Latvijā sastopamo Mycobacterium tuberculosis izolātu visa genoma ģenētiskās dažādības analīze
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Latvijas Universitāte
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Abstract
Tuberkuloze ir plaušu infekcijas slimība, kuru izraisa baktērija Mycobacterium tuberculosis. Starp
dažādiem Mycobacterium tuberculosis celmiem novērota atšķirīga ietekme uz infekcijas norises gaitu.
Pilna genoma sekvencēšana ir īpaši piemērota metode šīs baktērijas ģenētiskās piederības analīzei.
Pētījumā tika analizēta ģenētiskā piederība septiņiem Latvijā sastopamiem Mycobacterium
tuberculosis izolātiem, pamatojoties uz viena nukleotīda variācijām un insercijas sekvences IS6110
integrācijas pozīcijām genomā. Dati tika iegūti, izmantojot Ion Torrent nākamās paaudzes
sekvencēšanas tehnoloģijas. Datu analīze tika veikta ar datorprogrammu GATK, Samtools, snpEff,
VarScan, BRAT, Trimmomatic, FastTree, Mega 5.0 un programmēšanas valodu Perl, Python un C
palīdzību.
Visiem septiņiem izolātiem tika noteikta ģenētiskā piederība pie LAM saimes LAM-RUS ģenētiskās
apakšgrupas. Iegūtos rezultātus iespējams pielietot jaunu Mycobacterium tuberculosis celmu
genotipēšanas algoritmu izstrādē.
Atslēgvārdi: Nākamās paaudzes sekvencēšana, Mycobacterium tuberculosis, filoģenētiskā analīze
Tuberculosis is an infectious pulmonary disease, caused by bacterium Mycobacterium tuberculosis. It is observed that there is diverse impact on course of infection caused by various strains of Mycobacterium tuberculosis. Whole genome sequencing is particularly powerful technique for analysis of Mycobacterium tuberculosis genetic diversity. In this study the genetic relevance of seven Mycobacterium tuberculosis isolates from Latvia was analyzed based on single nucleotide variations and on integration positions of insertion sequence IS6110 in the genome. Data were obtained with Ion Torrent next-generation sequencing technology. Data analysis was performed with GATK, Samtools, snpEff, VarScan, BRAT, Trimmomatic, FastTree, Mega 5.0 and programming languages Perl, Python, C. It was determined that all seven isolates belong to LAM family LAM-RUS genetic subgroup. It is possible to apply these results in development of new Mycobacterium tuberculosis strain genotyping algorithms. Keywords: Next-generation sequencing, Mycobacterium tuberculosis, phylogenetic analysis
Tuberculosis is an infectious pulmonary disease, caused by bacterium Mycobacterium tuberculosis. It is observed that there is diverse impact on course of infection caused by various strains of Mycobacterium tuberculosis. Whole genome sequencing is particularly powerful technique for analysis of Mycobacterium tuberculosis genetic diversity. In this study the genetic relevance of seven Mycobacterium tuberculosis isolates from Latvia was analyzed based on single nucleotide variations and on integration positions of insertion sequence IS6110 in the genome. Data were obtained with Ion Torrent next-generation sequencing technology. Data analysis was performed with GATK, Samtools, snpEff, VarScan, BRAT, Trimmomatic, FastTree, Mega 5.0 and programming languages Perl, Python, C. It was determined that all seven isolates belong to LAM family LAM-RUS genetic subgroup. It is possible to apply these results in development of new Mycobacterium tuberculosis strain genotyping algorithms. Keywords: Next-generation sequencing, Mycobacterium tuberculosis, phylogenetic analysis