bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Genetic Distance as a Measure of Ongoing Transmission of
Mycobacterium tuberculosis
Authors: van der Spuy G. D. , Warren R. M. , Richardson M. , Beyers N. , Behr M. A. , van Helden P. D. 
Published: December 2003

ABSTRACT

The stability of the genotypic marker IS
6110
, used to define the epidemiology of
Mycobacterium tuberculosis
, is one of the most important factors influencing the interpretation of DNA fingerprint data. We propose that evolved strains should be considered together with clustered strains to represent chains of ongoing transmission. For the present study we used a large set of fingerprint data for strains collected between 1992 and 1998 from residents of a community with a high incidence of tuberculosis in Cape Town, South Africa. Interstrain genetic distances were calculated by counting the banding pattern mismatches in the IS
6110
DNA fingerprints of different isolates. These data demonstrate that the propensity to change by one or two bands is independent of the IS
6110
copy number. Hence, the genetic distance between pairs of isolates can be simply expressed as the number of differences in the banding patterns. From this foundation, a data set which identifies newly evolved strains has been generated. Inclusion of these evolved strains into various molecular epidemiological calculations significantly increased the estimate of ongoing transmission in this study setting. The indication is that nearly all cases of tuberculosis in this community are due to ongoing transmission. This has important implications for tuberculosis control, as it indicates that the control measures used at present are unable to reduce the level of transmission. This technique may also be applicable to the study of low-incidence tuberculosis outbreaks as well as the analysis of epidemiological data from other disease epidemics.
Improved Outcomes Associated with Limiting Identification of
Candida
spp. in Respiratory Secretions
Authors: Barenfanger Joan , Arakere Pushpalatha , Cruz Rafael Dela , Imran Adil , Drake Cheryl , Lawhorn Jerry , Verhulst Steven J. , Khardori Nancy 
Published: December 2003

ABSTRACT

Pneumonia due to infection with
Candida
spp. is extremely rare even though these yeasts are commonly cultured from respiratory secretions. The diagnosis of pneumonia due to
Candida
spp. should be made only by demonstrating tissue invasion of a biopsy specimen. Physicians might misinterpret the presence of
Candida
spp. in respiratory secretions as being the etiological agent of pneumonia. This study describes the practice of limiting identification (ID) of rapidly growing yeasts (i.e.,
Candida
spp.) in respiratory secretions and its impact on patients. Before November 2001, rapidly growing yeasts found in respiratory secretions were identified to the species level. After November, rapidly growing yeasts were reported as “yeasts, not
Cryptococcus
.” The group of patients with respiratory secretions processed before November 2001 is called the full ID group (
n
= 267); the group with samples processed after that date is called the limited ID group (
n
= 77). Full ID patients had an average length of hospital stay of 12.1 days/patient; that of limited ID patients was 10.1 days/patient, a decrease of 2 days/patient (
P
= 0.02). The full ID patients had an average cost of $9,407/patient; that of limited ID patients was $6,973/patient, a decrease of $2,434/patient (
P
= 0.03). Antifungal medications were used in 103 of 267 (39%) full ID patients and in 16 of 77 (21%) limited ID patients, a decrease of 18% (
P
= 0.004). Limited ID patients had a mortality rate of 14.3%; that of full ID patients was 18.7%, a decrease of 4.4% (
P =
0.37). This policy of limiting yeast ID did not impair the diagnosis of pneumonia. Rather, decreases in lengths of stay, costs, and administration of unnecessary antifungal therapy were observed after instituting this policy.
Characterization of a Novel Rapidly Growing
Mycobacterium
Species Associated with Sepsis
Authors: Hong Tao , Butler W. Ray , Hollis Frank , Floyd Margaret M. , Toney Sean R. , Tang Yi-Wei , Steele Cindy , Leggiadro Robert J. 
Published: December 2003

ABSTRACT

A rapidly growing mycobacterium was isolated five times from blood cultures from a 6-year-old female patient with relapsed pre-B-cell acute lymphocytic leukemia. All five isolates had identical nucleotide sequences for the first 500 bp of the 16S rRNA gene, indicative of a single species. High-performance liquid chromatography analysis of mycolic acids indicated that the species was similar to
Mycobacterium smegmatis.
Sequence analysis of the 16S rRNA gene (1,455 bp) for one isolate demonstrated that the species was closely related to
Mycobacterium diernhoferi
. Based on the phenotypic features and phylogenetic analysis, it was concluded that the isolates represented a novel rapidly growing
Mycobacterium
species. The name “
Mycobacterium hackensackense
” is proposed for this unique strain, 147-0552
T
, which was deposited in the American Type Culture Collection as ATCC BAA-823
T
.
Accuracy of Six Commercially Available Systems for Identification of Members of the Family
Vibrionaceae
Authors: O'Hara Caroline M. , Sowers Evangeline G. , Bopp Cheryl A. , Duda Sarah B. , Strockbine Nancy A. 
Published: December 2003

ABSTRACT

Six commercially available bacterial identification products were tested with
Vibrio alginolyticus
(12 strains),
V. cholerae
(30 strains),
Photobacterium
(
Vibrio
)
damselae
(10 strains), V.
fluvialis
(10 strains),
V. furnissii
(4 strains),
V. hollisae
(10 strains),
V. metschnikovii
(9 strains),
V. mimicus
(10 strains),
V. parahaemolyticus
(30 strains), and
V. vulnificus
(10 strains) to determine the accuracy of each system for identification. The products included API 20E, Crystal E/NF, MicroScan Neg ID2 and Rapid Neg ID3, and Vitek GNI+ and ID-GNB. Each product was tested only with those species that were listed in its database. Overall, the systems correctly identified 63.9, 80.9, 63.1, 73.6, 73.5, and 77.7% of the isolates to species level, respectively. Error rates ranged from 0.8% for the API 20E to 10.4% for the Rapid Neg ID3. The API 20E gave “no identification” for 13.1% of the isolates, while the Neg ID2, GNI+, ID-GNB, and Crystal were unable to identify 1.8, 2.9, 5.0, and 6.9%, respectively. For
V. cholerae
, specifically, accuracy ranged from 50.0 to 96.7%, with the API 20E having the worst performance and Crystal having the best.
V. fluvialis
presented the biggest challenge for the API 20E and the GNI+, with probabilities averaging 10%, while
V. mimicus
was a major problem with the Crystal E/NF, which identified none of the strains correctly. With the Neg ID2, correct answers were often obtained only after a modified inoculation of the panel with a bacterial suspension prepared with 0.85% NaCl. Additional tests required for identification often included growth in the absence of NaCl, which is not readily available in most clinical laboratories. The only product to correctly identify at least 90% of
V. cholerae
strains was the Crystal E/NF, and only three of the six products, the API 20E and both of the Vitek cards, correctly identified more than 90% of the
V. parahaemolyticus
strains. Thus, extreme care must be taken in the interpretation of answers from these six commercially available systems for the identification of
Vibrio
species.
Rapid Identification of Commonly EncounteredCandidaSpecies Directly from Blood Culture Bottles
Authors: Selvarangan Rangaraj , Bui Uyen , Limaye Ajit P. , Cookson Brad T. 
Published: December 2003

ABSTRACTWe report a rapid-cycle, real-time PCR method for identifying sixCandidaspp. directly from BACTEC blood culture bottles. Target sequences in the noncoding internal transcribed spacer regions of the rRNA operon were simultaneously amplified and interrogated with fluorescent probes to identifyCandida albicans,C. glabrata,C. parapsilosis,C. tropicalis,C. krusei, andC. lusitaniae; these account for 88% of the yeast species isolated from positive blood cultures in our laboratory. Any of the first four species can be identified in a single reaction using two fluorescent hybridization probe sets. The antifungal-resistant speciesC. kruseiandC. lusitaniaeare detected in a second reaction, also with two probe sets. The assay was validated with DNA extracted from BACTEC blood culture bottles positive for yeasts (n= 62) and was 100% concordant with culture identification based on biochemical and morphological features ofC. albicans(n= 22),C. parapsilosis(n= 10),C. tropicalis(n= 1)C. glabrata(n= 22),C. krusei(n= 2), andC. lusitaniae(n= 1). No cross-reactivity was observed in blood culture samples growing yeasts other than the above-mentioned species (n= 4), in those growing bacteria (n= 12), or in the absence of microbial growth. Our assay allows rapid (≤2 h) and specific detection of the most commonCandidaspp. directly from positive blood cultures and may facilitate delivery of optimal antifungal therapy.
Molecular Analysis of the VP7, VP4, VP6, NSP4, and NSP5/6 Genes of a Buffalo Rotavirus Strain: Identification of the Rare P[3] Rhesus Rotavirus-Like VP4 Gene Allele
Authors: Martella V. , Ciarlet M. , Pratelli A. , Arista S. , Terio V. , Elia G. , Cavalli A. , Gentile M. , Decaro N. , Greco G. , Cafiero M. A. , Tempesta M. , Buonavoglia C. 
Published: December 2003

ABSTRACT
We report the detection and molecular characterization of a rotavirus strain, 10733, isolated from the feces of a buffalo calf affected with diarrhea in Italy. Strain 10733 was classified as a P[3] rotavirus, as the VP8* trypsin cleavage product of the VP4 protein revealed a high amino acid identity (96.2%) with that of rhesus rotavirus strain RRV (P5B[3]), used as the recipient virus in the human-simian reassortant vaccine. Analysis of the VP7 gene product revealed that strain 10733 possessed G6 serotype specificity, a type common in ruminants, with an amino acid identity to G6 rotavirus strains ranging from 88 to 98%, to Venezuelan bovine strain BRV033, and Hungarian human strain Hun4. Phylogenetic analysis based on the VP7 gene of G6 rotaviruses identified at least four lineages and an apparent linkage between each lineage and the VP4 specificity, suggesting the occurrence of repeated interspecies transmissions and genetic reassortment events between ruminant and human rotaviruses. Moreover, strain 10733 displayed a bovine-like NSP4 and NSP5/6 and a subgroup I VP6 specificity, as well as a long electropherotype pattern. The detection of the rare P[3] genotype in ruminants provides additional evidence for the wide genetic and antigenic diversity of group A rotaviruses.
Development and Validation of a Quantitative Real-Time PCR Assay Using Fluorescence Resonance Energy Transfer Technology for Detection of
Aspergillus fumigatus
in Experimental Invasive Pulmonary Aspergillosis
Authors: O'Sullivan Cathal E. , Kasai Miki , Francesconi Andrea , Petraitis Vidmantas , Petraitiene Ruta , Kelaher Amy M. , Sarafandi Alia A. , Walsh Thomas J. 
Published: December 2003

ABSTRACT

Invasive pulmonary aspergillosis (IPA) is a frequently fatal infection in immunocompromised patients that is difficult to diagnose. Present methods for detection of
Aspergillus
spp. in bronchoalveolar lavage (BAL) fluid and in tissue vary in sensitivity and specificity. We therefore developed an
A. fumigatus
-specific quantitative real-time PCR-based assay utilizing fluorescent resonance energy transfer (FRET) technology. We compared the assay to quantitative culture of BAL fluid and lung tissue in a rabbit model of experimental IPA. Using an enzymatic and high-speed mechanical cell wall disruption protocol, DNA was extracted from samples of BAL fluid and lung tissues from noninfected and
A. fumigatus
-infected rabbits. A unique primer set amplified internal transcribed spacer regions (ITS) 1 and 2 of the rRNA operon. Amplicon was detected using FRET probes targeting a unique region of ITS1. Quantitation of
A. fumigatus
DNA was achieved by use of external standards. The presence of PCR inhibitors was determined by use of a unique control plasmid. The analytical sensitivity of the assay was ≤10 copies of target DNA. No cross-reactivity occurred with other medically important filamentous fungi. The assay results correlated with pulmonary fungal burden as determined by quantitative culture (
r
= 0.72, Spearman rank correlation;
P
≤ 0.0001). The mean number of genome equivalents detected in untreated animals was 3.86 log
10
(range, 0.86 to 6.39 log
10
) in tissue. There was a 3.53-log
10
mean reduction of
A. fumigatus
genome equivalents in animals treated with amphotericin B (AMB) (95% confidence interval, 3.38 to 3.69 log
10
;
P
≤ 0.0001), which correlated with the reduction of residual fungal burden in lung tissue measured in terms of log
10
CFU/gram. The enhanced quantitative sensitivity of the real-time PCR assay was evidenced by detection of
A. fumigatus
genome in infarcted culture-negative lobes, by a greater number of mean genome equivalents compared to the number of CFU per gram in tissue and BAL fluid, and by superior detection of therapeutic response to AMB in BAL fluid compared to culture. This real-time PCR assay using FRET technology is highly sensitive and specific in detecting
A. fumigatus
DNA from BAL fluid and lung tissue in experimental IPA.
Evaluation of S. aureus ID, a New Chromogenic Agar Medium for Detection of
Staphylococcus aureus
Authors: Perry John D. , Rennison Claire , Butterworth Lynne A. , Hopley Andrew L. J. , Gould F. Kate 
Published: December 2003

ABSTRACT

S. aureus ID (bioMérieux, La Balme Les Grottes, France) is a new chromogenic agar medium designed to enable the isolation of staphylococci and the specific identification of
Staphylococcus aureus. S. aureus
produces green colonies on this medium due to production of α-glucosidase. To evaluate this medium, a total of 350 wound swabs were cultured onto S. aureus ID, CHROMagar Staph. aureus, and conventional media routinely used in our laboratory. After 18 to 20 h of incubation, 96.8% of strains formed green colonies on S. aureus ID compared with 91.1% of strains forming mauve colonies on CHROMagar Staph. aureus. A total of 94.3% of strains were recovered within 18 to 20 h with conventional media. The sensitivity was increased after 48 h of incubation to 98.7, 96.2, and 95.6% with S. aureus ID, CHROMagar Staph. aureus, and conventional media, respectively. A total of 97.4% of green colonies on S. aureus ID were confirmed as
S. aureus
compared with 94.4% of mauve colonies on CHROMagar Staph. aureus. We conclude that S. aureus ID is a highly sensitive and specific medium for the isolation and identification of
S. aureus
from wound swabs.
rpoB
-Based Identification of Nonpigmented and Late-Pigmenting Rapidly Growing Mycobacteria
Authors: Adékambi Toïdi , Colson Philippe , Drancourt Michel 
Published: December 2003

ABSTRACT

Nonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) are increasingly isolated in clinical microbiology laboratories. Their accurate identification remains problematic because classification is labor intensive work and because new taxa are not often incorporated into classification databases. Also, 16S rRNA gene sequence analysis underestimates RGM diversity and does not distinguish between all taxa. We determined the complete nucleotide sequence of the
rpoB
gene, which encodes the bacterial β subunit of the RNA polymerase, for 20 RGM type strains. After using in-house software which analyzes and graphically represents variability stretches of 60 bp along the nucleotide sequence, our analysis focused on a 723-bp variable region exhibiting 83.9 to 97% interspecies similarity and 0 to 1.7% intraspecific divergence. Primer pair Myco-F-Myco-R was designed as a tool for both PCR amplification and sequencing of this region for molecular identification of RGM. This tool was used for identification of 63 RGM clinical isolates previously identified at the species level on the basis of phenotypic characteristics and by 16S rRNA gene sequence analysis. Of 63 clinical isolates, 59 (94%) exhibited <2% partial
rpoB
gene sequence divergence from 1 of 20 species under study and were regarded as correctly identified at the species level.
Mycobacterium abscessus
and
Mycobacterium mucogenicum
isolates were clearly distinguished from
Mycobacterium chelonae
;
Mycobacterium mageritense
isolates were clearly distinguished from “
Mycobacterium houstonense
.” Four isolates were not identified at the species level because they exhibited >3% partial
rpoB
gene sequence divergence from the corresponding type strain; they belonged to three taxa related to
M. mucogenicum
,
Mycobacterium smegmatis
, and
Mycobacterium porcinum
. For
M. abscessus
and
M. mucogenicum
, this partial sequence yielded a high genetic heterogeneity within the clinical isolates. We conclude that molecular identification by analysis of the 723-bp
rpoB
sequence is a rapid and accurate tool for identification of RGM.
Multilocus Sequence Typing of
Candidaglabrata
Reveals Geographically EnrichedClades
Authors: Dodgson Andrew R. , Pujol Claude , Denning David W. , Soll David R. , Fox Andrew J. 
Published: December 2003

ABSTRACT

The
haploid pathogenic yeast
Candida glabrata
is the second most
common
Candida
species isolated from cases of bloodstream
infection. The clinical relevance of
C. glabrata
is enhanced
by its reduced susceptibility to fluconazole. Despite this, little is
known of the epidemiology or population structure of this species. We
developed a multilocus sequence typing (MLST) scheme for
C.
glabrata
and used it to fingerprint a geographically diverse
collection of 107 clinical isolates and 2 reference strains.
Appropriate loci were identified by amplifying and sequencing fragments
of the coding regions of 11
C. glabrata
genes in 10 unrelated
isolates. The 6 most variable loci (
FKS
,
LEU2
,
NMT1
,
TRP1
,
UGP1
, and
URA3
) were
sequenced in the collection of 109 isolates. From the 3,345 bp
sequenced in each isolate, 81 nucleotide sites were found to be
variable. These defined 30 STs among the 109 strains. The technique was
validated by comparison with random amplified polymorphic DNA and the
complex DNA fingerprinting probes Cg6 and Cg12. MLST identified 5 major
clades among the isolates studied. Three of the clades exhibited
significant geographical bias. Our data demonstrate for the first time,
with such a large geographically diverse strain collection, that
distinct genetic clades of
C. glabrata
prevail in different
geographical
regions.
New Reverse Transcription-PCR Assay for Rapid and Sensitive Detection of Enterovirus Genomes in Cerebrospinal Fluid Specimens of Patients with Aseptic Meningitis
Authors: Jacques Jérôme , Carquin Jocelyne , Brodard Véronique , Moret Hélène , Lebrun Dorine , Bouscambert Maude , Motte Jacques , Rémy Gérard , Andréoletti Laurent 
Published: December 2003

ABSTRACT

Enterovirus (EV) detection by a new commercially available reverse transcription (RT)-PCR assay (Penter RT-PCR test) was compared with EV isolation from cell cultures and with EV detection by an in-house RT-PCR assay. Of the 54 cerebrospinal fluid specimens collected during a summer outbreak of aseptic meningitis, 52% were positive by cell culture versus 76% by in-house RT-PCR assay and 80% by the new RT-PCR test (52 versus 76 versus 80%;
P
= 0.003). This new reliable EV RNA detection test is suitable for clinical diagnosis of EV-related meningitis and may improve the management of EV-related neurological syndromes.
Caspofungin Activity against Clinical Isolates of Fluconazole-Resistant
Candida
Authors: Pfaller Michael A. , Messer Shawn A. , Boyken Linda , Rice Cassie , Tendolkar Shailesh , Hollis Richard J. , Diekema Daniel J. 
Published: December 2003

ABSTRACT

A total of 7,837 clinical isolates of
Candida
were tested against fluconazole, and 351 resistant (fluconazole MIC ≥ 64 μg/ml) isolates were identified (4% of the total tested). All fluconazole-resistant isolates were inhibited by caspofungin at concentrations that can be exceeded by standard doses (MIC at which 90% of the isolates were inhibited, 1 μg/ml; 99% of the MICs were ≤2 μg/ml).
Evaluation of Two Miniaturized Systems, MicroScan W/A and BBL Crystal E/NF, for Identification of Clinical Isolates of
Aeromonas
spp
Authors: Soler L. , Marco F. , Vila J. , Chacón M. R. , Guarro J. , Figueras M. J. 
Published: December 2003

ABSTRACT

Fifty-two clinical strains and 22 type and reference
Aeromonas
strains, previously genetically characterized by 16S rRNA gene restriction fragment length polymorphism, were identified in parallel with the MicroScan Walk/Away and BBL Crystal Enteric/Nonfermenter systems. The former identified only 14.8% of the isolates correctly, and the latter identified only 20.3% correctly, which indicates that neither of these systems is useful for this purpose.
Comparison of the Sequences of the Internal Transcribed Spacer Regions and
PbGP43
Genes of
Paracoccidioides brasiliensis
from Patients and Armadillos (
Dasypus novemcinctus
)
Authors: Hebeler-Barbosa Flavia , Morais Flavia V. , Montenegro Mario R. , Kuramae Eiko E. , Montes Beatriz , McEwen Juan G. , Bagagli Eduardo , Puccia Rosana 
Published: December 2003

ABSTRACT

Paracoccidioides brasiliensis
isolates from 10 nine-banded armadillos (
Dasypus novemcinctus
) were comparable with 19 clinical isolates by sequence analysis of the
PbGP43
gene and ribosomal internal transcribed spacer 1 (ITS1) and ITS2 and by random amplified polymorphic DNA. In this original ITS study, eight isolates differed by one or three sites among five total substitution sites.
Most Human Isolates ofMycobacterium aviumMav-A and Mav-B Are Strong Producers of Hemolysin, a Putative Virulence Factor
Authors: Rindi Laura , Bonanni Daniela , Lari Nicoletta , Garzelli Carlo 
Published: December 2003

ABSTRACTHemolysin was quantified in 58 isolates ofMycobacterium aviumfrom human, animal, and environmental sources. Human Mav-A and Mav-B isolates were the strongest producers; in contrast, animal and environmental Mav-A isolates and human, animal, and environmental Mav-C organisms were low-level producers. Hemolysin production was not restricted to isolates causing invasive infections.
Pseudomonas
Cross-Infection from Cystic Fibrosis Patients to Non-Cystic Fibrosis Patients: Implications for Inpatient Care of Respiratory Patients
Authors: Robinson P. , Carzino R. , Armstrong D. , Olinsky A. 
Published: December 2003

ABSTRACT

A 14-year-old boy with bronchiectasis secondary to chronic aspiration developed multiresistant
Pseudomonas aeruginosa
lower respiratory disease following several inpatient periods where accommodation and physiotherapy services were shared with cystic fibrosis (CF) patients known to be infected with the genetically identical strain of
P. aeruginosa
. Cross-infection with
P. aeruginosa
between CF patients and non-CF patients has not previously been described, and this finding raises significant issues relevant to the treatment of patients with non-CF suppurative lung disease.
Detection of Enterococcal Surface Protein Gene (
esp
) and Amplified Fragment Length Polymorphism Typing of Glycopeptide-Resistant
Enterococcus faecium
during Its Emergence in a Greek Intensive Care Unit
Authors: Routsi C. , Platsouka E. , Willems R. J. L. , Bonten M. J. M. , Paniara O. , Saroglou G. , Roussos C. 
Published: December 2003

ABSTRACT

The emergence of glycopeptide-resistant
Enterococcus faecium
(GREF) in a Greek intensive care unit was studied by amplified fragment length polymorphism analysis and
esp
gene detection. Three GREF clones harboring the
esp
gene were recovered from 17 out of 21 patients, indicating the dissemination of genetically homogenous and virulent strains of GREF.