bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serotype and Phage Type Distribution of
Salmonella
Strains Isolated from Humans, Cattle, Pigs, and Chickens in The Netherlands from 1984 to 2001
Authors: van Duijkeren E. , Wannet W. J. B. , Houwers D. J. , van Pelt W. 
Published: October 2002

ABSTRACT

We studied serotypes and phage types of
Salmonella
strains isolated from humans and animals in The Netherlands over the period 1984 to 2001. All human strains (
n
= 59,168) were clinical isolates. The animal strains (
n
= 65,567) were from clinical and nonclinical infections. All isolates were serotyped, and
Salmonella enterica
serovar Typhimurium and serovar Enteritidis strains were further phage typed. The most prevalent serotypes were as follows: in humans, serovars Typhimurium and Enteritidis; in cattle, serovars Typhimurium and Dublin; in pigs, serovar Typhimurium; and in chickens, serovars Enteritidis, Infantis, and Typhimurium. Serovar Enteritidis phage type 4 (pt 4) was the most common phage type in humans and chickens. Serovar Typhimurium pt 510 was the most prevalent serovar Typhimurium phage type in humans and pigs, pt 200 was the most prevalent serovar Typhimurium phage type in cattle, and pt 150 was the most prevalent serovar Typhimurium phage type in chickens. Analysis of the distribution of sero- and phage types during the study period indicated that types shifted over time in humans and animals. Serovar Typhimurium DT 104 emerged in 1991 in humans, cattle, pigs, and chickens and became the most common serovar Typhimurium phage type in 2001. In general, similar sero- and phage types were found in humans and animals, although distinct types were more common in animals. Between the animal species, the sero- and phage type distributions varied considerably.
Comparison of Quantitative Competitive PCR with LightCycler-Based PCR for Measuring Epstein-Barr Virus DNA Load in Clinical Specimens
Authors: Stevens Servi J. C. , Verkuijlen Sandra A. W. M. , Brule Adriaan J. C. van den , Middeldorp Jaap M. 
Published: October 2002

ABSTRACT

The aim of this study was to develop a LightCycler-based real-time PCR assay for monitoring the Epstein-Barr virus (EBV) DNA load in unfractionated whole blood. This assay was compared with quantitative competitive PCR (Q-PCR) for EBV. The LightCycler-based assay was highly sensitive and reproducible when quantifying plasmid DNA in either the presence or absence of healthy donor blood DNA. Amplifying plasmid DNA in DNA backgrounds from different donors slightly increased the variation of quantification, indicating that clinical specimen DNA has an influence on quantification. In most transplant recipients, a good correlation was observed between EBV DNA load dynamics determined by LightCycler and Q-PCR in follow-up samples, although the correlation between absolute values of EBV DNA loads was weak and occasional samples were false negative in the LightCycler assay. In 253 cross-sectional blood samples from patients with Burkitt's lymphoma, infectious mononucleosis, or human immunodeficiency virus infection, a weak but significant correlation between the two methods was found (
r
2
= 0.37,
P
< 0.001). Our results indicate that the clinical specimen DNA background may influence the absolute values of EBV DNA load in LightCycler analyses but that this effect is rare. LightCycler PCR is very well suited for monitoring of EBV DNA load dynamics, and its diagnostic value is comparable to that of Q-PCR. To avoid false negativity or underestimation of viral load, future internal calibration of the LightCycler is recommended. This would also enhance EBV load assay standardization and interinstitute comparisons.
Virologic and Serologic Identification of Minute Virus of Canines (Canine Parvovirus Type 1) from Dogs in Japan
Authors: Mochizuki Masami , Hashimoto Michiru , Hajima Takayuki , Takiguchi Mitsuyoshi , Hashimoto Akira , Une Yumi , Roerink Frank , Ohshima Takahisa , Parrish Colin R. , Carmichael Leland E. 
Published: October 2002

ABSTRACT
Minute virus of canines (MVC), also known as canine parvovirus type 1, was initially believed to be a nonpathogenic agent, since it was first isolated from canine fecal specimens in the late 1960s. However, subsequent pathological as well as epidemiological studies suggested that MVC is a pathogen of neonatal puppies and is widely distributed among domestic dogs in the United States. The virus also has been shown to cause fetal deaths. Nevertheless, the virus was not detected in dogs outside the United States until recently, presumably because of a lack of widespread availability of the only susceptible canine cell line, WRCC/3873D, used for MVC isolation. We examined 470 clinical specimens from 346 dogs by PCR and detected MVC-specific gene fragments from four diseased puppies (positive rate, 1.2%). Viruses were recovered from three PCR-positive rectal specimens by using WRCC/3873D and MDCK cells. The isolates possessed antigenic and genomic properties similar to those of the U.S. reference strain GA3 and were identified as MVC. In addition, seroepidemiological evidence that 5.0% of dogs possessed anti-MVC antibodies also indicated the presence of MVC infection among dogs in Japan. From this study and several recent European reports describing MVC field cases, it is evident that MVC is distributed among domestic dogs worldwide.
Collaborative Evaluation of Optimal Antifungal Susceptibility Testing Conditions for Dermatophytes
Authors: Fernández-Torres Belkys , Cabañes Francisco J. , Carrillo-Muñoz Alfonso J. , Esteban Alexandre , Inza Isabel , Abarca Lourdes , Guarro Josep 
Published: October 2002

ABSTRACT

A multicenter study was conducted to define the most suitable testing conditions for antifungal susceptibility of dermatophytes. Broth microdilution MICs of clotrimazole, itraconazole, and terbinafine were determined in three centers against 60 strains of dermatophytes. The effects of inoculum density (ca. 10
3
and 10
4
CFU/ml), incubation time (3, 7, and 14 days), endpoint criteria for MIC determination (complete [MIC-0] and prominent [MIC-2] growth inhibition), and incubation temperature (28 and 37°C) on intra- and interlaboratory agreement were analyzed. The optimal testing conditions identified were an inoculum of 10
4
CFU/ml, a temperature of incubation of 28°C, an incubation period of 7 days, and MIC-0.
False-Positive
Mycobacterium tuberculosis
Cultures in 44 Laboratories in The Netherlands (1993 to 2000): Incidence, Risk Factors, and Consequences
Authors: de Boer Annette S. , Blommerde Barbara , de Haas Petra E. W. , Sebek Maruschka M. G. G. , Lambregts-van Weezenbeek Kitty S. B. , Dessens Mirjam , van Soolingen Dick 
Published: October 2002

ABSTRACT

False-positive
Mycobacterium tuberculosis
cultures are a benchmark for the quality of laboratory processes and patient care. We studied the incidence of false-positive cultures, risk factors, and consequences for patients during the period from 1993 to 2000 in 44 peripheral laboratories in The Netherlands. The national reference laboratory tested 8,889
M. tuberculosis
isolates submitted by these laboratories. By definition, a culture was false positive (i) if the DNA fingerprint of the isolate was identical to that of an isolate from another patient processed within 7 days in the same laboratory, (ii) if the isolate was taken from a patient without clinical signs of tuberculosis, and/or (iii) if the false-positive test result was confirmed by the peripheral laboratory and/or the public health tuberculosis officer. We identified 213 false-positive cultures (2.4%). The overall incidence of false-positive cultures decreased over the years, from 3.9% in 1993 to 1.1% in 2000. Laboratories with false-positive cultures more often processed less than 3,000 samples per year (
P
< 0.05). Among 110 patients for whom a false-positive culture was identified from 1995 to 1999, we found that for 36% of the patients an official tuberculosis notification had been provided to the appropriate public health services, 31% of the patients were treated, 14% of the patients were hospitalized, and a contact investigation had been initiated for 16% of the patients. The application of DNA fingerprinting to identify false-positive
M. tuberculosis
cultures and the provision of feedback to peripheral laboratories are useful instruments to improve the quality of laboratory processes and the quality of medical care.
Molecular Detection and Seroepidemiology of the
Chlamydia pneumoniae
Bacteriophage (ΦCpn1)
Authors: Karunakaran Karuna P. , Blanchard James F. , Raudonikiene Ausra , Shen Caixia , Murdin Andrew D. , Brunham Robert C. 
Published: October 2002

ABSTRACT

Recent whole-genome analysis has demonstrated limited genetic variation in
Chlamydia pneumoniae
, with one strain (AR39) containing a 4,524 nucleotide single-stranded DNA bacteriophage, ΦCpn1. Using PCR, reverse transcription (RT)-PCR, and Western blotting, we confirmed the presence and functional expression of ΦCpn1 in
C. pneumoniae
strain AR39 and its absence in strain CWL029. Six additional epidemiologically distinct clinical isolates of
C. pneumoniae
also did not contain ΦCpn1. We generated recombinant viral protein 1 (Vp1) from ΦCpn1 in
Escherichia coli
and showed that Vp1 antigen is highly immunogenic in mice and that murine antisera readily recognize native Vp1 from
C. pneumoniae
strain AR39 elementary bodies (EB). We developed an enzyme-linked immunosorbent assay (ELISA) to measure antibodies to recombinant Vp1 in human sera collected from 32 patients with abdominal aortic aneurysm (AAA) and 40 controls. Among the 72 subjects, 61 had
C. pneumoniae
EB antibodies shown by ELISA. Antibodies to Vp1 were found in 39 of the 61 (64%) seropositive individuals and were significantly correlated with AAA (adjusted odds ratio, 13.9; 95% confidence interval, 1.1 to 175). Our studies indicate that phage-containing strains of
C. pneumoniae
are uncommonly found by isolation but may commonly infect individuals with vascular disease.
Precision and Accuracy of a Procedure for Detecting Recent Human Immunodeficiency Virus Infections by Calculating the Antibody Avidity Index by an Automated Immunoassay-Based Method
Authors: Suligoi Barbara , Galli Claudio , Massi Mario , Di Sora Fiorella , Sciandra Mauro , Pezzotti Patrizio , Recchia Olga , Montella Francesco , Sinicco Alessandro , Rezza Giovanni 
Published: October 2002

ABSTRACT

We evaluated the precision and accuracy of a procedure for detecting recent human immunodeficiency virus (HIV) infections, specifically, the avidity index (AI) calculated using a method based on an automated AxSYM HIV 1/2gO assay (Abbott). To evaluate precision, we performed multiple replicates on eight HIV-positive serum samples. To evaluate the accuracy in identifying recent infections (i.e., within 6 months of seroconversion), we used 216 serum samples from 47 persons whose dates of seroconversion were known. To evaluate the sensitivity and specificity of the procedure for different AI cutoff values, we performed receiver operating characteristic (ROC) analysis. To determine the effects of antiretroviral treatment, advanced stage of the disease (i.e., low CD4-cell count), and low HIV viral load on the AI, we analyzed 15 serum samples from 15 persons whose dates of seroconversion were unknown. The precision study showed that the procedure was robust (i.e., the total variance of the AI was lower than 10%). Regarding accuracy, the mean AI was significantly lower for samples collected within 6 months of seroconversion, compared to those collected afterwards (0.68 ± 0.16 versus 0.99 ± 0.10;
P
< 0.0001), with no overlap of the 95% confidence intervals. The ROC analysis revealed that an AI lower than 0.6 had a sensitivity of 33.3% and a specificity of 98.4%, compared to 87.9 and 86.3%, respectively, for an AI lower than 0.9. Antiretroviral treatment, low CD4-cell count, and low viral load had no apparent effect on the AI. In conclusion, this procedure is reproducible and accurate in identifying recent infections; it is automated, inexpensive, and easy to perform, and it provides a quantitative result with different levels of sensitivity and specificity depending on the selected cutoff.
Genetic Characterization and Sequence Heterogeneity of a Canadian Isolate of Swine Hepatitis E Virus
Authors: Pei Yanlong , Yoo Dongwan 
Published: October 2002

ABSTRACT
Swine hepatitis E virus (HEV) is a newly identified potentially zoonotic agent that is possibly transmitted to humans from pigs. Swine HEV is prevalent in pig populations and does not cause abnormal clinical symptoms in infected pigs, further implicating a likelihood of a risk of transmission to humans by normal contact. To date in North America, only one strain of swine HEV (strain US swine) has been fully sequenced. In the present study, we identified a swine HEV isolate from pigs in Canada, designated the Arkell strain, and determined the full length of the genomic sequence. The genome of Canadian strain Arkell consisted of 7,242 nucleotides, excluding the poly(A) tail of at least 15 A residues. The genome contained three open reading frames (ORFs), ORF1, ORF2, and ORF3, which had coding capacities for proteins of 1,708, 660, and 122 amino acids, respectively. Comparative analysis of the full-length genomic sequence indicated that the sequence of strain Arkell was distinct from those of all other known HEV isolates by 13 to 27% and shared the highest degrees of identity with human HEV isolates US-1 and US-2, HEV isolate US swine, and the human and swine HEV isolates recently isolated in Japan. On the basis of sequence similarities and phylogenetic analyses, HEV strain Arkell was grouped into genotype 3. The sequence of the Arkell swine HEV isolate differed from those of HEV isolate US swine and HEV isolate Japan swine by 13 and 14%, respectively. To date, two isolates of swine HEV (isolates Arkell and SK3 [D. Yoo et al., Clin. Diagn. Lab. Immunol. 8:1213-1219, 2001]) have been identified in Canadian pigs, and their sequences also differ from each other by 11.8%. Our studies indicate that, as with human HEV strains, swine HEV isolates exhibit extensive genetic heterogeneity.
Identification and Broad Dissemination of the CTX-M-14 β-Lactamase in Different
Escherichia coli
Strains in the Northwest Area of Spain
Authors: Bou German , Cartelle Monica , Tomas Maria , Canle Delia , Molina Francisca , Moure Rita , Eiros Jose Maria , Guerrero Antonio 
Published: October 2002

ABSTRACT

During the course of a molecular epidemiology study of mechanisms of antibiotic resistance in the area served by our hospital (516,000 inhabitants), we isolated the gene encoding CTX-M-14 β-lactamase. Thirty clinical strains (27
Escherichia coli
and 3
Klebsiella pneumoniae
isolates) with a phenotype of extended-spectrum β-lactamase were collected from January to October 2001 and studied for the presence of the CTX-M-14 β- lactamase gene. By isoelectric point determination, PCR, and nucleotide sequencing, we detected the presence of this gene in 17
E. coli
strains belonging to 15 different genotypes (REP-PCR) causing infections in 17 different patients. Epidemiological studies based on medical records did not suggest any relationship between the patients infected with these
E. coli
strains and, interestingly, 7 of 30 patients harboring strains with extended-spectrum β-lactamases never had contact with the hospital environment before the clinical
E. coli
isolation. Conjugation experiments revealed that this gene was plasmid mediated in the 17
E. coli
strains, and plasmid restriction fragment length polymorphisms showed 9 different patterns in the 17
E. coli
strains. By PCR, the sequence of the
tnpA
transposase gene of the insert sequence ISEcp-1 was detected in all the plasmids harboring the CTX-M-14 gene. These results strongly suggest that plasmid dissemination between different
E. coli
strains in addition to a mobile element (transposon) around the β-lactamase gene may be involved in the spreading of the CTX-M-14 gene. This study reinforces the hypothesis that the epidemiology of the prevalence of the β-lactamase genes is changing and should alert the medical community to the increase in the emergence of the CTX-M β-lactamases worldwide.
Severe Acquired Toxoplasmosis in Immunocompetent Adult Patients in French Guiana
Authors: Carme B. , Bissuel F. , Ajzenberg D. , Bouyne R. , Aznar C. , Demar M. , Bichat S. , Louvel D. , Bourbigot A. M. , Peneau C. , Neron P. , Dardé M. L. 
Published: October 2002

ABSTRACT

The most common presentation of symptomatic postnatally acquired toxoplasmosis in immunocompetent patients is painless cervical adenopathy. Acute visceral manifestations are associated in rare cases. We report 16 cases of severe primary toxoplasmosis diagnosed in French Guiana during a 6.5-year period. All of the subjects were immunocompetent adults hospitalized with clinical presentations consisting of a marked, nonspecific infectious syndrome accompanied by an altered general status with at least one visceral localization, mainly pulmonary involvement (14 cases). Acute toxoplasmosis was diagnosed according to the results of serological tests suggestive of recent primary infection and the absence of an alternative etiology. Recovery was rapid following specific antitoxoplasmosis treatment. Thirteen of the 16 patients had consumed game in the 2 weeks before the onset of the symptoms, and in eight cases the game was considered to have been undercooked.
Toxoplasma
strains, which were virulent in mice, were isolated from three patients. Microsatellite analysis showed that all of these isolates exhibited an atypical multilocus genotype, with one allele found only for isolates of this region.
Use of Epitope Mapping To Identify a PCR Template for Protein Amplification and Detection by Enzyme-Linked Immunosorbent Assay of Bovine Herpesvirus Type 1 Glycoprotein D
Authors: Joseph Tomy , Lyaku Japhet , Fredrickson Robert A. , Cepica Arnost , Kibenge Frederick S. B. 
Published: October 2002

ABSTRACT
Infection with bovine herpesvirus type 1 (BHV-1) occurs worldwide and causes serious economic losses due to the deaths of animals, abortions, decreased milk production, and loss of body weight. BHV-1 is frequently found in bovine semen and is transmitted through natural service and artificial insemination. The detection of BHV-1 in bovine semen is a long-standing problem in veterinary virology which is important in disease control schemes. In the present study, ordered deletions of the full-length BHV-1 glycoprotein open reading frame were used to identify an epitope recognized by a specific monoclonal antibody (MAb). A glycoprotein D fragment containing this epitope was then amplified using an in vitro protein amplification assay developed previously (J. Zhou, J. Lyaku, R. A. Fredrickson, and F. S. Kibenge, J. Virol. Methods 79:181-189, 1999), and the resulting peptide was detected by indirect enzyme-linked immunosorbent assay (ELISA) with the specific MAb. This method detected 0.0395 50% tissue culture infective dose of BHV-1 in raw bovine semen, which was 1,000-fold more sensitive than traditional PCR. We therefore conclude that this in vitro protein amplification assay combined with ELISA has superior sensitivity for direct virus detection in clinical samples.
Nosocomial Infections Caused by Multidrug-Resistant Isolates of
Pseudomonas putida
Producing VIM-1 Metallo-β-Lactamase
Authors: Lombardi Gianluigi , Luzzaro Francesco , Docquier Jean-Denis , Riccio Maria Letizia , Perilli Mariagrazia , Colì Alessandra , Amicosante Gianfranco , Rossolini Gian Maria , Toniolo Antonio 
Published: October 2002

ABSTRACT

Successful carbapenem-based chemotherapy for the treatment of
Pseudomonas
infections has been seriously hindered by the recent appearance of IMP- and VIM-type metallo-β-lactamases, which confer high-level resistance to carbapenems and most other β-lactams. Recently, multidrug-resistant
Pseudomonas putida
isolates for which carbapenem MICs were ≥32 μg/ml were recovered from cultures of urine from three inpatients in the general intensive care unit of the Ospedale di Circolo, Varese, Italy. Enzyme assays revealed production of a metallo-β-lactamase activity, while molecular analysis detected in each isolate a
bla
VIM-1
determinant carried by an apparently identical medium-sized plasmid. Conjugation experiments were unsuccessful in transferring the β-lactamase determinant to
Escherichia coli
or
Pseudomonas aeruginosa
. Macrorestriction analysis by pulsed-field gel electrophoresis demonstrated that the isolates were of clonal origin. PCR mapping and sequencing of the variable region of the plasmid-borne class 1 integron carrying the
bla
VIM-1
determinant (named In110) showed that the
bla
VIM-1
-containing cassette was identical to that previously found in strains of different species from other Italian hospitals and that the cassette array of In110 was not identical but clearly related to that of In70 (a
bla
VIM-1
-containing plasmid-borne integron from an
Achromobacter xylosoxidans
isolate), pointing to a common origin of this cassette and to a related evolutionary history of their cognate integrons.
Confirmation by 16S rRNA PCR of the COBAS AMPLICOR CT/NG Test for Diagnosis of
Neisseria gonorrhoeae
Infection in a Low-Prevalence Population
Authors: Diemert David J. , Libman Michael D. , Lebel Pierre 
Published: October 2002

ABSTRACT

The COBAS AMPLICOR CT/NG test is widely used for the diagnosis of
Neisseria gonorrhoeae
infection using genital swabs or urine samples. Although highly specific, cross-reactivity occurs with some nonpathogenic strains of
Neisseria
and
Lactobacillus
species. In low-prevalence populations, even highly specific assays may require confirmatory testing of positive results. We assessed the positive predictive value (PPV) of this test in a low-prevalence (0.5%) setting. Genital and urine specimens testing positive using the COBAS AMPLICOR NG test were retested using an investigational 16S rRNA PCR assay. Additionally, 737 specimens were tested in parallel by both culture and the above PCR protocol. Of 9,772 specimens tested in-house, 168 were positive by the AMPLICOR test; in addition, 62 AMPLICOR-positive specimens were referred to our laboratory for confirmatory testing, yielding 230 positive specimens. Of these, 72 were confirmed positive by 16S rRNA PCR, yielding a specificity of 98.7% and a PPV of 31.3%. Specificity was similar for all specimen types, whereas PPV varied with prevalence: specimens from males, females, urine specimens, and genital swabs had PPVs of 70.8, 13.3, 51.9, and 20.1%, respectively. The PPV was higher when the initial AMPLICOR optical density (OD) was ≥3.5 versus initial and repeat OD readings in an equivocal zone of ≥0.2 to <3.5 (65.1 versus 10.1%;
P
< 0.001). On repeat testing of specimens with ODs in the equivocal zone, 54 gave ODs of ≥0.2 and <2.0, 35 gave ODs of ≥2.0 and <3.5, and 12 gave ODs of ≥3.5, with 3.7, 20, and 33.3% confirmed positive, respectively (
P
= 0.004). Comparing PCR to culture as the “gold standard,” specificity increased from 96.8 to 99.9% when 16S rRNA PCR was performed on specimens positive by the COBAS AMPLICOR NG test. Confirmatory testing with a more specific method such as 16S rRNA PCR should be considered in low-prevalence populations, especially for specimens with an OD in the equivocal zone.