bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formate-Dependent Growth and Homoacetogenic Fermentation by a Bacterium from Human Feces: Description of
Bryantella formatexigens
gen. nov., sp. nov
Authors: Wolin Meyer J. , Miller Terry L. , Collins Matthew D. , Lawson Paul A. 
Published: October 2003

ABSTRACT

Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at −76°C. 16S rRNA gene sequencing identifies it as a distinct line within the
Clostridium coccoides
supra-generic rRNA grouping. We propose naming it
Bryantella formatexigens
gen. nov., sp. nov.
Multiplex Real-Time PCR Method To Identify Shiga Toxin Genes
stx1
and
stx2
and
Escherichia coli
O157:H7/H
−
Serotype
Authors: Jinneman Karen C. , Yoshitomi Ken J. , Weagant Stephen D. 
Published: October 2003

ABSTRACT

A multiplex real-time PCR method to simultaneously detect the
stx1
and
stx2
genes of Shiga toxin-producing
Escherichia coli
and a unique conserved single-nucleotide polymorphism in the
E. coli
O157:H7/H
−
uidA
gene has been developed. There is more than 98.6% sensitivity and 100% specificity for all three gene targets based on a panel of 138 isolates. The PCR efficiencies were ≥1.89, and as few as 6 CFU/reaction could be detected.
The High Salt Requirement of the Moderate Halophile
Chromohalobacter salexigens
DSM3043 Can Be Met Not Only by NaCl but by Other Ions
Authors: O'Connor Kathleen , Csonka Laszlo N. 
Published: October 2003

ABSTRACT

The growth rate of
Chromohalobacter salexigens
DSM 3043 can be stimulated in media containing 0.3 M NaCl by a 0.7 M concentration of other salts of Na
+
, K
+
, Rb
+
, or NH
4
+
, Cl
−
, Br
−
, NO
3
−
, or SO
4
2−
ions. To our knowledge, growth rate stimulation by a general high ion concentration has not been reported for any organism previously.
Distribution of Bovine Herpesvirus Type 5 DNA in the Central Nervous Systems of Latently, Experimentally Infected Calves
Authors: Vogel Fernanda Silveira Flôres , Caron Luizinho , Flores Eduardo Furtado , Weiblen Rudi , Winkelmann Evandro Reinoldo , Mayer Sandra Vanderli , Bastos Reginaldo Gaspar 
Published: October 2003

ABSTRACTBovine herpesvirus type 5 (BHV-5) is an alphaherpesvirus associated with meningoencephalitis, a disease highly prevalent in South America. In this study, we investigated the distribution of BHV-5 DNA in the brains of latently, experimentally infected calves by using a PCR for the glycoprotein B gene. Twelve calves inoculated intranasally with a Brazilian BHV-5 isolate were divided into two groups: group A calves (n= 4) were euthanized 55 days postinoculation (p.i.) for tissue collection; group B calves (n= 8) were submitted to dexamethasone administration at day 60 p.i. for reactivation of latent infection and were euthanized 50 days later. Latent infection was reactivated in all group B calves, as demonstrated by virus isolation from nasal secretions and/or seroconversion. Three calves developed neurological disease and died or were euthanized in extremis. For group A calves, viral DNA was consistently detected in the trigeminal ganglia (4/4), midbrain (4/4), thalamus (4/4), and olfactory cortex (4/4) and less frequently in the pons (3/4), cerebellum (3/4), anterior cerebral cortex (2/4), and olfactory bulb (2/4). For calves previously submitted to reactivation (group B), viral DNA was detected with roughly the same frequency in the same areas as for the group A calves. In addition, viral DNA was detected in the posterior (5/5) and dorso-lateral cortex (3/5). All DNA-positive tissues were negative for infectivity and viral antigens. These results demonstrated that latent BHV-5 DNA is present in several areas of the brain during latent infection and that virus reactivation may result in the establishment of latent infection in additional sites of the brain.
Etiology of Acute Diarrhea in Adults in Southwestern Nigeria
Authors: Okeke Iruka N. , Ojo Oladipupo , Lamikanra Adebayo , Kaper James B. 
Published: October 2003

ABSTRACT

Stool specimens from 113 adult outpatients with diarrhea in southwestern Nigeria and 63 controls were examined for bacterial and parasitic enteric pathogens. Enterohemorrhagic
Escherichia coli
(EHEC) (
P
< 0.02), enteroaggregative
E. coli
(EAEC) (
P
< 0.02), and
Entamoeba histolytica
(
P
< 0.0002) were significantly associated with diarrhea.
Salmonella
,
Shigella
, nontoxigenic
Vibrio cholerae
, other categories of diarrheagenic
E. coli
, as well as a variety of helminths were recovered more frequently from the stools of patients than from the stools of controls but did not show a significant association with disease. Multiple pathogens were recovered from 36.3% of specimens, and bloody diarrhea was commonly associated with
E. histolytica
and diarrheagenic
E. coli
infections. The majority of EHEC isolates were non-O157 strains that carried the
stx
2
gene. Of the 23 EHEC-infected patients, 12 (52.2%) presented during the 10th week of the study. EHEC strains isolated within this cluster were more likely to hybridize with the enterohemolysin gene probe, to be nonmotile and sorbitol positive, and to fail to agglutinate O157 antisera. Pulsed-field gel electrophoresis demonstrated that the only strains with
Xba
I profiles that occurred more than once were isolated during the 10th and 11th weeks of the study, suggesting an outbreak. The study has demonstrated that
E. histolytica
, EHEC, and EAEC are important diarrheal pathogens within the study area and that sporadic and epidemic EHEC infections occur in developing as well as developed countries. Routine surveillance for diarrheagenic
E. coli
, even only at the tertiary-care level, would be useful in identifying outbreaks and assist in identifying environmental reservoirs and transmission routes.
Molecular Detection and Identification of Influenza Viruses by Oligonucleotide Microarray Hybridization
Authors: Sengupta Srikumar , Onodera Kenji , Lai Alexander , Melcher Ulrich 
Published: October 2003

ABSTRACT
Microarrays of virus-specific oligonucleotides may provide a method of screening samples for the presence or absence of a large variety of viruses simultaneously. Influenza viruses are ideal for evaluating such microarrays because of their genetic and host diversity, and the availability of an extensive sequence database. A collection of 476 influenza virus-specific oligonucleotides was spotted onto glass slides as probes. Viral RNAs were reverse transcribed and amplified by PCR, and the products were labeled with cyanine dyes. The presence of viruses and their identities were determined by hybridization. The fluorescence intensities of oligonucleotide spots were highly reproducible within each slide and satisfactorily proportional between experiments. However, the intensities of probe spots completely complementary to target sequences varied from background to saturation. The variations did not correlate with base composition, nucleotide sequence, or internal secondary structures. Therefore, thresholds for determining whether hybridization to a spot should be judged as positive were assigned individually. Considering only positive spots from probes predicted to be monospecific for influenza virus species, subtype, host source, or gene segment, this method made correct identifications at the species, hemagglutinin subtype, and gene segment levels. Monospecific neuraminidase (NA) subtype probes were insufficiently diverse to allow confident NA subtype assignment. Incorporating positive spots from polyspecific probes into the identification scheme gave similar results. Overall, the results demonstrate the potential of microarray-based oligonucleotide hybridization for multiple virus detection.
Contribution of the PlateliaCandida-Specific Antibody and Antigen Tests to Early Diagnosis of SystemicCandida tropicalisInfection in Neutropenic Adults
Authors: Sendid Boualem , Caillot Denis , Baccouch-Humbert Bénédicte , Klingspor Lena , Grandjean Monique , Bonnin Alain , Poulain Daniel 
Published: October 2003

ABSTRACTThe PlateliaCandida-specific antigen and antibody assays (Bio-Rad Laboratories) were used to test serial serum samples from seven neutropenic adult patients with hematological malignancies who had developed systemicCandida tropicalisinfections. The diagnosis of candidiasis was based on a positive blood culture (all seven patients) and the isolation ofC. tropicalisfrom a normally sterile site (six patients). All patients received early antifungal therapy with amphotericin B and/or an azole derivative and had successful outcomes. When the combined assays were applied to sera collected at different time points before and after the first positive blood culture, all patients tested positive. In six patients, at least one positive test was obtained with sera collected, on average, 5 days (range, 2 to 10 days) prior to the first positive blood culture, while blood cultures were constantly negative. High and persistent mannanemias were detected in all patients during the neutropenic period. In five patients, an increased antibody response was detected when the patients recovered from aplasia. Controls consisted of 48 serum samples from 12 febrile neutropenic patients with aspergillosis (n= 4), bacteremia (n= 4), or no evidence of infection (n= 4). A low level of mannanemia was detected in only one serum sample, and none showed significantCandidaantibody titers. Our data thus confirm the value of the combined detection of mannanemia and antimannan antibodies in individuals at risk of candidemia and suggest that in neutropenic patients, an approach based on the regular monitoring of both markers could contribute to the earlier diagnosis ofC. tropicalissystemic infection.
Rapid Diagnosis of Mycobacterial Infections and Quantitation of
Mycobacterium tuberculosis
Load by Two Real-Time Calibrated PCR Assays
Authors: Broccolo Francesco , Scarpellini Paolo , Locatelli Giuseppe , Zingale Anna , Brambilla Anna M. , Cichero Paola , Sechi Leonardo A. , Lazzarin Adriano , Lusso Paolo , Malnati Mauro S. 
Published: October 2003

ABSTRACT

Sensitive and specific techniques to detect and identify
Mycobacterium tuberculosis
directly in clinical specimens are important for the diagnosis and management of patients with tuberculosis (TB). We developed two real-time PCR assays, based on the IS
6110
multicopy element and on the
senX3
-
regX3
intergenic region, which provide a rapid method for the diagnosis of mycobacterial infections. The sensitivity and specificity of both assays were established by using purified DNA from 71 clinical isolates and 121 clinical samples collected from 83 patients, 20 of whom were affected by TB. Both assays are accurate, sensitive, and specific, showing a complementary pattern of
Mycobacterium
recognition: broader for the IS
6110
-based assay and restricted to the
M. tuberculosis
complex for the
senX3
-
regX3
-based assay. Moreover, the addition of a synthetic DNA calibrator prior to DNA extraction allowed us to measure the efficiency of DNA recovery and to control for the presence of PCR inhibitors. The mycobacterial burden of the clinical samples, as assessed by direct microscopy, correlates with the
M. tuberculosis
DNA load measured by the
senX3
-
regX3
-based assay. In addition, reduced levels of
M. tuberculosis
DNA load are present in those patients subjected to successful therapy, suggesting a potential use of this assay for monitoring treatment efficacy. Therefore, these assays represent a fully controlled high-throughput system for the evaluation of mycobacterial burden in clinical specimens.
Fast and Accurate Quantitative Detection of
Helicobacter pylori
and Identification of Clarithromycin Resistance Mutations in
H
.
pylori
Isolates from Gastric Biopsy Specimens by Real-Time PCR
Authors: Lascols Christine , Lamarque Dominique , Costa Jean-Marc , Copie-Bergman Christiane , Le Glaunec Jeanne-Marie , Deforges Lionel , Soussy Claude-James , Petit Jean-Claude , Delchier Jean-Charles , Tankovic Jacques 
Published: October 2003

ABSTRACT

Rapid identification of patients infected with clarithromycin-resistant
Helicobacter pylori
without the need for culture can help to avoid useless prescriptions of clarithromycin. We developed and tested a routine real-time quantitative PCR assay dedicated to that purpose. One hundred ninety-six consecutive gastric biopsy specimens were examined by culture, histology performed by a trained physician, and rapid PCR with the LightCycler apparatus. Infection was defined as (i) positivity of culture, (ii) positivity of histology, or (iii) positivity of PCR if confirmed by positivity of a concomitant indirect test (serology or urea breath test). Susceptibility to clarithromycin was tested by E-test and PCR. The prevalence of infection was 33.7% (66 of 196 samples). The sensitivities of culture, histology, and PCR were 90.9% (60 of 66 samples), 87.9% (58 of 66 samples), and 97.0% (64 of 66 samples), respectively. The specificity of PCR was 94.6% (123 of 130 samples). The linearity of the PCR results was achieved over a 6-log range of input DNA, and we were able to accurately quantify as few as 300 bacteria and to qualitatively detect as few as 30 bacteria per DNA sample. For clarithromycin susceptibility testing, there was 98.2% (55 of 56 samples) concordance between E-test and PCR. Forty-eight strains were clarithromycin susceptible, and 9 strains were clarithromycin resistant. The single discrepancy concerned a culture which was a mixture of mutant and wild type, with a susceptible-to-resistant ratio of 11.5: the resistant population was detected by E-test but not by PCR. Our PCR assay is accurate for fast detection of
H. pylori
as well as of clarithromycin resistance and is also able to objectively determine bacterial density.
Association between Handling of Pet Treats and Infection with
Salmonella enterica
Serotype Newport Expressing the AmpC β-Lactamase, CMY-2
Authors: Pitout Johann D. D. , Reisbig Mark D. , Mulvey Mike , Chui Linda , Louie Marie , Crowe Larry , Church Deirdre L. , Elsayed Sameer , Gregson Dan , Ahmed Rafiq , Tilley Peter , Hanson Nancy D. 
Published: October 2003

ABSTRACT

Resistance to the extended-spectrum cephalosporins can occur in
Salmonella
species via the production of extended-spectrum and AmpC β-lactamases. We describe human infections with
Salmonella enterica
serotype Newport phage type 14 strains resistant to ceftazidime (CAZ) and cefoxitin (FOX) related to the handling of pet treats containing dried beef. These strains were isolated from five patients in Calgary, Alberta, Canada, during 2002 and were compared to a strain cultured from a commercial pet treat present at the property of one of the patients. The strains were resistant to FOX, CAZ, cefpodoxime, ampicillin, and chloramphenicol; intermediate resistant to ceftriaxone and cefotaxime; and sensitive to the aminoglycosides, ciprofloxacin, cefepime, and imipenem. Isoelectric focusing, multiplex PCR, and sequencing of the amplicons showed that all strains produced the plasmid-encoded AmpC β-lactamase, CMY-2. Restriction analysis of plasmid DNA following transformation demonstrated that
bla
CMY-2
was encoded on an approximately 140-kb plasmid. Pulsed-field gel electrophoresis showed the human and pet treat
Salmonella
strains to be highly related. This study is the first to implicate the transfer of multidrug-resistant
Salmonella
species through the handling of commercial pet treats containing animal products. In addition to documenting the first cases of human infection caused by CMY-2-producing
S. enterica
serotype Newport strains in Canada, this study illustrates the necessity of rapid and accurate laboratory-based surveillance in the identification of novel types of antimicrobial resistance.
Restriction Fragment Length Polymorphism Analysis of Ribosomal DNA Intergenic Regions Is Useful for Differentiating Strains of
Trichophyton mentagrophytes
Authors: Mochizuki Takashi , Ishizaki Hiroshi , Barton Richard C. , Moore Mary K. , Jackson Colin J. , Kelly Steven L. , Evans E. Glyn V. 
Published: October 2003

ABSTRACT

Twenty isolates of
Tricophyton mentagrophytes
var.
mentagrophytes
and 47 isolates of
T. mentagrophytes
var.
interdigitale
, identified by morphological characteristics, were screened by restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified internal transcribed spacer (ITS) region of ribosomal DNA (rDNA). Sixty isolates (14 of 20
T. mentagrophytes
var.
mentagrophytes
isolates and 46 of 47
T. mentagrophytes
var.
interdigitale
isolates) shared an identical ITS RFLP profile and were further investigated by using a probe targeted to the rDNA nontranscribed spacer (NTS) region. Polymorphisms were observed in the NTS regions of both
T. mentagrophytes
var.
mentagrophytes
and
T. mentagrophytes
var.
interdigitale
isolates. Twenty-three individual RFLP patterns (DNA types P-1 to P-12 and A-1 to A-11) were recognized and divided into two groups depending on the presence (P) or absence (A) of a 2.5-kb band, which correlated to a large extent with the morphological variety. Eleven of 14
T. metagrophytes
var.
mentagrophytes
isolates were A types, and all of the 46
T. mentagrophytes
var.
interdigitale
isolates were P types. A majority of strains (23 of 60 [38.3%]) were characterized by one RFLP pattern (pattern P-1), and eight types (P-1 to P-6, P-8, and P-9) accounted for 75% (45 of 60) of all strains, including all of the
T. mentagrophytes
var.
interdigitale
isolates. The remaining 15 types were represented by one only isolate and included all of the
T. mentagrophytes
var.
mentagrophytes
isolates. We conclude that RFLP analysis of the rDNA NTS region is a valuable technique for differentiation of
T. mentagrophytes
strains. Furthermore, by use of this method, there appears to be a greater degree of diversity among
T. mentagrophytes
var.
mentagrophytes
isolates than among
T. mentagrophytes
var.
interdigitale
isolates.
Effect of Duplicate Isolates of Methicillin-Susceptible and Methicillin-ResistantStaphylococcus aureuson Antibiogram Data
Authors: Horvat Rebecca T. , Klutman Neil E. , Lacy Melinda K. , Grauer Dennis , Wilson Marsha 
Published: October 2003

ABSTRACTDuplicateStaphylococcus aureusisolates were analyzed to determine the impact of multiple isolates from the same patient on annual antibiogram data. During a 6-year period (1996 to 2001), 3,227 patients with 4,844S. aureusisolates were evaluated. A total of 39% of patients with methicillin-resistantS. aureus(MRSA) (n= 860) and 23% of patients with methicillin-susceptibleS. aureus(MSSA) (n= 2,367) infections had duplicate isolates. Cumulative data show that 91% of the patients during this 6-year period with duplicate isolates (2 to 13 duplicates/year) did not switch between MSSA and MRSA but retained the originalS. aureusstrain whether it was MSSA or MRSA. Rates of MRSA were calculated for each year by using all isolates and then eliminating duplicates. The impact of duplicate MRSA and MSSA isolates was evaluated by using the ratio of isolates per patient such that ratios of >1.0 indicate >1 isolate per patient. The 6-year ratio for MRSA was 1.90 isolates/patient, and the ratio for MSSA was 1.35. A significant difference (P< 0.05) was noted in the MRSA rates in 4 of 6 years when duplicate isolates were removed. Common phenotypic antibiogram patterns were compared for all MRSA isolates during the 6-year period, and 64% were of a single antibiogram phenotype. Eighty-eight percent of patients with duplicate MRSA isolates had phenotypically identical multiple isolates. The rate of MRSA differs when duplicate isolates are removed from the antibiogram data.
emm
Typing of M Nontypeable Invasive Group A Streptococcal Isolates in Israel
Authors: Moses Allon E. , Hidalgo-Grass Carlos , Dan-Goor Mary , Jaffe Joseph , Shetzigovsky Ilanit , Ravins Miriam , Korenman Zinaida , Cohen-Poradosu Ronit , Nir-Paz Ran 
Published: October 2003

ABSTRACT

We performed
emm
typing of M nontypeable invasive group A streptococcal (GAS) isolates collected in a prospective population-based study in Israel. One hundred twenty of 131 isolates (92%) had
emm
sequences compatible with GAS, consisting of 51 different
emm
types. Eleven isolates were found to be group G streptococcus. Of the 120 isolates, 55 (46%) belonged to 32 types for which there were no typing sera available in the Streptococcal Reference Laboratory in Israel. The other 65 (64%) isolates, consisting of 19 types, had sera available and therefore could have been serotyped. Forty-three isolates had T and
emm
types which were not correlated according to standard M-typing protocols and were therefore missed. The principal effect of
emm
typing was the addition of 32 types not previously identified in Israel and the discovery of new associations between
emm
and T types.
emm
typing did not significantly change the proportion of M types; the five most common types were 3, 28, 2, 62, and 41. Twenty different types comprised 80% of all isolates. No new
emm
sequences were discovered.
emm
typing emphasized the unusually low incidence of M1 strains causing severe disease in Israel. As serological typing of GAS becomes more problematic due to lack of sera and the appearance of new
emm
types, reference laboratories should replace M typing with
emm
sequence typing. Development of a GAS vaccine relies on the
emm
type distributions in different geographical locations. In our study, 7% of isolates (types 41 and 62) are not included in a 26-valent vaccine that is being studied.
Decreased Vancomycin Susceptibility of Coagulase-Negative Staphylococci in a Neonatal Intensive Care Unit: Evidence of Spread of
Staphylococcus warneri
Authors: Center Kimberly J. , Reboli Annette C. , Hubler Robin , Rodgers Gail L. , Long Sarah S. 
Published: October 2003

ABSTRACT

Coagulase-negative staphylococci (CoNS) are important pathogens in premature neonates; decreasing glycopeptide susceptibility has been observed among these isolates. The epidemiology of colonization with CoNS, the organisms' vancomycin susceptibilities, and genetic relatedness were studied over 6 months in a tertiary-care neonatal unit. A total of 321 isolates of CoNS were isolated. Seventy-five percent of the infants were colonized at admission, and virtually all were colonized thereafter. Common species were
Staphylococcus epidermidis
(69%),
S. warneri
(12%),
S. haemolyticus
(9.7%), and
S. hominis
(5.6%). A total of 3.9% of CoNS isolates had decreased vancomycin susceptibility (DVS) (MICs > 2.0 μg/ml); isolate recovery was associated with a stay in a neonatal intensive care unit for >28 days (
P
= 0.039), vancomycin exposure (
P
= 0.021), and
S. warneri
colonization (
P
< 0.0001). Nine of 12 (75%) CoNS with DVS were
S. warneri
, had enhanceable high-level resistance in vitro, were indistinguishable or closely related by pulsed-field gel electrophoresis, and were different from 29 vancomycin-susceptible
S. warneri
isolates. Epidemiological analysis suggested unsuspected nosocomial spread. Species determination in certain settings may aid in the understanding of emerging nosocomial problems.