bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel 180- and 480-Base-Pair Insertions in African and African-American Strains of
Helicobacter pylori
Authors: McNulty Shannon L. , Mole Beth M. , Dailidiene Daiva , Segal Issy , Ally Reid , Mistry Rajesh , Secka Ousman , Adegbola Richard A. , Thomas Julian E. , Lenarcic Erik M. , Peek Richard M. , Berg Douglas E. , Forsyth Mark H. 
Published: December 2004

ABSTRACT

Helicobacter pylori
is a genetically diverse bacterial species that chronically infects human stomachs and sometimes causes severe gastroduodenal disease. Studies of polymorphic DNA sequences can suggest geographic origins of individual strains. Here, we describe a 180-bp insertion (ins180), which is just after the translation stop of a gene of unknown function, near the promoter of
jhp0152-
jhp0151
two-component signal transduction genes in strain J99, and absent from this site in strain 26695. This ins180 insertion was found in 9 of 9 Gambian (West African), 9 of 20 (45%) South African, and 9 of 40 (23%) Spanish strains but in only 2 of 20 (10%) North American strains and none of 20 Lithuanian, 20 Indian, and 20 Japanese strains. Four South African isolates that lacked ins180 and that belonged to an unusual outlier group contained a 480-bp insertion at this site (ins480), whereas none of 181 other strains screened contained ins480. In further tests 56% (10 of 18) of strains from African Americans but only 17% (3 of 18) of strains from Caucasian Americans carried ins180 (
P
< 0.05). Thus, the
H. pylori
strains of modern African Americans seem to retain traces of African roots, despite the multiple generations since their ancestors were taken from West Africa. Fragmentary ins180-like sequences were found at numerous sites in
H. pylori
genomes, always between genes. Such sequences might affect regulation of transcription and could facilitate genome rearrangement by homologous recombination. Apparent differences between African-American and Caucasian-American
H. pylori
gene pools may bear on our understanding of
H. pylori
transmission and disease outcome.
High Prevalence of Natural
Chlamydophila
Species Infection in Calves
Authors: Jee JunBae , Degraves Fred J. , Kim TeaYoun , Kaltenboeck Bernhard 
Published: December 2004

ABSTRACT

We investigated the acquisition and prevalence of
Chlamydophila
sp. infection in calves. Specimens were collected at weekly intervals from birth to week 12 postpartum from 40 female Holstein calf-dam pairs in a dairy herd. Real-time PCR detected, quantified, and differentiated
Chlamydophila
23S rRNA gene DNA from vaginal cytobrush swabs and milk samples. Chemiluminescence enzyme-linked immunosorbent assay with lysed
Chlamydophila abortus
or
Chlamydophila pecorum
elementary body antigens quantified antibodies against
Chlamydophila
spp. in sera.
Chlamydophila
sp. DNA was found in 61% of calves and 20% of dams in at least one positive quantitative PCR. In calves, clinically inapparent
C. pecorum
infection with low organism loads was fivefold more prevalent than
C. abortus
infection and was most frequently detected by vaginal swabs compared to rectal or nasal swabs. In dams,
C. abortus
dominated in milk and
C. pecorum
dominated in the vagina. The group size of calves correlated positively (
P
< 0.01) with
Chlamydophila
infection in quadratic, but not linear, regression. Thus, a doubling of the group size was associated with a fourfold increase in frequency and intensity of
Chlamydophila
infection. For groups of 14 or 28 calves, respectively, logistic regression predicted a 9 or 52% probability of infection of an individual calf and a 52 or 99.99% probability of infection of the group. Anti-
Chlamydophila
immunoglobulin M antibodies in
Chlamydophila
PCR-positive calves and dams and in dams that gave birth to calves that later became positive were significantly higher than in PCR-negative animals (
P
≤ 0.02). Collectively, crowding strongly enhances the frequency and intensity of highly prevalent
Chlamydophila
infections in cattle.
Emergence and Spread of Community-Associated Methicillin-ResistantStaphylococcus aureusin Rural Wisconsin, 1989 to 1999
Authors: Stemper Mary E. , Shukla Sanjay K. , Reed Kurt D. 
Published: December 2004

ABSTRACTWe investigated the emergence and spread of community-associated strains of methicillin-resistantStaphylococcus aureus(CA-MRSA) in central and northern Wisconsin by determining the temporal and clonal relationships and geographic expansion among 581 of 956 clinical isolates of MRSA collected between 1989 and 1999. Based on EcoRI plasmid profiles (PP), two types, PP-11 and PP-13, were highly stable over time and were consistently associated with multidrug-sensitive strains recovered from outpatients treated at Native American community clinics. Pulsed-field gel electrophoresis (PFGE) yielded six major clonal groups (MCGs) and 19 minor clonal groups. The six MCGs represented 82% of the isolates. All strains with either PP-11 or -13 were present in MCG-2. Eighty-nine percent of the isolates in MCG-2 originated from Native American clinics, and 90% belonged to two PFGE types (19 and 20), the types associated with an outbreak of MRSA in a Native American community in 1992. MCG-2 isolates were multidrug sensitive, harbored type IVa staphylococcal cassette chromosomemec, and were very closely related by PFGE to the Midwestern CA-MRSA strain MW2. MCG-2 strains were mostly obtained from skin infections and affected patients with a mean age of 24 (±18.0) years. MCG-2 strains spread to four additional Native American communities and 20 other communities. Our findings suggest that CA-MRSA in Wisconsin likely originated in Native American communities in the early 1990s and since has become widespread throughout the state. Two early CA-MRSA strains (WI-33 and WI-34) in Wisconsin represent progenitors of the MW2 strain, based on their almost indistinguishable genotypic characteristics.
Clinical and Laboratory Features of
Mycobacterium porcinum
Authors: Wallace Richard J. , Brown-Elliott Barbara A. , Wilson Rebecca W. , Mann Linda , Hall Leslie , Zhang Yansheng , Jost Kenneth C. , Brown June M. , Kabani Amin , Schinsky Mark F. , Steigerwalt Arnold G. , Crist Christopher J. , Roberts Glenn D. , Blacklock Zeta , Tsukamura Michio , Silcox Vella , Turenne Christine 
Published: December 2004

ABSTRACT

Recent molecular studies have shown
Mycobacterium porcinum
, recovered from cases of lymphadenitis in swine, to have complete 16S rDNA sequence identity and >70% DNA-DNA homology with human isolates within the
M. fortuitum
third biovariant complex. We identified 67 clinical and two environmental isolates of the
M. fortuitum
third biovariant sorbitol-negative group, of which 48 (70%) had the same PCR restriction enzyme analysis (PRA) profile as the
hsp65
gene of
M. porcinum
(ATCC 33776
T
) and were studied in more detail. Most U.S. patient isolates were from Texas (44%), Florida (19%), or other southern coastal states (15%). Clinical infections included wound infections (62%), central catheter infections and/or bacteremia (16%), and possible pneumonitis (18%). Sequencing of the 16S rRNA gene (1,463 bp) showed 100% identity with
M. porcinum
ATCC 33776
T
. Sequencing of 441 bp of the
hsp65
gene showed four sequevars that differed by 2 to 3 bp from the porcine strains. Clinical isolates were positive for arylsulfatase activity at 3 days, nitrate, iron uptake,
d
-mannitol, i-
myo
-inositol, and catalase at 68°C. They were negative for
l
-rhamnose and
d
-glucitol (sorbitol). Clinical isolates were susceptible to ciprofloxacin, sulfamethoxazole, and linezolid and susceptible or intermediate to cefoxitin, clarithromycin, imipenem, and amikacin.
M. porcinum
ATCC 33776
T
gave similar results except for being nitrate negative. These studies showed almost complete phenotypic and molecular identity between clinical isolates of the
M. fortuitum
third biovariant
d
-sorbitol-negative group and porcine strains of
M. porcinum
and confirmed that they belong to the same species. Identification of
M. porcinum
presently requires
hsp65
gene PRA or 16S rRNA or
hsp65
gene sequencing.
Varicella Seroprevalence and Molecular Epidemiology of Varicella-Zoster Virus in Argentina, 2002
Authors: Dayan Gustavo H. , Panero María S. , Debbag Roberto , Urquiza Ana , Molina Marta , Prieto Susana , del Carmen Perego María , Scagliotti Graciela , Galimberti Diana , Carroli Guillermo , Wolff Cristina , Schmid D. Scott , Loparev Vladimir , Guris Dalya , Seward Jane 
Published: December 2004

ABSTRACT
There is limited data on immunity against varicella-zoster virus (VZV) in adults in different parts of Argentina, and it is not known which VZV strains are circulating in Argentina. The objectives of this study were as follows: (i) to evaluate seroprevalence of varicella among adults, assessing the accuracy of clinical history and determining the sociodemographic factors associated with seropositivity; and (ii) to determine the VZV strains circulating in Argentina. A cross-sectional serological survey enrolling 2,807 women aged 15 to 49 years attending public health-care settings in four cities in Argentina (i.e., Buenos Aires, Salta, Mendoza, and Rosario) and one rural area was conducted from August to November 2002. Specimens for identification of VZV strains were obtained from vesicular lesions from 13 pediatric patients with varicella from different areas of the country. PCR amplification was used for genotyping. The overall seroprevalence of varicella antibodies was 98.5% (95% confidence interval, 98.0 to 98.9), ranging from 97.2% in central Buenos Aires to 99.3% in southern Buenos Aires and Salta. Varicella seroprevalence increased with age. Crowding and length of residence in the same place were associated with seropositivity. The positive predictive value of varicella history for immunity to varicella was 99.4%; however, the negative predictive value was 2.5%. The European genotype was identified in all viral specimens. In Argentina, seroprevalence in women more than 15 years old was high regardless of the area of residence. Negative or uncertain varicella history was not a good predictor of immunity. VZV genotype was stable in all areas of the country.
Detection of Immunoglobulin M Antibodies Specific for
Toxoplasma gondii
with Increased Selectivity for Recently Acquired Infections
Authors: Kaul Ravi , Chen Peilin , Binder Steven R. 
Published: December 2004

ABSTRACT

Toxoplasma gondii
infections can cause serious complications in pregnant women, leading to miscarriage, stillbirth, and birth defects. Definitive diagnosis of
T. gondii
acute infection is therefore critical for the clinical management of a mother and her fetus. Positive immunoglobulin M (IgM) results are not sufficient as evidence of recent infection, as these antibodies are often present for many months. Further, IgG avidity and differential agglutination tests, two tests used by reference laboratories to distinguish between recent and past infections, are not always in agreement, and both methods yield a significant number of indeterminate results. We report the development of a new toxoplasma IgM immunoassay that is performed by using a bead-based immunoassay on an automated analyzer (BioPlex 2200). Initial validation included 204 samples from pregnant women and 198 samples from asymptomatic healthy adults. An overall specificity of 99% was observed. Further, 100% sensitivity for acute infections was observed for 10 well-characterized seroconversion panels. We then examined 50 samples from pregnant women, all of which were IgM positive by ELISA, which had been fully evaluated in a reference laboratory. Of the 50 samples, 34 (68%) tested positive in the BioPlex 2200 toxoplasma IgM assay, of which 32 of 34 (94%) exhibited an acute or equivocal pattern by differential agglutination. Of the 16 negative samples, 15 (94%) showed high-IgG-avidity antibodies. Collectively, these results suggest that this new toxoplasma assay shows a preferential response to IgM antibodies produced by recent infections, reducing the number of positive results for pregnant women that will require extensive additional clinical evaluation.
Phenotypic and Molecular Detection of CTX-M-β-Lactamases Produced by
Escherichia coli
and
Klebsiella
spp
Authors: Pitout Johann D. D. , Hossain Ashfaque , Hanson Nancy D. 
Published: December 2004

ABSTRACT

Organisms producing CTX-M-β-lactamases are emerging around the world as a source of resistance to oxyiminocephalosporins such as cefotaxime (CTX). However, the laboratory detection of these strains is not well defined. In this study, a molecular detection assay for the identification of CTX-M-β-lactamase genes was developed and used to investigate the prevalence of these enzymes among clinical isolates of
Escherichia coli
and
Klebsiella
species in the Calgary Health Region during 2000 to 2002. In addition, National Committee for Clinical Laboratory Standards (NCCLS) recommendations were evaluated for the ability to detect isolates with CTX-M extended-spectrum β-lactamases (ESBLs). The PCR assay consisted of four primer sets and demonstrated 100% specificity and sensitivity for detecting different groups of CTX-M-β-lactamases in control strains producing well-characterized ESBLs. Using these primer sets, 175 clinical strains producing ESBLs were examined for the presence of CTX-M enzymes; 24 (14%) were positive for
bla
CTX-M-1-like
genes, 95 (54%) were positive for
bla
CTX-M-14-like
genes, and the remaining 56 (32%) were negative for
bla
CTX-M
genes. Following the NCCLS recommendations for ESBL testing, all of the control and clinical strains were detected when screened with cefpodoxime and when both cefotaxime and ceftazidime with clavulanate were used as confirmation tests.
Simultaneous Detection of
Staphylococcus aureus
and Coagulase-Negative Staphylococci in Positive Blood Cultures by Real-Time PCR with Two Fluorescence Resonance Energy Transfer Probe Sets
Authors: Sakai H. , Procop G. W. , Kobayashi N. , Togawa D. , Wilson D. A. , Borden L. , Krebs V. , Bauer T. W. 
Published: December 2004

ABSTRACT

A real-time PCR assay that uses two fluorescence resonance energy transfer probe sets and targets the
tuf
gene of staphylococci is described here. One probe set detects the
Staphylococcus
genus, whereas the other probe set is specific for
Staphylococcus aureus
. One hundred thirty-eight cultured isolates, which contained 41 isolates of staphylococci representing at least nine species, and 100 positive blood cultures that contained gram-positive cocci in clusters were tested. This assay was 100% sensitive and 100% specific for the detection of the
Staphylococcus
genus and of
S. aureus
.
Diarrhea Caused by Rotavirus in Children Less than 5 Years of Age in Hanoi, Vietnam
Authors: Nguyen Trung Vu , Le Van Phung , Le Huy Chinh , Weintraub Andrej 
Published: December 2004

ABSTRACT

Group A rotaviruses are the major cause of diarrhea in young children worldwide. From March 2001 to April 2002, 836 children less than 5 years of age were investigated in Hanoi, Vietnam. This included 587 children with diarrhea and 249 age-matched controls. Group A rotavirus was identified in 46.7% of the children with diarrhea and 3.6% of the controls, which was a significant difference. Within the diarrhea group, the highest prevalence was seen in children from 13 to 24 months of age, and the prevalence was higher in males than in females. The symptoms of acute diarrhea caused by rotavirus were watery diarrhea, vomiting, fever, and dehydration. A higher prevalence of rotavirus detection was obtained for children who had all of these symptoms, followed by those who had diarrhea with vomiting-dehydration, fever-dehydration, and dehydration. The high rates occurred from September to December, although the infection was encountered all year round. In 58 patients (21.2% of the rotavirus-infected children), rotavirus infection was detected in association with either diarrheagenic
Escherichia coli
or
Shigella
spp. The most frequent combinations were rotavirus-enteroaggregative
E. coli
and rotavirus-enteropathogenic
E. coli
. At least one enteropathogen was identified from about 64% percent of the samples. The bacterial infection may not have given rise to clinical symptoms of such severity. The present study demonstrates the burden of rotavirus diarrhea in Hanoi, Vietnam. Continuous surveillance of diarrhea caused by rotavirus in young children would play an important role in diagnosis, treatment, and prophylaxis in order to improve the health of children in Vietnam.
Clonal Expansion of a Globally Disseminated Lineage ofMycobacterium tuberculosiswith Low IS6110Copy Numbers
Authors: Warren R. M. , Victor T. C. , Streicher E. M. , Richardson M. , van der Spuy G. D. , Johnson R. , Chihota V. N. , Locht C. , Supply P. , van Helden P. D. 
Published: December 2004

ABSTRACTKnowledge of the clonal expansion ofMycobacterium tuberculosisand accurate identification of predominant evolutionary lineages in this species remain limited, especially with regard to low-IS6110-copy-number strains. In this study, 170M. tuberculosisisolates with ≤6 IS6110insertions identified in Cape Town, South Africa, were characterized by principal genetic grouping, restriction fragment length polymorphism analysis, spoligotyping, IS6110insertion site mapping, and variable-number tandem repeat (VNTR) typing. These analyses indicated that all but one of the isolates analyzed were members of principal genetic group 2 and of the same low-IS6110-copy-number lineage. The remaining isolate was a member of principal genetic group 1 and a different low-IS6110-copy-number lineage. Phylogenetic reconstruction suggests clonal expansion through sequential acquisition of additional IS6110copies, expansion and contraction of VNTR sequences, and the deletion of specific direct-variable-repeat sequences. Furthermore, comparison of the genotypic data of 91 representative low-IS6110-copy-number isolates from Cape Town, other southern African regions, Europe, and the United States suggests that certain low-IS6110-copy-number strain spoligotypes and IS6110fingerprints were acquired in the distant past. These clones have subsequently become widely disseminated and now play an important role in the global tuberculosis epidemic.
Genome Diversity of
Pseudomonas aeruginosa
Isolates from Cystic Fibrosis Patients and the Hospital Environment
Authors: Finnan Shirley , Morrissey John P. , O'Gara Fergal , Boyd E. Fidelma 
Published: December 2004

ABSTRACT

Pseudomonas aeruginosa
is a gram-negative rod that is ubiquitous in nature.
P. aeruginosa
is also the quintessential opportunistic pathogen, causing a wide variety of infections in compromised hosts. In cystic fibrosis patients,
P. aeruginosa
is the leading cause of death. In this study, the evolutionary genetic relationships among 17
P. aeruginosa
isolates were examined by comparative sequence analysis of the housekeeping gene encoding malate dehydrogenase and the chaperone
groEL
. The
P. aeruginosa
isolates examined included the sequenced strain PAO1, 11 strains recovered from cystic fibrosis patients in Ireland, 4 environmental isolates recovered from a hospital environment, and 1 isolate recovered from a plant rhizosphere. Phylogenetically, clinical and environmental isolates clustered together with one another on the
mdh
gene tree. At the
groEL
locus, among the 17 isolates examined, only two polymorphic sites were observed, highlighting the close genetic relationship between isolates from these different environments. Phenotypic analysis of 12 traits among our isolates, however, found that only clinical isolates produced phenazines and elastase. Furthermore, molecular analysis of the distribution of 15 regions associated with virulence showed that two of the environmental isolates examined lacked the majority of regions. Among the clinical isolates examined, the 15 virulence regions were variably present. The distribution of two prophages (Bacto1, Pf1) was also determined, with most isolates encoding both these regions. Of the four genomic islands (the flagellum island and PAGI
-
1, -2, and -3) examined, only two isolates contained the flagellum island, and PAGI
-
1, -2, and -3 were absent from all isolates tested. Our data demonstrate the significant role horizontal gene transfer and recombination, together with gene loss, play in the evolution of this important human pathogen.
Detection of
gyrA
and
parC
Mutations Associated with Ciprofloxacin Resistance in
Neisseria gonorrhoeae
by Use of Oligonucleotide Biochip Technology
Authors: Zhou Wenming , Du Weidong , Cao Huimin , Zhao Jianlong , Yang Sen , Li Wei , Shen Yujun , Zhang Shumei , Du Wenhui , Zhang Xuejun 
Published: December 2004

ABSTRACT

An oligonucleotide biochip that specifically detects point mutations in the
gyrA
and
parC
genes of
Neisseria gonorrhoeae
was designed and subsequently evaluated with 87 untreated clinical specimens. The susceptibilities of the
N. gonorrhoeae
strains were tested to determine the prevalence of ciprofloxacin-resistant strains in Anhui Province, People's Republic of China. Conventional DNA sequencing was also performed to identify mutations in
gyrA
and
parC
and to confirm the biochip data. The study demonstrates that all of the point mutations in the
gyrA
and
parC
genes of
N. gonorrhoeae
were easily discriminated by use of the oligonucleotide biochip. Fifteen different alteration patterns involved in the formation of ciprofloxacin resistance were identified by the biochip assay. Double mutations in both Ser91 and Asp95 of the GyrA protein were seen in all nonsensitive isolates. Double mutations in Ser91 and Asp95 of GyrA plus mutation of Glu91 or Ser87 of the ParC protein lead to significant high-level resistance to ciprofloxacin in
N. gonorrhoeae
isolates. The results obtained by use of the oligonucleotide biochip were identical to those obtained by use of DNA sequencing. In conclusion, the oligonucleotide biochip technology has potential utility for the rapid and reliable identification of point mutations in the drug resistance genes of
N. gonorrhoeae.
Real-Time PCR Assay for a Unique Chromosomal Sequence of
Bacillus anthracis
Authors: Bode Elizabeth , Hurtle William , Norwood David 
Published: December 2004

ABSTRACT

Real-time PCR has become an important method for the rapid identification of
Bacillus anthracis
since the 2001 anthrax mailings. Most real-time PCR assays for
B. anthracis
have been developed to detect virulence genes located on the pXO1 and pXO2 plasmids. In contrast, only two published chromosomal targets exist, the
rpoB
gene and the
gyrA
gene. In the present study, subtraction-hybridization with a plasmid-cured
B. anthracis
tester strain and a
Bacillus cereus
driver was used to find a unique chromosomal sequence. By targeting this region, a real-time assay was developed with the Ruggedized Advanced Pathogen Identification Device. Further testing has revealed that the assay has 100% sensitivity and 100% specificity, with a limit of detection of 50 fg of DNA. The results of a search for sequences with homology with the BLAST program demonstrated significant alignment to the recently published
B. anthracis
Ames strain, while an inquiry for protein sequence similarities indicated homology with an abhydrolase from
B. anthracis
strain A2012. The importance of this chromosomal assay will be to verify the presence of
B. anthracis
independently of plasmid occurrence.