bluuebunny/crossref_metadata_2025 huggingface dataset:
Blood Culture Contamination in Tanzania, Malawi, and the United States: a Microbiological Tale of Three Cities
Authors: Archibald Lennox K. , Pallangyo Kisali , Kazembe Peter , Reller L. Barth
Published: December 2006

We conducted retrospective, comparative analyses of contamination rates for cultures of blood obtained in the emergency rooms of Muhimbili National Hospital (MNH) in Dar es Salaam, Tanzania; Lilongwe Central Hospital (LCH) in central Malawi; and the Duke University Medical Center (DUMC) in the United States. None of the emergency room patients had indwelling intravascular devices at the time that the blood samples for cultures were obtained. In addition, we reviewed the contamination rates for a cohort of patients already hospitalized in the DUMC inpatient medical service, most of whom had indwelling intravascular devices. The bloodstream infection rates among the patients at MNH (
n
= 513) and LCH (
n
= 486) were similar (∼28%); the contamination rates at the two hospitals were 1.3% (7/513) and 0.8% (4/486), respectively. Of 54 microorganisms isolated from cultures of blood collected in the DUMC emergency room, 26 (48%) were identified as skin contaminants. Cultures of blood collected in the DUMC emergency room were significantly more likely to yield growth of contaminants than the cultures of blood collected in the emergency rooms at MNH and LCH combined (26/332 versus 11/1,003;
P
< 0.0001) or collected in the DUMC inpatient medical service (26/332 versus 7/283;
P
< 0.01). For the MNH and LCH blood cultures, lower contamination rates were observed when skin was disinfected with isopropyl alcohol plus tincture of iodine rather than isopropyl alcohol plus povidone-iodine. In conclusion, blood culture contamination was minimized in sub-Saharan African hospitals with substantially limited resources through scrupulous attention to aseptic skin cleansing and improved venipuncture techniques. Application of these principles when blood samples for culture are obtained in U.S. hospital emergency rooms should help mitigate blood culture contamination rates and the unnecessary microbiology workup of skin contaminants.
Prevalence and Sequence Variants of IS
481
in
Bordetella bronchiseptica
: Implications for IS
481
-Based Detection of
Bordetella pertussis
Authors: Register Karen B. , Sanden Gary N.
Published: December 2006

We report the prevalence in
Bordetella bronchiseptica
of IS
481
, a frequent target for diagnosis of
Bordetella pertussis
, as approximately 5%. However, PCR amplicons of the predicted size were detectable in 78% of IS
481
-negative strains. Our results suggest that PCR targeting IS
481
may not be sufficiently specific for reliable identification of
B. pertussis
.
First Case of
Staphylococcus pseudintermedius
Infection in a Human
Authors: Van Hoovels Lieve , Vankeerberghen Anne , Boel An , Van Vaerenbergh Kristien , De Beenhouwer Hans
Published: December 2006

We present the first clinical report of a
Staphylococcus pseudintermedius
infection in a human. Biochemically,
S. pseudintermedius
can be easily misidentified as
S. aureus
. Therefore, the final microbiological identification requires the combination of phenotypic and genotypic tests.
Relationship between Preexisting Anti-Varicella-Zoster Virus (VZV) Antibody and Clinical VZV Reactivation in Hematopoietic Stem Cell Transplantation Recipients
Authors: Onozawa Masahiro , Hashino Satoshi , Takahata Mutsumi , Fujisawa Fumie , Kawamura Takahito , Nakagawa Masao , Kahata Kaoru , Kondo Takeshi , Ota Shuichi , Tanaka Junji , Imamura Masahiro , Asaka Masahiro
Published: December 2006

Reactivation of latent varicella-zoster virus (VZV), presenting as localized zoster or as disseminated infection, is a common and potentially serious complication in hematopoietic stem cell transplantation (HSCT) recipients. We retrospectively studied anti-VZV immunoglobulin G titers by the immune adherence hemagglutination method after HSCT and also studied VZV DNA by real-time PCR during clinical VZV reactivation using cryopreserved serum samples. No significant difference was found between anti-VZV titers in 13 patients with VZV infection (localized zoster in 11 patients and disseminated zoster in 2 patients) and in 13 subjects without VZV infection at each time point after HSCT. Preexisting anti-VZV titers of disseminated zoster cases tended to be lower than those of localized zoster cases (
P
= 0.10). Serum VZV DNA copy numbers at the onset of disseminated zoster cases tended to be higher than those of localized zoster cases (
P
= 0.09). A strong inverse correlation was found between preexisting anti-VZV titer and serum VZV DNA at onset (
r
= −0.90,
P
= 0.006). In HSCT recipients, preexisting antibody does not prevent the development of VZV reactivation but may contribute to decreased viral load at onset, resulting in a mild clinical course.
Identification of New Genetic Regions More Prevalent in Nontypeable
Haemophilus influenzae
Otitis Media Strains than in Throat Strains
Authors: Xie Jingping , Juliao Patricia C. , Gilsdorf Janet R. , Ghosh Debashis , Patel Mayuri , Marrs Carl F.
Published: December 2006

Nontypeable (NT)
Haemophilus influenzae
strains cause significant respiratory illness and are isolated from up to half of middle ear aspirates from children with acute otitis media. Previous studies have identified two genes,
lic2B
and
hmwA
, that are associated with NT
H. influenzae
strains isolated from the middle ears of children with otitis media but that are not associated with NT
H. influenzae
strains isolated from the throats of healthy children, suggesting that they may play a role in virulence in otitis media. In this study, genomic subtraction was used to identify additional genetic regions unique to middle ear strains. The genome of NT
H. influenzae
middle ear strain G622 was subtracted from that of NT
H. influenzae
throat strain 23221, and the resultant gene regions unique to the middle ear strain were identified. Subsequently, the relative prevalence of the middle ear-specific gene regions among a large panel of otitis media and throat strains was determined by dot blot hybridization. By this approach, nine genetic regions were found to be significantly more prevalent in otitis media strains. Classification tree analysis of
lic2B
,
hmwA
, and the nine new potential otitis media virulence genes revealed two
H. influenzae
pathotypes associated with otitis media.
Direct Detection of
Mycobacterium tuberculosis
Complex DNA and Rifampin Resistance in Clinical Specimens from Tuberculosis Patients by Line Probe Assay
Authors: Traore Hamidou , van Deun Armand , Shamputa Isdore Chola , Rigouts Leen , Portaels Françoise
Published: December 2006

The INNO-LiPA.Rif TB test (LiPA) has only been applied to a limited number of clinical specimens. To assess the utility of this test for detecting
Mycobacterium tuberculosis
complex DNA and rifampin (RMP) resistance, 420 sputum samples comprising specimens from untreated (
n
= 160) and previously treated (
n
= 260) patients from 11 countries in Asia, Africa, Europe, and Latin America were tested. DNA was extracted from sputum samples by using a modification of the Boom's method, while the
rpoB
core region was amplified by nested PCR. The results were analyzed in conjunction with those obtained by Ziehl-Neelsen (ZN) microscopy and by culture on solid media. The LiPA test was positive for
M. tuberculosis
complex DNA in 389 (92.9%) specimens, including 92.0% (286 of 311) ZN-positive and 94.5% (103 of 109) ZN-negative specimens. Of these, 30.6% were RMP resistant. In contrast, 74.3% of the specimens were positive for
M. tuberculosis
by culture, and 30.8% of them were RMP resistant. LiPA detected
M. tuberculosis
complex DNA in 92.4% (110 of 119) of the culture-positive and 100.0% (41 of 41) of the culture-negative specimens from untreated patients. There was a 99.6% concordance between the RMP resistance as determined by culture and by the LiPA test. With an optimal DNA extraction method, LiPA allows rapid detection of
M. tuberculosis
complex DNA and RMP resistance directly from sputum specimens. LiPA can still provide useful information when culture fails for various reasons. The rapid availability of this information is necessary to adjust patient treatment and avoid the risk of amplification of drug resistance.
Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical Laboratory
Authors: Simmon Keith E. , Croft Ann C. , Petti Cathy A.
Published: December 2006

Laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. With the emergence of 16S rRNA gene sequencing as an identification tool, we evaluated the usefulness of SmartGene IDNS, a 16S rRNA sequence database and software program for microbial identification. Identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the SmartGene and MicroSeq databases. Of 300 isolates, SmartGene identified 295 (98%) to the genus level and 262 (87%) to the species level, with 5 (2%) being inconclusive. MicroSeq identified 271 (90%) to the genus level and 223 (74%) to the species level, with 29 (10%) being inconclusive. SmartGene and MicroSeq agreed on the genus for 233 (78%) isolates and the species for 212 (71%) isolates. Conventional methods identified 291 (97%) isolates to the genus level and 208 (69%) to the species level, with 9 (3%) being inconclusive. SmartGene, MicroSeq, and conventional identifications agreed for 193 (64%) of the results. Twenty-seven microorganisms were not represented in MicroSeq, compared to only 2 not represented in SmartGene. Overall, SmartGene IDNS provides comprehensive and accurate identification of a diverse group of bacteria and has the added benefit of being a user-friendly program that can be modified to meet the unique needs of clinical laboratories.
Simultaneous Quantification and Genotyping of Hepatitis B Virus for Genotypes A to G by Real-Time PCR and Two-Step Melting Curve Analysis
Authors: Liu Wen-Chun , Mizokami Masashi , Buti Maria , Lindh Magnus , Young Kung-Chia , Sun Koun-Tem , Chi Yun-Chan , Li Hsi-Hsien , Chang Ting-Tsung
Published: December 2006

Both the viral titer and the genotype significantly determine clinical outcomes and responses to antiviral treatment in chronic hepatitis B virus (HBV) infection. A method was developed for large-scale A-to-G genotyping with simultaneous viral quantification. The assay was run on a LightCycler instrument using hybridization probes. The genotype was determined from the melting points of the probes in a two-step manner. Set 1 amplicons differentiated genotypes B, E, and F from A, C, D, and G and simultaneously quantified viremia by real-time PCR. Melting curve analysis using the set 2-1 amplicon or the set 2-2 amplicon reaction mixture was then used to differentiate these genotype groups into single genotypes. HBV DNA quantification was consistent with that of the Amplicor assay and linear in a range from 10
2
to 10
13
copies/ml. By comparison with the restriction fragment length polymorphism method, 92.3% of 441 samples were accurately genotyped by the current assay. The method should be useful for genotyping and quantification of HBV DNA in areas where all genotypes exist.
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

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

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

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

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

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

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

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

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

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

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

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

Some 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

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

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

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

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

The 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

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.
Evidence of strong two-particle and three-particle dynamical correlation in compound multiplicity distribution in nucleus–nucleus interactions at 4.5 AGeV
Authors: Ghosh Dipak , Deb Argha , Biswas Subrata , Mandal Pasupati , Bhattacharyya Swarnapratim , Mallick Asok Kumar
Published: December 2006

This paper reports an investigation of two- and three-particle dynamical correlation in multiparticle production processes in terms of compound multiplicity (proton and pion) distributions. The data have been taken from 24Mg–AgBr and 12C–AgBr interactions at 4.5 AGeV. The experimental results are compared with those of Monte Carlo simulated events, assuming an independent emission of the compound multiplicity. The data exhibit strong two- and three-particle correlation in both forward and backward hemispheres in emission angle space for both data sets. PACS Nos.: 25.75–q, 24.60 Ky
Onset of convection in a viscoelastic-fluid-saturated sparselypacked porous layer using a thermal nonequilibrium model
Authors: Shivakumara I S , Malashetty M S , Chavaraddi K B
Published: December 2006

A linear stability analysis is carried out to study viscoelastic fluid convection in a sparsely packed horizontal porous layer heated from below. The viscoelastic fluid flow in the porous medium is modeled by using a modified Brinkman–Lapwood-extended Darcy model with the fluid viscosity different from the effective viscosity, which accounts for the viscoelastic properties and frictiondue to macroscopic shear. Besides, a two-field model for temperature each representing the solid and fluid phases separately is employed. The conditions for the occurrence of direct and Hopf bifurcations of the thermal convective instability are obtained analytically. It is shown that Hopf bifurcation occurs only if the retardation to relaxation-time ratio, Λ, is less than unity and the elasticity parameter, Γ, exceeds a threshold. Further, the effects of the viscoelastic parameters and the thermal nonequilibrium on the onset of convection are analyzed in detail.PACS No.: 47.55.–pb
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.
HOUSEHOLD HETEROGENEITY AND OPTIMAL INTER-TEMPORAL PRICING FOR A DURABLE-GOOD MONOPOLY
Authors: KOH WINSTON T.H.
Published: December 2006

In this paper, I extend the analysis in Koh (2006) to examine the optimality of inter-temporal price discrimination for a durable-good monopoly in a model where infinitely-lived households consume both durable goods and a stream of non-durable goods subject to different inter-temporal budget constraints. I also consider the multi-dimensional setting where households differ in both inter-temporal budget constraints and the utilities they derive from the consumption of the durable good.
Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms
Authors: Ghirardi Maria L. , Posewitz Matthew C. , Maness Pin-Ching , Dubini Alexandra , Yu Jianping , Seibert Michael
Published: December 2006

The photobiological production of H2 gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H2 production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O2 sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications.
Marital and Family Processes in the Context of Alcohol Use and Alcohol Disorders
Authors: Leonard Kenneth E. , Eiden Rina D.
Published: December 2006

Alcohol use is often part of the fabric of marriage and family life, and although it is associated with certain positive effects, excessive drinking and alcohol disorders can exert a negative effect on the marital development and on the development of children in the context of the family. This review considers evidence that alcohol influences and is influenced by marital/family processes, including transitions into marriage and parenthood, marital satisfaction, marital violence, parenting, and child development. The review discusses the importance of antisocial behavior and the need to examine women's drinking, and the joint impact of men's and women's drinking on marital/family processes. The review highlights the lack of studies in certain key areas, including the link between discordant drinking and violence and marital satisfaction, the role of alcohol in child neglect, and the potential role of marital conflict as a mediator or moderator of the relationship between alcohol and child functioning.
Climate Over the Past Two Millennia
Authors: Mann Michael E.
Published: December 2006

To assess the significance of modern climate change, it is essential to place recent observed changes in a longer-term context. This review assesses the evidence from both “proxy” climate data and theoretical climate model simulations with regard to the nature and causes of climate variability over a time interval spanning roughly the past two millennia. Evidence is reviewed for changes in temperature, drought, and atmospheric circulation over this timescale. Methods for reconstructing past climate from proxy data are reviewed and comparisons with the results of climate modeling studies are provided. The assessment provided affirms the role of natural (solar and volcanic) radiative forcing in past changes in large-scale mean temperature changes and in dynamical modes of climate variability such as the North Atlantic Oscillation (NAO) and El Niño/Southern Oscillation (ENSO) influencing large-scale climate. At hemispheric scales, late twentieth century warmth appears unprecedented in the context of at least the past 2000 years. This anomalous warmth can only be explained by modern anthropogenic forcing.
The Biology of NKT Cells
Authors: Bendelac Albert , Savage Paul B. , Teyton Luc
Published: December 2006

Recognized more than a decade ago, NKT cells differentiate from mainstream thymic precursors through instructive signals emanating during TCR engagement by CD1d-expressing cortical thymocytes. Their semi-invariant αβ TCRs recognize isoglobotrihexosylceramide, a mammalian glycosphingolipid, as well as microbial α-glycuronylceramides found in the cell wall of Gram-negative, lipopolysaccharide-negative bacteria. This dual recognition of self and microbial ligands underlies innate-like antimicrobial functions mediated by CD40L induction and massive Th1 and Th2 cytokine and chemokine release. Through reciprocal activation of NKT cells and dendritic cells, synthetic NKT ligands constitute promising new vaccine adjuvants. NKT cells also regulate a range of immunopathological conditions, but the mechanisms and the ligands involved remain unknown. NKT cell biology has emerged as a new field of research at the frontier between innate and adaptive immunity, providing a powerful model to study fundamental aspects of the cell and structural biology of glycolipid trafficking, processing, and recognition.
Isomerization Through Conical Intersections
Authors: Levine Benjamin G. , Martínez Todd J.
Published: December 2006

The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.
Gas-Phase Spectroscopy of Biomolecular Building Blocks
Authors: de Vries Mattanjah S. , Hobza Pavel
Published: December 2006

Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.
PGJ2-stimulated β-cell apoptosis is associated with prolonged UPR activation
Authors: Chambers Kari T. , Weber Sarah M. , Corbett John A.
Published: December 2006

Peroxisome proliferator-activated receptor-γ (PPARγ) ligands have been shown to possess anti-inflammatory properties that include the inhibition of transcription factor activation and the expression of inflammatory genes. Using pancreatic β-cells, we have shown that PPARγ ligands such as 15-deoxy-Δ12,14-prostaglandin J2(PGJ2) attenuate interferon-γ-induced signal transducer and activator of transcription 1 activation and interleukin (IL)-1β-induced nuclear factor-κB activation by a pathway that correlates with endoplasmic reticulum stress and the induction of the unfolded protein response (UPR). The UPR is a conserved cellular response activated by a number of cell stressors and is believed to alleviate the stress and promote cell survival. However, prolonged activation of the UPR results in cellular death by apoptosis. In this report, we have examined the effects of PGJ2on UPR activation and the consequences of this activation on cell survival. Consistent with induction of a cell death pathway, treatment of rat islets and RINm5F cells for 24 h with PGJ2results in caspase-3 activation and caspase-dependent β-cell death. The actions of these ligands do not appear to be selective for β-cells, because PGJ2stimulates macrophage apoptosis in a similar fashion. Associated with cell death is the enhanced phosphorylation of eukaryotic initiation factor 2α (eIF2α), and in cells expressing a mutant of eIF2α that cannot be phosphorylated, the stimulatory actions of PGJ2on caspase-3 activation are augmented. These findings suggest that, whereas PGJ2-induced UPR activation is associated with an inhibition of cytokine signaling, prolonged UPR activation results in cell death, and that eIF2α phosphorylation may function in a protective manner to attenuate cell death.
Effects of PYY1–36and PYY3–36on appetite, energy intake, energy expenditure, glucose and fat metabolism in obese and lean subjects
Authors: Sloth Birgitte , Holst Jens Juul , Flint Anne , Gregersen Nikolaj Ture , Astrup Arne
Published: December 2006

Peptide YY (PYY)3–36has been shown to produce dramatic reductions in energy intake (EI), but no human data exist regarding energy expenditure (EE), glucose and fat metabolism. Nothing is known regarding PYY1-36. To compare effects of PYY1–36and PYY3–36on appetite, EI, EE, insulin, glucose and free fatty acids (FFA) concentrations, 12 lean and 12 obese males participated in a blinded, randomized, crossover study with 90-min infusions of saline, 0.8 pmol·kg−1·min−1PYY1–36and PYY3–36. Only four participants completed PYY3–36infusions because of nausea. Subsequently, six lean and eight obese participants completed 0.2 pmol·kg−1·min−1PYY3–36and 1.6 pmol·kg−1·min−1PYY1–36infusions. PYY3–36at 0.8 pmol·kg−1·min−1produced reduced EI, lower ratings of well-being, increases in FFA, postprandial glucose (only 0.8 pmol·kg−1·min−1PYY3–36) and insulin concentrations, as well as heart rate and EE (only 0.8 pmol·kg−1·min−1PYY3–36). PYY1–36at 1.6 pmol·kg−1·min−1produced increased heart rate and postprandial insulin response. Ratings of appetite were opposite with infusions of 0.8 and 1.6 pmol·kg−1·min−1PYY1–36and seemed to depend on subjects being lean or obese. PYY3–36caused increased thermogenesis, lipolysis, postprandial insulin and glucose responses, suggestive of increased sympathoadrenal activity. PYY1–36had no effect on EI and no clear effects on appetite but resulted in increased heart rate and postprandial insulin response. However, highest tolerable dose of PYY1–36was probably not reached in the present study.
Physiological development of insulin secretion, calcium channels, and GLUT2 expression of pancreatic rat β-cells
Authors: Navarro-Tableros Victor , Fiordelisio Tatiana , Hernández-Cruz Arturo , Hiriart Marcia
Published: December 2006

Insulin secretion in mature β-cells increases vigorously when extracellular glucose concentration rises. Glucose-stimulated insulin secretion depends on Ca2+ influx through voltage-gated Ca2+ channels. During fetal development, this structured response is not well established, and it is after birth that β-cells acquire glucose sensitivity and a robust secretion. We compared some elements of glucose-induced insulin secretion coupling in β-cells obtained from neonatal and adult rats and found that neonatal cells are functionally immature compared with adult cells. We observed that neonatal cells secrete less insulin and cannot sense changes in extracellular glucose concentrations. This could be partially explained because in neonates Ca2+ current density and synthesis of mRNA α1 subunit Ca2+ channel are lower than in adult cells. Interestingly, immunostaining for α1B, α1C, and α1D subunits in neonatal cells is similar in cytoplasm and plasma membrane, whereas it occurs predominantly in the plasma membrane in adult cells. We also observed that GLUT2 expression in adult β-cells is mostly located in the membrane, whereas in neonatal cells glucose transporters are predominantly in the cytoplasm. This could explain, in part, the insensitivity to extracellular glucose in neonatal β-cells. Understanding neonatal β-cell physiology and maturation contributes toward a better comprehension of type 2 diabetes physiopathology, where alterations in β-cells include diminished L-type Ca2+ channels and GLUT2 expression that results in an insufficient insulin secretion.