bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome Type Analysis of Adenovirus Types 3 and 7 Isolated during Successive Outbreaks of Lower Respiratory Tract Infections in Children
Authors: Kim Yae-Jean , Hong Jung-Yun , Lee Hoan-Jong , Shin Seon-Hee , Kim Yun-Kyung , Inada Toshiki , Hashido Madoka , Piedra Pedro A.
Published: October 2003

Adenovirus is an important cause of respiratory infections in infants and children. Fifty-one serotypes have been identified, and adenovirus type 3 (Ad3) and Ad7 have often been associated with outbreaks of severe respiratory tract infections. Each serotype can be further divided into genome types based on the patterns of digestion of their DNAs with restriction enzymes. DNA restriction analysis was performed with 56 strains of Ad3 and 98 strains of Ad7 by using 12 restriction enzymes recognizing 6 bp (
Bam
HI,
Bcl
I,
Bgl
I,
Bgl
II,
Bst
EII,
Eco
RI,
Hin
dIII,
Hpa
I,
Sal
I,
Sma
I,
Xba
I, and
Xho
I). The virus strains were isolated during outbreaks of lower respiratory tract infections in children during an 11-year period from 1990 to 2000 in Seoul, Korea. Among the Ad3 strains, seven genome types were identified; Ad3a and six novel types (Ad3a13, Ad3a14, Ad3a15, Ad3a16, Ad3a17, and Ad3a18). Multiple genome types cocirculated during outbreaks, and some of these were isolated during the 11-year observation period, while others were restricted to particular outbreaks. For Ad7, two genome types, Ad7d and Ad7l, the latter of which is a novel genome type, were identified. A shift in genome types occurred from Ad7d to Ad7l during successive outbreaks. Mortality was 3.6% among children with Ad3 infections and 18% among children infected with either of the Ad7 genome types. In conclusion, the data confirm that Ad3 genome types are more diverse than those of Ad7 and suggest that shifts of genome types may occur during successive outbreaks of Ad3 and Ad7.
Segregation of Human Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia
Authors: Herring Belinda L. , Ge Ying C. , Wang Bin , Ratnamohan Mala , Zheng Frank , Cunningham Anthony L. , Saksena Nitin K. , Dwyer Dominic E.
Published: October 2003

The aim of this study was to determine which human immunodeficiency virus type 1 (HIV-1) subtypes were circulating in Australia and to correlate the subtypes with risk factors associated with the acquisition of HIV-1 infection. DNA was extracted from peripheral blood mononuclear cells, and HIV-1
env
genes were amplified and subtyped using heteroduplex mobility analysis, with selected samples sequenced and phylogenetic analysis performed. The HIV-1
env
subtypes were determined for 141 samples, of which 40 were from female patients and 101 were from male patients; 13 samples were from children. Forty-seven patients were infected by homosexual or bisexual contact, 46 were infected through heterosexual contact, 21 were infected from injecting drug use (IDU), 13 were infected by vertical transmission, 8 were infected from nosocomial exposure, and 6 were infected by other modes of transmission, including exposure to blood products, ritualistic practices, and two cases of intrafamilial transmission. Five subtypes were detected; B (
n
= 104), A (
n
= 5), C (
n
= 17), E (CRF01_AE;
n
= 13), and G (
n
= 2). Subtype B predominated in HIV-1 acquired homosexually (94% of cases) and by IDU (100%), whereas non-subtype B infections were mostly seen in heterosexually (57%) or vertically (22%) acquired HIV-1 infections and were usually imported from Africa and Asia. Subtype B strains of group M viruses predominate in Australia in HIV-1 transmitted by homosexual or bisexual contact and IDU. However, non-B subtypes have been introduced, mostly acquired via heterosexual contact.
Molecular Evidence of Persistent Echovirus 13 Meningoencephalitis in a Patient with Relapsed Lymphoma after an Outbreak of Meningitis in 2000
Authors: Archimbaud Christine , Bailly Jean-Luc , Chambon Martine , Tournilhac Olivier , Travade Philippe , Peigue-Lafeuille Hélène
Published: October 2003

Enteroviral meningoencephalitis was diagnosed in a patient with an immunodeficiency syndrome acquired after treatment with rituximab for a relapsed primary B-cell lymphoma. A second meningoencephalitic episode was diagnosed 6 months later and was successfully treated with a combination of immunoglobulins and pleconaril. The infection was persistent since the enterovirus genome was detected in five sequential specimens of cerebrospinal fluid collected over 9 months. An echovirus 13 isolate was isolated in the first three samples. The viral sequence encoding the VP1 capsid protein of the three isolates was determined and was compared with that of four control viruses. The virus isolates recovered from the patient shared >99% nucleotide sequence similarity with one another. In a phylogenetic tree, they were directly related to a control virus obtained from a patient hospitalized in 2000 during an outbreak of enterovirus meningitis. The epidemiological origin of a chronic echovirus infection in a patient with immune deficiency suggests that the echovirus had been continuously circulating in the general population after the outbreak that had revealed its emergence.
Predominance ofEhrlichia ewingiiin Missouri Dogs
Authors: Liddell Allison M. , Stockham Steven L. , Scott Michael A. , Sumner John W. , Paddock Christopher D. , Gaudreault-Keener Monique , Arens Max Q. , Storch Gregory A.
Published: October 2003

To investigate the species distribution ofEhrlichiapresent in Missouri dogs, we tested 78 dogs suspected of having acute ehrlichiosis and 10 healthy dogs. Blood from each dog was screened with a broad-range 16S rRNA gene PCR assay that detects known pathogenic species ofEhrlichiaandAnaplasma. The species was determined by using species-specific PCR assays and nucleotide sequencing.Ehrlichiaantibody testing was performed by using an indirect immunofluorescence assay withEhrlichia chaffeensisas the antigenic substrate. The broad-range assay detectedEhrlichiaorAnaplasmaDNA in 20 (26%) of the symptomatic dogs and 2 (20%) of the asymptomatic dogs.E. ewingiiaccounted for 20 (91%), andE. chaffeensisaccounted for 1 (5%) of the positives.Anaplasma phagocytophilumDNA was detected in one dog, and the sequences of regions of the 16S rRNA gene and thegroESLoperon amplified from the blood of this dog matched the published sequences of this organism. Antibodies reactive withE. chaffeensiswere detected in 14 (67%) of the 21 PCR-positive dogs and in 12 (19%) of the 64 PCR-negative dogs. Combining the results of PCR and serology indicated that 33 (39%) of 85 evaluable dogs had evidence of past or currentEhrlichiainfection. We conclude thatE. ewingiiis the predominant etiologic agent of canine ehrlichiosis in the areas of Missouri included in this survey.E. canis, a widely recognized agent of canine ehrlichiosis, was not detected in any animal. The finding ofE. ewingiiin asymptomatic dogs suggests that dogs could be a reservoir for thisEhrlichiaspecies.
Evaluation of the Hodge Test and the Imipenem-EDTA Double-Disk Synergy Test for Differentiating Metallo-β-Lactamase-Producing Isolates of
Pseudomonas
spp. and
Acinetobacter
spp
Authors: Lee K. , Lim Y. S. , Yong D. , Yum J. H. , Chong Y.
Published: October 2003

Gram-negative bacilli with acquired metallo-β-lactamase (MBL) production have been increasingly reported in some countries, necessitating their detection. The aim of this study was to evaluate the performance of the Hodge test and those of the imipenem (IPM)-EDTA, ceftazidime (CAZ)-mercaptopropionic acid (MPA), and CAZ-sodium mercaptoacetic acid (SMA) double-disk synergy tests (DDSTs). The efficiencies of testing CAZ-resistant and IPM-nonsusceptible isolates were also compared. Strains used for the evaluation were known IMP-1 and VIM-2 MBL-producing isolates and consecutive and CAZ-nonsusceptible isolates of pseudomonads and acinetobacters. The performance of the Hodge test was improved by addition of zinc sulfate (140 μg/disk) to an IPM disk. In DDSTs, EDTA (ca. 1,900 μg) disks were better at detecting MBL-producing strains among pseudomonads, while MPA (3 μl) and SMA (3 mg) disks performed better for acinetobacters. EDTA (ca. 750 μg)-plus-SMA (ca. 2 mg) disks performed better than EDTA, MPA, or SMA disks with both organisms. CAZ-SMA DDSTs failed to detect 22 of 80 (28%) MBL-producing acinetobacters. In conclusion, use of an IPM disk and an EDTA (750 μg)-plus-SMA (2 mg) disk improves performance, and testing IPM-nonsusceptible isolates rather than CAZ-resistant isolates could reduce screening work. Further evaluation of the test is required for the detection of other types of MBL-producing gram-negative bacilli.
Detection of a Point Mutation Associated with High-Level Isoniazid Resistance in
Mycobacterium tuberculosis
by Using Real-Time PCR Technology with 3′-Minor Groove Binder-DNA Probes
Authors: van Doorn H. Rogier , Claas Eric C. J. , Templeton Kate E. , van der Zanden Adri G. M. , te Koppele Vije Arianne , de Jong Menno D. , Dankert Jacob , Kuijper Ed J.
Published: October 2003

Tuberculosis remains one of the leading infectious causes of death worldwide. The emergence of drug-resistant strains of
Mycobacterium tuberculosis
is a serious public health threat. Resistance to isoniazid (INH) is the most prevalent form of resistance in
M. tuberculosis
and is mainly caused by mutations in the catalase peroxidase gene (
katG
). Among high-level INH-resistant isolates (MIC ≥ 2), 89% are associated with a mutation at codon 315 of
katG
. There is a need to develop rapid diagnostic tests to permit appropriate antibiotic treatment and to improve clinical management. Therefore, a single-tube real-time PCR, using a novel kind of probe (3′-minor groove binder-DNA probe), was developed to detect either the wild-type or the mutant codon directly in Ziehl-Neelsen-positive sputum samples. The detection limit of the assay for purified DNA was 5 fg per well (one mycobacterial genome), and with spiked sputum samples, it was 20 copies per well, corresponding to 10
3
mycobacteria per ml of sputum. Sputum samples from 20 patients living in Kazakhstan or Moldova and infected with monodrug- or multidrug-resistant
M. tuberculosis
and 20 sputum samples from patients infected with INH-susceptible
M. tuberculosis
were tested. The sensitivities and specificities of the probes were 70 and 94% for the wild-type probe and 82 and 100% for the mutant probe. Binding to either probe was nonambiguous. This real-time PCR allows the rapid identification of a mutant
katG
allele and can easily be implemented in a clinical microbiology laboratory.
Multiplexed, Real-Time PCR for Quantitative Detection of Human Adenovirus
Authors: Gu Z. , Belzer S. W. , Gibson C. S. , Bankowski M. J. , Hayden R. T.
Published: October 2003

Adenovirus infection is becoming increasingly recognized as a cause of morbidity and mortality in the immunosuppressed patient population. While early detection and quantitation of adenovirus in peripheral blood has been suggested as a means of directing and monitoring antiviral therapy in these patients, few methods have been published, particularly with respect to viral quantitation. A multiplexed real-time PCR assay was developed that can quantitatively detect a wide range of known serotypes of human adenovirus, including all of subgroups A to C. This assay was compared to a qualitative, Southern blot-based PCR assay by using 45 peripheral blood specimens from 16 patients. There was 100% concordance between the two tests in terms of qualitative results. The real-time assay detected adenovirus in patient samples at levels from <200 to 266,681 copies/ml of blood. By using control viral samples, sensitivity was demonstrated to less than 10 copies of viral genome per reaction and quantitative linearity was demonstrated from 10 to 10
6
copies of input viral DNA. Equivalent sensitivity and linearity were demonstrated for 15 different reference serotypes of adenovirus. Eleven other viral serotypes have complete target region sequence homology to one or more of the strains tested. No cross-reactivity was noted with other commonly isolated viral species. Sequence analysis showed no significant homology with any other human pathogens (bacterial or viral). This assay allows rapid, sensitive, and specific quantitation of adenovirus and may have a significant impact on the care of immunocompromised patients at risk for disseminated viral infection.
Human Metapneumovirus Infection in the Canadian Population
Authors: Bastien Nathalie , Ward Diane , Van Caeseele Paul , Brandt Ken , Lee Spencer H. S. , McNabb Gail , Klisko Brian , Chan Edward , Li Yan
Published: October 2003

Human metapneumovirus (hMPV), a newly discovered paramyxovirus, has been associated with acute respiratory tract infections (ARIs) ranging from upper ARIs to severe bronchiolitis and pneumonia. Important questions remain on the contribution of hMPV to ARIs and its impact on public health. During the 2001-2002 season, we conducted a collaborative study with four provincial public health laboratories to study the prevalence of this new virus in the Canadian population. A total of 445 specimens were collected from patients of all age groups with ARIs and were tested for the presence of hMPV by reverse transcription-PCR. Of these, 66 (14.8%) tested positive for hMPV. Positive specimens were found in all age groups and in all four provinces studied. Virus activity peaked in February and March. The age range of the patients with hMPV infection was 2 months to 93 years (median age, 25 years), with similar numbers of females (35%) and males (41%). Thirty-three percent (
n
= 22) of hMPV-infected patients were hospitalized; of these, 27% (
n
= 6) had rhinitis and pneumonia, 23% (
n
= 5) had bronchiolitis, and 9% (
n
= 2) had bronchitis. The hospitalization rates were significantly higher among patients <5 years of age (
P
= 0.0005) and those >50 years of age (
P
= 0.0044) than among those 6 to 50 years of age. Phylogenetic analysis of the F gene showed that two hMPV genetic clusters were cocirculating in the 2001-2002 season, and comparison with earlier studies suggests a temporal evolutionary pattern of hMPV isolates. These results provide further evidence of the importance of hMPV in ARIs, particularly in young children and elderly individuals.
Use of 16S rRNA Gene Sequencing for Rapid Identification and Differentiation ofBurkholderia pseudomalleiandB. mallei
Authors: Gee Jay E. , Sacchi Claudio T. , Glass Mindy B. , De Barun K. , Weyant Robbin S. , Levett Paul N. , Whitney Anne M. , Hoffmaster Alex R. , Popovic Tanja
Published: October 2003

Burkholderia pseudomalleiandB. mallei, the causative agents of melioidosis and glanders, respectively, are designated category B biothreat agents. Current methods for identifying these organisms rely on their phenotypic characteristics and an extensive set of biochemical reactions. We evaluated the use of 16S rRNA gene sequencing to rapidly identify these two species and differentiate them from each other as well as from closely related species and genera such asPandoraeaspp.,Ralstoniaspp.,Burkholderia gladioli,Burkholderia cepacia,Burkholderia thailandensis, andPseudomonas aeruginosa. We sequenced the 1.5-kb 16S rRNA gene of 56B. pseudomalleiand 23B. malleiisolates selected to represent a wide range of temporal, geographic, and origin diversity. Among all 79 isolates, a total of 11 16S types were found based on eight positions of difference. Nine 16S types were identified inB. pseudomalleiisolates based on six positions of difference, with differences ranging from 0.5 to 1.5 bp. Twenty-two of 23B. malleiisolates showed 16S rRNA gene sequence identity and were designated 16S type 10, whereas the remaining isolate was designated type 11. This report provides a basis for rapidly identifying and differentiatingB. pseudomalleiandB. malleiby molecular methods.
Detection of
Staphylococcus aureus
Enterotoxins A to D by Real-Time Fluorescence PCR Assay
Authors: Klotz M. , Opper S. , Heeg K. , Zimmermann S.
Published: October 2003

Staphylococcus aureus
is one of the most significant pathogens causing nosocomial and community-acquired infections. Among the secreted staphylococcal virulence factors, there is a growing list of enterotoxins which can induce gastroenteric syndrome and toxic shock syndrome. Here, we developed a real-time fluorescence PCR assay (TaqMan PCR) for the detection of genes encoding staphylococcal enterotoxins A, B, C1, and D (SEA, SEB, SEC1, and SED) of
S
.
aureus
as well as the
mecA
gene encoding methicillin resistance and the
femB
gene as a specific genomic marker for
S
.
aureus
. SEA to SED were selected because they are the four classically described enterotoxins of
S
.
aureus
and because they were detected by latex agglutination. In order to evaluate the reliability of TaqMan PCR, we investigated 93 isolates of
S
.
aureus
derived from patients at our hospital over 5 months and compared the results with data obtained by a commerciall available reversed passive latex agglutination assay (SET-RPLA) for these isolates. Thirteen enterotoxin genes were detected by TaqMan PCR; however, no proteins expressed by these genes were detected by SET-RPLA. As a result, more isolates of
S
.
aureus
(
n
= 44) were found positive by TaqMan PCR for one or more enterotoxin genes than by SET-RPLA for the respective proteins expressed by these genes (
n
= 40). We conclude that TaqMan PCR is more sensitive because it offers the possibility for determining enterotoxins on a genotypic basis. Additionally, the assay allows the parallel detection of genes for SEA to SED and methicillin resistance in
S
.
aureus
. Furthermore, real-time PCR is well suited for screening large numbers of samples at the same time, allowing rapid, reliable, efficient, and cost-saving routine laboratory diagnosis.
Six-Month Multicenter Study on Invasive Infections Due to Group B Streptococci in Argentina
Authors: Lopardo Horacio A. , Vidal Patricia , Jeric Paola , Centron Daniela , Paganini Hugo , Facklam Richard R. , Elliott John
Published: October 2003

There is little information about invasive infections by group B streptococci (GBS) and their antimicrobial susceptibilities in Latin America. We performed a prospective multicenter study to determine the serotype distribution and the antimicrobial susceptibility of GBS in Argentina. We identified 58 cases, but only 44 had sufficient data to be evaluated. Eight early-, four late-, and one fatal late, late-onset neonatal infections due to GBS were found. A total of 31 patients were adults with bacteremia, skin and soft tissue infections, osteomyelitis, arthritis, meningitis, abdominal infections, and renal abscess. Serotype III was prevalent in late-onset neonatal disease, and several serotypes (Ia/c, III, Ia, and II) were involved in early-onset neonatal infections. Serotypes II, Ia/c, III, and IV were commonly found in adults, with serotype II prevalent in younger adults (18 to 69 years old) and serotype Ia/c prevalent in elderly adults (>70 years old). The mortality rate attributable to GBS infections was 10.8%. All GBS were susceptible to penicillin and ceftriaxone. Resistance to clindamycin (1.7%), erythromycin (5.2%), azithromycin (5.2%), minocycline (69%), and tetracycline (72.4%), to high levels of kanamycin and amikacin (1.7%), and to intermediately high levels of gentamicin (1.7%) was observed. The bifunctional enzyme AAC6′-APH2" was detected in the isolate resistant to aminoglycosides, and other genetic determinants were identified in other resistant isolates:
tetM
and
tetO
in tetracycline-resistant streptococci and
mefA
and
ermTR
for efflux-mediated and inducible macrolide-lincosamide-streptogramin B-resistant streptococci, respectively. For clinical purposes and rapid and easy detection of high-level aminoglycoside-resistant GBS, a screening method that used 1,000-μg kanamycin disks is proposed.
Use of Turbidimetric Growth Curves for Early Determination of Antifungal Drug Resistance of Filamentous Fungi
Authors: Meletiadis Joseph , te Dorsthorst Debbie T. A. , Verweij Paul E.
Published: October 2003

A previously described microbroth kinetic system (J. Meletiadis, J. F. Meis, J. W. Mouton, and P. E. Verweij, J. Clin. Microbiol.
39:
478-484, 2001) based on continuous monitoring of changes in the optical density of fungal growth was used to describe turbidimetric growth curves of different filamentous fungi in the presence of increasing concentrations of antifungal drugs. Therefore, 24 clinical mold isolates, including
Rhizopus oryzae
,
Aspergillus fumigatus
,
Aspergillus flavus
, and
Scedosporium prolificans
, were tested against itraconazole, terbinafine, and amphotericin B according to NCCLS guidelines. Among various parameters of the growth curves, the duration of the lag phase was strongly affected by the presence of antifungal drugs. Exposure to increasing drug concentrations resulted in prolonged lag phases of the turbidimetric growth curves. The lag phases of the growth curves at drug concentrations which resulted in more than 50% growth (for itraconazole and terbinafine) and more than 75% growth (for amphotericin B) after 24 h of incubation for
R. oryzae
, 48 h for
Aspergillus
spp., and 72 h for
S. prolificans
were 4 h longer than the lag phases of the growth curves at the corresponding drug-free growth controls which varied from 4.4 h for
R. oryzae
, 6.5 h for
A. flavus
, 7.9 h for
A. fumigatus
, and 11.6 h for
S. prolificans
. The duration of the lag phases showed small experimental and interstrain variability, with differences of less than 2 h in most of the cases. Using this system, itraconazole and terbinafine resistance (presence of >50% growth) as well as amphotericin B resistance (presence of >75% growth) was determined within incubation periods of 5.0 to 7.7 h for
R. oryzae
(for amphotericin B resistance incubation for up to 12 h was required), 8.8 to 11.4 h for
A. fumigatus
, 6.7 to 8.5 h for
A. flavus
, and 13 to 15.6 h for
S. prolificans
while awaiting formal MIC determination by the NCCLS reference method.
Longitudinal Study of Intestinal
Entamoeba histolytica
Infections in Asymptomatic Adult Carriers
Authors: Blessmann Joerg , Ali Ibne Karim M. , Ton Nu Phuong A. , Dinh Binh T. , Ngo Viet Tram Q. , Le Van An , Clark C. Graham , Tannich Egbert
Published: October 2003

To gain insight into the dynamics of intestinal
Entamoeba histolytica
infection, a longitudinal study was performed over an observation period of 15 months with a group of 383 randomly selected adult individuals (mean age, 38.5 years) living in an area of amebiasis endemicity in central Vietnam. Ameba infection was diagnosed by using species-specific PCR and DNA extracted directly from fecal samples. The results indicated an
E. histolytica
prevalence of 11.2% and an annual new infection rate of 4.1% in the study population. Follow-up of the 43 individuals who were
E. histolytica
positive at enrollment suggested a regular exponential decline in infection of about 3% per month and a mean half-life of infection of more than 15 months. However, the reinfection rate for this group of participants was 2.7 times higher than that predicted for the study population as a whole. Both the reappearance of the parasite after successful treatment of
E. histolytica
infection and changes in “genetic fingerprints” of parasites during the course of infection revealed an annual new infection rate of about 11.5%. Thus, the mean half-life of
E. histolytica
infection was calculated to be 12.9 months (95% confidence interval, 10.2 to 15.6 months). Notably, none of the participants developed symptoms compatible with invasive intestinal amebiasis, and only one of the subjects developed an amebic liver abscess during the observation period.
Species Diversity and Polymorphism in theExophiala spiniferaClade Containing Opportunistic Black Yeast-Like Fungi
Authors: de Hoog G. S. , Vicente V. , Caligiorne R. B. , Kantarcioglu S. , Tintelnot K. , Gerrits van den Ende A. H. G. , Haase G.
Published: October 2003

A monophyletic group of black yeast-like fungi containing opportunistic pathogens aroundExophiala spiniferais analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genusExophiala) in addition to sympodial taxa (anamorph generaRamichloridiumandRhinocladiella). The new speciesExophiala oligosperma,Ramichloridium basitonum, andRhinocladiella similisare introduced and compared with their morphologically similar counterparts at larger phylogenetic distances outside theE. spiniferaclade.Exophiala jeanselmeiis redefined. New combinations are proposed inExophiala:Exophiala exophialaeforPhaeococcomyces exophialaeandExophiala heteromorphaforE. jeanselmeivar.heteromorpha.
Optimization of Real-Time PCR Assay for Rapid and Sensitive Detection of Eubacterial 16S Ribosomal DNA in Platelet Concentrates
Authors: Mohammadi Tamimount , Reesink Henk W. , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M.
Published: October 2003

A real-time PCR assay was developed for rapid detection of eubacterial 16S ribosomal DNA in platelet concentrates. The sensitivity of this assay can be hampered by contaminating DNA in the PCR reagents. Digestion of the PCR reagents with
Sau
3AI prior to PCR amplification was effective in eliminating this contaminating DNA without affecting the sensitivity of the assay.
National Department of Defense Surveillance Data for Antibiotic Resistance and
emm
Gene Types of Clinical Group A Streptococcal Isolates from Eight Basic Training Military Sites
Authors: Barrozo Christopher P. , Russell Kevin L. , Smith Tyler C. , Hawksworth Anthony W. , Ryan Margaret A. K. , Gray Gregory C.
Published: October 2003

Antibiotic resistance and
emm
gene types were examined from 692 Group A streptococci isolates from eight United States military basic training sites between 1998 and 2001. Macrolide resistance was associated with geographic sites and
emm
type. These data are useful for vaccine development initiatives and antimicrobial treatment considerations.
Real-Time PCR Assay Targets the 23S-5S Spacer for Direct Detection and Differentiation of
Legionella
spp. and
Legionella pneumophila
Authors: Herpers Bjorn L. , de Jongh Bartelt M. , van der Zwaluw Kim , van Hannen Erik J.
Published: October 2003

A real-time PCR for the ABI Prism 7000 system targeting the 23S-5S spacer of
Legionella
spp. was developed. Simultaneous detection and differentiation of
Legionella
spp. and
Legionella pneumophila
within 90 min and without post-PCR melting-curve analysis was achieved using two TaqMan probes. In sputum samples from 23 controls and 17 patients with legionellosis, defined by positive culture, urinary antigen testing, or seroconversion, 94% sensitivity and 100% specificity were observed.
Investigation of
Staphylococcus aureus
Isolates Identified as Erythromycin Intermediate by the Vitek-1 System: Comparison with Results Obtained with the Vitek-2 and Phoenix Systems
Authors: Tang Patrick , Low Donald E. , Atkinson Sandra , Pike Karen , Ashi-Sulaiman Aisha , Simor Andrew , Richardson Susan , Willey Barbara M.
Published: October 2003

We identified 69
Staphylococcus aureus
isolates that were erythromycin intermediate as reported by the Vitek-1 system using the GPS-105 card. Of the 57 strains that were available for further testing, all were erythromycin resistant by broth microdilution and the Phoenix system, while the Vitek-2 system identified 55 of 57 strains (96%) as erythromycin resistant. The majority of isolates (54 of 57 [95%]) exhibited the inducible MLS (macrolide-lincosamide-streptogramin family) phenotype, as shown by the double-disk test. We recommend that all
S. aureus
strains determined as erythromycin intermediate by the Vitek-1 system be interpreted as resistant to erythromycin.
Improved PCR for Detection of the Highly Leukotoxic JP2 Clone of
Actinobacillus actinomycetemcomitans
in Subgingival Plaque Samples
Authors: Poulsen Knud , Ennibi Oum-Keltoum , Haubek Dorte
Published: October 2003

The JP2 clone of
Actinobacillus actinomycetemcomitans
is associated with early-onset periodontitis in certain ethnic populations of African origin. Here, we describe and evaluate a set of primers for PCR to assay for the presence of
A. actinomycetemcomitans
and to discriminate between JP2-like strains and other genotypes in subgingival plaque samples.
Subtyping of
Salmonella enterica
Serovar Typhimurium Outbreak Strains Isolated from Humans and Animals in Iceland
Authors: Gudmundsdottir Sigrun , Hardardottir Hjordis , Gunnarsson Eggert
Published: October 2003

A total of 75
Salmonella enterica
serovar Typhimurium strains of various (mainly human and animal) origins were typed by pulsed-field gel electrophoresis (PFGE) and phage typing. These strains were collected during an outbreak in Iceland in 1999 and 2000. The typing revealed that 84% of the strains belonged to the same PFGE and phage type (PT), namely, PFGE type 1Aa and PT 1.
Dissemination of Extended-Spectrum β-Lactamase-Producing
Enterobacteriaceae
in Pediatric Intensive Care Units
Authors: Wu Tsu-Lan , Chia Ju-Hsin , Su Lin-Hui , Kuo An-Jing , Chu Chishih , Chiu Cheng-Hsun
Published: October 2003

To study the growing trend of extended-spectrum β-lactamase (ESBL)-producing
Enterobacteriaceae
in pediatric intensive care units (PICUs), 88 nonrepetitive ESBL-producing isolates were prospectively collected and analyzed by molecular methods during a 16-month period. The emergence and dissemination of ESBL-producing
Enterobacteriaceae
in PICUs are the consequence of the clonal dissemination of a few epidemic strains along with the horizontal transmission of resistance gene-carrying plasmids among bacterial organisms.
Detection of Differences in the Nucleotide and Amino Acid Sequences of Diphtheria Toxin fromCorynebacterium diphtheriaeandCorynebacterium ulceransCausing Extrapharyngeal Infections
Authors: Sing Andreas , Hogardt Michael , Bierschenk Suse , Heesemann Jürgen
Published: October 2003

WhileCorynebacterium ulceranscan mimic classical diphtheria, extrapharyngeal infections are extremely rare. Sequencing of the diphtheria toxin (DT)-encodingtoxgene of twoC. ulceransisolates from extrapharyngeal infections revealed differences fromC. diphtheriaeDT sequences, mainly in the translocation and receptor-binding domains.C. ulceranssupernatants were much less potent than supernatant fromC. diphtheriae. AC. ulceransDT-specific PCR is described below.
Evaluation of the TRUGENE
HCV 5
′
NC
Genotyping Kit with the New GeneLibrarian Module 3.1.2 for Genotyping of Hepatitis C Virus from Clinical Specimens
Authors: Germer Jeffrey J. , Majewski David W. , Rosser Michael , Thompson Amber , Mitchell P. Shawn , Smith Thomas F. , Elagin Slava , Yao Joseph D.C.
Published: October 2003

The TRUGENE
HCV 5′NC
genotyping kit (GeneLibrarian modules 3.1.1 and 3.1.2) and VERSANT HCV genotyping assay were compared by using 96 hepatitis C virus (HCV) RNA-positive patient specimens, including HCV genotypes 1, 2, 3, 4, 5, 6, and 10. The TRUGENE
HCV 5
′
NC
genotyping kit (GeneLibrarian module 3.1.2) yielded the most accurate genotyping results.
Molecular Analysis of Group A Streptococcal Isolates Associated with Scarlet Fever in Southern Taiwan between 1993 and 2002
Authors: Yan Jing-Jou , Liu Ching-Chuan , Ko Wen-Chien , Hsu Shui-Yuan , Wu Hsiu-Mei , Lin Yee-Shin , Lin Ming T. , Chuang Woei-Jer , Wu Jiunn-Jong
Published: October 2003

Collected between 1993 and 2002 at a Taiwanese university hospital, 77 group A streptococcus isolates associated with scarlet fever were grouped byemmtyping and pulsed-field gel electrophoresis. The predominance of anemm1clone before 1996 and the presence of genetically diverseemm1andemm4strains thereafter were found.
Detection of
Yersinia pestis
in Sputum by Real-Time PCR
Authors: Loïez Caroline , Herwegh Stéphanie , Wallet Frédéric , Armand Sylvie , Guinet Françoise , Courcol René J.
Published: October 2003

A 5′ nuclease PCR assay for detection of the
Yersinia pestis
plasminogen activator (
pla
) gene in human respiratory specimens with simulated
Y. pestis
infection was developed. An internal positive control was added to the reaction mixture in order to detect the presence of PCR inhibitors that are often found in biological samples. The assay was 100% specific for
Y. pestis
. In the absence of inhibitors, a sensitivity of 10
2
CFU/ml of respiratory fluid was obtained. When inhibitors were present, detection of
Y. pestis
DNA required a longer sample treatment time and an initial concentration of bacteria of at least 10
4
CFU/ml. The test's total turnaround time was less than 5 h. The assay described here is well suited to the rapid diagnosis of pneumonic plague, the form of plague most likely to result from a bioterrorist attack.
Surveillance for Respiratory Syncytial Virus in Infants Hospitalized for Acute Lower Respiratory Infection in Chile (1989 to 2000)
Authors: Avendaño Luis F. , Palomino María Angélica , Larrañaga Carmen
Published: October 2003

Hospitalized infants (4,618) were studied for lower respiratory infections from 1989 through 2000 by routine immunofluorescence assay and viral isolation. The hospitalization rate for respiratory syncytial virus (RSV) averaged 2% per year. The fatality rate was 0.1%. Monthly RSV detection varied from 14 to 88%, and epidemics lasted 3.5 to 6 months. From 1994 high-early versus low-late epidemic patterns alternately were observed, the first influenced by a group B strain.
Bipolaris spiciferaCauses Fungus Balls of the Sinuses and Triggers Polypoid Chronic Rhinosinusitis in an Immunocompetent Patient
Authors: Buzina Walter , Braun Hannes , Schimpl Kerstin , Stammberger Heinz
Published: October 2003

We report the rare case of a 19-year-old immunocompetent male suffering both from fungus balls of the sinuses and from chronic rhinosinusitis with massive polyposis. Endoscopic sinus surgery revealed grayish brown necrotic masses embedded in viscous eosinophilic mucus. Inoculated onto petri dishes, these masses as well as the mucus grew a dark pigmented fungus, which was identified asBipolaris spicifera.
Persistent Multiple Pulmonary Nodules in a Nonimmunocompromised Woman after Varicella-Related Myelitis Treated with Acyclovir
Authors: Schvoerer Evelyne , Frechin Valéry , Warter André , Gasser Bernard , Jouin Hervé , Gut Jean-Pierre , Stoll-Keller Françoise
Published: October 2003

Persistent multiple pulmonary nodules were observed on the chest X ray of a nonimmunocompromised woman 6 months after she was treated with acyclovir for a varicella-related myelitis without respiratory symptoms. Early antiviral therapy given for varicella infections might decrease the intensity of clinical symptoms without actually preventing the occurrence of varicella-zoster virus-related lesions such as the persistent pulmonary nodules reported here.
Generalized Deterministic Traffic Rules
Authors: Fuks Henryk , Boccara Nino
Published: October 2003

We study a family of deterministic models for highway traffic flow which generalize cellular automaton rule 184. This family is parameterized by the speed limit m and another parameter k that represents a "degree of aggressiveness" in driving, strictly related to the distance between two consecutive cars. We compare two driving strategies with identical maximum throughput: "conservative" driving with high speed limit and "aggressive" driving with low speed limit. Those two strategies are evaluated in terms of accident probability. We also discuss fundamental diagrams of generalized traffic rules and examine limitations of maximum achievable throughput. Possible modifications of the model are considered.
Exploiting Problem Structure as a Search Heuristic
Authors: Hogg Tad
Published: October 2003

Recent empirical and theoretical studies have shown that simple parameters characterizing constraint satisfaction problems predict whether they have a solution and the cost to solve them, on average. This paper examines the effectiveness of using these predictions as a heuristic for solving the graph coloring problem. Specifically, by adding some global information on the consequences of various choices, the use of these parameters can reduce the search required to find a solution. Current limitations of this approach, due to the high variance associated with the predictions, are also presented. More generally, observations of universal behaviors analogous to physical phase transitions can be applied to improve search methods.
Damage Propagation in a Diluted Asymmetric Neural Network
Authors: da Silva Crisógono R. , da Silva Ladário , Tamarit Francisco A.
Published: October 2003

We study numerically the nature of the retrieval attractors in an asymmetrically diluted Hopfield neural network through the damage propagation technique. We consider the damage evolution of two replicas, initially very close to each other and having both finite projection with one memorized pattern. By analyzing the asymptotic behavior of the damage, we characterize the dynamical nature of the retrieval attractors. We found, in the recognition phase, a dynamical phase transition separating chaotic and fixed point retrieval trajectories. We also present a conjugate field h associated with the damage, which destroys the dynamical transition and whose corresponding susceptibility presents a sharp peak at the critical parameter.
Cluster Counting: The Hoshen–Kopelman Algorithm Versus Spanning Tree Approaches
Authors: Babalievski F.
Published: October 2003

Two basic approaches to the cluster counting task in the percolation and related models are discussed. The Hoshen–Kopelman multiple labeling technique for cluster statistics is redescribed. Modifications for random and aperiodic lattices are sketched as well as some parallelized versions of the algorithm are mentioned. The graph-theoretical basis for the spanning tree approaches is given by describing the breadth first search and depth first search procedures. Examples are given for extracting the elastic and geometric "backbone" of a percolation cluster. An implementation of the "pebble game" algorithm using a depth first search method is also described.
Transformation of Diamond (sp3) to Graphite (sp2) Bonds by Ion-Impact
Authors: Saada David , Adler Joan , Kalish R.
Published: October 2003

The formation of point defects in diamond induced by an energetic displacement of a carbon atom out of its lattice site and the relaxation of the thereby disrupted crystal are studied by molecular dynamics simulations with the Tersoff potential. The displacement energy for Frenkel pair creation is calculated to be 52 eV, in agreement with experiments. It is found that the <100> split interstitial, with a bonding configuration which resembles graphite, is the most stable defect, and the disrupted region around it is rich in sp2-like (graphitic) bonds. This region extends several nanometers and is likely to be the elementary electrically conductive cell experimentally found in radiation-damaged diamond.
A New Approach to Image Reconstruction in Positron Emission Tomography Using Artificial Neural Networks
Authors: Bevilacqua A. , Bollini D. , Campanini R. , Lanconelli N. , Galli M.
Published: October 2003

This study investigates the possibility of using an Artificial Neural Network (ANN) for reconstructing Positron Emission Tomography (PET) images. The network is trained with simulated data which include physical effects such as attenuation and scattering. Once the training ends, the weights of the network are held constant. The network is able to reconstruct every type of source distribution contained inside the area mapped during the learning. The reconstruction of a simulated brain phantom in a noiseless case shows an improvement if compared with Filtered Back-Projection reconstruction (FBP). In noisy cases there is still an improvement, even if we do not compensate for noise fluctuations. These results show that it is possible to reconstruct PET images using ANNs. Initially we used a Dec Alpha; then, due to the high data parallelism of this reconstruction problem, we ported the learning on a Quadrics (SIMD) machine, suited for the realization of a small medical dedicated system. These results encourage us to continue in further studies that will make possible reconstruction of images of bigger dimension than those used in the present work (32 × 32 pixels).
Large Scale Simulations of Elastic Light Scattering by a Fast Discrete Dipole Approximation
Authors: Hoekstra A. G. , Grimminck M. D. , Sloot P. M. A.
Published: October 2003

Simulation of Elastic Light Scattering from arbitrary shaped particles in the resonance region (i.e., with a dimension of several wavelengths of the incident light) is a long standing challenge. By employing the combination of a simulation kernel with low computational complexity, implemented on powerful High Performance Computing systems, we are now able to push the limits of simulation of scattering of visible light towards particles with dimensions up to 10 micrometers. This allows for the first time the simulation of realistic and highly relevant light scattering experiments, such as scattering from human red — or white blood cells, or scattering from large soot — or dust particles. We use the Discrete Dipole Approximation to simulate the light scattering process. In this paper we report on a parallel Fast Discrete Dipole Approximation, and we will show the performance of the resulting code, running under PVM on a 32-node Parsytec CC. Furthermore, as an example we present results of a simulation of scattering from human white blood cells. In a first approximation the Lymphocyte is modeled as a sphere with a spherical inclusion. We investigate the influence of the position of the inner sphere, modeling the nucleus of a Lymphocyte, on the light scattering signals.
Algebraic Programming in the Hamiltonian Treatment of the Einstein–Maxwell Equations
Authors: Vulcanov Dumitru N.
Published: October 2003

We present new procedures in REDUCE language using the EXCALC package (adapted for IBM-PC machines) for algebraic programming in the hamiltonian formulation of Einstein–Maxwell equations. The dynamic and the constraint equations containing specific terms of the interaction of gravity with source-free electromagnetic field are translated into computer procedures. The results obtained by processing some examples of space-time models are presented.
Relaxation Criteria for Iterated Traffic Simulations
Authors: Kelly Terence , Nagel Kai
Published: October 2003

Iterative transportation microsimulations adjust traveler route plans by iterating between a microsimulation and a route planner. At each iteration, the route planner adjusts individuals' route choices based on the preceding microsimulations. Empirically, this process yields good results, but it is usually unclear when to stop the iterative process when modeling real-world traffic. This paper investigates several criteria to judge relaxation of the iterative process, emphasizing criteria related to traveler decision-making.
Microcanonical Optimization Applied to the Traveling Salesman Problem
Authors: Linhares Alexandre , Torreão José R. A.
Published: October 2003

Optimization strategies based on simulated annealing and its variants have been extensively applied to the traveling salesman problem (TSP). Recently, there has appeared a new physics-based metaheuristic, called the microcanonical optimization algorithm (μO), which does not resort to annealing, and which has proven a superior alternative to the annealing procedures in various applications. Here we present the first performance evaluation of μO as applied to the TSP. When compared to three annealing strategies (simulated annealing, microcanonical annealing and Tsallis annealing), and to a tabu search algorithm, the microcanonical optimization has yielded the best overall results for several instances of the euclidean TSP. This confirms μO as a competitive approach for the solution of general combinatorial optimization problems.
Universal Ratio χ in Two-Dimensional Square Random-Site Percolation
Authors: Malarz Krzysztof , Vidales Ana Maria
Published: October 2003

The percolation phenomena on two-dimensional square lattice is considered. The quotient χ of connectivity length ξ> above percolation threshold pc and ξ< below pc at the same small distance Δp is discussed. The results of two different algorithms and programs and agreement with theoretical/mathematical predications is presented, in contrast to previous contradictory Monte Carlo simulation results.
The Lattice Molecular Automaton(LMA): A Simulation System for Constructive Molecular Dynamics
Authors: Mayer Bernd , Rasmussen Steen
Published: October 2003

Molecular self-assembly is frequently encountered in biochemical systems generating higher order structures with well-defined functionalities. However, the driving forces underlying these processes are not well understood.

The Lattice Molecular Automaton (LMA) is a deterministic computational tool suitable for simulation of self-organization processes in large scale, molecular systems. This paper introduces the basic computational concepts needed to formulate molecular dynamics and self-assembly in a discrete field, cellular automaton environment: Molecular objects are encoded as data structures on a 2D triangular lattice. Propagating force particles together with kinetic and potential energy terms define simulation objects that specify molecular dynamics and force field properties. As an example, the simulation of polymer dynamics in an aqueous environment is shown.

In this paper we focus on the mathematical and algorithmic formulation of a variety of intra- and intermolecular interactions. Thermodynamical characteristics together with a variety of other physico-chemical properties of the LMA are discussed in detail in Ref. 1.
Analysis of Serial and Parallel Algorithms for Use in Molecular Dynamics.
Authors: Mazzone A. M.
Published: October 2003

This work analyzes the stability and accuracy of multistep methods, either for serial or parallel calculations, applied to molecular dynamics simulations. Numerical testing is made by evaluating the equilibrium configurations of mono-elemental crystalline lattices of metallic and semiconducting type (Ag and Si, respectively) and of a cubic CuY compound.
High and Low Temperature Series Estimates for the Critical Temperature of the 3D Ising Model
Authors: Salman Zaher , Adler Joan
Published: October 2003

We have analyzed low and high temperature series expansions for the three-dimensional Ising model on the simple cubic lattice. Our analysis of Butera and Comi's new 21-term high temperature series yields [Formula: see text] and from the 32-term low temperature series of Vohwinkel we find Kc=0.22167±0.00002, consistent with the high temperature series but with larger error bars. We discuss the reasons for the larger error bars on the low temperature side and compare these values with estimates from other series analyses and from simulations.