bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of 43StreptococcusSpecies by Pyrosequencing Analysis of thernpBGene
Authors: Innings Åsa , Krabbe Margareta , Ullberg Måns , Herrmann Björn 
Published: December 2005

ABSTRACTPyrosequencing technology was evaluated for identification of species within theStreptococcusgenus. Two variable regions in thernpBgene, which encodes the RNA subunit of endonuclease P, were sequenced in two reactions. Of 43 species, all could be identified to the species level except strains of the species pairsStreptococcus anginosus/S. constellatusandS. infantis/S. peroris. A total of 113 blood culture isolates were identified by pyrosequencing analysis of partialrnpBsequences. All but eight isolates could be unambiguously assigned to a specific species when the first 30 nucleotides of the two regions were compared to anrnpBdatabase comprising 107 streptococcal strains. Principal coordinate analysis of sequence variation of strains from viridans group streptococci resulted in species-specific clusters for the mitis and the salivarius groups but not for the anginosus group. The identification capacity of pyrosequencing was compared to the biochemical test systems VITEK 2 and Rapid ID 32 Strep. The concordance between pyrosequencing and VITEK 2 was 75%, and for Rapid ID 32 Strep the corresponding figure was 77%. Isolates with discrepant identifications in the three methods were subjected to entirernpBDNA sequence analysis that confirmed the identifications by pyrosequencing. In conclusion, pyrosequencing analysis of thernpBgene can reliably identifyStreptococcusspecies with high resolution.
Frequency and Possible Infection Control Implications of Gastrointestinal Colonization with Methicillin-Resistant
Staphylococcus aureus
Authors: Boyce John M. , Havill Nancy L. , Maria Benedicte 
Published: December 2005

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) is a major cause of health care-associated infections. Multiple factors, including transmission from unrecognized reservoirs of MRSA, are responsible for failure to control the spread of MRSA. We conducted prospective surveillance to determine the frequency of gastrointestinal colonization with MRSA among patients and its possible impact on nosocomial transmission of MRSA. Stool specimens submitted for
Clostridium difficile
toxin A/B assays were routinely inoculated on colistin-naladixic acid agar plates, and
S. aureus
was identified by using standard methods. Methicillin resistance was confirmed by growth on oxacillin-salt screening agar. For patients whose stool yielded MRSA, information regarding any previous cultures positive for MRSA or other organisms that would require contact precautions was obtained from the laboratory's computer system. During a 1-year period, 151 (9.8%) of 1,543 patients who had one or more stool specimens screened had MRSA in their stool. Ninety-three (62%) of the 151 patients had no previous history of MRSA colonization or infection. Of these 93, 75 were inpatients. Sixty (80%) of the 75 inpatients with no previous history of MRSA were not under “contact precautions.” The 60 patients would have spent an estimated total of 267 days without being placed under contact precautions if their positive stool cultures had not resulted in their being isolated. Placing patients under contact precautions based on their positive stool cultures prevented an estimated 35 episodes of MRSA transmission. We conclude that gastrointestinal colonization with MRSA may serve as an unrecognized reservoir from which transmission of MRSA may occur in health care facilities.
Clinical Significance of Hepatitis B Virus (HBV) Genotypes and Precore and Core Promoter Mutations Affecting HBV e Antigen Expression in Taiwan
Authors: Chen Chien-Hung , Lee Chuan-Mo , Lu Sheng-Nan , Changchien Chi-Sin , Eng Hock-Liew , Huang Chao-Min , Wang Jing-Houng , Hung Chao-Hung , Hu Tsung-Hui 
Published: December 2005

ABSTRACTTo assess the prevalence and clinical significance of hepatitis B virus (HBV) genotypes and precore and core promoter mutations in Taiwan, a cohort of 200 Taiwanese chronic hepatitis B patients was analyzed. The HBV genotypes and sequences of the precore and the core promoter regions were determined in 66 asymptomatic carriers and 134 patients who had liver biopsy-verified chronic hepatitis and liver cirrhosis. The HBV e-antigen (HBeAg)-negative patients had a higher frequency of mutations at core promoter nucleotides 1753 and 1773 and precore nucleotides 1846, 1896, and 1899 than HBeAg-positive patients. Among the 200 patients, the frequencies of genotype C, T1762 and A1764, C1753, T1766 and A1768, and A1896 mutations increased and the frequencies of T or G1752, T1773, G1799, and C1858 mutations decreased with advancing liver diseases. These factors were different between those with HBeAg-positive status and those with HBeAg-negative status. Based on multiple logistic regression analysis, the risk factors of liver cirrhosis for 200 patients were the presence of T1762 and A1764 mutations (odds ratio [OR] = 11.11; 95% confidence interval [CI] = 3.91 to 31.25;P< 0.001), age ≥35 years (OR = 3.42; 95% CI = 1.33 to 8.77;P= 0.011), and genotype C (OR = 2.87; 95% CI = 1.21 to 6.81;P= 0.017). Further categorical analysis found that 62.1% of patients with genotype C, T1762 and A1764 mutations and age ≥35 years had liver cirrhosis. None of the 55 patients infected with the genotype B, A1762 and G1764 wild type and age <35 years showed liver cirrhosis. In conclusion, our data suggest that pathogenic differences between HBeAg-positive and -negative patients may exist. In Taiwan, HBV genotype C and the T1762 and A1764 mutations may play a role in HBV-related liver cirrhosis, and these could serve as molecular markers for prediction of the clinical outcomes of chronic HBV patients.
Recurrent Melioidosis in Patients in Northeast Thailand Is Frequently Due to Reinfection Rather than Relapse
Authors: Maharjan Bina , Chantratita Narisara , Vesaratchavest Mongkol , Cheng Allen , Wuthiekanun Vanaporn , Chierakul Wirongrong , Chaowagul Wipada , Day Nicholas P. J. , Peacock Sharon J. 
Published: December 2005

ABSTRACT

Human melioidosis is associated with a high rate of recurrent disease, despite adequate antimicrobial treatment. Here, we define the rate of relapse versus the rate of reinfection in 116 patients with 123 episodes of recurrent melioidosis who were treated at Sappasithiprasong Hospital in Northeast Thailand between 1986 and 2005. Pulsed-field gel electrophoresis was performed on all isolates; isolates from primary and recurrent disease for a given patient different by one or more bands were examined by a sequence-based approach based on multilocus sequence typing. Overall, 92 episodes (75%) of recurrent disease were caused by the same strain (relapse) and 31 episodes (25%) were due to infection with a new strain (reinfection). The interval to recurrence differed between patients with relapse and reinfection; those with relapses had a median time to relapse of 228 days (range, 15 to 3,757 days; interquartile range [IQR], 99.5 to 608 days), while those with reinfection had a median time to reinfection of 823 days (range, 17 to 2,931 days; IQR, 453 to 1,211 days) (
P
= 0.0001). A total of 64 episodes (52%) occurred within 12 months of the primary infection. Relapse was responsible for 57 of 64 (89%) episodes of recurrent infection within the first year after primary disease, whereas relapse was responsible for 35 of 59 (59%) episodes after 1 year (
P
< 0.0001). Our data indicate that in this setting of endemicity, reinfection is responsible for one-quarter of recurrent cases. This finding has important implications for the clinical management of melioidosis patients and for antibiotic treatment studies that use recurrent disease as a marker for treatment failure.
Relationship between the Original Multiply Resistant South African Isolates ofStreptococcus pneumoniaefrom 1977 to 1978 and Contemporary International Resistant Clones
Authors: Reinert Ralf René , Jacobs Michael R. , Appelbaum Peter C. , Bajaksouzian Saralee , Cordeiro Soraia , van der Linden Mark , Al-Lahham Adnan 
Published: December 2005

ABSTRACTHigh-level penicillin G-resistant as well as multidrug-resistantStreptococcus pneumoniaeisolates were first described in South Africa in 1977. The relationship between these original multidrug-resistant South African isolates and other resistant clones was investigated. Twenty-six representative isolates isolated from initial outbreaks in South Africa from 1977 to 1978 were characterized by multilocus sequence typing and pulsed-field gel electrophoresis. Twenty-one isolates were penicillin resistant and five were penicillin intermediate, with variable susceptibilities to macrolides, clindamycin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole. Fourteen isolates were serotype 19A, 11 were serotype 6A, and one was serotype 14. Penicillin-resistant serotype 19A isolates belonged to three closely related sequence types (STs), ST 41 (n= 6), ST 1605 (n= 3), and ST 1656 (n= 1). Penicillin-resistant serotype 6A isolates belonged to two closely related STs, ST 1094 (n= 10) and ST 1607 (n= 1), and were not closely related to other international clones. The serotype 14 penicillin-intermediate isolate was not closely related to the other isolates from South Africa but was a predicted founder of a clonal group with 41 different STs. Five new STs, ST 1605, ST 1607, ST 1608, ST 1610, and ST 1656, are described for the first time in this study. New molecular methods have characterized the original multiply resistant South African pneumococcal isolates from 1977 to 1978 and have shown the relationships of these clones to major pneumococcal clones.
Distribution of Insertion- and Deletion-Associated Genetic Polymorphisms among Four
Mycobacterium tuberculosis
Phospholipase C Genes and Associations with Extrathoracic Tuberculosis: a Population-Based Study
Authors: Kong Y. , Cave M. D. , Yang D. , Zhang L. , Marrs C. F. , Foxman B. , Bates J. H. , Wilson F. , Mukasa L. N. , Yang Z. H. 
Published: December 2005

ABSTRACT

The
Mycobacterium tuberculosis
genome contains four phospholipase C (PLC)-encoding genes, designated
plcA
,
plcB
,
plcC
, and
plcD
, respectively. Each of the four genes contributes to the overall PLC activity of
M. tuberculosis.
PLC is hypothesized to contribute to
M. tuberculosis
virulence. Infection of
M. tuberculosis
strains carrying a truncated
plcD
gene is associated with the occurrence of extrathoracic tuberculosis. However, whether the other three
plc
genes are also associated with extrathoracic tuberculosis remains to be assessed. We investigated the insertion- and deletion-associated genetic diversity in all four
plc
genes among 682 epidemiologically and clinically well-characterized
M. tuberculosis
clinical isolates using PCR, DNA sequencing, and Southern hybridization. Two hundred sixty-six (39%) of the 682 isolates had an interruption in at least one of the four
plc
genes, most often associated with an IS
6110
insertion. The
plcD
gene interruption was the most common: it was observed in 233 (34%) of the isolates, compared to 4.7%, 4.1%, and 5.9% for
plcA
,
plcB
, and
plcC
gene interruption, respectively. The association between the
plc
gene genotypes and disease presentation was adjusted for clustering using generalized estimating equations for both bivariate and multivariate analyses. After controlling for the genotypes of the
plcABC
genes and the host-related risk factors, interruption in the
plcD
gene remained significantly associated with extrathoracic tuberculosis (odds ratio, 3.27; 95% confidence interval, 1.32 to 8.14). The data suggest that the
plcD
gene might play a more important role in the pathogenesis of thoracic TB than it does in the pathogenesis of extrathoracic TB.
Comparison of the Sodium Hydroxide Specimen Processing Method with the C
18
-Carboxypropylbetaine Specimen Processing Method Using Independent Specimens with Auramine Smear, the MB/BacT Liquid Culture System, and the COBAS AMPLICOR MTB Test
Authors: Padilla Eduardo , Manterola José M. , González Victoria , Thornton Charles G. , Quesada M. Dolores , Sánchez M. Dolores , Pérez Miguel , Ausina Vicente 
Published: December 2005

ABSTRACT

A study was performed to diagnose tuberculosis by smear, culture, and nucleic acid amplification. The study was comprised of two independent arms. Each arm used a different specimen processing method; in one arm, all specimens were processed with
N
-acetyl-
l
-cysteine-sodium hydroxide, and in the other arm, all specimens were processed with C
18
-carboxypropylbetaine and lytic enzymes. In each arm, all processed sediments were split for analysis by auramine smear, by culture using the MB/BacT liquid culture system and solid media, and by nucleic acid amplification using the COBAS AMPLICOR MTB test. In the
N
-acetyl-
l
-cysteine-sodium hydroxide arm, 1,468 specimens were analyzed: 65 were smear positive; 88 and 42 were culture positive for
Mycobacterium tuberculosis
and nontuberculous mycobacteria, respectively; and 103 were PCR positive. Relative to cultures positive for
M. tuberculosis
, the sensitivity and specificity of the smear were 68.2% and 99.6%, respectively, and those of PCR were 75.0% and 97.3%, respectively. In the C
18
-carboxypropylbetaine study arm, 1,423 specimens were analyzed: 44 were smear positive; 82 and 31 were culture positive for
M. tuberculosis
and nontuberculous mycobacteria, respectively; and 91 were PCR positive. The sensitivity and specificity of the smear were 48.8% and 99.7%, respectively, and those of PCR were 78.0% and 98.0%, respectively. When the two arms were compared, C
18
-carboxypropylbetaine specimen processing significantly increased the number of smear-negative and culture-positive specimens and significantly increased the PCR sensitivity among this same group of specimens while at the same time significantly reducing the inhibition rate.
DNA Polymorphism and Molecular Subtyping of the Capsular Gene Cluster of Group B
Streptococcus
Authors: Manning Shannon D. , Lacher David W. , Davies H. Dele , Foxman Betsy , Whittam Thomas S. 
Published: December 2005

ABSTRACT

Serotyping and other phenotypic methods are often used to characterize the capsular polysaccharide of group B streptococci (GBS). We describe a capsular genotyping method that utilizes PCR of capsular polysaccharide synthesis genes (
cps
) and restriction enzyme digestion. This method facilitates the detection of DNA polymorphism in
cps
genes and correlates well with serotyping.
Frequency and Species Distribution of Gliotoxin-Producing
Aspergillus
Isolates Recovered from Patients at a Tertiary-Care Cancer Center
Authors: Lewis Russell E. , Wiederhold Nathan P. , Lionakis Michail S. , Prince Randall A. , Kontoyiannis Dimitrios P. 
Published: December 2005

ABSTRACT

Aspergillus
isolates (
n
= 103) collected from cancer patients were screened to determine the taxonomic distribution and quantity of gliotoxin production. Gliotoxin was detected in 93% of
Aspergillus fumigatus
, 75% of
A. niger
, 25% of
A. terreus
, and 4% of
A. flavus
cultures. Gliotoxin concentrations were highest in cultures of
A. fumigatus
.
The Role of 16S rRNA Gene Sequencing in Identification of Microorganisms Misidentified by Conventional Methods
Authors: Petti C. A. , Polage C. R. , Schreckenberger P. 
Published: December 2005

ABSTRACT

Traditional methods for microbial identification require the recognition of differences in morphology, growth, enzymatic activity, and metabolism to define genera and species. Full and partial 16S rRNA gene sequencing methods have emerged as useful tools for identifying phenotypically aberrant microorganisms. We report on three bacterial blood isolates from three different College of American Pathologists-certified laboratories that were referred to ARUP Laboratories for definitive identification. Because phenotypic identification suggested unusual organisms not typically associated with the submitted clinical diagnosis, consultation with the Medical Director was sought and further testing was performed including partial 16S rRNA gene sequencing. All three patients had endocarditis, and conventional methods identified isolates from patients A, B, and C as a
Facklamia
sp.,
Eubacterium tenue
, and a
Bifidobacterium
sp. 16S rRNA gene sequencing identified the isolates as
Enterococcus faecalis
,
Cardiobacterium valvarum
, and
Streptococcus mutans
, respectively. We conclude that the initial identifications of these three isolates were erroneous, may have misled clinicians, and potentially impacted patient care. 16S rRNA gene sequencing is a more objective identification tool, unaffected by phenotypic variation or technologist bias, and has the potential to reduce laboratory errors.
Evaluation of the LightCycler
Staphylococcus
M
GRADE
Kits on Positive Blood Cultures That Contained Gram-Positive Cocci in Clusters
Authors: Shrestha Nabin K. , Tuohy Marion J. , Padmanabhan Ravindran A. , Hall Gerri S. , Procop Gary W. 
Published: December 2005

ABSTRACT

We evaluated the Roche LightCycler
Staphylococcus
M
GRADE
kits to differentiate between
Staphylococcus aureus
and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing
S. aureus
), the assay was 100% sensitive and 98.44% specific for
S. aureus
and 100% sensitive and specific for coagulase-negative staphylococci.
Validation of Performance of Plastic versus Glass Bottles for Culturing Anaerobes from Blood in BacT/ALERT SN Medium
Authors: Mirrett Stanley , Joyce Maria J. , Reller L. Barth 
Published: December 2005

ABSTRACT
To validate performance, we compared the new plastic BacT/ALERT (bioMérieux, Durham, NC) SN bottle to the current glass SN bottle with samples of blood obtained for culture from adults and found them comparable for both recovery and speed of detection of microorganisms. We conclude that the safety advantage of plastic bottles can be achieved without compromising performance.
Molecular Identification of Adenoviruses in Clinical Samples by Analyzing a Partial Hexon Genomic Region
Authors: Casas I. , Avellon A. , Mosquera M. , Jabado O. , Echevarria J. E. , Campos R. H. , Rewers M. , Perez-Breña P. , Lipkin W. I. , Palacios G. 
Published: December 2005

ABSTRACTHere we present a system for adenovirus detection and genotyping based on PCR amplification and phylogenetic analysis of a conserved hexon gene fragment. The system was validated using 157 sequences (86 previously typed and 71 clinical samples) and correctly identified species and serotype in 100% and 84% of sequences, respectively. Known associations between specific serotypes and clinical syndromes are verified. Possible new associations are described to allow further independent testing.
Clinical Significance of Mites in Urine
Authors: Dini Leigh A. , Frean John A. 
Published: December 2005

ABSTRACT
We report a case where a mite egg found in urine caused diagnostic confusion. The possibility of gut or bladder mite infection should be entertained only after repeated identification of mites in urine or stool samples from a symptomatic patient with no other cause for the symptoms and where the possibilities of contamination and spurious infection have been excluded.
The G Protein–Gated Potassium CurrentIK,AChIs Constitutively Active in Patients With Chronic Atrial Fibrillation
Authors: Dobrev D. , Friedrich A. , Voigt N. , Jost N. , Wettwer E. , Christ T. , Knaut M. , Ravens U. 
Published: December 2005

Background—The molecular mechanism of increased background inward rectifier current (IK1) in atrial fibrillation (AF) is not fully understood. We tested whether constitutively active acetylcholine (ACh)-activatedIK,AChcontributes to enhanced basal conductance in chronic AF (cAF).Methods and Results—Whole-cell and single-channel currents were measured with standard voltage-clamp techniques in atrial myocytes from patients with sinus rhythm (SR) and cAF. The selectiveIK,AChblocker tertiapin was used for inhibition ofIK,ACh. Whole-cell basal current was larger in cAF than in SR, whereas carbachol (CCh)-activatedIK,AChwas lower in cAF than in SR. Tertiapin (0.1 to 100 nmol/L) reducedIK,AChin a concentration-dependent manner with greater potency in cAF than in SR (−logIC50: 9.1 versus 8.2;P<0.05). Basal current contained a tertiapin-sensitive component that was larger in cAF than in SR (tertiapin [10 nmol/L]-sensitive current at −100 mV: cAF, −6.7±1.2 pA/pF, n=16/5 [myocytes/patients] versus SR, −1.7±0.5 pA/pF, n=24/8), suggesting contribution of constitutively activeIK,AChto basal current. In single-channel recordings, constitutively activeIK,AChwas prominent in cAF but not in SR (channel open probability: cAF, 5.4±0.7%, n=19/9 versus SR, 0.1±0.05%, n=16/9;P<0.05). Moreover,IK1channel open probability was higher in cAF than in SR (13.4±0.4%, n=19/9 versus 11.4±0.7%, n=16/9;P<0.05) without changes in other channel characteristics.Conclusions—Our results demonstrate that larger basal inward rectifier K+current in cAF consists of increasedIK1activity and constitutively activeIK,ACh. Blockade ofIK,AChmay represent a new therapeutic target in AF.
Mechanism of the salutary effects of flutamide on intestinal myeloperoxidase activity following trauma-hemorrhage: up-regulation of estrogen receptor-β-dependent HO-1
Authors: Yu Huang-Ping , Choudhry Mashkoor A , Shimizu Tomoharu , Hsieh Ya-Ching , Schwacha Martin G , Yang Shaolong , Chaudry Irshad H 
Published: December 2005

Abstract
Hemeoxygenase (HO)-1 induction following adverse circulatory conditions is known to be protective, and precastrated males have less intestinal damage than sham-operated males following trauma-hemorrhage (T-H). Previous studies have also shown that administration of flutamide up-regulated estrogen receptor (ER) expression in males following T-H. We hypothesized that flutamide administration in males following T-H up-regulates HO-1 via an ER-dependent pathway and protects against intestinal injury. Male Sprague-Dawley rats underwent T-H [mean blood pressure (MBP) 40 mmHg for 90 min and then resuscitation]. A single dose of flutamide (25 mg/kg body weight), with or without an ER antagonist (ICI 182,780), a HO enzyme inhibitor [chromium-mesoporphyrin (CrMP)], or vehicle, was administered subcutaneously during resuscitation. At 2 h after T-H or sham operation, intestinal myeloperoxidase (MPO) activity, intercellular adhesion molecule (ICAM)-1, cytokine-induced neutrophil chemoattractant (CINC)-1, and CINC-3 levels were measured. Intestinal ER-α, ER-β, androgen receptor, and HO-1 mRNA/protein levels were also determined. Results showed that T-H increased intestinal MPO activity, ICAM-1, CINC-1, and CINC-3 levels. These parameters were improved significantly in the flutamide-treated rats subjected to T-H. Flutamide treatment increased intestinal HO-1 and ER-β mRNA/protein levels as compared with vehicle-treated T-H rats. Administration of the ER antagonist ICI 182,780 or the HO inhibitor CrMP prevented the flutamide-induced attenuation of shock-induced intestinal damage. Thus, the salutary effects of flutamide administration on attenuation of intestinal injury following T-H are mediated via up-regulation of ER-β-dependent HO-1 expression.