bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Rapid Detection of Bloodstream Infections on Length of Hospitalization and Hospital Charges
Authors: Beekmann S. E. , Diekema D. J. , Chapin K. C. , Doern G. V. 
Published: July 2003

ABSTRACT
Current automated continuous-monitoring blood culture systems afford more rapid detection of bacteremia and fungemia than is possible with non-instrument-based manual methods. Use of these systems has not been studied objectively with respect to impact on patient outcomes, including hospital charges and length of hospitalization. We conducted a prospective, two-center study in which the time from the obtainment of the initial positive blood culture until the Gram stain was called was evaluated for 917 cases of bloodstream infection. Factors showing univariate associations with a shorter time to notification included higher body temperature and respiratory rate and higher percentage of immature neutrophils. Multiple linear regression models determined that the primary predictors of both increased microbiology laboratory and total hospital charges for patients with bloodstream infection were nonmicrobiologic and included length of stay and host factors such as the admitting service and underlying illness score. Significant microbiologic predictors of increased charges included the number of blood cultures obtained, nosocomial acquisition, and polymicrobial bloodstream infections. Accelerated failure time regression analysis demonstrated that microbiologic factors, including time until notification, organism group, and nosocomial acquisition, were independently associated with length of hospitalization after bacteremia, as were the factors of admitting service, gender, and age. Our data suggest that an increased time to notification of bloodstream infection is independently associated with increased length of stay. We conclude that the time to notification is an obvious target for efforts to shorten length of stay. The newest generation of automated continuous-monitoring blood culture systems, which shorten the time required to obtain a positive result, should impact length of hospitalization.
Genetic Polymorphism and Molecular Epidemiology ofLeishmania(Viannia)braziliensisfrom Different Hosts and Geographic Areas in Brazil
Authors: Cupolillo Elisa , Brahim Lúcia Regina , Toaldo Cristiane B. , de Oliveira-Neto Manoel Paes , de Brito Maria Edileuza Felinto , Falqueto Aloisio , de Farias Naiff Maricleide , Grimaldi Gabriel 
Published: July 2003

ABSTRACTNumerical zymotaxonomy and variability of the internal transcribed spacers (ITS) between the small and large subunits of the rRNA genes were used to examine strain variation and relationships in natural populations ofLeishmania(Viannia)braziliensis. A total of 101 strains from distinct hosts and Brazilian geographic regions were assigned to 15 zymodemes clustered in two major genetic groups. The great number of isolates (48.5%) placed in zymodeme IOC/Z-27 were collected on the Atlantic coast. The high molecular diversity found in populations in the Amazon Basin was related to the great number of sandfly vector(s) in that region. The results of the restriction fragment length polymorphism analysis of the ITS depicted considerable intraspecific variation. Genotypic groups A, B, and C contained 39, 40, and 22 isolates, which were divided into 16, 10, and 15 genotypes, respectively. The genetic polymorphism observed demonstrates the degree of diversity ofL.(V.)braziliensisstrains from different regions where they are endemic. The results reinforce the clonal theory forLeishmaniaparasites showing the genetic diversity of this pathogen and an association ofL.(V.)braziliensisgenotypes with specific transmission cycles, probably reflecting an adaptation of different clones to the vector species involved.
Evaluation of Real-Time PCR versus PCR with Liquid-Phase Hybridization for Detection of Enterovirus RNA in Cerebrospinal Fluid
Authors: Lai K. Kay-Yin , Cook Linda , Wendt Sharon , Corey Lawrence , Jerome Keith R. 
Published: July 2003

ABSTRACT

A LightCycler and two TaqMan real-time PCR assays were evaluated against an older PCR with liquid-phase hybridization method for the detection of enterovirus RNA in 74 patient samples. The two-step LightCycler and the two-step TaqMan formats correlated well with each other (
r
2
= 0.90) and were equally sensitive compared to the liquid-phase hybridization method, whereas the one-step recombinant
Tth
DNA polymerase format was rather insensitive, detecting enterovirus RNA in only about one-half of those patient samples previously positive by liquid-phase hybridization. The two-step TaqMan method was optimized utilizing 10 μl of cDNA and demonstrated the highest degree of analytical sensitivity among the methods evaluated in our study, being able to reproducibly quantify down to 510 copies of enteroviral RNA/ml of cerebrospinal fluid. This new assay can be performed in 4 h, is much less labor intensive, and showed less cross-reactivity with rhinovirus than the liquid-phase hybridization assay. Thus, the two-step TaqMan assay should prove useful in the diagnosis of enteroviral meningitis versus bacterial meningitis, thereby resulting in timely and appropriate clinical management that can amount to significant cost savings to the patient and health care system.
Evaluation of the NCCLS Extended-Spectrum β-Lactamase Confirmation Methods forEscherichia coliwith Isolates Collected during Project ICARE
Authors: Tenover Fred C. , Raney Patti M. , Williams Portia P. , Rasheed J. Kamile , Biddle James W. , Oliver Antonio , Fridkin Scott K. , Jevitt Laura , McGowan, John E. 
Published: July 2003

ABSTRACTTo determine whether confirmatory tests for extended-spectrum β-lactamase (ESBL) production inEscherichia coliare necessary, we selected 131E. coliisolates that met the National Committee for Clinical Laboratory Standards (NCCLS) screening criteria for potential ESBL production from the Project ICARE (Intensive Care Antimicrobial Resistance Epidemiology) strain collection. For all 131 isolates, the broth microdilution (BMD) MIC of at least one extended-spectrum cephalosporin was ≥2 μg/ml. For 21 of 131 (16%) isolates, the ESBL confirmatory test was positive; i.e., the BMD MICs of ceftazidime or cefotaxime decreased by ≥3 doubling dilutions in the presence of clavulanic acid (CA) or the disk diffusion zone diameters increased by ≥5 mm around ceftazidime or cefotaxime disks in the presence of CA. All 21 isolates were shown by PCR to contain at least one of the genesblaTEM,blaSHV, andblaOXA, and in isoelectric focusing (IEF) tests, all isolates demonstrated at least one β-lactamase band consistent with a TEM, SHV, or OXA enzyme. Of the 21 isolates, 3 showed a CA effect for cefotaxime by BMD but not by disk diffusion testing. A total of 59 (45%) of the 131 isolates demonstrated decreased susceptibility to cefpodoxime alone (MIC = 2 to 4 μg/ml), and none had a positive ESBL confirmatory test result. These were classified as false positives according to ESBL screen test results. For the remaining 51 (39%) isolates, the cefpodoxime MICs ranged from 16 to >128 μg/ml and the MICs for the other extended-spectrum cephalosporins were highly variable. All 51 isolates gave negative ESBL confirmatory test results. Most showed IEF profiles consistent with production of both a TEM and an AmpC β-lactamase, and representative isolates of several phenotypic groups showed changes in porin profiles; these 51 isolates were considered true negatives. In all, only 16% of 131E. coliisolates identified as potential ESBL producers by the current NCCLS screening criteria were confirmed as ESBL producers. Thus, changing the interpretation of extended-spectrum cephalosporins and aztreonam results from the susceptible to the resistant category without confirming the presence of an ESBL phenotype would lead to a large percentage of false resistance results and is not recommended. However, by increasing the cefpodoxime MIC screening breakpoint to ≥8 μg/ml, 45% of the false-positive results could be eliminated. NCCLS has incorporated this change in the cefpodoxime screening breakpoint in its recent documents.
Identification and Differentiation ofLeishmaniaSpecies in Clinical Samples by PCR Amplification of the Miniexon Sequence and Subsequent Restriction Fragment Length Polymorphism Analysis
Authors: Marfurt Jutta , Nasereddin Abed , Niederwieser Igor , Jaffe Charles L. , Beck Hans-Peter , Felger Ingrid 
Published: July 2003

ABSTRACTWe recently developed a new PCR-restriction fragment length polymorphism (RFLP)-based assay using the miniexon sequence from the genusLeishmania. Here we report the application of this new genotyping method to naturally infected clinical samples for the differentiation of New and Old WorldLeishmaniaspecies. Of the newly developed assay and four currently applied diagnostic tests (i.e., in vitro cultivation, serology, and two other molecular assays using either the small subunit-internal transcribed spacer sequence or a repetitive genomic sequence), the miniexon assay showed the highest sensitivity, 89.7%, compared to 70.6, 57.1, 51.7, and 79.3%, respectively. Species differentiation was robust and reliable compared with that by two otherLeishmaniagenotyping techniques. The assay provides a valuable tool for the identification ofLeishmaniadirectly from clinical samples and enables determination of the infecting species by a facile technique with high discrimination power. SinceLeishmaniacauses a broad spectrum of diseases distinguished by different parasite and host factors, detection and characterization of the infecting species is crucial for the confirmation of a diagnosis as well as the establishment of the clinical prognosis and the initiation of an adequate therapeutic approach. The miniexon PCR-RFLP assay will facilitate such determination and might improve diagnosis and treatment of leishmaniasis.
Improved Assay To Detect Neutralizing Antibody following Vaccination with Diluted or Undiluted Vaccinia (Dryvax) Vaccine
Authors: Newman Frances K. , Frey Sharon E. , Blevins Tamara P. , Mandava Mahendra , Bonifacio, Andres , Yan Lihan , Belshe Robert B. 
Published: July 2003

ABSTRACTThe assessment of immunogenicity of a diluted vaccinia vaccine for possible widespread use of a diluted vaccine in the event of a bioterrorist attack prompted us to focus on the development of a sensitive and specific plaque reduction neutralization (PRN) assay to assess the antibody response of volunteers to a vaccinia (Dryvax) vaccine. Two incubation times, 1 h or overnight (approximately 15 h), were explored for the neutralization step of the assay. In addition, serum samples were evaluated using both sonicated and nonsonicated virus in PRN assays with 1 and 15 h of incubation. The use of the overnight incubation method resulted in the detection of antibody in two vaccinated individuals who exhibited a take, i.e., a major reaction indicative of successive vaccination as defined by the Centers for Disease Control and Prevention, but did not have a fourfold increase in antibody to vaccinia virus by the 1-h-incubation method and increased the sensitivity from 94 to 100%. In addition to the increased sensitivity of the assay, we noted a significant increase (approximately 40-fold) in the PRN titer of serum samples tested with the 15-h-incubation method. The use of sonicated virus increased the reproducibility of the virus titers and PRN titers. Forty-two percent of the samples tested using sonicated virus had a PRN titer that was fourfold higher or greater than that of nonsonicated virus in the assay. A PRN titer that was threefold higher or greater was observed in more than half (58%) of the samples using sonicated virus. Therefore, the more sensitive, specific, and reproducible plaque neutralization assay for the detection of antibody to vaccinia virus is the method using a 15-h-incubation time and freshly sonicated vaccinia virus.
Rotavirus Diarrhea Severity Is Related to the VP4 Type in Mexican Children
Authors: Mota-Hernández Felipe , José Calva Juan , Gutiérrez-Camacho Claudia , Villa-Contreras Sofía , Arias Carlos F. , Padilla-Noriega Luis , Guiscafré-Gallardo Héctor , Guerrero María de Lourdes , López Susana , Muñoz Onofre , Contreras Juan F. , Cedillo Roberto , Herrera Ismael , Puerto Fernando I. 
Published: July 2003

ABSTRACT

This report is of a community-based case control study to assess whether the severity of acute diarrhea by rotavirus (RV) in young children is associated with a particular VP7 (G) or VP4 (P) RV serotype. Five hundred twenty children younger than 2 years of age with diarrhea lasting less than 3 days were age and gender matched with 520 children with no diarrhea. The G and P serotypes were determined with specific monoclonal antibodies, and the VP4 serotype specificity in a subgroup was confirmed by genotyping. Infection with a G3 serotype led to a higher risk of diarrhea than infection with a G1 serotype. Infection with a G3-nontypeable-P serotype was associated with more severe gastroenteritis than infection with a G3 (or G1) P1A[8] serotype. A child with diarrhea-associated dehydration was almost five times more likely to be infected with a G3-nontypeable-P serotype than a child without dehydration (
P
< 0.001). Moreover, the two predominant monotypes within serotype P1A[8] had significantly different clinical manifestations. In this study, the severity of RV-associated diarrhea was related to different P serotypes rather than to G serotypes. The relationship between serotype and clinical outcomes seems to be complex and to vary among different geographic areas.
Comparison of Culture Screening Methods for Detection of Nasal Carriage of Methicillin-Resistant
Staphylococcus aureus
: a Prospective Study Comparing 32 Methods
Authors: Safdar Nasia , Narans Leah , Gordon Barbara , Maki Dennis G. 
Published: July 2003

ABSTRACT

Screening for carriage of methicillin-resistant
Staphylococcus aureus
(MRSA) is fundamental to modern-day nosocomial infection control, both for epidemiologic investigation and day-to-day decisions on barrier isolation. Numerous microbiologic techniques have been advocated for screening for nasal carriage of MRSA, including the use of charcoal rather than rayon swabs, preincubation of swabs in Stuart's medium, preincubation of swabs in salt-containing trypticase soy broth (TSB), use of mannitol-salt agar (MSA), use of MSA containing oxacillin (MSA
Ox
), use of Mueller-Hinton agar containing oxacillin (MHA
Ox
), and the use of MSA containing lipovitellin with an oxacillin disk (MSAL
Ox
). We report a prospective clinical trial undertaken to test all of these methods concurrently. Patients at high risk for MRSA carriage were screened with eight consecutive nasal swabs (four standard rayon, four charcoal-coated rayon), which were processed by primary plating on MSA, MSA
Ox
, MHA
Ox
, and MSAL
Ox
; Stuart's preincubation for 72 h followed by plating on the solid media; overnight enrichment in salt-containing TSB followed by plating; and Stuart's preincubation for 72 h followed by overnight enrichment in TSB and plating. All of the above methods were repeated with charcoal swabs. Each patient was screened by 32 culture methods. Forty-three (42%) of 102 patients studied were positive for MRSA by one or more methods. Among the four media evaluated with direct plating, MSAL
Ox
was 11 to 25% more sensitive for detecting MRSA (MSAL
Ox
versus MSA
Ox
or MHA
Ox
or MSA, each
P
< 0.01). Preincubation in Stuart's medium for 72 h did not enhance recovery of MRSA. Enrichment in salt-containing TSB further increased yield 9%. MSAL
Ox
also showed the best specificity, 93%. Charcoal swabs showed no advantage over standard rayon swabs. Our results suggest that the highest yield will be achieved by using standard rayon swabs that are enriched overnight in TSB with inoculation onto MSAL
Ox
medium. Direct inoculation of swabs onto MSAL
Ox
allows detection of 90% of MRSA carriers.
Comparison of LightCycler-Based PCR, COBAS Amplicor CMV Monitor, and pp65 Antigenemia Assays for Quantitative Measurement of Cytomegalovirus Viral Load in Peripheral Blood Specimens from Patients after Solid Organ Transplantation
Authors: Pang Xiaoli L. , Chui Linda , Fenton Jayne , LeBlanc Barbara , Preiksaitis Jutta K. 
Published: July 2003

ABSTRACT

In order to evaluate the LightCycler-based PCR (LC-PCR) as a diagnostic assay technique, a classical pp65 antigenemia assay and the commercially available COBAS Amplicor CMV Monitor (CACM) assay were compared to the LC-PCR assay for the detection and quantitation of cytomegalovirus (CMV) load in 404 parallel specimens of peripheral blood from 66 patients after solid organ transplantation. A good correlation existed among these three assays (
r
≅ 0.6,
P
< 0.0001). The LC-PCR assay was the most sensitive (54% of specimens positive) compared to the CACM (48.6%) and the pp65 antigenemia (26%) assays. The LC-PCR assay detected all samples found positive by using both the CMV pp65 antigenemia assay and the CACM assay. The LC-PCR also had the widest dynamic range (from 250 to 10
7
DNA copies/ml of plasma). No cross-reactions were found among CMV and Epstein-Barr virus, varicella-zoster virus, or herpes simplex virus in the LC-PCR by using amplification with specifically designed primer pairs. Precision, expressed as the coefficient of variation, was <3% with standard DNA from cell cultures and between 6.55 and 14.1% with clinical specimens in repeat LC-PCR runs. One run of the LC-PCR took half of the time required for the semiautomated CACM procedure. Because of its sensitivity, specificity, cost-effectiveness, and simplicity, the LC-PCR assay could replace the pp65 antigenemia and the CACM assays as the preferred technique for the surveillance, diagnosis, and monitoring of response of CMV diseases in high-risk populations.
Environmental Isolation of
Balamuthia mandrillaris
Associated with a Case of Amebic Encephalitis
Authors: Schuster Frederick L. , Dunnebacke Thelma H. , Booton Gregory C. , Yagi Shigeo , Kohlmeier Candice K. , Glaser Carol , Vugia Duc , Bakardjiev Anna , Azimi Parvin , Maddux-Gonzalez Mary , Martinez A. Julio , Visvesvara Govinda S. 
Published: July 2003

ABSTRACT

This report describes the first isolation of the ameba
Balamuthia mandrillaris
from an environmental soil sample associated with a fatal case of amebic encephalitis in a northern California child. Isolation of the ameba into culture from autopsied brain tissue confirmed the presence of
Balamuthia
. In trying to locate a possible source of infection, soil and water samples from the child's home and play areas were examined for the presence of
Balamuthia
. The environmental samples (plated onto nonnutrient agar with
Escherichia coli
as a food source) contained, in addition to the ameba, a variety of soil organisms, including other amebas, ciliates, fungi, and nematodes, as contaminants. Presumptive
Balamuthia
amebas were recognized only after cultures had been kept for several weeks, after they had burrowed into the agar. These were transferred through a succession of nonnutrient agar plates to eliminate fungal and other contaminants. In subsequent transfers, axenic
Naegleria
amebas and, later, tissue cultures (monkey kidney cells) served as the food source. Finally, the amebas were transferred to cell-free axenic medium. In vitro, the
Balamuthia
isolate is a slow-growing organism with a generation time of ∼30 h and produces populations of ∼2 × 10
5
amebas per ml. It was confirmed as
Balamuthia
by indirect immunofluorescence staining with rabbit anti-
Balamuthia
serum and human anti-
Balamuthia
antibody-containing serum from the amebic encephalitis patient. The environmental isolate is similar in its antimicrobial sensitivities and identical in its 16S ribosomal DNA sequences to the
Balamuthia
isolate from the deceased patient.
Molecular Typing of Methicillin-Resistant
Staphylococcus aureus
: Can PCR Replace Pulsed-Field Gel Electrophoresis?
Authors: Strandén A. , Frei R. , Widmer A. F. 
Published: July 2003

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) is considered the “gold standard” for molecular typing of methicillin-resistant
Staphylococcus aureus
(MRSA). However, the method is time-consuming and expensive, and its discriminatory power may not be necessary in outbreak situations. We used a rapid multiplex PCR-based method with published primers and compared the results with those obtained by PFGE. A total of 75 clinical isolates were typed: 59 strains originated from our prospectively collected clinical strains and were epidemiologically unrelated; 16 strains came from an outbreak that was epidemiologically well defined in time and space. A primer mix of the
spa
gene, the
coa
gene, and the hypervariable region adjacent to
mec
A gene was used for multiplex PCR. Both PFGE and PCR clustered the 75 strains into 41 different genotypes. Concordance of the results was 100% for strains originating from the outbreak. Overall, both methods produced concordant results in 72% of cases. A total of 16% were clustered together by PFGE, but not by PCR and 12% were clustered together by PCR but not by PFGE, respectively. The turnaround time was only 8 h for PCR but 5 days for PFGE. This PCR-based method is excellent for rapid and inexpensive typing of MRSA in an outbreak setting, but the discriminatory power and reproducibility are still insufficient to replace PFGE in longitudinal studies in the endemic setting.
Evaluation of an Isothermal Signal Amplification Method for Rapid Detection of Methicillin-Resistant
Staphylococcus aureus
from Patient-Screening Swabs
Authors: Levi Katrina , Bailey Claire , Bennett Alexandra , Marsh Peter , Cardy Don L. N. , Towner Kevin J. 
Published: July 2003

ABSTRACT

A new molecular assay (CytAMP) utilizing isothermal signal-mediated amplification of RNA was evaluated for rapid detection of methicillin (oxacillin)-resistant
Staphylococcus aureus
(MRSA). The assay targeted the
coa
(coagulase) and
mecA
genes, thereby simultaneously identifying
S. aureus
and methicillin (oxacillin) resistance. Results were obtained in approximately 3.5 h as a color signal in 96-well microtiter plates. The detection limit was between 2 × 10
5
and 10
6
CFU/assay, equivalent to 4 × 10
6
to 2 × 10
7
CFU/ml in an overnight broth. This level of growth was obtained with an initial inoculum of 10 to 50 CFU. The CytAMP assay and a
mecA
-
femB
PCR assay both detected 113 MRSA strains among 396 clinical isolates of bacteria (CytAMP sensitivity and specificity were both 100% relative to those of PCR). Conventional culture detected 109 MRSA strains, but with 19 false-positive and 23 false-negative results relative to both molecular methods. Discrepancies were also observed for 100 enrichment broths containing MRSA screening swabs, with 11 broths culture negative but PCR positive. CytAMP and PCR were more in agreement, but six broths were CytAMP negative and PCR positive. Five of these contained 10
2
to 10
5
CFU/assay (below the CytAMP detection limit of 2 × 10
5
CFU/assay), and the sixth contained 10
6
CFU/assay. Overall, culture and CytAMP had similar sensitivities and specificities relative to those of PCR, but the CytAMP assay enabled swabs to be analyzed as a batch following overnight incubation in enrichment broth, with results reported before 12 noon the next day.