bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposition Rates of
Mycobacterium tuberculosis
IS
6110
Restriction Fragment Length Polymorphism Patterns
Authors: Eilers Paul H. C. , van Soolingen Dick , Thi Ngoc Lan Nguyen , Warren Rob M. , Borgdorff Martien W. 
Published: June 2004

ABSTRACT

To determine the rate at which IS
6110
restriction fragment length polymorphism (RFLP) patterns in
Mycobacterium tuberculosis
change over time, we applied a smooth nonparametric survival model to several data sets, including data from previous publications on the rate of change. The results strongly suggest a simple parametric model, with an instantaneous change at time zero and essentially a zero rate of change thereafter. Our interpretation of the results is that at the time of collection of the first isolate, more than one strain is present. We speculate that the selection of mutant strains is most likely during rapid growth, revival of the dormant bacteria, and/or adaptation to a new host. The parameter most accurately describing changing RFLP patterns is the proportion of isolates with band changes, rather than the half-life or the rate of change.
Molecular Evidence of Infections withBabesia gibsoniParasites in Japan and Evaluation of the Diagnostic Potential of a Loop-Mediated Isothermal Amplification Method
Authors: Ikadai Hiromi , Tanaka Hiroko , Shibahara Nona , Matsuu Aya , Uechi Masami , Itoh Naoyuki , Oshiro Sugao , Kudo Noboru , Igarashi Ikuo , Oyamada Takashi 
Published: June 2004

ABSTRACTDetection and analysis ofBabesia gibsoniinfection were performed with whole-blood samples collected between July 2002 and July 2003 from 945 and 137 dogs from the Aomori and Okinawa Prefectures of Japan, respectively, by PCR and loop-mediated isothermal amplification (LAMP). On the basis of the criterion for positivity by PCR, 3.9% (37 of 945) and 10.9% (15 of 137) of the dogs hadB. gibsoniDNA. All 37 positive animals from Aomori Prefecture were male Tosa dogs (Japanese mastiff). The 15 dogs from Okinawa Prefecture with positive PCR assay results were of various breeds, ages, and sexes. The 18S ribosomal DNA (18S rDNA) sequences from all samples showed 100% homology to each other and to publishedB. gibsonisequences. The limits of detection ofB. gibsoniparasitemia by the PCR and LAMP methods with an 18S rDNA-based primer set were 0.0005% each. A comparison of the PCR and LAMP methods with microscopic examination for the detection ofB. gibsoniinfections in blood samples from 945 field dogs in Aomori Prefecture and 137 field dogs in Okinawa Prefecture showed that 37 and 15 dogs, respectively, were positive by the PCR and LAMP methods and that 16 and 12 dogs, respectively, were positive by light microscopic examination. All samples found to be positive by microscopic examination were also positive by the PCR and LAMP methods. The results of the PCR and LAMP methods agreed for samples with positive results by either method. Moreover, nonspecific reactions were not observed by the LAMP method. These results suggest that the LAMP method provides a useful tool for the detection ofB. gibsoniinfections in dogs.
Distinct Diversity of the
cag
Pathogenicity Island among
Helicobacter pylori
Strains in Japan
Authors: Azuma Takeshi , Yamakawa Akiyo , Yamazaki Shiho , Ohtani Masahiro , Ito Yoshiyuki , Muramatsu Atsushi , Suto Hiroyuki , Yamazaki Yukinao , Keida Yoshihide , Higashi Hideaki , Hatakeyama Masanori 
Published: June 2004

ABSTRACT

The severity of
Helicobacter pylori
-related disease is correlated with the presence of a
cag
pathogenicity island (PAI). Genetic diversity within the
cag
PAI may have a modifying effect on the pathogenic potential of the infecting strain. We analyzed the complete
cag
PAI sequences of 11 representative Japanese strains according to their
vacA
genotypes and clinical effects and examined the relationship between the diversity of the
cag
PAI and clinical features. The
cag
PAI genes were divided into two major groups, a Western and a Japanese group, by phylogenetic analysis based on the entire
cag
PAI sequences. The predominant Japanese strains formed a Japanese cluster which was different from the cluster formed by Western strains. The diversity of the
cag
PAI was associated with the
vacA
and
cagA
genotypes. All strains with the s1c
vacA
genotype were in the Japanese cluster. In addition, all strains with the East Asian-type
cagA
genotype were also in the Japanese cluster. Patients infected with the Japanese-cluster strain had high-grade gastric mucosal atrophy. These results suggest that a distinct diversity of the
cag
PAI of
H. pylori
is present among Japanese strains and that this diversity may be involved in the development of atrophic gastritis and may increase the risk for gastric cancer.
Simple, Rapid Latex Agglutination Test for Serotyping of Pneumococci (Pneumotest-Latex)
Authors: Slotved H.-C. , Kaltoft M. , Skovsted I. C. , Kerrn M. B. , Espersen F. 
Published: June 2004

ABSTRACTThe “gold standard” for epidemiological typing ofStreptococcus pneumoniae(pneumococcus) is the capsular reaction test (Neufeld test) with antisera against the 90 pneumococcal polysaccharide capsules, i.e., serotyping. The method is labor intensive and requires a certain level of experience to be performed satisfactory, and thus it has been restricted for use in specialized reference or research laboratories. Surveillance of the serotype distribution of pneumococci that cause infections is important to secure an optimal composition of pneumococcal vaccines and to monitor antibiotic resistance in pneumococci. At Statens Serum Institut, a simple latex agglutination test for serotyping of pneumococci has been developed. The Pneumotest-Latex kit consists of 14 different pooled pneumococcus antisera (pools A to I and pools P to T) applied to latex particles. In a blind test of 352 isolates (with all 90 serotypes represented), 336 (95.5%) were typed or grouped correctly by the Pneumotest-Latex; in addition, 2 (7%) of 30 strains regarded as nontypeable or rough strains were serotyped, and the serotypes of these two isolates were confirmed by the capsular reaction test with type-specific antisera. The Pneumotest-Latex seems to be a sensitive method for serotyping or grouping of the majority of pneumococcal strains. By use of this ready-to-perform latex agglutination kit (Pneumotest-Latex), serotyping of pneumococci can gain more ground as a tool in prevention of pneumococcal diseases.
Sequence-Based Identification of Aerobic Actinomycetes
Authors: Patel Jean Baldus , Wallace Richard J. , Brown-Elliott Barbara A. , Taylor Tony , Imperatrice Carol , Leonard Deborah G. B. , Wilson Rebecca W. , Mann Linda , Jost Kenneth C. , Nachamkin Irving 
Published: June 2004

ABSTRACTWe investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the generaStreptomyces,Gordonia, andTsukamurellaand 10 taxa ofNocardiawere studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65hspgene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing ofNocardiaspecies revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences ofNocardia transvalensis,N. otitidiscaviarum, andN. novaisolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within theNocardiaspp. are unnamed at present. A major unresolved issue is the type strain ofN. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis.
Multiplex PCR for Distinguishing the Most Common Phase-1 Flagellar Antigens of
Salmonella
spp
Authors: Herrera-León Silvia , McQuiston John R. , Usera Miguel A. , Fields Patricia I. , Garaizar Javier , Echeita M. Aurora 
Published: June 2004

ABSTRACT

Most
Salmonella
serotypes alternatively express either phase-1 or phase-2 flagellar antigens, encoded by the
fliC
and
fljB
genes, respectively. Flagellar phase reversal for the identification of both flagellar antigens is not necessary at the genetic level. Variable internal regions of the
fliC
genes encoding the H:i, H:r, H:l,v, H:e,h, H:z
10
, H:b, and H:d antigens have been sequenced; and the specific sites for each antigen in selected
Salmonella
serotypes have been determined. These results, together with flagellar G-complex variable internal sequences obtained by the Foodborne and Diarrheal Diseases Branch at the Centers for Disease Control and Prevention in Atlanta, Ga., have been used to design a multiplex PCR to identify the G-complex antigens as well as the H:i, H:r, H:l,v, H:e,h, Hz
10
, H:b, and H:d first-phase antigens. These antigens are part of the most common
Salmonella
serotypes possessing first-phase flagellar antigens.
Salmonella enterica
serotype Enteritidis is identified by adding a specific primer pair published previously (P. G. Agron, R. L. Walker, H. Kinde, S. J. Sawyer, D. C. Hayes, J. Wollard, and G. L. Andersen, Appl. Environ. Microbiol. 67:4984-4991, 2001). This multiplex PCR includes 13 primers. A total of 161
Salmonella
strains associated with 72 different serotypes were tested. Each strain generated one first-phase-specific antigen fragment ranging from 100 to 500 bp;
Salmonella
serotype Enteritidis, however, generated two amplicons of 500 bp that corresponded to the G complex and a 333-bp serotype-specific amplicon, respectively. Twenty-three strains representing 19 serotypes with flagellar genes different from those targeted in this work did not generate any fragments. The method is quick, specific, and reproducible and is independent of the phase expressed by the bacteria when they are tested.
Etiology of Sporadic Cases of Pediatric Acute Gastroenteritis in Asturias, Spain, and Genotyping and Characterization of Norovirus Strains Involved
Authors: Boga José Antonio , Melón Santiago , Nicieza Inés , de Diego Isabel , Villar Mercedes , Parra Francisco , de Oña María 
Published: June 2004

ABSTRACT

From November 2000 to October 2001, a reverse transcription-PCR using primers directed to the norovirus RNA polymerase coding region was included in a viral and bacterial routine screening to diagnose sporadic cases of acute gastroenteritis among children in Asturias, Spain. The role of noroviruses (8.6% of the positively diagnosed cases) as the cause of sporadic pediatric gastroenteritis was evaluated with respect to the detection rates of other gastroenteritis-associated viruses and bacteria. The results indicated that noroviruses were less common than rotaviruses (36.9%),
Campylobacter
spp. (28.8%), and
Salmonella
spp. (18.4%) but more frequent than astroviruses (4.3%), adenoviruses (3.8%), and
Yersinia
spp. (2.2%). Mixed infections involving noroviruses were rarely observed (0.5%). The presence of a norovirus-associated pediatric gastroenteritis peak in summer, as well as the complete absence of norovirus-associated cases in colder months, challenges the view that norovirus infections exclusively have wintertime seasonality. On the other hand, phylogenetic analysis of the amplified fragments showed that the norovirus strains responsible were closely related. A further study using the full-length capsid region showed that these strains could be included into genogroup II, Bristol/Lorsdale cluster, and were closely related to the 1995 and 1996 U.S. subset of strains associated with outbreaks recorded worldwide between 1995 and 1996.
Comparison of Blood Smear, Antigen Detection, and Nested-PCR Methods for Screening Refugees from Regions Where Malaria Is Endemic after a Malaria Outbreak in Quebec, Canada
Authors: Ndao Momar , Bandyayera Etienne , Kokoskin Evelyne , Gyorkos Theresa W. , MacLean J. Dick , Ward Brian J. 
Published: June 2004

ABSTRACT

The importation of malaria into a region where it is not endemic raises many concerns, including the timely delivery of appropriate care, safety of the blood supply, and the risk of autochthonous transmission. There is presently no consensus on the best way to screen mobile populations for malaria. Between August 2000 and March 2001, 535 refugees arrived in Quebec, Canada, from Tanzanian camps. Within 4 weeks of resettlement of the first group of 224, the McGill University Centre for Tropical Diseases noted an outbreak of malaria across the province (15 cases over a 3-week period). This group (group 1) was traced and screened for malaria between 3 and 4 months after arrival in Canada. Subsequent groups of 106 and 205 refugees were screened immediately upon arrival in Canada (group 2) and immediately prior to their departure from refugee camps (group 3), respectively. A single EDTA-blood sample was obtained from 521 refugees for testing by thick and thin blood smears (groups 1 and 2), antigen detection (ICT Malaria Pf and OptiMAL; group 1 only), and nested PCR (all groups). Overall, 98 of 521 refugees were found to be infected (18.8%). The vast majority of infections (81 of 98) were caused by
Plasmodium falciparum
alone. Using PCR as the “gold standard,” both microscopy (sensitivity, 50%; specificity, 100%) and antigen detection (ICT sensitivity, 37.5%; ICT specificity, 100%; OptiMAL sensitivity, 29.1%; OptiMAL specificity, 95.6%) performed poorly. None of the PCR-positive subjects were symptomatic at the time of testing, and only two had recently had symptoms compatible with malaria (with or without diagnosis and treatment). Active surveillance of migrants from regions of intense malaria transmission can reduce the risk of morbidity in the migrant population and mitigate against transmission to the host population. Our data demonstrate that PCR is, by far, the most powerful tool for such surveillance.
DNA Sequence Analysis of the PorB Protein of Nonserotypeable Serogroup C ET-15 Meningococci Suggests a Potential Mutational Hot Spot on Their Serotype Antigens
Authors: Law Dennis K. S. , Henderson Averil M. , Tsang Raymond S. W. 
Published: June 2004

ABSTRACT

The nucleotide sequences of the PorB proteins from 28 nonserotypeable serogroup C ET-15 meningococci recovered from invasive meningococcal disease cases were determined. PCR amplification of the
porB
genes responsible for encoding the serotype antigen was used for DNA sequence determination and identification of the nature of the serotype antigen. DNA sequencing revealed that three strains were of serotype 2a, and of the remaining 25 strains, 20 were found to have an identical single point mutation in the region of the VR3 gene, which encodes surface-exposed loop VI, where the serotype 2a epitope resides. This nonsynonymous mutation was confirmed by synthetic peptide immunochemical analysis to confer new serospecificity to these serotype 2a mutants. This finding of a potential novel mutational hot spot on the PorB proteins of meningococci may have implications for pathogenesis and vaccine development.
High-Efficiency Detection of Severe Acute Respiratory Syndrome Virus Genetic Material
Authors: Weidmann Manfred , Zanotto Paolo M. D. A. , Weber Friedemann , Spiegel Martin , Brodt Hans Rheinhard , Hufert Frank T. 
Published: June 2004

ABSTRACT

A Taqman amplicon targeting the nucleocapsid gene of severe acute respiratory syndrome coronavirus (SARS-CoV) is 5 log
10
times more sensitive for SARS-CoV target RNA extracted from infected cells and 2.79 log
10
times more sensitive for RNA extracted from patient material of the index case in Frankfurt than an amplicon targeting the polymerase gene.
Incidence of Constitutive and Inducible Clindamycin Resistance in
Staphylococcus aureus
and Coagulase-Negative Staphylococci in a Community and a Tertiary Care Hospital
Authors: Schreckenberger Paul C. , Ilendo Elizabeth , Ristow Kathryn L. 
Published: June 2004

ABSTRACT

The incidences of inducible clindamycin resistance at two hospitals (an inner-city hospital and a suburban community hospital) were 7 and 12% for methicillin-resistant
Staphylococcus aureus
, 20 and 19% for methicillin-susceptible
S
.
aureus
, and 14 and 35% for coagulase-negative staphylococci, respectively. Given the variability of inducible resistance to clindamycin found in our two hospitals, we conclude that susceptibility testing of staphylococci should include the disk diffusion induction test (D-test).
Evaluation of the Methicillin-Resistant
Staphylococcus aureus
(MRSA)-Screen Latex Agglutination Test for Detection of MRSA of Animal Origin
Authors: Lee John H. , Jeong Jae-Myung , Park Yong-Ho , Choi Sung-Sun , Kim Yong-Hwan , Chae Joon-Seok , Moon Jin-San , Park Hyun , Kim Shin , Eo Seong-Kug 
Published: June 2004

ABSTRACT

Methicillin (oxacillin)-resistant staphylococci (MRS) have emerged as major clinical and epidemiological pathogens, and there have been frequent reports of MRS infections in the veterinary field. The MRSA-Screen latex agglutination test (Denka Seiken Co., Ltd., Tokyo, Japan) was compared with an oxacillin agar screen test, MIC determination, and
mecA
PCR assay, the “gold standard.” In an analysis of 15
mecA
-positive and 48
mecA
-negative
S
.
aureus
animal isolates, as well as 9
mecA
-positive and 147
mecA
-negative, coagulase-negative staphylococcal animal isolates, the latex agglutination test surpassed the widely used oxacillin agar screen method and MIC determination, with a sensitivity and a specificity of 100%. The MRSA-Screen test is a reliable and rapid method of detecting MRS in the veterinary field.
Utility of Reverse Transcriptase PCR for Rapid Diagnosis of Influenza A Virus Infection and Detection of Amantadine-Resistant Influenza A Virus Isolates
Authors: Pachucki Constance T. , Khurshid M. Aijaz , Nawrocki John 
Published: June 2004

ABSTRACTA reverse transcriptase PCR was developed to detect 50 or 5,000 RNA copies of influenza A virus per ml in throat swab specimens. The assay was more sensitive than the Directigen Flu A test. The technique was also used to detect amantadine-resistant isolates.
Sequencing and Sequence Analysis of VP7 and NSP5 Genes Reveal Emergence of a New Genotype of Bovine Group B Rotaviruses in India
Authors: Barman P. , Ghosh S. , Das S. , Varghese V. , Chaudhuri S. , Sarkar S. , Krishnan T. , Bhattacharya S. K. , Chakrabarti A. , Kobayashi N. , Naik T. N. 
Published: June 2004

ABSTRACT
Three bovine group B rotavirus strains were detected from diarrheic calves during a surveillance study of rotaviral diarrhea in West Bengal, India. The sequence analysis of VP7 and NSP5 genes of these strains demonstrates a high degree of sequence variation from other group B rotavirus strains, indicating the emergence of a new genotype.
Outbreak of Infection with Hepatitis A Virus (HAV) Associated with a Foodhandler and Confirmed by Sequence Analysis Reveals a New HAV Genotype IB Variant
Authors: Chironna Maria , Lopalco Pierluigi , Prato Rosa , Germinario Cinzia , Barbuti Salvatore , Quarto Michele 
Published: June 2004

ABSTRACT
An outbreak of infection with hepatitis A virus associated with a foodhandler and involving 26 subjects occurred in Southern Italy. Sequence analysis of the VP3-VP1 and VP1-P2A junctions confirmed that the outbreak was due to a point source and allowed the identification of a new genotype IB variant. This report confirms the usefulness of sequence-based molecular fingerprinting during outbreaks.
Evaluation of a New Particle Gel Immunoassay for Determination of Antibodies against
Treponema pallidum
Authors: Schmidt Bruno L. 
Published: June 2004

ABSTRACT

A new particle gel immunoassay (DiaMed AG, Cressier sur Morat, Switzerland) with three recombinant
Treponema pallidum
antigens was evaluated with serum samples from patients with syphilis (
n
= 124) and patients without syphilis (
n
= 490). It proved to be a simple, rapid (20 min), and useful test with sensitivity, specificity, and positive and negative predictive values of 91.9, 99.8, 99.2, and 98%, respectively.
First U.S. Report of Subcutaneous Phaeohyphomycosis Caused byVeronaea botryosain a Heart Transplant Recipient and Review of the Literature
Authors: Sutton D. A. , Rinaldi M. G. , Kielhofner M. 
Published: June 2004

ABSTRACTVeronaea botryosais a rare agent of human phaeohyphomycosis. We describe the first case of subcutaneous disease occurring in the United States, alert clinicians to the second report of a transplant-associated mycosis in a heart transplant recipient, extend the previously defined area of endemicity, and review the literature.
Subtype B Human Immunodeficiency Virus (HIV) Type 1 Mutant That Escapes Detection in a Fourth-Generation Immunoassay for HIV Infection
Authors: Gaudy Catherine , Moreau Alain , Brunet Sylvie , Descamps Jean-Michel , Deleplanque Pascale , Brand Denys , Barin Francis 
Published: June 2004

ABSTRACT
We report a case of human immunodeficiency virus (HIV) type 1 infection not detected by a highly sensitive combined antigen-antibody assay. The virus was a subtype B strain harboring a unique sequence within the immunodominant epitope of the transmembrane glycoprotein. Immunochemical analysis indicated that this sequence was probably responsible for the failure to detect HIV antibodies.
Serotonin modifies the sensitivity of the male silkmoth to pheromone
Authors: Gatellier Laureline , Nagao Takashi , Kanzaki Ryohei 
Published: June 2004

SUMMARYSerotonin is known to modulate the response of neuronal populations in the primary olfactory center of the moth olfactory system, the antennal lobe. Here, we analyzed the effects of serotonin on the behavior related to the restricted pheromone olfactory pathway of the male silkmoth, Bombyx mori. In order to understand the effects of serotonin at the behavioral level, we applied serotonin (10-5 mol l-1,10-4 mol l-1 and 10-3 mol l-1) to the brain and found that 10-4 mol l-1 serotonin increases the sensitivity to female pheromone whereas 10-3 mol l-1 serotonin had the opposite effect. Levels of serotonin in the brain were determined using HPLC with electrochemical detection. Inhibitory effects were observed after applying the serotonin antagonists mianserin(10-4 mol l-1) and ketanserin (10-3 mol l-1). Additionally, we quantified the circadian variation of serotonin in the brain using HPLC with electrochemical detection. Further,this variation correlated well with a circadian variation of the male sensitivity to pheromone. These results show that the serotonin-related enhancement of neuronal responses at the antennal lobe level is expressed at the behavioral level as a modulation of pheromone sensitivity and that the circadian variation of serotonin levels in the brain correlates with changes in the moth's pheromone sensitivity.