bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of Serogroups and Genotypes among Disease-Associated and Carried Isolates of
Neisseria meningitidis
from the Czech Republic, Greece, and Norway
Authors: Yazdankhah Siamak P. , Kriz Paula , Tzanakaki Georgina , Kremastinou Jenny , Kalmusova Jitka , Musilek Martin , Alvestad Torill , Jolley Keith A. , Wilson Daniel J. , McCarthy Noel D. , Caugant Dominique A. , Maiden Martin C. J. 
Published: November 2004

ABSTRACT
The distribution of serogroups and multilocus sequence types (STs) in collections of disease-associated and carried meningococci from the period 1991 to 2000 in three European countries (the Czech Republic, Greece, and Norway) was investigated. A total of 314 patient isolates and 353 isolates from asymptomatic carriers were characterized. The frequency distributions of serogroups and clone complexes differed among countries and between disease and carrier isolate collections. Highly significant differentiation was seen at each housekeeping locus. A marked positive association of serogroup C with disease was evidenced. The ST-11 complex was strongly positively associated with disease; associations for other clone complexes were weaker. The genetic diversity of the clone complexes differed. A single ST dominated the ST-11 clone complex, while the ST-41/44 complex exhibited greater levels of diversity. These data robustly demonstrated differences in the distribution of meningococcal genotypes in disease and carrier isolates and among countries. Further, they indicated that differences in genotype diversity and pathogenicity exist between meningococcal clone complexes.
Real-Time Quantitative PCR Assays for Detection andMonitoring of Pathogenic Human Viruses in ImmunosuppressedPediatricPatients
Authors: Watzinger F. , Suda M. , Preuner S. , Baumgartinger R. , Ebner K. , Baskova L. , Niesters H. G. M. , Lawitschka A. , Lion T. 
Published: November 2004

ABSTRACT

A
panel of 23 real-time PCR assays based on
Taq
Man
technology has been developed for the detection and monitoring of 16
different viruses and virus families including human polyomaviruses BK
virus and JC virus, human herpesviruses 6, 7, and 8, human
adenoviruses, herpes simplex viruses 1 and 2, varicella-zoster virus,
cytomegalovirus, Epstein-Barr virus, parvovirus B19, influenza A and B
viruses, parainfluenza viruses 1 to 3, enteroviruses, and respiratory
syncytial virus. The test systems presented have a broad dynamic range
and display high sensitivity, reproducibility, and specificity.
Moreover, the assays allow precise quantification of viral load in a
variety of clinical specimens. The ability to use uniform PCR
conditions for all assays permits simultaneous processing and detection
of many different viruses, thus economizing the diagnostic work. Our
observations based on more than 50,000 assays reveal the potential of
the real-time PCR tests to facilitate early diagnosis of infection and
to monitor the kinetics of viral proliferation and the response to
treatment. We demonstrate that, in immunosuppressed patients with
invasive virus infections, surveillance by the assays described may
permit detection of increasing viral load several days to weeks prior
to the onset of clinical symptoms. In virus infections for which
specific treatment is available, the quantitative PCR assays presented
provide reliable diagnostic tools for timely initiation of appropriate
therapy and for rapid assessment of the efficacy of antiviral treatment
strategies.
Assessment of the Target-Capture PCR Hepatitis B Virus (HBV) DNA Quantitative Assay and Comparison with Commercial HBV DNA Quantitative Assays
Authors: Shyamala Venkatakrishna , Arcangel Phillip , Cottrell Joshua , Coit Doris , Medina-Selby Angelica , McCoin Colin , Madriaga Dennis , Chien David , Phelps Bruce 
Published: November 2004

ABSTRACT

Recent clinical studies suggest that hepatitis B virus (HBV) load and genotype may be independent predictors of responses to antiviral therapies. However, it is difficult for clinicians to accurately determine viral loads in patient samples because results—both the values and the units of measure—can vary greatly among different tests. Accordingly, the World Health Organization (WHO) has produced the first international standard for HBV DNA for nucleic acid amplification technology (NAT) assays. In the present study, we describe the performance of the target-capture PCR HBV DNA quantitative assay for the quantitation of HBV DNA in clinical samples and reference panels. The range of quantitation was between 50 and 10
10
IU/ml. The sensitivity and accuracy of the target-capture PCR assay were demonstrated by using the HBV panel from Quality Control for Medical Diagnostics (QCMD) and the WHO HBV DNA standard. The target-capture PCR assay quantitated the six genotype A members of the QCMD panel and dilutions of the WHO HBV DNA standard within an accuracy of 74 to 142%. Compared to current serological methods, the assay offers window period reductions of 19 days prior to HBV surface antigen and 26 days prior to HBV e antigen detection. The target-capture PCR assay was also compared with four commercially available NAT assays, and the various units of measure were standardized with respect to the international units of the WHO HBV DNA standard. The target-capture PCR assay is a sensitive, accurate, high-throughput, rapid, and reproducible assay for the determination of HBV loads.
Development of a PCR-Restriction Fragment Length Polymorphism Assay for the Epidemiological Analysis of Shiga Toxin-Producing
Escherichia coli
Authors: Shima Kensuke , Terajima Jun , Sato Toshio , Nishimura Kazuhiko , Tamura Kazumichi , Watanabe Haruo , Takeda Yoshifumi , Yamasaki Shinji 
Published: November 2004

ABSTRACT

Six characteristic regions (I to VI) were identified in Shiga toxin 2 (Stx2) phages (T. Sato, T. Shimizu, M. Watarai, M. Kobayashi, S. Kano, T. Hamabata, Y. Takeda, and S. Yamasaki, Gene 309:35-48, 2003). Region V, which is ca. 10 kb in size and is located in the upstream region of the Stx operons, includes the most distinctive region among six Stx phages whose genome sequences have been determined. In this study, we developed a PCR-restriction fragment length polymorphism (RFLP) assay for the epidemiological analysis of Shiga toxin-producing
Escherichia coli
(STEC) on the basis of the diversity of region V. When region V was amplified by long and accurate-PCR (LA-PCR) with five control
E. coli
strains carrying six different Stx phages such as
E. coli
strains C600 (Stx1 phage), C600 (933W phage), C600 (Stx2 phage-I), C600 (Stx2 phage-II), and O157:H7 Sakai strain RIMD0509952 (VT1-Sakai phage and VT2-Sakai phage), an expected size of the band was obtained. Restriction digest of each PCR product with BglI or EcoRV also gave the expected sizes of banding patterns and discriminated the RFLPs of five control strains. When a total of 204 STEC O157 strains were analyzed by LA-PCR, one to three bands whose sizes ranged from 8.2 to 14 kb were obtained. Two STEC O157 strains, however, did not produce any bands. Subsequent restriction digest of the PCR products with BglI or EcoRV differentiated the RFLPs of 202 STEC O157 strains into 24 groups. The RFLP patterns of pulsed-field gel electrophoresis (PFGE) of representative strains of STEC O157 divided into 24 groups were well correlated with those of PCR-RFLP when STEC O157 strains were isolated in the same time period and in the close geographic area. To evaluate the PCR-RFLP assay developed here, ten strains, each isolated from four different outbreaks in different areas in Japan (Tochigi, Hyogo, Aichi, and Fukuoka prefecture), were examined to determine whether the strains in each group showed the same RFLP patterns in the PCR-RFLP assay. In accordance with the results of PFGE except for strains isolated in an area (Fukuoka), which did not produce any amplicon, ten strains in each group demonstrated the same RFLP pattern. Taken together, these data suggest that the PCR-RFLP based on region V is as useful as PFGE but perhaps more simple and rapid than PFGE for the molecular epidemiological analysis of STEC strains during sporadic and common source outbreaks.
Carious Dentine Provides a Habitat for a Complex Array of Novel
Prevotella
-Like Bacteria
Authors: Nadkarni Mangala A. , Caldon C. Elizabeth , Chhour Kim-Ly , Fisher Ilana P. , Martin F. Elizabeth , Jacques Nicholas A. , Hunter Neil 
Published: November 2004

ABSTRACT

Previous analysis of the microbiology of advanced caries by culture and real-time PCR emphasized the high incidence and abundance of gram-negative anaerobic species, particularly
Prevotella
-like bacteria. The diversity of
Prevotella
-like bacteria was further explored by analyzing pooled bacterial DNA from lesions of carious dentine. This was achieved by amplification of a region of the 16S ribosomal DNA with a
Prevotella
genus-specific forward primer and a universal bacterial reverse primer, followed by cloning and sequencing. Cultured
Prevotella
species commonly associated with oral tissues constituted only 12% of the
Prevotella
clones isolated from advanced carious lesions. The remaining 88% consisted of a diverse range of phylotypes. These included five clusters of previously recognized but uncultured oral
Prevotella
spp. and a major cluster containing
Prevotella
-like bacteria most closely related to uncharacterized rumen bacteria. Cluster-specific primers were designed, and the numbers of bacteria within clusters were quantified by real-time PCR, confirming the abundance of these organisms. The data indicated that advanced dental caries provides a unique environment for a complex array of novel and uncultured
Prevotella
and
Prevotella
-like bacteria which, in some cases, may dominate the diverse polymicrobial community associated with the disease.
Quantification of
Leishmania infantum
DNA by a Real-Time PCR Assay with High Sensitivity
Authors: Mary Charles , Faraut Françoise , Lascombe Laurie , Dumon Henri 
Published: November 2004

ABSTRACT

A real-time PCR was developed to quantify
Leishmania infantum
kinetoplast DNA and optimized to reach a sensitivity of 0.0125 parasites/ml of blood. In order to analyze the incidence of heterogeneity and number of minicircles, we performed comparative PCR by using the
Leishmania
DNA polymerase gene as a reporter. Assays performed in both promastigote and amastigote stages showed variations among different
L. infantum
and
Leishmania donovani
strains and the stability of the minicircle numbers for a particular strain. Analysis of blood samples from a patient who presented with Mediterranean visceral leishmaniasis confirmed the reliability of such an assay for
Leishmania
quantification in biological samples and allowed an estimation of positivity thresholds of classical tests used for direct diagnosis of the disease; positivity thresholds were in the range of 18 to 42, 0.7 to 42, and 0.12 to 22.5 parasites/ml for microscopic examination, culture, and conventional PCR, respectively. At the time of diagnosis, parasitemia could vary by a wide range (32 to 188,700 parasites/ml, with a median of 837 parasites/ml), while in bone marrow, parasite load was more than 100 parasites per 10
6
nucleated human cells. After successful therapy, parasitemia levels remain lower than 1 parasite/ml. In the immunocompromised host, relapses correlate with an increase in the level of parasitemia, sometimes scanty, justifying the need for assays with high sensitivity. Such sensitivity allows the detection of
Leishmania
DNA in the blood of 21% of patients with no history of leishmaniasis living in the Marseilles area, where leishmaniasis is endemic. This technique may be useful for epidemiologic and diagnostic purposes, especially for the quantification of parasitemia at low levels during posttherapy follow-up.
Metallo-β-Lactamase-Producing Gram-Negative Bacilli: Laboratory-Based Surveillance in Cooperation with 13 Clinical Laboratories in the Kinki Region of Japan
Authors: Nishio Hisaaki , Komatsu Masaru , Shibata Naohiro , Shimakawa Kouichi , Sueyoshi Noriyuki , Ura Toshiro , Satoh Kaori , Toyokawa Masahiro , Nakamura Tatsuya , Wada Yasunao , Orita Tamaki , Kofuku Tomomi , Yamasaki Katsutoshi , Sakamoto Masako , Kinoshita Shohiro , Aihara Masanori , Arakawa Yoshichika 
Published: November 2004

ABSTRACT

A total of 19,753 strains of gram-negative rods collected during two 6-month periods (October 2000 to March 2001 and November 2001 to April 2002) from 13 clinical laboratories in the Kinki region of Japan were investigated for the production of metallo-β-lactamases (MBLs). MBLs were detected in 96 (0.5%) of the 19,753 isolates by the broth microdilution method, the 2-mercaptopropionic acid inhibition test, and PCR and DNA sequencing analyses. MBL-positive isolates were detected in 9 of 13 laboratories, with the rate of detection ranging between 0 and 2.6% for each laboratory. Forty-four of 1,429 (3.1%)
Serratia marcescens
, 22 of 6,198 (0.4%)
Pseudomonas aeruginosa
, 21 of 1,108 (1.9%)
Acinetobacter
spp., 4 of 544 (0.7%)
Citrobacter freundii
, 3 of 127 (2.4%)
Providencia rettgeri
, 1 of 434 (0.2%)
Morganella morganii
, and 1 of 1,483 (0.1%)
Enterobacter cloacae
isolates were positive for MBLs. Of these 96 MBL-positive strains, 87 (90.6%), 7 (7.3%), and 2 (2.1%) isolates carried the genes for IMP-1-group MBLs, IMP-2-group MBLs, and VIM-2-group MBLs, respectively. The class 1 integrase gene,
intI1
, was detected in all MBL-positive strains, and the
aac
(
6
′)
-Ib
gene was detected in 37 (38.5%) isolates. Strains with identical PCR fingerprint profiles in a random amplified polymorphic DNA pattern analysis were isolated successively from five separate hospitals, suggesting the nosocomial spread of the organism in each hospital. In conclusion, many species of MBL-positive gram-negative rods are distributed widely in different hospitals in the Kinki region of Japan. The present findings should be considered during the development of policies and strategies to prevent the emergence and further spread of MBL-producing bacteria.
Occurrence of Extended-Spectrum β-Lactamases in Members of the Genus
Shigella
in the Republic of Korea
Authors: Kim Seonghan , Kim Junyoung , Kang Yeonho , Park Yongkeun , Lee Bokkwon 
Published: November 2004

ABSTRACT

A nationwide survey was carried out in Korea to assess the prevalence of
Shigella
strains producing extended-spectrum β-lactamases (ESBLs). From 1991 to 2002, 5,911 clinical strains were isolated and screened for resistance to extended-spectrum cephalosporins. Twenty of the
Shigella
isolates were ESBL positive, based on the synergistic effects between clavulanate and selected β-lactams (ceftazidime and cefotaxime). Nucleotide sequence analysis of these isolates revealed that they harbored
bla
TEM-19
(eight isolates),
bla
TEM-15
(five isolates),
bla
TEM-52
(six isolates),
bla
TEM-17
(one isolate),
bla
TEM-20
(one isolate), and
bla
CTX-M-14
(three isolates). All the ESBL-encoding genes in this study were carried in conjugable plasmids. Thus, TEM-19, TEM-15, TEM-52, and CTX-M-14 β-lactamases can be considered common Korean ESBL types in
Shigella sonnei
and are probably transmitted through interspecies spread between medical facilities and the community in Korea. This is the first report of the presence of TEM-17, TEM-19, and TEM-20 in Korea and in
S. sonnei
.
Dual-Probe Assay for Rapid Detection of Drug-Resistant
Mycobacterium tuberculosis
by Real-Time PCR
Authors: Wada Takayuki , Maeda Shinji , Tamaru Aki , Imai Shigeyoshi , Hase Atsushi , Kobayashi Kazuo 
Published: November 2004

ABSTRACT

Mutations in particular nucleotides of genes coding for drug targets or drug-converting enzymes lead to drug resistance in
Mycobacterium tuberculosis
. For rapid detection of drug-resistant
M. tuberculosis
in clinical specimens, a simple and applicable method is needed. Eight TaqMan minor groove binder (MGB) probes, which discriminate one-base mismatches, were designed (dual-probe assay with four reaction tubes). The target of six MGB probes was the
rpoB
gene, which is involved in rifampin resistance; five probes were designed to detect for mutation sites within an 81-bp hot spot of the
rpoB
gene, and one probe was designed as a tuberculosis (TB) control outside the
rpoB
gene hot-spot. We also designed probes to examine codon 315 of
katG
and codon 306 of
embB
for mutations associated with resistance to isoniazid and ethambutol, respectively. Our system was
M. tuberculosis
complex specific, because neither nontuberculous mycobacteria nor bacteria other than mycobacteria reacted with the system. Detection limits in direct and preamplified analyses were 250 and 10 fg of genomic DNA, respectively. The system could detect mutations of the
rpoB
,
katG
, and
embB
genes in DNAs extracted from 45 laboratory strains and from sputum samples of 27 patients with pulmonary TB. This system was much faster (3 h from DNA preparation) than conventional drug susceptibility testing (3 weeks). Results from the dual-MGB-probe assay were consistent with DNA sequencing. Because the dual-probe assay system is simple, rapid, and accurate, it can be applied to detect drug-resistant
M. tuberculosis
in clinical laboratories.
Porphyromonas uenonis
sp. nov., a Pathogen for Humans Distinct from
P. asaccharolytica
and
P. endodontalis
Authors: Finegold Sydney M. , Vaisanen Marja-Liisa , Rautio Merja , Eerola Erkki , Summanen Paula , Molitoris Denise , Song Yuli , Liu Chengxu , Jousimies-Somer Hannele 
Published: November 2004

ABSTRACT

Three
Porphyromonas
species (
Porphyromonas asaccharolytica
,
P. endodontalis
, and the novel species that is the subject of the present report,
P. uenonis
) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents.
P. asaccharolytica
is distinguished from the other two species by virtue of production of α-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from
P. endodontalis
phenotypically and was designated a
P. endodontalis
-like organism for some time. However,
P. endodontalis
is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore,
P. uenonis
is glycerol positive in the Biolog AN Microplate system. Both
P. asaccharolytica
and
P. uenonis
are positive by 13 other tests in the Biolog system, whereas
P. endodontalis
is negative by all of these tests.
P. asaccharolytica
grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and
P. endodontalis
but less than 2% sequence difference between the novel species and
P. asaccharolytica.
Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from
P. asaccharolytica.
We propose the name
Porphyromonas uenonis
for the novel species. We have recovered
P. uenonis
from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children.
ThecagPathogenicity Island ofHelicobacter pyloriIs Disrupted in the Majority of Patient Isolates from Different Human Populations
Authors: Kauser Farhana , Khan Aleem A. , Hussain M. Abid , Carroll Ian M. , Ahmad Naheed , Tiwari Santosh , Shouche Yogesh , Das Bimal , Alam Mahfooz , Ali S. Mahaboob , Habibullah C. M. , Sierra Rafaela , Megraud Francis , Sechi Leonardo A. , Ahmed Niyaz 
Published: November 2004

ABSTRACTThecagpathogenicity island (cag-PAI) is one of the major virulence determinants ofHelicobacter pylori. The chromosomal integrity of this island or the lack thereof is speculated to play an important role in the progress of the gastroduodenal pathology caused byH. pylori. We determined the integrity of thecag-PAI by using specific flanking and internally anchored PCR primers to know the biogeographical distribution of strains carrying fully integralcag-PAI with proinflammatory behavior in vivo. Genotypes based on eight selected loci were studied in 335 isolates obtained from eight different geographic regions. Thecag-PAI appeared to be disrupted in the majority of patient isolates throughout the world. Conservation ofcag-PAI was highest in Japanese isolates (57.1%). However, only 18.6% of the Peruvian and 12% of the Indian isolates carried an intactcag-PAI. The integrity ofcag-PAI in European and African strains was minimal. All 10 strains from Costa Rica had rearrangements. Overall, a majority of the strains of East Asian ancestry were found to have intactcag-PAI compared to strains of other descent. We also found that thecagEandcagTgenes were less often rearranged (18%) than thecagAgene (27%). We attempted to relatecag-PAI rearrangement patterns to disease outcome. Deletion frequencies ofcagA,cagE, andcagTgenes were higher in benign cases than in isolates from severe ulcers and gastric cancer. Conversely, thecagApromoter and the left end of thecag-PAI were frequently rearranged or deleted in isolates linked to severe pathology. Analysis of thecag-PAI genotypes with a different biogeoclimatic history will contribute to our understanding of the pathogen-host interaction in health and disease.
Prevalence and Characterization of Leukotoxin-Producing
Staphylococcus intermedius
in Isolates from Dogs and Pigeons
Authors: Futagawa-Saito Keiko , Sugiyama Tsukasa , Karube Sayaka , Sakurai Naomi , Ba-Thein William , Fukuyasu Tsuguaki 
Published: November 2004

ABSTRACT

Staphylococcus intermedius
isolates from dogs (
n
= 44) and pigeons (
n
= 62) were categorized into 12 types by intergenic ribosomal DNA spacer polymorphism analysis. All isolates from pigeons were
lukS
positive and all isolates from dogs were
lukS
and
lukF
positive by dot blot analysis. The mean leukotoxicity titer for dog isolates was at least 129-fold higher than that for pigeon isolates.
Complexity ofKlebsiella pneumoniaeIsolates Resistant to Both Cephamycins and Extended-Spectrum Cephalosporins at a Teaching Hospital in Taiwan
Authors: Yan Jing-Jou , Ko Wen-Chien , Wu Hsiu-Mei , Tsai Shu-Huei , Chuang Chin-Luan , Wu Jiunn-Jong 
Published: November 2004

ABSTRACTAmong 99 clinicalKlebsiella pneumoniaeisolates resistant to cefoxitin and extended-spectrum cephalosporins, coexistence of AmpC (DHA-1, CMY-2, or CMY-8) and extended-spectrum β-lactamases (CTX-M and/or SHV) was detected in a total of 35. The remainder produced AmpC (n= 42), extended-spectrum β-lactamases (n= 9), metallo-β-lactamases (n= 2), or none of these enzymes (n= 11). Phenotypic characteristics of these isolates were demonstrated.