bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-Assisted Surveillance for Detecting Clonal Outbreaks of Nosocomial Infection
Authors: Hacek Donna M. , Cordell Ralph L. , Noskin Gary A. , Peterson Lance R. 
Published: March 2004

ABSTRACT
Whole-house surveillance for healthcare-associated infection is no longer the recommended practice because of the large personnel time investment required. We developed a computer-based tracking system using microbiologic data as an aid in detecting potential outbreaks of healthcare-associated infections on a hospital-wide basis. Monthly total isolates of 25 clinically significant hospital pathogens were tallied from 1991 to 1998 to form a database for future comparison. Two different algorithm tools (based on increases of organism numbers over baseline) were applied to determine alert thresholds for suspected outbreaks using this information. The first algorithm (2SD) defined an alert as two standard deviations above the mean monthly number of isolates. The second (MI) defined an alert as either a 100% increase from the baseline organism number over 2 months or a ≥50% increase (compared to baseline) during a three-consecutive-month period. These two methods were compared to standard infection control professional surveillance (ICP) for the detection of clonal outbreaks over 12 months. Overall, a total of seven clonal outbreaks were detected during the 1-year study. Using standard methods, ICP investigated nine suspected outbreaks, four of which were associated with clonal microbes. The 2SD method signaled a suspected outbreak 15 times, of which three were clonal and ICP had detected one. The MI method signaled a suspected outbreak 30 times; four of these were clonal, and ICP had detected one. The sensitivity and specificity values for ICP, 2SD, and MI for detecting clonal outbreaks were 57, 43, and 57% and 17, 83, and 67%, respectively. Statistical methods applied to clinical microbiology laboratory information system data efficiently supplement infection control efforts for outbreak detection.
Surveillance of Childhood Influenza Virus Infection: What Is the Best Diagnostic Method To Use for Archival Samples?
Authors: Frisbie Brent , Tang Yi-Wei , Griffin Marie , Poehling Katherine , Wright Peter F. , Holland Kathy , Edwards Kathryn M. 
Published: March 2004

ABSTRACT
Despite the clinical importance of influenza virus in pediatric respiratory infections, the optimal set of diagnostic tests to use when conducting studies using archival samples is not clear. In this study, we compared diagnostic tests for influenza virus in 75 children younger than 5 years of age who presented with symptomatic respiratory infection during one of four influenza seasons, had negative viral cultures for other respiratory pathogens, and had both an archival nasal aspirate obtained at the time of illness and serology spanning that influenza season. For all eligible children, we compared the results of viral culture performed at the time of collection with serology and PCR of archival nasal aspirates. Using real-time viral culture as the “gold standard,” the test characteristics of PCR of archival nasal aspirates (sensitivity, 82%; specificity, 100%) and serology (sensitivity, 82%; specificity, 87%) were similar. The relatively low sensitivity of PCR of archival nasal samples in this study compared to that of PCR of fresh samples in a previous study suggests that RNA degradation occurred despite storage of the specimens at −70°C. RNA degradation would also explain why only 11 (52%) of 21 archival nasal samples that had positive influenza virus cultures at the time of collection had positive repeat cultures in the summer of 2000. Thus, in archival specimens stored at −70°C, PCR was more sensitive than viral culture. However, testing of fresh specimens had the highest yield in this study. Studies of optimal methods for specimen storage are needed.
Laboratory Detection of
Haemophilus influenzae
with Decreased Susceptibility to Nalidixic Acid, Ciprofloxacin, Levofloxacin, and Moxifloxacin Due to
gyrA
and
parC
Mutations
Authors: Pérez-Vázquez María , Román Federico , Aracil Belén , Cantón Rafael , Campos José 
Published: March 2004

ABSTRACT

The detection of clinical isolates with decreased fluoroquinolone susceptibilities and a resistance mechanism is of epidemiological and clinical interest. We studied the susceptibilities of 62 clinical isolates and 2 American Type Culture Collection reference strains of
Haemophilus influenzae
to ciprofloxacin, levofloxacin, moxifloxacin, and nalidixic acid by the microdilution and disk diffusion methods. The ciprofloxacin MICs for 34 of the isolates were ≥0.12 μg/ml (range, 0.12 to 32 μg/ml), and the ciprofloxacin MICs for 28 matched control isolates were ≤0.06 μg/ml. In addition, we sequenced the quinolone resistance-determining regions (QRDRs) of
gyrA
and
parC
of all strains. The log
2
MICs of all quinolones were plotted against the inhibition zone diameters. The MICs and inhibition zone diameters selected to screen for the resistance mechanism were based on the susceptibility distribution data and the presence or absence of amino acid changes in the QRDRs of GyrA and ParC. Strains for which ciprofloxacin MICs were ≤0.06 μg/ml, levofloxacin and moxifloxacin MICs were ≤0.03 μg/ml, and nalidixic acid MICs were ≤2.0 μg/ml lacked modifications in the QRDR of GyrA. In contrast, all strains for which ciprofloxacin, levofloxacin, and moxifloxacin MICs were ≥0.5 μg/ml and the vast majority of those for which nalidixic acid MICs were ≥32 μg/ml exhibited amino acid changes in GyrA and ParC. Nalidixic acid and the other three fluoroquinolones studied could be used to screen
H. influenzae
isolates for the detection of decreased susceptibilities to quinolones due to the acquisition of two amino acid changes in the QRDRs of GyrA and ParC (sensitivity, >95%; specificity, >80%).
Characterization of Three New Enterococcal Species,
Enterococcus
sp. nov. CDC PNS-E1,
Enterococcus
sp. nov. CDC PNS-E2, and
Enterococcus
sp. nov. CDC PNS-E3, Isolated from Human Clinical Specimens
Authors: Carvalho Maria da Glória S. , Steigerwalt Arnold G. , Morey Roger E. , Shewmaker Patricia Lynn , Teixeira Lúcia M. , Facklam Richard R. 
Published: March 2004

ABSTRACT

As a reference laboratory, the
Streptococcus
Laboratory at the Centers for Disease Control and Prevention (CDC) is frequently asked to confirm the identity of unusual or difficult-to-identify catalase-negative, gram-positive cocci. In order to accomplish the precise identification of these microorganisms, we have systematically applied analysis of whole-cell protein profiles (WCPP) and DNA-DNA reassociation experiments, in conjunction with conventional physiological tests. Using this approach, we recently focused on the characterization of three strains resembling the physiological groups I (strain SS-1730), II (strain SS-1729), and IV (strain SS-1728) of enterococcal species. Two strains were isolated from human blood, and one was isolated from human brain tissue. The results of physiological testing were not consistent enough to allow confident inclusion of the strains in any of the known enterococcal species. Resistance to vancomycin was detected in one of the strains (SS-1729). Analysis of WCPP showed unique profiles for each strain, which were not similar to the profiles of any previously described
Enterococcus
species. 16S ribosomal DNA (rDNA) sequencing results revealed three new taxa within the genus
Enterococcus
. The results of DNA-DNA relatedness experiments were consistent with the results of WCPP analysis and 16S rDNA sequencing, since the percentages of homology with all 25 known species of
Enterococcus
were lower than 70%. Overall, the results indicate that these three strains constitute three new species of
Enterococcus
identified from human clinical sources, including one that harbors the
vanA
gene. The isolates were provisionally designated
Enterococcus
sp. nov. CDC Proposed New Species of
Enterococcus
1 (CDC PNS-E1), type strain SS-1728
T
(= ATCC BAA-780
T
= CCUG 47860
T
);
Enterococcus
sp. nov. CDC PNS-E2, type strain SS-1729
T
(= ATCC BAA-781
T
= CCUG 47861
T
); and
Enterococcus
sp. nov. CDC PNS-E3, type strain SS-1730
T
(= ATCC BAA-782
T
= CCUG 47862
T
).
Antibiotic-Associated Diarrhea Accompanied by Large-Scale Alterations in the Composition of the Fecal Microbiota
Authors: Young Vincent B. , Schmidt Thomas M. 
Published: March 2004

ABSTRACT
Alterations in the diversity of the gut microbiota are believed to underlie the development of antibiotic-associated diarrhea (AAD). A molecular phylogenetic analysis was performed to document temporal changes in the diversity of fecal bacteria of a patient who developed AAD. Antibiotic administration was associated with distinct changes in the diversity of the gut microbiota, including a marked decrease in the prevalence of butyrate-producing bacteria. Following the discontinuation of the antibiotic, resolution of diarrhea was accompanied by a reversal of these changes, providing the first direct evidence linking changes in the community structure of the gastrointestinal bacteria with the development of AAD.
Simultaneous Detection of
Entamoeba histolytica
,
Giardia lamblia
, and
Cryptosporidium parvum
in Fecal Samples by Using Multiplex Real-Time PCR
Authors: Verweij Jaco J. , Blangé Roy A. , Templeton Kate , Schinkel Janke , Brienen Eric A. T. , van Rooyen Marianne A. A. , van Lieshout Lisette , Polderman Anton M. 
Published: March 2004

ABSTRACT

Entamoeba histolytica
,
Giardia lamblia
, and
Cryptosporidium
are three of the most important diarrhea-causing parasitic protozoa. For many years, microscopic examination of stool samples has been considered to be the “gold standard” for diagnosis of
E. histolytica
,
G. lamblia
,
and C. parvum
infections. Recently, more specific and sensitive alternative methods (PCR, enzyme-linked immunosorbent assay, and direct fluorescent-antibody assay) have been introduced for all three of these parasitic infections. However, the incorporation in a routine diagnostic laboratory of these parasite-specific methods for diagnosis of each of the respective infections is time-consuming and increases the costs of a stool examination. Therefore, a multiplex real-time PCR assay was developed for the simultaneous detection of
E. histolytica
,
G. lamblia
, and
C. parvum
in stool samples. The multiplex PCR also included an internal control to determine efficiency of the PCR and detect inhibition in the sample. The assay was performed on species-specific DNA controls and a range of well-defined stool samples, and it achieved 100 percent specificity and sensitivity. The use of this assay in a diagnostic laboratory would provide sensitive and specific diagnosis of the main parasitic diarrheal infections and could improve patient management and infection control.
Comparison of the Semisolid Agar Antifungal Susceptibility Test with the NCCLS M38-P Broth Microdilution Test for Screening of Filamentous Fungi
Authors: Kuzucu Cigdem , Rapino Barbara , McDermott Laura , Hadley Susan 
Published: March 2004

ABSTRACT

Antifungal susceptibility testing of pathogenic molds is being developed. A simple screening semisolid agar antifungal susceptibility (SAAS) test accurately measures susceptibilities of yeasts. The performance of the SAAS screening test for filamentous fungi was assessed by comparing MICs of four antifungals (amphotericin B [AMB], AMB lipid complex [ABEL], itraconazole [ITZ], and posaconazole [POS]) for 54 clinical mold isolates with the results of the National Committee for Clinical Laboratory Standards (NCCLS) proposed broth microdilution method (M38-P). The SAAS test utilized inocula stabbed into tubes of 0.5% semisolid heart infusion agar. In both tests MICs were read after incubation at 35°C for 48 h. The isolates tested were
Aspergillus fumigatus
,
Aspergillus niger
,
Aspergillus flavus
, other
Aspergillus
spp.,
Fusarium
spp.,
Penicillium
sp.,
Mucor
sp.,
Scedosporium prolificans
,
Trichophyton
sp., and an unidentified dematiaceous mold. Concordance of test results was determined as the percent agreement of MICs ± 1 dilution. The overall agreement between the tests for each drug was as follows: AMB, 94%; ABEL, 83%; ITZ, 94%; POS, 94%. For the
Aspergillus
spp., all but one were susceptible to ITZ by SAAS test; all were susceptible to POS (MIC range, 0.25 to 4 μg/ml). Three of six non-
Aspergillus
molds that were resistant to AMB and ABEL by SAAS (MIC ≥ 2 μg/ml) were also resistant by the NCCLS test. The SAAS test compared favorably to the NCCLS broth microdilution test for molds, and most of the clinical isolates tested were susceptible to all four drugs.
Improved Antigenic Methods for Differential Diagnosis of Bovine, Caprine, and Cervine Alphaherpesviruses Related to Bovine Herpesvirus 1
Authors: Keuser Véronique , Schynts Frédéric , Detry Bruno , Collard Alfred , Robert Béatrice , Vanderplasschen Alain , Pastoret Paul-Pierre , Thiry Etienne 
Published: March 2004

ABSTRACTThe control of infectious bovine rhinotracheitis induced by bovine herpesvirus 1 (BoHV-1) requires sensitive and specific diagnostic assays. As BoHV-1 is antigenically and genetically related to four other alphaherpesviruses of ruminants—namely, BoHV-5, caprine herpesvirus 1 (CpHV-1), cervine herpesvirus 1 (CvHV-1) and CvHV-2—diagnostic tests able to discriminate BoHV-1 from these related viruses are needed to avoid misdiagnosis, especially because some of these viruses are able to cross the species barrier. In this study, murine monoclonal antibodies (MAbs) specific for BoHV-1, BoHV-5, CpHV-1, CvHV-1, and CvHV-2 were produced with the aim of setting up an immunofluorescence assay able to discriminate between these related herpesviruses. Produced MAbs were selected for their viral specificity by enzyme-linked immunosorbent assay and indirect immunofluorescence staining of virus-infected cells. Radioimmunoprecipitation characterization of the selected MAbs revealed that four of them are directed against glycoprotein C (gC) and one of them is directed against gD of these related viruses. The obtained results demonstrate that the antibodies produced allow an unambiguous discrimination of each of the four alphaherpesviruses related to BoHV-1.
Hairpin Primers for Simplified Single-Nucleotide Polymorphism Analysis of
Mycobacterium tuberculosis
and Other Organisms
Authors: Hazbón Manzour Hernando , Alland David 
Published: March 2004

ABSTRACT

We describe a novel, simple, rapid, and highly sensitive method to detect single-nucleotide polymorphisms (SNPs) in
Mycobacterium tuberculosis
and other organisms. Amplification refractory mutation (ARMS) SNP assays were modified by converting the SNP-detecting linear primers in the ARMS assay to hairpin-shaped primers (HPs) through the addition of a 5′ tail complementary to the 3′ end of the linear primer. The improved ability of these primers to detect SNPs in
M. tuberculosis
was compared in a real-time PCR with SYBR-I green dye. Linear primers resulted in incorrect or indeterminate allele designation for 6 of the 13 SNP alleles tested in seven different SNP assays, while HPs determined the correct SNP in all cases. We compared the cycle threshold differences (Δ

C
t

) between the reactions containing primer-template matches and the reactions containing primer-template mismatches (where a larger Δ

C
t

indicates a more robust assay). The use of HPs dramatically improved the mean Δ

C
t

values for the SNP assays (7.6 for linear primers and 11.2 for HPs). We designed 98 different HP assays for SNPs previously associated with resistance to the antibiotic isoniazid to test the large-scale utility of the HP approach. Assay design was successful in 72.4%, 83.7%, 88.8%, and 92.9% of the assays after one to four rounds of assay design, respectively. HP SNP assays are simple, sensitive, robust, and inexpensive. These advantages favor the application of this technique for SNP assays of
M. tuberculosis
and other organisms.
Preferential Presence of Decorin-Binding Protein B (BBA25) and BBA50 Antibodies in Cerebrospinal Fluid of Patients with Neurologic Lyme Disease
Authors: Fikrig Erol , Coyle Patricia K. , Schutzer Steven E. , Chen Manchuan , Deng Zhidian , Flavell Richard A. 
Published: March 2004

ABSTRACT

Borrelia burgdorferi
antibodies preferentially present in cerebrospinal fluid (CSF) were examined by differentially probing a
B. burgdorferi
expression library with CSF and sera from patients with neurologic Lyme disease. Several phage clones selectively reacted with CSF, and these genes were then expressed in recombinant form and used to detect specific antibody in an enzyme-linked immunosorbent assay. Decorin-binding protein B (BBA25) and BBA50 (hypothetical protein) elicited immunoglobulin G (IgG) or IgM detectable in CSF—but not sera—of patients, demonstrating preferential antibody production during neuroborreliosis.
Parasitic Mycelial Forms of
Coccidioides
Species in Mexican Patients
Authors: Muñoz B. , Castañón L. R. , Calderón I. , Vázquez M. E. , Manjarrez M. E. 
Published: March 2004

ABSTRACT

Of 26 cases of coccidioidomycosis reported here, 15 showed hyphae, atypical parasitic structures of
Coccidioides
spp. in fresh cytologic and/or histologic specimen preparations. The finding of this morphology could have implications which should be considered, especially when the disease affects areas of nonendemicity.
Human Monoclonal Antibody Fragment Specific for Glycoprotein G in Herpes Simplex Virus Type 2 with Applications for Serotype-Specific Diagnosis
Authors: Bugli Francesca , Manzara Stefania , Torelli Riccardo , Graffeo Rosalia , Santangelo Rosaria , Cattani Paola , Fadda Giovanni 
Published: March 2004

ABSTRACT
A combinatorial library was used to select a human monoclonal antibody fragment (Fab) with high affinity for G glycoprotein in herpes simplex virus type 2 (HSV-2). Tests with 112 clinical specimens demonstrated successful discrimination between HSV-2 and HSV-1, showing the potential of Fab as a low-cost tool for HSV subtyping in clinical diagnosis.
Susceptibility Pattern and Molecular Type of Species-Specific
Candida
in Oropharyngeal Lesions of Indian Human Immunodeficiency Virus-Positive Patients
Authors: Abdul Lattif Ali , Banerjee Uma , Prasad Rajendra , Biswas Ashutosh , Wig Naveet , Sharma Neeraj , Haque Absarul , Gupta Nivedita , Baquer Najma Z. , Mukhopadhyay Gauranga 
Published: March 2004

ABSTRACT

A study of oropharyngeal candidiasis (OPC) in Indian human immunodeficiency virus (HIV)/AIDS patients was conducted over a period of 15 months. This study revealed that 75% of the HIV/AIDS patients had OPC. MIC testing revealed that 5% of the
Candida
isolates were fluconazole resistant. A correlation between CD4
+
-T-cell counts and development of OPC in HIV/AIDS patients was also observed. Molecular typing of
C. albicans
isolates showed that all were genetically unrelated.
Evaluation of Different Methods To Detect Methicillin Resistance in Small-Colony Variants of
Staphylococcus aureus
Authors: Kipp Frank , Becker Karsten , Peters Georg , von Eiff Christof 
Published: March 2004

ABSTRACT

To evaluate different methods for their abilities to detect methicillin resistance in small-colony variants (SCVs) of
Staphylococcus aureus
, 11 different methicillin-resistant
S. aureus
(MRSA) clones with the SCV phenotype were used in this study. The slow growth of SCVs often makes testing by disk diffusion or by automated methods invalid. Only detection of the
mecA
gene by PCR and the MRSA-Screen latex agglutination test using a higher colony number were shown to be reliable methods to rapidly detect methicillin resistance in these variants.
Assessment of Evolution of Pandemic
Vibrio parahaemolyticus
by Multilocus Sequence Typing
Authors: Chowdhury Nandini Roy , Stine O. Colin , Morris J. Glenn , Nair G. B. 
Published: March 2004

ABSTRACT

The genetic relatedness of 81 isolates of
Vibrio parahaemolyticus
was assessed by multilocus sequence typing. The strain with serotype O3:K6 emerged as a pandemic pathogen in 1996, with subsequent expansion to include strains having serotypes O1:KUT, O4:K68, and O1:K25. Sequence data from
gyrB
,
recA
,
dnaE
, and
gnd
revealed that 16 distinct serogroups isolated prior to the pandemic were highly variable and only isolates of serogroup O3:K6 shared two alleles with the pandemic strains. The pandemic strains regardless of serotype were clonal, with 51 of 54 isolates having the identical allelic profile (AP). Serotype alone did not adequately define a pandemic strain: among O1:KUT strains tested, seven strains with the identical pandemic AP carried previously described pandemic markers, while five nonpandemic strains had five distinct APs. Our sequence data provide strong molecular support for the clonal origin of pandemic
V. parahaemolyticus
O3:K6 and suggest that strains within such a clonal group may acquire previously identified serotypes.
Evaluation of Penicillin Binding Protein 2a Latex Agglutination Assay for Identification of Methicillin-Resistant
Staphylococcus aureus
Directly from Blood Cultures
Authors: Chapin Kimberle C. , Musgnug Michael C. 
Published: March 2004

ABSTRACT

The penicillin binding protein 2a (PBP2a) latex agglutination test using a blood culture pellet was compared to the oxacillin screen agar method using isolated colonies. For blood cultures positive for
Staphylococcus aureus
(
n
= 70), the direct PBP2a test was 18% sensitive and 100% specific. The PBP2a test shows poor sensitivity when used directly with positive blood cultures.
Stability of Mueller-Hinton Agar Supplemented with Glucose and Methylene Blue for Disk Diffusion Testing of Fluconazole and Voriconazole
Authors: Pfaller M. A. , Boyken L. , Messer S. A. , Hollis R. J. , Diekema D. J. 
Published: March 2004

ABSTRACT

The shelf life of Mueller-Hinton agar supplemented with 2% glucose and methylene blue (0.5 μg/ml) (MH-GMB) prepared in the laboratory to test disk diffusion of voriconazole and fluconazole was assessed using quality control (QC) strains of
Candida albicans
ATCC 90028,
Candida krusei
ATCC 6258, and
Candida parapsilosis
ATCC 22019. MH-GMB agar plates were prepared as described in National Committee for Clinical Laboratory Standards document M44-P, and isolates were tested using 25-μg fluconazole disks and 1-μg voriconazole disks over a 36-day period. Zone diameters for fluconazole and voriconazole varied by no more than 4 mm over the study period, and 95 to 100% of results were within the established QC limits for the strains tested. Prepared MH-GMB agar plates provide acceptable performance for disk diffusion testing for at least 30 days when stored at 5°C.
Identification of a
Mycobacterium tuberculosis
Strain with Stable, Low-Level Resistance to Isoniazid
Authors: Madison Bereneice M. , Siddiqi Salman H. , Heifets Leonid , Gross Wendy , Higgins Mike , Warren Nancy , Thompson Anthony , Morlock Glenn , Ridderhof John C. 
Published: March 2004

ABSTRACT

We have identified a potential quality control strain of
Mycobacterium tuberculosis
to monitor isoniazid susceptibility testing. This strain (strain A) has a stable phenotypic low-level resistance to isoniazid, has a mutation of C (−15) → T in the
inhA
promoter region, and gave consistent susceptibility test results in 141 laboratories.
Cytomegalovirus Quantitation by Real-Time PCR Is Unaffected by Delayed Separation of Plasma from Whole Blood
Authors: Nesbitt Shannon E. , Cook Linda , Jerome Keith R. 
Published: March 2004

ABSTRACT
A previous study suggested that delayed sample preparation can cause a false-positive plasma cytomegalovirus (CMV) PCR. We evaluated 78 samples submitted for CMV testing, and we report that a 24-h delay in plasma separation did not affect viral quantitation by real-time PCR. Laboratories should evaluate specimen handling requirements for their own PCR technology.