bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tsukamurella strandjordae
sp. nov., a Proposed New Species Causing Sepsis
Authors: Kattar Mireille M. , Cookson Brad T. , Carlson LaDonna C. , Stiglich Susan K. , Schwartz Margot A. , Nguyen Trang T. , Daza Riza , Wallis Carolyn K. , Yarfitz Stuart L. , Coyle Marie B. 
Published: July 2002

ABSTRACT

We have isolated a gram-positive, weakly acid-alcohol-fast, irregular rod-shaped bacterium from cultures of blood from a 5-year-old girl with acute myelogenous leukemia. This isolate was compared with 14 other strains including reference strains of
Tsukamurella
species by a polyphasic approach based on physiological and biochemical properties, whole-cell short-chain fatty acid and mycolic acid analyses, DNA-DNA hybridization, and sequencing of the 16S rRNA gene. This isolate represents a new taxon within the genus
Tsukamurella
for which we propose the name
Tsukamurella strandjordae
sp. nov. Our study also revealed that
Tsukamurella paurometabola
ATCC 25938 represents a misnamed
Tsukamurella inchonensis
isolate and confirms that
Tsukamurella wratislaviensis
belongs to the genus
Rhodococcus
.
Quantitation of Bacteria in Bone Marrow from Patients with Typhoid Fever: Relationship between Counts and Clinical Features
Authors: Wain John , Bay Phan Van Be , Vinh Ha , Duong Nguyen M. , Diep To Song , Walsh Amanda L. , Parry Christopher M. , Hasserjian Robert P. , Ho Vo Anh , Hien Tran T. , Farrar Jeremy , White Nicholas J. , Day Nicholas P. J. 
Published: July 2002

ABSTRACT

Enteric fever is the only bacterial infection of humans for which bone marrow examination is routinely recommended. A prospective study of the concentrations of bacteria in the bone marrow and their relationship to clinical features was conducted with 120 Vietnamese patients with suspected enteric fever, of whom 89 had confirmed typhoid fever. Ninety-three percent of the
Salmonella enterica
serovar Typhi samples isolated were resistant to ampicillin, chloramphenicol, and co-trimoxazole. For 81 patients with uncomplicated typhoid and satisfactory bone marrow aspirates, the number of serovar Typhi CFU in bone marrow aspirates was a median value of 9 (interquartile range [IQR], 1 to 85; range, 0.1 to 1,580) compared to 0.3 (IQR, 0.1 to 10; range, 0.1 to 399) CFU/ml in simultaneously sampled blood. The ratio of individual blood counts to bone marrow counts was 10 (IQR, 2.3 to 97.5). The number of bacteria in blood but not bone marrow was correlated inversely with the duration of preceding fever. Thus, with increasing duration of illness the ratio of bone marrow-to-blood bacterial concentrations increased; the median ratio was 4.8 (IQR, 1 to 27.5) during the first week compared with 158 (IQR, 60 to 397) during the third week. After lysing the host cells, the median ratio of viable bone marrow to blood increased, reflecting the higher concentration of intracellular serovar Typhi in the bone marrow. Effective antibiotic pretreatment had a significantly greater effect in reducing blood counts compared to bone marrow counts (
P
< 0.001). Thus, bacteria in the bone marrow of typhoid patients are less affected by antibiotic treatment than bacteria in the blood. The numbers of bacteria in bone marrow correlated negatively with the white blood cell (
R
= −0.3,
P
= 0.006) and platelet counts (
R
= −0.32,
P
= 0.01) and positively with fever clearance time after treatment (
R
= 0.4,
P
< 0.001). The bacterial load in bone marrow therefore may reflect the clinical course of the infection, and high levels may suppress neutrophil proliferation.
Genetic Variation among Human Isolates of Uninucleated Cyst-Producing
Entamoeba
Species
Authors: Verweij Jaco J. , Polderman Anton M. , Clark C. Graham 
Published: July 2002

ABSTRACT

Twelve human infections with
Entamoeba
spp. producing uninucleated cysts were studied. DNA was extracted from infected feces and used to amplify part of the ameba small-subunit rRNA gene. Sequence analysis identified four distinct types of
Entamoeba
, all of which are related to
Entamoeba polecki
and
E. chattoni
and two of which have not been reported previously. Whether these genetic types represent different species is unclear. We propose that the agent of all human infections with uninucleated cyst-producing
Entamoeba
species be reported as “
E. polecki
-like.”
Utility of Paired BACTEC MYCO/F LYTIC Blood Culture Vials for Detection of Bacteremia, Mycobacteremia, and Fungemia
Authors: Archibald Lennox K. , Dobbie Hamish , Kazembe Peter , Nwanyanwu Okey , McKnight Celeste , Byrne Terry , Addison Rachel M. , Bell Michael , Reller L. Barth , Jarvis William R. 
Published: July 2002

ABSTRACT
In previous bloodstream infection studies in Malawi, we inoculated blood from a single venesection into a single BACTEC MYCO/F LYTIC (MFL) vial. Inoculation of one vial, however, would be expected to reduce the sensitivity of bloodstream pathogen detection with MFL vials. To ascertain the degree of this loss of sensitivity, blood was drawn from each of 228 febrile, adult inpatients in Malawi and 5 ml of each blood sample was inoculated into each of two MFL vials. Of 228 paired vials, 51 (22%) were both positive, 172 (75%) were both negative, and 5 (3%) had discordant results. Bloodstream infection would have been detected in 11 (92%) of 12 patients with mycobacteremia and 38 (92%) of 41 patients with bacteremia had only one MFL vial been inoculated. Our study shows that a second MFL vial does not significantly increase diagnostic sensitivity.
Antifungal Susceptibility Testing of Fluconazole by Flow Cytometry Correlates with Clinical Outcome
Authors: Wenisch Christoph , Moore Caroline B. , Krause Robert , Presterl Elisabeth , Pichna Peter , Denning David W. 
Published: July 2002

ABSTRACT

Susceptibility testing of fungi by flow cytometry (also called fluorescence-activated cell sorting [FACS]) using vital staining with FUN-1 showed a good correlation with the standard M27-A procedure for assessing MICs. In this study we determined MICs for blood culture isolates from patients with candidemia by NCCLS M27-A and FACS methods and correlated the clinical outcome of these patients with in vitro antifungal resistance test results. A total of 24 patients with candidemia for whom one or more blood cultures were positive for a
Candida
sp. were included. Susceptibility testing was performed by NCCLS M27-A and FACS methods. The correlation of MICs (NCCLS M27-A and FACS) and clinical outcome was calculated. In 83% of the cases, the MICs of fluconazole determined by FACS were within 1 dilution of the MICs determined by the NCCLS M27-A method. For proposed susceptibility breakpoints, there was 100% agreement between the M27-A and FACS methods. In the FACS assay, a fluconazole MIC of <1 μg/ml was associated with cure (
P
< 0.001) whereas an MIC of ≥1 μg/ml was associated with death (
P
< 0.001). The M27-A-derived fluconazole MICs did not correlate with outcome (
P
= 1 and
P
= 0.133).
Molecular Identification of Microorganisms from Endodontic Infections
Authors: Rolph H. J. , Lennon A. , Riggio M. P. , Saunders W. P. , MacKenzie D. , Coldero L. , Bagg J. 
Published: July 2002

ABSTRACT

A relatively wide range of bacteria have been isolated from root canals using standard culture techniques. However, only 50% of the bacteria in the oral cavity are cultivable (S. S. Socransky et al., Arch. Oral Biol. 8:278–280, 1963); hence, bacterial diversity in endodontic infections is underestimated. This study used a PCR-based 16S rRNA gene assay, followed by cloning and sequencing of 16S rRNA amplicons from a small subset of samples to assess the diversity of bacteria present in infected root canals. A total of 41 clinical samples from 15 de novo and 26 refractory cases of endodontic infections were assessed. Of these samples, 44% were positive by culture and 68% were positive by PCR. Eight samples were selected for further analysis. Of these, the two de novo cases yielded sequences related to those of the genera
Enterococcus, Lactobacillus, Propionibacterium
, and
Streptococcus
and two clones were related to previously uncultivated bacteria, while the sinus-associated, de novo case yielded sequences related to those of the genera
Lactobacillus, Pantoea, Prevotella
, and
Selenomonas
. The five refractory cases produced clones which were related to the genera
Capnocytophaga, Cytophaga, Dialister, Eubacterium, Fusobacterium, Gemella, Mogibacterium, Peptostreptococcus, Prevotella, Propionibacterium, Selenomonas, Solobacterium, Streptococcus
, and
Veillonella
and two clones representing previously uncultivated bacteria. The phylogenetic positions of several clones associated with the
Clostridiaceae
and
Sporomusa
subgroups of the
Firmicutes
grouping are also shown. This study demonstrates that molecular techniques can detect the presence of bacteria in endodontic infections when culture techniques yield a negative result and can be used to identify a wider range of endodontic-infection-related bacteria including the presence of previously unidentified or unculturable bacteria.
Genetic Diversity of
Streptococcus suis
Strains Isolated from Pigs and Humans as Revealed by Pulsed-Field Gel Electrophoresis
Authors: Berthelot-Hérault Florence , Marois Corinne , Gottschalk Marcelo , Kobisch Marylène 
Published: July 2002

ABSTRACT

The genetic diversity of 123
Streptococcus suis
strains of capsular types 2, 1/2, 3, 7, and 9, isolated from pigs in France and from humans in different countries, was evaluated by pulsed-field gel electrophoresis (PFGE) of DNA restricted with
Sma
I. The method was highly discriminative (
D
= 0.98), results were reproducible, and the PFGE analysis was easy to interpret. Among all
S. suis
strains, 74 PFGE patterns were shown. At 60% homology, three groups (A, B, and C) were identified, and at 69% homology, eight subgroups (a to h) were observed. Strains isolated from diseased pigs or from humans were statistically clustered in group B, especially in subgroup d. By contrast,
S. suis
strains isolated from clinically healthy pigs were preferentially included in subgroup b of group A. Relationships could be established between capsular types 1/2, 3, and 9 and groups A, e, and B, respectively.
S. suis
strains isolated from humans were homogeneous, and a very high level of association between these strains and four DNA patterns was observed. The PFGE used in this study is a very useful tool for evaluating the genetic diversity of
S. suis
strains, and it would be used for epidemiological investigations.
PCR Detection and DNA Sequence Analysis of the Regulatory Region of Lymphotropic Papovavirus in Peripheral Blood Mononuclear Cells of an Immunocompromised Rhesus Macaque
Authors: Lednicky John A. , Halvorson Steven J. , Butel Janet S. 
Published: July 2002

ABSTRACT
A lymphotropic papovavirus (LPV) archetypal regulatory region was amplified from DNA from the blood of an immunocompromised rhesus monkey. We believe this is the first nonserological evidence of LPV infection in rhesus monkeys.
Streptococcus sinensis
sp. nov., a Novel Species Isolated from a Patient with Infective Endocarditis
Authors: Woo Patrick C. Y. , Tam Dorothy M. W. , Leung Kit-Wah , Lau Susanna K. P. , Teng Jade L. L. , Wong Michelle K. M. , Yuen Kwok-Yung 
Published: July 2002

ABSTRACT

A bacterium was isolated from the blood culture of a patient with infective endocarditis. The cells were facultative anaerobic, nonsporulating, gram-positive cocci arranged in chains. The bacterium grows on sheep blood agar as alpha-hemolytic, gray colonies of 0.5 to 1 mm in diameter after 24 h of incubation at 37°C in ambient air. Growth also occurs in 10 or 40% bile and on bile esculin agar but not in 6% NaCl. No enhancement of growth is observed in 5% CO
2
. It is nongroupable with Lancefield groups A, B, C, D, F, or G antisera and is resistant to optochin and bacitracin. The organism is aflagellated and is nonmotile at both 25 and 37°C. It is Voges-Proskauer test positive. It produces leucine arylamidase and β-glucosidase but not catalase, urease, lysine decarboxylase, or ornithine decarboxylase. It hydrolyzes esculin and arginine. It utilizes glucose, lactose, salicin, sucrose, pullulan, trehalose, cellobiose, hemicellulase, mannose, maltose, and starch. 16S rRNA gene sequencing showed that there were 3.6, 3.7, 4.3, 4.7, and 5.9% differences between the 16S rRNA gene sequence of the bacterium and those of
Streptococcus gordonii
,
Streptococcus intermedius
,
Streptococcus constellatus
,
Streptococcus sanguis
, and
Streptococcus anginosus
, respectively. The G+C content of it (mean ± standard deviation) was 53.0% ± 2.9%. Based on phylogenetic affiliation, it belongs to the mitis or anginosus group of
Streptococcus
. For these reasons a new species,
Streptococcus sinensis
sp. nov., is proposed, for which HKU4 is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an emerging cause of infective endocarditis.
Temperature-Mediated Heteroduplex Analysis Performed by Using Denaturing High-Performance Liquid Chromatography To Identify Sequence Polymorphisms in
Mycobacterium tuberculosis
Complex Organisms
Authors: Cooksey Robert C. , Morlock Glenn P. , Holloway Brian P. , Limor Josef , Hepburn Michael 
Published: July 2002

ABSTRACT

PCR products containing sequence polymorphisms were prepared from six mycobacterial genes, denatured, mixed with reference PCR products, and reannealed; the mixtures were then examined with a denaturing high-performance liquid chromatography system (WAVE) equipped with a temperature-controlled alkalated polystyrene divinyl benzene column. Mismatching of bases in heteroduplexes of the PCR products causes elution patterns of the DNA from the column to be altered. The six mycobacterial genes studied were
oxyR
, in which a specific polymorphism (G
1031
A) is found only in certain species of the
Mycobacterium tuberculosis
complex, and five genes in which mutations associated with antituberculosis drug resistance have been found. The resistance genes (with affected drug and PCR product sizes given parenthetically) were
rpoB
(rifampin; 258 bp),
katG
(isoniazid; 205 bp),
pncA
(pyrazinamide; 579 bp);
rpsL
(streptomycin; 196 bp), and
embB
(ethambutol; 185 bp). Elution patterns of heteroduplexes of all 20 polymorphisms studied shifted detectably at column temperatures ranging from 65.3 to 68°C and elution times of 3.5 to 6 min. These results show that temperature-mediated heteroduplex analysis is a potentially useful genotypic screen for mutations associated with antituberculosis drug resistance and for the G
1031
A polymorphism in
oxyR
. The method may allow users to detect novel as well as heterogeneous mutations without using expensive kits or detection labels.
Detection of Plasmid-Mediated AmpC β-Lactamase Genes in Clinical Isolates by Using Multiplex PCR
Authors: Pérez-Pérez F. Javier , Hanson Nancy D. 
Published: July 2002

ABSTRACTTherapeutic options for infections caused by gram-negative organisms expressing plasmid-mediated AmpC β-lactamases are limited because these organisms are usually resistant to all the β-lactam antibiotics, except for cefepime, cefpirome, and the carbapenems. These organisms are a major concern in nosocomial infections and should therefore be monitored in surveillance studies. Six families of plasmid-mediated AmpC β-lactamases have been identified, but no phenotypic test can differentiate among them, a fact which creates problems for surveillance and epidemiology studies. This report describes the development of a multiplex PCR for the purpose of identifying family-specific AmpC β-lactamase genes within gram-negative pathogens. The PCR uses six sets ofampC-specific primers resulting in amplicons that range from 190 bp to 520 bp and that are easily distinguished by gel electrophoresis.ampCmultiplex PCR differentiated the six plasmid-mediatedampC-specific families in organisms such asKlebsiella pneumoniae,Escherichia coli,Proteus mirabilis, andSalmonella entericaserovar Typhimurium. Family-specific primers did not amplify genes from the other families ofampCgenes. Furthermore, this PCR-based assay differentiated multiple genes within one reaction. In addition, WAVE technology, a high-pressure liquid chromatography-based separation system, was used as a way of decreasing analysis time and increasing the sensitivity of multiple-gene assays. In conclusion, a multiplex PCR technique was developed for identifying family-specificampCgenes responsible for AmpC β-lactamase expression in organisms with or without a chromosomal AmpC β-lactamase gene.
Efficient Particle Production by Minimal Gag Constructs Which Retain the Carboxy-Terminal Domain of Human Immunodeficiency Virus Type 1 Capsid-p2 and a Late Assembly Domain
Authors: Accola Molly A. , Strack Bettina , Göttlinger Heinrich G. 
Published: July 2002

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) Gag precursor Pr55

gag

by itself is capable of assembling into retrovirus-like particles (VLP). In the present study, we attempted to identify the minimal Gag sequences required for the formation of VLP. Our results show that about 80% of Pr55

gag

can be either deleted or replaced by heterologous sequences without significantly compromising VLP production. The smallest chimeric molecule still able to efficiently form VLP was only about 16 kDa. This minimal Gag construct contained the leucine zipper domain of the yeast transcription factor GCN4 to substitute for the assembly function of nucleocapsid (NC), followed by a P-P-P-P-Y motif to provide late budding (L) domain function, and retained only the myristylation signal and the C-terminal capsid-p2 domain of Pr55

gag

. We also show that the L domain function of HIV-1 p6

gag

is not dependent on the presence of an active viral protease and that the NC domain of Pr55

gag

is dispensable for the incorporation of Vpr into VLP.
Conserved Surface-Exposed K/R-X-K/R Motifs and Net Positive Charge on Poxvirus Complement Control Proteins Serve as Putative Heparin Binding Sites and Contribute to Inhibition of Molecular Interactions with Human Endothelial Cells: a Novel Mechanism for Evasion of Host Defense
Authors: Smith Scott A. , Mullin Nick P. , Parkinson John , Shchelkunov Sergei N. , Totmenin Alexei V. , Loparev V. N. , Srisatjaluk Ratchapin , Reynolds David N. , Keeling Kristen L. , Justus David E. , Barlow Paul N. , Kotwal Girish J. 
Published: July 2002

ABSTRACTVaccinia virus complement control protein (VCP) has been shown to possess the ability to inhibit both classical and alternative complement pathway activation. The newly found ability of this protein to bind to heparin has been shown in previous studies to result in uptake by mast cells, possibly promoting tissue persistence. It has also been shown to reduce chemotactic migration of leukocytes by blocking chemokine binding. In addition, this study shows that VCP—through its ability to bind to glycosaminoglycans (heparin-like molecules) on the surface of human endothelial cells—is able to block antibody binding to surface major histocompatibility complex class I molecules. Since heparin binding is critical for many functions of this protein, we have attempted to characterize the molecular basis for this interaction. Segments of this protein, generated by genetic engineering of the DNA encoding VCP into thePichia pastorisexpression system, were used to localize the regions with heparin binding activity. These regions were then analyzed to more specifically define their properties for binding. It was found that the number of putative binding sites (K/R-X-K/R), the overall positive charge, and the percentage of positively charged amino acids within the protein were responsible for this interaction.
Human T-Cell Lymphotropic Virus Type 1-Infected T Lymphocytes Impair Catabolism and Uptake of Glutamate by Astrocytes via Tax-1 and Tumor Necrosis Factor Alpha
Authors: Szymocha Raphaël , Akaoka Hideo , Dutuit Magali , Malcus Christophe , Didier-Bazes Marianne , Belin Marie-Françoise , Giraudon Pascale 
Published: July 2002

ABSTRACTHuman T-cell lymphotropic virus type 1 (HTLV-1) is the causative agent of a chronic progressive myelopathy called tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM). In this disease, lesions of the central nervous system (CNS) are associated with perivascular infiltration by lymphocytes. We and others have hypothesized that these T lymphocytes infiltrating the CNS may play a prominent role in TSP/HAM. Here, we show that transient contact of human or rat astrocytes with T lymphocytes chronically infected by HTLV-1 impairs some of the major functions of brain astrocytes. Uptake of extracellular glutamate by astrocytes was significantly decreased after transient contact with infected T cells, while the expression of the glial transporters GLAST and GLT-1 was decreased. In two-compartment cultures avoiding direct cell-to-cell contact, similar results were obtained, suggesting possible involvement of soluble factors, such as cytokines and the viral protein Tax-1. Recombinant Tax-1 and tumor necrosis factor alpha (TNF-α) decreased glutamate uptake by astrocytes. Tax-1 probably acts by inducing TNF-α, as the effect of Tax-1 was abolished by anti-TNF-α antibody. The expression of glutamate-catabolizing enzymes in astrocytes was increased for glutamine synthetase and decreased for glutamate dehydrogenase, the magnitudes of these effects being correlated with the level of Tax-1 transcripts. In conclusion, Tax-1 and cytokines produced by HTLV-1-infected T cells impair the ability of astrocytes to manage the steady-state level of glutamate, which in turn may affect neuronal and oligodendrocytic functions and survival.
Human Cytomegalovirus Infection of Placental Cytotrophoblasts In Vitro and In Utero: Implications for Transmission and Pathogenesis
Authors: Fisher Susan , Genbacev Olga , Maidji Ekaterina , Pereira Lenore 
Published: July 2002

ABSTRACTHuman cytomegalovirus (CMV) is the leading cause of prenatal viral infection. Affected infants may suffer intrauterine growth retardation and serious neurologic impairment. Analysis of spontaneously aborted conceptuses shows that CMV infects the placenta before the embryo or fetus. In the human hemochorial placenta, maternal blood directly contacts syncytiotrophoblasts that cover chorionic villi and cytotrophoblasts that invade uterine vessels, suggesting possible routes for CMV transmission. To test this hypothesis, we exposed first-trimester chorionic villi and isolated cytotrophoblasts to CMV in vitro. In chorionic villi, syncytiotrophoblasts did not become infected, although clusters of underlying cytotrophoblasts expressed viral proteins. In chorionic villi that were infected with CMV in utero, syncytiotrophoblasts were often spared, whereas cytotrophoblasts and other cells of the villous core expressed viral proteins. Isolated cytotrophoblasts were also permissive for CMV replication in vitro; significantly, infection subsequently impaired the cytotrophoblasts' ability to differentiate and invade. These results suggest two possible routes of CMV transmission to the fetus: (i) across syncytiotrophoblasts with subsequent infection of the underlying cytotrophoblasts and (ii) via invasive cytotrophoblasts within the uterine wall. Furthermore, the observation that CMV infection impairs critical aspects of cytotrophoblast function offers testable hypotheses for explaining the deleterious effects of this virus on pregnancy outcome.