bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disseminated Infection Caused by
Scedosporium prolificans
in a Patient with Acute Multilineal Leukemia
Authors: de Batlle J. , Motjé M. , Balanzà R. , Guardia R. , Ortiz R. 
Published: December 2019

ABSTRACT

In this report, we describe a case of disseminated infection caused by
Scedosporium prolificans
(
S. inflatum
) in a patient affected by chemotherapy-induced acute multilineal leukemia and neutropenia. For the fungus isolated in four blood cultures, high MICs of currently available antifungal agents were found. Postmortem examination revealed multiorgan involvement.
Bartonella vinsonii
subsp.
berkhoffii
as an Agent of Afebrile Blood Culture-Negative Endocarditis in a Human
Authors: Roux Véronique , Eykyn Susannah J. , Wyllie Sarah , Raoult Didier 
Published: December 2019

ABSTRACT

We report a case of endocarditis in a human infected with
Bartonella vinsonii
subsp.
berkhoffii
, which causes bacteremia and endocarditis in dogs. Bacterial identification was established by PCR amplification and sequencing of an intergenic spacer region (ITS1), 16S ribosomal DNA, and a gene encoding citrate synthase (
gltA
).
Bartonella
antibodies were detected by immunofluorescence.
Detection of
Legionella
Species in Respiratory Specimens Using PCR with Sequencing Confirmation
Authors: Cloud J. L. , Carroll K. C. , Pixton P. , Erali M. , Hillyard D. R. 
Published: December 2019

ABSTRACT

Legionella
spp. are a common cause of community-acquired respiratory tract infections and an occasional cause of nosocomial pneumonia. A PCR method for the detection of legionellae in respiratory samples was evaluated and was compared to culture. The procedure can be performed in 6 to 8 h with a commercially available DNA extraction kit (Qiagen, Valencia, Calif.) and by PCR with gel detection. PCR is performed with primers previously determined to amplify a 386-bp product within the 16S rRNA gene of
Legionella pneumophila
. We can specifically detect the clinically significant
Legionella
species including
L. pneumophila
,
L. micdadei
,
L. longbeachae
,
L. bozemanii
,
L. feeleii
, and
L. dumoffii
. The assay detects 10 fg (approximately two organisms) of legionella DNA in each PCR. Of 212 clinical specimens examined by culture, 100% of the culture-positive samples (31 of 31) were positive by this assay. By gel detection of amplification products, 12 of 181 culture-negative samples were positive for
Legionella
species by PCR, resulting in 93% specificity. Four of the 12 samples with discrepant results (culture negative, PCR positive) were confirmed to be positive for
Legionella
species by sequencing of the amplicons. The legionella-specific PCR assay that is described demonstrates high sensitivity and high specificity for routine detection of legionellae in respiratory samples.
Molecular Epidemiology of
Staphylococcus epidermidis
in a Neonatal Intensive Care Unit over a Three-Year Period
Authors: Villari P. , Sarnataro C. , Iacuzio L. 
Published: December 2019

ABSTRACT

Coagulase-negative staphylococci, especially
Staphylococcus epidermidis
, are increasingly important nosocomial pathogens, particularly in critically ill neonates. A 3-year prospective surveillance of nosocomial infections in a neonatal intensive care unit (NICU) was performed by traditional epidemiologic methods as well as molecular typing of microorganisms. The aims of the study were (i) to quantify the impact of
S. epidermidis
on NICU-acquired infections, (ii) to establish if these infections are caused by endemic clones or by incidentally occurring bacterial strains of this ubiquitous species, (iii) to evaluate the use of different methods for the epidemiologic typing of the isolates, and (iv) to characterize the occurrence and the spread of staphylococci with decreased glycopeptide susceptibility. Results confirmed that
S. epidermidis
is one of the leading causes of NICU-acquired infections and that the reduced glycopeptide susceptibility, if investigated by appropriate detection methods such as population analysis, is more common than is currently realized. Typing of isolates, which can be performed effectively through molecular techniques such as pulsed-field gel electrophoresis but not through antibiograms, showed that many of these infections are due to clonal dissemination and, thus, are potentially preventable by strict adherence to recommended infection control practices and the implementation of programs aimed toward the reduction of the unnecessary use of antibiotics. These strategies are also likely to have a significant impact on the frequency of the reduced susceptibility of staphylococci to glycopeptides, since this phenomenon appears to be determined either by more resistant clones transmitted from patient to patient or, to a lesser extent, by strains that become more resistant as a result of antibiotic pressure.
Contamination and Sensitivity Issues with a Real-Time Universal 16S rRNA PCR
Authors: Corless C. E. , Guiver M. , Borrow R. , Edwards-Jones V. , Kaczmarski E. B. , Fox A. J. 
Published: December 2019

ABSTRACT

A set of universal oligonucleotide primers specific for the conserved regions of the eubacterial 16S rRNA gene was designed for use with the real-time PCR Applied Biosystems 7700 (TaqMan) system. During the development of this PCR, problems were noted with the use of this gene as an amplification target. Contamination of reagents with bacterial DNA was a major problem exacerbated by the highly sensitive nature of the real-time PCR chemistry. This was compounded by the use of a small amplicon of approximately 100 bases, as is necessary with TaqMan chemistry. In an attempt to overcome this problem, several methodologies were applied. Certain treatments were more effective than others in eliminating the contaminating DNA; however, to achieve this there was a decrease in sensitivity. With UV irradiation there was a 4-log reduction in PCR sensitivity, with 8-methoxypsoralen activity facilitated by UV there was between a 5- and a 7-log reduction, and with DNase alone and in combination with restriction digestion there was a 1.66-log reduction. Restriction endonuclease treatment singly and together did not reduce the level of contaminating DNA. Without the development of ultrapure
Taq
DNA polymerase, ultrapure reagents, and plasticware guaranteed to be free of DNA, the implementation of a PCR for detection of eubacterial 16S rRNA with the TaqMan system will continue to be problematical.
Zinc Salts Inactivate Clinical Isolates of Herpes Simplex Virus In Vitro
Authors: Arens Max , Travis Sharon 
Published: December 2019

ABSTRACTUsing a standard plaque assay and clinical isolates of herpes simplex virus (HSV), we have tested the ability of zinc salts to inactivate HSV. Virus was treated by incubation at 37°C with zinc salts in morpholinepropanesulfonic acid-buffered culture medium and was then diluted and plated onto CV-1 cells for detection and quantitation of remaining infectious virus. Of 10 randomly chosen clinical isolates (five HSV type 1 [HSV-1] isolates and five HSV-2 isolates), seven were inactivated >98% by treatment in vitro with 50 mM zinc gluconate for 2 h and nine were inactivated >97% by treatment with zinc lactate. The effect was concentration dependent. With an HSV-1 isolate, 50 mM zinc gluconate or zinc lactate caused 100% inactivation, 15 mM caused 98 to 99% inactivation, and 5 mM caused 63 to 86% inactivation. With an HSV-2 isolate, 50 and 15 mM zinc gluconate caused 30% inactivation and 5 and 1 mM caused less than 9% inactivation, whereas 50 and 15 mM zinc lactate caused greater than 92% inactivation and 5 and 1 mM caused 37 and 26% inactivation, respectively. The ability of the zinc salts to inactivate HSV was not related to pH in the pH range of 6.1 to 7.6 since inactivation by zinc gluconate or zinc lactate in that pH range was 99.7 to 100% with a 2-h treatment with 50 mM zinc salt. Short (5-min) treatments of selected isolates with zinc gluconate, zinc lactate, zinc acetate, or zinc sulfate yielded inactivation rates of 0 to 55%.
Identification of Enterotoxigenic
Escherichia coli
Harboring Longus Type IV Pilus Gene by DNA Amplification
Authors: Gutiérrez-Cázarez Zita , Qadri Firdausi , Albert M. John , Girón Jorge A. 
Published: December 2019

ABSTRACT

DNA amplification of
lngA
, the structural gene of longus type IV pilus produced by human enterotoxigenic
Escherichia coli
(ETEC) was achieved by the use of specific oligonucleotide primers designed from the nucleotide sequence of
lngA
. A 630-bp fragment representing the entire
lngA
gene was amplified in eight prototype strains previously characterized as longus positive. Five ETEC strains producing colonization factor antigen III (CFA III) (also a type IV pilus) were also positive by PCR, confirming the DNA homology between CFA III and longus. None of the non-ETEC and non-
E. coli
enteropathogens studied showed the 0.63-kbp amplicon. The procedure thus detected only ETEC strains harboring type IV pili genes with or without other colonization factors. Except for five
lngA
PCR-positive, probe-positive strains, all
lngA
PCR-positive strains produced the pilin as demonstrated by immunoblotting. To test the amplification procedure in a clinical setting, a collection of 264 fresh clinical
E. coli
strains isolated from 88 Mexican children with diarrhea was screened by PCR. Among 82 ETEC isolates found, 30 (36.5%) were
lngA
PCR-positive. Twenty-seven percent of the children shed ETEC that possessed
lngA
. In parallel with DNA probes or PCR protocols to detect enterotoxin genes, the
lngA
PCR method may prove useful for detection of ETEC harboring type IV pilus genes in epidemiological studies.
A PCR-Colorimetric Microwell Plate Hybridization Assay for Detection of
Mycobacterium tuberculosis
and
M. avium
from Culture Samples and Ziehl-Neelsen-Positive Smears
Authors: Rossi Maria Cristina , Gori Andrea , Zehender Gianguglielmo , Marchetti Giulia , Ferrario Giulio , De Maddalena Chiara , Catozzi Lidia , Bandera Alessandra , Esposti Anna Degli , Franzetti Fabio 
Published: December 2019

ABSTRACT

Differentiation between
Mycobacterium tuberculosis
and
M. avium
is essential for the treatment of mycobacterial infections. We have developed an easy and rapid detection assay for the diagnosis of mycobacterial diseases. This is a PCR-hybridization assay based on selective amplification of a 16S rRNA gene sequence using pan-
Mycobacterium
primers followed by hybridization of the amplification products to biotinylated
M. tuberculosis
and
M. avium
-specific probes. A total of 55 mycobacterial isolates were tested. For all isolates, results concordant with those of conventional identification methods were obtained. Moreover, we developed a method for extraction of DNA from Ziehl-Neelsen-positive smears which allows the recovery of intact target DNA in our PCR-hybridization assay. Our method was able to confirm all culture results for 59 Ziehl-Neelsen-positive smears from clinical specimens (35 sputum, 11 lymph node biopsy, 6 stool, 4 pus, 2 urine, and 1 pericardial fluid specimens). These data suggest that our PCR-hybridization assay, which is simple to perform and less expensive than commercial probe methods, may be suitable for the identification of
M. tuberculosis
and
M. avium
. It could become a valuable alternative approach for the diagnosis of mycobacterial infections when applied directly to DNA extracted from Ziehl-Neelsen-positive smears as well.
Evaluation of the VITEK 2 System for Rapid Identification of Yeasts and Yeast-Like Organisms
Authors: Graf Barbara , Adam Thomas , Zill Edith , Göbel Ulf B. 
Published: December 2019

ABSTRACT

The new VITEK 2 system is a fully automated system dedicated to the identification and susceptibility testing of microorganisms. In conjunction with the VITEK ID-YST card the VITEK 2 system allows the identification of clinically important yeasts and yeast-like organisms in 15 h due to a sensitive fluorescence-based technology. The ID-YST card consists of 47 biochemical reactions. The database comprises 51 taxa, including newly described species. In this study we evaluated the reliability of the VITEK ID-YST card for the identification of yeasts and yeast-like organisms encountered in a clinical microbiology laboratory. A total of 241 strains representing 21 species were studied. The strains were isolated from clinical samples within a period of 60 days prior to the identification. The tests were performed using 24-h to 55-h subcultures on Sabouraud-gentamicin-chloramphenicol agar. Each strain was tested in parallel using the ID 32C strip as a comparison method combined with microscopic morphology and an agglutination test for
C. krusei
. Overall, 222 strains (92.1%) were unequivocally identified including 11 isolates (4.6%) identified with low discrimination resolved by simple additional tests. Ten strains (4.1%) for which results were given with low discrimination could not be unequivocally identified with supplemental tests, 4 strains (1.7%) were misidentified and 5 strains (2.1%) could not be identified. In conclusion, we found that the VITEK 2 system is a rapid and accurate method for the identification of medically important yeasts and yeast-like organisms.
Effects of Bovine Herpesvirus Type 1 Infection in Calves with Maternal Antibodies on Immune Response and Virus Latency
Authors: Lemaire Mylène , Weynants Vincent , Godfroid Jacques , Schynts Frédéric , Meyer Gilles , Letesson Jean-Jacques , Thiry Etienne 
Published: December 2019

ABSTRACTThe presence of maternally derived antibodies can interfere with the development of an active antibody response to antigen. Infection of seven passively immunized young calves with a virulent strain of bovine herpesvirus type 1 (BHV-1) was performed to determine whether they could become seronegative after the disappearance of maternal antibodies while latently infected with BHV-1. Four uninfected calves were controls. All calves were monitored serologically for 13 to 18 months. In addition, the development of a cell-mediated immune response was assessed by an in vitro antigen-specific gamma interferon (IFN-γ) production assay. All calves had positive IFN-γ responses as early as 7 days until at least 10 weeks after infection. However, no antibody rise was observed after infection in the three calves with the highest titers of maternal antibodies. One of the three became seronegative by virus neutralization test at 7 months of age like the control animals. This calf presented negative IFN-γ results at the same time and was classified seronegative by enzyme-linked immunosorbent assay at around 10 months of age. This calf was latently infected, as proven by virus reexcretion after dexamethasone treatment at the end of the experiment. In conclusion, this study demonstrated that BHV-1-seronegative latent carriers can be obtained experimentally. In addition, the IFN-γ assay was able to discriminate calves possessing only passively acquired antibodies from those latently infected by BHV-1, but it could not detect seronegative latent carriers. The failure to easily detect such animals presents an epidemiological threat for the control of BHV-1 infection.
Application of Pulsed-Field Gel Electrophoresis and Binary Typing as Tools in Veterinary Clinical Microbiology and Molecular Epidemiologic Analysis of Bovine and HumanStaphylococcus aureusIsolates
Authors: Zadoks Ruth , van Leeuwen Willem , Barkema Herman , Sampimon Otlis , Verbrugh Henri , Schukken Ynte Hein , van Belkum Alex 
Published: December 2019

ABSTRACTThirty-eight bovine mammaryStaphylococcus aureusisolates from diverse clinical, temporal, and geographical origins were genotyped by pulsed-field gel electrophoresis (PFGE) afterSmaI digestion of prokaryotic DNA and by means of binary typing using 15 strain-specific DNA probes. Seven pulsed-field types and four subtypes were identified, as were 16 binary types. Concordant delineation of genetic relatedness was documented by both techniques, yet based on practical and epidemiological considerations, binary typing was the preferable method. Genotypes of bovine isolates were compared to 55 previously characterized humanS. aureusisolates through cluster analysis of binary types. Genetic clusters containing strains of both human and bovine origin were found, but bacterial genotypes were predominantly associated with a single host species. Binary typing proved an excellent tool for comparison ofS. aureusstrains, including methicillin-resistantS. aureus, derived from different host species and from different databases. For 28 bovineS. aureusisolates, detailed clinical observations in vivo were compared to strain typing results in vitro. Associations were found between distinct genotypes and severity of disease, suggesting strain-specific bacterial virulence. Circumstantial evidence furthermore supports strain-specific routes of bacterial dissemination. We conclude that PFGE and binary typing can be successfully applied for genetic analysis ofS. aureusisolates from bovine mammary secretions. Binary typing in particular is a robust and simple method and promises to become a powerful tool for strain characterization, for resolution of clonal relationships of bacteria within and between host species, and for identification of sources and transmission routes of bovineS. aureus.
Development and Evaluation of a Molecular Viability Assay for
Pneumocystis carinii
Authors: Maher Nancy , Vermund Sten , Lasbury Mark , Lee C.-H. , Bartlett Marilyn , Unnasch Thomas R. 
Published: December 2019

ABSTRACT

Despite recent declines in incidence,
Pneumocystis carinii
pneumonia (PCP) remains the most commonly occurring opportunistic illness among persons with AIDS in the United States. While
P. carinii
DNA has been detected in patient respiratory specimens and in air samples collected from various indoor environments housing PCP patients, the viability of these organisms is unknown. For this reason, we have developed and evaluated a molecular viability assay for
P. carinii
. This method is based upon the detection of
P. carinii
mRNA by a reverse transcription-PCR that employs specific primers from a member of the heat shock protein 70 family. Under optimal assay conditions, these primers were capable of detecting as few as 100 viable trophozoites as determined by ethidium bromide staining, while no signal was obtained from 10
6
trophozoites killed by heat, desiccation, or UV radiation. This assay was also capable of distinguishing
P. carinii
from other common fungi present in the air. Therefore, this molecular viability assay may be useful in conjunction with standard bioaerosol collection devices and procedures for the detection of viable
P. carinii
collected from various indoor environments. It may also be useful in confirming the presence of viable trophozoites in respiratory specimens collected by noninvasive techniques from putatively infected individuals.
Prevalence ofCryptococcus neoformansvar.neoformans(Serotype D) andCryptococcus neoformansvar.grubii(Serotype A) Isolates in New York City
Authors: Steenbergen Judith N. , Casadevall Arturo 
Published: December 2019

ABSTRACTAnalysis of 40 New York CityCryptococcus neoformansisolates revealed that 39 were typeable, of which 85 and 12.5% wereCryptococcus neoformansvar.grubii(serotype A) andCryptococcus neoformansvar.neoformans(serotype D), respectively. The prevalence of serotype D isolates in New York City appears to be significantly higher than indicated by previous studies of North American isolates.
Prevalence of Polyclonal
mefA
-Containing Isolates among Erythromycin-Resistant Group A Streptococci in Southern Taiwan
Authors: Yan Jing-Jou , Wu Hsiu-Mei , Huang Ah-Huei , Fu Hsiu-Mei , Lee Chen-Ting , Wu Jiunn-Jong 
Published: December 2019

ABSTRACT

A total of 204 nonrepetitive isolates of group A streptococci (GAS), including 107 randomly collected between 1992 and 1995 and 66 and 31 consecutively collected in 1997 and 1998, respectively, from a university hospital in southern Taiwan were examined to determine the prevalence and mechanisms of erythromycin resistance among these isolates. Resistance to erythromycin was detected in 129 isolates (63.2%) by the agar dilution test. Of these, 42 isolates (32.6%) were assigned to the constitutive macrolide, lincosamide, and streptogramin B resistance (cMLS) phenotype, and all carried the
ermB
gene; 4 (3.1%) were assigned to the inducible MLS resistance (iMLS) phenotype, and all harbored the
ermTR
gene; and 83 (64.3%) were erythromycin resistant but susceptible to clindamycin (M phenotype), and all possessed the
mefA
gene. Distributed by years, the rates of erythromycin resistance and different phenotypes were 61.7% (53.0% cMLS, 6.1% iMLS, and 40.9% M phenotype) between 1992 and 1995, 62.1% (12.2% cMLS and 87.8% M phenotype) in 1997, and 71.0% (9.1% cMLS and 90.9% M phenotype) in 1998. Pulsed-field gel electrophoresis showed that all but 2 cMLS isolates were clonal in origin, and 17 clones were detected among the M-phenotype isolates. These results indicate that the high incidence and increasing rate of erythromycin-resistant GAS in southern Taiwan are due to the prevalence of multiple M-phenotype clones and that clindamycin may be the drug of choice for the treatment of infections with GAS in penicillin-hypersensitive patients in this area.
Genomic Variability of
Haemophilus influenzae
Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR
Authors: Gomez-De-Leon Patricia , Santos Jose I. , Caballero Javier , Gomez Demostenes , Espinosa Luz E. , Moreno Isabel , Piñero Daniel , Cravioto Alejandro 
Published: December 2019

ABSTRACT

Genomic fingerprints from 92 capsulated and noncapsulated strains of
Haemophilus influenzae
from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint patterns were detected in the
H. influenzae
strains. Isolates from patients with different diseases were represented by a variety of patterns, which clustered into two major groups. Of the 37 strains isolated from cases of meningitis, 24 shared patterns and were clustered into five groups within a similarity level of 1.0. One fragment of 1.25 kb was common to all meningitis strains.
H. influenzae
strains from healthy carriers presented fingerprint patterns different from those found in strains from sick children. Isolates from healthy individuals were more variable and were distributed differently from those from patients. The results show that ERIC-PCR provides a powerful tool for the determination of the distinctive pathogenicity potentials of
H. influenzae
strains and encourage its use for molecular epidemiology investigations.
Differentiation of
Borrelia burgdorferi
Sensu Lato on the Basis of RNA Polymerase Gene (
rpoB
) Sequences
Authors: Lee Seung-Hyun , Kim Bum-Joon , Kim Jong-Hyun , Park Kyung-Hee , Kim Seo-Jeong , Kook Yoon-Hoh 
Published: December 2019

ABSTRACT

We determined the nucleotide sequences (329 bp) of the
rpoB
DNAs from 22 reference strains of
Borrelia
. No insertions or deletions were observed. Deduced amino acid sequences of amplified
rpoB
DNA comprised 109 amino acid residues (N
450
to M
558
[
Escherichia coli
numbering]). All amino acid sequences were identical with the exception of those of
Borrelia lusitaniae
PotiB2 (T
461
→A) and
B. bissettii
DN127 (I
498
→V). Each species of
B. burgdorferi
sensu lato was differentiated as a distinct entity in the phylogenetic tree constructed by a neighbor-joining method.
B. burgdorferi
sensu lato could be distinguished from
B. turicatae
and
B. hermsii
, which are associated with relapsing fever. Seventeen Korean isolates could be identified by PCR-linked direct sequencing and restriction analysis of the
rpoB
DNA. These results suggest that
rpoB
DNA is useful for identification and characterization of
Borrelia
. In addition, we developed the rapid species identification method using the species-specific primer sets based on
rpoB
gene sequences.