bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence ofBorrelia lonestariDNA inAmblyomma americanum(Acari: Ixodidae) Removed from Humans
Authors: Stromdahl Ellen Y. , Williamson Phillip C. , Kollars Thomas M. , Evans Sandra R. , Barry Ryan K. , Vince Mary A. , Dobbs Nicole A. 
Published: December 2003

ABSTRACTWe used a nested PCR withBorreliaflagellin gene (flaB) primers and DNA sequencing to determine ifBorrelia lonestariwas present inAmblyomma americanumticks removed from military personnel and sent to the Tick-Borne Disease Laboratory of the U.S. Army Center for Health Promotion and Preventive Medicine. In our preliminary investigation, we detectedBorreliasequences in 19 of 510A. americanumadults and nymphs from Ft. A. P. Hill, Va. During the 2001 tick season, theflaBprimers were used to test allA. americanumsamples as they were received, and 29 of 2,358A. americanumsamples tested individually or in small pools were positive. PCRs with 2,146A. americanumsamples in 2002 yielded 26 moreBorrelia-positive samples. The positive ticks in 2001 and 2002 were from Arkansas, Delaware, Kansas, Kentucky, Maryland, New Jersey, North Carolina, Tennessee, and Virginia. The last positive sample of the 2001 season was a pool of larvae. To further investigate larval infection, we collected and tested questingA. americanumlarvae from Aberdeen Proving Ground, Md.; 4 of 33 pools (40 larvae per pool) were positive. Infection of unfed larvae provides evidence of the maintenance ofB. lonestariby means of transovarial transmission. Sequence analysis revealed that the amplicons were identical to sequences of theB. lonestari flaBgene in GenBank. Despite the low prevalence of infection, the risk ofB. lonestaritransmission may be magnified becauseA. americanumis often abundant and aggressive, and many tick bite victims receive multiple bites.
Denaturing High-Performance Liquid Chromatography for Detecting and Typing Genital Human Papillomavirus
Authors: Li Jianduan , Gerhard Daniela S. , Zhang Zhengyan , Huettner Phyllis C. , Wright Jason , Nguyen Loan , Lu Danielle , Rader Janet S. 
Published: December 2003

ABSTRACT
Human papillomaviruses (HPVs) are important in the development of human cancers, including cervical and oral tumors. However, most existing methods for HPV typing cannot routinely distinguish among the more than 100 distinct types of HPV or the natural HPV intratypic variants that have also been documented. To address this problem, we developed a novel method, general primer-denaturing high-performance liquid chromatography (GP-dHPLC), for the detection and typing of genital HPV using an automated 96-well plate format. GP-dHPLC uses general primer PCR (GP-PCR) to amplify the viral DNA and then analyzes the GP-PCR products by denaturing high-performance liquid chromatography (dHPLC). A number of different primer pairs with homology to most known genital HPV types were tested, and the L1C1-L1C2M pair specific for the L1 region of the viral genome was chosen. A set of HPV standard control patterns, consisting of those for HPV types 16, 18, 31, 33, 39, 45, 51, 52, 56, 58, 59, 6, and 11, was established for genital HPV typing. One hundred eighty-six frozen and formalin-fixed cervical cancer tissue samples were analyzed for the presence of HPV and the HPV type by this method, and 95.8% of them were found to contain HPV DNA. GP-dHPLC accurately discriminated among HPV variants that differed by as little as one nucleotide. Several new variants of HPV types 16, 18, 39, 45, 52, and 59 were identified. Moreover, multiple HPV infections were detected in 26.6% of the samples. Our results indicate that HPV typing by GP-dHPLC permits discrimination of common genital HPV types, detection of multiple HPV infections, and identification of HPV variants in clinical samples.
Molecular Analysis of
Cryptococcus neoformans
Mitochondrial Cytochrome
b
Gene Sequences
Authors: Biswas Swarajit Kumar , Wang Li , Yokoyama Koji , Nishimura Kazuko 
Published: December 2003

ABSTRACT

Mitochondrial cytochrome
b
genes (
cyt b
) of 40 strains of
Cryptococcus neoformans
were partially sequenced to determine the genetic relations. With the exception of the type strain of
C. neoformans
var.
neoformans
, all strains contained introns in their sequences. Analysis of 386 bp of coding sequence from each strain under investigation revealed a total of 27 (6.99%) variable nucleotide sites and categorized isolates of
C. neoformans
into nine
cyt b
types.
C. neoformans
var.
gattii
included
cyt b
types I to V, and
C. neoformans
var.
neoformans
comprised types VI to IX.
cyt b
types were correlated with serotypes. All strains with
cyt b
types I, IV, and V were serotype B. All other strains except IFM 5878 (serotype B) with
cyt b
types II and III were serotype C. Serotype D strains had
cyt b
types VI and IX, and serotype A strains were
cyt b
type VIII. Of four serotype AD strains, one was
cyt b
type VII and the remaining three were type VIII. The phylogenetic tree based on deduced amino acid sequences divided the strains only into
C. neoformans
var.
neoformans
and
C. neoformans
var.
gattii
. These results indicate that
cyt b
sequences are effective for DNA typing as well as phylogenetic analysis of
C. neoformans
.
Borna Disease Virus RNA in Immunocompromised Patients in Southwestern France
Authors: Cotto Emmanuelle , Neau Didier , Cransac-Neau Martine , Auriacombe Marc , Pellegrin Jean-Luc , Ragnaud Jean-Marie , Fillet Anne-Marie , Belnard Magali , Fleury Hervé , Lafon Marie-Edith 
Published: December 2003

ABSTRACT
Borna disease virus (BDV) is a neurotropic RNA virus with a wide host range. Human infections, although controversial, have been described in Europe, Asia, and the United States. The present study investigated the existence of BDV infections in immunocompromised human beings, namely, 82 human immunodeficiency virus (HIV)-infected and 80 therapeutically immunosuppressed patients. BDV p40 RNAs were detected in peripheral white blood cells with reverse transcription-nested PCR and hybridization in, respectively, 11 (13.41%) and 1 (1.25%) of the two groups of patients. BDV p24 RNAs were identified in only one of those. BDV RNA was detected in the absence of any neuropsychiatrical illness, suggesting that BDV infections may occur in asymptomatic carriers. The severity and particularity of cellular immunosuppression could explain the significantly increased detection of BDV RNA in HIV-infected patients.
Comparison of Antibiotic Resistance and Serotype Composition of Carriage and Invasive Pneumococci among Bangladeshi Children: Implications for Treatment Policy and Vaccine Formulation
Authors: Saha Samir K. , Baqui Abdullah H. , Darmstadt Gary L. , Ruhulamin M. , Hanif Mohammed , El Arifeen Shams , Santosham Mathuram , Oishi Kazunori , Nagatake Tsuyoshi , Black Robert E. 
Published: December 2003

ABSTRACT

The nasopharyngeal carriage of
Streptococcus pneumoniae
is thought to pose a risk for invasive pneumococcal diseases, and the evaluation of carriage strains is thus often used to inform antibiotic treatment and vaccination strategies for these diseases. In this study, the age-specific prevalences, resistance to antibiotics, and serotype distributions of 1,340 carriage strains were analyzed and compared to 71 pneumococcal strains isolated from the cerebrospinal fluid of children under 5 years old with meningitis. Overall, the nasal carriage rate was 47%. One-fourth (26%) of the infants under 1 month of age and one-half (48%) of the infants under 12 months of age were colonized with
S. pneumoniae
. Rural children were colonized earlier than those from urban areas. Approximately one-fourth and one-half of the cases of pneumococcal meningitis occurred in the first 3 and 6 months of life, respectively. The respective rates of resistance for carriage and meningitis strains to penicillin (7 and 3%), cotrimoxazole (77 and 69%), and erythromycin (2 and 1%) were similar, whereas chloramphenicol resistance was lower among carriage strains (3%) than among meningitis strains (15.5%). The predominant serogroups of carriage and invasive isolates were variable and widely divergent. Thus, hypothetical 7-, 9-, and 11-valent vaccines, based on the predominant carriage strains of the present study, would cover only 23, 26, and 30%, respectively, of the serotypes causing meningitis. Further, currently available 7-, 9-, and 11-valent vaccines would protect against only 26, 43, and 48%, respectively, of these meningitis cases. In conclusion, while the surveillance of carriage strains for resistance to antibiotics appears useful in the design of empirical treatment guidelines for invasive pneumococcal disease, data on the serotypes of carriage strains have limited value in vaccine formulation strategies, particularly for meningitis cases.
Risk Factors Associated with
Campylobacter jejuni
Infections in Curaçao, Netherlands Antilles
Authors: Endtz Hubert P. , van West Hanneke , Godschalk Peggy C. R. , de Haan Lidewij , Halabi Yaskara , van den Braak Nicole , Kesztyüs Barbara I. , Leyde Ewald , Ott Alewijn , Verkooyen Roel , Price Lawrence J. , Woodward David L. , Rodgers Frank G. , Ang C. Wim , van Koningsveld Rinske , van Belkum Alex , Gerstenbluth Izzy 
Published: December 2003

ABSTRACT

A steady increase in the incidence of Guillain-Barré syndrome (GBS) with a seasonal preponderance, almost exclusively related to
Campylobacter jejuni
, and a rise in the incidence of laboratory-confirmed
Campylobacter
enteritis have been reported from Curaçao, Netherlands Antilles. We therefore investigated possible risk factors associated with diarrhea due to epidemic
C. jejuni
. Typing by pulsed-field gel electrophoresis identified four epidemic clones which accounted for almost 60% of the infections. One hundred six cases were included in a case-control study. Infections with epidemic clones were more frequently observed in specific districts in Willemstad, the capital of Curaçao. One of these clones caused infections during the rainy season only and was associated with the presence of a deep well around the house. Two out of three GBS-related
C. jejuni
isolates belonged to an epidemic clone. The observations presented point toward water as a possible source of
Campylobacter
infections.
Molecular Evidence for Dissemination of Unique
Campylobacter jejuni
Clones in Curaçao, Netherlands Antilles
Authors: Duim Birgitta , Godschalk Peggy C. R. , van den Braak Nicole , Dingle Kate E. , Dijkstra Jeroen R. , Leyde Ewald , van der Plas Jan , Colles Frances M. , Endtz Hubert P. , Wagenaar Jaap A. , Maiden Martin C. J. , van Belkum Alex 
Published: December 2003

ABSTRACT

Campylobacter jejuni
isolates (
n
= 234) associated with gastroenteritis and the Guillain-Barré syndrome (GBS) in the island of Curaçao, Netherlands Antilles, and collected from March 1999 to March 2000 were investigated by a range of molecular typing techniques. Data obtained by pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), automated ribotyping, and sequence analysis of the short variable region of the flagellin gene (
flaA
) were analyzed separately and in combination. Similar groupings were obtained by all methods, with the data obtained by MLST and AFLP analysis exhibiting the highest degree of congruency. MLST identified 29 sequence types, which were assigned to 10 major clonal complexes. PFGE, AFLP analysis, and ribotyping identified 10, 9, and 8 of these clonal groups, respectively; however, these three techniques permitted subdivision of the clonal groups into more different types. Members of seven clonal groups comprising 107 isolates were obtained from November 1999 to February 2000, and no distinguishing characteristics were identified for two GBS-associated strains. The sequence type 41 (ST-41), ST-508, and ST-657 clonal complexes and their corresponding AFLP types have been rare or absent in the
Campylobacter
data sets described to date. We conclude that several clonal complexes of
C. jejuni
are associated with human disease in Curaçao, and some of these have not been reported elsewhere. Furthermore, given the observation that
C. jejuni
-associated diseases appear to be more severe from November to February, it can be speculated that this may be due to the presence of virulent clones with a limited span of circulation.
Detection of the Hepatitis B Virus X Protein (HBx) Antigen and Anti-HBx Antibodies in Cases of Human Hepatocellular Carcinoma
Authors: Hwang Guang-Yuh , Lin Chuang-Yu , Huang Li-Mei , Wang Yan-Hsiung , Wang Jing-Chyi , Hsu Ching-Ting , Yang Sheng-Shun , Wu Cheng-Chung 
Published: December 2003

ABSTRACT

Hepatitis B virus X protein (HBx) expressed in
Escherichia coli
DH5α by recombinant DNA technology was purified to homogeneity by use of glutathione-Sepharose beads. Immunological characterization of the recombinant HBx protein was performed. Specific binding between the anti-HBx monoclonal antibody and HBx protein showed the specificity of the recombinant HBx protein. The intact HBx protein of the factor Xa-digested glutathione
S
-transferase-HBx fusion protein was further purified and was used as an antigen for screening the titers of anti-HBx antibodies in sera. Titers of anti-HBx in sera from 20 patients with hepatocellular carcinoma (HCC), 20 patients with chronic hepatitis (CH), and 20 healthy individuals were evaluated by Western blotting and a quantitative enzyme-linked immunosorbent assay. The results indicated that 70% of sera from HCC patients and 5% of sera from CH patients contained antibodies with significant binding to the HBx protein. Western blotting of HBx protein in liver extracts from 20 HCC patients was also performed by using the anti-HBx monoclonal antibody. Results showed that 85% of HCC patients' liver tissues contained a specific HBx protein with the same molecular size as the purified intact HBx. Full correlation was found between anti-HBx antibody positivity in serum and HBx protein positivity in HCC tissues. The data demonstrated that the etiology of HCC is involved with hepatitis B virus (HBV) infection and that HBx in particular plays a role in the development of HBV-related HCC.
Concordance ofHelicobacter pyloriStrains within Families
Authors: Kivi Mårten , Tindberg Ylva , Sörberg Mikael , Casswall Thomas H. , Befrits Ragnar , Hellström Per M. , Bengtsson Carina , Engstrand Lars , Granström Marta 
Published: December 2003

ABSTRACTHelicobacter pyloriinfection is typically acquired in early childhood, and a predominantly intrafamilial transmission has been postulated. To what extent family members share the same strains is poorly documented. Our aim was to explore patterns of shared strains within families by using molecular typing. Family members ofH. pylori-infected 10- to 12-year-old index children identified in a school survey were invited to undergo gastroscopy. Bacterial isolates were typed with random amplified polymorphic DNA and PCR-restriction fragment length polymorphism of the genesureA-B,glmM, orflaA. The presence or absence of thecagpathogenicity island, a bacterial virulence factor, was determined by PCR. GelCompar II software, supplemented with visual inspection, was used in the cluster analysis. In 39 families, 104 individuals contributed 208 bacterial isolates from the antrum and corpus. A large proportion, 29 of 36 (81%) of the offspring in a sibship, harbored the same strain as at least one sibling. Mother-offspring strain concordance was detected in 10 of 18 (56%) of the families. Of 17 investigated father-offspring relations in eight families, none were strain concordant. Spouses were infected with the same strains in 5 of 23 (22%) of the couples. Different strains in the antrum and corpus were found in 8 of 104 (8%) of the subjects. Our family-based fingerprinting study demonstrates a high proportion of shared strains among siblings. Transmission between spouses seems to be appreciable. The data support mother-child and sib-sib transmission as the primary transmission pathways ofH. pylori.
Persistence of Two Genotypes of
Neisseria gonorrhoeae
during Transmission
Authors: Martin I. M. C. , Ghani A. , Bell G. , Kinghorn G. , Ison C. A. 
Published: December 2003

ABSTRACT

Isolates of
Neisseria gonorrhoeae
were tested using a highly discriminatory typing method,
opa
typing, to examine the genetic diversity over a 2-year study period of isolates from all consecutive patients with gonorrhea attending the Genitourinary Medicine clinic in Sheffield, United Kingdom. Two
opa
genotypes were detected throughout the 2-year time period and comprised 41% of all strains tested. The persistence of two
opa
types was investigated further to determine the apparent genetic stability, by examining the ability of isolates to undergo intragenic and intergenic recombination and mutation in vitro. Intragenic recombination or mutation involving the
opa
genes of
N. gonorrhoeae
in the selected isolates was not detected, but intergenic recombination did occur.
opa
genes of
N. gonorrhoeae
in vivo appear to diversify primarily through intergenic recombination. Intergenic recombination in vivo would require the presence of a mixed gonococcal infection, in which an individual is concurrently colonized with more than one strain of
N. gonorrhoeae
. We propose that the level of diversity of
opa
genotypes in a population is linked to the degree of sexual mixing of individuals and the incidence of mixed infections of
N. gonorrhoeae
.
Association of the Presence of
Helicobacter
in Gallbladder Tissue with Cholelithiasis and Cholecystitis
Authors: Silva Cíntia Presser , Pereira-Lima Júlio Carlos , Oliveira Adriana Gonçalves , Guerra Juliana Becattini , Marques Daniela Lemos , Sarmanho Letícia , Cabral Mônica Maria Demas Álvares , Queiroz Dulciene Maria Magalhães 
Published: December 2003

ABSTRACT

The presence of
Helicobacter
DNA species has been investigated in the biliary epithelium of patients with biliary diseases. However, conflicting results have been observed that may have been due to the small number of subjects studied, difficulty in obtaining a healthy control group, absence of controlling for confounding factors, or differences among populations. Therefore, we investigated the presence of
Helicobacter
species by culture and nested PCR of 16S rRNA genes in gallbladder tissue and bile from 46 Brazilian subjects with and 18 without cholelithiasis. The control group was mainly composed of liver donors and of patients who had submitted to cholecystectomy as part of the surgical treatment for morbid obesity. No
Helicobacter
species were grown from the bile or gallbladder tissues.
Helicobacter
DNA was detected in the gallbladder tissue and bile from 31.3 and 42.9% of the patients, respectively. In a logistic regression model, cholelithiasis was positively and independently associated with the female gender (
P
= 0.02), increasing age (
P
= 0.002), and the presence of
Helicobacter
DNA in the gallbladder tissue (
P
= 0.009). The presence of
Helicobacter
DNA in the bile was not associated with cholelithiasis (
P
= 0.8). A significant association between the presence of
Helicobacter
DNA in the gallbladder epithelium and histological cholecystitis, even after adjusting for gender and age (
P
= 0.002), was also observed. The sequences of the 16S rRNA genes were >99% similar to that of
Helicobacter pylori
. In conclusion, our results support the hypothesis that
Helicobacter
is associated with the pathogenesis of human cholelithiasis and cholecystitis.
Use of the Roche LightCycler Instrument in a Real-Time PCR for
Trichomonas vaginalis
in Urine Samples from Females and Males
Authors: Hardick Justin , Yang Samuel , Lin Shin , Duncan Della , Gaydos Charlotte 
Published: December 2003

ABSTRACT

Trichomonas vaginalis
is the agent of a highly prevalent sexually transmitted infection (STI) that can result in vaginitis, urethritis, and preterm birth. Traditional methods of diagnosis, including wet preparation, can be unreliable. In this study, we describe the adaptation of an existing PCR method for specific detection of
T. vaginalis
DNA into a rapid real-time PCR assay based on fluorescence resonance energy transfer (FRET) probe chemistry. The FRET-based assay described demonstrated high sensitivity with a detection limit of 1.06 organisms, as well as a high specificity. A total of 253 urine samples collected prospectively from both men and women were tested for
T. vaginalis
DNA with both the FRET-based assay and a previously validated PCR assay. When the validated PCR assay was used as the “gold standard” and after discrepancies had been resolved, our FRET-based assay demonstrated an analytical sensitivity and specificity of 90.1 and 100%, respectively. Overall results suggest that FRET-based assays can provide rapid, accurate, and high-throughput detection of
T. vaginalis
and may prove useful in clinical settings and for large-scale screening programs.
Molecular Epidemiology of Penicillin-Susceptible Non-β-Lactam-Resistant
Streptococcus pneumoniae
Isolates from Greek Children
Authors: Bogaert D. , Hermans P. W. M. , Grivea I. N. , Katopodis G. S. , Mitchell T. J. , Sluijter M. , de Groot R. , Beratis N. G. , Syrogiannopoulos G. A. 
Published: December 2003

ABSTRACT

A total of 128
Streptococcus pneumoniae
isolates that were susceptible to penicillin but resistant to non-β-lactam agents were isolated from young carriers in Greece and analyzed by antibiotic susceptibility testing, serotyping, restriction fragment end labeling (RFEL), and antibiotic resistance genotyping. The serotypes 6A/B (49%), 14 (14%), 19A/F (11%), 11A (9%), 23A/F (4%), 15B/C (2%), and 21 (2%) were most prevalent in this collection. Of the isolates, 65% were erythromycin resistant, while the remaining isolates were tetracycline and/or trimethoprim-sulfamethoxazole resistant. Fifty-nine distinct RFEL types were identified. Twenty different RFEL clusters, harboring 2 to 19 strains each, accounted for 76% of all strains. Confirmatory multilocus sequence typing analysis of the genetic clusters showed the presence of three international clones (Tennessee
23F
-4, England
14
-9, and Greece
6B
-22) representing 30% of the isolates. The
erm
(B) gene was present in 70% of the erythromycin-resistant isolates, whereas 18 and 8% contained the
mef
(A) and
mef
(E) genes, respectively. The pneumococci representing
erm
(B),
erm
(A), and
mef
genes belonged to distinct genetic clusters. In total, 45% of all isolates were tetracycline resistant. Ninety-six percent of these isolates contained the
tet
(M) gene. In conclusion, penicillin-susceptible pneumococci resistant to non-β-lactams are a genetically heterogeneous group displaying a variety of genotypes, resistance markers, and serotypes. This suggests that multiple genetic events lead to non-β-lactam-resistant pneumococci in Greece. Importantly, most of these genotypes are capable of disseminating within the community.