin-Hong , Tsui Stephen Kwok-Wing , Sung Joseph Jao-Yiu 
Published: March 2006

ABSTRACT

Hepatitis B virus (HBV) with T-1856 of the precore region is always associated with C-1858 (i.e., TCC at nucleotides 1856 to 1858), and it is reported only in genotype C HBV isolates. We aimed to investigate the phylogenetic, virological, and clinical characteristics of HBV isolates bearing TCC at nucleotides 1856 to 1858. We have previously reported on the presence of two major subgroups in genotype C HBV, namely, HBV genotype Cs (Southeast Asia) and HBV genotype Ce (Far East). We have designed a novel 5′ nuclease technology based on the nucleotide polymorphism (C or A) at nucleotide 2733 to differentiate the two genotype C HBV subgroups. The mutations at the basal core promoter and precore regions were analyzed by direct sequencing. Among 214 genotype C HBV-infected patients, 31% had TCC, 37% had CCC, 3% had CTC, and 29% had CCT at nucleotides 1856 to 1858. All except one HBV strain with TCC at nucleotides 1856 to 1858 belonged to subgroup Cs, which has been reported only in Hong Kong; Guangzhou, China; and Vietnam. HBV with TCC at nucleotides 1856 to 1858 was associated with the G1898A mutation (64%). Patients infected with HBV harboring TCC had more liver cirrhosis than those infected with HBV harboring CCC (18% versus 5%;
P
= 0.008), and more of the patients infected with HBV harboring TCC were positive for HBeAg (58% versus 36%;
P
= 0.01) and had higher median alanine aminotransferase levels (65 IU/liter versus 49 IU/liter;
P
= 0.006); but similar proportions of patients infected with HBV harboring TCC and those infected with HBV harboring CCT had liver cirrhosis (18% versus 13%;
P
= 0.43). In summary, we report that HBV with TCC at nucleotides 1856 to 1858 of the precore region might represent a specific HBV strain associated with more aggressive liver disease than other genotype C HBV strains.
Multicenter Laboratory Validation of the BACTEC MGIT 960 Technique for Testing Susceptibilities of
Mycobacterium tuberculosis
to Classical Second-Line Drugs and Newer Antimicrobials
Authors: Rüsch-Gerdes Sabine , Pfyffer Gaby E. , Casal Manuel , Chadwick Maureen , Siddiqi Salman 
Published: March 2006

ABSTRACT

The BACTEC MGIT 960 system, a fully automated, nonradiometric, noninvasive system for detection and drug susceptibility testing of mycobacteria, was evaluated for the ability to test susceptibilities to second-line drugs. In this study, which was carried out in three phases (phase I, mostly susceptible strains; phase II, mostly resistant strains; phase III, final testing of the optimal drug concentrations found in phases I and II), we established the critical concentrations for seven drugs to be tested in the BACTEC MGIT 960 system compared to the BACTEC 460TB system. The critical concentrations for the seven drugs used in the MGIT 960 system are as follows: amikacin, 1.0 μg/ml; capreomycin, 2.5 μg/ml; ethionamide, 5.0 μg/ml; protionamide, 2.5 μg/ml; ofloxacin, 2.0 μg/ml; rifabutin, 0.5 μg/ml; linezolid, 1.0 μg/ml. Our results demonstrate that the BACTEC MGIT 960 system is an accurate method for rapid testing of the susceptibilities of
Mycobacterium tuberculosis
to second-line drugs.
Sensitivities of Antigen Detection and PCR Assays Greatly Increased Compared to That of the Standard Culture Method for Screening for Group B Streptococcus Carriage in Pregnant Women
Authors: Rallu Fabien , Barriga Peter , Scrivo Carole , Martel-Laferrière Valérie , Laferrière Céline 
Published: March 2006

ABSTRACT

Group B streptococcus (GBS) is a major cause of serious infections in neonates. The 2002 revised guidelines of the Centers for Disease Control and Prevention (CDC) for the prevention of perinatal GBS disease recommend that all pregnant women be screened for GBS carriage at between 35 and 37 weeks of gestation and that intrapartum antibiotic prophylaxis be given to carriers. We studied the performances of four different GBS detection assays in the context of antenatal screening. Between May and August 2004, the 605 vaginorectal swab specimens received at our bacteriology laboratory for GBS antenatal detection were tested by the four assays. The standard culture method was done according to the CDC recommendations. The three experimental assays performed with the growth from the selective enrichment (LIM) broth (Todd-Hewitt broth with 15 μg/ml nalidixic acid and 10 μg/ml colistin) after overnight incubation were a GBS antigen detection assay (PathoDx) and two PCR assays (for
cfb
and
scpB
). The most accurate assay was the
scpB
PCR (sensitivity, 99.6%; specificity, 100%), followed by the
cfb
PCR (sensitivity, 75.3%; specificity, 100%), GBS antigen detection (sensitivity, 57.3%; specificity, 99.5%), and standard culture (sensitivity, 42.3%; specificity, 100%). The GBS antigen detection assay was found to be more sensitive than the standard culture method, and moreover, the assay has a low cost and is easy to perform in all obstetrical centers which have access to the most basic of diagnostic microbiology services. We believe that antigen detection on incubated LIM broth should replace the standard culture method for screening for GBS carriage at 35 to 37 weeks of gestation. The impact of the greater sensitivities of PCR assays on the diminution of neonatal GBS infections remains to be demonstrated.
Comparison of Conventional PCR with Real-Time PCR and Branched DNA-Based Assays for Hepatitis C Virus RNA Quantification and Clinical Significance for Genotypes 1 to 5
Authors: Sarrazin Christoph , Gärtner Barbara C. , Sizmann Dorothea , Babiel Rainer , Mihm Ulrike , Hofmann Wolf Peter , von Wagner Michael , Zeuzem Stefan 
Published: March 2006

ABSTRACTThe key parameter for diagnosis and management of hepatitis C virus (HCV) infection is HCV RNA. Standardization of HCV RNA assays to IU is mainly based on genotype 1 panels. Little is known about the variability of commercially available HCV RNA assays for quantification of different genotypes. Two real-time reverse transcription (RT)-PCR assays (COBAS TaqMan HCV Test for use with the High-Pure System [HPS/CTM] and COBAS Ampliprep/COBAS TaqMan HCV Test [CAP/CTM]), one standard RT-PCR assay (COBAS Amplicor HCV Monitor 2.0 [CAM]), and one signal amplification assay (Versant Quantitative 3.0 [branched DNA {bDNA}]) were compared for quantification of genotypes 1 to 5 (n= 108). Using CAM as a reference assay for genotype 1-infected patients, the mean interassay differences compared with CAP/CTM, HPS/CTM, and bDNA were 0.16, −0.13, and −0.48 log10IU/ml HCV RNA, respectively. Comparison of CAM with CAP/CTM, HPS/CTM, and bDNA for the remaining genotypes showed the following results, respectively: 2a/c, −0.24, −0.78, and −0.49; 2b, −0.21, −0.18, and −0.64; 3a, 0.13, −1.04, and −0.55; 4, −0.52, −1.51, and −0.05; and 5, −0.28, −1.00, and −0.24 log IU/ml HCV RNA. A correct decision for treatment discontinuation in genotype 1 patients at week 12 was possible only when the same assay was used at baseline and week 12. Comparison of CAM with the CAP/CTM assay showed equal quantifications of genotype 1, 2, 3, and 5 samples, while genotype 4 samples were slightly underestimated. For the HPS/CTM assay, a significant underestimation of the HCV RNA concentrations of genotypes 2a/c, 3, 4, and 5 was observed. For the bDNA assay, a constant lower quantification of genotypes 1 to 3 was detected.
Prevalence and Spread of Enterohepatic
Helicobacter
Species in Mice Reared in a Specific-Pathogen-Free Animal Facility
Authors: Bohr U. R. M. , Selgrad M. , Ochmann C. , Backert S. , König W. , Fenske A. , Wex T. , Malfertheiner P. 
Published: March 2006

ABSTRACT

Infections with enterohepatic
Helicobacter
species (EHS) can change the results of animal experiments. However, there is little information about the prevalence of EHS in noncommercial animal facilities. The aim of this study was to investigate the prevalence and the spread of EHS in specific-pathogen-free (SPF) mice. Fecal samples of 40 mouse lines were analyzed for members of the family
Helicobacteraceae
using a group-specific PCR targeting the 16S rRNA gene. Additional experiments were carried out to evaluate the spread of EHS among mice harbored in different caging systems.
Helicobacter
species were detected in 87.5% of the mouse lines tested. Five different
Helicobacter
species were identified:
H. ganmani
,
H. hepaticus
,
H. typhlonicus
, and the putative
Helicobacter
species represented by the isolates hamster B and MIT 98-5357.
Helicobacter
infection did not spread between animals in neighboring cages when individually ventilated cages were used; in contrast, when the mice were reared in open-air cages, EHS were found to spread from cage to cage. However, the spread was prevented by adding polycarbonate filter tops to the cages. When
Helicobacter-
negative and infected mice shared the same cage, transmission of the infection occurred in 100% within 2 weeks. Furthermore, we found that mice from commercial breeding facilities may carry undetected
Helicobacter
infections. Taken together, we show that infection with EHS may frequently occur and spread easily in mice reared under SPF conditions despite extensive safety precautions. Moreover, there is a high prevalence of rather uncommon
Helicobacter
species that may be a consequence of the current routine procedures used for health screening of SPF mice.
A Successful, Diverse Disease-Associated Lineage of Nontypeable Pneumococci That Has Lost the Capsular Biosynthesis Locus
Authors: Hanage W. P. , Kaijalainen T. , Saukkoriipi A. , Rickcord J. L. , Spratt B. G. 
Published: March 2006

ABSTRACT

Streptococcus pneumoniae
strains which fail to produce a polysaccharide capsule are commonly isolated from carriage and disease contexts. Here we use a multilocus approach to distinguish genuine nontypeable pneumococci from closely related nontypeable streptococcal isolates in a data set of 121 untypeable pneumococci from nasopharyngeal swabs and middle ear fluid of Finnish children and demonstrate that 70 of these belong to a pneumococcal lineage which has lost its capsular locus. Strains of this relatively old lineage include sequence types 344, 448, and 449. Comparison with the multilocus sequence typing database shows that strains of this lineage have spread intercontinentally and have been isolated from carriage, mucosal, and invasive disease. Furthermore we note a particular association of this nontypeable lineage with outbreaks of conjunctivitis. The diversification and geographic spread of this lineage suggest that loss of capsule is not inconsistent with long-term persistence and raise questions about the capsule's role in pneumococcal transmission.
In Vitro Susceptibilities of
Candida
spp. to Caspofungin: Four Years of Global Surveillance
Authors: Pfaller M. A. , Boyken L. , Hollis R. J. , Messer S. A. , Tendolkar S. , Diekema D. J. 
Published: March 2006

ABSTRACT

Caspofungin is being used increasingly as therapy for invasive candidiasis. Prospective sentinel surveillance for emergence of in vitro resistance to caspofungin among invasive
Candida
spp. isolates is indicated. We determined the in vitro activity of caspofungin against 8,197 invasive (bloodstream or sterile-site) unique patient isolates of
Candida
collected from 91 medical centers worldwide from 1 January 2001 to 31 December 2004. We performed antifungal susceptibility testing according to the Clinical and Laboratory Standards Institute (CLSI, formerly NCCLS) M27-A2 method and used a 24-h prominent inhibition endpoint for determination of the MIC. Of 8,197 invasive
Candida
spp. isolates, species distribution was as follows: 54%
Candida albicans
, 14%
C. glabrata
, 14%
C. parapsilosis
, 11%
C. tropicalis
, 3%
C. krusei
, and 4% other
Candida
spp. Overall, caspofungin was very active against
Candida
(MIC
50
/MIC
90
, 0.03/0.25 μg/ml; 98.2% were inhibited at a MIC of ≤0.5 μg/ml and 99.7% were inhibited at a MIC of ≤1 μg/ml). Results by species (expressed as MIC
50
/MIC
90
and the percentage inhibited at ≤1 μg/ml) were as follows:
C. albicans
, 0.03/0.06, 99.9;
C. glabrata
, 0.03/0.06, 99.9;
C. parapsilosis
, 0.5/0.5, 99.0;
C. tropicalis
, 0.03/0.06, 99.7;
C. krusei
, 0.12/0.5, 99.0; and
C. guilliermondii
, 0.5/1, 94.4. Of the 25 isolates with caspofungin MICs of >1 μg/ml, 12 isolates were
C. parapsilosis
, 6 isolates were
C. guilliermondii
, 2 isolates were
C. rugosa
, and 1 isolate each was
C. albicans
,
C. glabrata
,
C. krusei
,
C. lusitaniae
, and
C. tropicalis
. There was no significant change in caspofungin activity over the 4-year study period. Likewise, there was no difference in activity by geographic region. Caspofungin has excellent in vitro activity against invasive clinical isolates of
Candida
from centers worldwide. Our prospective sentinel surveillance reveals no evidence of emerging caspofungin resistance among invasive clinical isolates of
Candida
.
Peptide Mimotopes Selected from a Random Peptide Library for Diagnosis of Epstein-Barr Virus Infection
Authors: Casey Joanne L. , Coley Andrew M. , Street Graham , Parisi Kathy , Devine Peter L. , Foley Michael 
Published: March 2006

ABSTRACTEpstein-Barr virus (EBV) is a ubiquitous, worldwide infectious agent that causes infectious mononucleosis, affecting >90% of the world's population. Currently, enzyme-linked immunosorbent assay, mostly with purified preparations of EBV cell extracts to capture immunoglobulin M (IgM) antibodies in patients' serum, is used for primary diagnosis. Our objective was to determine whether a small set of peptides could contain sufficient immunogenic information to replace solid-phase antigens in EBV diagnostics. Using monoclonal antibodies, we selected four peptides that mimic different epitopes of EBV from a phage-displayed random peptide library. To assess their diagnostic value, we screened a panel of 62 individual EBV IgM sera for their reactivities with the peptides alone. For all peptides, there was a clear distinction between the EBV-positive and the EBV-negative samples, resulting in 100% specificity. The sensitivities were 88%, 85%, 71%, and 54% for peptides F1, A3, gp125, and A2, respectively. Any combination of peptides increased the sensitivity, indicating that individual peptides react with different subsets of antibodies. Furthermore, when the F1 and the gp125 peptides were coupled to bovine serum albumin and screened against 216 serum samples, there were dramatic improvements in sensitivities (95% and 92%, respectively) and little cross-reactivity with the other peptides encountered during acute viral infections, including rheumatoid factor. This study shows the potential for the use of peptide mimotopes as alternatives to the complex antigens used in current serodiagnostics for EBV infection.
Single-Nucleotide Repeat Analysis for Subtyping
Bacillus anthracis
Isolates
Authors: Stratilo Chad W. , Lewis Christopher T. , Bryden Louis , Mulvey Michael R. , Bader Doug 
Published: March 2006

ABSTRACT

Single-nucleotide repeats (SNRs) are variable-number tandem repeats that display very high mutation rates. In an outbreak situation, the use of a marker system that exploits regions with very high mutation rates, such as SNRs, allows the differentiation of isolates with extremely low levels of genetic diversity. This report describes the identification and analysis of SNR loci of
Bacillus anthracis
. SNR loci were selected in silico, and the loci with the highest diversity were used to design and test locus-specific primers against a number of
B. anthracis
strains with the same multilocus variable-number tandem repeat analysis (MLVA) genotype. SNR markers that allowed strains with the same MLVA genotype to be differentiated from each other were identified. The resulting SNR marker system can be used as a molecular epidemiological tool in a natural outbreak or bioterrorism event, offering the best chance of distinguishing very closely related isolates.
Multiple Viral Infections and Genomic Divergence among Noroviruses during an Outbreak of Acute Gastroenteritis
Authors: Sasaki Yukiko , Kai Akemi , Hayashi Yukinao , Shinkai Takayuki , Noguchi Yayoi , Hasegawa Michiya , Sadamasu Kenji , Mori Kohji , Tabei Yukiko , Nagashima Mami , Morozumi Satoshi , Yamamoto Tomoko 
Published: March 2006

ABSTRACT
An epidemic outbreak of both norovirus (NV) and astrovirus (ASV) occurred on a research ship surveying Tokyo Bay, causing acute gastroenteritis in 26 of its 37 crew members. The presence of viral pathogens in fecal specimens was analyzed, and noroviruses were identified by reverse transcription-PCR in 18 (48.6%) of these specimens. In addition, astroviruses were identified in 14 (37.8%) of the fecal samples from the affected crew members, and multiple viral infections of both NV and ASV were observed in 6 cases. The genogrouping of the NV-positive samples was then examined by dot blot hybridization, and it was determined that all of the isolates were from genogroup II (GII). No bacterial pathogens were subsequently isolated from fecal specimens. Furthermore, a variety of NV strains were identified by sequencing and single-stranded conformational polymorphism (SSCP) analyses of PCR products from the fecal samples. One recombinant NV isolate, Minato/14, was identified as a recombinant NV strain of GII/6 and GII/1. The other NV isolates from this outbreak were classified into three NV genotypes (GII/1 [Minato/10], GII/4 [Minato/33], and GII/5 [Minato/6]). Furthermore, ASVs in positive samples were determined to belong to serotypes 1 and 2 by sequencing analysis. Our findings thus indicate that coinfections with NV and ASV, including a number of NV genotypes, persisted during an outbreak of gastroenteritis in a closed environment.