bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serotypes, Virulence Genes, and Intimin Types of Shiga Toxin (Verotoxin)-Producing
Escherichia coli
Isolates from Human Patients: Prevalence in Lugo, Spain, from 1992 through 1999
Authors: Blanco J. E. , Blanco M. , Alonso M. P. , Mora A. , Dahbi G. , Coira M. A. , Blanco J. 
Published: January 2004

ABSTRACT

We have analyzed the prevalence of Shiga toxin-producing
Escherichia coli
(STEC) in stool specimens of patients with diarrhea or other gastrointestinal alterations from the Xeral-Calde Hospital of Lugo City (Spain). STEC strains were detected in 126 (2.5%) of 5,054 cases investigated, with a progressive increase in the incidence from 0% in 1992 to 4.4% in 1999. STEC O157:H7 was isolated in 24 cases (0.5%), whereas non-O157 STEC strains were isolated from 87 patients (1.7%). STEC strains were (after
Salmonella
and
Campylobacter
strains) the third most frequently recovered enteropathogenic bacteria. A total of 126 human STEC isolates were characterized in this study. PCR showed that 43 (34%) isolates carried
stx
1
genes, 45 (36%) possessed
stx
2
genes and 38 (30%) carried both
stx
1
and
stx
2
. A total of 88 (70%) isolates carried an
ehxA
enterohemolysin gene, and 70 (56%) isolates possessed an
eae
intimin gene (27 isolates with type γ1, 20 with type β1, 8 with type ζ, 5 with type γ2, and 3 with type ε). STEC isolates belonged to 41 O serogroups and 66 O:H serotypes, including 21 serotypes associated with hemolytic uremic syndrome and 30 new serotypes not previously reported among human STEC strains in other studies. Although the 126 STEC isolates belonged to 81 different seropathotypes (associations between serotypes and virulence genes), only four accounted for 31% of isolates. Seropathotype O157:H7
stx
1
stx
2
eae-
γ1
ehxA
was the most common (13 isolates) followed by O157:H7
stx
2
eae-
γ1
ehxA
(11 isolates), O26:H11
stx
1
eae-
β1
ehxA
(11 isolates), and O111:H-
stx
1
stx
2
eae-
γ2
ehxA
(4 isolates). Our results suggest that STEC strains are a significant cause of human infections in Spain and confirm that in continental Europe, infections caused by STEC non-O157 strains are more common than those caused by O157:H7 isolates. The high prevalence of STEC strains (both O157:H7 and non-O157 strains) in human patients, and their association with serious complications, strongly supports the utilization of protocols for detection of all serotypes of STEC in Spanish clinical microbiology laboratories.
Use of Real-Time PCR To Resolve Slide Agglutination Discrepancies in Serogroup Identification of
Neisseria meningitidis
Authors: Mothershed Elizabeth A. , Sacchi Claudio T. , Whitney Anne M. , Barnett Gwen A. , Ajello Gloria W. , Schmink Susanna , Mayer Leonard W. , Phelan Maureen , Taylor Thomas H. , Bernhardt Scott A. , Rosenstein Nancy E. , Popovic Tanja 
Published: January 2004

ABSTRACT

Neisseria meningitidis
is a leading cause of bacterial meningitis and septicemia in children and young adults in the United States. Rapid and reliable identification of
N. meningitidis
serogroups is crucial for judicious and expedient response to cases of meningococcal disease, including decisions about vaccination campaigns. From 1997 to 2002, 1,298
N. meningitidis
isolates, collected in the United States through the Active Bacterial Core surveillance (ABCs), were tested by slide agglutination serogrouping (SASG) at both the ABCs sites and the Centers for Disease Control and Prevention (CDC). For over 95% of isolates, SASG results were concordant, while discrepant results were reported for 58 isolates. To resolve these discrepancies, we repeated the SASG in a blinded fashion and employed
ctrA
and six serogroup-specific PCR assays (SGS-PCR) to determine the genetic capsule type. Seventy-eight percent of discrepancies were resolved, since results of the SGS-PCR and SASG blinded study agreed with each other and confirmed the SASG result at either state health laboratories or CDC. This study demonstrated the ability of SGS-PCR to efficiently resolve SASG discrepancies and identified the main cause of the discrepancies as overreporting of these isolates as nongroupable. It also reemphasized the importance of adherence to quality assurance procedures when performing SASG and prompted prospective monitoring for SASG discrepancies involving isolates collected through ABCs in the United States.
Development of a Real-Time Reverse-Transcription PCR for Detection of Newcastle Disease Virus RNA in Clinical Samples
Authors: Wise Mark G. , Suarez David L. , Seal Bruce S. , Pedersen Janice C. , Senne Dennis A. , King Daniel J. , Kapczynski Darrell R. , Spackman Erica 
Published: January 2004

ABSTRACT

A real-time reverse-transcription PCR (RRT-PCR) was developed to detect avian paramyxovirus 1 (APMV-1) RNA, also referred to as Newcastle disease virus (NDV), in clinical samples from birds. The assay uses a single-tube protocol with fluorogenic hydrolysis probes. Oligonucleotide primers and probes were designed to detect sequences from a conserved region of the matrix protein (M) gene that recognized a diverse set (
n
= 44) of APMV-1 isolates. A second primer-probe set was targeted to sequences in the fusion protein (F) gene that code for the cleavage site and detect potentially virulent NDV isolates. A third set, also directed against the M gene, was specific for the North American (N.A.) pre-1960 genotype that includes the common vaccine strains used in commercial poultry in the United States. The APMV-1 M gene, N.A. pre-1960 M gene, and F gene probe sets were capable of detecting approximately 10
3
, 10
2
, and 10
4
genome copies, respectively, with in vitro-transcribed RNA. Both M gene assays could detect approximately 10
1
50% egg infective doses (EID
50
), and the F gene assay could detect approximately 10
3
EID
50
. The RRT-PCR test was used to examine clinical samples from chickens experimentally infected with the NDV strain responsible for a recent epizootic in the southwestern United States. Overall, a positive correlation was obtained between the RRT-PCR results and virus isolation for NDV from clinical samples.
Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria
Authors: Lefmann Michael , Honisch Christiane , Böcker Sebastian , Storm Niels , von Wintzingerode Friedrich , Schlötelburg Cord , Moter Annette , van den Boom Dirk , Göbel Ulf B. 
Published: January 2004

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for the identification of mycobacteria. Full-length 16S rDNA reference sequences of 12 type strains of
Mycobacterium
spp. frequently isolated from clinical specimens were determined by PCR, cloning, and sequencing. For MALDI-TOF MS-based comparative sequence analysis, mycobacterial 16S rDNA signature sequences (∼500 bp) of the 12 type strains and 24 clinical isolates were PCR amplified using RNA promoter-tagged forward primers. T7 RNA polymerase-mediated transcription of forward strands in the presence of 5-methyl ribo-CTP maximized mass differences of fragments generated by base-specific cleavage. In vitro transcripts were subsequently treated with RNase T1, resulting in G-specific cleavage. Sample analysis by MALDI-TOF MS showed a specific mass signal pattern for each of the 12 type strains, allowing unambiguous identification. All 24 clinical isolates were identified unequivocally by comparing their detected mass signal pattern to the reference sequence-derived in silico pattern of the type strains and to the in silico mass patterns of published 16S rDNA sequences. A 16S rDNA microheterogeneity of the
Mycobacterium xenopi
type strain (DSM 43995) was detected by MALDI-TOF MS and later confirmed by Sanger dideoxy sequencing. In conclusion, analysis of 16S rDNA amplicons by MS after base-specific cleavage of RNA transcripts allowed fast and reliable identification of the
Mycobacterium tuberculosis
complex and ubiquitous mycobacteria (mycobacteria other than tuberculosis). The technology delivers an open platform for high-throughput microbial identification on the basis of any specific genotypic marker region.
Detection of Severe Acute Respiratory Syndrome Coronavirus in Blood of Infected Patients
Authors: Ng Lisa F. P. , Wong Michelle , Koh Susie , Ooi Eng-Eong , Tang King-Fai , Leong Hoe-Nam , Ling Ai-Ee , Agathe Lora V. , Tan Jenny , Liu Edison T. , Ren Ee-Chee , Ng Lee-Ching , Hibberd Martin L. 
Published: January 2004

ABSTRACT
Severe acute respiratory syndrome (SARS) has caused major outbreaks worldwide, resulting in an urgent need to obtain sensitive and accurate diagnosis of this disease. PCR-based detection methods were developed for use on a variety of samples, including blood. Eighteen subjects were investigated, and results indicated that blood samples contain sufficient virus for detection by using quantitative real-time PCR.
Rapid Immunochromatographic Test Using Recombinant SAG2 for Detection of Antibodies against
Toxoplasma gondii
in Cats
Authors: Huang Xiaohong , Xuan Xuenan , Hirata Haruyuki , Yokoyama Naoaki , Xu Longshan , Suzuki Naoyoshi , Igarashi Ikuo 
Published: January 2004

ABSTRACT

An immunochromatographic test using recombinant truncated surface antigen 2 for detection of antibodies against
Toxoplasma gondii
was developed. Evaluation of detection of the antibody in mice and cats suggests that this test is rapid, simple, accurate, relatively inexpensive, and suitable for use under field conditions.
Nissui Glucose Fermentative Gram-Negative Rod Identification System EB-20 Gives a Unique Profile for Typical Non-Sorbitol-Fermenting
Escherichia coli
O157:H7
Authors: Kodaka H. , Uesaka Y. , Kashitani F. 
Published: January 2004

ABSTRACT

The 98 non-sorbitol-fermenting (NSF)
Escherichia coli
O157:H7 strains identified on a Nissui glucose fermentative gram-negative rod identification system (EB-20) gave a unique biochemical profile number that was not detected in 85 pathogenic and 13 nonpathogenic
E. coli
strains. Thus, EB-20 is useful for the identification of NSF
E. coli
O157:H7 and provides a simple, cost-effective, and reliable tool for clinical laboratories.
Development of an Immunochromatographic Test with Recombinant EMA-2 for the Rapid Detection of Antibodies against
Babesia equi
in Horses
Authors: Huang Xiaohong , Xuan Xuenan , Xu Longshan , Zhang Shoufa , Yokoyama Naoaki , Suzuki Naoyoshi , Igarashi Ikuo 
Published: January 2004

ABSTRACT

An immunochromatographic test (BeICT) for the rapid detection of antibodies against
Babesia equi
was developed. It clearly differentiated
B. equi-
infected horses from
B. caballi-
infected and uninfected horses. The agreement with enzyme-linked immunosorbent assay results was 96.7% in the detection of field sera. The results suggest that BeICT is rapid, simple, reliable, and suitable for use to detect
B. equi
infection in the field.
Molecular Epidemiology of the Iron Utilization Genes of Enteroaggregative
Escherichia coli
Authors: Okeke Iruka N. , Scaletsky Isabel C. A. , Soars Elizabeth H. , Macfarlane Louissa R. , Torres Alfredo G. 
Published: January 2004

ABSTRACT

Enteroaggregative
Escherichia coli
(EAEC) strains are etiologic agents of acute and persistent diarrhea. In this study, the results of phenotypic assays suggested that EAEC strains possess specialized iron acquisition systems. Genes required for the synthesis (
iucA
) or transport (
fepC
) of siderophores, and genes encoding siderophore (
fyuA
,
ireA
, and
iroN
) or heme transport (
chu
) receptors or hemoglobin proteases (
pic
and
hbp
), were sought in EAEC strains which have been characterized with respect to known virulence genes and phylogeny. The
chuA
,
iucA
,
fyuA
,
fepC
, and
pic
genes were detected in 33, 76.2, 85.7, 33, and 61.9% of these EAEC strains, respectively, and the other genes were absent. The majority of EAEC strains possessed genes encoding multiple iron transport systems, and there was no phylogenetic correlation in the distribution of the majority of these loci, as is typical for EAEC. The notable exceptions were
chuA
and
fepC
(which is associated with the
prrA-modA-fepC
pathogenicity island); these genes were restricted to the EAEC2 and DAEC2 phylogenetic groups, which could represent pathogenic subsets. When collections of EAEC strains isolated during case-control studies in Nigeria and Brazil were examined, no association of the presence of either
chuA
or
iucA
alone with diarrhea was seen, but both genes together were present in significantly more strains from cases than from controls in the Nigerian collection (
P
< 0.05). It is possible that the presence of both genes marks at least some virulent strains. The data also demonstrate geographical variation in the association of iron utilization genes with disease in EAEC.
Possible High Rate of Transmission of Nontypeable
Haemophilus influenzae
, Including β-Lactamase-Negative Ampicillin-Resistant Strains, between Children and Their Parents
Authors: Watanabe Hiroshi , Hoshino Kazuhiko , Sugita Rinya , Asoh Norichika , Watanabe Kiwao , Oishi Kazunori , Nagatake Tsuyoshi 
Published: January 2004

ABSTRACT

The possible transmission of nontypeable
Haemophilus influenzae
between children and their parents was evaluated in 18 pairs of subjects from 15 families. Of the 33 isolates, 31 were found to be β-lactamase negative, including 10 β-lactamase-negative, ampicillin (AMP)-resistant (BLNAR) strains (AMP MIC, ≥1.0 μg/ml) and 2 were β-lactamase producing. Molecular typing by pulsed-field gel electrophoresis (PFGE) showed that 10 BLNAR isolates had 6 patterns, 23 non-BLNAR isolates had 13 patterns, and these patterns were different from each other, except for 1 pattern. As a result, the PFGE patterns in 14 of 18 pairs were indistinguishable and those in 4 pairs were different. These data indicate a possible high rate of intrafamilial transmission of nontypeable
H. influenzae
, including BLNAR strains, between children and their parents.
Method for Testing for Human Papillomavirus Infection in Patients with Cervical Intraepithelial Disease
Authors: Lin Hsing-Pei , Huang Yang-Yang , Wu Hsueh-Yin , Kao Jau-Tsuen 
Published: January 2004

ABSTRACT
To determine whether DNA detection of high-risk human papillomavirus could represent a reliable screening technique and a useful follow-up method, we investigated the performance of the Hybrid Capture II assay in detecting high-grade cervical lesions. The test positivity at 1.86 pg/ml had a high sensitivity (94.7%) and improved specificity. It was also a suitable follow-up method for detecting the recurrence of cervical intraepithelial disease in patients.
Amplified Fragment Length Polymorphism Fingerprinting Is an Effective Technique To Distinguish
Streptococcus pneumoniae
from Other Streptococci and an Efficient Alternative to Pulsed-Field Gel Electrophoresis for Molecular Typing of Pneumococci
Authors: Neeleman Chris , Klaassen Corné H. W. , de Valk Hanneke A. , de Ruiter Maaike T. , Mouton Johan W. 
Published: January 2004

ABSTRACT
Amplified fragment length polymorphism versus pulsed-field gel electrophoresis was used for fingerprinting of 85 macrolide-resistant pneumococcal isolates identified by using primarily phenotypic methods. Confirmation of identification by 16S rRNA sequencing revealed that 27 isolates were actually nonpneumococci. Amplified fragment length polymorphism but not pulsed-field gel electrophoresis offered simultaneous and accurate discrimination between pneumococci and nonpneumococcal species.
PCR-Based Genotyping of
Mycobacterium tuberculosis
with New GC-Rich Repeated Sequences and IS
6110
Inverted Repeats Used as Primers
Authors: Kotłowski Roman , Shamputa Isdore Chola , El Aila Nabil Abdullah , Sajduda Anna , Rigouts Leen , van Deun Armand , Portaels Françoise 
Published: January 2004

ABSTRACT

In the present study we attempted to develop a PCR-based epidemiological tool for the differentiation of
Mycobacterium tuberculosis
isolates. Use of the designed primers Mtb1 (5′-CCG-GCG-GGG-CCG-GCG-G) and Mtb2 (5′-CGG-CGG-CAA-CGG-CGG-C) targeting frequently repeated 16-bp sequences in combination with primers sited at the inverted repeats flanking IS
6110
allowed differentiation of
M. tuberculosis
isolates.
Improving the Bacteriological Diagnosis of Tuberculous Meningitis
Authors: Thwaites Guy E. , Chau Tran Thi Hong , Farrar Jeremy J. 
Published: January 2004

ABSTRACT
We made a bacteriological diagnosis of tuberculous meningitis in 107 of 132 (81%) adults with clinical tuberculous meningitis: acid-fast bacilli were seen in 77 of 132 (58%) and cultured from 94 of 132 (71%). Volume of cerebrospinal fluid, duration of symptoms, cerebrospinal fluid neutrophils, lactate, and glucose were all independently associated with bacteriological confirmation.
Evaluation of the NCCLS M44-P Disk Diffusion Method for Determining Susceptibilities of 276 Clinical Isolates of
Cryptococcus neoformans
to Fluconazole
Authors: Pfaller M. A. , Messer S. A. , Boyken L. , Rice C. , Tendolkar S. , Hollis R. J. , Diekema D. J. 
Published: January 2004

ABSTRACT

We evaluated the NCCLS M44-P fluconazole disk diffusion method in comparison with the NCCLS M27-A2 broth microdilution method for determining the susceptibility of 276 isolates of
Cryptococcus neoformans
. Disk diffusion testing was performed using Mueller-Hinton agar supplemented with 2% glucose and 0.5 μg of methylene blue/ml. Among the 276 isolates, 259 (93.8%) were susceptible, 16 (5.8%) were susceptible—dose dependent, and 1 (0.4%) was resistant to fluconazole as determined by the NCCLS broth microdilution method. The overall categorical agreement between the two methods was 86%, with 0% very major errors, 2% major errors, and 12% minor errors. The disk diffusion method using Mueller-Hinton agar supplemented with glucose and methylene blue appears to be a useful approach for determining the fluconazole susceptibility of C.
neoformans.
Helicobacter
Species in the Intestinal Mucosa of Patients with Ulcerative Colitis
Authors: Oliveira Adriana Gonçalves , Sanna Maria das Graças Pimenta , Rocha Gifone Aguiar , Rocha Andreia Maria Camargos , Santos Adriana , Dani Renato , Marinho Frederico Passos , Moreira Liano Sia , Ferrari Maria de Lourdes Abreu , Moura Sílvia Beleza , Castro Lúcia Porto Fonseca , Queiroz Dulciene Maria Magalhães 
Published: January 2004

ABSTRACT

In a search for
Helicobacter
species in the intestinal mucosae of 42 patients with ulcerative colitis (UC) and 74 without UC, only
H. pylori
was found. Although the bacterium was detected in UC patients by culture (7.1%) and nested PCR (19.0%), its presence was not associated with the disease (
P
= 0.13).
Susceptibilities to Different Antibiotics of
Helicobacter pylori
Strains Isolated from Patients at the Pediatric Medical Center of Tehran, Iran
Authors: Falsafi Tahereh , Mobasheri Fatemeh , Nariman Farahnaz , Najafi Mehri 
Published: January 2004

ABSTRACT

Antibiotic susceptibility testing of 70 pediatric
Helicobacter pylori
isolates was performed by using screening agar and disk diffusion methods. Resistance to metronidazole and tinidazole was 72 to 79% and 71 to 81% by modified disk diffusion and 77% and 78% by screening agar, respectively. Susceptibilities to amoxicillin, ampicillin, clarithromycin, tetracycline, erythromycin, and ciprofloxacin were 58, 69, 75, 68, 68, and 65%, respectively.
Mutations Including IS
6110
Insertion in the Gene Encoding the MPB64 Protein of Capilia TB-Negative
Mycobacterium tuberculosis
Isolates
Authors: Hirano Kazue , Aono Akio , Takahashi Mitsuyoshi , Abe Chiyoji 
Published: January 2004

ABSTRACT

A simple immunochromatographic assay, Capilia TB, using anti-MPB64 monoclonal antibodies, is a kit for discriminating between the
Mycobacterium tuberculosis
complex and mycobacteria other than tubercle bacilli. The sensitivity of the kit was estimated to be 99.2% (381 of 384 samples). The sequencing analysis revealed that all of the Capilia TB-negative isolates had mutations within the
mpb64
gene, leading to the production of an incomplete protein as a result of a deletion of the C-terminal region of the protein.
Eight-Year Survey of Human Rotavirus Strains Demonstrates Circulation of Unusual G and P Types in Hungary
Authors: Bányai Krisztián , Gentsch Jon R. , Glass Roger I. , Új Mária , Mihály Ilona , Szücs György 
Published: January 2004

ABSTRACT
Between 1992 and 2000, a total of 4,173 rotavirus-positive samples were collected from two areas of Hungary. Of these, 2,020 specimens (48.4%) were analyzed for G serotype, using monoclonal antibody-based immunoassay and reverse transcription-PCR. By the two methods, 1,789 samples were specified as G1 (62%), G2 (12.2%), G3 (1.4%), G4 (6.4%), G6 (1.0%), G9 (2.9%), or mixed infection (2.6%), and the remaining 231 (11.4%) could not be G typed. The linkage between G and P type, subgroup specificity, and RNA profile was investigated with a sample subset. Among these specimens, we identified both the four globally common strains (P[8],G1 subgroup II (sgII); P[4],G2 sgI; P[8],G3 sgII; and P[8],G4 sgII) and six uncommon strains (P[6],G4 sgII; P[9],G3 sgI; P[9],G6 sgI; P[14],G6 sgI; P[8],G9 sgII; and P[8],G9 sgI). All strains with P[8], P[6], P[9], and P[14] specificities had a long electropherotype, whereas most of those carrying a P[4] specificity were associated with a short electropherotype. Although once considered to be rare, P[9],G6 and P[8],G9 rotavirus strains represent potentially important new serotypes in Hungary.
Reduced Etiological Role for Enteropathogenic
Escherichia coli
in Cases of Diarrhea in Brazilian Infants
Authors: Rodrigues Josias , Thomazini Cristiane M. , Morelli Alexandra , de Batista Georgea C. M. 
Published: January 2004

ABSTRACT

Previously common in Brazil, enteropathogenic
Escherichia coli
(EPEC) strains of serogroups O55, O111, and O119 are now rare, while enteroadherent strains other than EPEC, belonging to serogroups such as O125, were prevalent among 126 diarrheic infants less than 1 year old who were surveyed. None of these strains had the EPEC bundle-forming pilus (
bfpA
) gene.
Use of Genome Selected Repeated Sequences Increases the Sensitivity of PCR Detection of
Tropheryma whipplei
Authors: Fenollar Florence , Fournier Pierre-Edouard , Robert Catherine , Raoult Didier 
Published: January 2004

ABSTRACT

The availability of the
Tropheryma whipplei
genome offers the putative possibility of choosing logical DNA targets. We applied a PCR assay (targeting repeated sequences of
T. whipplei
) to samples from patients with Whipple's disease and to those from members of a control group. When compared to the results seen with regular PCR, the sensitivity of repeat PCR was significantly enhanced (
P
= 0.02) without alteration of its specificity.
Specific Oligonucleotide Primers for Identification ofCladophialophora carrionii, a Causative Agent of Chromoblastomycosis
Authors: Abliz Paride , Fukushima Kazutaka , Takizawa Kayoko , Nishimura Kazuko 
Published: January 2004

ABSTRACTCladophialophora carrioniiis one of the relatively common causative agents of chromoblastomycosis. We have developed the specific oligonucleotide primer set based on the internal transcribed spacer regions of ribosomal DNA for the rapid identification of this pathogen. PCR with this primer set amplified a 362-bp amplicon fromC. carrioniistrains. From other relevant dematiaceous species, including medically important dematiaceous fungi, such asFonsecaea pedrosoi,Phialophora verrucosa, andExophiala dermatitidis, and eight species of medically important yeasts, such asCandida albicansandCryptococcus neoformansvar.neoformans, the primer set did not produce any amplicon. PCR with this primer set may be a useful tool for the identification ofC. carrionii.