Complete Genome of the Attenuated Sparfloxacin-Resistant Streptococcus agalactiae Strain 138spar

Pridgeon, Julia W.; Zhang, Dunhua; Zhang, Lee

doi:10.1128/genomea.00431-14

Cited by 4 publications

(3 citation statements)

References 14 publications

(17 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An Ion Torrent PGM (Life Technologies, Inc., Carlsbad, CA) was used for sequencing after extracting DNA from stationary-phase cells of GB1 using standard techniques as described by Thijs et al ( 6 ). In total, 1.52 million reads (mean length 265 bases) generated 403 Mb of data (>362 M Q20 bases) in Torrent Suite 4.2.1.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus

et al. 2016

View full text Add to dashboard Cite

show abstract

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Representation of the eight genomic islands predicted using the same software by comparing the S. agalactiae GBS85147 strain against the 16 complete genomes of the S. agalactiae species obtained from the NCBI database. From the inner to outer ring (black) we used the genome of S. agalactiae GBS85147 strain as a reference, followed by GC - (purple) and GC + (green) content, the strains of S. agalactiae 09mas018883 [ 35 ], 138P [ 56 ], 138spar [ 57 ], 2603 V/R [ 58 ], A909 [ 59 ], CNCTC10/84 [ 60 ], COH1 [ 61 ], GBS1-NY [ 62 ], GBS2-NM [ 62 ], GBS6 [ 62 ], GD201008-001 [ 32 ], ILRI005 [ 63 ], ILRI112 [ 63 ], NGBS061 [ 64 ], NGBS572 [ 64 ] and SA20-06 [ 65 ] respectively. The last external ring in 4A display the pathogenic islands while the last external ring in 4B display the genomic islands, respectively …”

Section: Insight From the Genome Sequencementioning

confidence: 99%

Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of type Ia isolated from human oropharynx

Aguiar

Mariano

Viana

et al. 2016

Stand in Genomic Sci

View full text Add to dashboard Cite

Streptococcus agalactiae, also referred to as Group B Streptococcus, is a frequent resident of the rectovaginal tract in humans, and a major cause of neonatal infection. The pathogen can also infect adults with underlying disease, particularly the elderly and immunocompromised ones. In addition, S. agalactiae is a known fish pathogen, which compromises food safety and represents a zoonotic hazard. This study provides valuable structural, functional and evolutionary genomic information of a human S. agalactiae serotype Ia (ST-103) GBS85147 strain isolated from the oropharynx of an adult patient from Rio de Janeiro, thereby representing the first human isolate in Brazil. We used the Ion Torrent PGM platform with the 200 bp fragment library sequencing kit. The sequencing generated 578,082,183 bp, distributed among 2,973,022 reads, resulting in an approximately 246-fold mean coverage depth and was assembled using the Mira Assembler v3.9.18. The S. agalactiae strain GBS85147 comprises of a circular chromosome with a final genome length of 1,996,151 bp containing 1,915 protein-coding genes, 18 rRNA, 63 tRNA, 2 pseudogenes and a G + C content of 35.48 %.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-016-0158-6) contains supplementary material, which is available to authorized users.

show abstract

“…Pridgeon et al successfully generated an attenuated S. agalactiae strain 138spar from tilapia-derived S. agalactiae serotype Ib strain 138P in laboratory using a sparfloxacin resistance strategy; comparative genome analysis indicated that S. agalactiae 138spar had 22 deletions larger than 6 bp and 26 SNVs [ 7 , 9 ]. Although S. agalactiae serotype Ib strain can cause infection and diseases in various fishes and amphibians, there is no report of its pathogenicity to humans, and comparative genome and phylogenetic studies indicate that S. agalactiae serotype Ia and Ib are distantly related [ 6 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016

Wang

Huang

et al. 2015

BMC Genomics

View full text Add to dashboard Cite

BackgroundStreptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia.MethodsWe performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains.ResultsThe genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes.ConclusionsThe genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2026-y) contains supplementary material, which is available to authorized users.

show abstract

Complete Genome of the Attenuated Sparfloxacin-Resistant Streptococcus agalactiae Strain 138spar

Cited by 4 publications

References 14 publications

Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus

Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus

Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of type Ia isolated from human oropharynx

Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016

Contact Info

Product

Resources

About