bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Discrimination of
Listeria monocytogenes
Strains by Microtemperature Gradient Gel Electrophoresis
Authors: Tominaga Tatsuya 
Published: June 2006

ABSTRACT

Microtemperature gradient gel electrophoresis (μ-TGGE) was examined for use for the rapid subtyping of
Listeria monocytogenes
strains. Comparison of genomes between
L. monocytogenes
strains F2365 and H7858 identified a sequence encoding a portion of the PRT/PTS system IIA 2 protein domain as appropriate for μ-TGGE analysis. Thirty-one strains belonging to 10 different serovar types were tested by PCR, and sequence analysis of the amplified products revealed that the strains comprise 11 groups. All 55 possible pairs within the 11 groups were examined by μ-TGGE analysis. Of these, 47 pairs could be successfully discriminated, with a total electrophoresis time of only 7 min. Moreover, Cy3/Cy5 labeling allowed rapid identification of the sequence type in unknown strains of
L. monocytogenes
isolated from meat. These findings collectively indicate that μ-TGGE can be used for the rapid analysis of
L. monocytogenes
strains, facilitating determination of routes of contamination when these bacteria are found in food products.
Identification and Characterization of Variable-Number Tandem-Repeat Markers for Typing of
Brucella
spp
Authors: Whatmore Adrian M. , Shankster Stephen J. , Perrett Lorraine L. , Murphy Terry J. , Brew Simon D. , Thirlwall Rachel E. , Cutler Sally J. , MacMillan Alastair P. 
Published: June 2006

ABSTRACT

Members of the genus
Brucella
infect many domesticated and wild animals and cause serious zoonotic infection in humans. The availability of discriminatory molecular typing tools to inform and assist conventional epidemiological approaches would be invaluable in controlling these infections, but efforts have been hampered by the genetic homogeneity of the genus. We report here on a molecular subtyping system based on 21 variable-number tandem-repeat (VNTR) loci consisting of 13 previously unreported loci and 8 loci previously reported elsewhere. This approach was applied to a collection of 121
Brucella
isolates obtained worldwide and representing all six classically recognized
Brucella
species. The size of repeats selected for inclusion varied from 5 to 40 bp giving VNTR loci with a range of diversities. The number of alleles detected ranged from 2 to 21, and Simpson's diversity index values ranged from 0.31 to 0.92. This assay divides the 121 isolates into 119 genotypes, and clustering analysis results in groups that, with minor exceptions, correspond to conventional species designations. Reflecting this, the use of six loci in isolation was shown to be sufficient to determine species designation. On the basis of the more variable loci, the assay could also discriminate isolates originating from restricted geographical sources, indicating its potential as an epidemiological tool. Stability studies carried out in vivo and in vitro showed that VNTR profiles were sufficiently stable such that recovered strains could readily be identified as the input strain. The method described here shows great potential for further development and application to both epidemiological tracing of
Brucella
transmissions and in determining relationships between isolates worldwide.
Staphylococcus aureus
Carriage Patterns and the Risk of Infections Associated with Continuous Peritoneal Dialysis
Authors: Nouwen Jan , Schouten Jeroen , Schneebergen Peter , Snijders Susan , Maaskant Jolanda , Koolen Marjan , van Belkum Alex , Verbrugh Henri A. 
Published: June 2006

ABSTRACT

The epidemiology and risks of
Staphylococcus aureus
carriage in continuous peritoneal dialysis (CPD) patients was studied in a single tertiary-care institution. On outpatient visits samples for culture were routinely taken prospectively from the CPD catheter exit site and the vestibulum nasi. Seventy-five patients with at least one culture positive for
S. aureus
in this period were included: 43 had genotypically identical
S. aureus
strains in over 80% of the cultures and were classified as persistent carriers; 32 were intermittent carriers. Persistent carriage was associated with a threefold higher risk for CPD-related infections and sixfold higher rates of vancomycin consumption compared to those for the intermittent carriers. No methicillin or vancomycin resistance was detected.
Rapid Detection of Rifampin Resistance in
Mycobacterium tuberculosis
by Pyrosequencing Technology
Authors: Jureen Pontus , Engstrand Lars , Eriksson Solveig , Alderborn Anders , Krabbe Margareta , Hoffner Sven E. 
Published: June 2006

ABSTRACT

We developed an assay for rapid detection of rifampin resistance in
Mycobacterium tuberculosis
based on Pyrosequencing technology, involving a technique for real-time sequencing. A 180-bp region of the
rpoB
gene was amplified in clinical isolates of both rifampin-resistant and -susceptible
M. tuberculosis
. The PCR products were subjected to Pyrosequencing analysis using four different sequencing primers in four overlapping reactions. These four sequencing reactions covered the 81-bp region where >96% of the mutations associated with rifampin resistance are located. The results were compared to those obtained with two other molecular methods, the line probe assay and cycle sequencing, and the phenotypic BACTEC method. The genotypic determination methods all detected the mutations that previously have been correlated with rifampin resistance. In addition, Pyrosequencing analysis and the two other molecular methods found additional mutations within the
rpoB
gene in phenotypically susceptible strains. We found that Pyrosequencing technology, in particular, offers high accuracy, short turnaround time, and a potentially high throughput in detection of rifampin resistance in
M. tuberculosis
.
Combining Multiplex Reverse Transcription-PCR and a Diagnostic Microarray To Detect and Differentiate Enterovirus 71 and Coxsackievirus A16
Authors: Chen Tsan-Chi , Chen Guang-Wu , Hsiung Chao Agnes , Yang Jyh-Yuan , Shih Shin-Ru , Lai Yiu-Kay , Juang Jyh-Lyh 
Published: June 2006

ABSTRACT
Cluster A enteroviruses, including enterovirus 71 (EV71) and coxsackievirus A16 (CA16), are known to cause hand-foot-and-mouth disease (HFMD). Despite the close genetic relationship between these two viruses, EV71 is generally known to be a more perpetuating pathogen involved in severe clinical manifestations and deaths. While the serotyping of enteroviruses is mostly done by conventional immunological methods, many clinical isolates remain unclassifiable due to the limited number of antibodies against enterovirus surface proteins. Array-based assays are able to detect several serotypes with high accuracy. We combined an enterovirus microarray with multiplex reverse transcription-PCR to try to develop a method of sensitively and accurately detecting and differentiating EV71 and CA16. In an effort to design serotype-specific probes for detection of the virus, we first did an elaborate bioinformatic analysis of the sequence database derived from different enterovirus serotypes. We then constructed a microarray using 60-mer degenerate oligonucleotide probes covalently bound to array slides. Using this enterovirus microarray to study 144 clinical specimens from patients infected with HFMD or suspected to have HFMD, we found that it had a diagnostic accuracy of 92.0% for EV71 and 95.8% for CA16. Diagnostic accuracy for other enteroviruses (non-EV71 or -CA16) was 92.0%. All specimens were analyzed in parallel by real-time PCR and subsequently confirmed by neutralization tests. This highly sensitive array-based assay may become a useful alternative in clinical diagnostics of EV71 and CA16.
Evaluation of a Multiple-Cycle, Recombinant Virus, Growth Competition Assay That Uses Flow Cytometry To Measure Replication Efficiency of Human Immunodeficiency Virus Type 1 in Cell Culture
Authors: Dykes Carrie , Wang Jiong , Jin Xia , Planelles Vicente , An Dong Sung , Tallo Amanda , Huang Yangxin , Wu Hulin , Demeter Lisa M. 
Published: June 2006

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) replication efficiency or fitness, as measured in cell culture, has been postulated to correlate with clinical outcome of HIV infection, although this is still controversial. One limitation is the lack of high-throughput assays that can measure replication efficiency over multiple rounds of replication. We have developed a multiple-cycle growth competition assay to measure HIV-1 replication efficiency that uses flow cytometry to determine the relative proportions of test and reference viruses, each of which expresses a different reporter gene in place of
nef
. The reporter genes are expressed on the surface of infected cells and are detected by commercially available fluorescence-labeled antibodies. This method is less labor-intensive than those that require isolation and amplification of nucleic acids. The two reporter gene products are detected with similar specificity and sensitivity, and the proportion of infected cells in culture correlates with the amount of viral p24 antigen produced in the culture supernatant. HIV replication efficiencies of six different drug-resistant site-directed mutants were reproducibly quantified and were similar to those obtained with a growth competition assay in which the relative proportion of each variant was measured by sequence analysis, indicating that recombination between the
pol
and reporter genes was negligible. This assay also reproducibly quantified the relative fitness conferred by protease and reverse transcriptase sequences containing multiple drug resistance mutations, amplified from patient plasma. This flow cytometry-based growth competition assay offers advantages over current assays for HIV replication efficiency and should prove useful for the evaluation of patient samples in clinical trials.
Molecular Epidemiology of Group A Rotavirus Diarrhea among Children in Buenos Aires, Argentina, from 1999 to 2003 and Emergence of the Infrequent Genotype G12
Authors: Castello A. A. , Argüelles M. H. , Rota R. P. , Olthoff A. , Jiang B. , Glass R. I. , Gentsch J. R. , Glikmann G. 
Published: June 2006

ABSTRACT
To examine the epidemiology of rotaviruses in Buenos Aires, Argentina, we screened 1,212 stool samples from children with diarrhea in the southern district of Buenos Aires from 1999 to 2003. We identified 187 samples (15.4%) that were positive for group A rotavirus by use of antigen enzyme-linked immunosorbent assay. Among these specimens, 112 were available for typing: 93 (83.0%) were single-type infections, 9 (8.0%) were mixed-type infections with more than one G or P type, and 10 (8.9%) were G and/or P nontypeable. In contrast to the findings in our last study, from 1996 to 1998, genotype P[4], G2 strains were almost completely absent and P[8], G1 and P[8], G4 strains were dominant, representing more than 80% of the G and P types found. Genotypes G2 and G9 were detected in few samples, and type G3 was completely absent. We identified several uncommon genotype G12 strains, representing the first detections outside of Asia and the United States, by sequencing. Using a genotype G12-specific reverse transcription-PCR, we identified eight (6.7%) positive samples for the 1999 to 2003 period. The high degree of sequence identity between recent G12 isolates from Argentina, the United States, and Asian countries suggests a relatively recent introduction(s) of these strains into humans from a common progenitor. The Argentinean G12 strains belonged to genotype P[9], similar to most of the recently described Asian G12 strains. The finding of G12 strains in several other regions of the world raises the possibility that G12 may be emerging globally and suggests that surveillance for this strain should be conducted routinely.
Genetically Diverse Group A Streptococci from Children in Far-Western Nepal Share High Genetic Relatedness with Isolates from Other Countries
Authors: Sakota Varja , Fry Alicia M. , Lietman Thomas M. , Facklam Richard R. , Li Zhongya , Beall Bernard 
Published: June 2006

ABSTRACT

The genetic diversity of group A streptococci (GAS) throughout much of the world has not been adequately explored. To assess genetic variation among GAS in western Nepal, 120 noninvasive GAS, collected from eight different villages, were genetically characterized using
emm
typing,
sof
sequencing, and multilocus sequence typing (MLST). A high level of genetic diversity was observed among these isolates, with 51 genotypes based upon 51 multilocus sequence types (STs), 45
emm
sequence types, and 28
sof
sequence types. On the basis of shared ST
-emm
and
sof
-
emm
associations, 40 of the 51 genotypes were identical or highly related to genotypes characterized from locations outside of Nepal, even though most of the
emm
sequence and clonal types are rare among GAS within the United States. When analyzing all known STs highly related to Nepal STs, only one example of similar STs shared between a
sof
PCR-positive strain and a
sof
PCR-negative strain was observed. Since previous data indicate free exchange of MLST loci between
sof
-positive and
sof
-negative strains, there is possibly selection against the expansion of subclones resulting from horizontal transfers of
sof
or
emm
genes between
sof
-positive and
sof
-negative strains. All 45
emm
types encountered in Nepal have also been documented from other countries. These data, together with data encompassing the past decade of
emm
type surveillance, support the possibility that most existing GAS
emm
types have been discovered. Similarly, since most (40/51) strain types were highly related to strains found elsewhere, it is likely that a major fraction of the existing GAS clonal complexes have been discovered.
Analysis of the 5′ Noncoding Region versus the NS5b Region in Genotyping Hepatitis C Virus Isolates from Blood Donors in France
Authors: Cantaloube Jean-François , Laperche Syria , Gallian Pierre , Bouchardeau Françoise , de Lamballerie Xavier , de Micco Philippe 
Published: June 2006

ABSTRACT
The 5′ noncoding region (5′ NCR) of the hepatitis C virus (HCV) has become the standard for genotyping even though several reports show that its use can result in classification errors. The purpose of this study was to perform genotyping based on sequence analysis of the NS5b region in a set of 357 HCV strains isolated from blood donors in France in 2002 and 2003. Results were compared with those previously obtained using 5′ NCR analysis, and HCV subtype distribution was reevaluated. Twenty-six of 120 strains (∼22%) initially identified as genotype 1b by 5′ NCR region sequence analysis were reclassified as genotype 1a by NS5b region sequence analysis. Similarly, 14 of 23 strains (∼61%) initially identified as 2a/2c were reclassified as non-2a and non-2c subtypes, and 12 of 22 strains (∼45%) initially identified as 4c/4d subtypes were reclassified as non-4c and non-4d subtypes. Sequence analysis of the NS5b region also revealed 5 putative new subtype 2 variants and 2 putative new subtype 4 variants. Although these findings demonstrated full agreement between 5′ NCR and NS5b sequence analysis with regard to type classification, genotyping based on phylogenetic analysis of the NS5b region is more accurate for subtype determination than genotyping based on analysis of the 5′ NCR. Sequence analysis of the NS5b region is mandatory for epidemiologic studies.
Acute Cholecystitis Accompanied by Acute Pancreatitis Potentially Caused by
Dolosigranulum pigrum
Authors: Lin Jung-Chung , Hou Shu-Jin , Huang Li-Ung , Sun Jun-Ren , Chang Wei-Kuo , Lu Jang-Jih 
Published: June 2006

ABSTRACT

We report a case of acute cholecystitis accompanied by acute pancreatitis and caused by
Dolosigranulum pigrum
in a 76-year-old male with gallstones.
D. pigrum
was isolated from a blood culture and confirmed by biochemistry tests and 16S rRNA sequencing. The isolate was susceptible to the β-lactams ampicillin, penicillin, cephalothin, ceftriaxone, ceftazidime, chloramphenicol, and vancomycin but was intermediate to erythromycin and clindamycin. The patient recovered without sequelae after treatment with appropriate antibiotics for two weeks.
Diagnosis of Mixed
Plasmodium malariae
and
P. vivax
Infection in a Development Aid Volunteer by Examination of Bone-Marrow Specimens by Real-Time PCR
Authors: Imirzalioglu Can , Soydan Nedim , Schaller Markus , Bretzel Reinhard G. , Chakraborty Trinad , Domann Eugen 
Published: June 2006

ABSTRACT

Mixed
Plasmodium malariae
and
P. vivax
infections in humans are reported very infrequently. The case of a 27-year-old male who sustained malaria quartana/tertiana caused by an unbalanced mixed
P. malariae
-
P. vivax
infection is reported here. Conventional tests and serology for malarial parasites were uniformly negative. Identification and quantification of the parasites were accomplished by examining bone-marrow specimens using specific real-time TaqMan PCR.
Antimicrobial Agent of Susceptibilities and Antiseptic Resistance Gene Distribution among Methicillin-Resistant
Staphylococcus aureus
Isolates from Patients with Impetigo and Staphylococcal Scalded Skin Syndrome
Authors: Noguchi Norihisa , Nakaminami Hidemasa , Nishijima Setsuko , Kurokawa Ichiro , So Hiromu , Sasatsu Masanori 
Published: June 2006

ABSTRACT

The susceptibilities to antimicrobial agents of and distributions of antiseptic resistance genes in methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated between 1999 and 2004 in Japan were examined. The data of MRSA strains that are causative agents of impetigo and staphylococcal scalded skin syndrome (SSSS) were compared with those of MRSA strains isolated from patients with other diseases. The susceptibilities to antiseptic agents in MRSA isolates from patients with impetigo and SSSS were higher than those in MRSA isolates from patients with other diseases. The distribution of the
qacA/B
genes in MRSA strains isolated from patients with impetigo and SSSS (1.3%, 1/76) was remarkably lower than that in MRSA strains isolated from patients with other diseases (45.9%, 95/207). Epidemiologic typings of staphylococcal cassette chromosome
mec
(SCC
mec
) and pulsed-field gel electrophoresis (PFGE) showed that MRSA strains isolated from patients with impetigo and SSSS had type IV SCC
mec
(75/76), except for one strain, and 64.5% (49/76) of the strains had different PFGE types. In addition, the patterns of restriction digestion of all tested
qacA/B
plasmid in MRSA isolates having different PFGE types were identical. The results showed that a specific MRSA clone carrying
qacA/B
was not prevalent, but
qacA/B
was spread among health care-associated MRSA strains. Therefore, it was concluded that the lower distribution rate of
qacA/B
resulted in higher susceptibilities to cationic antiseptic agents in MRSA isolated from patients with impetigo and SSSS.
Plant Pathogen Forensics: Capabilities, Needs, and Recommendations
Authors: Fletcher J. , Bender C. , Budowle B. , Cobb W. T. , Gold S. E. , Ishimaru C. A. , Luster D. , Melcher U. , Murch R. , Scherm H. , Seem R. C. , Sherwood J. L. , Sobral B. W. , Tolin S. A. 
Published: June 2006

SUMMARYA biological attack on U.S. crops, rangelands, or forests could reduce yield and quality, erode consumer confidence, affect economic health and the environment, and possibly impact human nutrition and international relations. Preparedness for a crop bioterror event requires a strong national security plan that includes steps for microbial forensics and criminal attribution. However, U.S. crop producers, consultants, and agricultural scientists have traditionally focused primarily on strategies for prevention and management of diseases introduced naturally or unintentionally rather than on responding appropriately to an intentional pathogen introduction. We assess currently available information, technologies, and resources that were developed originally to ensure plant health but also could be utilized for postintroduction plant pathogen forensics. Recommendations for prioritization of efforts and resource expenditures needed to enhance our plant pathogen forensics capabilities are presented.
Cell Wall Assembly in
Saccharomyces cerevisiae
Authors: Lesage Guillaume , Bussey Howard 
Published: June 2006

SUMMARY

An extracellular matrix composed of a layered meshwork of β-glucans, chitin, and mannoproteins encapsulates cells of the yeast
Saccharomyces cerevisiae
. This organelle determines cellular morphology and plays a critical role in maintaining cell integrity during cell growth and division, under stress conditions, upon cell fusion in mating, and in the durable ascospore cell wall. Here we assess recent progress in understanding the molecular biology and biochemistry of cell wall synthesis and its remodeling in
S. cerevisiae
. We then review the regulatory dynamics of cell wall assembly, an area where functional genomics offers new insights into the integration of cell wall growth and morphogenesis with a polarized secretory system that is under cell cycle and cell type program controls.
Defenses against Oxidative Stress inNeisseria gonorrhoeae: a System Tailored for a Challenging Environment
Authors: Seib Kate L. , Wu Hsing-Ju , Kidd Stephen P. , Apicella Michael A. , Jennings Michael P. , McEwan Alastair G. 
Published: June 2006

SUMMARYNeisseria gonorrhoeaeis a host-adapted pathogen that colonizes primarily the human genitourinary tract. This bacterium encounters reactive oxygen and reactive nitrogen species as a consequence of localized inflammatory responses in the urethra of males and endocervix of females and also of the activity of commensal lactobacilli in the vaginal flora. This review describes recent advances in the understanding of defense systems against oxidative stress inN. gonorrhoeaeand shows that while some of its defenses have similarities to the paradigm established withEscherichia coli, there are also some key differences. These differences include the presence of a defense system against superoxide based on manganese ions and a glutathione-dependent system for defense against nitric oxide which is under the control of a novel MerR-like transcriptional regulator. An understanding of the defenses against oxidative stress inN. gonorrhoeaeand their regulation may provide new insights into the ways in which this bacterium survives challenges from polymorphonuclear leukocytes and urogenital epithelial cells.
IS
CR
Elements: Novel Gene-Capturing Systems of the 21st Century?
Authors: Toleman Mark A. , Bennett Peter M. , Walsh Timothy R. 
Published: June 2006

SUMMARY

“Common regions” (CRs), such as Orf513, are being increasingly linked to mega-antibiotic-resistant regions. While their overall nucleotide sequences show little identity to other mobile elements, amino acid alignments indicate that they possess the key motifs of IS
91
-like elements, which have been linked to the mobility
ent
plasmids in pathogenic
Escherichia coli
. Further inspection reveals that they possess an IS
91
-like origin of replication and termination sites (
ter
IS), and therefore CRs probably transpose via a rolling-circle replication mechanism. Accordingly, in this review we have renamed CRs as IS
CR
s to give a more accurate reflection of their functional properties. The genetic context surrounding IS
CR
s indicates that they can procure 5′ sequences via misreading of the cognate
ter
IS, i.e., “unchecked transposition.” Clinically, the most worrying aspect of IS
CR
s is that they are increasingly being linked with more potent examples of resistance, i.e., metallo-β-lactamases in
Pseudomonas aeruginosa
and co-trimoxazole resistance in
Stenotrophomonas maltophilia
. Furthermore, if IS
CR
elements do move via “unchecked RC transposition,” as has been speculated for IS
CR
1, then this mechanism provides antibiotic resistance genes with a highly mobile genetic vehicle that could greatly exceed the effects of previously reported mobile genetic mechanisms. It has been hypothesized that bacteria will surprise us by extending their “genetic construction kit” to procure and evince additional DNA and, therefore, antibiotic resistance genes. It appears that IS
CR
elements have now firmly established themselves within that regimen.