| 1. |
- Mushtaq, Mamoona, et al.
(författare)
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Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics
- 2015
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: The genus Brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. In a previous study a group of strongly haemolytic isolates from pigs and mallards was provisionally described as a new species within genus Brachyspira, "B. suanatina", and enteropathogenic properties were demonstrated in a porcine challenge model. Methods: In the current study characterization of B. suanatina was performed on the basis of cell morphology, growth characteristics, enzyme profiles, DNA-DNA hybridization (DDH) and whole genome comparisons. The draft genome sequence of B. suanatina strain AN4859/03 was determined and compared with the available genomes of all valid species of Brachyspira. Results: According to morphological traits, growth characteristics and enzymatic profiles, B. suanatina was similar to the type strain of B. hyodysenteriae, but using the recommended threshold value of 70 % similarity by DDH it did not belong to any of the recognized Brachyspira species (range 16-64 % similarity). This was further supported by average nucleotide identity values. Phylogenetic analysis performed using housekeeping genes and core genomes of all valid Brachyspira sp. and "B. hampsonii" revealed that B. suanatina and B. intermedia formed a clade distinct from B. hyodysenteriae. By comparing the genomes of the three closely related species B. intermedia, B. hyodysenteriae and B. suanatina similar profiles of general genomic features and distribution of genes in different functional categories were obtained. However, the genome size of B. hyodysenteriae was smallest among the species, suggesting the possibility of reductive evolution in the divergence of this species. A bacteriophage region and a putative plasmid sequence were also found in the genome of B. suanatina strain AN4859/03. Conclusions: The results of our study suggest that despite being similar to B. hyodysenteriae phenotypically, B. suanatina should be regarded as a separate species based on its genetic characteristics. Based on characteristics presented in this report we propose that strains AN4859/03, AN1681:1/04, AN2384/04 and Dk12570-2 from pigs in Sweden and Denmark, and strains AN3949:2/02 and AN1418:2/01 isolated from mallards in Sweden, represent a unique species within genus Brachyspira. For this new species we propose the name B. suanatina for which the type strain is AN4859/03T (=ATCC® BAA-2592TM = DSM 100974T).
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| 2. |
- Zubair, Saima
(författare)
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Bioinformatics analysis of bacterial pathogens from East African camels : comparative genomics of Streptococcus agalactiae and Staphylococcus aureus
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The camel is the most valuable livestock species in arid and semi-arid regions in the Greater Horn of Africa. Streptococcus agalactiae and Staphylococcus aureus are important pathogens for a wide range of hosts including camels, cattle and humans. Streptococcus agalactiae has been reported to cause infections of the skin, the respiratory tract, the mammary gland and the vaginal tract in camels. Staphylococcus aureus has been isolated from the nasal cavity, wound infections and mastitis from camels. Both pathogens account for decline in health and productivity of camels, hence causing economic losses to the inhabitants of arid and semi arid lands. To define candidate virulence traits in these bacteria, we compared the genomes of S. agalactiae and S. aureus. We sequenced and completely assembled the genomes of two S. agalactiae isolates ILRI005 and ILRI112 from abscessed case camels and an S. aureus isolate ILRI_Eymole1/1 from the nasal swab of camel in Kenya. To perform comparative analysis, we also sequenced and assembled an S. agalactiae isolate 09mas018883 from subclinical mastitis case cattle in Sweden. Mapping assembly, de novo assembly and post-assembly genome finishing were performed to obtain completely assembled genomes. Comparative genomics approach was applied to explore the genetic heterogeneity, core genome construction and protein repertoire comparison of these novel genomes, and to highlight potential virulence factors that could have contributed to the pathogenicity of these isolates in their hosts. Newly sequenced camel S. agalactiae genomes were compared with human and cattle S. agalactiae genomes. This comparison revealed that the two camel isolates were genetically close to each other but relatively distinct from other isolates, while cattle isolate 09mas018883 was genetically closer to the human isolates. Large proportion of the isolate-specific genes of the camel S. agalactiae isolates was clustered in putative phage insertions and genomic islands suggesting the lateral transfer of these putative phages. The two camel S. agalactiae isolates shared a novel potential virulent locus, the CRISPR2 (Cluster Regularly Interspaced Palindromic Repeats) locus. The two cattle S. agalactiae isolates and three human S. agalactiae isolates contained similar putative phage insertions. Important potential pathogenic factors found in all S. agalactiae isolates were CRISPR1 locus, cyl locus, capsular polysaccharide locus and pilus islands. Phylogenetic analysis of novel camel S. aureus genome of strain type ST30 and previously sequenced human S. aureus genomes of type Clonal Complex 30 (CC30) revealed that camel S. aureus isolate is genetically distinct from human S. aureus isolates of the same sequence type. Important features were also identified such as genes encoding bacterial adhesins and secretory proteins. The availability of genomic sequences of S. agalactiae and S. aureus from camels, their detailed bioinformatics analysis and identified potential virulence factors will foster the development of control measures such as molecular diagnostic assays and vaccines for control of S. agalactiae and S. aureus infections in camels. This will ensure improvement in health and productivity of camels.
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| 3. |
- Zubair, Saima, et al.
(författare)
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Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel
- 2015
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), similar to 18 % were within the variable genome (shared among multiple but not all isolates) and similar to 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.
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| 4. |
- Zubair, Saima, et al.
(författare)
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Genome sequence of Streptococcus agalactiae strain 09mas018883, isolated from a Swedish cow
- 2013
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Ingår i: Genome Announcements. - 2169-8287. ; 1, s. 1-2
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Tidskriftsartikel (refereegranskat)abstract
- We announce the complete genome sequence of Streptococcus agalactiae strain 09mas018883, isolated from the milk of a cow with clinical mastitis. The availability of this genome may allow identification of candidate genes, leading to discovery of antigens that might form the basis for development of a vaccine as an alternative means of mastitis control.
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| 5. |
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