| 1. |
- Nicklasson, Matilda, 1978, et al.
(författare)
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Pseudomonas boanensis sp. nov., a bacterium isolated from river water used for household purposes in Boane District, Mozambique
- 2022
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 72:7
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Tidskriftsartikel (refereegranskat)abstract
- A Gram- negative rod with a single polar flagellum was isolated from a freshwater reservoir used for household purposes in Boane District, near Maputo, Mozambique, and designated as strain DB1T. Growth was observed at 30???42 ??C (optimum, 30???37 ??C) and with 0.5???1.5 % NaCl. Whole- genome-, rpoD- and 16S rRNA- based phylogenies revealed this isolate to be distant from other Pseudomonas species with Pseudomonas resinovorans, Pseudomonas furukawaii and Pseudomonas lalkuanensis being the closest relatives. Phenotypic analyses of strain DB1T showed marked differences with respect to type strains P. resinovorans CCUG 2473T, P. lalkuanensis CCUG 73691T, P. furukawaii CCUG 75672T and Pseudomonas otiditis CCUG 55592T. Taken together, our results indicate that strain DB1T is a representative of a novel species within the genus Pseudomonas for which the name Pseudomonas boanensis is proposed. The type strain is DB1T (=CCUG 62977T=CECT 30359T).
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| 2. |
- Zamora, L, et al.
(författare)
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Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout (Oncorhynchus mykiss).
- 2012
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 1618-0984 .- 0723-2020. ; 35:1, s. 24-9
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Tidskriftsartikel (refereegranskat)abstract
- Genotypic and phenotypic analyses were performed on five Gram-negative, catalase and oxidase-positive, rod-shaped bacteria isolated from the gill and liver of four rainbow trout. Studies based on comparative 16S rRNA gene sequence analysis showed that the five new isolates shared 99.8-100% sequence similarity and that they belong to the genus Chryseobacterium. The nearest phylogenetic neighbours of the strain 701B-08(T) were Chryseobacterium ureilyticum F-Fue-04IIIaaaa(T) (99.1% 16S rRNA gene sequence similarity) and Chryseobacterium joosteii LMG 18212(T) (98.6%). DNA-DNA hybridization values between the five isolates were 91-99% and ranged from 2 to 53% between strain 701B-08(T) and the type strains of phylogenetically closely related species of Chryseobacterium. Strain 701B-08(T) had a DNA G+C content of 36.3 mol%, the major fatty acids were iso-C(15:0), iso-C(17:1)ω9c, C(16:1)ω6c and iso-C(17:0) 3-OH and the predominant respiratory quinone was MK-6. The novel isolates were distinguished from related Chryseobacterium species by physiological and biochemical tests. The genotypic and phenotypic properties of the isolates from rainbow trout suggest their classification as representatives of a novel species of the genus Chryseobacterium, for which the name Chryseobacterium oncorhynchi sp. nov. is proposed. The type strain is 701B-08(T) (=CECT 7794(T)=CCUG 60105(T)).
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| 3. |
- Moore, Edward R.B. 1954, et al.
(författare)
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Applications of MALDI-TOF and SARAMIS analyses for the identification of closely related clinically-relevant bacterial species
- 2009
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Ingår i: Proceedings of the 12th Conference in Genomics and Proteomics of Human Pathogens: Target molecules and biomarkers in the characterisation of microbes in disease and the environment, June 25-26, London, UK.
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Konferensbidrag (refereegranskat)abstract
- Identification of prokaryotes in the complexity of microbial diversity is increasingly problematic for clinical diagnoses. Among the most difficult problems for clinical diagnostics is the identification of bacteria within “complexes” of closely related species, comprising pathogenic and non-pathogenic species with limited differentiating characteristics. However, these species complexes are composed of micro-organisms with different virulence potentials and it is essential to be able to obtain and confirm reliable identifications. A “polyphasic” multi-locus sequence analysis (MLSA) strategy may be applied for the typing and identification (species- and sub-species-levels) of bacteria, including “first-phase” comparisons of partial 16S rRNA gene sequences and subsequent “second-phase” analyses of one or more conserved house-keeping genes, for identification to the species level. These genotypic data are being used to correlate with the data obtained by MALDI-TOF (matrix-assisted laser desorption-ionisation time-of-flight) IC-MS (intact-cell mass-spectrometry) and analysed with the SARAMIS (Spectral Archive And Microbial Identification System) software and database package. The high reproducibility, rapid speed and low cost of MALDI-TOF IC-MS analyses makes the methodology ideal for processing large numbers of microbiological samples sent to the clinical lab for identification. The question of the resolution able to be obtained, using MALDI-TOF IC-MS was addressed by focusing analyses on bacteria comprising clinically-relevant species-complexes. The SARAMIS analysis of the MALDI-TOF IC-MS data was observed to be able to compare spectra from bacteria, yeast and fungi with reference spectra maintained in a database, identify the most closely related bacterial species with statistically-relevant confidence values and type strains to sub-species levels. The analyses are applicable to nearly all micro-organisms with high reproducibility.
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| 4. |
- Moore, Edward R.B. 1954, et al.
(författare)
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Polyphasic phenotypic and genotypic analyses for diagnosing closely related clinically-relevant bacteria
- 2007
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Ingår i: Proceedings of the XXIX Congreso Chileno de Microbología, December 3-5, Viña del Mar, Chile. ; , s. 44-45
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Konferensbidrag (refereegranskat)abstract
- The majority of known pathogenic bacteria have been recognised for more than a century. However, reliable identification of specific pathogens within the increasing complexity of bacterial diversity is becoming more problematic for clinical diagnoses. DNA sequencing and genotyping of bacteria has helped enable recognition of the extensive diversity of microorganisms in the environment and the same approaches are more recently being adopted in clinical microbiology. Genotypic methods are especially suited to the analyses of the “difficult-to-cultivate” organisms, as well as bacteria that pose significant health risks during cultivation. Traditional phenotyping, as well as genotyping by 16S rRNA gene sequence analysis, in many cases are able to provide only good estimations of identifications, although they may be able to provide information on what an isolate is not. In some cases of clinical diagnoses, such information may be useful and adequate. However, such analyses are often not able to provide definitive identifications. Among the most difficult problem for diagnoses in clinical cases, is the identification of organisms within “complexes” of closely related species, e.g., the Burkholderia cepacia “complex”, the Mycobacterium tuberculosis “complex”, the Streptococcus mitis “complex”, etc. These, so called “complexes” are comprised of closely related pathogenic and non-pathogenic species or genomovars, with limited phenotypic and genotypic differentiating characteristics, e.g., the 16S rRNA gene sequence differences among such organisms is less than 1.0%. Because these species “complexes” are comprised of organisms with different pathogenic and virulence potential and different treatment regimen, it is essential to be able to provide reliable identifications to the clinicians. Genotyping of bacteria provides the means for detailed, high-resolution differentiation and identification of organisms, as well as epidemiological monitoring. For identification of clinical isolates, a “multi-locus sequence analysis (MLSA)”, is used, including “first-phasic” comparisons of partial 16S rRNA gene sequences, for identification to the sub-genus level, and subsequent analyses of one or more “house-keeping” genes, for identification to the species level. However, not all house-keeping genes are equally useful for all taxa. Thus, the key to effective identifications, with respect to the speed and cost of analyses, and the resolution and reproducibility of identifications, depends upon the selection of the most applicable house-keeping genes, i.e., those with adequately high levels of resolution among the most closely related species. Protocols and results for species-resolving MLSA, using “house-keeping” genes enable effective differentiation of clinically-relevant closely related species of respective genera of Burkholderia, Mycobacterium, Streptococcus and Staphylococcus, as well as Pseudomonas and Stenotrophomonas. Furthermore, Matrix-Assisted Laser Desorption Ionization Time-of-Flight mass-spectrometry (MALDI-TOF MS), in combination with Spectral Archive And Microbial Identification System (SARAMIS) software analyses, were able to further define species-level differentiation among the most closely-related members of species “complexes”. MALDI-TOF MS, generating cell protein profiles, may exhibit even higher levels of resolution than the most discriminating genotypic analyses for species, as well as strain, identifications. These phenotypic data, as well as traditional phenotypic data, and genotypic MLSA data are correlated in the polyphasic assessment and definition of selected species “complexes”.
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| 5. |
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| 6. |
- Svensson, Liselott A, et al.
(författare)
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New genotypic and phenotypic analyses of clinically-relevant Gram-negative, non-fermenting bacteria: MALDI-TOF MS as a rapid, high-resolution method for identifying and typing microorganisms
- 2010
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Ingår i: 20th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objectives. Identification of Gram-negative, non-fermenting bacilli, using phenotypic characterization is problematic. Many of the species of this group are frequent nosocomial infectious agents and are ubiquitous in the environment. The aims of this study were to assess the resolving capacities of “house-keeping” gene sequences, including 16S rRNA, atpD, gyrB, recA, rpoB and rpoD, and to compare a multi-locus sequence analysis (MLSA) with matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry analyses for identifying and typing strains of Achromobacter, Bordetella, Burkholderia, Pseudomonas, and Stenotrophomonas species. Methods. Genotypic analyses. Type strains of the focus genera and species-complexes, other well-characterised reference strains and selected clinically-relevant strains representing a range of phenotypic and genotypic similarities were included in this study. Partial genes, 16S rRNA, atpD, recA, gyrB and rpoD recA were amplified by PCR and sequenced. DNA-DNA hybridisation analyses were carried out on selected strains for confirmation of species designations. MALDI-TOF analysis. Bacterial biomass were prepared from cultures on agar medium and analysed by MALDI-TOF MS, in the positive mode, using the SARAMIS software for analysis (1) Results. MLSA, using the respective house keeping genes were able to differentiate and identify the most closely related species of the analysed taxa and cluster analyses showed similarities of branching order between species that correlated well between different genes. However, different genes were not equally effective in differentiating species of the different genera. The MALDI-TOF analyses were effective in differentiating the most closely related species of the respective genera. Good correlation was observed between the results of MALDI-TOF MS and MLSA data. Conclusion. In most cases, clinically-relevant isolates and strains of Gram negative, non-fermenting bacilli exhibited good agreement between the methods of this study. In some cases, strains previously defined as given species were observed to be genotypically more similar to other species, as well as some strains with highly aberrant phenotypes were almost genotypically identical to the type strain. MALDI-TOF identification was very well correlated to the MLSA results, and is a much less expensive and effectively able to reduce identification times by 24-48 hours. (1) Vanlaere E et al. J. Microbiol. Meth. 75: 279-286 (2008).
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| 7. |
- Svensson, Liselott A, et al.
(författare)
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Stenotrophomonas species differentiation by MLSA of gyrB and rpoD and identification of isolates from clinical and environmental samples
- 2009
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Ingår i: FEMS 2009 - 3rd Congress of European Microbiologists.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Background: Stenotrophomonas species are commonly observed in clinical and environmental samples. S. maltophilia is associated with respiratory infections, is recognized as the third most common nosocomial Gram-negative, non-fermenting bacterium and is isolated from a range of environmental ecosystems, often exhibiting biodegradation and other biotechnological potential. Identification of Stenotrophomonas spp. is famously problematic, due to lack of phenotypic markers, as well as limited 16S rRNA gene sequence differentiation. Objectives: The aim of this study was to determine the applicability of “house-keeping” genes gyrB and rpoD as biomarkers for species-level differentiation within Stenotrophomonas. Methods: Selected regions from gyrB and rpoD of Stenotrophomonas spp., including all type strains, were amplified by PCR and sequenced, for comparative analyses. Results: Comparative sequence analyses of targeted regions of gyrB and rpoD enabled effective resolution of all species in Stenotrophomonas. Dissimilarities between the sequences of the type strains of S. maltophilia and other Stenotrophomonas spp. ranged from 10.2 – 14.7 % (gyrB) and 13.0 – 21.7 % (rpoD). Inter-species sequence dissimilarities of gyrB and rpoD ranged from 7.2 % --18.0 % and from 5.5 % - 22.8%, respectively. Compared with Stenotrophomonas spp. 16S rRNA gene sequence dissimilarities, (0.9 – 3.1 %), both house keeping genes exhibit better capacity for reliably differentiating Stenotrophomonas species. Clinical isolates identified as S. maltophilia were analysed by gyrB and rpoD sequence analyses. These data elucidated high levels of sequence dissimilarities among isolates, bringing into question the identifications determined by traditional methods, as well as the resolution of the taxonomy of Stenotrophomonas. These questions are being addressed in more detail. Conclusions: Analyses of house-keeping genes gyrB and rpoD exhibited effective species-level differentiation for Stenotrophomonas, which can be applied, in combination with 16S rRNA gene sequence analyses to provide an MLSA strategy for genotypic analyses for reliable identifications of isolates from clinical and environmental samples.
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| 8. |
- Zamora, L, et al.
(författare)
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Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss).
- 2012
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 1618-0984 .- 0723-2020. ; 35:2, s. 86-91
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Tidskriftsartikel (refereegranskat)abstract
- Eighteen isolates of a Gram-negative, catalase and oxidase-positive, rod-shaped bacterium, recovered from diseased rainbow trout (Oncorhynchus mykiss), were characterized, using a polyphasic taxonomic approach. Studies based on comparative 16S rRNA gene sequence analysis showed that that the eighteen new isolates shared 99.2-100% sequence similarities. Phylogenetic analysis revealed that isolates from trout belonged to the genus Flavobacterium, showing the highest sequence similarities to F. chungangense (98.6%), F. frigidimaris (98.1%), F. hercynium (97.9%) and F. aquidurense (97.8%). DNA-DNA reassociation values between the trout isolates (exemplified by strain 631-08(T)) and five type strains of the most closely related Flavobacterium species exhibited less than 27% similarity. The G+C content of the genomic DNA was 33.0 mol%. The major respiratory quinone was observed to be menaquinone 6 (MK-6) and iso-C(15:0), C(15:0) and C(16:1) ω7c the predominant fatty acids. The polar lipid profile of strain 631-08(T) consisted of phosphatidylethanolamine, unknown aminolipids AL1 and AL3, lipids L1, L2, L3 and L4 and phospholipid PL1. The novel isolates were differentiated from related Flavobacterium species by physiological and biochemical tests. On the basis of the evidence from this polyphasic study, it is proposed that the isolates from rainbow trout be classified as a new species of the genus Flavobacterium, Flavobacterium oncorhynchi sp. nov. The type strain is 631-08(T) (= CECT 7678(T) = CCUG 59446(T)).
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| 9. |
- Brudey, Karine, et al.
(författare)
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Molecular epidemiology of Mycobacterium tuberculosis in western Sweden.
- 2004
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Ingår i: Journal of clinical microbiology. - 0095-1137. ; 42:7, s. 3046-51
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Tidskriftsartikel (refereegranskat)abstract
- The genetic diversity of Mycobacterium tuberculosis isolates among patients from Sweden was determined by a combination of two PCR-based techniques (spoligotyping and variable number of tandem repeats analysis). It resulted in a clustering of 23.6% of the isolates and a rate of recent transmission of 14.1%. The clustered isolates mainly belonged to the Haarlem family (23.2%), followed by the Beijing (9.8%), Latin American and Mediterranean (LAM; 8%), and East African-Indian (EAI; 6.2%) families. A comparison of the spoligotypes with those in the international spoligotyping database showed that 62.5% of the clustered isolates and 36.6% of all isolates typed were grouped into six major shared types. A comparison of the spoligotypes with those in databases for Scandinavian countries showed that 33% of the isolates belonged to an ill-defined T family, followed by the EAI (22%), Haarlem (20%), LAM (11%), Central Asian (5%), X (5%), and Beijing (4%) families. Both the highest number of cases and the proportion of clustered cases were observed in patients ages 15 to 39 years. Nearly 10% of the isolates were resistant to one or more drugs (essentially limited to isoniazid monoresistance). However, none of the strains were multidrug resistant. Data on the geographic origins of the patients showed that more than two-thirds of the clustered patients with tuberculosis were foreign-born individuals or refugees. These results are explained on the basis of both the historical links within specific countries and recently imported cases of tuberculosis into Sweden.
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| 10. |
- Karlsson, R., et al.
(författare)
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Proteotyping: Proteomic characterization, classification and identification of microorganisms - A prospectus
- 2015
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 38:4, s. 246-257
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Forskningsöversikt (refereegranskat)abstract
- Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels. (C) 2015 Elsevier GmbH. All rights reserved.
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