bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Characterization of a Specific Glycopeptidolipid Containing a Novel
N
-Acyl-Deoxy Sugar from
Mycobacterium intracellulare
Serotype 7 and Genetic Analysis of Its Glycosylation Pathway
Authors: Fujiwara Nagatoshi , Nakata Noboru , Maeda Shinji , Naka Takashi , Doe Matsumi , Yano Ikuya , Kobayashi Kazuo 
Published: November 2006

ABSTRACT

The nontuberculous
Mycobacterium avium-Mycobacterium intracellulare
complex (MAC) is distributed ubiquitously in the environment and is an important cause of respiratory and lymphatic disease in humans and animals. These species produce polar glycopeptidolipids (GPLs), and of particular interest is their serotype-specific antigenicity. Structurally, GPLs contain an
N
-acylated tetrapeptide-amino alcohol core that is glycosylated at the C terminal with 3,4-di-
O
-methyl rhamnose and at the
d
-
allo
-threonine with a 6-deoxy-talose. This serotype nonspecific GPL is found in all MAC species. The serotype-specific GPLs are further glycosylated with a variable haptenic oligosaccharide at 6-deoxy-talose. At present, 31 distinct serotype-specific GPLs have been identified on the basis of oligosaccharide composition, and the complete structures of 14 serotype-specific GPLs have been defined. It is considered that the modification of the GPL structure plays an important role in bacterial physiology, pathogenesis, and host immune responses. In this study, we defined the complete structure of a novel serotype 7 GPL that has a unique terminal amido sugar. The main molecular mass is 1,874, and attached to the tetrapeptide-amino alcohol core is the serotype 7-specific oligosaccharide unit of 4-2′-hydroxypropanoyl-amido-4,6-dideoxy-2-
O
-methyl-β-hexose-(1→3)-α-
l
-rhamnose-(1→3)-α-
l
-rhamnose-(1→3)-α-
l
-rhamnose-(1→2)-α-
l
-6-deoxy-talose. Moreover, we isolated and characterized the serotype 7-specific gene cluster involved in glycosylation of the oligosaccharide. Nine open reading frames (ORFs) were observed in the cluster. Based on the sequence homology, the ORFs are thought to participate in the biosynthesis of the serotype 7 GPL.
Prospective Evaluation of the Hybrid Capture 2 and AMPLICOR Human Papillomavirus (HPV) Tests for Detection of 13 High-Risk HPV Genotypes in Atypical Squamous Cells of Uncertain Significance
Authors: Halfon Philippe , Trepo Elisabeth , Antoniotti Gilles , Bernot Catherine , Cart-Lamy Philippe , Khiri Hacène , Thibaud Didier , Marron Jean , Martineau Agnès , Pénaranda Guillaume , Benmoura Dominique , Blanc Bernard 
Published: November 2006

ABSTRACT

The use of high-risk human papillomavirus (hrHPV) testing as an adjunct to cervical cytology in population-based screening programs is currently based on DNA hybridization and PCR assays. The aim of this study was to prospectively assess the diagnostic performance of the Hybrid Capture 2 test (HC2; Digene Corporation) in comparison with that of the recently developed PCR-based AMPLICOR HPV test (Roche Molecular Systems) for the detection of 13 hrHPV types. A reverse line blot hybridization assay (Innogenetics) was used as an internal reference standard in discordant cases. Two hundred seventy-one patients with atypical squamous cells of uncertain significance (ASCUS) in cervical samples underwent hrHPV testing. The chi-square test was performed to compare respective proportions. Totals of 160/271 (59%) and 156/271 (58%) were found to be positive for hrHPV with HC2 and AMPLICOR, respectively. Concordant results were obtained for 235 (86.7%) of the 271 samples (kappa statistic, 0.73 ± 0.04). Considering types 26, 53, and 66 as oncogenic types, negative predictive values (NPVs) of HC2 and AMPLICOR were 92.8% and 87.8%, respectively (difference was not significant), and their respective accuracies were 94.8% and 91.9% (difference was not significant). Considering types 26, 53, and 66 as not oncogenic, the respective HC2 and AMPLICOR NPVs were 92.8% and 97.4% (difference was not significant), and accuracy was significantly higher for the AMPLICOR assay (95.9% versus 90.8% for HC2) (
P
< 0.05). For ASCUS samples, the NPV was 92.8% for HC2 testing and might be compromised if the copy number of HPV DNA was low. The NPV was 97.4% for the AMPLICOR assay and might be compromised if HPV types 26, 53, and 66 were considered oncogenic. The accuracy of these two assays is good and is compatible with routine clinical use in the triage of ASCUS cases.
Antibiotic-Resistant Invasive Pneumococcal Clones in Italy
Authors: Gherardi Giovanni , Fallico Loredana , Del Grosso Maria , Bonanni Federica , D'Ambrosio Fabio , Manganelli Riccardo , Palù Giorgio , Dicuonzo Giordano , Pantosti Annalisa 
Published: November 2006

ABSTRACT

A total of 105 multiple-antibiotic-resistant invasive pneumococcal isolates recovered in Italy from 2001 to 2003 were genetically characterized. Of these, 40 were penicillin-nonsusceptible (PNSSP) and 65 were penicillin-susceptible (PSSP)
Streptococcus pneumoniae
strains. Among the PNSSP isolates, 8 and 11 different restriction profiles were obtained for the
pbp2b
and
pbp2x
genes, respectively. Clonal groups were established on the basis of analysis of both pulsed-field gel electrophoresis (PFGE) types and multilocus sequence typing (MLST). Several international clones, such as Spain
23F
-1/ST81, Spain
6B
-2/ST90, Spain
9V
-3/ST156, and Sweden
15A
-25/ST263, were identified among the PNSSP isolates. Other, smaller clones, such as the minor Spanish 19F clone/ST88 and Denmark
14
-32/ST230, were also found. Among the PSSP isolates, clones related to England
14
-9/ST9, Greece
6B
-22/ST273, and Portugal
19F
-21/ST177 were found. In addition, two large clones comprised nonvaccine serotypes. One, comprising serotype 3 isolates, corresponded to the clone Netherlands
3
-31/ST180; the other, comprising serotype 15B/C isolates, ST474, was not related to any previously described clone. Two small clusters related to the newly described clones Greece
21
-30/ST193 and Netherlands
15B
-37/ST199 included isolates with unrelated PFGE profiles. An unusual finding was the inability to obtain the MLST allelic profile for an isolate of serotype 19A, belonging to the Sweden
15A
-25/ST263 clone, due to a large deletion of the
xpt
gene. Capsular switching was observed among both PNSSP and PSSP isolates and involved also serotypes not included in the 7-valent pneumococcal conjugate vaccine (PCV7), such as serotypes 15B/C and 19A. Since antibiotic-resistant nonvaccine serotype clones are present in Italy, continuous monitoring of pneumococcal epidemiology should be carried out in the PCV7 era.
Evidence for a Link between Parasite Genotype and Outcome of Infection with
Entamoeba histolytica
Authors: Ali Ibne Karim M. , Mondal Utpal , Roy Shantanu , Haque Rashidul , Petri William A. , Clark C. Graham 
Published: November 2006

ABSTRACT

The factors determining whether a person infected with
Entamoeba histolytica
develops disease remain obscure. To investigate whether the parasite genome contributes to the outcome, we have investigated the distribution of parasite genotypes among
E. histolytica
-infected individuals in Bangladesh. Samples were obtained from individuals who either were asymptomatic, had diarrhea/dysentery, or had developed a liver abscess. Genotypes were determined by using six tRNA-linked polymorphic markers, and their distributions among the three sample groups were evaluated. A significant population differentiation in the genotype distribution was found for four of the six individual markers as well as for the combined genotypes, suggesting that the parasite genome does contribute in some way to the outcome of infection with
E. histolytica
. The markers themselves do not indicate the nature of the underlying genetic differences, but they may be linked to loci that do have an impact on the outcome of infection.
PCR-Based Diagnosis of
Naegleria
sp. Infection in Formalin-Fixed and Paraffin-Embedded Brain Sections
Authors: Schild Marc , Gianinazzi Christian , Gottstein Bruno , Müller Norbert 
Published: November 2006

ABSTRACT

We developed a real-time PCR which allowed the highly sensitive detection of
Naegleria fowleri
in histological brain tissue sections from experimentally infected mice. This genus-specific small-subunit (18S) rRNA gene-based PCR can complement conventional (immuno-) histology for the diagnosis of primary amoebic meningoencephalitis in paraffin-embedded brain necropsy specimens that had been fixed in formalin buffered with phosphate-buffered saline.
A Multiplex Ligase Detection Reaction-Fluorescent Microsphere Assay for Simultaneous Detection of Single Nucleotide Polymorphisms Associated with
Plasmodium falciparum
Drug Resistance
Authors: Carnevale Eric P. , Kouri Drew , DaRe Jeana T. , McNamara David T. , Mueller Ivo , Zimmerman Peter A. 
Published: November 2006

ABSTRACT

Incomplete malaria control efforts have resulted in a worldwide increase in resistance to drugs used to treat the disease. A complex array of mutations underlying antimalarial drug resistance complicates efficient monitoring of parasite populations and limits the success of malaria control efforts in regions of endemicity. To improve the surveillance of
Plasmodium falciparum
drug resistance, we developed a multiplex ligase detection reaction-fluorescent-microsphere-based assay (LDR-FMA) that identifies single nucleotide polymorphisms (SNPs) in the
P. falciparum dhfr
(9 alleles),
dhps
(10 alleles), and
pfcrt
(3 alleles) genes associated with resistance to Fansidar and chloroquine. We evaluated 1,121 blood samples from study participants in the Wosera region of Papua New Guinea, where malaria is endemic. Results showed that 468 samples were
P. falciparum
negative and 453 samples were
P. falciparum
positive by a
Plasmodium
species assay and all three gene assays (concordance, 82.2%). For
P. falciparum
infections where the assay for each gene was positive, 2 samples carried resistance alleles for all three genes, 299 carried resistance alleles for
dhfr
and
pfcrt
, 131 carried resistance alleles for only one gene (
dhfr
[
n
= 40],
dhps
[
n
= 1], or
pfcrt
[
n
= 90]), and 21 carried only sensitive alleles at all three genes. Mixed-strain infections characterized 100 samples. Overall, 95.4% (432/453) of
P. falciparum
-infected samples carried at least one allele associated with resistance to Fansidar or chloroquine. In view of the fact that 86.3% (391/453) of
P. falciparum
-infected samples carried
pfcrt
mutations, chloroquine is largely ineffective against
P. falciparum
in Papua New Guinea. Surveillance of additional
dhfr
and
dhps
polymorphisms in order to monitor the continued effectiveness of Fansidar is recommended.
Controlled Clinical Comparison of VersaTREK and BacT/ALERT Blood Culture Systems
Authors: Mirrett Stanley , Hanson Kimberly E. , Reller L. Barth 
Published: November 2006

ABSTRACT

To assess the relative yields in automated microbial detection systems of bacteria and yeasts isolated from the blood of adult patients with suspected sepsis, we compared the new VersaTREK system (VTI) (TREK Diagnostic Systems, Cleveland, OH) to the BacT/ALERT 3D system (3D) (bioMérieux, Inc., Durham, NC). Identical protocols were followed for the two systems. Paired aerobic (REDOX 1) and anaerobic (REDOX 2) VTI media were compared with standard aerobic (SA) and anaerobic (SN) 3D media; each of the four culture bottles was filled with 6 to 9 ml of blood. All bottles flagged positive by the instruments were subcultured to determine both true-positive (growth) and false-positive (no growth) cultures. Additionally, to assess false-negative bottles, terminal subcultures were done on all negative companion bottles to true-positive bottles. All isolates were identified by standard methods. All 4 bottles were adequately filled and yielded 413 clinically significant isolates in 5,389 (79%) of the 6,786 4-bottle sets obtained. Although no overall difference in yield or in time to detection was detected between the two systems, significantly more streptococci and enterococci as a group were detected by VTI. Moreover, significantly more microorganisms were detected by VTI for patients receiving antimicrobial therapy. The two systems were comparable (
P
, not significant) at detecting the 179 unimicrobial episodes of bacteremia seen. False-positive rates for aerobic and anaerobic bottles, respectively, were 1.6% and 0.9% for VTI and 0.7% and 0.8% for 3D. We conclude that the VTI and 3D systems are comparable for detection of bloodstream infections with bacteria or yeasts.
Isolation and Antimicrobial Susceptibilities of Chlamydial Isolates from Western Barred Bandicoots
Authors: Kumar Swati , Kutlin Andrei , Roblin Patricia , Kohlhoff Stephan , Bodetti Tracey , Timms Peter , Hammerschlag Margaret R. 
Published: November 2006

ABSTRACT

A range of species of
Chlamydiales
have previously been detected in a variety of Australian marsupials, including koalas and western barred bandicoots. Thirty-seven ocular, urogenital, or nasal swabs were obtained from 21 wild western barred bandicoots.
Chlamydia
culture and antibiotic susceptibility testing were performed for cycloheximide-treated HEp-2 cells in 96-well microtiter plates.
Chlamydia
spp. were isolated from 11 specimens from 9 (42.8%) bandicoots. All isolates were identified as
Chlamydiales
by conventional PCR with 16S and 23S rRNA gene primers specific to
Chlamydiales
and were confirmed to be
Chlamydia pneumoniae
by a
C. pneumoniae
-specific
ompA
-based real-time PCR assay and 16S rRNA and 23S rRNA gene signature sequence analyses. The MICs of azithromycin, doxycycline, ciprofloxacin, and enrofloxacin for 10
C. pneumoniae
isolates from these bandicoots ranged from 0.015 to 1 μg/ml, 0.25 to 1 μg/ml, 0.25 to 2 μg/ml, and 0.25 to 0.5 μg/ml, respectively. The MICs at which 90% of isolates were inhibited and the minimal bactericidal concentrations were within the ranges reported previously for human isolates of
C. pneumoniae.
Globicatella sanguinis
Is an Etiological Agent of Ventriculoperitoneal Shunt-Associated Meningitis
Authors: Seegmüller I. , van der Linden M. , Heeg C. , Reinert R. R. 
Published: November 2006

ABSTRACT

Globicatella sanguinis
is a very rare isolate in clinical samples. We present a case of meningitis in a 69-year-old female patient after implantation of an external left ventricular drainage due to a hydrocephalus. She recovered after antibiotic treatment with ceftriaxone.
Catabacter hongkongensisgen. nov., sp. nov., Isolated from Blood Cultures of Patients from Hong Kong and Canada
Authors: Lau Susanna K. P. , McNabb Alan , Woo Gibson K. S. , Hoang Linda , Fung Ami M. Y. , Chung Liliane M. W. , Woo Patrick C. Y. , Yuen Kwok-Yung 
Published: November 2006

ABSTRACTFour bacterial isolates were recovered from the blood cultures of four patients, two of whom were from Hong Kong and two of whom were from Canada. The two Hong Kong strains were isolated from a 48-year-old man with intestinal obstruction and secondary sepsis (strain HKU16T) and from a 39-year-old man with acute appendicitis (strain HKU17), while the two Canadian strains were isolated from a 74-year-old man with biliary sepsis (strain CA1) and from a 66-year-old woman with metastatic carcinoma and sepsis (strain CA2). While the first three patients survived, the last patient died 2 weeks after the episode of bacteremia. All four isolates are strictly anaerobic, nonsporulating, gram-positive coccobacilli that were unidentified by conventional phenotypic tests and commercial identification systems. They grow on sheep blood agar as nonhemolytic pinpoint colonies after 48 h of incubation at 37°C in an anaerobic environment. All are catalase positive and motile, with flagella. They produce acid from arabinose, glucose, mannose, and xylose. They do not produce indole or reduce nitrate. They are sensitive to penicillin, vancomycin, and metronidazole but resistant to cefotaxime. 16S rRNA gene sequence analysis showed 16.0%, 16.8%, and 21.0% base differences fromClostridium propionicum,Clostridium neopropionicum, andAtopobium minutum, respectively. The G+C content of strain HKU16Tis 40.2% ± 2.2%. Based on their phylogenetic affiliation, unique G+C content, and phenotypic characteristics, we propose a new genus and species,Catabacter hongkongensisgen. nov., sp. nov., to describe the bacterium, for which HKU16 is the type strain, and suggest that it be assigned to a new family,Catabacteriaceae. The gastrointestinal tract was probably the source of the bacterium for at least three of the four patients. The isolation of a catalase-positive, motile, nonsporulating, anaerobic gram-positive bacillus in clinical laboratories should raise the possibility ofC. hongkongensis.Further studies should be performed to ascertain the epidemiology and other disease associations of this bacterium.
Development and Clinical Application of a Panfungal PCR Assay To Detect and Identify Fungal DNA in Tissue Specimens
Authors: Lau Anna , Chen Sharon , Sorrell Tania , Carter Dee , Malik Richard , Martin Patricia , Halliday Catriona 
Published: November 2006

ABSTRACTGiven the rise in the incidence of invasive fungal infections (IFIs) and the expanding spectrum of fungal pathogens, early and accurate identification of the causative pathogen is essential. We developed a panfungal PCR assay that targets the internal transcribed spacer 1 (ITS1) region of the ribosomal DNA gene cluster to detect fungal DNA in fresh and formalin-fixed, paraffin-embedded (PE) tissue specimens from patients with culture-proven (n= 38) or solely histologically proven (n= 24) IFIs. PCR products were sequenced and compared with sequences in the GenBank database to identify the causal pathogen. The molecular identification was correlated with results from histological examination and culture. The assay successfully detected and identified the fungal pathogen in 93.6% and 64.3% of culture-proven and solely histologically proven cases of IFI, respectively. A diverse range of fungal genera were identified, including species ofCandida,Cryptococcus,Trichosporon,Aspergillus,Fusarium,Scedosporium,Exophiala,Exserohilum,Apophysomyces,Actinomucor, andRhizopus. For five specimens, molecular analysis identified a pathogen closely related to that identified by culture. All PCR-negative specimens (n= 10) were PE tissues in which fungal hyphae were visualized. The results support the use of the panfungal PCR assay in combination with conventional laboratory tests for accurate identification of fungi in tissue specimens.
Mucor circinelloides
Was Identified by Molecular Methods as a Cause of Primary Cutaneous Zygomycosis
Authors: Iwen Peter C. , Sigler Lynne , Noel Rhonda K. , Freifeld Alison G. 
Published: November 2006

ABSTRACT

A case of primary cutaneous zygomycosis caused by
Mucor circinelloides
is described. Histopathology showed typical hyphae along with chlamydospores. The isolate was identified by molecular and phenotypic methods. The utility of sequence analysis of the internal transcribed spacer region is highlighted; however, further studies are needed to assess species genetic heterogeneity.
First Reported Infections Caused by Three Newly Described Genera in the Family
Xanthomonadaceae
Authors: LaSala P. Rocco , Segal Jonathan , Han Faye S. , Tarrand Jeffrey J. , Han Xiang Y. 
Published: November 2006

ABSTRACT

Members of the family of
Xanthomonadaceae
are typically characterized as environmental organisms. With the exception of
Stenotrophomonas maltophilia
, these organisms are infrequently implicated as human pathogens. We describe three cases of central venous catheter-associated bloodstream infections caused by
Dokdonella koreensis
,
Aquimonas voraii
, and a
Luteibacter
sp., all newly named genera within the family
Xanthomonadaceae
. The three patients all had histories of underlying hematological disorders, presented with fever, and recovered fully following treatment. These isolates required 16S rRNA gene sequencing for identification and, unlike
S. maltophilia
, demonstrated susceptibility to most antibiotics tested. This report represents the first description of human infections caused by these organisms.
Distribution of
Mycoplasma pneumoniae
and
Mycoplasma salivarium
in the Synovial Fluid of Arthritis Patients
Authors: Johnson Sheena M. , Bruckner Felix , Collins David 
Published: November 2006

ABSTRACT

By use of a very sensitive nested PCR method targeting part of the strongly conserved mycoplasmal 16S RNA genes,
Mycoplasma pneumoniae
was found in the synovial fluid of 19/24 (79%) of rheumatoid arthritis patients, 6/6 (100%) of patients with nonrheumatoid inflammatory arthritis, and 8/10 (80%) of osteoarthritis patients attending the rheumatology clinic for drainage of joint effusions. It was not found in the synovial exudates of 13 people attending the orthopedic clinic with traumatic knee injuries or undergoing surgery for knee replacement. However,
M. pneumoniae
was detected in 2/4 synovial biopsy specimens from orthopedic patients with traumatic knee injuries.
M. pneumoniae
was associated with the increased synovial fluids found in arthritic flares but was not found in the synovial fluids of trauma patients.
Mycoplasma salivarium
occurred sporadically.
Mycoplasma fermentans
had previously been isolated from patients with inflammatory cellular infiltrates, such as rheumatoid arthritis, but it was not detected for osteoarthritic patients from either clinic. It is possible that these organisms may contribute to chronic inflammation within the joints.
Identification of Group A Porcine Rotavirus Strains Bearing a Novel VP4 (P) Genotype in Italian Swine Herds
Authors: Martella V. , Ciarlet M. , Bányai K. , Lorusso E. , Arista S. , Lavazza A. , Pezzotti G. , Decaro N. , Cavalli A. , Lucente M. S. , Corrente M. , Elia G. , Camero M. , Tempesta M. , Buonavoglia C. 
Published: November 2006

ABSTRACT
The VP4 gene of a G5 Italian porcine rotavirus strain, 344/04-1, was nontypeable by PCR genotyping. The amino acid sequence of the full-length VP4 protein had low identity (≤76.6%) with the homologous sequences of representative strains of the remaining P genotypes, providing evidence for a novel P genotype.
Inhibition of the Secretory Pathway by Foot-and-Mouth Disease Virus 2BC Protein Is Reproduced by Coexpression of 2B with 2C, and the Site of Inhibition Is Determined by the Subcellular Location of 2C
Authors: Moffat Katy , Knox Caroline , Howell Gareth , Clark Sarah J. , Yang H. , Belsham Graham J. , Ryan Martin , Wileman Thomas 
Published: November 2006

ABSTRACT
Infection of cells with picornaviruses can lead to a block in protein secretion. For poliovirus this is achieved by the 3A protein, and the consequent reduction in secretion of proinflammatory cytokines and surface expression of major histocompatibility complex class I proteins may inhibit host immune responses in vivo. Foot-and-mouth disease virus (FMDV), another picornavirus, can cause persistent infection of ruminants, suggesting it too may inhibit immune responses. Endoplasmic reticulum (ER)-to-Golgi apparatus transport of proteins is blocked by the FMDV 2BC protein. The observation that 2BC is processed to 2B and 2C during infection and that individual 2B and 2C proteins are unable to block secretion stimulated us to study the effects of 2BC processing on the secretory pathway. Even though 2BC was processed rapidly to 2B and 2C, protein transport to the plasma membrane was still blocked in FMDV-infected cells. The block could be reconstituted by coexpression of 2B and 2C, showing that processing of 2BC did not compromise the ability of FMDV to slow secretion. Under these conditions, 2C was located to the Golgi apparatus, and the block in transport also occurred in the Golgi apparatus. Interestingly, the block in transport could be redirected to the ER when 2B was coexpressed with a 2C protein fused to an ER retention element. Thus, for FMDV a block in secretion is dependent on both 2B and 2C, with the latter determining the site of the block.