bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread Skin and Soft-Tissue Infections Due to Two Methicillin-Resistant
Staphylococcus aureus
Strains Harboring the Genes for Panton-Valentine Leucocidin
Authors: Diep Binh An , Sensabaugh George F. , Somboona Naraporn S. , Carleton Heather A. , Perdreau-Remington Françoise 
Published: May 2004

ABSTRACT

Infections caused by community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) are emerging as a major public health problem. CA-MRSA has been associated previously with skin and soft-tissue infection (SSTI) and with carriage of staphylococcal cassette chromosome
mec
(SCC
mec
) type IV and the Panton-Valentine leucocidin (PVL) virulence factor. To assess the clonal distribution of PVL-carrying strains and the association with SSTI in the San Francisco Bay area, we surveyed six collections of
S. aureus
isolates—671 isolates in all—collected between 1997 and 2002 originating from inpatient and outpatient clinical specimens and from a community-based sampling. Isolates were genotyped by pulsed-field gel electrophoresis, multilocus restriction fragment typing, and multilocus sequence typing and assayed for the PVL virulence factor. The
S. aureus
populations showed a high proportion of PVL-carrying strains, with frequencies ranging up to 70% in MRSA isolated from jail inmate patients and 69% in MRSA from patients receiving surgical treatment at an outpatient clinic specializing in treating SSTIs. PVL-carrying isolates were identified in nine clonal groups, but 88.5% of the PVL-carrying MRSA isolates belonged to only two clonal groups. These two clonal groups carried the SCC
mec
type IV resistance determinant and were more likely than other clonal groups to be recovered from SSTI sites than from other sites (
P
< 0.0001). There is evidence of clonal replacement over the period from 1999 to 2002, with one of these two clonal groups being supplanted by the other.
Rapid Quantification of Drug Resistance Gene Expression in
Candida albicans
by Reverse Transcriptase LightCycler PCR and Fluorescent Probe Hybridization
Authors: Frade Joao P. , Warnock David W. , Arthington-Skaggs Beth A. 
Published: May 2004

ABSTRACT

We developed a rapid, sensitive, and reproducible assay to quantify
Candida albicans ACT1
,
CDR1
,
CDR2
,
ERG11
, and
MDR1
mRNA using a two-step reverse transcription and LightCycler real-time PCR (RT-LightCycler PCR) method with sequence-specific hybridization probes. We compared RT-LightCycler PCR with Northern hybridization for quantitative analysis of gene expression in isolates with various fluconazole susceptibilities. Specificity of each LightCycler PCR was verified by LightCycler melting curve analysis and agarose gel electrophoresis of amplified products. Correlation of quantification results between RT-LightCycler PCR and Northern hybridization yielded correlation coefficients of ≥0.91 for all genes except
MDR1
(0.74). In this case, reduced correlation was due to the inability of Northern hybridization to accurately quantify the high
MDR1
expression in a susceptible dose-dependent isolate which was shown by RT-LightCycler PCR to overexpress
MDR1
>200-fold relative to the other isolates tested. In four isolates, low levels of
CDR2
mRNA were detected by RT-LightCycler PCR but were undetectable by Northern hybridization. mRNA quantification by RT-LightCycler PCR correlates with Northern hybridization and offers additional advantages, including increased sensitivity and speed of analysis, along with lower RNA concentration requirements and an increased dynamic range of signal detection.
Comparison of Two Real-Time Quantitative Assays for Detection of Severe Acute Respiratory Syndrome Coronavirus
Authors: Hourfar Michael K. , Roth W. Kurt , Seifried Erhard , Schmidt Michael 
Published: May 2004

ABSTRACT

The new severe acute respiratory syndrome (SARS) coronavirus (CoV), described in February 2003, infected a total of 8,439 people. A total of 812 people died due to respiratory insufficiency. Close contact with symptomatic patients appeared to be the main route of transmission. However, potential transmission by blood transfusion could not be definitely excluded. Two real-time SARS-specific PCR assays were assessed for their sensitivities, agreement of test results, and intra-assay variabilities. Both assays rely on reverse transcription and amplification of extracted RNA. Dilutions of gamma-irradiated cell culture supernatants of SARS CoV-infected Vero E6 cells were prepared to determine the precisions, linear ranges, and accuracies of the assays. The linear range for the Artus RealArt HPA-Coronavirus assay (Artus assay) was 1 × 10
2
to 1 × 10
7
copies/ml, and that for the Roche LightCycler SARS CoV Quantification kit (Roche assay) was 1 × 10
4
to 2 × 10
8
copies/ml. The detection limit of the Roche assay was 3,982.1 copies/ml, whereas that of the Artus assay was 37.8 copies/ml. Detection limits were calculated with a standard preparation that was recommended for use by the World Health Organization. However, quantification of CoV in this preparation may be imprecise. In summary, both assays are suitable for quantitative measurement of SARS CoV at the high concentrations expected in sputum samples. The Artus assay is also suitable for detection of SARS CoV at the low concentrations found in serum samples.
Detection ofCandidain Concentrated Oral Rinse Cultures by Real-Time PCR
Authors: White P. Lewis , Williams David W. , Kuriyama Tomoari , Samad Shamim A. , Lewis Michael A. O. , Barnes Rosemary A. 
Published: May 2004

ABSTRACTThe incidence of oral candidosis has increased in recent years, largely as a result of the emergence of human immunodeficiency virus infection and the more widespread use of immunosuppressive chemotherapy. This development has been associated with a need for more reliable methods for the detection ofCandida. The present study assessed the performance of a real-time PCR and two block-based PCRs for the detection ofCandidain 193 concentrated oral rinse culture (CRC) specimens. A total of 102 CRC specimens were positive by culture forCandida; and 96, 90, and 75 of these were also positive by real-time, N18-specific, and internal transcribed spacer (ITS)-specific PCRs, respectively. The five false-negative results by the real-time PCR were all non-Candida albicanspositive by culture. Of the 91 culture-negative CRC specimens, 20, 41, and 44 were positive by the real-time PCR and the N18- and ITS-specific PCRs, respectively. All three PCRs detected fungal DNA in 8 culture-negative CRC specimens, with a further 30 being positive by two of the three PCRs. A total of 32 CRC specimens wereCandidafree by all methods. In summary, a real-time PCR that provides a sensitive, specific, and rapid alternative technique for detection ofCandidain the mouth is described.
Comparison of Two 3ABC Enzyme-Linked Immunosorbent Assays for Diagnosis of Multiple-Serotype Foot-and-Mouth Disease in a Cattle Population in an Area of Endemicity
Authors: Bronsvoort B. M. de C. , Sørensen K. J. , Anderson J. , Corteyn A. , Tanya V. N. , Kitching R. P. , Morgan K. L. 
Published: May 2004

ABSTRACTThe development of a serological test for foot-and-mouth disease virus (FMDV) which is quick and easy to use, which can identify all seven serotypes, and which can differentiate vaccinated from convalescing or potential virus carriers would be a major advance in the epidemiological toolkit for FMDV. The nonstructural polyprotein 3ABC has recently been proposed as such an antigen, and a number of diagnostic tests are being developed. This paper evaluates the performance of two FMDV tests for antibodies to nonstructural proteins in an unvaccinated cattle population from a region of Cameroon with endemic multiple-serotype FMD. The CHEKIT-FMD-3ABC bo-ov (CHEKIT) enzyme-linked immunosorbent assay (ELISA) (Bommeli Diagnostics/Intervet) is a commercially available test that was compared with a competitive 3ABC ELISA (C-ELISA) developed in Denmark. The tests were compared with the virus neutralization test as the “gold standard.” Diagnostic sensitivity and specificity were examined over a range of test cutoffs by using receiver operating characteristic curves, which allowed comparison of the overall performance of each test. The results indicated that the CHEKIT ELISA kit was 23% sensitive and 98% specific and the Danish C-ELISA was 71% sensitive and 90% specific at the recommended cutoff. These results have important implications if the tests are to be used to screen herds or individual cattle in surveillance programs, at border crossings for import-export clearance, or following emergency vaccination in an outbreak situation.
Serotyping of 800 Strains of
Erysipelothrix
Isolated from Pigs Affected with Erysipelas and Discrimination of Attenuated Live Vaccine Strain by Genotyping
Authors: Imada Yumiko , Takase Ai , Kikuma Reiko , Iwamaru Yoshifumi , Akachi Shigehiro , Hayakawa Yûji 
Published: May 2004

ABSTRACT

Eight hundred
Erysipelothrix
strains isolated between 1992 and 2002 from swine with erysipelas in Japan were serotyped. Thirty-seven, 47, 73, and 643 strains were isolated from animals with acute septicemia, urticaria, chronic endocarditis, and chronic arthritis, respectively, of which 381, 146, 254, and 19 isolates belonged to serotypes 1a, 1b, and 2b and other serotypes, respectively. All serotype 1a isolates were further examined for acriflavine resistance and their genotypes to discriminate them from the attenuated live vaccine strain, defined as serotype 1a, which is resistant to 0.02% acriflavine and which shows low levels of pathogenicity in mice. Of the serotype 1a isolates, 64.6% were acriflavine resistant, with 98.4% of these acriflavine-resistant strains having been isolated from animals with chronic arthritis. By randomly amplified polymorphic DNA (RAPD) analysis, almost all the acriflavine-resistant serotype 1a strains showed the 253-bp band characteristic of vaccine strains and were easily discriminated from all 113 strains of acriflavine-sensitive serotype 1a strains from animals with acute and subacute swine erysipelas. The incidence of acriflavine-resistant strains of the distinctive RAPD type 1-2 was markedly higher than that of the other RAPD types and serotypes. RAPD type 1-2 strains also included a specific group identifiable by restriction fragment length polymorphism DNA analysis. Furthermore, the pathogenicities of 29 isolates of RAPD type 1-2 for mice were lower than those of the 21 isolates of other RAPD types. Our results indicate that RAPD type 1-2 strains are live vaccine strains and that 37% of the cases of chronic swine erysipelas detected in the past 11 years in Japan have occurred as a side effect of live vaccine use.
Simultaneous Analysis of Multiple Staphylococcal Enterotoxin Genes by an Oligonucleotide Microarray Assay
Authors: Sergeev Nikolay , Volokhov Dmitriy , Chizhikov Vladimir , Rasooly Avraham 
Published: May 2004

ABSTRACT

Staphylococcal enterotoxins (SEs) are a family of 17 major serological types of heat-stable enterotoxins that are one of the leading causes of gastroenteritis resulting from consumption of contaminated food. SEs are considered potential bioweapons. Many
Staphylococcus aureus
isolates contain multiple SEs. Because of the large number of SEs, serological typing and PCR typing are laborious and time-consuming. Furthermore, serological typing may not always be practical because of antigenic similarities among enterotoxins. We report on a microarray-based one-tube assay for the simultaneous detection and identification (genetic typing) of multiple enterotoxin (
ent
) genes. The proposed typing method is based on PCR amplification of the target region of the
ent
genes with degenerate primers, followed by characterization of the PCR products by microchip hybridization with oligonucleotide probes specific for each
ent
gene. We verified the performance of this method by using several other techniques, including PCR amplification with gene-specific primers, followed by gel electrophoresis or microarray hybridization, and sequencing of the enterotoxin genes. The assay was evaluated by analysis of previously characterized staphylococcal isolates containing 16
ent
genes. The microarray assay revealed that some of these isolates contained additional previously undetected
ent
genes. The use of degenerate primers allows the simultaneous amplification and identification of as many as nine different
ent
genes in one
S. aureus
strain. The results of this study demonstrate the usefulness of the oligonucleotide microarray assay for the analysis of multitoxigenic strains, which are common among
S. aureus
strains, and for the analysis of microbial pathogens in general.
Evaluation of “Helicobacter heilmannii” Subtypes in the Gastric Mucosas of Cats and Dogs
Authors: Priestnall Simon L. , Wiinberg Bo , Spohr Anette , Neuhaus Britta , Kuffer Manuela , Wiedmann Martin , Simpson Kenneth W. 
Published: May 2004

ABSTRACTInfection with candidatus “Helicobacter heilmannii” is associated with gastritis and mucosa-associated lymphoid tissue lymphoma in people. Infection with “H. heilmannii” type 1 predominates (80%) and is thought to be acquired from dogs, cats, or pigs. We further examined the zoonotic potential of dogs and cats by amplifying gastric DNA from cats (n= 45) and dogs (n= 10) with primers against “H. heilmannii”ureBand 16S rRNA genes and sequencing the products. Fluorescence in situ hybridization (FISH) with eubacterial and “H. heilmannii”-specific probes was employed to directly visualize “H. heilmannii” types and their intragastric distribution.ureBsequences of “H. heilmannii” amplicons clustered with human and feline isolates of “H. heilmannii” and were distinct from the “H. heilmannii”-like organisms (HHLO)H. felis,H. salomonis, andH. bizzozeronii. 16S ribosomal DNA sequences in 20 “H. heilmannii”-infected cats and dogs were distinct from “H. heilmannii” type 1 and “H. suis” and clustered with “H. heilmannii” types 2 and 4. FISH confirmed the presence of “H. heilmannii” types 2 and 4 in dogs but failed to definitively characterize the “H. heilmannii” types present in cats. In infected dogs, “H. heilmannii” inhabited the gastric mucus and glands, and in dogs coinfected with other HHLO it shared the same gastric niche. The results indicate that dogs and cats are predominantly colonized by “H. heilmannii” bacteria that are distinct from type 1 and from “H. suis.” As “H. heilmannii” type 1 predominates in people, the zoonotic risk posed by dogs and cats is likely small.
Hyperinvasive Neonatal Group B Streptococcus Has Arisen from a Bovine Ancestor
Authors: Bisharat Naiel , Crook Derrick W. , Leigh James , Harding Rosalind M. , Ward Phil N. , Coffey Tracey J. , Maiden Martin C. , Peto Tim , Jones Nicola 
Published: May 2004

ABSTRACT

The genetic relatedness and evolutionary relationships between group B streptococcus (GBS) isolates from humans and those from bovines were investigated by phylogenetic analysis of multilocus sequence typing data. The collection of isolates consisted of 111 GBS isolates from cows with mastitis and a diverse global collection of GBS isolates from patients with invasive disease (
n
= 83) and carriers (
n
= 69). Cluster analysis showed that the majority of the bovine isolates (93%) grouped into one phylogenetic cluster. The human isolates showed greater diversity and clustered separately from the bovine population. However, the homogeneous human sequence type 17 (ST-17) complex, known to be significantly associated with invasive neonatal disease, was the only human lineage found to be clustered within the bovine population and was distinct from all the other human lineages. Split decomposition analysis revealed that the human isolate ST-17 complex, the major hyperinvasive neonatal clone, has recently arisen from a bovine lineage.
Correlation between Viral Loads of Cytomegalovirus in Blood and Bronchoalveolar Lavage Specimens from Lung Transplant Recipients Determined by Histology and Immunohistochemistry
Authors: Chemaly Roy F. , Yen-Lieberman Belinda , Castilla Elias A. , Reilly Amy , Arrigain Susana , Farver Carol , Avery Robin K. , Gordon Steven M. , Procop Gary W. 
Published: May 2004

ABSTRACT

Cytomegalovirus (CMV) is an important pathogen in lung transplant recipients. Early detection of CMV end-organ disease should help with treatment management. We determined the CMV viral load by hybrid capture in bronchoalveolar lavage (BAL) fluid samples from patients who had undergone lung transplantation. For 39 of these samples (from 25 patients), corresponding transbronchial biopsy samples were available for CMV immunohistochemistry (IHC). The CMV IHC results were interpreted and categorized as positive or negative, and the positive results were subcategorized as typical if cells with both significant nuclear enlargement or Cowdry A-type inclusions and positive staining were present or as atypical if definitive nuclear staining was seen but significant nuclear enlargement was not. Diagnostic CMV viral inclusions were reported in the anatomic diagnosis, based on hematoxylin-eosin staining alone, for three (8%) of the biopsy samples. CMV was detected by IHC in 13 (33%) samples (5 typical, 8 atypical). The median CMV viral load in BAL samples was 0 copies/ml for BAL samples from patients with IHC-negative biopsy samples; 47,678 copies/ml for BAL samples from patients with biopsy samples with positive, atypical staining; and 1,548,827 copies/ml for BAL samples from patients with biopsy samples with positive, typical staining (
P
< 0.001). Compared to routine pathology of biopsy samples, the use of IHC increased the diagnostic yield of CMV. Also, the CMV viral load in BAL fluid samples increased along with immunoreactivity from negative to positive, atypical staining to positive, typical staining. The CMV viral load determined with the end-organ sample, the BAL fluid sample, was higher than the corresponding viral load determined with blood. Both IHC and determination of the CMV viral load in BAL samples may be useful for the detection of individuals at risk for the development of fulminant invasive CMV disease.
Systematic 16S rRNA Gene Sequencing of Atypical Clinical Isolates Identified 27 New Bacterial Species Associated with Humans
Authors: Drancourt M. , Berger P. , Raoult D. 
Published: May 2004

ABSTRACTClinical microorganisms isolated during a 5-year study in our hospital that could not be identified by conventional criteria were studied by 16S rRNA gene sequence analysis. Each isolate yielded a ≥1,400-bp sequence containing <5 ambiguities which was compared with the GenBank 16S rRNA gene library; 1,404 such isolates were tested, and 120 were considered unique (27 isolates) or rare (≤10 cases reported in the literature) human pathogens. Eleven new species, “Actinobaculum massiliae,” “CandidatusActinobaculum timonae,”Paenibacillus sanguinis, “CandidatusBacteroides massiliae,”Chryseobacterium massiliae, “CandidatusChryseobacterium timonae,”Paenibacillus massiliensis, “CandidatusPeptostreptococcus massiliae,” “CandidatusPrevotella massiliensis,”Rhodobacter massiliensis, and “CandidatusVeillonella atypica” were identified. Sixteen species were obtained from humans for the first time. Our results show the important role that 16S rRNA gene sequence-based bacterial identification currently plays in recognizing unusual and emerging bacterial diseases.
Use of β-Lactamase Inhibitors in Disk Tests To Detect Plasmid-Mediated AmpC β-Lactamases
Authors: Black Jennifer A. , Thomson Kenneth S. , Pitout Johann D. D. 
Published: May 2004

ABSTRACT
Seeking a simple disk test for detection of organisms producing plasmid-mediated AmpC β-lactamases, we evaluated the diagnostic utility of the β-lactamase inhibitors 48-1220 (Ro 48-1220) and LN-2-128. Using NCCLS disk methodology, inhibition zone diameters were determined for five β-lactam antibiotics tested alone and in combination with 20 μg of either 48-1220 or LN-2-128. Using an increase of ≥4 mm in zone diameter in the presence of an inhibitor as a positive test, cefotetan with LN-2-128 and 48-1220 was adequate for the detection of organisms producing plasmid-mediated AmpCs (specificity of 90% and sensitivity of 100%).
Human Papillomavirus Type 16 Viral Load Is Higher in Human Immunodeficiency Virus-Seropositive Women with High-Grade Squamous Intraepithelial Lesions Than in Those with Normal Cytology Smears
Authors: Lefevre Jonas , Hankins Catherine , Money Deborah , Rachlis Anita , Pourreaux Karina , Coutlée François 
Published: May 2004

ABSTRACT

Human papillomavirus type 16 (HPV-16) viral load in cervicovaginal lavage samples collected from 66 human immunodeficiency virus-seropositive women was inversely correlated with blood CD4 count (
P
= 0.002). HPV-16 viral load was 81-fold higher in women with cervical smears suggestive of high-grade lesions (median, 4,425,883 copies/μg of DNA) than in women with normal smears (median, 54,576), controlling for age (
P
= 0.006).
Comparison of Chlorhexidine and Tincture of Iodine for Skin Antisepsis in Preparation for Blood Sample Collection
Authors: Barenfanger Joan , Drake Cheryl , Lawhorn Jerry , Verhulst Steven J. 
Published: May 2004

ABSTRACT
Rates of contamination of blood cultures obtained when skin was prepared with iodine tincture versus chlorhexidine were compared. For iodine tincture, the contamination rate was 2.7%; for chlorhexidine, it was 3.1%. The 0.41% difference is not statistically significant. Chlorhexidine has comparable effectiveness and is safer, cheaper, and preferred by staff, so it is an alternative to iodine tincture.
Outbreak of
Burkholderia cepacia
Bacteremia in a Pediatric Hospital Due to Contamination of Lipid Emulsion Stoppers
Authors: Doit C. , Loukil C. , Simon A.-M. , Ferroni A. , Fontan J.-E. , Bonacorsi S. , Bidet P. , Jarlier V. , Aujard Y. , Beaufils F. , Bingen E. 
Published: May 2004

ABSTRACT

We describe a 7-month outbreak of nosocomial
Burkholderia cepacia
bacteremia involving eight children in a pediatric hospital and the results of epidemiological investigations. A
B. cepacia
strain genotypically identical to the blood isolates was recovered from the upper surface of capped rubber stoppers of bottles of a commercial lipid emulsion used for parenteral nutrition.
CorynebacteriumSpecies Isolated from Bone and Joint Infections Identified by 16S rRNA Gene Sequence Analysis
Authors: Roux Véronique , Drancourt Michel , Stein Andreas , Riegel Philippe , Raoult Didier , La Scola Bernard 
Published: May 2004

ABSTRACTBy the use of 16S rRNA gene sequence analysis we identified 28 of 31Corynebacteriumspp. isolated from bone and joint infections, including species never before isolated in such infections. Phenotypic analysis led to the correct identification of 8 of 31. 16S rRNA gene sequence analysis appears to be a good technique for identification of clinical strains ofCorynebacteriumspp.
Further Evaluation of a Rapid Diagnostic Test for Melioidosis in an Area of Endemicity
Authors: O'Brien Mathew , Freeman Kevin , Lum Gary , Cheng Allen C. , Jacups Susan P. , Currie Bart J. 
Published: May 2004

ABSTRACT

Immunochromatographic test (ICT) kits for the rapid detection of immunoglobulin G (IgG) and IgM antibodies to
Burkholderia pseudomallei
were compared to the indirect hemagglutination (IHA) assay. In 138 culture-confirmed melioidosis cases, sensitivities were 80, 77, and 88% for IHA, ICT IgG, and ICT IgM, respectively. In a prospective study of 160 consecutive sera samples sent for melioidosis serology, respective specificities were 91, 90, and 69, positive predictive values were 41, 32, and 18, and negative predictive values were 99, 98, and 100%. ICT IgM kits are unreliable for diagnosis of melioidosis, but ICT IgG kits may be useful for diagnosing travelers presenting with possible melioidosis who return from regions where melioidosis is endemic.