bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Identification of the Main Opportunistic Mucorales by PCR-Restriction Fragment Length Polymorphism
Authors: Machouart M. , Larché J. , Burton K. , Collomb J. , Maurer P. , Cintrat A. , Biava M. F. , Greciano S. , Kuijpers A. F. A. , Contet-Audonneau N. , de Hoog G. S. , Gérard A. , Fortier B. 
Published: March 2006

ABSTRACT

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera
Absidia
,
Mucor
,
Rhizopus
, and
Rhizomucor
, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis.
Correlation of MIC with Outcome for
Candida
Species Tested against Voriconazole: Analysis and Proposal for Interpretive Breakpoints
Authors: Pfaller M. A. , Diekema D. J. , Rex J. H. , Espinel-Ingroff A. , Johnson E. M. , Andes D. , Chaturvedi V. , Ghannoum M. A , Odds F. C. , Rinaldi M. G. , Sheehan D. J. , Troke P. , Walsh T. J. , Warnock D. W. 
Published: March 2006

ABSTRACT

Developing interpretive breakpoints for any given organism-drug combination requires integration of the MIC distribution, pharmacokinetic and pharmacodynamic parameters, and the relationship between the in vitro activity and outcome from both in vivo and clinical studies. Using data generated by standardized broth microdilution and disk diffusion test methods, the Antifungal Susceptibility Subcommittee of the Clinical and Laboratory Standards Institute has now proposed interpretive breakpoints for voriconazole and
Candida
species. The MIC distribution for voriconazole was determined using a collection of 8,702 clinical isolates. The overall MIC
90
was 0.25 μg/ml and 99% of the isolates were inhibited at ≤1 μg/ml of voriconazole. Similar results were obtained for 1,681
Candida
isolates (16 species) from the phase III clinical trials. Analysis of the available data for 249 patients from six phase III voriconazole clinical trials demonstrated a statistically significant correlation (
P
= 0.021) between MIC and investigator end-of-treatment assessment of outcome. Consistent with parallel pharmacodynamic analyses, these data support the following MIC breakpoints for voriconazole and
Candida
species: susceptible (S), ≤1 μg/ml; susceptible dose dependent (SDD), 2 μg/ml; and resistant (R), ≥4 μg/ml. The corresponding disk test breakpoints are as follows: S, ≥17 mm; SDD, 14 to 16 mm; and R, ≤13 mm.
Chronic Colonization with
Pandoraea apista
in Cystic Fibrosis Patients Determined by Repetitive-Element-Sequence PCR
Authors: Atkinson R. M. , LiPuma J. J. , Rosenbluth D. B. , Dunne W. M. 
Published: March 2006

ABSTRACT

Pandoraea apista
is recovered with increasing frequency from the lungs of patients with cystic fibrosis (CF) and may represent an emerging pathogen (I. M. Jorgensen et al., Pediatr. Pulmonol. 36:439-446, 2003). We identified two CF patients from our hospital whose sputum specimens were culture positive for
P. apista
over the course of several years. Repetitive-element-sequence PCR was employed to determine whether sequential isolates that were recovered from these patients represented a single clone and whether each patient had been chronically colonized with the same strain. Banding patterns generated with ERIC primers, REP primers, and BOX primers showed that individual patient isolates had a high degree of similarity (>97%) and were considered identical. However, only the banding patterns from the ERIC primers and BOX primers were able to show that the strains from patients I and II were unique (similarity indices of 79.8% and 70.0%, respectively). We concluded that all strains of
P. apista
from patient I were identical, as were all strains from patient II, establishing chronic colonization. Only two of the three methods employed indicate that the strains from the two patients are distinct. This implied that the organism was not transferred from one patient to the other, suggesting that the choice of methodology could generate misleading results when examining person-to-person transmission regarding this organism.
Detection of New Methicillin-Resistant
Staphylococcus aureus
Clones Containing the Toxic Shock Syndrome Toxin 1 Gene Responsible for Hospital- and Community-Acquired Infections in France
Authors: Durand Geraldine , Bes Michèle , Meugnier Helene , Enright Mark C. , Forey Françoise , Liassine Nadia , Wenger Aline , Kikuchi Ken , Lina Gerard , Vandenesch François , Etienne Jerome 
Published: March 2006

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) clones harboring the toxic shock syndrome toxin 1 (
tst
) gene have been detected in France and in Switzerland since 2002. During a passive survey conducted between 2002 and 2003, we collected 103
tst-
positive
S. aureus
isolates from 42 towns in France, of which 27 were resistant to methicillin. The
tst-
positive MRSA belonged to two clones: a major clone comprising 25 isolates of sequence type (ST) 5 and
agr
group 2 and a minor clone comprising two isolates of ST30 and
agr3
. The
tst
-positive MRSA clones were associated with both hospital-acquired (12 cases) and community-acquired (8 cases) infections. The MRSA clones were mainly isolated from children (overall median age, 3 years). They caused a variety of clinical syndromes, including toxic shock syndrome and suppurative infections. Both clones were found to harbor a type IV staphylococcal chromosomal cassette
mec
(SCC
mec
) and to have similar antibiotic resistance profiles (usually resistant to oxacillin, kanamycin, and tobramycin and with intermediate resistance to fusidic acid). The origin of these clones is unclear. The
tst
-positive
agr2
MRSA clone has the same sequence type (ST5) of two pandemic nosocomial MRSA clones, namely, the Pediatric clone and the New York/Japan clone. These findings suggest that all these clones are phylogenetically related. The pulsotype of the
tst
-positive MRSA clones differed from that of methicillin-sensitive
S. aureus
(MSSA) clones by a single band involving the SCC
mec
element. These findings suggest that the
tst
-positive MRSA clones may have emerged from their respective MSSA counterparts.
Use of Various Common Isolation Media To Evaluate the New VITEK 2 Colorimetric GN Card for Identification of
Burkholderia pseudomallei
Authors: Lowe Peter , Haswell Helen , Lewis Kirsty 
Published: March 2006

ABSTRACT

The use of automated systems in the modern microbiology laboratory is becoming commonplace as the pressure of cost containment impacts on staff resources. With increased international travel and threats of bioterrorism, recognition and accurate identification of organisms such as
Burkholderia pseudomallei
is important. In areas where this organism is endemic, identification is not usually problematic. This study evaluates the performance of the new VITEK 2 colorimetric GN card for the identification of this organism. A total of 103 previously identified clinical isolates were tested with the new card with isolates taken from MacConkey agar, Columbia horse blood agar, Columbia sheep blood agar, and Trypticase soy agar in order to determine identification performance and to see if there was any variability in results due to the agar. Columbia horse blood agar produced the highest rates of identification (81%), followed by Trypticase soy agar (78%), Columbia sheep blood agar (75%), and MacConkey agar (63%). There was considerable variability in some of the reactions obtained. Seven isolates failed to identify from any of the agars used. This study highlights issues with the identification of this organism with the new VITEK 2 GN card. Enhancements of the algorithm parameters for the GN card are warranted and are in progress. Laboratory personnel need to be aware of the current limitations with this GN card and the software (version 4.02 or older for the VITEK 2 60/XL and version 1.02 or older for VITEK 2 Compact) and rely on clinical history, a high index of suspicion, and basic microbiology tests to confirm the identification of this organism.
Simultaneous Detection and Identification of
Candida
,
Aspergillus
, and
Cryptococcus
Species by Reverse Line Blot Hybridization
Authors: Playford E. Geoffrey , Kong Fanrong , Sun Ying , Wang Hui , Halliday Catriona , Sorrell Tania C. 
Published: March 2006

ABSTRACT

We report on a reverse line blot (RLB) assay, utilizing fungal species-specific oligonucleotide probes to hybridize with internal transcribed spacer 2 region sequences amplified using a nested panfungal PCR. Reference and clinical strains of 16
Candida
species (116 strains),
Cryptococcus neoformans
(five strains of
Cryptococcus neoformans
var.
neoformans
, five strains of
Cryptococcus neoformans
var.
grubii
, and six strains of
Cryptococcus gatti
), and five
Aspergillus
species (68 strains) were all correctly identified by the RLB assay. Additional fungal species (16 species and 26 strains) not represented on the assay did not exhibit cross-hybridization with the oligonucleotide probes. In simulated clinical specimens, the sensitivity of the assay for
Candida
spp. and
Aspergillus
spp. was 10
0.5
cells/ml and 10
2
conidia/ml, respectively. This assay allows sensitive and specific simultaneous detection and identification of a broad range of fungal pathogens.
Rhino-Orbitocerebral Mucormycosis Caused by
Apophysomyces elegans
Authors: Liang Kimberly P. , Tleyjeh Imad M. , Wilson Walter R. , Roberts Glenn D. , Temesgen Zelalem 
Published: March 2006

ABSTRACT

Rhino-orbitocerebral mucormycosis (ROCM) caused by more common zygomycetes (e.g.,
Mucor
) is known to cause rapidly fatal infections in immunocompromised patients.
Apophysomyces elegans
is an emerging zygomycete that has been reported to cause invasive cutaneous and rhino-orbitocerebral infections in immunocompetent individuals. Limited data exist describing the syndrome of ROCM caused by
A. elegans
. We describe a recent case and performed a comprehensive literature review to delineate the clinical characteristics of ROCM caused by
A. elegans
. Our case is a 50-year-old man with diabetes mellitus who presented with facial pain and right eye proptosis. Endoscopic sinus sampling revealed
A. elegans
. He was treated with liposomal amphotericin B and multiple debridements, with no disease on 1.5-year follow-up examination. Seven cases were identified on literature review, including the present case. Most patients (86%) were male, with a mean age of 40 years. Most patients (71%) did not have predisposing medical conditions. Three patients had predisposing head trauma. All presented with facial and/or periorbital pain. All had magnetic resonance imaging or computed tomography of the head showing intraorbital and/or sinus inflammation. Diagnosis was confirmed by histopathology and deep tissue culture in all cases. All patients required eye exenteration and extensive surgical debridement, in addition to intravenous amphotericin B. Six of the seven patients (86%) recovered. ROCM caused by
A. elegans
is rarely reported in the literature. Most such infections occurred in immunocompetent patients, often after facial trauma. Survival in ROCM caused by
A. elegans
is favorable in reported cases, with prompt surgical debridement and antifungal therapy.
Two Quality Control Exercises Involving Nucleic Acid Amplification Methods for Detection of
Mycoplasma pneumoniae
and
Chlamydophila pneumoniae
and Carried Out 2 Years Apart (in 2002 and 2004)
Authors: Loens K. , Beck T. , Ursi D. , Pattyn S. , Goossens H. , Ieven M. 
Published: March 2006

ABSTRACT

The quality performance of laboratories for the detection of
Mycoplasma pneumoniae
and
Chlamydophila pneumoniae
by two quality control (QC) exercises with a 2-year interval was investigated. For the 2002 QC exercise, specimens were spiked with
M. pneumoniae
at concentrations of 5,000, 500, 50, and 0 color-changing units (CCU)/100 μl. The limit of detectability was 50 CCU/100 μl. Therefore, this concentration was omitted from the 2004 panel and was excluded from the analysis. In 2002, 2 out of 12 participants obtained 100% correct results, 2 out of 12 produced false-positive results, and 10 out of 12 had between 0 out of 9 and 8 out of 9 correct positive results. In 2004, correct results were obtained in 15 out of 18 tests, and no false-positive results were reported. In 2002, specimens were spiked with
C. pneumoniae
at concentrations of 490, 49, 4.9, and 0 inclusion-forming units/100 μl (IFU/100 μl). In the 2004 panel, samples spiked with a lower dilution of 0.49 IFU/100 μl were added to the panel. For the
C. pneumoniae
QC, correct results were produced in 12 out of 16 and 13 out of 18 tests in 2002 and in 2004, respectively. Both multiplex PCR and nucleic acid sequence-based amplification (NASBA) formats scored a smaller number of samples positive than the monoplex reactions.
Characteristics of
Streptococcus pseudopneumoniae
Isolated from Purulent Sputum Samples
Authors: Keith Elaine R. , Podmore Roslyn G. , Anderson Trevor P. , Murdoch David R. 
Published: March 2006

ABSTRACT

Streptococcus pseudopneumoniae
is a recently described streptococcus that is phenotypically and genetically distinct from
Streptococcus pneumoniae
and other viridans streptococci. Key characteristics of
S. pseudopneumoniae
are the absence of a pneumococcal capsule, insolubility in bile, resistance or indeterminate susceptibility to optochin when incubated in 5% CO
2
but susceptibility to optochin when incubated in ambient air, and a positive reaction with the AccuProbe DNA probe hybridization test. The clinical importance of this bacterium is currently unknown. We report the characteristics and associated clinical data of 35 strains of
S. pseudopneumoniae
isolated from sputum samples from 33 patients. All isolates produced a positive result with the NOW
S. pneumoniae
antigen test (Binax, Inc.). No isolate was resistant to penicillin, but 60% were resistant to erythromycin and 77% were resistant to tetracycline. All patients had lower respiratory tract symptoms, 79% had chronic obstructive pulmonary disease (COPD), and 33% had chest radiographic infiltrates. Compared with matched control patients who had
Streptococcus pneumoniae
isolated from sputum, patients with
S. pseudopneumoniae
infection were more likely to have a history of COPD (odds ratio [OR], 5.0; 95% confidence interval [CI], 1.67 to 20.11) or exacerbation of COPD (OR, 6.5; 95% CI, 2.61 to 16.20). Further research is needed to better characterize the epidemiology of
S. pseudopneumoniae
colonization and the role of
S. pseudopneumoniae
in COPD and other diseases.
Evaluation of the Phoenix 100 ID/AST System and NID Panel for Identification of
Enterobacteriaceae
,
Vibrionaceae
, and Commonly Isolated Nonenteric Gram-Negative Bacilli
Authors: O'Hara Caroline M. 
Published: March 2006

ABSTRACT

The Phoenix 100 ID/AST system (Becton Dickinson Co., Sparks, Md.) is an automated system for the identification and antimicrobial susceptibility testing of bacterial isolates. This system with its negative identification (NID) panel was evaluated for its accuracy in the identification of 507 isolates of the family
Enterobacteriaceae
, 57 other nonenteric gram-negative isolates that are commonly isolated in clinical microbiology laboratories, and 138 isolates of the family
Vibrionaceae
. All of the isolates had been characterized by using approximately 48 conventional tube biochemicals. Of the 507 isolates of the
Enterobacteriaceae
, 456 (89.9%) were correctly identified to the genus and species levels. The five isolates of
Proteus penneri
required an off-line indole test, as suggested by the system to differentiate them from
Proteus vulgaris
. The identifications of 20 (3.9%) isolates were correct to the genus level but incorrect at the species level. Two (0.4%) isolates were reported as “no identification.” Misidentifications to the genus and species levels occurred for 29 (5.7%) isolates of the
Enterobacteriaceae
. These incorrect identifications were spread over 14 different genera. The most common error was the misidentification of
Salmonella
species. The shortest time for a correct identification was 2 h 8 min. The longest time was 12 h 27 min, for the identification of a
Serratia marcescens
isolate. Of the 57 isolates of nonenteric gram-negative bacilli (
Acinetobacter
,
Aeromonas
,
Burkholderia
,
Plesiomonas
,
Pseudomonas
, and
Stenotrophomonas
spp.), 48 (84.2%) were correctly identified to the genus and species levels and 7 (12.3%) were correctly identified to the genus level but not to the species level. The average time for a correct identification was 5 h 11 min. Of the
Vibrionaceae
spp., 123 (89.1%) were correctly identified at the end of the initial incubation period, which averaged 4 h. Based on the findings of this study, the Phoenix 100 ID/AST system NID panel falls short of being an acceptable new method for the identification of the
Enterobacteriaceae
,
Vibrionaceae
, and gram-negative nonenteric isolates that are commonly encountered in many hospital microbiology laboratories.
Evaluation of Phenotypic and Molecular Methods for Detection of Oxacillin Resistance in Members of the
Staphylococcus sciuri
Group
Authors: Stepanović Srdjan , Hauschild Tomasz , Dakić Ivana , Al-Doori Zainab , Švabić-Vlahović Milena , Ranin Lazar , Morrison Donald 
Published: March 2006

ABSTRACT

In this paper we report on an experimental evaluation of phenotypic and molecular methods as means for the detection of oxacillin resistance in members of the
Staphylococcus sciuri
group. A total of 109
S. sciuri
group member isolates (92
S. sciuri
isolates, 9
S. lentus
isolates, and 8
S. vitulinus
isolates) were tested by the disk diffusion method, the agar dilution method, the oxacillin salt-agar screening method, slide latex agglutination for PBP 2a, and PCR assay for
mecA
as the reference method. The
mecA
gene was detected in 29
S. sciuri
isolates, and the true-positive and true-negative results of the other tests were defined on the basis of the presence or the absence of the
mecA
gene. For the different methods evaluated, the sensitivities and specificities were as follows: for the disk diffusion test with a 1-μg oxacillin disk, 100% and 55.9%, respectively; for the disk diffusion test with a 30-μg cefoxitin disk, 93.5% and 100%, respectively; for the agar dilution method, 100% and 50%, respectively; for the oxacillin salt-agar screen test (with 6 μg of oxacillin per ml and 4% NaCl) 100% and 100%, respectively; and for the slide latex agglutination test for PBP 2a, 100% and 100%, respectively. The disk diffusion test with various β-lactam antibiotics was performed to evaluate their use for the prediction of oxacillin resistance. The results indicate that meropenem, cefazolin, cefamandole, cefuroxime, cefotetan, cefoperazone, cefotaxime, ceftriaxone, moxalactam, cefaclor, and cefprozil may be used as surrogate markers of oxacillin resistance, although further studies of their use for the detection of oxacillin resistance are required.
High Incidence of
Alloiococcus otitidis
in Children with Otitis Media, Despite Treatment with Antibiotics
Authors: Harimaya Atsushi , Takada Ryuta , Hendolin Panu H. , Fujii Nobuhiro , Ylikoski Jukka , Himi Tetsuo 
Published: March 2006

ABSTRACT

Acute otitis media (AOM) and otitis media with effusion (OME) are common diseases in childhood.
Alloiococcus otitidis
is a newly recognized species of gram-positive bacterium which was recently discovered as a pathogen associated with OME. Although some studies show that
A. otitidis
is frequently detected in children with OME, no study is available concerning the clinical efficiency of antibiotics against this organism. The prevalence of
A. otitidis
in 116 middle ear effusion specimens from 36 AOM and 52 OME patients was examined by culture and PCR. In addition, the prevalence of the bacterium was retrospectively investigated in relation to antibiotic use.
A. otitidis
was detected in 20 (50%) AOM and 47 (61%) OME specimens. The organism was the most frequent bacterium in AOM as well as in OME and was highly detected even in patients who had been treated with antibiotics, such as beta-lactams or erythromycin. The incidence of
A. otitidis
in our study was higher than that in Western countries, and our results suggest that drug-resistant strains of
A. otitidis
may be frequently spread in Japanese children. Our study suggests that antibiotics such as beta-lactams or erythromycin may not be sufficiently effective to eliminate this organism. Further investigation is expected to reveal the clinical role of the organism in otitis media.
Validation of String Test for Diagnosis of
Helicobacter pylori
Infections
Authors: Velapatiño Billie , Balqui Jacqueline , Gilman Robert H. , Bussalleu Alejandro , Quino Willi , Finger S. Alison , Santivañez Livia , Herrera Phabiola , Piscoya Alejandro , Valdivia Jose , Cok Jaime , Berg Douglas E. 
Published: March 2006

ABSTRACT

The method of recovering
Helicobacter pylori
DNA or viable cells absorbed on a string that a person has swallowed and that is retrieved an hour later (string test) should be a useful alternative to traditional analysis of cells or DNA obtained by endoscopy, which is invasive, uncomfortable, relatively costly, and ill-suited for community-based and pediatric studies. Here we assayed the sensitivity and validity of the string test versus conventional endoscopic biopsy for detecting and analyzing
H. pylori
infection. Forty-four people with gastric complaints were studied using both
H. pylori
culture and urease gene (
ureB
) PCR.
H. pylori
organisms cultured from strings and biopsy specimens from the same patients were fingerprinted by the randomly amplified polymorphic DNA (RAPD) method. Biopsy sections were also hematoxylin and eosin and silver stained for
H. pylori
detection.
H. pylori
was cultured from 80% of strings and detected by PCR from 91% of strings from participants whose biopsies had been
H. pylori
positive by culture, PCR, and/or histology. Strains recovered from strings and biopsy specimens yielded identical or closely related RAPD profiles in each of the 24 cases tested. We conclude that the string test is a useful method for
H. pylori
recovery and analysis when relatively noninvasive procedures are needed.