bluuebunny/crossref_metadata_2025_split huggingface dataset:
Existence of a True Phosphofructokinase in
Bacillus sphaericus
: Cloning and Sequencing of the
pfk
Gene
Authors: Alice Alejandro F. , Pérez-Martínez Gaspar , Sánchez-Rivas Carmen 
Published: November 2002

ABSTRACT

Some strains of
Bacillus sphaericus
are entomopathogenic to mosquito larvae, which transmit diseases, such as filariasis and malaria, affecting millions of people worldwide. This species is unable to use hexoses and pentoses as unique carbon sources, which was proposed to be due to the lack of glycolytic enzymes, such as 6-phosphofructokinase (PFK). In this study, PFK activity was detected and the
pfk
gene was cloned and sequenced. Furthermore, this gene was shown to be present in strains belonging to all the homology groups of this heterogeneous species, in which PFK activity was also detected. A careful sequence analysis revealed the conservation of different catalytic and regulatory residues, as well as the enzyme's phylogenetic affiliation with the family of allosteric ATP-PFK enzymes.
Quantitative Determination of Bile Salt Hydrolase Activity in Bacteria Isolated from the Small Intestine of Chickens
Authors: Knarreborg Ane , Engberg Ricarda M. , Jensen Søren K. , Jensen Bent B. 
Published: November 2002

ABSTRACT

A quantitative assay based on high-performance liquid chromatography analysis of bile salts and bacterial protein determination was established for investigating bile salt hydrolase (BSH) activity in bacteria isolated from the small intestine of chickens. Bacteria were isolated using various media and were subsequently grouped according to cell morphology, fermentation profile, and 16S ribosomal DNA sequence. Representative isolates from each bacterial group were assayed for BSH activity. The isolates differed in BSH activity with respect to the state of growth and preculturing with and without taurochenodeoxycholate. The highest levels of BSH activity were found with
Enterococcus faecium
and
Clostridium perfringens
.
Incorporation of DNA and Protein Precursors into Macromolecules by Bacteria at −15
o
C
Authors: Christner Brent C. 
Published: November 2002

ABSTRACT

DNA and protein precursors were incorporated into trichloroacetic acid-precipitated material by bacterial cell suspensions during incubation for 50 to 100 days at −15
o
C. Incorporation did not occur at −70
o
C and was inhibited by antibiotics. The results demonstrate that bacteria can perform macromolecular synthesis under conditions that mimic entrapment in glacial ice.
Virulence Properties and Serotypes of Shiga Toxin-Producing
Escherichia coli
from Healthy Australian Cattle
Authors: Hornitzky Michael A. , Vanselow Barbara A. , Walker Keith , Bettelheim Karl A. , Corney Bruce , Gill Paul , Bailey Graham , Djordjevic Steven P. 
Published: November 2002

ABSTRACT

The virulence properties and serotypes of complex Shiga toxin-producing
Escherichia coli
(cSTEC) were determined in two studies of healthy cattle in eastern Australia. In the first, a snapshot study, 84 cSTEC isolates were recovered from 37 of 1,692 (2.2%) fecal samples collected from slaughter-age cattle from 72 commercial properties. The second, a longitudinal study of three feedlots and five pasture beef properties, resulted in the recovery of 118 cSTEC isolates from 104 animals. Of the 70 serotypes identified, 38 had not previously been reported.
Identification of a Replicon from pTXL1, a Small Cryptic Plasmid from
Leuconostoc mesenteroides
subsp.
mesenteroides
Y110, and Development of a Food-Grade Vector
Authors: Biet Franck , Cenatiempo Yves , Fremaux Christophe 
Published: November 2002

ABSTRACT

A 2,665-bp cryptic plasmid, pTXL1, isolated from
Leuconostoc mesenteroides
subsp.
mesenteroides
Y110 was identified. This plasmid harbors a replicon localized on a 1,300-bp fragment. Two observations suggested that pTXL1 does not belong to rolling-circle replication (RCR)-type plasmids and most likely replicates via a theta mechanism. These hypotheses are supported by the observation that no detectable single-stranded intermediate was found for the replicon and that, unlike in RCR-type plasmids, the pTXL1 replicon sequence lacks an open reading frame encoding a replicase. The small-sized pTXL1 plasmid is stable and, according to its origin, can be considered in the “generally recognized as safe” category. Its ability to replicate in several lactic acid bacteria was exploited to develop a vector producing mesentericin Y105, a class II anti-
Listeria
bacteriocin. With this new vector, a recombinant industrial
Leuconostoc cremoris
strain able to produce mesentericin Y105 was constructed.
Vancomycin-Resistant Enterococci in Humans and Imported Chickens in Japan
Authors: Ozawa Yoshiyuki , Tanimoto Koichi , Nomura Takahiro , Yoshinaga Masao , Arakawa Yoshichika , Ike Yasuyoshi 
Published: November 2002

ABSTRACT

The phenotypes and genotypes of 22 VanA-type vancomycin-resistant enterococci that had been isolated in Japan were examined. The VanA resistance determinant was plasmid mediated in each of the 22 strains. Of the 22 strains, 8 were isolated from different patients and 11 and 3 were obtained from different samples of chickens imported from Thailand and France, respectively. Three of the strains that were isolated from patients and the 11 strains isolated from the Thai chickens showed high-level vancomycin resistance (MICs, 512 to 1,024 μg/ml) and low-level teicoplanin resistance (MICs, 0.5 to 4 μg/ml). Each of these strains had three amino acid substitutions in the N-terminal region of the deduced VanS sequence. L50 was converted to V, E54 was converted to Q, and Q69 was converted to H compared to the
vanS
gene sequence of Tn
1546
.
Disruption of
narH
,
narJ
, and
moaE
Inhibits Heterotrophic Nitrification in
Pseudomonas
Strain M19
Authors: Nemergut D. R. , Schmidt S. K. 
Published: November 2002

ABSTRACT

Interruptions in three nitrate reductase-related genes,
narH
,
narJ,
and
moaE
, inhibited heterotrophic nitrification in
Pseudomonas
strain M19. No nitrate was detected in the medium, and nitrification proceeded in the presence of a nitrate reductase inhibitor. Heterotrophic nitrification was greatly stimulated by the addition of nitrate.
Enumeration of
Legionella
CFU by Colony Hybridization Using Specific DNA Probes
Authors: Satoh Wakako , Nakata Mayumi , Yamamoto Hiroyuki , Ezaki Takayuki , Hiramatsu Keiichi 
Published: November 2002

ABSTRACT

Oligonucleotide probes and colony hybridization (CH) were applied to enumerate organisms of the genus
Legionella
in cooling tower water. The CH counts indicated almost the same results as CFU counts in cultivated samples derived from the water. It was concluded that it is possible to substitute the CH procedure for the conventional one.
Real-Time PCR for Detection and Differentiation ofEntamoeba histolyticaandEntamoeba disparin Fecal Samples
Authors: Blessmann Joerg , Buss Heidrun , Nu Phuong A. Ton , Dinh Binh T. , Ngo Quynh T. Viet , Van An Le , Alla Mohamed D. Abd , Jackson Terry F. H. G. , Ravdin Jonathan I. , Tannich Egbert 
Published: November 2002

ABSTRACTA closed-tube, real-time PCR assay was developed for sensitive and specific detection and differentiation of the two closely related intestinal protozoan parasitesEntamoeba histolyticaandEntamoeba dispardirectly from human feces. The assay is performed with the LightCycler system using fluorescence-labeled detection probes and primers amplifying a 310-bp fragment from the high-copy-number, ribosomal DNA-containing ameba episome. The assay was able to detect as little as 0.1 parasite per g of feces. The two pairs of primers used were specific for the respective ameba species, and results were not influenced by the presence of otherEntamoebaspecies even when present in exceeding amounts. PCR was evaluated using several hundred stool samples from areas of amebiasis endemicity in Vietnam and South Africa, and results were compared with those of microscopy and ameba culture. PCR was found to be significantly more sensitive than microscopy or culture, as all samples positive by microscopy and 22 out of 25 (88%) samples positive by culture were also positive by PCR, but PCR revealed a considerable number of additionalE. histolytica-orE. dispar-positive samples. Compared to culture and subsequent ameba differentiation by isoenzyme analysis, PCR was 100% specific for each of the twoEntamoebaspecies. Interestingly, the comparison with PCR revealed that culture, in particular, underestimatesE. histolyticainfections. Given the high sensitivity and specificity of the developed PCR assay, the inability of microscopy to distinguish between the two ameba species, and the time it takes to culture and subsequently differentiate entamoebae by isoenzyme analysis, this assay is more suitable than microscopy or culture to correctly diagnose intestinalE. histolyticaorE. disparinfection.
Detection of Human Respiratory Syncytial Virus in Respiratory Samples by LightCycler Reverse Transcriptase PCR
Authors: Whiley David M. , Syrmis Melanie W. , Mackay Ian M. , Sloots Theo P. 
Published: November 2002

ABSTRACT
Laboratory diagnosis of human respiratory syncytial virus (hRSV) infections has traditionally been performed by virus isolation in cell culture and the direct fluorescent-antibody assay (DFA). Reverse transcriptase PCR (RT-PCR) is now recognized as a sensitive and specific alternative for detection of hRSV in respiratory samples. Using the LightCycler instrument, we developed a rapid RT-PCR assay for the detection of hRSV (the LC-RT-PCR) with a pair of hybridization probes that target the hRSV L gene. In the present study, 190 nasopharyngeal aspirate samples from patients with clinically recognized respiratory tract infections were examined for hRSV. The results were then compared to the results obtained with a testing algorithm that combined DFA and a culture-augmented DFA (CA-DFA) assay developed in our laboratory. hRSV was detected in 77 (41%) specimens by LC-RT-PCR and in 75 (39%) specimens by the combination of DFA and CA-DFA. All specimens that were positive by the DFA and CA-DFA testing algorithm were positive by the LC-RT-PCR. The presence of hRSV RNA in the two additional LC-RT-PCR-positive specimens was confirmed by a conventional RT-PCR method that targets the hRSV N gene. The sensitivity of LC-RT-PCR was 50 PFU/ml; and this, together with its high specificity and rapid turnaround time, makes the LC-RT-PCR suitable for the detection of hRSV in clinical specimens.
Laboratory Diagnosis and Genetic Analysis of an Echovirus 30-Associated Outbreak of Aseptic Meningitis in Taiwan in 2001
Authors: Wang Jen-Ren , Tsai Huey-Pin , Huang Sen-Wen , Kuo Pin-Hwa , Kiang David , Liu Ching-Chuan 
Published: November 2002

ABSTRACT
A large outbreak of aseptic meningitis occurred from April to November 2001 in Taiwan. Of the 1,130 enterovirus-infected patients, echovirus 30 (E30) infection was diagnosed in 188 (16.6%), with the patients having various clinical manifestations including aseptic meningitis (73.9%), young infant fever (6.9%), respiratory symptoms or herpangina (13.3%), or others (5.9%). The majority of the E30-infected patients were between 3 and 10 years old. Of the 264 E30 strains identified, 94.3, 71, and 67.4% were isolated from RD, MRC-5, and A549 cells, respectively. Primary isolation of E30 required mean times of 3.7 days for RD cells and 4.1 days for MRC-5 and A549 cells. Among all E30-positive patients, virus was most frequently isolated from throat swab specimens (85.2%) and, to a lesser extent, stool (76.4%) or cerebrospinal fluid (70.1%) specimens. The virus isolates were initially identified as echovirus 4 (E4) on the basis of immunofluorescence staining with anti-E4 and anti-E30 (Bastianni prototype) monoclonal antibodies. However, upon performance of the neutralization test, E30-specific reverse transcription-PCR, and sequencing of the VP1 gene, the results identified these isolates as E30, not E4, indicating that the reagent used to type E30, which is produced with the Bastianni strain as the immunogen, is inadequate for the identification of recent E30 isolates in Taiwan. Phylogenetic analyses of the VP1 genes of these isolates showed that their sequences differed from those of E30 isolates from the GenBank database by 9.1 to 25.2%, suggesting that this outbreak was caused by a new variant strain of E30 introduced into Taiwan in 2000 that resulted in the widespread aseptic meningitis epidemic in 2001.
Multiple Genetic Typing of
Salmonella enterica
Serotype Typhimurium Isolates of Different Phage Types (DT104, U302, DT204b, and DT49) from Animals and Humans in England, Wales, and Northern Ireland
Authors: Liebana Ernesto , Garcia-Migura Lourdes , Clouting Carol , Clifton-Hadley Felicity A. , Lindsay Elisabeth , Threlfall E. John , McDowell Stanley W. J. , Davies Robert H. 
Published: November 2002

ABSTRACT

Salmonella enterica
serotype Typhimurium is a common cause of salmonellosis among humans and animals in England, Wales, and Northern Ireland. Phage types DT104 and U302 were the most prevalent types in both livestock and humans in 2001. In addition,
Salmonella
serotype Typhimurium DT204b was responsible for a recent international outbreak involving England. A total of 119 isolates from humans (
n
= 28) and animals or their environment (
n
= 91), belonging to DT104 (
n
= 66), U302 (
n
= 33), DT204b (
n
= 12), and DT49 (
n
= 8), were fingerprinted by a combination of well-established genetic methods (pulsed-field gel electrophoresis [PFGE],
Pst
I/
Sph
I [PS] ribotyping, and plasmid profiling). The different techniques identified different degrees of polymorphism (from greatest to least, plasmid profiling [40 types], PS ribotyping [34 types], and PFGE [23 types]). It seems clear that a prevalent genomic clone, as well as a variety of less frequent clones, is present for each of the phage types. In most cases, the prevalent clones appeared within isolates from several animal species and from several geographical locations. We did not find clear evidence of a higher degree of diversity for any of the animal species included, or of any link between isolates from particular animal species and humans. The data presented show the inaccuracy of drawing epidemiological conclusions based on a single fingerprinting method. Strains that share one of the markers do not necessarily belong to the same clone, and a multiple typing approach is required to enable enough discrimination to track strains for epidemiological investigations.
Two Different Families ofhopQAlleles inHelicobacter pylori
Authors: Cao Ping , Cover Timothy L. 
Published: November 2002

ABSTRACTHelicobacter pylorigenomes contain about 30 differenthopgenes, which encode outer membrane proteins. In this study, we analyzed genetic diversity in theH. pylori hopQ(omp27) locus, which corresponds to HP1177 in the genome ofH. pylorireference strain 26695.hopQand its flanking genes were PCR amplified from multipleH. pyloristrains, and the nucleotide sequences were determined. This analysis revealed the existence of two different families ofhopQalleles. Type IhopQalleles are present in the genomes of two fully sequencedH. pyloristrains, whereas the existence of type IIhopQalleles has not previously been recognized. Type I and type IIhopQalleles are 75 to 80% identical in nucleotide sequences and encode predicted outer membrane proteins that are 68 to 72% identical in amino acid sequences. PCR-based methods were developed to enable rapid differentiation between type I and type IIhopQalleles. Type IhopQalleles were found significantly more commonly incag+/type s1-vacAstrains from patients with peptic ulcer disease than incag-negative/s2-vacAstrains from patients without ulcer disease (P< 0.001). Determination ofhopQallelic types provides a new method for classification ofH. pyloristrains. Further studies in multiple populations of patients are indicated to evaluate the usefulness of this approach for distinguishing potentially ulcerogenicH. pyloristrains from less virulent strains.
Testing Genotypic and Phenotypic Resistance in Human Immunodeficiency Virus Type 1 Isolates of Clade B and Other Clades from Children Failing Antiretroviral Therapy
Authors: Brindeiro Patrícia A. , Brindeiro Rodrigo M. , Mortensen Cláudio , Hertogs Kurt , De Vroey Veronique , Rubini Norma P. M. , Sion Fernando S. , De Sá Carlos A. M. , Machado Deisy M. , Succi Regina C. M. , Tanuri Amilcar 
Published: November 2002

ABSTRACT

The emergence of resistance to antiretroviral drugs is a major obstacle to the successful treatment of human immunodeficiency virus type 1 (HIV-1)-infected patients. In this work, we correlate clinical and virological trends such as viral load (VL) and CD4 counts to genotypic and phenotypic antiretroviral (ARV) resistance profiles of HIV-1 isolates from the B and non-B subtypes found in vertically infected children failing ARV therapy. Plasma samples were collected from 52 vertically HIV-1-infected children failing different ARV therapies. Samples underwent HIV-1
pol
sequencing and phenotyping and were clustered into subtypes by phylogenetic analysis. Clinical data from each patient were analyzed together with the resistance (genotypic and phenotypic) data obtained. Thirty-five samples were from subtype B, 10 samples were non-B (subtypes A, C, and F), and 7 were mosaic samples. There was no significant difference concerning treatment data between B and non-B clades. Prevalence of known drug resistance mutations revealed slightly significant differences among B and non-B subtypes: L10I, 21 and 64%, K20R, 13 and 43%, M36I, 34 and 100%, L63P, 76 and 36%, A71V/T, 24 and 0%, and V77I, 32 and 0%, respectively, in the protease (0.0001 ≤
P
≤ 0.0886), and D67N, 38 and 8%, K70R, 33 and 0%, R211K, 49 and 85%, and K219Q/E, 31 and 0%, respectively, in the reverse transcriptase (0.0256 ≤
P
≤ 0.0704). Significant differences were found only in secondary resistance mutations and did not reflect significant phenotypic variation between clade B and non-B.
Helicobacter cetorumsp. nov., a Urease-PositiveHelicobacterSpecies Isolated from Dolphins and Whales
Authors: Harper C. G. , Feng Y. , Xu S. , Taylor N. S. , Kinsel M. , Dewhirst F. E. , Paster B. J. , Greenwell M. , Levine G. , Rogers A. , Fox J. G. 
Published: November 2002

ABSTRACTA novel helicobacter with the proposed nameHelicobacter cetorum, sp. nov. (type strain MIT 99-5656; GenBank accession numberAF 292378), was cultured from the main stomach of two wild, stranded Atlantic white-sided dolphins (Lagenorhynchus acutus) and from the feces of three captive cetaceans (a Pacific white-sided dolphin [Lagenorhynchus obliquidens]; an Atlantic bottlenose dolphin [Tursiops truncatus]; and a beluga whale [Delphinapterus leucas]). The infected captive cetaceans were either subclinical, or clinical signs included intermittent regurgitation, inappetance, weight loss, and lethargy. Ulcers were observed in the esophagus and forestomach during endoscopic examination in two of the three captive animals. In the third animal, esophageal linear erosions were visualized endoscopically, and histopathological evaluation of the main stomach revealed multifocal lymphoplasmacytic gastritis with silver-stained spiral-shaped bacteria.Helicobacter cetorumis a fusiform gram-negative bacterium with a single bipolar flagellum. The isolates grow under microaerobic conditions at 37 and 42°C but not at 25°C.H. cetorumis urease, catalase, and oxidase positive, and it is sensitive to cephalothin. The isolates from the wild, stranded dolphins were sensitive to nalidixic acid, whereas the isolates from the collection animals were resistant. By 16S rRNA sequencing it was determined thatH. cetorumrepresented a distinct taxon that clusters most closely withH. pylori.Further studies are necessary to determine the role ofH. cetorumin the development of gastric ulcers and gastritis of cetaceans. This is the first description and formal naming of a novelHelicobacterspecies from a marine mammal.
Determining the Genetic Structure of the Natural Population of
Staphylococcus aureus
: a Comparison of Multilocus Sequence Typing with Pulsed-Field Gel Electrophoresis, Randomly Amplified Polymorphic DNA Analysis, and Phage Typing
Authors: Grundmann Hajo , Hori Satoshi , Enright Mark C. , Webster Carol , Tami Adriana , Feil Edward J. , Pitt Tyrone 
Published: November 2002

ABSTRACT

We used a sample of
Staphylococcus aureus
strains that are carried by humans and that are representative of the natural population of
S. aureus
strains in order to assess the value of multilocus sequence typing (MLST), pulsed-field gel electrophoresis, randomly amplified polymorphic DNA analysis, and phage typing as epidemiological tools. Only MLST was able to define clonal complexes unambiguously. All DNA-based typing approaches achieved a high degree of agreement, implying phylogenetic concordance, but predicted epidemiological associations with variable accuracy.
Stability of Variable-Number Tandem Repeats of Mycobacterial Interspersed Repetitive Units from 12 Loci in Serial Isolates ofMycobacterium tuberculosis
Authors: Savine Evgueni , Warren Robin M. , van der Spuy Gian D. , Beyers Nulda , van Helden Paul D. , Locht Camille , Supply Philip 
Published: November 2002

ABSTRACTVariable number tandem repeats (VNTRs) of elements named mycobacterial interspersed repetitive units (MIRUs) have previously been identified in 12 minisatellite loci of theMycobacterium tuberculosisgenome. These markers allow reliable high-throughput genotyping ofM. tuberculosisand represent a portable approach to global molecular epidemiology ofM. tuberculosis. To assess their temporal stability, we genotyped 123 serial isolates, separated by up to 6 years and belonging to a variety of distinct IS6110restriction fragment length polymorphism (RFLP) families, from 56 patients who had positive sputum cultures. All 12 MIRU VNTR loci were completely identical within the groups of serial isolates in 55 out of 56 groups (98.2%), although 11 pairs of isolates from the same patients with conserved MIRU VNTRs displayed slightly different IS6110RFLP profiles. In a single case, serial isolates with an unchanged IS6110RFLP profile showed a change in 1 out of 12 MIRU VNTR loci. These results indicate that MIRU VNTRs are stable over time and therefore are suitable for reliable follow-up of patients chronically infected with tuberculosis over long periods. Moreover, they support MIRU VNTR genotyping as a powerful first-line method followed by subtyping by IS6110RFLP to define ongoing transmission clusters.