bluuebunny/crossref_metadata_2025 huggingface dataset:
Smallpox and
pan
-Orthopox Virus Detection by Real-Time 3′-Minor Groove Binder TaqMan Assays on the Roche LightCycler and the Cepheid Smart Cycler Platforms
Authors: Kulesh David A. , Baker Robert O. , Loveless Bonnie M. , Norwood David , Zwiers Susan H. , Mucker Eric , Hartmann Chris , Herrera Rafael , Miller David , Christensen Deanna , Wasieloski Leonard P. , Huggins John , Jahrling Peter B.
Published: February 2004

We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and
pan
-orthopox virus DNAs. The assays are based on TaqMan 3′-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the
pan
-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 × 10
7
, 1.24 × 10
5
, 1.24 × 10
3
, and 1.24 × 10
1
genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs. However, all five assays had nearly 100% sensitivity on both machines with samples above the LOD (>12 gene copies). These real-time PCR assays represent a battery of tests to screen for and confirm the presence of variola virus DNA. The early detection of a smallpox outbreak is crucial whether the incident is an act of bioterrorism or an accidental occurrence.
Epidemiology and Etiology of Sexually Transmitted Infection among Hotel-Based Sex Workers in Dhaka, Bangladesh
Authors: Nessa Khairun , Waris Shama-A , Sultan Zafar , Monira Shirajum , Hossain Maqsud , Nahar Shamsun , Rahman Habibur , Alam Mahbub , Baatsen Pam , Rahman Motiur
Published: February 2004

The prevalence of sexually transmitted infections (STIs) and reproductive tract infections (RTIs) among hotel-based sex workers (HBSWs) in Dhaka, Bangladesh, was studied. A total of 400 HBSWs were enrolled in the study during April to July 2002. Endocervical swabs, high vaginal swabs, and blood samples from 400 HBSWs were examined for
Neisseria gonorrhoeae
(by culture),
Chlamydia trachomatis
(by PCR),
Trichomonas vaginalis
(by microscopy), antibody to
Treponema pallidum
(by both rapid plasma reagin and
Treponema pallidum
hemagglutination tests), and antibody to herpes simplex virus type 2 (HSV-2) (by enzyme-linked immunosorbent assay). Sociodemographic information as well as gynecological and obstetric information was collected. Among the HBSWs, 228 women (57%) were symptomatic and 172 (43%) were asymptomatic, 35.8% were positive for
N. gonorrhoeae
, 43.5% were positive for
C. trachomatis
, and 4.3% were positive for
T. vaginalis
. A total of 8.5% had syphilis, 34.5% were positive for HSV-2, and 86.8% were positive for at least one RTI or STI. There was no significant difference between the prevalences of STIs among the symptomatic and asymptomatic HBSWs. These data suggested a high prevalence of STIs, particularly gonorrhea and chlamydia, among HBSWs in Dhaka.
Direct Amplification and Genotyping of
Dientamoeba fragilis
from Human Stool Specimens
Authors: Peek Ron , Reedeker Freek R. , van Gool Tom
Published: February 2004

Dientamoeba fragilis
is a globally occurring parasite that has been recognized as a causative agent of gastrointestinal symptoms. A single-round PCR was developed to detect
D. fragilis
DNA directly from human stool samples. The genetic diversity of
D. fragilis
from 93 patients and 6 asymptomatic carriers was examined by PCR followed by restriction fragment length polymorphism and sequencing of part of the small-subunit rRNA gene. The data show that
D. fragilis
sequences can be studied directly from fecal specimens despite the absence of a cyst stage and without the need for prior culturing. In addition, the results suggest strongly that
D. fragilis
shows remarkably little variation in its small-subunit rRNA gene.
Genetic Diversity of Cell-Invasive Erythromycin-Resistant and -Susceptible Group A Streptococci Determined by Analysis of the
RD2
Region of the
prtF1
Gene
Authors: Spinaci Cinzia , Magi Gloria , Zampaloni Claudia , Vitali Luca A. , Paoletti Claudia , Catania Maria R. , Prenna Manuela , Ferrante Luigi , Ripa Sandro , Varaldo Pietro E. , Facinelli Bruna
Published: February 2004

The
RD2
region of the internalization-associated gene
prtF1
, which encodes the fibronectin-binding repeat domain type 2 of protein F1, plays a crucial role in the entry of group A streptococci (GAS) into epithelial cells. A molecular study of the variability of the
RD2
region was carried out with 77 independent Italian GAS, 66 erythromycin resistant (ER) and 11 erythromycin susceptible (ES), which had previously been investigated for the association between erythromycin resistance and ability to enter human respiratory cells. The amplicons obtained from PCR analysis of the
RD2
region were consistent with a number of
RD2
repeats ranging from one to five, more frequently four (
n
= 30), three (
n
= 27), and one (
n
= 18). A new method to type cell-invasive GAS (
RD2
typing) was developed by combining PCR analysis of the
RD2
region and restriction analysis of PCR products with endonucleases
Hae
III,
Dde
I, and
Hin
fI. Overall, 10
RD2
types (a to j) were distinguished (all detected among the 66 ER isolates, four detected among the 11 ES isolates). Comparison and correlation of
RD2
typing data with the genotype and phenotype of macrolide resistance and with data from PCR M typing and
Sma
I macrorestriction analysis allowed us to identify 41 different clones (31 among the 66 ER isolates and 10 among the 11 ES isolates). Three major clones accounted for 40% of the isolates (47% of ER strains). Some ES isolates appeared to be related to ER isolates with identical combinations of
RD2
type and
emm
type. While simultaneous use of different typing methods is essential for a thorough investigation of GAS epidemiology,
RD2
typing may be especially helpful in typing cell-invasive GAS.
Serotypes, Virulence Genes, and Intimin Types ofShiga Toxin (Verotoxin)-ProducingEscherichia coliIsolatesfrom Cattle in Spain and Identification of a New Intimin VariantGene(eae-ξ)
Authors: Blanco M. , Blanco J. E. , Mora A. , Dahbi G. , Alonso M. P. , González E. A. , Bernárdez M. I. , Blanco J.
Published: February 2004

A total of 514 Shiga toxin-producingEscherichia coli(STEC) isolates from diarrheic and healthy cattle in Spain were characterized in this study. PCR showed that 101 (20%) isolates carriedstx1genes, 278 (54%) possessedstx2genes, and 135 (26%) possessed bothstx1andstx2. Enterohemolysin (ehxA) and intimin (eae) virulence genes were detected in 326 (63%) and in 151 (29%) of the isolates, respectively. STEC isolates belonged to 66 O serogroups and 113 O:H serotypes (including 23 new serotypes). However, 67% were of one of these 15 serogroups (O2, O4, O8, O20, O22, O26, O77, O91, O105, O113, O116, O157, O171, O174, and OX177) and 52% of the isolates belonged to only 10 serotypes (O4:H4, O20:H19, O22:H8, O26:H11, O77:H41, O105:H18, O113:H21, O157:H7, O171:H2, and ONT:H19). Although the 514 STEC isolates belonged to 164 different seropathotypes (associations between serotypes and virulence genes), only 12 accounted for 43% of isolates. Seropathotype O157:H7stx2eae-γ1ehxA(46 isolates) was the most common, followed by O157:H7stx1stx2eae-γ1ehxA(34 isolates), O113:H21stx2(25 isolates), O22:H8stx1stx2ehxA(15 isolates), O26:H11stx1eae-β1ehxA(14 isolates), and O77:H41stx2ehxA(14 isolates). Forty-one (22 of serotype O26:H11) isolates had intiminβ 1, 82 O157:H7 isolates possessed intimin γ1, three O111:H- isolates had intimin type γ2, one O49:H- strain showed intimin type δ, 13 (six of serotype O103:H2) isolates had intimin type ε and eight (four of serotype O156:H-) isolates had intimin ζ. We have identified a new variant of theeaeintimin gene designated ξ (xi) in two isolates of serotype O80:H-. The majority (85%) of bovine STEC isolates belonged to serotypes previously found for human STEC organisms and 54% to serotypes associated with STEC organisms isolated from patients with hemolytic uremic syndrome. Thus, this study confirms that cattle are a major reservoir of STEC strains pathogenic for humans.
Prevalence, Risk Factors, and Genetic Diversity of
Bartonella henselae
Infections in Pet Cats in Four Regions of the United States
Authors: Guptill L. , Wu C.-C. , HogenEsch H. , Slater L. N. , Glickman N. , Dunham A. , Syme H. , Glickman L.
Published: February 2004

Blood was collected from a convenience sample of 271 pet cats aged 3 months to 2 years (mean age, 8 months, median and mode, 6 months) between May 1997 and September 1998 in four areas of the United States (southern California, Florida, metropolitan Chicago, and metropolitan Washington, D.C.). Sixty-five (24%) cats had
Bartonella henselae
bacteremia, and 138 (51%) cats were seropositive for
B. henselae
. Regional prevalences for bacteremia and seropositivity were highest in Florida (33% and 67%, respectively) and California (28% and 62%, respectively) and lowest in the Washington, D.C. (12% and 28%, respectively) and Chicago (6% and 12%, respectively) areas. No cats bacteremic with
B. clarridgeiae
were found. The 16S rRNA type was determined for 49
B. henselae
isolates. Fourteen of 49 cats (28.6%) were infected with 16S rRNA type I, 32 (65.3%) with 16S rRNA type II, and three (6.1%) were coinfected with 16S rRNA types I and II. Flea infestation was a significant risk factor for
B. henselae
bacteremia (odds ratio = 2.82, 95% confidence interval, 1.1 to 7.3). Cats ≥13 months old were significantly less likely to be bacteremic than cats ≤6 months old (odds ratio = 0.18, 95% confidence interval, 0.05 to 0.61). Flea infestation, adoption from a shelter or as a stray cat, hunting, and being from Florida or California were significant risk factors for
B. henselae
seropositivity. DNA fingerprint was significantly associated with region (
P
= 0.03) and indoor/outdoor status of cats (
P
= 0.03).
GenotypicAnalysis ofMycobacterium tuberculosisin Bangladesh andPrevalence of the BeijingStrain
Authors: Banu Sayera , Gordon Stephen V. , Palmer Si , Islam Reazul , Ahmed Shakeel , Alam Khan Mashrequl , Cole Stewart T. , Brosch Roland
Published: February 2004

Genotypic analysis was performed on 48Mycobacterium tuberculosiscomplex strains collected from a hospital in Dhaka city. Deletion analysis showed that the isolates were allM. tuberculosis;13 of them were found to be of the “ancestral” type, while 35 were of the “modern” type, indicating that both endemic (ancestral type) and epidemic (modern type) strains cause tuberculosis in Bangladesh. Genotyping based on the spoligotype and variable-number tandem repeats (VNTR) of mycobacterial interspersed repetitive units (MIRU) was also done. A total of 34 strains (71%) were grouped by spoligotyping into nine different clusters; the largest comprised 15 isolates of the Beijing genotype, whereas the remaining eight clusters consisted of two to five isolates. MIRU-VNTR typing detected 32 different patterns among 44 tested strains, and the 15 Beijing strains were further discriminated by MIRU-VNTR typing (7 distinct patterns for the 15 isolates). These results indicate that MIRU-VNTR typing, along with spoligotyping and deletion analysis, can be used effectively for molecular epidemiological studies to determine ongoing transmission clusters; to our knowledge, this is the first report about the type of strains prevailing in Bangladesh.
Genetic Characterization and Antibiotic Resistance of
Campylobacter jejuni
Isolated from Meats, Water, and Humans in Sweden
Authors: Lindmark H. , Harbom B. , Thebo L. , Andersson L. , Hedin G. , Osterman B. , Lindberg T. , Andersson Y. , Westöö A. , Olsson Engvall E.
Published: February 2004

The incidence of
Campylobacter jejuni
has increased during the last decade, and today it is the leading cause of bacterial enteritis in most developed countries. Still, there is a lack of knowledge about infection routes and to what extent identified sources are responsible for spreading the bacterium to humans. The major objective of this work was to explore the genetic similarity between
C. jejuni
isolated from different sources.
C. jejuni
isolated from patients (
n
= 95), five types of meat (
n
= 71), and raw water (
n
= 11) during the year 2000 were subtyped by pulsed-field gel electrophoresis (PFGE). The pulsotypes obtained after digestion with
Sma
I revealed not only that
C. jejuni
is genetically diverse but also that specific pulsotypes occur frequently. Five clusters comprising 88 of the 162
Sma
I-digested isolates were obtained. After digestion with
Kpn
I most isolates in four of the five clusters were still indistinguishable, while the fifth cluster was strongly dissolved. The clusters comprised high frequencies of human and meat isolates, while only one of nine water isolates belonged to a cluster. The largest cluster comprised 21 human isolates, one raw water isolate, and seven chicken meat isolates, originating from at least six different broiler flocks. Low frequencies of antibiotic resistance were revealed when the meat and water isolates were tested for sensitivity to six antibiotics. Interestingly, the five isolates resistant to quinolones displayed similar or identical pulsotypes. The results showed that PFGE has proved useful in identifying clones and will be used in future work focusing on identification and eradication of the major reservoirs for common clones.
Use of theTrypanosoma cruziRecombinant Complement Regulatory Protein To Evaluate Therapeutic Efficacy following Treatment of Chronic Chagasic Patients
Authors: Meira Wendell S. F. , Galvão Lúcia M. C. , Gontijo Eliane D. , Machado-Coelho George L. L. , Norris Karen A. , Chiari Egler
Published: February 2004

One of the greatest concerns in Chagas' disease is the absence of reliable methods for the evaluation of chemotherapy efficacy in treated patients. The tests available to evaluate cure after the specific treatment are the complement-mediated lysis (CoML) and flow cytometry tests, but they are not feasible for routine clinical use. In this study, we evaluated an enzyme-linked immunosorbent assay (ELISA) based on the recombinantTrypanosoma cruzicomplement regulatory protein (rCRP) as a method to determine parasite clearance in comparison to the CoML and other methods such as conventional serology, hemoculture, and PCR in serum samples of 31 patients collected before and after the treatment, monitored for an average of 27.7 months after chemotherapy. The results showed that the percentage of patient samples that were positive by rCRP ELISA was reduced from 100 to 70.3, 62.5, 71.4, and 33.4% in the first, second, third, and fourth years after treatment, respectively, while the samples positive by CoML were reduced to 85.2, 81.2, 71.4, and 33.4% during the same period, demonstrating the same significant tendency in the reduction of positive samples. On the other hand, the conventional serology (CS) tests did not present this reduction. The percentage of samples positive by PCR was initially 77.4% and decreased to 55.5, 68.7, 47.7, and 50.0% at the fourth year after treatment, confirming the drastic clearance of circulating parasites after treatment. Our results strongly suggest that the rCRP ELISA was capable of detecting the early therapeutic efficacy in treated patients and confirmed its superiority over the CS tests and parasitologic methods.
Identification and H
2
O
2
Production of Vaginal Lactobacilli from Pregnant Women at High Risk of Preterm Birth and Relation with Outcome
Authors: Wilks Mark , Wiggins Rebecca , Whiley Angela , Hennessy Enid , Warwick Simon , Porter Helen , Corfield Anthony , Millar Michael
Published: February 2004

Lactobacilli, principally the strains that are hydrogen peroxide (H
2
O
2
) producing, may have a protective effect against vaginal colonization by pathogenic species such as those that cause bacterial vaginosis. Previous reports have also suggested that H
2
O
2
-producing lactobacilli in the vagina may protect pregnant women against ascending infection of the chorioamniotic membranes and uterine cavity. We report the identification and H
2
O
2
production of lactobacilli isolated from vaginal swabs collected at 20 weeks' gestation from a population of pregnant women at high risk of preterm birth. We also report the correlation between identification and H
2
O
2
production in relation to the outcomes of chorioamnionitis and preterm birth. Lactobacilli were identified by partial 16S rRNA gene sequencing. H
2
O
2
production by isolates was determined by a semiquantitative method. The most commonly isolated species were
L. crispatus
,
L. gasseri
,
L. vaginalis
and
L. jensenii
. Amounts of H
2
O
2
produced by lactobacilli varied widely. The presence of lactobacilli producing high levels of H
2
O
2
in the vagina of this population of pregnant women was associated with a reduced risk of bacterial vaginosis at 20 weeks' gestation and subsequent chorioamnionitis.
L. jensenii
and
L. vaginalis
produced the highest levels of H
2
O
2
. We postulate that H
2
O
2
-producing lactobacilli are able to reduce the incidence of ascending infections of the uterus and the subsequent production of proinflammatory molecules which are important in the pathogenesis of chorioamnionitis and preterm birth.
Purification and Characterization of a 43-Kilodalton Extracellular Serine Proteinase from
Cryptococcus neoformans
Authors: Yoo Jae il , Lee Yeong Seon , Song Chul-Yong , Kim Bong Su
Published: February 2004

An extracellular proteinase was purified from culture filtrates of
Cryptococcus neoformans
NHPY24 by DEAE ion-exchange chromatography and gelatin affinity column chromatography with azoalbumin as the substrate. The molecular mass of the purified enzyme was 43 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, its pH optimum was 7.0 to 8.0, and maximal activity was obtained at pH 7.5 and 37°C. By isoelectric focusing, the purified enzyme had a pI of 4.77. Enzyme activity was inhibited by serine proteinase inhibitors such as phenylmethylsulfonyl fluoride and diisopropylfluorophosphate. The purified enzyme was thus a serine proteinase. It hydrolyzed natural substrates including hemoglobin, β-casein, and gamma globulin.
Viable but Nonculturable Bacteria Are Present in Mouse and Human Urine Specimens
Authors: Anderson Marc , Bollinger Daphne , Hagler Ashley , Hartwell Hadley , Rivers Bryan , Ward Kristie , Steck Todd R.
Published: February 2004

The presence of viable but nonculturable bacteria in human clean-catch and mouse bladder-isolated urine specimens was investigated. Viable but nonculturable bacteria are alive but do not give rise to visible growth under nonselective growth conditions. Urine specimens obtained from human female volunteers with or without an active urinary tract infection were found to contain, on average, significantly more viable than culturable forms of bacteria. Additional support for the presence of viable but nonculturable cells in urine specimens considered sterile was obtained from examination of urine specimens obtained directly from the bladder of healthy mice. Because the viability assay used to study the viable but nonculturable condition is by necessity growth independent, and hence indirect, the accuracy of this assay that scores cells with intact cell membranes as being viable was studied. Greater than 95% of
Escherichia coli
cells exposed to lethal doses of UV irradiation were found to lose their membrane integrity within a day, a time frame similar to that used to examine urine specimens. These data suggest that viable but nonculturable cells can occur within regions of the urinary tract previously considered sterile.
Comparison of Sensitivities of Virus Isolation, Antigen Detection, and Nucleic Acid Amplification for Detection of Equine Influenza Virus
Authors: Quinlivan Michelle , Cullinane Ann , Nelly Maura , van Maanen Kees , Heldens Jacco , Arkins Sean
Published: February 2004

Four seronegative foals aged 6 to 7 months were exposed to an aerosol of influenza strain A/Equi/2/Kildare/89 at 10
6
50% egg infective doses (EID
50
)/ml. Nasopharyngeal swabs were collected for 10 consecutive days after challenge. Virus isolation was performed in embryonated eggs, and the EID
50
was determined for all positive samples. The 50% tissue culture infective dose was determined using Madin-Darby canine kidney (MDCK) cells. Samples were also tested by an in vitro enzyme immunoassay test, Directigen Flu A, and by reverse transcription-PCR (RT-PCR) using nested primers from the nucleoprotein gene and a single set of primers from the matrix gene. RT-PCR using the matrix primers and virus isolation in embryonated eggs proved to be the most sensitive methods for the detection of virus. The Directigen Flu A test was the least sensitive method. The inclusion of 2% fetal calf serum in the viral transport medium inhibited the growth of virus from undiluted samples in MDCK cells but was essential for the maintenance of the virus titer in samples subjected to repeated freeze-thaw cycles.
Comparison of Mycosis IC/F and Plus Aerobic/F Media for Diagnosis of Fungemia by the Bactec 9240 System
Authors: Meyer Marie-Hélène , Letscher-Bru Valérie , Jaulhac Benoît , Waller Jocelyn , Candolfi Ermanno
Published: February 2004

Fungemia is associated with a high mortality rate. We compared the performance of the Mycosis IC/F selective fungal medium and the Plus Aerobic/F standard bacteriological medium for the diagnosis of fungemia on the Bactec 9240 automatic system. We retrospectively analyzed 550 blood culture pairs composed of one Mycosis IC/F vial and one Plus Aerobic/F vial, drawn in 187 patients with fungemia. The positivity rate by vial was significantly higher on Mycosis IC/F medium than on Plus Aerobic/F medium (88.0% versus 74.9%,
P
< 0.0001). The positivity rate for fungus detection on Plus Aerobic/F medium fell to 26.9% when bacteria were present in the same vial. The positivity rate by patient was also significantly higher on Mycosis IC/F medium than on Plus Aerobic/F medium (92.5% versus 75.9%,
P
< 0.0001). A marked superiority of Mycosis IC/F medium was demonstrated for diagnosis of
Candida glabrata
fungemia (31 of 31, 100%, versus 18 of 31, 58.1%,
P
< 0.0001). The mean detection time was significantly shorter on Mycosis IC/F medium than on Plus Aerobic/F medium (28.9 ± 22.2 h versus 36.5 ± 24.6 h,
P
< 0.0001). The mean time saving was 8.8 h for
Candida albicans
and 43.7 h for
C. glabrata
. Mycosis IC/F medium enabled more sensitive and earlier diagnosis, particularly for the two strains most frequently responsible for fungemia,
C. albicans
and
C. glabrata
, and also in the event of the concomitant presence of both yeasts and bacteria. In patients with risk factors, it would thus appear to be sensible to draw a Mycosis IC/F vial in addition to the standard bacteriological vials.
Multicenter Evaluation of the VERSANT Hepatitis B Virus DNA 3.0 Assay
Authors: Yao Joseph D. C. , Beld Marcel G. H. M. , Oon Lynette Lin Ean , Sherlock Christopher H. , Germer Jeffrey , Menting Sandra , Se Thoe Su Yun , Merrick Linda , Ziermann Rainer , Surtihadi Johan , Hnatyszyn H. James
Published: February 2004

The VERSANT hepatitis B virus (HBV) 3.0 Assay (branched DNA [bDNA]) (referred to herein as VERSANT 3.0) was evaluated at four external sites for analytical sensitivity, specificity, reproducibility, linearity of quantification, and limits of detection. In addition, each of the test evaluation sites provided HBV DNA-positive clinical samples that were previously analyzed by one of three commercially available HBV DNA quantitative tests: Digene Hybrid Capture II HBV DNA Test (Digene); VERSANT HBV DNA 1.0 Assay (bDNA) (VERSANT 1.0); and COBAS AMPLICOR HBV Monitor Test (COBAS AMPLICOR). These samples were reexamined using VERSANT 3.0. The results from these studies showed that VERSANT 3.0 has high specificity (99.3%), excellent reproducibility (between-run coefficient of variation [CV] = 1.6 to 9.4%; within-run CV = 6.5 to 20.7%), and a broad linear range of quantification (2.0 × 10
3
to 1.0 × 10
8
HBV DNA copies/ml) that facilitate the monitoring of HBV DNA levels at diagnosis and throughout the course of treatment. In general, correlation was very good between results obtained from clinical samples analyzed by VERSANT 3.0 and the comparative HBV DNA quantitative assays (VERSANT 1.0,
R
2
= 0.900; Digene,
R
2
= 0.985; COBAS AMPLICOR,
R
2
= 0.771). The greatest differences in comparative quantitation occurred at HBV DNA levels approaching the limits of the dynamic ranges for the comparative assays. The performance characteristics of the new VERSANT 3.0 assay demonstrated that it provides a reliable and robust method for routinely monitoring serum HBV DNA levels in assessing disease activity and determining response to antiviral treatment.
Molecular Characterization of Resistance to Mupirocin in Methicillin-Susceptible and -Resistant Isolates of
Staphylococcus aureus
from Nasal Samples
Authors: Chaves Fernando , García-Martínez Jesus , de Miguel Sonia , Otero Joaquín R.
Published: February 2004

A total of 15 of 101 (14.8%) nasal methicillin-resistant
Staphylococcus aureus
(MRSA) isolates exhibited mupirocin resistance (Mup
r
) compared with 1 of 154 (0.6%) methicillin-susceptible
Staphylococcus aureus
isolates. A total of 14 (93%) isolates exhibiting high-level Mup
r
belonged to a single clone. Horizontal plasmid transfer and transmission of Mup
r
strains contribute to a high incidence of Mup
r
MRSA at our institution.
Comparison of
Acinetobacter baumannii
Isolates from United Kingdom Hospitals with Predominant Northern European Genotypes by Amplified-Fragment Length Polymorphism Analysis
Authors: Spence Richard P. , van der Reijden Tanny J. K. , Dijkshoorn Lenie , Towner Kevin J.
Published: February 2004

Acinetobacter baumannii
isolates collected between 1999 and 2001 from 46 United Kingdom hospitals were compared with previously identified northern European genotypes by amplified-fragment length polymorphism (AFLP) analysis. Two predominant northern European genotypes associated with outbreaks in the mid-1980s had been superseded by new outbreak-associated genotypes.
Development of a New Serological Test for SerotypingHaemophilus parasuisIsolates and Determination of Their Prevalence in North America
Authors: Tadjine M. , Mittal K. R. , Bourdon S. , Gottschalk M.
Published: February 2004

Haemophilus parasuiscauses polyserositis in swine. Fifteen serovars have been characterized by immunodiffusion test, but many field strains are not typeable. Isolates (n= 300) ofH. parasuisfrom animals in North America were serotyped by a new indirect hemagglutination test. The test was rapid and effective for serotyping ofH. parasuis, and serovars 4, 5, 13, and 7 were the most prevalent serotypes.
Use of an Internal Positive Control in a Multiplex Reverse Transcription-PCR To Detect West Nile Virus RNA in Mosquito Pools
Authors: Eisler Diane L. , McNabb Alan , Jorgensen Danielle R. , Isaac-Renton Judith L.
Published: February 2004

We report on the use of West Nile virus Armored RNA as an internal positive control (IPC) for the extraction and reverse transcription-PCR (RT-PCR) of RNA extracted from field-collected mosquitoes and on a multiplex real-time Taqman RT-PCR to simultaneously detect the 3′ noncoding region of West Nile virus and the West Nile virus NS5-2 region comprising the IPC. Mosquito pools from the province of British Columbia, Canada (
n
= 635), were tested in duplicate and found to be negative for West Nile virus and positive for the IPC. Known West Nile virus-positive supernatants from mosquito pools from the provinces of Alberta and Manitoba were tested in duplicate and found to be positive for both regions of the West Nile virus genome. The mean cycle threshold (Ct) value for the IPC in batch extraction controls ± 2 standard deviations was found to be 36.43 ± 1.78 cycles. IPCs of 98.4% (624) of West Nile virus-negative pools fell within this range, indicating the reproducibility of RNA extraction and RT-PCR for pools varying in mosquito genus and number. A comparison of mosquito pool genera revealed no significant genus effect on the Ct value of the IPC. The incorporation of West Nile virus Armored RNA as an IPC allows monitoring of RNA extraction and RT-PCR and detection of false-negative results due to failures in these processes or to PCR inhibition, respectively.
Identification of a New Type of
Babesia
Species in Wild Rats (
Bandicota indica
) in Chiang Mai Province, Thailand
Authors: Dantrakool Anchalee , Somboon Pradya , Hashimoto Tetsuo , Saito-Ito Atsuko
Published: February 2004

A new type of rodent babesia, which resembled
Babesia microti
but was phylogenetically placed closest, with the highest level of statistical support, to
Babesia canis
, a canine babesia, was identified in Thai
Bandicota indica
in Thai provinces to which malaria is endemic. Close watch should be kept on human babesiosis in Thailand.
Resolution of Discrepant Results for
Candida
Species Identification by Using DNA Probes
Authors: Coignard Catherine , Hurst Steven F. , Benjamin Lynette E. , Brandt Mary E. , Warnock David W. , Morrison Christine J.
Published: February 2004

Candida
species bloodstream isolates were collected from institutions participating in an active, population-based surveillance for candidemia. Species identifications were performed locally and then confirmed at the Centers for Disease Control and Prevention (CDC) by phenotype-based methods. Discrepancies in species identification between the referring institution and the CDC were noted for 43 of 935 isolates (4.6%). A DNA probe-based species identification system (PCR-enzyme immunoassay [EIA]) was then used to resolve these discrepancies. The PCR-EIA result was identical to the CDC phenotypic identification method for 98% of the isolates tested. The most frequently misidentified species was
Candida glabrata
(37% of all discrepant identifications). Such misidentifications could lead to the administration of inappropriate therapy given the propensity of
C. glabrata
to develop resistance to azole antifungal drugs.
Detection of the
Candida
Antigen Mannan in Cerebrospinal Fluid Specimens from Patients Suspected of Having
Candida
Meningitis
Authors: Verduyn Lunel Frans M. , Voss Andreas , Kuijper Ed J. , Gelinck L. B. S. , Hoogerbrugge Peter M. , Liem K. L. , Kullberg Bart Jan , Verweij Paul E.
Published: February 2004

Cerebrospinal fluid samples from five patients from which
Candida
cells were cultured were tested for the presence of mannan. Samples from four patients categorized as having proven candidosis reacted positively. Samples from the remaining patient and from patients with other central nervous system infections were negative. Detection of mannan may be valuable in the diagnosis of
Candida
meningitis.
Direct Colorimetric Assay for Rapid Detection of Rifampin-Resistant
Mycobacterium tuberculosis
Authors: Abate Getahun , Aseffa Abraham , Selassie Alemayehu , Goshu Solomon , Fekade Bekele , WoldeMeskal Dawit , Miörner Håkan
Published: February 2004

The colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay was standardized for direct detection of rifampin-resistant
Mycobacterium tuberculosis
in sputum samples. The sensitivity and specificity of the direct MTT assay matched those of the standard indirect susceptibility assay on 7H10 medium, and interpretable results were obtained for 98.5% of the samples within 2 weeks. Traditional methods of in vitro drug susceptibility testing are time consuming and laborious. Susceptibility tests on clinical isolates require 6 to 9 weeks, and tests conducted directly on smear-positive samples take about 3 weeks (International Union Against Tuberculosis and Lung Disease, The public health service national tuberculosis reference laboratory and the national laboratory network. Minimum requirements, role and operation in a low-income country, Paris, France, 1998, and P. T. Kent and G. P. Kubica, Public health mycobacteriology. A guide for the level III laboratory, Centers for Disease Control and Prevention, Atlanta, Ga., 1985). More-rapid methods are available but are very expensive for routine use under program conditions in countries with high levels of tuberculosis endemicity.
Characterization of
Haemophilus segnis
, an Important Cause of Bacteremia, by 16S rRNA Gene Sequencing
Authors: Lau Susanna K. P. , Woo Patrick C. Y. , Mok Mo-yin , Teng Jade L. L. , Tam Victoria K. P. , Chan Katie K. H. , Yuen Kwok-yung
Published: February 2004

We describe the application of 16S rRNA gene sequencing in defining eight cases of bacteremia due to
Haemophilus
species other than
Haemophilus influenzae
(non-
H. influenzae
bacteremia) during a 7-year period. The first case of acute pyelonephritis due to
Haemophilus segnis
is also reported. In contrast to the extremely rare incidence of
H. segnis
infections reported previously, our results suggested that
H. segnis
is an important cause of non-
H. influenzae
bacteremia.
Development, Implementation, and Impact of Acceptability Criteria for Serologic Tests for Infectious Diseases
Authors: Crump John A. , Corder Jennifer R. , Henshaw Nancy G. , Reller L. Barth
Published: February 2004

Serologic testing is essential for the diagnosis of some infectious diseases and yet is fraught with potential pitfalls. All parts of the diagnostic process must be optimized to ensure that serologic tests perform adequately. Recognizing that a lack of clinical data and correctly timed, paired sera frequently led to uninterpretable serology results at our laboratory, we developed and implemented simple acceptability criteria for serologic tests. We assessed the impact of these criteria by comparing submissions and results for the year before and the year after implementation of the criteria. The number of serologic tests performed declined by 25% after implementation of the acceptability criteria, despite an increase in requests for serologic tests. Inappropriate testing of acute-phase sera alone fell from 49 to 0% (
P
< 0.001) for the tests monitored. Appropriate submission of paired sera rose from 9 to 19% (
P
= 0.006). The proportion of results classified as interpretable rose from 52 to 100% (
P
< 0.001). We recommend that acceptability criteria be developed and applied to samples submitted to clinical microbiology laboratories for serologic testing.
Evaluation of Commercial Enzyme-Linked Immunosorbent Assay Kits for Detection of Tuberculosis in Argentinean Population
Authors: Imaz María Susana , Comini Marcelo Alberto , Zerbini Elsa , Sequeira María Delfina , Latini Omar , Claus Juan Daniel , Singh Mahavir
Published: February 2004

Pathozyme-Myco G (Myco G), M, A, and TB complex plus (Omega Diagnostics Ltd., Alloa, Scotland) were evaluated for the serological diagnosis of pulmonary tuberculosis (TB) in an Argentinean population. Sera from 58 patients with pulmonary TB, 24 subjects with pulmonary mycobacteriosis or mycoses (pulmonary MM group), and 45 subjects with other underlying disorders (control group) were analyzed. The sensitivities of the tests ranged from 29% (Myco M) to 82% (Myco G) in smear-positive patients (17 subjects) and from 29% (TB complex plus) to 49% (Myco G) in smear-negative patients (41 subjects). The specificities of the assays varied from 93% (Myco M) to 100% (Myco G and TB complex plus) in controls and from 62% (Myco A) to 96% (TB complex plus) in the pulmonary MM group. Overall, for the diagnosis of smear-negative patients, Myco G had the best characteristics, with a sensitivity of 49% and specificities of 100% for controls and 75% for the pulmonary MM group; after its combination with TB complex plus, its sensitivity improved to 59%. Nevertheless, despite its relatively poor capacity to discriminate between pulmonary TB and pulmonary MM, Myco G, alone or in combination with TB complex plus, would be a useful diagnostic tool for patients with suspected pulmonary TB living in areas where the relative prevalence of pulmonary MM was low.
Genotypic and Phenotypic Characterization of Drug-Resistant
Mycobacterium tuberculosis
Isolates from Rural Districts of the Western Cape Province of South Africa
Authors: Streicher E. M. , Warren R. M. , Kewley C. , Simpson J. , Rastogi N. , Sola C. , van der Spuy G. D. , van Helden P. D. , Victor T. C.
Published: February 2004

Genotypic and phenotypic analysis of drug-resistant
Mycobacterium tuberculosis
isolates from the Western Cape Province of South Africa showed that drug resistance is widespread and recently transmitted. Multidrug-resistant (MDR) isolates comprise 40% of this collection, and a large pool of isoniazid monoresistance may be a future source of MDR tuberculosis.
Virulence Properties and Characteristics of Shiga Toxin-Producing
Escherichia coli
in São Paulo, Brazil, from 1976 through 1999
Authors: Vaz T. M. I. , Irino K. , Kato M. A. M. F. , Dias Â. M. G. , Gomes T. A. T. , Medeiros M. I. C. , Rocha M. M. M. , Guth B. E. C.
Published: February 2004

Twenty-nine Shiga toxin-producing
Escherichia coli
(STEC) strains were identified in a collection of 2,607 isolates from patients with diarrhea in São Paulo, Brazil, from 1976 to 1999. The STEC strains belonged mainly to serotypes O111:HNM (HNM, nonmotile) (13 of 29 [44.8%]), O111:H8 (7 of 29 [24%]), and O26:H11 (4 of 29 [13.8%]);
stx
1
eae
(26 of 29 [89.6%]), in combination with either enterohemorrhagic
E. coli hlyA
(11 of 26 [42%]) or
astA
(24 of 26 [92.3%]), prevailed. The O111 STEC strains were distinguished by their inability to decarboxylate lysine. The predominance of STEC O111 and O26 since the late 1970s and the identification of STEC serotypes O55:H19, O93:H19, and O118:H16 in association with human infections in Brazil are described for the first time.
Evaluation of Sensititre Automated Reading and Incubation System for Automated Reading of Sensititre Broth Microdilution Susceptibility Plates
Authors: Chapin Kimberle C. , Musgnug Michael C.
Published: February 2004

The Sensititre Automated Reading and Incubation System (ARIS) performs automated reading of Sensititre identification and susceptibility plates. ARIS susceptibility results were compared to manually read results. A total of 212 isolates (3,352 organism-antimicrobial agent combinations) yielded 99.4% essential agreement and categorical error rates of 0.2% minor, 0% major, and 1.0% very major. ARIS yields accurate susceptibility results compared to plates read manually.
Onychomycosis Due to
Emericella quadrilineata
Authors: Gugnani Harish C. , Vijayan Vanan K. , Tyagi Puneet , Sharma Sonal , Stchigel Alberto M. , Guarro Josep
Published: February 2004

Nondermatophytic fungi are increasingly being reported as etiological agents of onychomycosis. We describe here a case of hand nail infection caused by
Emericella quadrilineata
(anamorph
Aspergillus tetrazonus
), a species not so far known to be an etiological agent of onychomycosis.
Enterococcus cecorum
Empyema Thoracis Successfully Treated with Cefotaxime
Authors: Woo Patrick C. Y. , Tam Dorothy M. W. , Lau Susanna K. P. , Fung Ami M. Y. , Yuen Kwok-Yung
Published: February 2004

We report the first case of
Enterococcus cecorum
empyema thoracis and spontaneous bacterial peritonitis in a 44-year-old man with underlying cirrhosis. The patient responded to cefotaxime (MIC, 0.25 μg/ml) treatment and drainage of the empyema. Susceptibility of
E. cecorum
to expanded-spectrum cephalosporins could be due to its production of types of penicillin-binding proteins similar to those produced by
Streptococcus
species rather than to those produced by
Enterococcus
species (as predicted by phylogenetic analysis of the 16S rRNA gene sequences).
Culture-Negative Pericarditis Caused by
Neisseria meningitidis
Serogroup C
Authors: Moumile Kaoutar , Carbonnelle Etienne , Dessemme Philippe , Tamisier Daniel , Iserin Franck , Houdouin Véronique , Nassif Xavier , Berche Patrick
Published: February 2004

We describe a case of primary purulent culture-negative pericarditis caused by
Neisseria meningitidis
serogroup C occurring in an 8-month-old previously healthy boy, which was detected in pericardial fluid by broad-spectrum PCR amplification.
Isolation of
Neosartorya pseudofischeri
from Blood: First Hint of Pulmonary Aspergillosis
Authors: Järv H. , Lehtmaa J. , Summerbell R. C. , Hoekstra E. S. , Samson R. A. , Naaber P.
Published: February 2004

We report a case of invasive pulmonary aspergillosis caused by
Neosartorya pseudofischeri
S. W. Peterson [anamorph
Aspergillus thermomutatus
(Paden) S. W. Peterson]. The diagnosis was initially based on a positive blood culture for a strain isolated from a neutropenic patient by means of a BACTEC 9050 blood culture system. The final diagnosis was established based on X-ray and computer tomography scan results as well as the detection of
Aspergillus
antigen in the patient's serum.
Treatment of Meningitis Due to Methicillin-Resistant
Staphylococcus epidermidis
with Linezolid
Authors: Krueger Wolfgang A. , Kottler Bernd , Will Bernd E. , Heininger Alexandra , Guggenberger Heinz , Unertl Klaus E.
Published: February 2004

Methicillin-resistant
Staphylococcus epidermidis
(MRSE) can cause nosocomial meningitis in the presence of prosthetic devices. Vancomycin is the treatment of choice, but its penetration into the cerebrospinal fluid is poor, especially in cases without severe meningeal inflammation. We successfully used linezolid to treat a case of posttraumatic MRSE meningitis with a low-level inflammatory response. Therapeutic effectiveness was documented microbiologically and by the simultaneous measurement of linezolid levels in serum and cerebrospinal fluid.
A THEORETICAL REVIEW OF HEAVY QUARKONIUM INCLUSIVE DECAYS
Authors: VAIRO ANTONIO
Published: February 2004

In this brief review, we summarize the current theoretical knowledge of heavy quarkonium inclusive decays, with emphasis on recent progress made in the framework of QCD effective field theories. In the appendix, we list the imaginary parts of the matching coefficients of dimensions six and eight NRQCD four-fermion operators as presently known.
DIMENSION OF THE UNIVERSE AND REPRESENTATION OF THE WAVE FUNCTION
Authors: WU ZHONG CHAO
Published: February 2004

Using the right representation in the evaluation of the creation probability of the universe, one can show that the external dimension of the Freund–Rubin model is min (s,n-s), where s is the rank of the antisymmetric field strength in the model.
SOME CONSEQUENCES OF NONCOMMUTATIVE WORLDSHEET OF SUPERSTRING
Authors: KAMANI DAVOUD
Published: February 2004

In this paper some properties of the superstring with noncommutative worldsheet are studied. We study the noncommutativity of the spacetime, generalization of the Poincaré symmetry of the superstring, the changes of the metric, antisymmetric tensor and dilaton.
NEW STRINGS WITH WORLDSHEET SUPERSYMMETRY
Authors: NICHOLS A. , MANVELYAN R. , SAVVIDY G. K.
Published: February 2004

Using worldsheet superfields we suggest a supersymmetric extension of the tensionless strings theory with perimeter action. It possesses an additional global fermionic symmetry which is similar in many ways to BRST symmetry.
MEDIUM-INDUCED GLUON RADIATION AND JET QUENCHING IN HEAVY-ION COLLISIONS
Authors: SALGADO CARLOS A.
Published: February 2004

In this brief review, we summarize the new developments on the description of gluon radiation by energetic quarks traversing a medium as well as the observable consequences in high-energy heavy-ion collisions. Information about the initial state is essential for a reliable interpretation of the experimental results and will also be reviewed. Comparison with experimental data from RHIC and expectation for the future LHC will be given.
LOW ENERGY NEUTRINO PHYSICS AFTER SNO AND KamLAND
Authors: OBERAUER L.
Published: February 2004

In the recent years important discoveries in the field of low energy neutrino physics (Eν in the ≈ MeV range) have been achieved. Results of the solar neutrino experiment SNO show clearly flavor transitions from νe to νμ,τ. In addition, the long standing solar neutrino problem is basically solved. With KamLAND, an experiment measuring neutrinos emitted from nuclear reactors at large distances, evidence for neutrino oscillations has been found. The values for the oscillation parameters, amplitude and phase, have been restricted. In this paper the potential of future projects in low energy neutrino physics is discussed. This encompasses future solar and reactor experiments as well as the direct search for neutrino masses. Finally the potential of a large liquid scintillator detector in an underground laboratory for supernova neutrino detection, solar neutrino detection, and the search for proton decay p→K+ν is discussed.
ELEMENTARY PARTICLES AND SPIN REPRESENTATIONS
Authors: MARANER PAOLO
Published: February 2004

We emphasize that the group-theoretical considerations leading to SO (10) unification of electroweak and strong matter field components naturally extend to spacetime components, providing a truly unified description of all generation degrees of freedoms in terms of a single chiral spin representation of one of the groups SO (13,1), SO (9,5), SO (7,7) or SO (3,11). The realization of these groups as higher-dimensional spacetime symmetries produces unification of all fundamental fermions is a single spacetime spinor.
VACUUM ELECTROMAGNETIC MODES IN FRIEDMAN–ROBERTSON–WALKER UNIVERSE
Authors: DARIESCU CIPRIAN , DARIESCU MARINA-AURA
Published: February 2004

The aim of the present paper is to analyze the rich structure of the vacuum electromagnetic modes in a radiation dominated FRW universe. It turns out that the nontrivial solutions for the four-vector potential, sharing the Fab=0 property, are affecting the behavior of the minimally coupled scalar boson, in comparison not only to the Minkowskian manifold but also to the closed Robertson–Walker background.
FOUR LECTURES ON THE GAUGE/GRAVITY CORRESPONDENCE
Authors: BERTOLINI MATTEO
Published: February 2004

We review in a pedagogical manner some of the efforts aimed at extending the gauge/gravity correspondence to nonconformal supersymmetric gauge theories in four dimensions. After giving a general overview, we discuss in detail two specific examples: fractional D-branes on orbifolds and D-branes wrapped on supersymmetric cycles of Calabi–Yau spaces. We explore in particular which gauge theory information can be extracted from the corresponding supergravity solutions, and what the remaining open problems are. We also briefly explain the connection between these and other approaches, such as fractional branes on conifolds, branes suspended between branes, M5-branes on Riemann surfaces and M-theory on G2-holonomy manifolds, and discuss the role played by geometric transitions in all that.