bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Proficiency Testing on Results of the Microscopic Agglutination Test for Diagnosis of Leptospirosis
Authors: Chappel R. J. , Goris M. , Palmer M. F. , Hartskeerl R. A. 
Published: December 2004

ABSTRACT

A proficiency testing scheme for the leptospirosis microscopic agglutination test was provided to 37 laboratories in 23 countries in 2002 (round 1) and to 60 laboratories in 34 countries in 2003 (round 2). Thirty-four laboratories participated in both rounds. Each panel consisted of five rabbit serum samples, four of which were antisera raised against pathogenic serovars of
Leptospira
. One of these samples was a mixture of two different antisera. The rates of false-negative results, calculated on the basis of the assumption that serovars within a serogroup will cross-react, were 11% for round 1 and 14% for round 2. There were regional differences in the rates of false-negative results. The titers reported by laboratories testing for the same sample with the same serovar varied widely. Laboratories that had previously participated in round 1 reported fewer false-negative results in round 2 than new participants (10 and 21%, respectively [
P
= 0.002]) and reported 0.56 false-negative results per participant, whereas new participants reported 1.23 false-negative results per participant (
P
= 0.041). Laboratories that had previously participated also reported fewer false-negative results in round 2 than in round 1 when samples common to both rounds were tested (5 and 15%, respectively [
P
= 0.028]). The titers reported by the new participants were, on average, lower than those reported by the laboratories that had participated previously (
P
= 0.019) and were significantly more variable (
P
= 0.001). Analysis of these results suggests a positive impact of proficiency testing on the testing performance of the participating laboratories.
Evaluation of a Bedside Immunochromatographic Test for Detection of Adenovirus in Respiratory Samples, by Comparison to Virus Isolation, PCR, and Real-Time PCR
Authors: Fujimoto Tsuguto , Okafuji Teruo , Okafuji Takao , Ito Masahiro , Nukuzuma Soichi , Chikahira Masatsugu , Nishio Osamu 
Published: December 2004

ABSTRACT

An immunochromatography (IC) kit for human adenovirus (HAdV) was evaluated with 138 patient nasopharyngeal samples. The samples were collected at a sentinel clinic in Japan from January through June 2003. Patients were diagnosed by clinical manifestation of pharyngoconjunctival fever (
n
= 38) or exudative tonsillitis (
n
= 100). The IC kit was positive for 84% (116 of 138) of patients diagnosed at bedside. The remaining extract solution of the IC kit test was transferred into maintenance medium and tested via laboratory diagnoses. The IC kit had 95% sensitivity (116 of 122 patients) with HAdV isolation (isolation) as the standard and 91% sensitivity (116 of 128 patients) with PCR as the standard. All of the IC kit-positive samples were isolation and PCR positive. Similarly, all the isolation-positive samples were PCR positive. Twenty-two IC kit-negative samples were evaluated by real-time PCR. Six samples were IC kit negative and isolation positive and contained 3.8 × 10
7
to 2.5 × 10
9
copies of the HAdV genome/ml. Five samples that were only PCR positive contained 3.0 × 10
4
to 3.8 × 10
5
copies of the HAdV genome/ml, but one sample was real-time PCR negative. We conclude that the IC kit is a useful bedside diagnostic tool for HAdV infections because it has 95% sensitivity (compared to isolation), but a negative result does not always rule out HAdV infection.
AspergillusGalactomannan Enzyme Immunoassay and Quantitative PCR for Diagnosis of Invasive Aspergillosis with Bronchoalveolar Lavage Fluid
Authors: Musher Benjamin , Fredricks David , Leisenring Wendy , Balajee S. Arunmozhi , Smith Caitlin , Marr Kieren A. 
Published: December 2004

ABSTRACTInvasive pulmonary aspergillosis (IPA) is frequent and often fatal in hematopoietic stem cell transplant patients. Diagnosis requires microbiological or histopathologic demonstration of the organism in tissues; however, cultivation ofAspergillusspecies from respiratory secretions has low diagnostic sensitivity. Assays to detectAspergillusantigen or DNA in bronchoalveolar lavage (BAL) fluid could facilitate earlier diagnosis, thereby guiding optimal therapy and obviating the need for additional costly and potentially morbid diagnostic evaluation. We evaluated the performance of a galactomannan enzyme immunoassay (GM EIA; Bio-Rad) by using a range of index cutoffs to define positivity and a quantitative PCR (qPCR) assay for the detection ofAspergillusspecies from BAL samples of patients with proven and probable IPA (case patients;n= 49) and without IPA (control patients;n= 50). The sensitivity of the GM EIA was 61% with an index cutoff of 1.0 and 76% with an index cutoff of 0.5; the corresponding specificities were 98 and 94%, respectively. The sensitivity and specificity of qPCR assay were 67 and 100%, respectively. The sensitivity with 22 culture-negative BAL specimens from patients with IPA was 41% for GM EIA with an index cutoff of 1.0, 59% for GM EIA with an index cutoff of 0.5, and 36% for qPCR assay. GM EIA indices and DNA quantities corresponded to BAL fungal burdens, with culture-positive samples having larger amounts of antigen and DNA compared to culture-negative samples. GM EIA and qPCR assay add to the sensitivity of BAL for diagnosing IPA in high-risk patients, with excellent specificity. Adjunctive use of these tests may reduce dependence on invasive diagnostic procedures.
Culture-Independent Identification of Periodontitis-Associated
Porphyromonas
and
Tannerella
Populations by Targeted Molecular Analysis
Authors: de Lillo A. , Booth V. , Kyriacou L. , Weightman A. J. , Wade W. G. 
Published: December 2004

ABSTRACT

Periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. About half of the oral microflora is unculturable; and 16S rRNA PCR, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. In the present study, a PCR primer set specific for the genera
Porphyromonas
and
Tannerella
was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep sites in subjects with periodontitis and shallow sites in age- and sex-matched controls. A total of 308 clones were sequenced and found to belong to one of six
Porphyromonas
or
Tannerella
species or phylotypes, one of which,
Porphyromonas
P3, was novel.
Tannerella forsythensis
was found in significantly higher proportions in patients than in controls.
Porphyromonas catoniae
and
Tannerella
phylotype BU063 appeared to be associated with shallow sites. Targeted culture-independent molecular ecology studies have a valuable role to play in the identification of bacterial targets for further investigations of the pathogenesis of bacterial infections.
Genotypic and Phenotypic Heterogeneity amongMycobacterium tuberculosisIsolates from Pulmonary Tuberculosis Patients
Authors: Shamputa Isdore Chola , Rigouts Leen , Eyongeta Lovet Achale , El Aila Nabil Abdullah , van Deun Armand , Salim Abdul Hamid , Willery Eve , Locht Camille , Supply Philip , Portaels Françoise 
Published: December 2004

ABSTRACTAlthough the heterogeneity ofMycobacterium tuberculosispopulations and the existence of mixed infections are now generally accepted, systematic studies on their relative importance are rare. In the present study, 10 individual colonies of eachM. tuberculosisisolate (primary isolate) from 97 tuberculosis patients in a primarily human immunodeficiency virus-negative population were screened for heterogeneity and detectable mixed infections by spoligotyping, IS6110-based restriction fragment length polymorphism analysis, and mycobacterial interspersed repetitive unit-variable number of tandem repeat typing. The MICs of antituberculosis drugs for colonies with divergent fingerprints were determined. Infections with different bacterial subpopulations were detected in the samples from eight patients (8.2%), and the frequency of detectable mixed infections in the study population was estimated to be 2.1%. Genotypic variations were found to be independent of the drug susceptibilities, and the various molecular markers evolved independently in most cases. The predominant strains and the primary isolates always had concordant drug susceptibility and MIC testing results. These findings have implications on the interpretation of molecular epidemiology results for patient follow-up and in transmission studies.
Nicoletella semolinagen. nov., sp. nov., a New Member ofPasteurellaceaeIsolated from Horses with Airway Disease
Authors: Kuhnert Peter , Korczak Bożena , Falsen Enevold , Straub Reto , Hoops Anneliese , Boerlin Patrick , Frey Joachim , Mutters Reinier 
Published: December 2004

ABSTRACTGram-negative, nonmotile bacteria that are catalase, oxidase, and urease positive are regularly isolated from the airways of horses with clinical signs of respiratory disease. On the basis of the findings by a polyphasic approach, we propose that these strains be classified asNicoletella semolinagen. nov, sp. nov., a new member of the familyPasteurellaceae. N. semolinareduces nitrate to nitrite but is otherwise biochemically inert; this includes the lack of an ability to ferment glucose and other sugars. Growth is fastidious, and the isolates have a distinctive colony morphology, with the colonies being dry and waxy and looking like a semolina particle that can be moved around on an agar plate without losing their shape. DNA-DNA hybridization data and multilocus phylogenetic analysis, including 16S rRNA gene (rDNA),rpoB, andinfBsequencing, clearly placedN. semolinaas a new genus in the familyPasteurellaceae. In all the phylogenetic trees constructed,N. semolinais on a distinct branch displaying ∼5% 16S rDNA, ∼16%rpoB, and ∼20%infBsequence divergence from its nearest relative within the familyPasteurellaceae. High degrees of conservation of the 16S rDNA (99.8%),rpoB(99.6%), andinfB(99.7%) sequences exist within the species, indicating thatN. semolinaisolates not only are phenotypically homogeneous but also are genetically homogeneous. The type strain ofN. semolinais CCUG43639T(DSM16380T).
“
Bacteroides nordii
” sp. nov. and “
Bacteroides salyersae
” sp. nov. Isolated from Clinical Specimens of Human Intestinal Origin
Authors: Song Y. L. , Liu C. X. , McTeague M. , Finegold S. M. 
Published: December 2004

ABSTRACT

Two groups of unknown bacteria, which phenotypically resemble members of the
Bacteroides fragilis
group but phylogenetically display >5% 16S rRNA gene sequence divergence from their nearest validly described species,
Bacteroides thetaiotaomicron
, were characterized by phenotypic and molecular taxonomic methods. Phylogenetically and phenotypically, the unidentified bacteria displayed a relatively close association with each other. However, a 16S rRNA gene sequence divergence of approximately 4% between the two unknown bacteria, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct, and each group may represent a previously unknown subline within the
Bacteroides
phylogenetic cluster. Subsequent DNA-DNA hybridization studies confirmed that the two novel organisms were indeed distinct from each other. The previously described species closest to both of them is
B. thetaiotaomicron
(approximately 94% sequence similarity), but they can be differentiated easily from
B. thetaiotaomicron
by virtue of not utilizing trehalose. DNA-DNA pairing studies also documented the separateness of the unknown species and
B. thetaiotaomicron
. Based on the phenotypic and phylogenetic findings, two new species, “
Bacteroides nordii
” sp. nov. and “
Bacteroides salyersae
” sp. nov, are proposed. The G+C content of the DNA is 41.4 mol% for
Bacteroides nordii
and 42.0 mol% for
Bacteroides salyersae
. The type strains of
Bacteroides nordii
and
Bacteroides salyersae
are WAL 11050 (ATCC BAA-998 or CCUG 48943) and WAL 10018 (ATCC BAA-997 or CCUG 48945), respectively.
Detection of Methicillin-Resistant
Staphylococcus aureus
Directly from Nasal Swab Specimens by a Real-Time PCR Assay
Authors: Warren David K. , Liao Robert S. , Merz Liana R. , Eveland Michael , Dunne W. Michael 
Published: December 2004

ABSTRACT

Screening for colonization with methicillin-resistant
Staphylococcus aureus
(MRSA) is a key aspect of infection control to limit the nosocomial spread of this organism. Current methods for the detection of MRSA in clinical microbiology laboratories, including molecularly based techniques, require a culture step and the isolation of pure colonies that result in a minimum of 20 to 24 h until a result is known. We describe a qualitative in vitro diagnostic test for the rapid detection of MRSA directly from nasal swab specimens (IDI-MRSA; Infectio Diagnostic, Inc., Sainte-Foy, Québec, Canada), based upon a real-time PCR and direct detection of MRSA via amplicon hybridization with a fluorogenic target-specific molecular beacon probe. Samples from 288 patients were analyzed for the presence of MRSA with the IDI-MRSA assay, compared to detection by either direct plating or enrichment broth selective culture methods. The diagnostic values for this MRSA screening method were 91.7% sensitivity, 93.5% specificity, 82.5% positive predictive value, and 97.1% negative predictive value when compared to culture-based methods. The time from the start of processing of specimen to result was approximately 1.5 h. In our hands, the IDI-MRSA assay is a sensitive and specific test for detection of nasal colonization with MRSA and providing for same-day results, allowing more efficient and effective use of infection control resources to control MRSA in health care facilities.
Phenotypic Profiles of Enterotoxigenic
Escherichia coli
Associated with Early Childhood Diarrhea in Rural Egypt
Authors: Shaheen Hind I. , Khalil Sami B. , Rao Malla R. , Abu Elyazeed Remon , Wierzba Thomas F. , Peruski Leonard F. , Putnam Shannon , Navarro Armando , Morsy Badria Z. , Cravioto Alejandro , Clemens John D. , Svennerholm Ann-Mari , Savarino Stephen J. 
Published: December 2004

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) causes substantial diarrheal morbidity and mortality in young children in countries with limited resources. We determined the phenotypic profiles of 915 ETEC diarrheal isolates derived from Egyptian children under 3 years of age who participated in a 3-year population-based study. For each strain, we ascertained enterotoxin and colonization factor (CF) expression, the O:H serotype, and antimicrobial susceptibility. Sixty-one percent of the strains expressed heat-stable enterotoxin (ST) only, 26% expressed heat-labile enterotoxin (LT) alone, and 12% expressed both toxins. The most common CF phenotypes were colonization factor antigen I (CFA/I) (10%), coli surface antigen 6 (CS6) (9%), CS14 (6%), and CS1 plus CS3 (4%). Fifty-nine percent of the strains did not express any of the 12 CFs included in our test panel. Resistance of ETEC strains to ampicillin (63%), trimethoprim-sulfamethoxazole (52%), and tetracycline (43%) was common, while resistance to quinolone antibiotics was rarely detected. As for the distribution of observed serotypes, there was an unusually wide diversity of O antigens and H types represented among the 915 ETEC strains. The most commonly recognized composite ETEC phenotypes were ST CS14 O78:H18 (4%), ST (or LTST) CFA/I O128:H12 (3%), ST CS1+CS3 O6:H16 (2%), and ST CFA/I O153:H45 (1.5%). Temporal plots of diarrheal episodes associated with ETEC strains bearing common composite phenotypes were consistent with discrete community outbreaks either within a single or over successive warm seasons. These data suggest that a proportion of the disease that is endemic to young children in rural Egypt represents the confluence of small epidemics by clonally related ETEC strains that are transiently introduced or that persist in a community reservoir.
Practical Implementation of a Multiplex PCR for Acute Respiratory Tract Infections in Children
Authors: Gruteke Paul , Glas Afina S. , Dierdorp Mirjam , Vreede Willem B. , Pilon Jan-Willem , Bruisten Sylvia M. 
Published: December 2004

ABSTRACT

Molecular testing for acute respiratory infections (ARIs) has documented value but limited implementation due to questions that typically slow the acceptance of new tests. This study sought to address these questions and achieve implementation. Rhinovirus was added to a nested multiplex PCR (M-PCR), increasing its diagnostic yield. Over one winter, three hospital pediatric departments used the M-PCR to complement their direct fluorescent-antibody assay (DFA) for respiratory syncytial virus (RSV). Clinicians recorded “pretest probability estimates” (using continuous scales for various pathogen groups) for comparison with test results; treatments and test turnaround times were also recorded. Transnasal and throat swabs, with or without nasopharyngeal aspirate (NPA), were M-PCR tested. NPA-containing sample sets found to be RSV positive by DFA were not further tested. Single PCR for human metapneumovirus (hMPV) was performed retrospectively. Of 178 ARI episodes representing 172 patients, NPA was included in 97 sample sets; 54 (56%) were determined to be RSV positive. The other NPA-containing sample sets (
n
= 43) yielded 27 findings (63%), and the swab-only sets (
n
= 81) yielded 47 findings (58%); rhinovirus was found most often. Testing for hMPV yielded seven positive results. M-PCR median turnaround times were 4 days in swab-only samples and 5 days with NPA. Antibiotics were prescribed in 50 episodes, at rates similar for RSV and rhinovirus. Pretest probability estimates of a viral cause were lower in episodes caused by rhinovirus than in episodes caused by RSV. The hospitals continued to use M-PCR for NPA-containing samples found to be RSV negative by DFA. Test implementation is more likely with higher diagnostic yield and a protocol that reflects day-to-day clinical and laboratory operations.
Genetic Profile of an Oka Varicella Vaccine Virus Variant Isolated from an Infant with Zoster
Authors: Sauerbrei Andreas , Rubtcova Elena , Wutzler Peter , Schmid D. Scott , Loparev Vladimir N. 
Published: December 2004

ABSTRACT
Varicella virus vaccine strain Oka (V-Oka) has in rare cases caused zoster in vaccinated people. Despite broad usage of V-Oka, little is known about varicella-zoster virus genomic sequence variation of strains in vaccine and isolates from patients with vaccine adverse events. Direct sequencing of 20 regions of V-Oka-GSK was compared to the sequences of the original V-Oka-Biken, GlaxoSmithKline Oka vaccine (V-Oka-GSK), and Oka-parental (P-Oka) strains. We analyzed single nucleotide polymorphisms (SNP) differentiating the Oka parental and Oka vaccine strains identified in open reading frames (ORFs) 6, 9A, 10, 21, 31, 39, 50, 51, 52, 54, 55, and 59 and eight base substitutions within ORF 62. Sixteen of these SNP impose an amino acid change in the corresponding gene product. The genotypic analysis revealed that (i) both V-Oka-GSK and V-Oka-Biken comprise mixtures of strains represented in variable proportion from lot to lot; (ii) V-Oka-GSK/zoster isolated from the zoster patient had six wild-type SNP in ORF 9A, 10, 21, 52, 55, and 62 (mutation 108838); (iii) none of the six revertant SNP would reliably discriminate Oka vaccine from the wild type; and (iv) the genomic variation found in V-Oka/zoster might be associated with changes in the biological behavior of the virus. Further studies will be needed to identify potential virulence factors in variant vaccine strains.
Prevalence and Mechanisms of Erythromycin Resistance in Group A and Group B
Streptococcus
: Implications for Reporting Susceptibility Results
Authors: Desjardins M. , Delgaty K. L. , Ramotar K. , Seetaram C. , Toye B. 
Published: December 2004

ABSTRACT

Increased rates of erythromycin resistance among group B
Streptococcus
(GBS) and group A
Streptococcus
(GAS) have been reported. Cross-resistance to clindamycin may be present, depending on the mechanism of resistance. We determined the prevalence of macrolide-resistant determinants in GBS and GAS isolates to guide the laboratory reporting of erythromycin and clindamycin susceptibility. Susceptibilities were determined by the disk diffusion and broth microdilution methods. Inducible and constitutive resistance to clindamycin was determined by the double-disk diffusion method. The presence of the
ermTR
,
ermB
, and
mefA
genes was confirmed by PCR. Of the 338 GBS isolates, 55 (17%) were resistant to erythromycin, whereas 26 (8%) were resistant to clindamycin. The
erm
methylase gene was identified in 48 isolates, 22 of which had inducible resistance to clindamycin and 26 of which had constitutive resistance to clindamycin. The remaining seven resistant isolates had
mefA
. Of the 593 GAS isolates, 49 (8%) and 6 (1%) isolates were resistant to erythromycin and clindamycin, respectively. Erythromycin resistance was due to
mefA
in 33 isolates, whereas 14 isolates had
erm
-mediated resistance (9 isolates had inducible resistance and 5 isolates had constitutive resistance). In our population, erythromycin resistance in GAS was predominantly mediated by
mefA
and erythromycin resistance in GBS was predominantly mediated by
erm
. Regional differences in mechanisms of resistance need to be taken into consideration when deciding whether to report clindamycin susceptibility results on the basis of in vitro test results. Testing by the double-disk diffusion method would be an approach that could be used to address this issue, especially for GAS.
Detection of Four
Plasmodium
Species in Blood from Humans by 18S rRNA Gene Subunit-Based and Species-Specific Real-Time PCR Assays
Authors: Rougemont Mathieu , Van Saanen Madeleine , Sahli Roland , Hinrikson Hans Peter , Bille Jacques , Jaton Katia 
Published: December 2004

ABSTRACT

There have been reports of increasing numbers of cases of malaria among migrants and travelers. Although microscopic examination of blood smears remains the “gold standard” in diagnosis, this method suffers from insufficient sensitivity and requires considerable expertise. To improve diagnosis, a multiplex real-time PCR was developed. One set of generic primers targeting a highly conserved region of the 18S rRNA gene of the genus
Plasmodium
was designed; the primer set was polymorphic enough internally to design four species-specific probes for
P. falciparum
,
P. vivax
,
P. malarie
, and
P. ovale
. Real-time PCR with species-specific probes detected one plasmid copy of
P. falciparum
,
P. vivax
,
P. malariae
, and
P. ovale
specifically. The same sensitivity was achieved for all species with real-time PCR with the 18S screening probe. Ninety-seven blood samples were investigated. For 66 of them (60 patients), microscopy and real-time PCR results were compared and had a crude agreement of 86% for the detection of plasmodia. Discordant results were reevaluated with clinical, molecular, and sequencing data to resolve them. All nine discordances between 18S screening PCR and microscopy were resolved in favor of the molecular method, as were eight of nine discordances at the species level for the species-specific PCR among the 31 samples positive by both methods. The other 31 blood samples were tested to monitor the antimalaria treatment in seven patients. The number of parasites measured by real-time PCR fell rapidly for six out of seven patients in parallel to parasitemia determined microscopically. This suggests a role of quantitative PCR for the monitoring of patients receiving antimalaria therapy.