bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of an Oxacillin Disk Screening Test for Detection of Penicillin- and Ceftriaxone-Resistant Pneumococci
Authors: Jetté Louise P. , Sinave Christian 
Published: December 2019

ABSTRACT

In a context of worldwide emergence of resistance among
Streptococcus pneumoniae
strains, early detection of strains with decreased susceptibility to β-lactam antibiotics is important for clinicians. If the 1-μg oxacillin disk diffusion test is used as described by the National Committee for Clinical Laboratory Standards, no interpretation is available for strains showing zone sizes of ≤19 mm, and there is presently no disk diffusion test available for screening cephalosporin resistance. The zones obtained by the diffusion method by using the 1-μg oxacillin disk were compared with penicillin MICs for 1,116 clinical strains and with ceftriaxone MICs for 695 of these strains. Among the 342 strains with growth up to the 1-μg oxacillin disk margin, none were susceptible (MIC, ≤0.06 μg/ml), 62 had intermediate resistance (MIC, 0.12 to 1.0 μg/ml), and 280 were resistant (MIC, ≥2.0 μg/ml) to penicillin. For ceftriaxone, among 98 strains with no zone of inhibition in response to oxacillin, 68 had intermediate resistance (MIC, 1.0 μg/ml), and 22 were resistant (MIC, ≥2.0 μg/ml). To optimize the use of the disk diffusion method, we propose that the absence of a zone of inhibition around the 1-μg oxacillin disk be regarded as an indicator of nonsusceptibility to penicillin and ceftriaxone and recommend that such strains be reported as nonsusceptible to these antimicrobial agents, pending the results of a MIC quantitation method.
Contaminations Occurring in Fungal PCR Assays
Authors: Loeffler Juergen , Hebart Holger , Bialek Ralf , Hagmeyer Lars , Schmidt Diethard , Serey Francois-Prâseth , Hartmann Matthias , Eucker Jan , Einsele Hermann 
Published: December 2019

ABSTRACT

Successful in vitro amplification of fungal DNA in clinical specimens has been reported recently. In a collaboration among five European centers, the frequency and risk of contamination due to airborne spore inoculation or carryover contamination in fungal PCR were analyzed. The identities of all contaminants were specified by cycle sequencing and GenBank analysis. Twelve of 150 PCR assays that together included over 2,800 samples were found to be contaminated (3.3% of the negative controls were contaminated during the DNA extraction, and 4.7% of the PCR mixtures were contaminated during the amplification process). Contaminants were specified as
Aspergillus fumigatus
,
Saccharomyces cerevisiae
, and
Acremonium
spp. Further analysis showed that commercially available products like zymolyase powder or 10× PCR buffer may contain fungal DNA. In conclusion, the risk of contamination is not higher in fungal PCR assays than in other diagnostic PCR-based assays if general precautions are taken.
Isolation of Lyme DiseaseBorreliafrom Puffins (Fratercula arctica) and Seabird Ticks (Ixodes uriae) on the Faeroe Islands
Authors: Gylfe Åsa , Olsen Björn , Straševičius Darius , Marti Ras Nuria , Weihe Pál , Noppa Laila , Östberg Yngve , Baranton Guy , Bergström Sven 
Published: December 2019

ABSTRACTThis is the first report on the isolation of Lyme diseaseBorreliafrom seabirds on the Faeroe Islands and the characteristics of its enzootic cycle. The major components of theBorreliacycle include the puffin (Fratercula arctica) as the reservoir andIxodes uriaeas the vector. The importance of this cycle and its impact on the spread of human Lyme borreliosis have not yet been established.Borreliaspirochetes isolated from 2 of 102 sampled puffins were compared to the borreliae previously obtained from seabird ticks,I. uriae. Therrf-rrlintergenic spacer and therrsand theospCgenes were sequenced and a series of phylogenetic trees were constructed. Sequence data and restriction fragment length polymorphism analysis grouped the strains together withBorrelia garinii. In a seroepidemiological survey performed with residents involved in puffin hunting on the Faeroe Islands, 3 of 81 serum samples were found to be positive by two commonly used clinical tests: a flagellin-based enzyme-linked immunosorbent assay (ELISA) and Western blotting. These three positive serum samples also had high optical density values in a whole-cell ELISA. The finding of seropositive Faeroe Islanders who are regularly exposed toI. uriaeindicate that there may be a transfer ofB. gariniiby this tick species to humans.
Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of
Escherichia coli
: High-Resolution Typing Method with Phylogenetic Significance
Authors: Arnold Catherine , Metherell Lou , Willshaw Geraldine , Maggs Anthony , Stanley John 
Published: December 2019

ABSTRACT

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains of
Escherichia coli
. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species
E. coli
, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselective
Eco
RI primer (
Eco
+0) and a labelled selective
Mse
I primer (
Mse
+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of
E. coli
infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.
Typing of Human Enteroviruses by Partial Sequencing of VP1
Authors: Oberste M. Steven , Maher Kaija , Kilpatrick David R. , Flemister Mary R. , Brown Betty A. , Pallansch Mark A. 
Published: December 2019

ABSTRACT

Human enteroviruses (family
Picornaviridae
) are the major cause of aseptic meningitis and also cause a wide range of other acute illnesses, including neonatal sepsis-like disease, acute flaccid paralysis, and acute hemorrhagic conjunctivitis. The neutralization assay is usually used for enterovirus typing, but it is labor-intensive and time-consuming and standardized antisera are in limited supply. We have developed a molecular typing system based on reverse transcription-PCR and nucleotide sequencing of the 3′ half of the genomic region encoding VP1. The standard PCR primers amplify approximately 450 bp of VP1 for most known human enterovirus serotypes. The serotype of an “unknown” may be inferred by comparison of the partial VP1 sequence to those in a database containing VP1 sequences for the prototype strains of all 66 human enterovirus serotypes. Fifty-one clinical isolates of known serotypes from the years 1991 to 1998 were amplified and sequenced, and the antigenic and molecular typing results agreed for all isolates. With one exception, the nucleotide sequences of homologous strains were at least 75% identical to one another (>88% amino acid identity). Strains with homologous serotypes were easily discriminated from those with heterologous serotypes by using these criteria for identification. This method can greatly reduce the time required to type an enterovirus isolate and can be used to type isolates that are difficult or impossible to type with standard immunological reagents. The technique may also be useful for the rapid determination of whether viruses isolated during an outbreak are epidemiologically related.
Direct Quantification of the Enteric Bacterium
Oxalobacter formigenes
in Human Fecal Samples by Quantitative Competitive-Template PCR
Authors: Sidhu H. , Holmes R. P. , Allison M. J. , Peck A. B. 
Published: December 2019

ABSTRACT

Homeostasis of oxalic acid appears to be regulated, in part, by the gut-associated bacterium
Oxalobacter formigenes
. The loss of this bacterium from the gut flora is associated with an increased susceptibility to hyperoxaluria, a condition which can lead to the formation of calcium oxalate crystalluria and kidney stones. In order to identify and quantify the presence of
O. formigenes
in clinical specimens, a quantitative-PCR-based assay system utilizing a competitive DNA template as an internal standard was developed. This quantitative competitive-template PCR test allows for the rapid, highly specific, and reproducible quantification of
O. formigenes
in fecal samples and provides a prototype for development of DNA-based quantitative assays for enteric bacteria.
Femur Osteomyelitis Due to a Mixed Fungal Infection in a Previously Healthy Man
Authors: Cimerman M. , Gunde-Cimerman N. , Zalar P. , Perkovic T. 
Published: December 2019

ABSTRACT

We describe a previously healthy, 22-year-old man who, after a closed fracture of the femur and subsequent operation, developed chronic osteomyelitis. Within a few days, infected bone fragments, bone, and wound drainage repeatedly yielded three different filamentous fungi:
Aspergillus fumigatus
,
Aspergillus flavus
, and
Chalara ellisii
. Histologic examination of the bone revealed septate hyphae. After sequential necrotomies of the femur and irrigation-suction drainage with added antimycotic therapy, the infection ceased and the fracture healed. This case is unique in that it is the only known instance in which a long bone was affected in an immunocompetent individual, with no evidence of any systemic infection, by a mixed population of two different
Aspergillus
spp. and the rare filamentous fungus
C. ellisii
. Environmental factors that could potentiate the infection include blood and edema fluid resulting from the surgical procedure and the presence of the osteosynthetic plate.
Isolation of
Malassezia furfur
from a Cat
Authors: Crespo M. J. , Abarca M. L. , Cabañes F. J. 
Published: December 2019

ABSTRACT

During a survey of the occurrence of
Malassezia
species in the external ear canals of cats without otitis externa,
Malassezia furfur
was isolated. This is the first report of the isolation of
M. furfur
from cats.
Evaluation of the Digene Hybrid Capture II CT-ID Test for Detection of
Chlamydia trachomatis
in Endocervical Specimens
Authors: Girdner Jennifer L. , Cullen Allison P. , Salama Teresa G. , He Ling , Lorincz Attila , Quinn Thomas C. 
Published: December 2019

ABSTRACT

The performance characteristics of the new signal amplification-based Hybrid Capture (HC) II CT-ID test system (Digene, Silver Spring, Md.) with endocervical specimens were compared to those of tissue culture and PCR (AMPLICOR CT PCR; Roche Molecular Systems, Branchburg, N.J.) for detection of
Chlamydia trachomatis
in 587 women. HC II CT-ID identified 62 of 65 confirmed
C. trachomatis
-positive patients (sensitivity of 95.4%) and was negative for 517 of 522 patients who were negative by culture and PCR (specificity of 99.0%). Twelve of the 65 confirmed positive patients were negative by culture but were identified by both HC II CT-ID and PCR (sensitivity of culture was 81.5% [
P
< 0.01]). In comparison, PCR detected 59 of 65 positive specimens (sensitivity of 90.8%) and had a specificity of 99.6% (520 of 522). These results demonstrate that the Digene HC II CT-ID test is a highly sensitive and specific assay for the detection of
C. trachomatis
infection in endocervical specimens.
First-Glance Diagnosis of
Strongyloides stercoralis
Autoinfection by Stool Microscopy
Authors: Sing Andreas , Leitritz Lorenz , Bogner Johannes R. , Heesemann Jürgen 
Published: December 2019

ABSTRACT

We report a case of autoinfection due to
Strongyloides stercoralis
in a 27-year-old Ethiopian AIDS patient living in Germany for nearly 3 years. This case was diagnosed on the basis of a single-view field in microscopy of a freshly obtained formalin-fixed stool specimen showing both rhabditiform and filariform larvae. The diagnosis of autoinfection by microscopy is discussed in detail.
Pseudoepidemic of
Aspergillus niger
Infections Traced to Specimen Contamination in the Microbiology Laboratory
Authors: Laurel Valerie L. , Meier Patricia A. , Astorga Alicia , Dolan Donna , Brockett Royce , Rinaldi Michael G. 
Published: December 2019

ABSTRACT

We report a pseudo-outbreak of
Aspergillus niger
that followed building construction in our clinical microbiology laboratory. Because outbreaks of invasive aspergillosis have been linked to hospital construction, strategies to minimize dust in patient care areas are common practice. We illustrate that the impact of false-positive cultures on patient care should compel laboratories to prevent specimen contamination during construction.
Misclassification of Susceptible Strains of
Staphylococcus aureus
as Methicillin-Resistant
S. aureus
by a Rapid Automated Susceptibility Testing System
Authors: Ribeiro Julival , Vieira F. D. , King Tom , D’Arezzo Julia B. , Boyce John M. 
Published: December 2019

ABSTRACT

Eight
Staphylococcus aureus
strains initially identified by Vitek GPS-BS or GPS-SA cards as resistant to oxacillin, but susceptible to most non-beta-lactam antibiotics, were found on further testing to be susceptible to oxacillin and ceftizoxime by disk diffusion tests. For all these strains, the MICs of oxacillin were ≤0.5 μg/ml by agar dilution tests, and the strains were oxacillin susceptible when tested by the BBL Crystal MRSA ID and a Vitek machine with GPS-101 cards. None grew on oxacillin-salt agar screening plates. None were positive for
mecA
gene sequences by PCR. When
S. aureus
strains tested by Vitek GPS-SA or GPS-BS cards appear resistant to only penicillin and oxacillin, a confirmatory test such as the oxacillin-salt agar screening method should be performed.
Identification of Medically Relevant
Trichosporon
Species Based on Sequences of Internal Transcribed Spacer Regions and Construction of a Database for
Trichosporon
Identification
Authors: Sugita Takashi , Nishikawa Akemi , Ikeda Reiko , Shinoda Takako 
Published: December 2019

ABSTRACT

The nucleotide sequences of the internal transcribed spacer (ITS) 1 and 2 regions in the rRNA gene were determined by directly sequencing PCR-amplified fragments for all of the species (17 species and five varieties) in the genus
Trichosporon
. Comparative sequence analysis suggests that six medically relevant species,
T. asahii
,
T. asteroides
,
T. cutaneum
,
T. inkin
,
T. mucoides
, and
T. ovoides
, can be readily identified by their ITS sequences. In addition, the sequence analysis showed that conspecific strains have fewer than 1% nucleotide differences in the ITS 1 and 2 regions overall. Molecular phylogenetic trees are also presented.
Differentiation of
Helicobacter pylori
Isolates Based on Lectin Binding of Cell Extracts in an Agglutination Assay
Authors: Hynes Sean O. , Hirmo Siiri , Wadström Torkel , Moran Anthony P. 
Published: December 2019

ABSTRACT

Plant and animal lectins with various carbohydrate specificities were used to type 35 Irish clinical isolates of
Helicobacter pylori
and the type strain NCTC 11637 in a microtiter plate assay. Initially, a panel of eight lectins with the indicated primary specificities were used:
Anguilla anguilla
(AAA),
Lotus tetragonolobus
(Lotus A), and
Ulex europaeus
I (UEA I), specific for α-
l
-fucose;
Solanum tuberosum
(STA) and
Triticum vulgaris
(WGA), specific for β-
N
-acetylglucosamine;
Glycine max
(SBA), specific for β-
N
-acetylgalactosamine;
Erythrina cristagali
(ECA), specific for β-galactose and β-
N
-acetylgalactosamine; and
Lens culinaris
(LCA), specific for α-mannose and α-glucose. Three of the lectins (SBA, STA, and LCA) were not useful in aiding in strain discrimination. An optimized panel of five lectins (AAA, ECA, Lotus A, UEA I, and WGA) grouped all 36 strains tested into eight lectin reaction patterns. For optimal typing, pretreatment by washing bacteria with a low-pH buffer to allow protein release, followed by proteolytic degradation to eliminate autoagglutination, was used. Lectin types of treated samples were stable and reproducible. No strain proved to be untypeable by this system. Electrophoretic and immunoblotting analyses of lipopolysaccharides (LPSs) indicated that the lectins interact primarily, but not solely, with the O side chain of
H. pylori
LPS.
Epidemiological Analysis of Sequential
Pseudomonas aeruginosa
Isolates from Chronic Bronchiectasis Patients without Cystic Fibrosis
Authors: Pujana I. , Gallego L. , Martín G. , López F. , Canduela J. , Cisterna R. 
Published: December 2019

ABSTRACT

PCR fingerprinting was used for the epidemiological investigation of 64
Pseudomonas aeruginosa
isolates collected from 16 chronic bronchiectasis patients without cystic fibrosis: 56% of the patients harbored one clone, 12.5% carried a single major type with minor variants, and 31.5% carried two clones. Only a minority of the acquisitions of antibiotic resistance was related to the acquisition of exogenous strains. Mucoid and nonmucoid sets of isolates did not display any consistent differences in their patterns. The genetic similarity among the clones ranged from 10 to 69%. Cross-infection or common-source exposure did not appear to have occurred.
Variation in Microbial Identification System Accuracy for Yeast Identification Depending on Commercial Source of Sabouraud Dextrose Agar
Authors: Kellogg James A. , Bankert David A. , Chaturvedi Vishnu 
Published: December 2019

ABSTRACT

The accuracy of the Microbial Identification System (MIS; MIDI, Inc.) for identification of yeasts to the species level was compared by using 438 isolates grown on prepoured BBL Sabouraud dextrose agar (SDA) and prepoured Remel SDA. Correct identification was observed for 326 (74%) of the yeasts cultured on BBL SDA versus only 214 (49%) of yeasts grown on Remel SDA (
P
< 0.001). The commercial source of the SDA used in the MIS procedure significantly influences the system’s accuracy.
Proficiency of Clinical Laboratories in Spain in Detecting Vancomycin-Resistant
Enterococcus
spp
Authors: Alonso-Echanove Juan , Robles Belen , Jarvis William R. ,   The Spanish VRE Study Group
Published: December 2019

ABSTRACT

Studies in a variety of U.S. clinical laboratories have demonstrated difficulty in detecting intermediate and low-level vancomycin-resistant enterococci (VRE). The misclassification of “at least intermediate resistant isolates” as vancomycin susceptible may have both clinical implications and a negative impact on measures to control the spread of VRE. No published study has assessed the ability of clinical laboratories in Europe to detect VRE. So, the apparent low prevalence of VRE in European hospitals may be, in part, secondary to the inability of these laboratories to detect all VRE. In an effort to assess European laboratories’ proficiency in detecting VRE, we identified 22 laboratories in Spain and asked them to test four VRE strains and one susceptible enterococcal strain from the Centers for Disease Control and Prevention collection. Each organism was tested by the routine antimicrobial susceptibility testing method used by each laboratory. Overall, VRE were correctly identified in 61 of 88 (69.1%) instances. The accuracy of VRE detection varied with the level of resistance and the antimicrobial susceptibility method. The high-level-resistant strain (
Enterococcus faecium
; MIC, 512 μg/ml) was accurately detected in 20 of 22 (91.3%) instances, whereas the intermediate-resistant isolate (
Enterococcus gallinarum
; MIC, 8 μg/ml) was accurately detected in only 11 of 22 (50%) instances. Classification errors occurred in 27 of 88 (30.9%) instances. Misclassification as vancomycin susceptible was the most common error (16 of 27 [59.3%] instances). Our study shows that the participating Spanish laboratories had an overall acceptable proficiency in detecting VRE but that a substantial proportion of VRE isolates with low or intermediate levels of resistance were not detected. We recommend that studies be conducted to validate laboratory proficiency testing as an important step in the prevention and control of the spread of antimicrobial resistance.
Identification of
Burkholderia
spp. in the Clinical Microbiology Laboratory: Comparison of Conventional and Molecular Methods
Authors: van Pelt Cindy , Verduin Cees M. , Goessens Wil H. F. , Vos Margreet C. , Tümmler Burkhard , Segonds Christine , Reubsaet Frans , Verbrugh Henri , van Belkum Alex 
Published: December 2019

ABSTRACT

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus
Burkholderia
are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as
Burkholderia cepacia
(
n
= 51),
B. gladioli
(
n
= 14),
Ralstonia pickettii
(
n
= 6),
B. multivorans
(
n
= 2),
Stenotrophomonas maltophilia
(
n
= 3), and
Pseudomonas aeruginosa
(
n
= 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as
Burkholderia
spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of
B. cepacia
appeared to be the API 20NE test. None of the biochemical assays successfully grouped the
B. gladioli
strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different
Burkholderia
spp. With this method,
B. gladioli
was also reliably classified in a separate group. For the laboratory diagnosis of
B. cepacia
, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a
Burkholderia
phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended.