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PubMed1970

Differentiation of Serratia from Enterobacter on the basis of nucleoside phosphotransferase production.

Precoated cellulose thin-layer chromatograms were used to detect the production of guanosine 5'-phosphate from guanosine and p-nitrophenylphosphate by whole-cell preparations. One-hundred per cent of Serratia (163 strains) and 84% of E. liquefaciens (15 of 18 strains) produced the nucleotide. All other Enterobacter (23 strains), Klebsiella (10 strains), and E. coli (10 strains) were negative for the production of this nucleotide. The entire test procedure could be carried out in 4 hr. It is proposed that E. liquefaciens is more closely related to Serratia than Enterobacter and that reclassification of these organisms should be investigated.

Chromatography, Thin Layer↗
PubMed2025

An update on clinically relevant, rare, and emerging Candida and Saccharomycotina yeasts that have been recently reclassified from Candida.

SUMMARYMany yeast species causing life-threatening invasive infections that were formerly classified in the genus Candida have been reclassified due to their evolutionary and phylogenetic relationships elucidated by DNA sequencing methods that are increasingly using whole genomes. This review explores the evolving taxonomy, epidemiology, and clinical implications of clinically relevant, rare, emerging Candida and Saccharomycotina yeasts that have recently been reclassified from Candida. This article highlights the urgent need for intensified research efforts to enhance knowledge and improve outcomes in the management of infections caused by these yeasts. Communicating results from molecular phylogenetic studies of yeasts, which lead to their reclassification, is of great importance to the medical mycology community to implement such results in clinical practice.

Humans↗
PubMed2003

Antigens and alternatives for control of Anaplasma marginale infection in cattle.

Anaplasmosis, a tick-borne cattle disease caused by the rickettsia Anaplasma marginale, is endemic in tropical and subtropical areas of the world. The disease causes considerable economic loss to both the dairy and beef industries worldwide. Analyses of 16S rRNA, groESL, and surface proteins have resulted in the recent reclassification of the order Rickettsiales. The genus Anaplasma, of which A. marginale is the type species, now also includes A. bovis, A. platys, and A. phagocytophilum, which were previously known as Ehrlichia bovis, E. platys, and the E. phagocytophila group (which causes human granulocytic ehrlichiosis), respectively. Live and killed vaccines have been used for control of anaplasmosis, and both types of vaccines have advantages and disadvantages. These vaccines have been effective in preventing clinical anaplasmosis in cattle but have not blocked A. marginale infection. Thus, persistently infected cattle serve as a reservoir of infective blood for both mechanical transmission and infection of ticks. Advances in biochemical, immunologic, and molecular technologies during the last decade have been applied to research of A. marginale and related organisms. The recent development of a cell culture system for A. marginale provides a potential source of antigen for the development of improved killed and live vaccines, and the availability of cell culture-derived antigen would eliminate the use of cattle in vaccine production. Increased knowledge of A. marginale antigen repertoires and an improved understanding of bovine cellular and humoral immune responses to A. marginale, combined with the new technologies, should contribute to the development of more effective vaccines for control and prevention of anaplasmosis.

Anaplasma marginale↗
PubMed1980

Specification of surface mating systems among conjugative drug resistance plasmids in Escherichia coli K-12.

Representative plasmids for most incompatibility groups in Escherichia coli K-12 were transferred to a "bald" strain to compare transfer frequencies for liquid and solid media. Standard broth matings were used for a liquid environment, but for solid surface mating, conjugation was allowed to take place on nutrient plates before washing off the cells for transconjugant selection on plates containing appropriate drugs. Plasmids that determine rigid pili transferred at least 2,000x better on plates than in broth. Some plasmids that determine thick flexible pili transferred 45 to 470x better, whereas others transferred equally well in both environments, as did plasmids of the I complex, which determine thin flexible pili. These results clearly distinguished a number of surface mating systems where most plasmids were derepressed for transfer and determined conjugative pili constitutively. The temperature-independent IncH2 plasmid R831b transferred best on plates, but other IncH plasmids transferred equally well in broth. This inconsistency led to the reclassification of R831b as IncM.

Conjugation, Genetic↗
PubMed2003

Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:flavin adenine dinucleotide oxidoreductase (TftC) of Burkholderia cepacia AC1100.

Burkholderia cepacia AC1100 uses 2,4,5-trichlorophenoxyacetic acid, an environmental pollutant, as a sole carbon and energy source. Chlorophenol 4-monooxygenase is a key enzyme in the degradation of 2,4,5-trichlorophenoxyacetic acid, and it was originally characterized as a two-component enzyme (TftC and TftD). Sequence analysis suggests that they are separate enzymes. The two proteins were separately produced in Escherichia coli, purified, and characterized. TftC was an NADH:flavin adenine dinucleotide (FAD) oxidoreductase. A C-terminally His-tagged fusion TftC used NADH to reduce either FAD or flavin mononucleotide (FMN) but did not use NADPH or riboflavin as a substrate. Kinetic and binding property analysis showed that FAD was a better substrate than FMN. TftD was a reduced FAD (FADH(2))-utilizing monooxygenase, and FADH(2) was supplied by TftC. It converted 2,4,5-trichlorophenol to 2,5-dichloro-p-quinol and then to 5-chlorohydroxyquinol but converted 2,4,6-trichlorophenol only to 2,6-dichloro-p-quinol as the final product. TftD interacted with FADH(2) and retarded its rapid oxidation by O(2). A spectrum of possible TftD-bound FAD-peroxide was identified, indicating that the peroxide is likely the active oxygen species attacking the aromatic substrates. The reclassification of the two enzymes further supports the new discovery of FADH(2)-utilizing enzymes, which have homologues in the domains Bacteria and Archaea.

Bacterial Proteins↗
PubMed1968

Taxonomy of Azotomonas species.

The ability of two strains of Azotomonas insolita and one strain classified only as Azotomonas species to use molecular nitrogen was investigated by use of several techniques. Molecular (15)N(2) incorporation by growing cultures of Azotomonas was inconsistent and limited. In addition, attempts to demonstrate nitrogen fixation in growing cultures by the radioactive (13)N(2) technique were negative. Experiments were done in which the total nitrogen content of a culture was determined by a micro-Kjeldahl method. None of these experiments resulted in a significant increase in total nitrogen. Attempts to show a diauxie effect, that is, transition from growth on NH(4) (+) to N(2), were also unsuccessful. Nitrogen fixation by cell-free extracts of A. insolita was negative, as determined by reduction of N(2) to NH(3), and reduction of cyanide, of acetylene, and of azide. These negative results suggest that the taxonomic reclassification of the genus Azotomonas should be considered.

Bacteria↗
PubMed1995

Genetic and biochemical characterization of Citrobacter rodentium sp. nov.

An unusual bacterial pathogen of laboratory mice has been previously classified as an atypical biotype of Citrobacter freundii. Designated C. freundii biotype 4280, this bacterium is the etiologic agent of transmissible murine clonic hyperplasia. An eaeA gene has been shown to be present in this organism and to be necessary for virulence in laboratory mice. However, other biotypes of C. freundii lack DNA homology with the eaeA gene. Because of the recent reclassification in which five named species and three unnamed species, all previously considered C. freundii, were described, we determined the taxonomic status of C. freundii biotype 4280. With a battery of biochemical tests and DNA relatedness studies, three isolates of C. freundii biotype 4280 were shown to be members of an unnamed Citrobacter species, designated species 9. In total, six isolates of Citrobacter species 9, but none of the type strains of the other eight named species or of the two remaining unnamed species of Citrobacter, were shown to possess DNA homology with both the eaeA and the eaeB genes. Species 9 was named Citrobacter rodentium sp. nov.

Animals↗
PubMed1998

Evaluation of bias in diagnostic-test sensitivity and specificity estimates computed by discrepant analysis.

When a new diagnostic test is potentially more sensitive than the reference test used to classify persons as infected or uninfected, a substantial number of specimens from infected persons may be reference-test negative but new-test positive. Discrepant analysis involves the performance of one or more additional tests with these specimens, reclassification as infected those persons for whom the new-test-positive results are confirmed, and recalculation of the estimates of new-test sensitivity and specificity by using the revised classification. This approach has been criticized because of the bias introduced by the selective use of confirmation testing. Under conditions appropriate for evaluating a nucleic acid amplification (NAA) test for Chlamydia trachomatis infection with cell culture as the reference test, we compared the bias in estimates based on the discrepant-analysis classification of persons as infected or uninfected with that in estimates based on the culture classification. We concluded that the bias in estimates of NAA-test specificity based on discrepant analysis is small and generally less than that in estimates based on culture. However, the accuracy of discrepant-analysis-based estimates of NAA-test sensitivity depends critically on whether culture specificity is equal to or is slightly less than 100%, and it is affected by competing biases that are not fully taken into account by discrepant analysis.

Bacteriological Techniques↗
PubMed1999

Abiotrophia elegans strains comprise 8% of the nutritionally variant streptococci isolated from the human mouth.

Ninety-one isolates of nutritionally variant streptococci (NVS) that were previously isolated from the human mouth were regarded as consisting of 7 Streptococcus defectivus isolates, 78 Streptococcus adjacens isolates, and 6 Gemella morbillorum isolates. However, recent references to the taxonomic reclassification of NVS, from S. defectivus to Abiotrophia defectiva and from S. adjacens to Abiotrophia adiacens, and the newly introduced species Abiotrophia elegans as a third Abiotrophia species, emphasize the need for genetic analyses for identification of NVS. When PCR-restriction fragment length polymorphism (RFLP) and phylogenetic distances were examined based on 16S rRNA gene sequences, the results indicated that 7 of the 91 NVS isolates were closely related to A. elegans. These seven isolates consisted of four isolates previously identified as G. morbillorum and three isolates previously identified as S. adjacens. Two isolates previously identified as G. morbillorum were related to A. adiacens. In biochemical tests, A. elegans and the seven isolates related to it possessed arginine dihydrolase (ADH) activity but the other Abiotrophia species did not. As a result, A. elegans strains comprised 8% of the 91 NVS isolates. Our findings suggest that A. elegans, A. adiacens, and A. defectiva exist in the human mouth in proportions of about 1:11:1 and that A. elegans can be genetically distinguished from the other two Abiotrophia species by PCR-RFLP analysis of 16S rRNA gene sequences and can be biochemically distinguished by ADH activity.

Food Microbiology↗
PubMed2004

Mycobacterium africanum genotyping using novel spacer oligonucleotides in the direct repeat locus.

This study involves a first evaluation of 25 novel spacer oligonucleotides in addition to the 43 routine spacers for molecular characterization of a panel of 65 isolates of tubercle bacilli from different geographic origins that were initially classified as Mycobacterium africanum based on phenotypic characters. The 68-spacer format defined four additional patterns, and three groups were identified. The relatively homogeneous groups A1 and A2 included strains from West Africa, and A3-1 included strains from East Africa. The presence of deletion region RD9 confirmed the reclassification of the M. africanum subtype II spoligopattern within group A3-1 as Mycobacterium tuberculosis. These isolates may represent a diverging branch of M. tuberculosis in Africa. The use of new spacers also suggested an undergoing evolution of M. africanum subtype I in West Africa. Our results showed that the strain differentiation within the M. tuberculosis complex is improved by using novel spacers, and extensive studies using new-generation spoligotyping may be helpful to better understand the evolution of M. africanum.

Africa↗
PubMed1978

Classification of the New Jersey serotype of vesicular stomatitis virus into two subtypes.

We propose a reclassification of five strains of the New Jersey serotype of vesicular stomatitis virus into two subtypes designated Concan and Hazelhurst. This subclassification into two subtypes is based on reciprocal differences in antibody neutralization of virion infectivity, nucleotide base sequence homology, oligonucleotide maps of virion RNA, and interference by defective-interfering particles.

Base Sequence↗
PubMed2001

Porcine teschoviruses comprise at least eleven distinct serotypes: molecular and evolutionary aspects.

Nucleotide sequencing and phylogenetic analysis of 10 recognized prototype strains of the porcine enterovirus (PEV) cytopathic effect (CPE) group I reveals a close relationship of the viral genomes to the previously sequenced strain F65, supporting the concept of a reclassification of this virus group into a new picornavirus genus. Also, nucleotide sequences of the polyprotein-encoding genome region or the P1 region of 28 historic strains and recent field isolates were determined. The data suggest that several closely related but antigenically and molecular distinct serotypes constitute one species within the proposed genus Teschovirus. Based on sequence data and serological data, we propose a new serotype with strain Dresden as prototype. This hitherto unrecognized serotype is closely related to porcine teschovirus 1 (PTV-1, former PEV-1), but induces type-specific neutralizing antibodies. Sequencing of field isolates collected from animals presenting with neurological disorders prove that other serotypes than PTV-1 may also cause polioencephalomyelitis of swine.

3' Untranslated Regions↗
PubMed2001

Evolutionary relationships among parvoviruses: virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses.

The current classification of parvoviruses is based on virus host range and helper virus dependence, while little data on evolutionary relationships among viruses are available. We identified and analyzed 472 sequences of parvoviruses, among which there were (virtually) full-length genomes of all 41 viruses currently recognized as individual species within the family Parvoviridae. Our phylogenetic analysis of full-length genomes as well as open reading frames distinguished three evolutionary groups of parvoviruses from vertebrates: (i) the human helper-dependent adeno-associated virus (AAV) serotypes 1 to 6 and the autonomous avian parvoviruses; (ii) the bovine, chipmunk, and autonomous primate parvoviruses, including human viruses B19 and V9; and (iii) the parvoviruses from rodents (except for chipmunks), carnivores, and pigs. Each of these three evolutionary groups could be further subdivided, reflecting both virus-host coevolution and multiple cross-species transmissions in the evolutionary history of parvoviruses. No parvoviruses from invertebrates clustered with vertebrate parvoviruses. Our analysis provided evidence for negative selection among parvoviruses, the independent evolution of their genes, and recombination among parvoviruses from rodents. The topology of the phylogenetic tree of autonomous human and simian parvoviruses matched exactly the topology of the primate family tree, as based on the analysis of primate mitochondrial DNA. Viruses belonging to the AAV group were not evolutionarily linked to other primate parvoviruses but were linked to the parvoviruses of birds. The two lineages of human parvoviruses may have resulted from independent ancient zoonotic infections. Our results provide an argument for reclassification of Parvovirinae based on evolutionary relationships among viruses.

Animals↗
PubMed2002

Sequencing of porcine enterovirus groups II and III reveals unique features of both virus groups.

The molecular classification of the porcine enterovirus (PEV) groups II and III was investigated. The sequence of the almost complete PEV-8 (group II) genome reveals that this virus has unique L and 2A gene regions. A reclassification of this group into a new picornavirus genus is suggested. PEV group III viruses are typical enteroviruses. They differ from other enteroviruses by a prolonged stem-loop D of the 5'-cloverleaf structure.

3' Untranslated Regions↗
PubMed2005

The importance of acknowledging clinical uncertainty in the diagnosis of epilepsy and non-epileptic events.

BACKGROUND: Failure to recognise diagnostic uncertainty between the epilepsies and non-epileptic events may be a factor in high rates of misdiagnosis. AIMS: To explore the results of acknowledging diagnostic uncertainty in a cohort of children presenting with paroxysmal events. METHODS: Children (29 days-16th birthday) with new presentations of paroxysmal disorders were ascertained through outpatients, admissions, and accident and emergency over a two year period in a district hospital with a catchment population of 500,000. Cases were classified by diagnosis at entry and 6-30 months later. A random selection of cases was independently assessed. RESULTS: A total of 684 cases were ascertained. Attacks were initially classified as febrile seizures (n = 212), acute symptomatic epileptic seizures (n = 5), epilepsies (n = 83), unclassified (possible epilepsy) (n = 90), isolated epileptic seizures (n = 51), and non-epileptic events (n = 243). Case review enabled reclassification of 61 of those initially unclassified--31 to an epilepsy and 27 to non-epileptic events. In 29 the final diagnosis was never clarified. These were 23 cases with confusing or absent histories and six with short lived seizure clusters. Prognosis for these 29 cases was good; 75% had been discharged. None were on long term medication. The diagnosis in the 131 cases confirmed as epilepsy was stable. Independent review of a random sample showed full concordance with one neurologist and 20% uncertainty with another. CONCLUSION: In addition to definite epilepsy or non-epileptic events it is helpful to recognise a group of cases where the diagnosis is uncertain-unclassified paroxysmal events. Reassessment of these cases enables accurate diagnosis and may prevent a hasty and incorrect diagnosis of epilepsy.

Adolescent↗
PubMed1990

Increasing asthma prevalence in a rural New Zealand adolescent population: 1975-89.

A survey of asthma symptoms and spirometry in 435 adolescent schoolchildren was undertaken in 1989 in a rural, largely Maori population. The survey questionnaires were identical to those used in a 1975 survey at the same school. The prevalence of reported asthma or wheeze significantly increased from 26.2% to 34.0%. This increase occurred in groups reporting asthma, and also those reporting wheeze unassociated with colds, but without a previous diagnosis of asthma. There was a tendency for a rise in reported wheeze in Europeans (24.3% to 27.4%) and a significant rise in Maoris (27.1% to 36.2%). The reclassification of other respiratory problems did not account for the increase. Data from this study provides evidence that there has been a rise in the prevalence of asthma in this New Zealand population over a time period of 14 years.

Adolescent↗
PubMed1996

Patients, society, and the increase in self medication.

Self medication with over the counter medicines has long been a feature of the lay health system. With the reclassification of certain drugs, the public can buy preparations that were previously available only prescription. Sales of over the counter medicines are now equivalent to a third of the NHS drugs bill; governments throughout the world see self medication as a way of shifting some of the cost of health care onto consumers. The trend towards increased self care and with it the increasing empowerment of patients has many potential benefits; collaboration between doctors and pharmacists will be critical.

Attitude of Health Personnel↗
PubMed1997

Birth defects in infants conceived by intracytoplasmic sperm injection: an alternative interpretation.

OBJECTIVE: To test the hypothesis that liveborn infants conceived by intracytoplasmic sperm injection are at an increased risk of having a major birth defect. DESIGN: Reclassification of the birth defects reported in infants born after intracytoplasmic sperm injection in Belgium and comparison with prevalence estimated in Western Australian population by means of same classification system. SETTING AND SUBJECTS: 420 liveborn infants who were conceived after intracytoplasmic sperm injection in Belgium and 100,454 liveborn infants in Western Australia delivered during the same period. MAIN OUTCOME MEASURES: Estimates of birth prevalence of birth defects and comparisons of odds ratios between cohort conceived after intracytoplasmic sperm injection and Western Australian infants. RESULTS: Infants born after intracytoplasmic sperm injection were twice as likely as Western Australian infants to have a major birth defect (odds ratio 2.03 (95% confidence interval 1.40 to 2.93); P = 0.0002) and nearly 50% more likely to have a minor defect (1.49 (0.48 to 4.66); P = 0.49). Secondary data-led analyses, to be interpreted with caution, found an excess of major cardiovascular defects (odds ratio 3.99), genitourinary defects (1.33), and gastrointestinal defects (1.84), in particular cleft palate (5.11) and diaphragmatic hernia (7.73). CONCLUSIONS: These results do not confirm the apparently reassuring results published by the Belgian researchers of intracytoplasmic sperm injection. Further research is clearly required. Meanwhile, doctors practising intracytoplasmic sperm injection should bear this alternative interpretation in mind when they counsel couples and obtain informed consent for the procedure.

Adolescent↗