bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective Study of the Performance of Vibrational Spectroscopies for Rapid Identification of Bacterial and Fungal Pathogens Recovered from Blood Cultures
Authors: Maquelin K. , Kirschner C. , Choo-Smith L.-P. , Ngo-Thi N. A. , van Vreeswijk T. , Stämmler M. , Endtz H. P. , Bruining H. A. , Naumann D. , Puppels G. J. 
Published: January 2003

ABSTRACTRapid identification of microbial pathogens reduces infection-related morbidity and mortality of hospitalized patients. Raman spectra and Fourier transform infrared (IR) spectra constitute highly specific spectroscopic fingerprints of microorganisms by which they can be identified. Little biomass is required, so that spectra of microcolonies can be obtained. A prospective clinical study was carried out in which the causative pathogens of bloodstream infections in hospitalized patients were identified. Reference libraries of Raman and IR spectra of bacterial and yeast pathogens highly prevalent in bloodstream infections were created. They were used to develop identification models based on linear discriminant analysis and artificial neural networks. These models were tested by carrying out vibrational spectroscopic identification in parallel with routine diagnostic phenotypic identification. Whereas routine identification has a typical turnaround time of 1 to 2 days, Raman and IR spectra of microcolonies were collected 6 to 8 h after microbial growth was detected by an automated blood culture system. One hundred fifteen samples were analyzed by Raman spectroscopy, of which 109 contained bacteria and 6 contained yeasts. One hundred twenty-one samples were analyzed by IR spectroscopy. Of these, 114 yielded bacteria and 7 were positive for yeasts. High identification accuracy was achieved in both the Raman (92.2%, 106 of 115) and IR (98.3%, 119 of 121) studies. Vibrational spectroscopic techniques enable simple, rapid, and accurate microbial identification. These advantages can be easily transferred to other applications in diagnostic microbiology, e.g., to accelerate identification of fastidious microorganisms.
Evaluation of 11 PCR Assays for Species-Level Identification of
Campylobacter jejuni
and
Campylobacter coli
Authors: On Stephen L. W. , Jordan Penelope J. 
Published: January 2003

ABSTRACT

We examined the sensitivity and specificity of 11 PCR assays described for the species identification of
Campylobacter jejuni
and
Campylobacter coli
by using 111 type, reference, and field strains of
C. jejuni
,
C. coli
, and
Campylobacter lari
. For six assays, an additional 21 type strains representing related
Campylobacter
,
Arcobacter
, and
Helicobacter
species were also included. PCR tests were initially established in the laboratory by optimizing conditions with respect to five type and reference strains of
C. jejuni
,
C. coli
, and
C. lari
. One PCR test for
C. coli
failed to give appropriate results during this initial setup phase and was not evaluated further. The remaining 10 assays were used to examine heated lysate and purified DNA templates as appropriate of well-characterized type, reference, and field strains of
C. jejuni
(
n
= 62),
C. coli
(
n
= 34), and
C. lari
(
n
= 15). The tests varied considerably in their sensitivity and specificity for their respective target species. No assay was found to be 100% sensitive and/or specific for all
C. jejuni
strains tested, but four assays for
C. coli
gave appropriate responses for all strains examined. Between one and six strains of
C. jejuni
gave amplicons in four of seven
C. jejuni
PCR tests only where purified DNA was used as the template; corresponding results were seen with one strain of
C. coli
in each of three assays for the latter species. Our findings indicate that a polyphasic strategy for PCR-based identification should be used to identify
C. jejuni
and
C. coli
strains. The data may assist laboratories in selecting assays suited for their needs and in designing evaluations of future PCR tests aimed to identify these species.
Characterization of Members of the
Legionellaceae
Family by Automated Ribotyping
Authors: Cordevant Christophe , Tang Jane S. , Cleland David , Lange Marc 
Published: January 2003

ABSTRACT

In order to implement a new and reliable method for characterizing different species of
Legionella
, a genetic fingerprinting study with an automated ribotyping system (RiboPrinter) was completed with members of this genus which were deposited at the American Type Culture Collection. The RiboPrinter examined the different patterns of
Eco
RI digestion fragments from the rRNA operons of 110 strains, representing 48 of the 49 described
Legionella
species as well as 70 serogroups of those species. Distinctive and consistent patterns were obtained for the type strains of the 48 species investigated.
Legionella pneumophila
subsp.
fraseri
and
L. pneumophila
subsp.
pascullei
each generated a specific pattern, whereas
L. pneumophila
subsp.
pneumophila
produced six different fingerprint patterns. No correlation seemed to exist between the ribotypes obtained and the 15 serotypes of
L. pneumophila
. For the other species, those with two known serogroups presented two distinctive patterns with the RiboPrinter with the exception of
L. hackeliae
and
L. quinlivanii
, which yielded only one pattern. We also encountered ribotypes for strains which were not identified to the species level. The ribotypes generated for these strains with the RiboPrinter did not match those generated for known type strains, suggesting the putative description of new serogroups or species. Although the automated system did not have sufficient discriminatory ability to serve as an epidemiological tool in a clinical setting, it appeared to be a powerful tool for general genomic analysis of the
Legionella
isolates (e.g., determination of new species) and assessment of the interrelationship among
Legionella
strains through the RiboPrinter database connection.
Antimicrobial Susceptibility Testing of Carbapenems: Multicenter Validity Testing and Accuracy Levels of Five Antimicrobial Test Methods for Detecting Resistance in
Enterobacteriaceae
and
Pseudomonas aeruginosa
Isolates
Authors: Steward Christine D. , Mohammed Jasmine M. , Swenson Jana M. , Stocker Sheila A. , Williams Portia P. , Gaynes Robert P. , McGowan, John E. , Tenover Fred C. 
Published: January 2003

ABSTRACT

From January 1996 to May 1999, Project ICARE (Intensive Care Antimicrobial Resistance Epidemiology) received 448 nonduplicate clinical isolates of
Enterobacteriaceae
and
Pseudomonas aeruginosa
that were reported to be imipenem intermediate or resistant. However, broth microdilution (BMD) confirmatory testing at the Project ICARE central laboratory confirmed this result in only 11 of 123 (8.9%)
Enterobacteriaceae
isolates and 241 of 325 (74.2%)
P. aeruginosa
isolates. To investigate this overdetection of imipenem resistance, we tested 204 selected isolates from the Project ICARE collection plus five imipenem-resistant challenge strains at the Centers for Disease Control and Prevention against imipenem and meropenem by agar dilution, disk diffusion, Etest (AB BIODISK North America, Inc., Piscataway, N.J.), two MicroScan WalkAway conventional panels (Neg MIC Plus 3 and Neg Urine Combo 3) (Dade MicroScan, Inc., West Sacramento, Calif.), and two Vitek cards (GNS-116 containing meropenem and GNS-F7 containing imipenem) (bioMérieux Vitek, Inc., Durham, N.C.). The results of each test method were compared to the results of BMD testing using in-house-prepared panels. Seven imipenem-resistant and five meropenem-resistant isolates of
Enterobacteriaceae
and 43 imipenem-resistant and 21 meropenem-resistant isolates of
P. aeruginosa
were identified by BMD. For
Enterobacteriaceae
, the imipenem and meropenem test methods produced low numbers of very major and major errors. All test systems in the study produced low numbers of very major and major errors when
P. aeruginosa
was tested against imipenem and meropenem, except for Vitek testing (major error rate for imipenem, 20%). Further testing conducted in 11 of the participating ICARE hospital laboratories failed to pinpoint the factors responsible for the initial overdetection of imipenem resistance. However, this study demonstrated that carbapenem testing difficulties do exist and that laboratories should consider using a second, independent antimicrobial susceptibility testing method to validate carbapenem-intermediate and -resistant results.
Attempted Isolation of
Nanobacterium
sp. Microorganisms from Upper Urinary Tract Stones
Authors: Drancourt Michel , Jacomo Véronique , Lépidi Hubert , Lechevallier Eric , Grisoni Vincent , Coulange Christian , Ragni Edith , Alasia Claude , Dussol Bertrand , Berland Yvon , Raoult Didier 
Published: January 2003

ABSTRACT

A single team has reported isolation of nanobacteria in human and bovine blood products, as well as, more recently, kidney stones. This has raised controversy. To confirm the data, we searched for nanobacteria from 10 aseptically removed upper urinary tract (UUT) stones. We used scanning electronic microscopy (SEM) with four stones and culture of stones on either 3T6 fibroblast monolayers or liquid RPMI medium. Detection of nanobacteria was made with a commercially available monoclonal antibody, 16S ribosomal DNA amplification with specific primers, and transmission electronic microscopy (TEM) of inoculated cells. SEM showed nanoparticles in four of four UUT stones similar to those recently described. TEM of inoculated 3T6 cell monolayers has shown transient intracytoplasmic vacuolar formations containing 200- to 500-nm particles in 3 of 10 cell cultures. Gimenez staining, Hoechst staining, and specific monoclonal immunofluorescence failed to reveal nanobacteria. Finally, we could not grow
Nanobacterium
sp. microorganisms by the techniques described. Although with SEM, we observed nanoparticles morphologically similar to nanobacteria, we failed to isolate
Nanobacterium
sp. microorganisms in culture and to prove the bacterial nature of these nanoparticles in stones.
M Protein Gene Type Distribution among Group A Streptococcal Clinical Isolates Recovered in Mexico City, Mexico, from 1991 to 2000, and Durango, Mexico, from 1998 to 1999: Overlap with Type Distribution within the United States
Authors: Espinosa Luz Elena , Li Zhongya , Barreto Demostenes Gomez , Jaimes Ernesto Calderon , Rodriguez Romeo S. , Sakota Varja , Facklam Richard R. , Beall Bernard 
Published: January 2003

ABSTRACT

To examine the type distribution of pathogenic group A streptococcal (GAS) strains in Mexico, we determined the
emm
types of 423 GAS isolates collected from ill patients residing in Mexico (Durango or Mexico City). These included 282 throat isolates and 107 isolates from normally sterile sites. Of the other isolates, 38 were recovered from other miscellaneous infections. A total of 31 different
emm
types were found, revealing a broad overlap between commonly occurring
emm
types in Mexico and the United States. The information obtained in this study is consistent with the possibility that multivalent, M type-specific vaccines prepared for GAS strain distribution within the United States could theoretically protect against the majority of GAS strains causing disease in the two cities surveyed in Mexico.
Identification of
Haemophilus influenzae
Serotypes by Standard Slide Agglutination Serotyping and PCR-Based Capsule Typing
Authors: LaClaire Leslye L. , Tondella Maria Lucia C. , Beall David S. , Noble Corie A. , Raghunathan Pratima L. , Rosenstein Nancy E. , Popovic Tanja 
Published: January 2003

ABSTRACT

To resolve discrepancies in slide agglutination serotyping (SAST) results from state health departments and the Centers for Disease Control and Prevention (CDC), we characterized 141 of 751 invasive
Haemophilus influenzae
isolates that were identified in the United States from January 1998 to December 1999 through an active, laboratory-based, surveillance program coordinated by the CDC. We found discrepancies between the results of SAST performed at state health departments and those of PCR capsule typing performed at the CDC for 56 (40%) of the isolates characterized: 54 isolates that were identified as a particular serotype by SAST were shown to be unencapsulated by PCR, and two isolates that were reported as serotypes b and f were found to be serotypes f and e, respectively, by PCR. The laboratory error most likely to affect the perceived efficacy of the conjugate
H. influenzae
type b (Hib) vaccine was the misidentification of isolates as serotype b: of 40 isolates identified as serotype b by SAST, 27 (68%) did not contain the correlating capsule type genes. The frequency of errors fell substantially when standardized reagents and routine quality control of SAST were used during a study involving three laboratories. An overall 94% agreement between SAST and PCR results showed that slide agglutination could be a valid and reliable method for serotyping
H. influenzae
if the test was performed correctly, in accordance with standardized and recommended procedures. An ongoing prospective analysis of all
H. influenzae
surveillance isolates associated with invasive disease in children less than 5 years old will provide more accurate national figures for the burden of invasive disease caused by Hib and other
H. influenzae
serotypes.
Evaluation of Broth Microdilution Testing Parameters and Agar Diffusion Etest Procedure for Testing Susceptibilities of
Aspergillus
spp. to Caspofungin Acetate (MK-0991)
Authors: Espinel-Ingroff Ana 
Published: January 2003

ABSTRACT

The NCCLS M38-A document does not describe guidelines for testing caspofungin acetate (MK-0991) and other echinocandins against molds. This study evaluated the susceptibilities of 200 isolates of
Aspergillus fumigatus
,
A. flavus
,
A. nidulans
,
A. niger
, and
A. terreus
to caspofungin (MICs and minimum effective concentrations [MECs]) by using standard RPMI 1640 (RPMI) and antibiotic medium 3 (M3), two inoculum sizes (10
3
and 10
4
CFU/ml), and two MIC determination criteria (complete [MICs-0] and prominent growth inhibition [MICs-2]) at 24 and 48 h. Etest MICs were also determined. In general, caspofungin MIC-2 and MEC pairs were comparable with both media and inocula (geometric mean ranges of MECs and MICs, respectively, with larger inoculum: 0.12 to 0.64 μg/ml and 0.12 to 0.44 μg/ml with RPMI versus 0.04 to 0.51 μg/ml and 0.03 to 0.21 μg/ml with M3); however, MEC results were less influenced by testing conditions than MICs, especially with the larger inoculum. Overall, the agreement between caspofungin Etest MICs and broth dilution values was higher with MECs obtained with M3 (>90%) and the large inoculum than under the other testing conditions. Because RPMI is a more stable and chemically defined medium than M3, the determination at 24 h of the easier visual MECs with RPMI and the inoculum recommended in the M38-A document appears to be a suitable procedure at present for in vitro testing of caspofungin against
Aspergillus
spp. Future in vitro correlations with in vivo outcome of both microdilution and Etest procedures may detect more-relevant testing conditions.
Thymidine-Dependent Small-Colony Variants of
Staphylococcus aureus
Exhibit Gross Morphological and Ultrastructural Changes Consistent with Impaired Cell Separation
Authors: Kahl Barbara C. , Belling Gunnar , Reichelt Rudolf , Herrmann Mathias , Proctor Richard A. , Peters Georg 
Published: January 2003

ABSTRACT

Thymidine-dependent small-colony variants (SCV) of
Staphylococcus aureus
exhibited unusual colony morphology with “fried-egg” or pinpoint white colonies on agar plates and pleomorphic cocci as determined by Gram staining. Electron microscopy revealed enlarged cocci with incomplete or multiple cross walls consistent with impaired cell separation. Fried-egg SCV phenotypes could be reversed by thymidine supplementation.
Identification of
Candida
spp. by Randomly Amplified Polymorphic DNA Analysis and Differentiation between
Candida albicans
and
Candida dubliniensis
by Direct PCR Methods
Authors: Bautista-Muñoz Consuelo , Boldo Xavier M. , Villa-Tanaca Lourdes , Hernández-Rodríguez César 
Published: January 2003

ABSTRACT

Because
Candida
species have innately highly variable antifungal susceptibilities, the availability of a fast and reliable species identification test is very important so that suitable and effective therapeutic measures may be taken. Using three oligonucleotide primers, we established a randomly amplified polymorphic DNA (RAPD) analysis method that enabled direct identification of the most common opportunistic pathogenic
Candida
species. RAPD analysis revealed a characteristic molecular fingerprint for each
Candida
species. Differences between the profiles for
Candida albicans
and
C. dubliniensis
were evident. RAPD analysis is a relatively easy, reproducible, and reliable technique that can be useful in providing genetic fingerprints for the identification of strains. In addition, a collection of different
C. albicans
strains was identified by a specific PCR based on multiple secreted aspartic proteinase (
SAP
) genes and the dipeptidyl aminopeptidase (
DAP2
) gene. Our findings demonstrate that PCR based upon the
SAP
and
DAP2
sequences is a simple, rapid, clear, and direct technique for the identification and differentiation of
C. albicans
and
C. dubliniensis
.
Changes in Patterns of Antimicrobial Susceptibility and Integron Carriage among
Shigella sonnei
Isolates from Southwestern Korea during Epidemic Periods
Authors: Oh Jae Young , Yu Hak Sun , Kim Sung Ki , Seol Seong Yong , Cho Dong Taek , Lee Je Chul 
Published: January 2003

ABSTRACT

Shigella sonnei
isolates from southwestern Korea during the epidemic periods of 1998 to 2000 were genetically related. The antimicrobial susceptibilities of the outbreak-related isolates changed annually. All isolates carried class 2 integrons, and the outbreak-related isolates from 1999 also carried class 1 integrons. The antimicrobial susceptibilities of
S. sonnei
isolates are readily changed by antibiotic selective pressures, and integrons are responsible for resistance to antimicrobial agents commonly used to treat shigellosis.
Phenotypes and Genotypes of Erythromycin-Resistant Pneumococci in Italy
Authors: Montanari Maria Pia , Mingoia Marina , Cochetti Ileana , Varaldo Pietro Emanuele 
Published: January 2003

ABSTRACT

Of 120 erythromycin-resistant pneumococci isolated in Italian hospitals, 39 (32.5%) were M-type isolates, carrying the
mef
gene alone. The
mef
gene was also detected, together with
erm
(AM), in one constitutively resistant isolate and in five isolates of the partially inducible phenotype. Among the 45
mef
-positive isolates, 25 (55.6%) carried
mef
(A) and 20 (44.4%) carried
mef
(E) as observed from PCR-restriction fragment length polymorphism analysis of a 1,743-bp amplicon. The same result was obtained by a similar method applied to a more common 348-bp amplicon.
Antigen Detection Assay for Identification ofPenicillium marneffeiInfection
Authors: Chaiyaroj Sansanee C. , Chawengkirttikul Runglawan , Sirisinha Stitaya , Watkins Pramuan , Srinoulprasert Yuttana 
Published: January 2003

ABSTRACTTwo recently produced monoclonal antibodies were used to develop an antigen capture enzyme-linked immunosorbent assay (ELISA) for rapid diagnosis ofPenicillium marneffei. The method was evaluated with 53 patients with culture-confirmed penicilliosis and 240 controls. The diagnostic sensitivity, specificity, and accuracy of the ELISA were 92.45, 97.5, and 96.59%, respectively.
Comparison of Washing and Swabbing Procedures for Collecting Genital Fluids To Assess Shedding of Human Immunodeficiency Virus Type 1 (HIV-1) RNA in Asymptomatic HIV-1-Infected Women
Authors: Andréoletti Laurent , Grésenguet Gérard , Chomont Nicolas , Matta Mathieu , Quiniou Yann , Si-Mohamed Ali , Bélec Laurent 
Published: January 2003

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) RNA was detected by means of ultrasensitive reverse transcription-PCR assay of 19 cervicovaginal lavage, 21 cervical mucus, 18 vaginal wall, and 17 vaginal fornix paired samples from 25 asymptomatic HIV-1-infected women (76, 84, 72, and 68%, respectively;
P
> 0.5). Levels of HIV-1 RNA in cervicovaginal wash samples were highly correlated with those in paired endocervical mucus samples (
r
= 0.71;
P
= 0.0006), indicating that cervicovaginal washing and endocervical swabbing are equivalent collection procedures.
Characterization of the First Extended-Spectrum Beta-Lactamase-ProducingSalmonellaIsolate Identified in Canada
Authors: Mulvey Michael R. , Soule Geoff , Boyd David , Demczuk Walter , Ahmed Rafiq 
Published: January 2003

ABSTRACTA singleSalmonella entericaserovar Typhimurium isolate with an UT2 phage type producing an extended-spectrum beta-lactamase (ESBL) was identified in Canada in 2000. The isolate harbored two plasmids, one containing ablaTEM-1gene and the other containing ablaSHV-2agene. The ESBL gene was located on a 70-kb transferable plasmid which also carried tetracycline and trimethoprim resistance elements.
Epidemiology and Antimicrobial Susceptibilities of 111
Campylobacter fetus
subsp.
fetus
Strains Isolated in Québec, Canada, from 1983 to 2000
Authors: Tremblay Carole , Gaudreau Christiane , Lorange Manon 
Published: January 2003

ABSTRACT

The epidemiology and antimicrobial susceptibilities of 111
Campylobacter fetus
subsp
. fetus
strains isolated from 103 patients from 1983 to 2000 in Québec, Canada, were determined. The median number of patients infected annually with this bacteria was seven, with an incidence of 0.1 per 100,000 population. The male-to-female ratio was 1.1 to 1.0. The patients originated from 13 of the 18 Québec socioeconomic regions. The age range of the patients was 6 months to 90 years old, 53% being ≥70 years old and 2% being <20 years old. The isolation site was blood for 69% of the patients, stools for 20%, and other body fluids for 11% of them. Three patients suffered a relapse, with the same strain being isolated from the same site at different times as confirmed by pulse-field gel electrophoresis. All isolates were susceptible to ampicillin, gentamicin, meropenem, and imipenem, with 90% minimal inhibitory concentrations of 4, 1, 0.12, and ≤0.06 μg/ml, respectively. Three percent and two percent of the strains were, respectively, resistant and intermediate to ciprofloxacin. Thirty-four percent of the strains were resistant to tetracycline. There was a nonsignificant increase in resistance to ciprofloxacin (
P
= 0.27) and to tetracycline (
P
= 0.65) in recent years. The percentages of intermediate and resistant MICs were, respectively, 12 and 1% for cefotaxime and 71 and 0% for erythromycin. All strains were β-lactamase negative.
Processing Sputum Specimens in a Refrigerated Centrifuge Does Not Increase the Rate of Isolation of
Mycobacterium tuberculosis
Authors: Selvakumar N. , Govindan Dakshayani , Chandu Naik Ashok , Frieden Thomas R. , Narayanan P. R. 
Published: January 2003

ABSTRACT

A total of 1,047 sputum samples from pulmonary tuberculosis patients was collected in cetyl pyridinium chloride-sodium chloride solution. Each sample was divided into two parts and randomly allocated for the isolation of
Mycobacterium tuberculosis
, with one part to be processed by the standard method and the other by a modified method. In the standard method, the samples were processed by using nonrefrigerated centrifuges, while in the modified method, they were processed by using a refrigerated centrifuge. Fifty-seven samples that yielded contaminants were excluded, and the remaining 990 samples were taken up for analysis. The rates of isolation of
M. tuberculosis
with the standard and modified methods were 48.6 and 48.1%, respectively, and the difference was not statistically significant (McNemar's test;
P
> 0.5). However, 51% of the positive cultures were isolated within 2 weeks with the modified method compared to 37% with the standard method (chi-square test;
P
< 0.001). The results of the study reveal that processing of sputum samples in a refrigerated centrifuge does not improve the rate of isolation but will result in rapid isolation of
M. tuberculosis
.