bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strains of
Escherichia coli
O157:H7 Differ Primarily by Insertions or Deletions, Not Single-Nucleotide Polymorphisms
Authors: Kudva Indira T. , Evans Peter S. , Perna Nicole T. , Barrett Timothy J. , Ausubel Frederick M. , Blattner Frederick R. , Calderwood Stephen B. 
Published: July 2002

ABSTRACT

Escherichia coli
O157:H7 (O157) strains demonstrate varied pulsed-field gel electrophoresis patterns following
Xba
I digestion, which enable epidemiological surveillance of this important human pathogen. The genetic events underlying PFGE differences between strains, however, are not defined. We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the
Xba
I restriction enzyme sites in the genome. Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the
Xba
I sites polymorphic between strains rather than single-nucleotide polymorphisms in the
Xba
I sites themselves. These insertions and deletions were found to be uniquely localized within the regions of the genome that are specific to O157 compared to
E. coli
K-12 (O islands), suggesting that strain-to-strain variation occurs in these O islands. These results may be utilized to devise novel strain-typing tools for this pathogen.
Chemiosmotic Energy Conservation with Na
+
as the Coupling Ion during Hydrogen-Dependent Caffeate Reduction by
Acetobacterium woodii
Authors: Imkamp Frank , Müller Volker 
Published: July 2002

ABSTRACT

Cell suspensions of
Acetobacterium woodii
prepared from cultures grown on fructose plus caffeate catalyzed caffeate reduction with electrons derived from molecular hydrogen. Hydrogen-dependent caffeate reduction was strictly Na
+
dependent with a

K
m

for Na
+
of 0.38 mM; Li
+
could substitute for Na
+
. The sodium ionophore ETH2120, but not protonophores, stimulated hydrogen-dependent caffeate reduction by 280%, indicating that caffeate reduction is coupled to the buildup of a membrane potential generated by primary Na
+
extrusion. Caffeate reduction was coupled to the synthesis of ATP, and again, ATP synthesis coupled to hydrogen-dependent caffeate reduction was strictly Na
+
dependent and abolished by ETH2120, but not by protonophores, indicating the involvement of a transmembrane Na
+
gradient in ATP synthesis. The ATPase inhibitor
N
,
N
′-dicyclohexylcarbodiimide (DCCD) abolished ATP synthesis, and at the same time, hydrogen-dependent caffeate reduction was inhibited. This inhibition could be relieved by ETH2120. These experiments are fully compatible with a chemiosmotic mechanism of ATP synthesis with Na
+
as the coupling ion during hydrogen-dependent caffeate reduction by
A
.
woodii
.
Evolutionary Analysis by Whole-Genome Comparisons
Authors: Bansal Arvind K. , Meyer Terrance E. 
Published: July 2002

ABSTRACTA total of 37 complete genome sequences of bacteria, archaea, and eukaryotes were compared. The percentage of orthologous genes of each species contained within any of the other 36 genomes was established. In addition, the mean identity of the orthologs was calculated. Several conclusions result: (i) a greater absolute number of orthologs of a given species is found in larger species than in smaller ones; (ii) a greater percentage of the orthologous genes of smaller genomes is contained in other species than is the case for larger genomes, which corresponds to a larger proportion of essential genes; (iii) before species can be specifically related to one another in terms of gene content, it is first necessary to correct for the size of the genome; (iv) eukaryotes have a significantly smaller percentage of bacterial orthologs after correction for genome size, which is consistent with their placement in a separate domain; (v) the archaebacteria are specifically related to one another but are not significantly different in gene content from the bacteria as a whole; (vi) determination of the mean identity of all orthologs (involving hundreds of gene comparisons per genome pair) reduces the impact of errors in misidentification of orthologs and to misalignments, and thus it is far more reliable than single gene comparisons; (vii) however, there is a maximum amount of change in protein sequences of 37% mean identity, which limits the use of percentage sequence identity to the lower taxa, a result which should also be true for single gene comparisons of both proteins and rRNA; (viii) most of the species that appear to be specifically related based upon gene content also appear to be specifically related based upon the mean identity of orthologs; (ix) the genes of a majority of species considered in this study have diverged too much to allow the construction of all-encompassing evolutionary trees. However, we have shown that eight species of gram-negative bacteria, six species of gram-positive bacteria, and eight species of archaebacteria are specifically related in terms of gene content, mean identity of orthologs, or both.
Firm but Slippery Attachment of
Deinococcus geothermalis
Authors: Kolari M. , Schmidt U. , Kuismanen E. , Salkinoja-Salonen M. S. 
Published: July 2002

ABSTRACT

Bacterial biofilms impair the operation of many industrial processes.
Deinococcus geothermalis
is efficient primary biofilm former in paper machine water, functioning as an adhesion platform for secondary biofilm bacteria. It produces thick biofilms on various abiotic surfaces, but the mechanism of attachment is not known. High-resolution field-emission scanning electron microscopy and atomic force microscopy (AFM) showed peritrichous adhesion threads mediating the attachment of
D. geothermalis
E50051 to stainless steel and glass surfaces and cell-to-cell attachment, irrespective of the growth medium. Extensive slime matrix was absent from the
D. geothermalis
E50051 biofilms. AFM of the attached cells revealed regions on the cell surface with different topography, viscoelasticity, and adhesiveness, possibly representing different surface layers that were patchily exposed. We used oscillating probe techniques to keep the tip-biofilm interactions as small as possible. In spite of this, AFM imaging of living
D. geothermalis
E50051 biofilms in water resulted in repositioning but not in detachment of the surface-attached cells. The irreversibly attached cells did not detach when pushed with a glass capillary but escaped the mechanical force by sliding along the surface. Air drying eliminated the flexibility of attachment, but it resumed after reimmersion in water. Biofilms were evaluated for their strength of attachment.
D. geothermalis
E50051 persisted 1 h of washing with 0.2% NaOH or 0.5% sodium dodecyl sulfate, in contrast to biofilms of
Burkholderia cepacia
F28L1 or the well-characterized biofilm former
Staphylococcus epidermidis
O-47.
Deinococcus radiodurans
strain DSM 20539
T
also formed tenacious biofilms. This paper shows that
D. geothermalis
has firm but laterally slippery attachment not reported before for a nonmotile species.
Improved Detection of Amphotericin B-Resistant Isolates of
Candida lusitaniae
by Etest
Authors: Peyron Florence , Favel Anne , Michel-Nguyen Annie , Gilly Magali , Regli Patrick , Bolmström Anne 
Published: July 2002

ABSTRACT

Both intrinsic and acquired resistance to amphotericin B have been documented for
Candida lusitaniae
. Amphotericin B remains the drug of choice for many critical fungal infections, and the detection of resistance is essential to monitor treatment effectively. The limitations of the National Committee for Clinical Laboratory Standards (NCCLS) reference methodology for detection of amphotericin B resistance are well documented, and several alternative methods have been proposed. Etest assays with RPMI and antibiotic medium 3 (AM3) agar were compared to the NCCLS M27-A broth macrodilution method using AM3 for amphotericin B resistance testing with 49 clinical isolates of
C. lusitaniae
. The panel included nine isolates with known or presumed resistance to amphotericin B on the basis of in vivo and/or in vitro data. The distribution of amphotericin B MICs by Etest with RPMI ranged from 0.032 to 16 μg/ml and was bimodal. All of the putatively resistant isolates were inhibited by amphotericin B at ≥0.38 μg/ml and could be categorized as resistant using this breakpoint. Etest with AM3 yielded a broader amphotericin B MIC range (0.047 to 32 μg/ml), and there were six putatively resistant isolates for which MICs were >1 μg/ml. The separation of putatively susceptible and resistant isolates was less obvious. Broth macrodilution with AM3 generated a unimodal distribution of MICs (ranging from 0.032 to 2 μg/ml) and failed to discriminate most of the putatively resistant isolates at both 24 and 48 h. Etest using RPMI and, to a lesser extent, using AM3 provided better discrimination between amphotericin B-resistant and -susceptible isolates of
C. lusitaniae
.
Evaluation of Pulsed-Field Gel Electrophoresis in Epidemiological Investigations of Meningococcal Disease Outbreaks Caused by
Neisseria meningitidis
Serogroup C
Authors: Popovic Tanja , Schmink Susanna , Rosenstein Nancy A. , Ajello Gloria W. , Reeves Michael W. , Plikaytis Brian , Hunter Susan B. , Ribot Efrain M. , Boxrud David , Tondella Maria L. , Kim Chung , Noble Corie , Mothershed Elizabeth , Besser John , Perkins Bradley A. 
Published: July 2002

ABSTRACT

Since 1990, the frequency of
Neisseria meningitidis
serogroup C (NMSC) outbreaks in the United States has increased. Based on multilocus enzyme electrophoresis (MEE), the current molecular subtyping standard, most of the NMSC outbreaks have been caused by isolates of several closely related electrophoretic types (ETs) within the ET-37 complex. We chose 66 isolates from four well-described NMSC outbreaks that occurred in the United States from 1993 to 1995 to evaluate the potential of pulsed-field gel electrophoresis (PFGE) to identify outbreak-related isolates specific for each of the four outbreaks and to differentiate between them and 50 sporadic isolates collected during the outbreak investigations or through active laboratory-based surveillance from 1989 to 1996. We tested all isolates collected during the outbreak investigations by four other molecular subtyping methods: MEE, ribotyping (
Cla
I), random amplified polymorphic DNA assay (two primers), and serotyping and serosubtyping. Among the 116 isolates, we observed 11 clusters of 39
Nhe
I PFGE patterns. Excellent correlation between the PFGE and the epidemiological data was observed, with an overall sensitivity of 85% and specificity of 71% at the 95% pattern relatedness breakpoint using either 1.5 or 1.0% tolerance. For all four analyzed outbreaks, PFGE would have given public health officials additional support in declaring an outbreak and making appropriate public health decisions.
International Multicenter Evaluation of Latex Agglutination Tests for Identification of
Staphylococcus aureus
Authors: van Griethuysen Arjanne , Bes Michèle , Etienne Jerome , Zbinden Reinhard , Kluytmans Jan 
Published: July 2002

ABSTRACT

A newly marketed rapid agglutination kit for the identification of
Staphylococcus aureus
, Slidex Staph Plus (bioMérieux), was compared to Staphaurex Plus (Murex Diagnostics) and Pastorex Staph-Plus (Sanofi Diagnostics Pasteur). The study took place in three clinical microbiology laboratories in three different European countries. A total of 892 staphylococcal isolates, including 278 methicillin-sensitive
S. aureus
(MSSA) isolates, 171 methicillin-resistant
S. aureus
(MRSA) isolates, and 443 coagulase-negative staphylococcal isolates, were analyzed. The sensitivities (MSSA/MRSA) and specificities, respectively, were 98.2% (98.9%/97.1%) and 98.9% for Slidex Staph Plus, 98.2% (98.2%/98.2%) and 96.2% for Staphaurex Plus, and 98.7% (98.6%/98.8%) and 95.7% for Pastorex Staph Plus. The specificity of the Slidex Staph Plus kit was statistically significantly higher than the specificities of Staphaurex Plus and Pastorex Staph-Plus. The Slidex Staph Plus is a very reliable test for the identification of
S. aureus
.
Value of Throat Swab in Diagnosis of Melioidosis
Authors: Wuthiekanun Vanaporn , Suputtamongkol Yupin , Simpson A. J. H. , Kanaphun Panida , White N. J. 
Published: July 2002

ABSTRACT
Throat swab (TS) cultures were performed for 1,011 patients with melioidosis and 3,524 healthy subjects or patients with other diseases. The specificity of TS culture for the diagnosis of melioidosis was 100%, and the overall sensitivity was 36% (24% for sputum-negative patients and 79% for sputum-positive patients). Direct plating of the TS specimen on Ashdown's medium was rapid (colonies were usually evident within 24 h) but only 63% sensitive compared to the results of primary culture in a selective broth. A throat swab should be cultured in all cases of suspected melioidosis.
Emergence of G9 P[6] Human Rotaviruses in Argentina: Phylogenetic Relationships among G9 Strains
Authors: Bok Karin , Palacios Gustavo , Sijvarger Karina , Matson David , Gomez Jorge 
Published: July 2002

ABSTRACT
Because rotavirus diarrhea can be reduced through vaccination and because current vaccine candidates provide protection against only the most common G antigenic types (G1 to G4), detection of uncommon G types is one of the main goals of rotavirus surveillance. After a 2-year nationwide rotavirus surveillance study in Argentina concluded, surveillance was continued and an increase of G9 prevalence in several Argentine cities was detected. During this period G9 strains predominated in the south, and a gradient of decreasing G9 prevalence was observed from south to north (41 to 0%). Sequence analysis of gene 9, encoding the G antigen, showed that Argentine strains cluster with most G9 isolates from other countries, showing less than 2% nucleotide divergence among them, but are distinctive from them in that they present some unique amino acid changes. Our results agree with reports of increased G9 prevalence in other parts of the world, suggesting the need to incorporate G9 into candidate rotavirus vaccines.
Isolation and Characterization of Polymorphic DNA from
Entamoeba histolytica
Authors: Zaki Mehreen , Clark C. Graham 
Published: July 2002

ABSTRACT

An important gap in our understanding of the epidemiology of amebiasis is what determines the outcome of
Entamoeba histolytica
infections. To investigate the possible existence of invasive and noninvasive strains as one factor, the ability to differentiate individual isolates of
E. histolytica
is necessary. Two new loci containing internal repeats, locus 1-2 and locus 5-6, have been isolated. Each contains a single repeat block with two types of related direct repeats arranged in tandem. Southern blot analysis suggests that both loci are multicopy and may themselves be arranged in tandem arrays. Three other previously reported, internally repetitive loci containing at least two repeat blocks each with one or more related repeat units were also investigated. PCR was used to study polymorphism at each of these loci, which was detected to various degrees in each case. Variation was seen in the total number of bands obtained per isolate and their sizes. Nucleotide sequence comparison of loci 1-2 and 5-6 in five axenic isolates revealed differences in the number of repeat units, which correlated with the observed PCR product size variation, and in repeat sequence. Use of multiple loci collectively allowed differentiation of a majority of the 13 isolates studied, and we believe that these loci have the potential to be used as polymorphic molecular markers for investigating the epidemiology of
E. histolytica
and the potential existence of genetically distinct invasive and noninvasive strains.
Detection and Culture of
Bartonella quintana, Serratia marcescens
, and
Acinetobacter
spp. from Decontaminated Human Body Lice
Authors: La Scola Bernard , Fournier Pierre-Edouard , Brouqui Philippe , Raoult Didier 
Published: July 2002

ABSTRACT

As part of a survey for trench fever among homeless people in Marseilles, France, we attempted isolation of
Bartonella quintana
from body lice. A decontamination protocol of immersion in 70% ethanol with 0.2% iodine was devised and was tested with a laboratory colony of body lice. Lice which had been experimentally contaminated with either
Escherichia coli, Staphylococcus epidermidis
, or
Acinetobacter
spp. were successfully decontaminated, and this process did not prevent the culture of
B. quintana
from these lice. One hundred sixty-one lice obtained from homeless patients were studied by the protocol.
B. quintana
was isolated on axenic medium from 15 of 161 body lice and was detected in 41 of 161 lice by PCR.
Acinetobacter
spp. and
Serratia marcescens
were also isolated from body lice. The sensitivities of PCR and culture of
B. quintana
were 98 and 36%, respectively. These procedures may be useful for epidemiologic studies of trench fever and for the recovery of strains for characterization and comparison.
Development of Molecular Methods for Identification of
Schizophyllum commune
from Clinical Samples
Authors: Buzina Walter , Lang-Loidolt Doris , Braun Hannes , Freudenschuss Kurt , Stammberger Heinz 
Published: July 2002

ABSTRACT

In the last 50 years, to our knowledge, only 16 cases of diseases caused by
Schizophyllum commune
in humans have been reported. Within only 6 months, we found four isolates of this basidiomycetous fungus, obtained from patients suffering from chronic sinusitis. The cultures of the isolated fungi showed neither clamp connections nor fruiting bodies (basidiocarps), which are distinctive features for
S. commune
, but fast-growing cottony white mycelium only. This was harvested, and DNA was extracted. The internal transcribed spacer region of the ribosomal DNA (rDNA) was amplified with fungus-specific primers, and the PCR products were sequenced. Two strains of
S. commune
, collected from branches of a European hornbeam (
Carpinus betulus
) and a tree of heaven (
Ailanthus altissima
), respectively; four specimens from the herbarium of the Institute of Botany, Karl-Franzens-University Graz; and two strains from internationally known culture collections (CBS 340.81 [ATCC 44201] and CBS 405.96) were investigated in the same way. The sequence data of all strains were compared and showed homology of over 99% in this 660-bp-long fragment of rDNA. With these results, a map of restriction enzyme cutting sites and a primer set specific for
S. commune
were created for reliable identification of this human pathogenic fungus.
Comparative Evaluation of Penicillin, Ampicillin, and Imipenem MICs and Susceptibility Breakpoints for Vancomycin-Susceptible and Vancomycin-Resistant
Enterococcus faecalis
and
Enterococcus faecium
Authors: Weinstein Melvin P. 
Published: July 2002

ABSTRACT

Although imipenem has in vitro activity against
Enterococcus faecalis
and Food and Drug Administration-approved indications for treatment of infections caused by this microorganism, there are no NCCLS guidelines for susceptibility testing of imipenem versus enterococci. Therefore, the in vitro activities of penicillin, ampicillin, imipenem, and vancomycin against 201 blood isolates of
E. faecalis
and 24 blood isolates of
Enterococcus faecium
were compared. The susceptibility of isolates to penicillin or ampicillin accurately predicted the in vitro activity of imipenem. Since the susceptibility of enterococci to imipenem can be predicted by the results obtained by testing of penicillin or ampicillin, testing of imipenem by clinical laboratories probably is not necessary.
Development and Evaluation of Real-Time PCR-Based Fluorescence Assays for Detection of
Chlamydia
pneumoniae
Authors: Tondella Maria Lucia C. , Talkington Deborah F. , Holloway Brian P. , Dowell Scott F. , Cowley Karyn , Soriano-Gabarro Montse , Elkind Mitchell S. , Fields Barry S. 
Published: July 2002

ABSTRACT

Chlamydia
pneumoniae
is an important respiratory pathogen recently associated with atherosclerosis and several other chronic diseases. Detection of
C. pneumoniae
is inconsistent, and standardized PCR assays are needed. Two real-time PCR assays specific for
C. pneumoniae
were developed by using the fluorescent dye-labeled TaqMan probe-based system. Oligonucleotide primers and probes were designed to target two variable domains of the
ompA
gene, VD2 and VD4. The limit of detection for each of the two PCR assays was 0.001 inclusion-forming unit. Thirty-nine
C. pneumoniae
isolates obtained from widely distributed geographical areas were amplified by the VD2 and VD4 assays, producing the expected 108- and 125-bp amplification products, respectively. None of the
C. trachomatis
serovars,
C. psittaci
strains, other organisms, or human DNAs tested were amplified. The amplification results of the newly developed assays were compared to the results of culturing and two nested PCR assays, targeting the 16S rRNA and
ompA
genes. The assays were compared by testing
C. pneumoniae
purified elementary bodies, animal tissues, 228 peripheral blood mononuclear cell (PBMC) specimens, and 179 oropharyngeal (OP) swab specimens obtained from ischemic stroke patients or matched controls. The real-time VD4 assay and one nested PCR each detected
C. pneumoniae
in a single, but different, PBMC specimen. Eleven of 179 OP specimens (6.1%) showed evidence of the presence of
C. pneumoniae
in one or more tests. The real-time VD4 assay detected the most positive results of the five assays. We believe that this real-time PCR assay offers advantages over nested PCR assays and may improve the detection of
C. pneumoniae
in clinical specimens.
PCR-Based Diagnosis of Acute and Chronic Cutaneous Leishmaniasis Caused by
Leishmania
(
Viannia
)
Authors: Weigle Kristen A. , Labrada Luz Angela , Lozano Caterin , Santrich Cecilia , Barker Douglas C. 
Published: July 2002

ABSTRACT

We evaluated PCR methods for diagnosis of acute and chronic cutaneous leishmaniasis (CL) in an area of Colombia where
Leishmania
(
Viannia
) is endemic. The PCR method specifically amplified whole linearized minicircle kinetoplast DNA (kDNA) of the
Leishmania
subgenus
Viannia
from biopsy lysates. PCR products were detected in agarose gels. For 255 acute cases, this PCR method had greater sensitivity (75.7%) than each conventional method, i.e., microscopic examination of Giemsa-stained lesion scraping (46.7%), biopsy culture (55.3%), aspirate culture (46.3%), and the conventional methods combined (70.2%). Among 44 cases of chronic CL, amplification of biopsy DNA was more sensitive (45.5%) than the individual (4.5 to 27.7%) and combined (27.3%) conventional methods. The detection of kDNA in biopsies from chronic lesions was enhanced by a chemiluminescent dot blot hybridization, which produced a sensitivity of 65.8% when alone and 90.9% when in combination with DNA extraction of biopsy lysates (
P
< 0.001). Three biopsies from 84 skin lesions of other etiologies were falsely positive by PCR (specificity, 96.4%). PCR detected kDNA more frequently in biopsies (detection level, 83.9%) than in aspirates (74.7%) from 103 cases of acute CL. Among aspirates from 53 chronic cases of CL, the alternative methods, DNA extraction and hybridization, increased sensitivity from 41.5 to 56.6% (
P
> 0.05). This enhanced PCR method in chronic biopsies was so much more sensitive than conventional methods that it should be considered the preferred diagnostic method for chronic CL. These findings support the appropriate incorporation of PCR into diagnostic strategies for cutaneous leishmaniasis.
Septicemia Due to
Pasteurella pneumotropica
: 16S rRNA Sequencing for Diagnosis Confirmation
Authors: Frebourg Noëlle Barbier , Berthelot Gilles , Hocq Raymond , Chibani Ahmed , Lemeland Jean-François 
Published: July 2002

ABSTRACT

Bacteremia due to
Pasteurella pneumotropica
occurs infrequently. We report a case of septicemia in a 72-year-old woman who had no underlying illness. The microorganism was isolated from 10 blood cultures and identified by conventional and molecular methods. This is the first reported case of
P. pneumotropica
septicemia in an immunocompetent patient. The history of
P. pneumotropica
diseases in animals and humans and their varied clinical features are reviewed.