bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of
cfxA
and
cfxA2
, the β-Lactamase Genes of
Prevotella
spp., in Clinical Samples from Dentoalveolar Infection by Real-Time PCR
Authors: Iwahara Kaori , Kuriyama Tomoari , Shimura Satoshi , Williams David W. , Yanagisawa Maki , Nakagawa Kiyomasa , Karasawa Tadahiro 
Published: January 2006

ABSTRACT

While most bacteria involved in dentoalveolar infection are highly susceptible to penicillin, some
Prevotella
strains exhibit resistance to this agent through the production of β-lactamase. The production of β-lactamase by
Prevotella
spp. is in turn associated with the expression of the genes
cfxA
and
cfxA2
. The aim of the present study was to determine the prevalence of
cfxA
and
cfxA2
in
Prevotella
strains by use of real-time PCR and to assess the performance of this molecular method for the direct detection of the genes in 87 clinical samples (pus and root canal exudates) from dentoalveolar infection. Production of β-lactamase by each isolate was determined using a nitrocefin disk. β-Lactamase production was seen in 31% of
Prevotella
isolates, while all isolates of other species were β-lactamase negative. The penicillin resistance of isolates strongly correlated with the production of β-lactamase. Real-time PCR was found to detect the
cfxA
and
cfxA2
genes from at least five cells per reaction mixture (5 × 10
3
CFU/ml of pus). Using real-time PCR, the presence of
cfxA
and
cfxA2
was evident for all 48 β-lactamase-positive
Prevotella
strains. In contrast, neither β-lactamase-negative
Prevotella
(
n
= 91) or non-
Prevotella
(
n
= 31) strains were positive for the genes. In this study, 31 of the 87 samples yielded β-lactamase-positive
Prevotella
results, and
cfxA
and
cfxA2
were detected in all 31 samples. Of the 56 culture-negative samples, 8 (14%) were positive for
cfxA
and
cfxA2
by the real-time PCR. This sensitive and specific molecular method offers a rapid clinical test for aiding in the selection of an appropriate antibiotic for treatment of dentoalveolar infection. Although penicillin remains largely effective in the treatment of dentoalveolar infection, β-lactamase-stable antibiotics should be considered in cases in which β-lactamase-positive
Prevotella
strains are involved.
Virological, Serological, and Clinical Features of an Outbreak of Acute Gastroenteritis Due to Recombinant Genogroup II Norovirus in an Infant Home
Authors: Tsugawa Takeshi , Numata-Kinoshita Kazuko , Honma Shinjiro , Nakata Shuji , Tatsumi Masatoshi , Sakai Yoshiyuki , Natori Katsuro , Takeda Naokazu , Kobayashi Shinichi , Tsutsumi Hiroyuki 
Published: January 2006

ABSTRACT
Norovirus (NV) is an important cause of acute nonbacterial gastroenteritis worldwide. Recently, several sporadic cases due to naturally occurring recombinant NVs have been reported. In January 2000, there was an outbreak of gastroenteritis in an infant home in Sapporo, Japan. Of 34 residents of the home that were less than 2 years old, 23 developed gastrointestinal symptoms and NV infection was confirmed by conventional reverse transcription-PCR to detect the RNA polymerase region of genogroup II NV. In this virus, the RNA polymerase region shared 86% nucleotide identity with Hawaii virus but only 77% with Mexico virus; however, its capsid region shared only 70% identity with Hawaii virus but 90% with Mexico virus. On the other hand, both regions shared a higher 96% nucleotide identity with Arg320 virus, which was found in Mendoza, Argentina, in 1995 and considered to be a recombinant of Hawaii and Mexico viruses. The findings indicate that the virus involved in the outbreak was similar and may have evolved from the Arg320 virus. Clinically the cases were more severe than those of previously reported sporadic or outbreak cases of NV infection.
Long-Term Population-Based Genotyping Study of
Mycobacterium tuberculosis
Complex Isolates in the French Departments of the Americas
Authors: Brudey Karine , Filliol Ingrid , Ferdinand Séverine , Guernier Vanina , Duval Philippe , Maubert Bertrand , Sola Christophe , Rastogi Nalin 
Published: January 2006

ABSTRACT

The three French overseas departments of the Americas are characterized both by insular (Guadeloupe and Martinique) and continental (French Guiana) settings with a tuberculosis case detection rate that varies from less than 10 per 100,000 per year in insular areas to an estimated incidence of more than 55 per 100,000 in French Guiana. Under a long-term genotyping program, more than three-fourths of all the
Mycobacterium tuberculosis
isolates (
n
= 744) received from the three settings were fingerprinted over a 10-year period (1994 to 2003) by spoligotyping and variable number of tandem DNA repeats (VNTRs) in order to understand the current trends in their detection rates, drug resistance, and groups and subpopulations at risk of contracting the disease and to pinpoint the circulating phylogeographical clades of the bacilli. The major difference in the study populations was the nationality of the patients, with a high percentage of immigrants from high-incidence neighboring countries in French Guiana and a low but increasing percentage in the French Caribbean. The rate of recent transmission was calculated to be 49.3% in French Guiana, compared to 27.2% and 16.9% in Guadeloupe and Martinique, respectively. At the phylogeographic level, 77.9% of the isolates studied belonged to four major clades (Haarlem, Latin-American and Mediterranean, T, and X) which are already reported from neighboring Caribbean islands in an international database and may underline potential interregional transmission events.
Use of a Mycobacteriophage-Based Assay for Rapid Assessment of Susceptibilities of
Mycobacterium tuberculosis
Isolates to Isoniazid and Influence of Resistance Level on Assay Performance
Authors: Galí N. , Domínguez J. , Blanco S. , Prat C. , Alcaide F. , Coll P. , Ausina V. 
Published: January 2006

ABSTRACT

We standardized and assessed the performance of an in-house microtiter assay for determining the susceptibilities of
Mycobacterium tuberculosis
clinical isolates to isoniazid based on mycobacteriophage amplification technology. Seventy isolates (43 resistant and 27 sensitive according to the BACTEC 460 radiometric method and MIC determination) were studied. The isoniazid resistance molecular mechanism was previously determined by sequencing the entire
katG
gene and the
mabA-inhA
regulatory region. The sensitivity of the mycobacteriophage-based assay in detecting isoniazid resistance was 86.1%, the specificity achieved was 92.6%, and the overall accuracy was 88.6%. In order to assess the possible influence of resistance levels on the mycobacteriophage-based-assay sensitivity, the results were analyzed according to the isoniazid MICs. All the isolates exhibiting high-level resistance (MIC ≥ 2 μg/ml) were scored as resistant by the mycobacteriophage-based assay (100% concordance), and 95% showed mutations or deletions in the catalytic domain of the
katG
gene. In contrast, 26.1% of the low-level-resistance strains (MICs, 0.25 to 1 μg/ml) were misclassified, and 66.7% had alterations in the
mabA-inhA
regulatory region. The mycobacteriophage-based assay could be used as a rapid method to detect the isoniazid susceptibility pattern, although data from those areas with high rates of low-level-resistance strains should be interpreted with caution. The features of the assay make it suitable for widespread application due to its low technical demand and cost.
Development and Validation of a Rotor-Gene Real-Time PCR Assay for Detection, Identification, and Quantification of
Chlamydia trachomatis
in a Single Reaction
Authors: Jalal Hamid , Stephen Hannah , Curran Martin D. , Burton Janet , Bradley Michelle , Carne Christopher 
Published: January 2006

ABSTRACT

A multitarget real-time PCR (MRT-PCR) for detection of
Chlamydia trachomatis
DNA was developed and validated. There were three targets for amplification in a single reaction: the cryptic plasmid (CP), the major outer membrane protein (MOMP) gene, and an internal control. The assay had the following characteristics: (i) detection and confirmation of the presence of
C. trachomatis
DNA in a single reaction, (ii) detection of all genovars of
C. trachomatis
without any cross-reactivity with pathogenic bacteria or commensal organisms of the oropharynx and genital tract, (iii) a 95% probability of detection with three copies of MOMP and one copy of CP per reaction mixture, (iv) identification of the inhibition of amplification, (v) a quantitative dynamic range of 25 to 250,000 genome copies per reaction mixture, (vi) high intra- and interassay reproducibilities, and (vii) correct identification of all samples in the validation panel. There were 146 COBAS Amplicor PCR (Amplicor PCR)-positive samples and 122 Amplicor PCR-negative samples in the panel. MRT-PCR detected CP DNA alone in 6 (4%) Amplicor PCR-positive samples and both CP and MOMP DNAs in 140 (96%) of 146 Amplicor PCR-positive samples. The quantity of MOMP DNA in 95 (68%) of 140 samples was within the dynamic range of the assay. The median
C. trachomatis
load in these samples was 321 genome copies per reaction mixture (range, 26 to 40,137 genome copies per reaction mixture). Due to the inclusion of two different
C. trachomatis
-specific targets, the assay confirmed 259 (97%) of 268 results in a single reaction. This assay could be used in the qualitative format for the routine detection of
C. trachomatis
and in the quantitative format for study of the pathogenesis of
C. trachomatis
-associated diseases. The assay demonstrated the potential to eliminate the need for confirmatory testing in almost all samples, thus reducing the turnaround time and the workload.
Listeria monocytogenes
Serotype 4b Strains Belonging to Lineages I and III Possess Distinct Molecular Features
Authors: Liu Dongyou , Lawrence Mark L. , Gorski Lisa , Mandrell Robert E. , Ainsworth A. Jerald , Austin Frank W. 
Published: January 2006

ABSTRACT

A collection of
Listeria monocytogenes
serotype 4b strains belonging to lineages I and III were examined by PCR and Southern blot analysis using species-, virulence-, and serotype-specific primers and probes. Whereas four serotype 4b lineage I strains reacted in PCR with the serotype 4b-, 4d-, and 4e-specific ORF2110 and virulence-specific
lmo1134
and
lmo2821
primers, all nine serotype 4b lineage III strains were negative by ORF2110 and
lmo1134
primers. In addition, the nine serotype 4b lineage III strains formed two separate groups through their reactions in PCR with virulence-specific
lmo2821
primers. Southern blot analysis using species-specific
lmo0733
and virulence-specific
lmo2821
gene probes largely confirmed the PCR results. These findings indicate that
L. monocytogenes
serotype 4b strains belonging to lineages I and III possess distinct molecular features.
Four-Year Persistence of a SingleCandida albicansGenotype Causing Bloodstream Infections in a Surgical Ward Proven by Multilocus Sequence Typing
Authors: Viviani Maria Anna , Cogliati Massimo , Esposto Maria Carmela , Prigitano Anna , Tortorano Anna Maria 
Published: January 2006

ABSTRACTThe present study represents the first application of multilocus sequence typing to retrospectively investigate a suspected outbreak ofCandida albicansbloodstream infection cases that occurred in the same hospital ward between July 1987 and October 1991. Results demonstrated that eight bloodstream infections were caused by the same strain, endemic in the ward, over a 4-year period.
Clonal Spread of Serogroup W135 Meningococcal Disease in Turkey
Authors: Kilic Abdullah , Urwin Rachel , Li Haijing , Saracli Mehmet A. , Stratton Charles W. , Tang Yi-Wei 
Published: January 2006

ABSTRACTSix cases ofNeisseria meningitidisserogroup W135 meningococcal infection have been reported in Turkey since 2003. Seven isolates recovered from four meningococcal meningitis patients and two asymptomatic carriers produced three distinct pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing and antigen gene sequencing showed that five isolates were indistinguishable from ST-11 (ET-37) serogroup W135 meningococci, which were first isolated in Saudi Arabia and were responsible for the worldwide outbreak among Hajj pilgrims and their contacts in 2000. The remaining two isolates, which had related PFGE patterns, differed from each other at only one of the genetic loci characterized but were not related to the ST-11 clonal complex. None of the six individuals recalled contact with a pilgrim or had traveled on the Hajj. These six individuals exhibited no time or place relationships to each other, except for the two asymptomatic carriers, who were soldiers and served in the same military unit. These data demonstrate that serogroup W135 meningococci with different genotypes, including the Hajj epidemic strain, are endemic in Turkey.
Comparative Study of the New Colorimetric VITEK 2 Yeast Identification Card versus the Older Fluorometric Card and of CHROMagar Candida as a Source Medium with the New Card
Authors: Aubertine C. L. , Rivera M. , Rohan S. M. , Larone D. H. 
Published: January 2006

ABSTRACT
The new VITEK 2 colorimetric card was compared to the previous fluorometric card for identification of yeast. API 20C was considered the “gold standard.” The new card consistently performed better than the older card. Isolates from CHROMagar Candida plates were identified equally as well as those from Sabouraud dextrose agar.
Does Nasal Cocolonization by Methicillin-Resistant Coagulase-Negative Staphylococci and Methicillin-Susceptible
Staphylococcus aureus
Strains Occur Frequently Enough To Represent a Risk of False-Positive Methicillin-Resistant
S. aureus
Determinations by Molecular Methods?
Authors: Becker Karsten , Pagnier Isabelle , Schuhen Brigitte , Wenzelburger Frauke , Friedrich Alexander W. , Kipp Frank , Peters Georg , von Eiff Christof 
Published: January 2006

ABSTRACT

By analyzing the colonization of the anterior nares in cardiothoracic surgery patients on admission, nasal cocolonization by methicillin-susceptible
Staphylococcus aureus
and methicillin-resistant coagulase-negative staphylococci was detected in 8/235 (3.4%) specimens. Consequently, in a low-methicillin-resistant
S. aureus
(MRSA) setting, a molecular MRSA screening test targeting the
mecA
gene and an
S. aureus
-specific gene in parallel and applied directly to clinical specimens would be associated with an unacceptable positive predictive value of about 40%.
Evaluation of Three Diagnostic Methods, Including Real-Time PCR, for Detection of
Dientamoeba fragilis
in Stool Specimens
Authors: Stark D. , Beebe N. , Marriott D. , Ellis J. , Harkness J. 
Published: January 2006

ABSTRACT

Dientamoeba fragilis
is a protozoan parasite of humans that infects the mucosa of the large intestine and is associated with gastrointestinal disease. We developed a 5′ nuclease (TaqMan)-based real-time PCR assay, targeting the small subunit rRNA gene, for the detection of
D. fragilis
in human stool specimens and compared its sensitivity and specificity to conventional PCR and microscopic examination by a traditional modified iron-hematoxylin staining procedure. Real-time PCR exhibited 100% sensitivity and specificity.
Utility of the VITEK 2 Advanced Expert System for Identification of Extended-Spectrum β-Lactamase Production in
Enterobacter
spp
Authors: Schwaber Mitchell J. , Navon-Venezia Shiri , Chmelnitsky Inna , Leavitt Azita , Schwartz David , Carmeli Yehuda 
Published: January 2006

ABSTRACT

Forty clinical isolates of
Enterobacter
spp. were identified as extended-spectrum β-lactamase (ESBL) producers by disk diffusion. The VITEK 2 Advanced Expert System (AES) identified the ESBL phenotype in only 25 isolates (62.5%), and erroneously reported cephalosporin susceptibility in 11 isolates (28%). Refinements in the AES are required in order to improve ESBL detection in
Enterobacter
.
Diagnostic Oligonucleotide Microarray Fingerprinting of
Bacillus
Isolates
Authors: Chandler Darrell P. , Alferov Oleg , Chernov Boris , Daly Don S. , Golova Julia , Perov Alexander , Protic Miroslava , Robison Richard , Schipma Matthew , White Amanda , Willse Alan 
Published: January 2006

ABSTRACT

A genome-independent microarray and new statistical techniques were used to genotype
Bacillus
strains and quantitatively compare DNA fingerprints with the known taxonomy of the genus. A synthetic DNA standard was used to understand process level variability and lead to recommended standard operating procedures for microbial forensics and clinical diagnostics.
Rapid, Noninvasive Diagnosis of Visceral Leishmaniasis in India: Comparison of Two Immunochromatographic Strip Tests for Detection of Anti-K39 Antibody
Authors: Sundar Shyam , Maurya Radheshyam , Singh Rakesh K. , Bharti K. , Chakravarty Jaya , Parekh Ashish , Rai Madhukar , Kumar Kailash , Murray Henry W. 
Published: January 2006

ABSTRACT
Used with blood or serum, a new anti-K39 antibody immunochromatographic strip test (IT-Leish; DiaMed AG) proved sensitive (range, 99 to 100%) and specific (range, 95 to 100%) for the noninvasive serodiagnosis of visceral leishmaniasis in India. Used with serum, the IT-Leish test and the existing Kalazar Detect test (InBios International, Inc.) yielded comparable results for symptomatic infection and identified apparent subclinical infection in 15 to 32% of healthy residents in a region where visceral leishmaniasis is highly endemic.
Safe
Mycobacterium tuberculosis
DNA Extraction Method That Does Not Compromise Integrity
Authors: Warren Robin , de Kock Marianna , Engelke Erica , Myburgh Roseline , Gey van Pittius Nico , Victor Thomas , van Helden Paul 
Published: January 2006

ABSTRACT

Concern has been raised about the efficacy of the heat killing of mycobacteria during the isolation of DNA. We demonstrate a method that allows for the efficient killing of
Mycobacterium tuberculosis
without compromising DNA integrity for subsequent molecular investigation. This method reduces the risk of infection to the research scientist.
Utility of Extended Blood Culture Incubation for Isolation of
Haemophilus, Actinobacillus, Cardiobacterium, Eikenella
, and
Kingella
Organisms: a Retrospective Multicenter Evaluation
Authors: Petti Cathy A. , Bhally Hasan S. , Weinstein Melvin P. , Joho Kim , Wakefield Teresa , Reller L. Barth , Carroll Karen C. 
Published: January 2006

ABSTRACT

The incidence of and average time to detection for
Haemophilus, Actinobacillus, Cardiobacterium, Eikenella
, and
Kingella
(HACEK) bacteria in blood cultures with standard incubation and the utility of extended incubation of blood culture bottles were reviewed at four tertiary care microbiology laboratories. HACEK organisms were isolated from 35 (<0.005%) of 59,203 positive blood cultures. None of 407 blood cultures with extended incubation grew HACEK or other bacteria. Bacteremia from HACEK bacteria is rare, and extended incubation of blood cultures to recover HACEK bacteria is unnecessary.
Multiple-Locus Variable-Number Tandem Repeat Analysis for Typing of
Staphylococcus epidermidis
Authors: Johansson Anders , Koskiniemi Satu , Gottfridsson Per , Wiström Johan , Monsen Tor 
Published: January 2006

ABSTRACT

We applied a high-resolution PCR-based typing method, multiple-locus variable-number tandem repeat analysis (MLVA), for discrimination of 30 multidrug-resistant clinical isolates of
Staphylococcus epidermidis
. The results of MLVA were congruent with results obtained by pulsed-field gel electrophoresis (PFGE). MLVA generated discrete character data, and its discriminatory capacity was comparable to that of PFGE.
Prevalence and Evolution of Methicillin-Resistant
Staphylococcus aureus
in Spanish Hospitals between 1996 and 2002
Authors: Vindel A. , Trincado P. , Gómez E. , Cabrera R. , Boquete T. , Solá C. , Valdezate S. , Saez-Nieto J. A. 
Published: January 2006

ABSTRACT

Pulsed-field gel electrophoretic analysis of 2,144 methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from patients in Spanish hospitals over a 7-year period revealed 17 predominant profiles. Typing showed the replacement of Iberian clone E1 (ST247-MRSA-I) by two prevalent clones, E7 and E8, that are closely related to each other and have the same genetic background as ST125-MRSA-IV.
Rapid Identification ofMycobacterium tuberculosisBeijing Genotypes on the Basis of the Mycobacterial Interspersed Repetitive Unit Locus 26 Signature
Authors: Rao K. Rajender , Ahmed Niyaz , Srinivas Sriramula , Sechi Leonardo A. , Hasnain Seyed E. 
Published: January 2006

ABSTRACTMycobacterium tuberculosisBeijing strains are prevalent in many parts of the world and often give rise to large institutional outbreaks. Such highly transmissible strains, often associated with multidrug resistance, are likely underrepresented in outbreaks reported from developing countries, mainly due to nonavailability of fast detection methods suitable in epidemiological surveillance studies. We evaluated a PCR assay based on amplification of mycobacterial interspersed repetitive unit locus 26 as a stand-alone method for unambiguous identification of Beijing strains. The method was used on blinded samples from 10 standard strains whose Beijing status was already confirmed by spoligotyping. All 10 strains were accurately identified, and their profiles were corroborated successfully with spoligotypes. The method was also applied to 70 different non-Beijing clinical isolates from different countries to allow discrimination of isolates. Owing to its accuracy, simplicity, and rapidity, the assay can be employed in laboratory-level testing of isolates linked to certain outbreaks. The test can also be adopted for direct application on clinical samples to save time on culturing bacilli for genotyping.
First Isolation of
Bartonella alsatica
from a Valve of a Patient with Endocarditis
Authors: Raoult Didier , Roblot France , Rolain Jean-Marc , Besnier Jean-Marc , Loulergue Joëlle , Bastides Frédéric , Choutet Patrick 
Published: January 2006

ABSTRACT

We report the first documented case of endocarditis in a man infected with
Bartonella alsatica
, which causes bacteremia in healthy wild rabbits.
B. alsatica
was identified by serology and culture and by PCR of an aortic valve specimen.
B. alsatica
should be added to the list of zoonotic agents of blood culture-negative endocarditis.
Nocardia cyriacigeorgica
Septicemia
Authors: Elsayed Sameer , Kealey Angela , Coffin Carla S. , Read Ron , Megran David , Zhang Kunyan 
Published: January 2006

ABSTRACT

We report two cases of
Nocardia cyriacigeorgica
septicemia and disseminated infection in the setting of profound immunodeficiency. In both instances, diagnosis was rapidly facilitated by 16S rRNA gene sequencing of blood culture isolates. These constitute the first confirmed reports of
Nocardia cyriacigeorgica
bloodstream infection in humans.
Specimens from a Vesicular Lesion Caused by Molluscum Contagiosum Virus Produced a Cytopathic Effect in Cell Culture That Mimicked That Produced by Herpes Simplex Virus
Authors: Bell Constance A. , Eberly Allison P. , Takata Geraldine , Combs Raelene K. , Deweese Nathan E. , Whelen A. Christian 
Published: January 2006

ABSTRACT
Infection with molluscum contagiosum virus, a poxvirus, normally has a typical clinical presentation; therefore, laboratory confirmation is infrequently sought and the virus is rarely isolated in culture. As reported herein, viral culture of specimens from atypical lesions may produce an abortive infection in limited cell lines and a cytopathic effect suggestive of herpes simplex virus.