bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Serotype-Specific DNA Microarray for Identification of Some
Shigella
and Pathogenic
Escherichia coli
Strains
Authors: Li Yayue , Liu Dan , Cao Boyang , Han Weiqing , Liu Yanqun , Liu Fenxia , Guo Xi , Bastin David A. , Feng Lu , Wang Lei 
Published: December 2006

ABSTRACT

Shigella
and pathogenic
Escherichia coli
are major causes of human infectious diseases and are responsible for millions of cases of diarrhea worldwide every year. A convenient and rapid method to identify highly pathogenic serotypes of
Shigella
and
E. coli
is needed for large-scale epidemiologic study, timely clinical diagnosis, and reliable quarantine of the pathogens. In this study, a DNA microarray targeting O-serotype-specific genes was developed to detect 15 serotypes of
Shigella
and
E. coli
, including
Shigella sonnei
;
Shigella flexneri
type 2a;
Shigella boydii
types 7, 9, 13, 16, and 18;
Shigella dysenteriae
types 4, 8, and 10; and
E. coli
O55, O111, O114, O128, and O157. The microarray was tested against 186 representative strains of all
Shigella
and
E. coli
O serotypes, 38 clinical isolates, and 9 strains of other bacterial species that are commonly present in stool samples and was shown to be specific and reproducible. The detection sensitivity was 50 ng genomic DNA or 10
4
CFU per ml in mock stool specimens. This is the first report of a microarray for serotyping
Shigella
and pathogenic
E. coli
. The method has a number of advantages over traditional bacterial culture and antiserum agglutination methods and is promising for applications in basic microbiological research, clinical diagnosis, food safety, and epidemiological surveillance.
Candida pseudorugosa
sp. nov., a Novel Yeast Species from Sputum
Authors: Li Juan , Xu Ying-Chun , Bai Feng-Yan 
Published: December 2006

ABSTRACT

Two yeast strains, strains XH 1026 and XH 1164, isolated from the sputum of an intensive care unit patient with acute pneumonia, were originally identified as
Candida albicans
and
C. tropicalis
, respectively. Sequence analysis of the 26S rRNA gene D1/D2 domain and the internal transcribed spacer (ITS) region indicated that the two strains represent a novel yeast species closely related to
C. rogusa
. The name
Candida pseudorugosa
sp. nov. is therefore proposed (type strain, AS 2.3107 [CBS 10433]). The new species is able to grow at 42°C and is resistant or insusceptible to amphotericin B (MIC, 2 μg/ml), caspofungin (MIC, 64 μg/ml), itraconazole (MIC, 1 μg/ml), and nystatin (MIC, 16 μg/ml); dose-dependent susceptible to fluconazole (MIC, 16 μg/ml); and susceptible to flucytosine (MIC, 0.125 μg/ml) and voriconazole (MIC, 0.125 to 0.25 μg/ml). The code for
C. pseudorugosa
sp. nov. provided by the API 20C AUX system is identical to that for
C. rugosa
. The colonies of the new species on CHROMagar Candida appear blue-green, similar to those of
C. albicans
. In addition to the molecular method based on D1/D2 domain or ITS region sequencing, use of the combination of the API system and CHROMagar Candida is helpful for the correct identification of
C. pseudorugosa
sp. nov.
Detection of
Giardia lamblia
Antigens in Human Fecal Specimens by a Solid-Phase Qualitative Immunochromatographic Assay
Authors: Garcia Lynne S. , Garcia John Paul 
Published: December 2006

ABSTRACT

The SIMPLE-READ
Giardia
rapid assay (Medical Chemical Corporation) is a solid-phase qualitative immunochromatographic assay that detects
Giardia lamblia
in aqueous extracts of human fecal specimens. Testing 106
Giardia
-positive and 104
Giardia
-negative stool specimens yielded a sensitivity of 97.2% and a specificity of 100% for the SIMPLE-READ
Giardia
rapid assay.
Phylogenetic Comparisons Reveal Multiple Acquisitions of the Toxin Genes by Enterotoxigenic
Escherichia coli
Strains of Different Evolutionary Lineages
Authors: Turner Sue M. , Chaudhuri Roy R. , Jiang Zhi-Dong , DuPont Herbert , Gyles Carlton , Penn Charles W. , Pallen Mark J. , Henderson Ian R. 
Published: December 2006

ABSTRACT

Escherichia coli
is a diverse bacterial species which is widely distributed in the environment but also exists as a commensal and pathogen of different host species. Human intestinal pathogenic
E. coli
causes over 160 million cases of diarrhea and an estimated 1 million deaths per year. The majority of deaths are attributable to one pathovar of
E. coli
, namely, enterotoxigenic
E. coli
. The pathogenesis of enterotoxigenic
E. coli
is dependent on the production of a colonization factor to promote adhesion to the intestinal epithelium and the elaboration of heat-labile or heat-stable toxins which induce a secretory diarrhea. Despite the high morbidity and mortality associated with enterotoxigenic
E. coli
infection, little is known of the genetic background of this global pathogen. Here we demonstrate by multilocus sequence typing that enterotoxigenic
E. coli
isolates are present in all phylogenetic lineages of
E. coli
, indicating that acquisition of the toxin genes may be sufficient to generate an enterotoxigenic
E. coli
strain. In addition, screening of diarrheal isolates for the presence of additional genes previously associated with the virulence of enterotoxigenic
E. coli
revealed that they were not abundant. These observations have significant implications for disease epidemiology and for the design of effective vaccines.
Misidentification of a Mucoid Strain of
Salmonella enterica
Serotype Choleraesuis as
Hafnia alvei
by the Vitek GNI+ Card System
Authors: Wang Teresa K. F. , Yam Wing-Cheong , Yuen Kwok-Yung , Wong Samson S. Y. 
Published: December 2006

ABSTRACT

Nontyphoidal salmonellae are among the most common causes of bacterial gastroenteritis worldwide. They are also notable causes of extraintestinal infections, including bacteremia and vascular infections.
Salmonella enterica
serotype Choleraesuis is typically associated with invasive infections. We report a patient who had an infected intra-abdominal aortic aneurysm due to an unusually mucoid strain of
Salmonella enterica
serotype Choleraesuis. The isolate was erroneously identified as
Hafnia alvei
by the Vitek GNI+ card system. A blood culture isolate taken from the same patient 9 months earlier was also identified as
H. alvei
by the Vitek GNI+ card system. Despite an apparent cure with intravenous amoxicillin-clavulanic acid at that time, the
Salmonella
infection had not been cleared and manifested as a ruptured infected abdominal aortic aneurysm. Repeated passage of the strain yielded nonmucoid colonies, which were correctly identified by the API and PHOENIX systems. The isolates from the aneurysm and the former bacteremic episode were found to be identical using pulsed field gel electrophoresis. The fallibility of automated bacterial identification systems is highlighted. Such errors are especially important for isolates in which in vitro antibiotic susceptibility testing does not correlate with the clinical success of treatment, as illustrated by
Salmonella
infections.
Use of Smear-Positive Samples To Assess the PCR-Based Genotype MTBDR Assay for Rapid, Direct Detection of the
Mycobacterium tuberculosis
Complex as Well as Its Resistance to Isoniazid and Rifampin
Authors: Somoskovi Akos , Dormandy Jillian , Mitsani Dimitra , Rivenburg Jeremy , Salfinger Max 
Published: December 2006

ABSTRACT

Isoniazid (INH) and rifampin (RIF) are two of the most important antituberculosis drugs, and resistance to both of these drugs can often result in treatment failure and fatal clinical outcome. Resistance to these two first-line drugs is most often attributed to mutations in the
katG
,
inhA
, and
rpoB
genes. Historically, the identification and testing of the susceptibility of
Mycobacterium tuberculosis
complex (MTBC) strains takes weeks to complete. Rapid detection of resistance using the PCR-based Genotype MTBDR assay (Hain Lifescience GmbH, Nehren, Germany) has the potential to significantly shorten the turnaround time from specimen receipt to reporting of results of susceptibility testing. Therefore, the aim of the present study was to determine (i) the sensitivity and accuracy of the Genotype MTBDR assay for the detection of MTBC strains and (ii) the ability of the assay to detect the presence of INH and RIF resistance-associated mutations in
katG
and
rpoB
from samples taken directly from smear-positive clinical specimens. The results were compared with those obtained with the reference BACTEC 460TB system combined with standard DNA sequencing analysis methods for
katG
,
inhA
, and
rpoB
. A total of 92 drug-resistant and 51 pansusceptible smear-positive specimens were included in the study. The Genotype MTBDR assay accurately and rapidly detected MTBC strains in 94.4% of the 143 specimens and showed a sensitivity of 94.4% for
katG
and 90.9% for
rpoB
when used directly on smear-positive specimens. The assay correctly identified INH resistance in 48 (84.2%) of the 57 specimens containing strains with resistance to high levels of INH (0.4 μg/ml) and RIF resistance in 25 (96.2%) of the 26 specimens containing RIF-resistant strains.
Bacterial Identification, Clinical Significance, and Antimicrobial Susceptibilities of
Acinetobacter ursingii
and
Acinetobacter schindleri
, Two Frequently Misidentified Opportunistic Pathogens
Authors: Dortet Laurent , Legrand Patrick , Soussy Claude-James , Cattoir Vincent 
Published: December 2006

ABSTRACT

The species belonging to the
Acinetobacter
genus are currently reported as opportunistic pathogens in hospitalized patients with underlying predispositions. However, except for the
Acinetobacter calcoaceticus-Acinetobacter baumannii
complex, the identification of other species is frequently unreliable, especially for
Acinetobacter ursingii
and
Acinetobacter schindleri
, newly described in 2001. Thus, the clinical significance, phenotypic features, and antimicrobial susceptibilities of these two misidentified species remain unclear. Of 456
Acinetobacter
sp. clinical strains isolated from 2002 to 2005 in Henri Mondor Hospital, 15 isolates (10
A. ursingii
and 5
A. schindleri
isolates) were studied. They were characterized using a phenotypic approach (API 20 NE and VITEK 2 systems), 16S rRNA gene sequencing, and susceptibility to antimicrobial agents with evaluation of impact in clinical relevance. The two corresponding type strains were also included for comparison. All isolates were identified to the species level using molecular tools, whereas the phenotypic methods remained unreliable due to the absence of these two species in the manufacturers' databases. However, the API 20 NE system appeared to be a reasonably reliable phenotypic alternative for the identification of
A. ursingii
when the numerical code 0000071 was found. Conversely, no discriminative phenotypic alternative existed for
A. schindleri
isolates. Concerning antimicrobial susceptibility,
A. ursingii
strains appeared to be more resistant to antibiotics than
A. schindleri
strains, which could imply therapeutic consequences. Finally, the prevalence of infections caused by
A. ursingii
and
A. schindleri
(representing 9.7% and 4.8% of non-
A. calcoaceticus-A. baumannii
complex strains, respectively) seems to be underestimated.
Identification of a Novel, Invasive, Not-Yet-Cultivated
Treponema
sp. in the Large Intestine of Pigs by PCR Amplification of the 16S rRNA Gene
Authors: Mølbak Lars , Klitgaard Kirstine , Jensen Tim K. , Fossi Marja , Boye Mette 
Published: December 2006

ABSTRACT

Laser capture microdissection in combination with fluorescent in situ hybridization was used to identify an unknown species of spirochetes from the pig colonic mucosa. The 16S rRNA gene was PCR amplified, and the closest related type strain was
Treponema bryantii
T
(90.1%). The spirochete, here named “
Candidatus
Treponema suis,
”
was associated with colitis, including invasion of the surface epithelium as well as superficial parts of the mucosa.
Monitoring of Stool Microbiota in Subjects with Diarrhea Indicates Distortions in Composition
Authors: Mai Volker , Braden Christopher R. , Heckendorf Jill , Pironis Baiba , Hirshon Jon Mark 
Published: December 2006

ABSTRACT
We utilized denaturing gradient gel electrophoresis profiling to survey stool microbiota in 175 persons with diarrhea and 113 asymptomatic persons in a diarrhea surveillance study. Compared with healthy controls, the microbiota profiles in diarrhea cases more frequently exhibited decreased diversity and strong bands indicating the overgrowth of selected bacteria or bacterial groups.
Pneumonia and Septicemia Caused by
Burkholderia thailandensis
in the United States
Authors: Glass Mindy B. , Gee Jay E. , Steigerwalt Arnold G. , Cavuoti Dominick , Barton Theresa , Hardy R. Doug , Godoy Daniel , Spratt Brian G. , Clark Thomas A. , Wilkins Patricia P. 
Published: December 2006

ABSTRACT

Burkholderia thailandensis
is closely related to
Burkholderia pseudomallei
, the causative agent of melioidosis. It is generally considered avirulent and previously has been reported to occur only in Southeast Asia. We report the first case of pneumonia and septicemia caused by
B. thailandensis
in the United States.
Assessing the Genetic Diversity of the Aldolase Genes of
Plasmodium falciparum
and
Plasmodium vivax
and Its Potential Effect on Performance of Aldolase-Detecting Rapid Diagnostic Tests
Authors: Lee Nelson , Baker Joanne , Bell David , McCarthy James , Cheng Qin 
Published: December 2006

ABSTRACT

Malaria-specific rapid diagnostic tests (RDTs) targeting aldolase show highly variable sensitivities. We assessed diversity in
Plasmodium falciparum
and
P. vivax
aldolases by sequencing the coding genes from parasites of various origins. The results show that aldolases are highly conserved, indicating that antigenic diversity is not a cause of variable RDT sensitivity.
Array-Based Identification of Species of the GeneraAbiotrophia,Enterococcus,Granulicatella,andStreptococcus
Authors: Tung Sheng Kai , Teng Lee Jene , Vaneechoutte Mario , Chen Hung Mo , Chang Tsung Chain 
Published: December 2006

ABSTRACTSome species of enterococci and streptococci are difficult to differentiate by phenotypic traits. The feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. The aim of this study was to expand the array to identify species ofAbiotrophia(1 species),Enterococcus(18 species),Granulicatella(3 species), andStreptococcus(31 species and 6 subspecies). The method consisted of PCR amplification of the ribosomal DNA intergenic spacer (ITS) regions, followed by hybridization of the digoxigenin-labeled PCR products to a panel of oligonucleotide probes (16- to 30-mers) immobilized on a nylon membrane. Probes could be divided into three categories: species specific, group specific, and supplemental probes. All probes were designed either from the ITS regions or from the 3′ ends of the 16S rRNA genes. A collection of 312 target strains (162 reference strains and 150 clinical isolates) and 73 nontarget strains was identified by the array. Most clinical isolates were isolated from blood cultures or deep abscesses, and only those strains having excellent species identification with the Rapid ID 32 STREP system (bioMérieux Vitek, Taipei, Taiwan) were used for array testing. The test sensitivity and specificity of the array were 100% (312/312) and 98.6% (72/73), respectively. The whole procedure of array hybridization took about 8 h, starting from isolated colonies, and the hybridization patterns could be read by the naked eye. The oligonucleotide array is accurate for identification of the above microorganisms and could be used as a reliable alternative to phenotypic identification methods.
Brain Abscess Caused by
Streptococcus pyogenes
in a Previously Healthy Child
Authors: Dehority Walter , Uchiyama Satoshi , Khosravi Arya , Nizet Victor 
Published: December 2006

ABSTRACT

Responsible for many childhood diseases, group A
Streptococcus
(GAS) is a rare cause of central nervous system infections. We report the case of a previously healthy boy with brain abscesses caused by M/
emm
type 12 GAS and review the case in the context of the published literature and recent epidemiological data.
Evaluation of a New Chromogenic Medium, MRSA
Select
, for Detection of Methicillin-Resistant
Staphylococcus aureus
Authors: Louie Lisa , Soares Deirdre , Meaney Helen , Vearncombe Mary , Simor Andrew E. 
Published: December 2006

ABSTRACT

We compared MRSA
Select
to mannitol-salt agar with 8 μg/ml cefoxitin for the detection of methicillin-resistant
Staphylococcus aureus
(MRSA) from 6,199 clinical samples submitted for MRSA screening. The sensitivities and specificities of MRSA
Select
and mannitol-salt agar with cefoxitin were 98% and 92% versus 90% and 78%, respectively (
P
< 0.0001). Most (96%) MRSA were detected after overnight incubation using MRSA
Select
.
Rapid Screening of Topoisomerase Gene Mutations by a Novel Melting Curve Analysis Method for Early Warning of Fluoroquinolone-Resistant
Streptococcus pneumoniae
Emergence
Authors: Fukushima Kazuko Y. , Hirakata Yoichi , Sugahara Kazuyuki , Yanagihara Katsunori , Kondo Akira , Kohno Shigeru , Kamihira Shimeru 
Published: December 2006

ABSTRACT

We developed a real-time PCR assay combined with melting curve analysis for rapidly genotyping quinolone resistance-determining regions (QRDR) of topoisomerase genes in
Streptococcus pneumoniae
. This assay was not only accurate for the screening of fluoroquinolone (FQ) resistance but also relevant as an early warning system for detecting preexisting single QRDR mutations.
Emergence of Ofloxacin Resistance in
Mycobacterium tuberculosis
Clinical Isolates from China as Determined by
gyrA
Mutation Analysis Using Denaturing High-Pressure Liquid Chromatography and DNA Sequencing
Authors: Shi Ruiru , Zhang Jianyuan , Li Chuanyou , Kazumi Yuko , Sugawara Isamu 
Published: December 2006

ABSTRACT

A high rate of double point mutations in
gyrA
(56% of 87 ofloxacin-resistant
Mycobacterium tuberculosis
clinical isolates) indicates the emergence of fluoroquinolone resistance. This is the first report to describe denaturing high-pressure liquid chromatography analysis of mutations in
gyrA
of
M. tuberculosis
in a large number of clinical isolates.
Evaluation ofEntamoeba histolyticaAntigen and Antibody Point-of-Care Tests for the Rapid Diagnosis of Amebiasis
Authors: Leo Megan , Haque Rashidul , Kabir Mamun , Roy Shantanu , Lahlou Rita Marie , Mondal Dinesh , Tannich Egbert , Petri William A. 
Published: December 2006

ABSTRACTThe bedside diagnosis of amebiasis could improve patient care. In Bangladesh and Vietnam, a novel and simple-to-useEntamoeba histolyticarapid antigen test had 97% sensitivity and 100% specificity compared to the results of a standard enzyme-linked immunosorbent assay antigen detection method, and a rapid antibody test had 89 to 100% sensitivity and 89 to 95% specificity.
Escherichia coli
Isolates Associated with Uncomplicated and Complicated Cystitis and Asymptomatic Bacteriuria Possess Similar Phylogenies, Virulence Genes, and O-Serogroup Profiles
Authors: Takahashi Akira , Kanamaru Sojun , Kurazono Hisao , Kunishima Yasuharu , Tsukamoto Taiji , Ogawa Osamu , Yamamoto Shingo 
Published: December 2006

ABSTRACT

The genetic and serological characteristics of
Escherichia coli
isolates from patients with uncomplicated cystitis (UC), complicated cystitis (CC), and complicated asymptomatic bacteriuria (CASB) were determined. Phylogenetic group B2 was predominant in all categories. The prevalences of 14 out of 18 virulence factor genes were similar among the three categories, while
pap
,
iha
,
ompT
, and
PAI
were more frequently seen in isolates associated with UC than CC or CASB.
PREDICTING US 2001 RECESSION, COMPOSITE LEADING ECONOMIC INDICATORS, STRUCTURAL CHANGE AND MONETARY POLICY
Authors: MOSTAGHIMI MEHDI 
Published: December 2006

In an attempt to predict a peak in the US economy using a classical statistical decision methodology and a Bayesian methodology and using the 1996 revised composite leading economic indicators (CLI), it is learned that the Bayesian models have generally outperformed the classical statistical ones and, among the Bayesian models, the two using two and three consecutive CLI growth rates are superior in reliability and in accuracy. These two models, however, failed to correctly predict the 2001 recession. In investigating the reasons behind their failures, we learned that: (1) if the concurrent data for the economic structure of 1983–1999 are used for the prediction, they have also been able to predict the 2001 recession correctly, but their overall reliability is not as strong as before; (2) given the overwhelming weight of the monetary policy tools in the CLI-1996 design and the combination of the economic and political events in the year 2000, the less than expected effectiveness of the monetary policy since 2001 has contributed to this failure; and (3) a possible structural change in the US economy since 2000 has also contributed to this prediction failure.
Novel in vivo imaging shows up-regulation of death receptors by paclitaxel and correlates with enhanced antitumor effects of receptor agonist antibodies
Authors: Gong Jing , Yang David , Kohanim Saady , Humphreys Robin , Broemeling Lyle , Kurzrock Razelle 
Published: December 2006

Abstract
Susceptibility to apoptosis by tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) is mediated through cognate death receptor signaling. We hypothesized that auto-amplification of this apparatus would enhance antitumor effects in vivo and could be optimized using the results obtained from novel imaging techniques. We therefore imaged mice bearing human colorectal cancer (Colo205) tumor xenografts with HGS-ETR1 and HGS-ETR2 agonist antibodies to TRAIL receptor-1 (TRAIL-R1) and TRAIL-R2, respectively, after radiolabeling the antibodies. Paclitaxel significantly increased in vivo expression of TRAIL-R1 and TRAIL-R2 in a time-dependent manner. The imaging results were confirmed by immunoblots for steady-state protein levels (&gt;20-fold increase in TRAIL-R1 and TRAIL-R2 levels in tumor xenografts by 48 h after paclitaxel administration). TRAIL-R1 and TRAIL-R2 mRNA expression did not change, suggesting that these effects were posttranscriptional. Sequential treatment with paclitaxel followed by HGS-ETR1 or HGS-ETR2 after 48 h resulted in markedly enhanced antitumor activity against Colo205 mouse xenografts. Our experiments suggest that sequential taxane treatment followed by TRAIL-R agonist antibodies could be applied in the clinic, and that novel imaging techniques using radiolabeled receptor antibodies may be exploitable to optimize sequence timing and patient selection. [Mol Cancer Ther 2006;5(12):2991–3000]