Biomedical subjects

M Goodfellow

Publications and source records attributed to M Goodfellow.

At least 55 records · Page 3Linked to original sources

PubMed1998

Nocardia, nocardiosis and mycetoma.

The recent emergence of invasive infections due to Nocardia spp., including nosocomial outbreak, is now evident. Newer molecular diagnostic and typing methods are developed. Although sulfonamide-based therapy is generally effective, optimal treatment may be guided by antimicrobial susceptibility testing of isolates. The improved classification of nocardiae and other related genera such as actinomadurae, using the 16S ribosomal RNA sequencing, provide a sound basis for improved diagnostic methods for the identification of members of clinically significant species. The commonest cause of eumycetoma in Sudan is Madurella mycetomatis, and Streptomyces somaliensis and Actinomadura madurae for actinomycetoma. The humoral immunity response in actinomycetoma patients and in experimental mice was measured and significant titre of anti-P24 antibody was demonstrated.

Actinomycetales↗

PubMed1997

Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology.

Pyrolysis mass spectrometry is a well established analytical tool that has received a considerable boost from the development of low cost, dedicated instruments and sophisticated statistical analyses on personal computers. Further analytical developments, especially in the area of neural networks, are pushing the technology to the forefront of methods for the discrimination and identification of microorganisms and their products. The speed and reproducibility of pyrolysis mass spectrometry and its applicability to a wide range of microorganisms make it an attractive method for epidemiological studies. For inter-strain comparisons, the method is at least as discriminatory as conventional typing systems and usually gives discrimination similar to that of nucleic acid fingerprinting techniques. There has been some success in using neural networks to make identifications across pyrolysis mass spectrometric batches. Further development of methods used to handle data from multiple PyMS analyses can be expected to extend the value of pyrolysis mass spectrometry in clinical microbiology.

Bacteria↗

PubMed1997

Classification of photobacteria associated with spoilage of fish products by numerical taxonomy and pyrolysis mass spectrometry.

Forty strains of luminous and non-luminous Photobacterium phosphoreum isolates from cod (Gadus morhua) and seven reference strains of psychrotolerant and mesophilic photobacteria were examined for 156 unit characters in a numerical taxonomic study. The fish strains were isolated from the intestines, from spoiled products and by using a specific detection method. The data were analysed using the similarity coefficient and the unweighted pair-group with arithmetic averages algorithm. In addition twenty-six of the fish isolates and five reference strains were analysed by Curie-point pyrolysis mass spectrometry. The mesophilic and psychrotolerant photobacteria were clearly separated in each of the analyses. Both procedures indicated that the spoilage isolates of P. phosphoreum had originated from the live fish as strains from the fish intestines and from the spoiled products were recovered in the same sub-groups. One sub-group of psychrotolerant P. phosphoreum strains, which was selected in modified atmosphere packed fish stored at low temperature, was also highlighted using each of the methods. The importance of classifying food spoilage bacteria has been shown and a simple key generated for the identification of luminous and non-luminous isolates of Photobacterium phosphoreum.

Fish Products↗

PubMed1997

Evaluation of Streptomyces species-groups by pyrolysis mass spectrometry.

Curie-point pyrolysis mass spectrometry was used to evaluate the taxonomic integrity of three subclusters, provisionally labelled S. albidoflavus, S. anulatus and S. halstedii, which formed a species-group in an extensive numerical phenetic survey of the genus Streptomyces. Excellent agreement was found between the results of the triplicate analyses of each strain while the duplicated strains clustered adjacent to one another. Sequential principal component-canonical variates analysis of the experimental data collected on the 32 representative organisms showed that the S. albidoflavus strains formed a distinct group. This result taken together with earlier chemical, molecular and numerical taxonomic data indicates that the S. albidoflavus subcluster corresponds to a distinct species. In contrast, the subclusters equated with S. anulatus and S. halstedii were found to be heterogeneous and hence in need of further study. However, it is evident from the present investigation that Curie-point pyrolysis mass spectrometry provides a rapid and reproducible way of evaluating the taxonomic integrity of Streptomyces species-groups.

Mass Spectrometry↗

PubMed1997

An investigation of the intra-generic structure of Rothia by pyrolysis mass spectrometry.

Previous studies of the genus Rothia have indicated that members of the only species, Rothia dentocariosa, are heterogeneous and may form more than one species. To study the intrageneric taxonomic structure of the Rothia taxon eighteen strains identified as R. dentocariosa, including reference organisms from culture collections (3 strains), isolates from healthy subjects (5 strains) and from clinical sources (10 strains) were examined using pyrolysis mass spectrometry. The ordination plots of the pyrolysis data indicated that all the strains clustered in a closely related group, with the exception of three strains which out-grouped. Phenotypic testing and fatty acid data indicated that the latter three strains are probably misclassified in the genus Rothia. Reanalysis of the PyMS data including only the fifteen authentic Rothia strains indicated that ten of these organisms formed a group which included the type strain, R. dentocariosa NCTC 10917. Four out of the remaining five organisms formed a diffuse group; the remaining strain was recovered as a single member cluster. These data indicate that R. dentocariosa is heterogeneous though at present there are no suitable criteria for assigning members of this taxon to more than one species.

Actinomycetales↗

PubMed1997

Polyphasic taxonomic study of clinically significant actinomadurae including the description of Actinomadura latina sp.nov.

Thirty-one strains received either as Actinomadura madurae or Actinomadura pelletieri were assigned to four phena, clusters 1 to 4, in a numerical phenetic survey of the genus Actinomadura. Clusters 2 and 4 corresponded to the validly described species A. madurae and A. pelletieri whereas clusters 1 and 3 encompassed strains received as A. madurae and A. pelletieri, respectively. The two clusters that contained A. madurae strains formed a single taxon when a dataset lacking the antibiotic sensitivity entries was examined. Results from pyrolysis mass spectrometric and DNA amplification fingerprinting analyses underpinned the taxonomic status of clusters 2, 3 and 4 and suggested that the A. madurae strains accounted for a relatively wide range of variation. It is proposed that the cluster 3 strains be given species status within the genus Actinomadura given the congruence found between the chemical, molecular and numerical phenetic data. The name Actinomadura latina is proposed for the new taxon. The type strain is DSM 43382.

Actinomycetales↗

PubMed1997

Typing of the fish pathogen Listonella (Vibrio) anguillara by pyrolysis mass spectrometry.

Twenty-eight representatives of Listonella (Vibrio) anguillara serovars O1, O2 and O3 were compared by Curie-point pyrolysis mass spectrometry (PyMS). The representatives of serovars O1 and O3 formed discrete, homogeneous groups in ordination plots of the PyMS data. Strains from serovar O2 were recovered in two groups, one of which encompassed six strains including the type strain of the species and the reference strain for serovar O2, and the other included two strains which showed cross-reactions between serovars O2 and O5. The almost complete agreement found between the PyMS and the serological data suggests that pyrolysis mass spectrometry will prove to be an effective method for interstrain comparison within the species Listonella anguillara.

Animals↗

PubMed1997

Long-term identification of streptomycetes using pyrolysis mass spectrometry and artificial neural networks.

Sixteen reference strains and thirteen fresh isolates of three putatively novel Streptomyces species were examined six times over twenty months using pyrolysis mass spectrometry to examine the long-term reproducibility of the procedure. The reference strains and new isolates were correctly identified using information in each of the datasets and operational fingerprinting, but direct statistical comparison of the datasets for strain identification was unsuccessful between datasets. Artificial neural networks were also used to identify the strains held in the datasets. Neural networks trained with pyrolysis mass spectra from a single dataset were found to successfully identify the reference strains and fresh isolates in that dataset but were unable to identify many of the strains in the other datasets. However, a neural network trained on representative pyrolysis mass spectra from each of the first three datasets were found to identify the reference strains and fresh isolates in those three datasets and in the three subsequent datasets. Therefore, artificial neural network analysis of pyrolysis mass spectrometric data can provide a rapid, cost-effective, accurate and long-term reproducible way of identifying and typing microorganisms.

Humans↗

PubMed1997

Differentiation of Mycobacterium senegalense from related non-chromogenic mycobacteria using pyrolysis mass spectrometry.

Twenty-six representative strains of Mycobacterium chelonae, Mycobacterium fortuitum, Mycobacterium peregrinum and Mycobacterium senegalense were compared by Curie point pyrolysis mass spectrometry. The M. chelonae and M. senegalense strains formed distinct groups. A third, relatively diffuse group, contained the M. fortuitum and M. peregrinum strains. These results, together with those from corresponding analyses, suggest that pyrolysis mass spectrometry provides a rapid and reliable way of distinguishing between members of closely related mycobacterial species which are difficult to differentiate using conventional taxonomic procedures.

Mass Spectrometry↗

PubMed1997

A proposal to reclassify Nocardia pinensis Blackall et al. as Skermania piniformis gen. nov., comb. nov.

The type strain of Nocardia pinensis was the subject of chemotaxonomic and 16S ribosomal DNA sequencing studies. The resultant nucleotide sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordona, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella, and phylogenetic trees were generated by using the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, and neighbor-joining methods. It was evident from the phylogenetic analyses that N. pinensis represents a distinct phyletic line that is most closely associated with the Gordona clade. This genealogical evidence, together with chemotaxonomic and phenotypic data derived from this and previous studies, indicates that N. pinensis merits generic status within the family Nocardiaceae. Therefore, we propose that N. pinensis Blackall et al. 1989 be reclassified as Skermania piniformis gen. nov., comb. nov. The type strain of Skermania piniformis cleaved an array of conjugated substrates based on the fluorophores 7-amino-4-methylcoumarin and 4-methylumbelliferone.

Bacteriological Techniques↗

PubMed1997

Inter- and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences.

In order to clarify interspecific relationships and to investigate the intraspecific phylogenetic structure of the genus Saccharomonospora, 16S to 23S ribosomal DNA (16S-23S) and 23S to 5S ribosomal DNA (23S-5S) internally transcribed spacers (ITSs) were used for sequence analyses. The 16S-23S and 23S-5S ITSs from 22 Saccharomonospora strains were amplified by PCR and directly sequenced. The average levels of nucleotide similarity of the 16S-23S and 23S-5S ITSs for the four valid species were 87.6% +/- 3.9% and 83% +/- 2.2%, respectively. For the most part, intraspecific sequence differences were not found in the two ITSs; the only exception was Saccharomonospora glauca K194, which differed from other S. glauca strains by 1 bp in the 23S-5S ITS. The Saccharomonospora viridis strains had a smaller 16S-23S ITS region than the other strains, which may be useful for differentiating these organisms from other Saccharomonospora species. The characteristics of the two ITS regions make them more useful than 16S rRNA sequences as a tool for defining and identifying Saccharomonospora strains. However, Saccharomonospora azurea K161T had two types of 23S-5S ITSs; rrnB, separated by XhoI digestion, had two additional nucleotides inserted between positions 52 and 55. Most of the 16S-23S and 23S-5S ITS sequences of S. azurea K161T and strains of "Saccharomonospora caesia" were identical; the only exception was rrnB in S. azurea K161T. The lengths and levels of sequence divergence of the two ITSs of Saccharomonospora sp. strain K180 were different from the lengths and levels of sequence divergence of the ITSs of other species. These findings suggest that a taxonomic revision of the genus Saccharomonospora is necessary. Two trees based on 16S-23S and 23S-5S ITS sequences revealed distinct interspecific relationships in the genus Saccharomonospora.

Actinomycetales↗

PubMed1997

Biodiversity of bradyrhizobia nodulating Lupinus spp.

The genetic structure of Bradyrhizobium isolates recovered from three Lupinus species (Lupinus campestris, Lupinus montanus, and Lupinus exaltatus) grown in Mexico was examined. Among 41 Bradyrhizobium isolates, 18 electrophoretic types (ETs) were distinguished by multilocus enzyme electrophoresis of five metabolic enzymes. The mean genetic diversity, 0.64, indicated that there was great genetic diversity in the population sampled. Most isolates (63%) fell into two closely related clusters (clusters I and II) and were the types most frequently isolated from the root nodules of L. montanus and L. campestris. ET cluster III isolates were frequent nodule occupants of L. exaltatus. The isolates also were assigned to three main groups by using Curie point pyrolysis mass spectrometry. In general, the multilocus enzyme electrophoretic data and pyrolysis mass spectrometric data agreed. We determined the 16S rRNA sequences of representative Lupinus isolates and of Bradyrhizobium japonicum USDA 6T and found that the lupine isolates were highly related to the B. japonicum type strain, although not all B. japonicum type strains (subcultures maintained in different bacterial collections) had identical small-subunit rRNA.

Bacterial Proteins↗

PubMed1997

Mycobacterium novocastrense sp. nov., a rapidly growing photochromogenic mycobacterium.

A strain isolated from a biopsy sample taken from a slowly spreading skin granulation on a child's hand was found to have properties consistent with its classification in the genus Mycobacterium. An almost complete gene sequence of the 16S rRNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available for mycobacteria, and phylogenetic trees were inferred with four tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycolic acid pattern and a number of other phenotypic features, notably its ability to form yellow pigmented colonies when incubated in the light. The name proposed for this new species is Mycobacterium novocastrense. The type strain is DSM 44203.

DNA, Bacterial↗

PubMed1996

Attempts to find phenotypic markers of the virulence plasmid of Rhodococcus equi.

Four isolates of Rhodococcus equi, from pneumonic foals, and containing the 85 kb virulence plasmid, a porcine isolate containing an 80 kb plasmid, and their plasmid cured derivatives, were examined for 239 phenotypic properties in an attempt to find characters other than the virulence-associated protein (VapA) which might be encoded by the virulence plasmid in organisms grown at 37 degrees C. Tests chosen included those which have previously given variable results for R. equi isolates, since such variability might be attributed to plasmid curing, and characteristics which have been described as properties of plasmids of Rhodococcus species other than R. equi. Tests included cadmium resistance, Congo red binding, resistance to 26 antibiotics, conventional clinical microbiological tests, utilization of 95 different carbon sources, enzymatic activities in API ZYM, fluorogenic assays for exo- and endopeptidase, glycosidase activities, and testosterone degradation. Apart from production of VapA by foal isolates, no phenotypic property was identified in the plasmid-positive isolates. Phenotypic characteristics of R. equi that have not been described before, and might be useful in identification were: metabolism of N-acetyl-beta D-glucopyranoside, alpha- and beta-hydroxybutyric, alpha-ketobutyric and N-acetyl-glutamic acids, of methylpyruvate, heptanoate, nonanoate and stearate esters; exopeptidase activity against alanine-alanine-tyrosine, alanine-phenylalanine-lysine, glycine-arginine, lysine-alanine, and valine-glycine-alanine; endopeptidase activity against arginine and methionine; and hydrolysis of bis-phosphate ester.

Amino Acids↗

PubMed1995

A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences.

Partial sequences of the 16S rRNA genes of the type strains of nine species of the genus Nocardia were determined following the isolation and cloning of the amplified genes. These sequences were aligned with the sequences of representatives of the genera Corynebacterium, Gordona, Mycobacterium, Rhodococcus, and Tsukamurella, and phylogenetic trees were inferred by using the Fitch-Margoliash and neighbor-joining methods. The genus Nocardia formed a distinct clade that was most closely associated with the genus Rhodococcus. The average level of sequence similarity found among the type strains of the Nocardia species was 97.2 +/- 0.7%. Two sublines were recognized within the Nocardia clade; one encompassed Nocardia asteroides and related species, and the other encompassed Nocardia otitidiscaviarum and allied taxa. Separation of the two sublines is based on differences in helix 37-1. The results of isoprenoid quinone analyses provided evidence that nocardiae can be distinguished from all other actinomycete taxa on the basis of their characteristic menaquinone profiles. Nocardiae typically contain hexahydrogenated menaquinones with eight isoprene units in which the two end units are cyclized.

Base Sequence↗

PubMed1995

A phylogenetic analysis of the genus Saccharomonospora conducted with 16S rRNA gene sequences.

Nearly complete sequences of 16S rRNA genes of representative strains of the genus Saccharomonospora were determined following the isolation and cloning of the amplified genes. The sequences were aligned with those of representatives of the family Pseudonocardiaceae, and a phylogenetic tree was inferred by the neighbor-joining method. The genus Saccharomonospora formed a distinct clade within the evolutionary radiation encompassed by the family Pseudonocardiaceae. The average nucleotide similarity value found between the type strains of the four validly described Saccharomonospora species was 97.5% +/- 1.0%. The most distant relationship was found between Saccharomonospora azurea and Saccharomonospora viridis K73 (96.3% similarity). In contrast, Saccharomonospora azurea K161 and "Saccharomonospora caesia" K163 had identical 16S rRNA gene sequences. The nucleotide sequence data suggest that the genus Saccharomonospora contains several new centers of variation.

Actinomycetales↗

PubMed1995

Rapid growth and increased biomass yield of Mycobacterium farcinogenes and some related taxa in broth and agar media.

A broth medium containing yeast extract (4 g/l), glucose (15 g/l), magnesium sulphate (0.5 g/l), tri-sodium citrate (1.5 g/l), potassium sulphate (0.5 g/l), ammonium ferric citrate (trace) and buffered with potassium di-hydrogen phosphate (5 g/l) was formulated and found to support a luxuriant growth of Mycobacterium farcinogenes strains that was superior to the conventional media used before. Similar results were obtained with M. senegalense strains and with representatives of the genera Gordona, Mycobacterium, Nocardia, Rhodococcus and Tsukamurella. Out of 13 diverse agar-based media, M. farcinogenes was found to grow particularly well on Mueller Hinton's medium, followed, in order of decreasing growth rate, by modified Bennett's, DST, tryptic soya and glucose yeast extract agars.

Animals↗

PubMed1994

Theoretical and practical aspects of the quantification of biodiversity among microorganisms.

The quantification of biodiversity among microorganisms has to address both theoretical and practical aspects. Species concepts are often at variance with those applied in macroorganisms, and satisfactory concepts suitable for general use in bacteria and fungi have yet to be formulated. Molecular approaches have not yet provided a universal solution to this key issue. Quantification in habitats such as soil is difficult as isolation procedures yield only a small and skewed selection of the microorganisms present. Indices of taxonomic or phylogenetic diversity have potential in the quantification of microbial diversity at a range of ranks, but the non-equivalence of ranks and representatives of the taxa detected have to be addressed. Chemical and molecular methods have immense potential in the quantification of microbial diversity in environmental samples; 16S rRNA has shown particular promise with bacteria, but as yet the fungi lack a universal probe. A greater awareness of the limitations of existing approaches and methodologies used by microbiologists is needed, but significant progress can be anticipated as new technologies are developed and become more widely adopted.

Bacteria↗