bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Significance and Epidemiologic Analyses of
Mycobacterium avium
and
Mycobacterium intracellulare
among Patients without AIDS
Authors: Han Xiang Y. , Tarrand Jeffrey J. , Infante Rosa , Jacobson Kalen L. , Truong Mylene 
Published: September 2005

ABSTRACT

The clinical significance and prevalence of
Mycobacterium avium
and
Mycobacterium intracellulare
were analyzed in a cohort of 7,472 patients who, from 1999 to 2003, sought care at the University of Texas M.D. Anderson Cancer Center, Houston, and had cultures performed for mycobacteria. Patients were stratified for age, sex, and underlying diseases, and bacteria were identified by 16S rRNA gene sequencing.
M. avium
was isolated in 62 (0.83%) of 7,472 patients and
M. intracellulare
in 65 (0.87%). Clinically, only 10 of the 62 (16.2%) patients with
M. avium
had probable to definite evidence of infection, whereas the majority (83.8%) had weak evidence of infection. Sex and age did not affect the isolation or infection of
M. avium
. Hematological tumors predisposed to
M. avium
colonization but not infection. In contrast, 41 of the 65 (63.1%) patients with
M. intracellulare
had probable to definite infection, a level much higher than those with
M. avium
(
P
< 0.001).
M. intracellulare
was more prevalent in women (1.33% of 3,311) than in men (0.50% of 4,161) (
P
< 0.001), and underlying diseases had no effect in women. Men with lung cancer had a higher prevalence (1.37%) than men without (0.34%) (4.0-fold;
P
< 0.001), but it was similar to that in women. A marked age trend for the isolation of
M. intracellulare
among women was noted: 0.27% (1-fold) for ages of <50 years, 0.85% (3.1-fold) for ages 50 to 59 years, 1.50% (5.6-fold) for ages 60 to 69 years, and 3.74% (13.9-fold) for ages ≥70 years (trend,
P
< 0.001). The combined rate for women ≥50 was 1.86% (95% confidence interval [1.30 to 2.42%]) (6.9-fold). Together, these results suggest that, among non-AIDS patients,
M. intracellulare
is more pathogenic and tends to infect women increasingly beyond menopause (age ≥50 years) regardless of underlying disease. The prevalence rate of 1.86% in postmenopausal women suggests the need to further investigate the public health significance of
M. intracellulare
.
Quantitative Detection of Hepatitis C Virus (HCV) RNA in Saliva and Gingival Crevicular Fluid of HCV-Infected Patients
Authors: Suzuki Tetsuro , Omata Kazuhiko , Satoh Tazuko , Miyasaka Takahiro , Arai Chiaki , Maeda Munehiro , Matsuno Tomonori , Miyamura Tatsuo 
Published: September 2005

ABSTRACT
The search for hepatitis C virus (HCV) in body fluids other than blood is important when assessing possible nonparenteral routes of viral transmission. However, the role of oral fluids in HCV transmission remains controversial. Here we quantitatively determined HCV RNA in saliva and gingival crevicular fluid (GCF) of anti-HCV-positive patients. Most patients (14 of 18; 78%) whose saliva specimens were negative had HCV RNA in their GCF. Most patients (20 of 26; 77%) had higher HCV RNA levels in their GCF than in their saliva. Although there was not a statistically significant correlation between the serum viral load and HCV level in saliva or GCF, patients with low serum HCV loads were less likely to have detectable HCV in their saliva. These findings have important implications for medical personnel and suggest that epidemiological studies designed to understand the significance of the oral route of transmission of HCV are warranted.
Detection of Vi-Negative
Salmonella enterica
Serovar Typhi in the Peripheral Blood of Patients with Typhoid Fever in the Faisalabad Region of Pakistan
Authors: Baker Stephen , Sarwar Yasra , Aziz Hafsa , Haque Asma , Ali Aamir , Dougan Gordon , Wain John , Haque Abdul 
Published: September 2005

ABSTRACT

The synthesis and transportation proteins of the Vi capsular polysaccharide of
Salmonella enterica
serovar Typhi (serovar Typhi) are encoded by the
viaB
operon, which resides on a 134-kb pathogenicity island known as SPI-7. In recent years, Vi-negative strains of serovar Typhi have been reported in regions where typhoid fever is endemic. However, because Vi negativity can arise during in vitro passage, the clinical significance of Vi-negative serovar Typhi is not clear. To investigate the loss of Vi expression at the genetic level, 60 stored strains of serovar Typhi from the Faisalabad region of Pakistan were analyzed by PCR for the presence of SPI-7 and two genes essential for Vi production:
tviA
and
tviB
. Nine of the sixty strains analyzed (15%) tested negative for both
tviA
and
tviB
; only two of these strains lacked SPI-7. In order to investigate whether this phenomenon occurred in vivo, blood samples from patients with the clinical symptoms of typhoid fever were also investigated. Of 48 blood samples tested, 42 tested positive by
fliC
PCR for serovar Typhi; 4 of these were negative for
tviA
and
tviB
. Three of these samples tested positive for SPI-7. These results demonstrate that
viaB
-negative, SPI-7-positive serovar Typhi is naturally occurring and can be detected by PCR in the peripheral blood of typhoid patients in this region. The method described here can be used to monitor the incidence of Vi-negative serovar Typhi in regions where the Vi vaccine is used.
Seminational Surveillance of Fungemia in Denmark: Notably High Rates of Fungemia and Numbers of Isolates with Reduced Azole Susceptibility
Authors: Arendrup Maiken Cavling , Fuursted Kurt , Gahrn-Hansen Bente , Jensen Irene Møller , Knudsen Jenny Dahl , Lundgren Bettina , Schønheyder Henrik C. , Tvede Michael 
Published: September 2005

ABSTRACT

The aim of this study was to present the first set of comprehensive data on fungemia in Denmark including the distribution of species and range of susceptibility to major antifungal compounds based on a seminational surveillance study initiated in 2003. The catchment area of the participating hospitals had a population of 2.8 million, or 53% of the Danish population. A total of 303 episodes of fungemia were registered (annual rate, 11 of 100,000 people or 0.49 of 1,000 hospital discharges).
Candida
species accounted for 97.4% of the fungal pathogens.
C. albicans
was the predominant species (63%), but the proportion varied from 57% to 72% among participating departments of clinical microbiology.
C. glabrata
was the second most frequent species (20%; range, 8% to 32%).
C. krusei
was a rare isolate (3%) and occurred only at two of the participating hospitals. Retrospective data retrieved from the Danish laboratory systems documented a continuous increase of candidemia cases since the early 1990s. For the 272 susceptibility-tested isolates, MICs of amphotericin B and caspofungin were within the limits expected for the species or genus. However, decreased azole susceptibility, defined as a fluconazole MIC of >8 μg/ml and/or itraconazole MIC of >0.125 μg/ml, was detected for 11
Candida
isolates that were neither
C. glabrata
nor
C. krusei
. Including intrinsically resistant fungi, we detected decreased susceptibility to fluconazole and/or itraconazole in 87 (32%) current Danish bloodstream fungal isolates. We showed a continuous increase of fungemia in Denmark and an annual rate in 2003 to 2004 higher than in most other countries. The proportion of bloodstream fungal isolates with reduced susceptibility to fluconazole and/or itraconazole was also notably high.
Development and Validation of an Immunoassay for Identification of Recent Human Immunodeficiency Virus Type 1 Infections and Its Use on Dried Serum Spots
Authors: Barin Francis , Meyer Laurence , Lancar Rémi , Deveau Christiane , Gharib Myriam , Laporte Anne , Desenclos Jean-Claude , Costagliola Dominique 
Published: September 2005

ABSTRACT
The objective was to develop and to validate an immunossay to identify recent human immunodeficiency virus type 1 (HIV-1) infections that can be used on dried serum spots (DSS). A single, indirect enzyme-linked immunosorbent assay was developed to quantify antibodies toward four HIV-1 antigens: consensus peptides of the immunodominant epitope of gp41 (IDE), consensus V3 peptides, recombinant integrase, and recombinant p24. The parameters of the logistic regression used to classify the samples were estimated on a training sample (210 serum samples) using resampling techniques to get stable estimates and then applied to a validation sample (761 serum samples). The IDE and V3 peptides were the best able to discriminate between the antibodies present in serum from recently (≤6 months) infected individuals and those with long-lasting infection. Combined quantification of antibody binding to these two synthetic antigens allowed us to identify recent infections with an area under the receiver operating characteristic curve of 0.949 and a sensitivity of 88.3%, with a specificity of 97.6% in patients with long-term infection (but not AIDS) and 86.0% in patients suffering from AIDS with a threshold of 0.50 in the validation sample. This simple immunoassay can be used to identify recently HIV-1-infected patients. Its performance is compatible with its use in population-based studies including DSS.
Porphyromonas somerae
sp. nov., a Pathogen Isolated from Humans and Distinct from
Porphyromonas levii
Authors: Summanen Paula H. , Durmaz Bengül , Väisänen Marja-Liisa , Liu Chengxu , Molitoris Denise , Eerola Erkki , Helander Ilkka M. , Finegold Sydney M. 
Published: September 2005

ABSTRACT

Porphyromonas levii
is an anaerobic, pigmented gram-negative bacillus originally isolated from bovine rumen. We describe 58 human clinical strains of
P. levii
-like organisms, isolated from various human clinical specimens that are phenotypically similar to the type strain of
P. levii
, a rumen isolate (ATCC 29147). Our biochemical, comparative 16S rRNA sequence analyses, and DNΑ-DNA relatedness studies indicate that the human
P. levii
-like organisms are similar to each other but genetically different from the
P. levii
type strain isolated from bovine rumen. We therefore propose the name
Porphyromonas somerae
to encompass the human
P. levii
-like organisms.
P. somerae
was predominantly isolated from patients with chronic skin and soft tissue or bone infections, especially in the lower extremities.
Method for Rapid Identification and Differentiation of the Species of the
Mycobacterium chelonae
Complex Based on 16S-23S rRNA Gene Internal Transcribed Spacer PCR-Restriction Analysis
Authors: Khan Izhar U. H. , Selvaraju Suresh B. , Yadav Jagjit S. 
Published: September 2005

ABSTRACT

Members of the
Mycobacterium chelonae
complex (MCC), including
M. immunogenum
,
M. chelonae
, and
M. abscessus
, have been associated with nosocomial infections and occupational hypersensitivity pneumonitis due to metalworking fluid (MWF) exposures. In order to minimize these health hazards, an effective and rapid assay for detection of MCC species and differentiation of MCC species from other species of rapidly growing mycobacteria (RGM) and from one another is warranted. Here we report such a method, based on the variable 16S-23S rRNA gene internal transcribed spacer (ITS) region.
Mycobacterium
genus-specific primers derived from highly conserved sequences in the ITS region and the flanking 16S rRNA gene were used. Specificity of the primers was verified using the MCC member species, 11 non-MCC RGM species, 3 slow-growing mycobacterial (SGM) species (two strains each), and 19 field isolates, including 18 MCC isolates (from in-use MWF) and one non-MCC isolate (from reverse osmosis water). The ITS amplicon size of
M. immunogenum
varied from those of
M. chelonae
and
M. abscessus
. Sequencing of the ∼250-bp-long ITS amplicons of the three MCC member species showed differences in 24 to 34 bases, thereby yielding variable deduced restriction maps. ITS PCR-restriction analysis using the in silico-selected restriction enzyme MaeII or HphI differentiated the three MCC members from one another and from other RGM and SGM species without sequencing. The enzyme MaeII discriminated all three member species; however, HphI could only differentiate
M. immunogenum
from
M. chelonae
and
M. abscessus
. Use of an optimized rapid DNA template preparation step based on direct cell lysis in the PCR tube added to the simplicity and adaptability of the developed assay.
Molecular Typing ofMycobacterium tuberculosisby Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis, a More Accurate Method for Identifying Epidemiological Links between Patients with Tuberculosis
Authors: van Deutekom Henk , Supply Philip , de Haas Petra E. W. , Willery Eve , Hoijng Susan P. , Locht Camille , Coutinho Roel A. , van Soolingen Dick 
Published: September 2005

ABSTRACTIS6110fingerprinting ofMycobacterium tuberculosisis the standard identification method in studies on transmission of tuberculosis. However, intensive epidemiological investigation may fail to confirm transmission links between patients clustered by IS6110-restriction fragment length polymorphism (RFLP) typing. We applied typing based on variable numbers of tandem repeats (VNTRs) of mycobacterial interspersed repetitive units (MIRUs) to isolates from 125 patients in 42 IS6110clusters, for which thorough epidemiological data were available, to investigate the potential of this method in distinguishing epidemiologically linked from nonlinked patients. Of seven IS6110clusters without epidemiological links, five were split by MIRU-VNTR typing, while nearly all IS6110clusters with proven or likely links displayed conserved MIRU-VNTR types. These results provide molecular evidence that not all clusters determined on the basis of multibanded IS6110RFLP patterns necessarily reflect transmission of tuberculosis. They support the use of MIRU-VNTR typing as a more reliable and faster method for transmission analysis.
Development of a Multiplex PCR and SHV Melting-Curve Mutation Detection System for Detection of Some SHV and CTX-M β-Lactamases of
Escherichia coli
,
Klebsiella pneumoniae
, and
Enterobacter cloacae
in Taiwan
Authors: Chia Ju-Hsin , Chu Chishih , Su Lin-Hui , Chiu Cheng-Hsun , Kuo An-Jing , Sun Chien-Feng , Wu Tsu-Lan 
Published: September 2005

ABSTRACT

Infection by extended-spectrum β-lactamase (ESBL)-producing
Enterobacteriaceae
has been increasing in Taiwan. Accurate identification of the ESBL genes is necessary for surveillance and for epidemiological studies of the mode of transmission in the hospital setting. We describe herein the development of a novel system, which consists of a multiplex PCR to identify
bla
SHV
,
bla
CTX-M-3
-like, and
bla
CTX-M-14
-like genes and a modified SHV melting-curve mutation detection method to rapidly distinguish six prevalent
bla
SHV
genes (
bla
SHV-1
,
bla
SHV-2
,
bla
SHV-2a
,
bla
SHV-5
,
bla
SHV-11
, and
bla
SHV-12
) in Taiwan. Sixty-five clinical isolates, which had been characterized by nucleotide sequencing of the
bla
SHV
and
bla
CTX-M
genes, were identified by the system. The system was then used to genotype the ESBLs from 199 clinical isolates, including 40
Enterobacter cloacae
, 68
Escherichia coli
, and 91
Klebsiella pneumoniae
, collected between August 2002 and March 2003. SHV-12 (80 isolates) was the most prevalent type of ESBL identified, followed in order of frequency by CTX-M-3 (65 isolates) and CTX-M-14 (36 isolates). Seventeen (9%) of the 199 clinical isolates harbored both SHV- and CTX-M-type ESBLs. In contrast to
Enterobacter cloacae
, the majority of which produced SHV-type ESBLs,
E. coli
and
K. pneumoniae
were more likely to possess CTX-M-type ESBLs. Three rare CTX-M types were identified through sequencing of the
bla
CTX-M-3
-like (CTX-M-15) and
bla
CTX-M-14
-like (CTX-M-9 and CTX-M-13) genes. The system appears to provide an efficient differentiation of ESBLs among
E. coli
,
K. pneumoniae
, and
Enterobacter cloacae
in Taiwan. Moreover, the design of the system can be easily adapted for similar purposes in areas where different ESBLs are prevalent.
Human Parainfluenza Virus 4 Outbreak and the Role of Diagnostic Tests
Authors: Lau Susanna K. P. , To Wing-kin , Tse Philomena W. T. , Chan Alex K. H. , Woo Patrick C. Y. , Tsoi Hoi-wah , Leung Annie F. Y. , Li Kenneth S. M. , Chan Paul K. S. , Lim Wilina W. L. , Yung Raymond W. H. , Chan Kwok-hung , Yuen Kwok-yung 
Published: September 2005

ABSTRACT
Owing to the difficulties in isolating the virus and the lack of routine surveillance, the clinical significance of human parainfluenza virus 4 (HPIV-4) is less well defined than that of the other human parainfluenza viruses. We describe the first outbreak of HPIV-4 infection in a developmental disabilities unit, involving 38 institutionalized children and three staff members, during a 3-week period in autumn 2004. Most subjects had upper respiratory tract infections (URTI), while lower respiratory tract infections (LRTI) occurred in three children (7%), one complicated by respiratory failure requiring ventilation support. All patients recovered. Nasopharyngeal aspirates tested for HPIV-4 were positive by reverse transcriptase PCR (RT-PCR) in all 41 cases (100%), by direct immunofluorescence in 29 of 39 tested cases (74%), and by cell cultures in 6 of 37 cases (16%), and serum was positive for antibodies against HPIV-4 in all 35 cases (100%) with serum samples available. In addition, RT-PCR detected HPIV-4 in four children (three LRTI and one URTI) out of 115 patients with community-acquired respiratory tract infection. Molecular analysis of the 1,198-bp phosphoprotein sequences showed that HPIV-4 isolates among the cases were genetically similar, whereas the community controls were more genetically distant, supporting nosocomial transmission of a single HPIV-4 genotype during the outbreak. Moreover, the HPIV-4 causing the outbreak is more closely related to HPIV-4A than HPIV-4B. HPIV-4 may be an important cause of more severe respiratory illness in children. The present RT-PCR assay is a sensitive, specific, and rapid method for the diagnosing HPIV-4 infection. To better define the epidemiology and clinical spectrum of disease of HPIV-4 infections, HPIV-4 should be included in the routine panels of respiratory virus detection on respiratory specimens.
“Bacteroides goldsteiniisp. nov.” Isolated from Clinical Specimens of Human Intestinal Origin
Authors: Song Yuli , Liu Chengxu , Lee Julia , Bolaňos Mauricio , Vaisanen Marja-Liisa , Finegold Sydney M. 
Published: September 2005

ABSTRACTPhenotypic and phylogenetic studies were performed on an unknown gram-negative, strictly anaerobic, rod-shaped bacterium isolated from human clinical specimens. This organism was indole negative, resistant to 20% bile, produced acetic and a lesser amount of succinic acids as the major end products of glucose metabolism, and possessed a G+C content of approximately 43 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was a member of theCytophaga-Flavobacter-Bacteroidesphylum of gram-negative bacteria and formed a close association (with an average sequence similarity of 93.6%) with the second subcluster of thePorphyromonascluster in theBacteroidessubgroup. Phylogenetically and phenotypically it resembledBacteroides merdae; however, a 16S rRNA gene sequence divergence of approximately 5.5% between the unknown bacterium andB. merdae, as well as distinguishable biochemical characteristics, demonstrate that the unknown bacterium is genotypically and phenotypically distinct and represents a previously unknown subline within thePorphyromonasphylogenetic cluster. Furthermore, a DNA-DNA reassociation value of 17.8% between isolates WAL 12034T(the type strain of this novel taxon) and ATCC 43184T(B. merdaetype strain) also documented the separateness of the unknown species andB. merdae. Based on the phenotypic and phylogenetic findings, a new species, “Bacteroides goldsteiniisp. nov,” is proposed. The G+C content of the DNA is 43 mol% forBacteroides. The type strain of “B. goldsteinii” is WAL 12034T(= CCUG 48944T= ATCC BAA-1180T).
Discrimination of
Streptococcus pneumoniae
from Viridans Group Streptococci by Genomic Subtractive Hybridization
Authors: Suzuki Nao , Seki Mitsuko , Nakano Yoshio , Kiyoura Yusuke , Maeno Masao , Yamashita Yoshihisa 
Published: September 2005

ABSTRACT

Two oligonucleotide primer sets for the discrimination of
Streptococcus pneumoniae
from “pneumococcus-like” oral streptococcal isolates by PCR were developed. Genomic subtractive hybridization was performed to search for differences between
Streptococcus pneumoniae
strain WU2 and the most closely related oral streptococcus,
Streptococcus mitis
strain 903. We identified 19 clones that contained
S. pneumoniae-
specific nucleotide fragments that were absent from the chromosomal DNA of typical laboratory strains of
S. mitis
and other oral bacteria. Subsequently, oligonucleotide PCR primers for the detection of
S. pneumoniae
were designed from the sequences of the subtracted DNA fragments, and the specificities of the 19 primer sets were evaluated by PCR using chromosomal DNAs extracted from four
S. pneumoniae
clinical isolates and from 20 atypical organisms classified as
S. mitis
or
S. oralis
, which harbored genes encoding the pneumococcal virulence factors autolysin (
lytA
) or pneumolysin (
ply
), as templates. Of the 19 primer sets, two (Spn9802 and Spn9828) did not amplify PCR products from any of the pneumococcus-like streptococcal strains that we examined. The genes containing the Spn9802 and Spn9828 sequences encoded proteins of unknown function that did not correspond to any previously described proteins in other bacteria. These new oligonucleotide primers may be very useful for early and correct diagnosis of
S. pneumoniae
infections.
Comparison of Visual 24-Hour and Spectrophotometric 48-Hour MICs to CLSI Reference Microdilution MICs of Fluconazole, Itraconazole, Posaconazole, and Voriconazole for
Candida
spp.: a Collaborative Study
Authors: Espinel-Ingroff A. , Barchiesi F. , Cuenca-Estrella M. , Fothergill A. , Pfaller M. A. , Rinaldi M. , Rodriguez-Tudela J. L. , Verweij P. E. 
Published: September 2005

ABSTRACT

A multicenter (six-center) study evaluated the performance (interlaboratory reproducibility, compatibility with reference methods, and categorical agreement) of 24-h visual and 48-h spectrophotometric MICs. MICs of fluconazole, itraconazole, voriconazole, and posaconazole were compared to reference 48-h microdilution broth visual MICs (CLSI [formerly NCCLS] M27-A2 document) for 71 isolates of
Candida
spp. that included 10 fluconazole-resistant strains. Twenty readings (5%) were reported as showing no growth at 24 h, mostly for
Candida dubliniensis
and from a single center. The overall interlaboratory agreement of 24-h visual readings and 48-h spectrophotometric MICs, as well their compatibility with reference values, were excellent with the four triazoles for most of the species (93 to 99%, within 3 dilutions). The categorical agreement between the investigational reading conditions and reference values was good with fluconazole and voriconazole (93 to 97%) but lower with itraconazole (86 to 88%), due primarily to minor errors. There were only 0 to 3% very major errors with these three triazoles; the number of substantial errors (more than three dilutions) was also low (<2%) with posaconazole. These data suggest that the performance of both investigational MIC readings gives results similar to those of reference MICs. Since spectrophotometric MICs are more objective and the 24-h time period would shorten the MIC determination of azoles, the description of either of these two reading conditions in the M27-A2 document should be considered by the CLSI subcommittee in addition to or instead of the longer, less practical, and more subjective 48-h visual MIC reading.