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16S rRNA amplicon sequencing of biopsy samples taken from Finnish dairy cattle

ABSTRACT: 16S rRNA amplicon sequencing of biopsy samples taken from Finnish dairy cattle

PROVIDER: PRJEB75508 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13508700_1.fastq.gz	Fastqsanger.gz
	ERR13508700_2.fastq.gz	Fastqsanger.gz
	ERR13508800_1.fastq.gz	Fastqsanger.gz
	ERR13508800_2.fastq.gz	Fastqsanger.gz
	ERR13508701_1.fastq.gz	Fastqsanger.gz

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Project description:Background Bordetella pertussis is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years. Methodology/Principal Findings The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of the genome of Tohama I, the strain of which the genome has been sequenced [21]. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared to the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to ion transport, metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481. Conclusion/Significance Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations. Keywords: comparetive genomic hybridisation

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16S rRNA amplicon sequencing of biopsy samples taken from Finnish dairy cattle

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