19977 reference strain genome  (ATCC)

Journal: Emerging Infectious Diseases

Article Title: High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks

doi: 10.3201/eid2003.131106

Figure Lengend Snippet: Twenty-four Mycobacterium abscessus group strain genomes analyzed for genetic relatedness*

Article Snippet: To replicate data from the Papworth cystic fibrosis outbreak clusters 1 and 2 ( ) by using a similar approach, we mapped sequencing reads from the subset of 6 Papworth isolates, together with reads with from the 3 Seattle cystic fibrosis isolates and soft tissue strain CRM-0020 from Brazil , onto the M. abscessus type strain ATCC 19977 T reference genome by using BWA software ( ).

Techniques:

Journal: Emerging Infectious Diseases

Article Title: High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks

doi: 10.3201/eid2003.131106

Figure Lengend Snippet: Neighbor-joining phylogenetic tree based on whole-genome multiple alignment of 24 Mycobacterium abscessus group genomes. Genomes in were aligned by using Mugsy , core segments of the alignment were identified by using Phylomark , and resulting concatenated nucleotide sequences were used for construction of the midpoint-rooted neighbor-joining phylogenetic tree by using MEGA . Strains from an outbreak of M. abscessus subsp. massiliense infections at a cystic fibrosis center in Seattle, Washington, USA, are indicated in red; strains from an outbreak of M. abscessus subsp. massiliense infections at a cystic fibrosis center in Papworth, UK, are indicated in blue (cluster 1) and purple (cluster 2); strains from Brazil are indicated in magenta; and the M. abscessus subsp. massiliense type strain is indicated in green. Boostrap values obtained after 100 iterations were ≥97 for all nodes of the tree except 70 for the node separating strain M115 from the outbreak cluster and 40 and 41 for 2 nodes within the Papworth cluster 1 . SNPs, single-nucleotide polymorphisms.

Article Snippet: To replicate data from the Papworth cystic fibrosis outbreak clusters 1 and 2 ( ) by using a similar approach, we mapped sequencing reads from the subset of 6 Papworth isolates, together with reads with from the 3 Seattle cystic fibrosis isolates and soft tissue strain CRM-0020 from Brazil , onto the M. abscessus type strain ATCC 19977 T reference genome by using BWA software ( ).

Techniques:

Journal: Emerging Infectious Diseases

Article Title: High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks

doi: 10.3201/eid2003.131106

Figure Lengend Snippet: Venn diagram of core single-nucleotide polymorphisms (SNPs) shared by outbreak localities. Core segments of the Mugsy alignment of the 20 Mycobacterium abscessus subsp. massiliense genomes were parsed for SNPs shared by different subsets of outbreak localities. Each field in the Venn diagram represents nucleotides that are identical among isolates of that field but different in other isolates represented on the diagram and non–outbreak-related M. abscessus subsp. massiliense strains 1S-151–0930, 5S-0817, M115, M139, M154, and the type strain CCUG 48898 T . Details on SNPs and genes they affect are shown in the .

Article Snippet: To replicate data from the Papworth cystic fibrosis outbreak clusters 1 and 2 ( ) by using a similar approach, we mapped sequencing reads from the subset of 6 Papworth isolates, together with reads with from the 3 Seattle cystic fibrosis isolates and soft tissue strain CRM-0020 from Brazil , onto the M. abscessus type strain ATCC 19977 T reference genome by using BWA software ( ).

Techniques:

Journal: Emerging Infectious Diseases

Article Title: High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks

doi: 10.3201/eid2003.131106

Figure Lengend Snippet: Detection of rpoB and secA1 SNP signature in the Mycobacterium abscessus group and rapidly growing mycobacteria*

Article Snippet: To replicate data from the Papworth cystic fibrosis outbreak clusters 1 and 2 ( ) by using a similar approach, we mapped sequencing reads from the subset of 6 Papworth isolates, together with reads with from the 3 Seattle cystic fibrosis isolates and soft tissue strain CRM-0020 from Brazil , onto the M. abscessus type strain ATCC 19977 T reference genome by using BWA software ( ).

Techniques: In Silico

Journal: Emerging Infectious Diseases

Article Title: High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks

doi: 10.3201/eid2003.131106

Figure Lengend Snippet: Neighbor-joining phylogenetic tree based on 13-target multilocus sequences types from 20 Mycobacterium abscessus subsp. massiliense genomes. Electronic PCR was performed on the M. abscessus subsp. massiliense genomes listed in by using primer pairs for 13 housekeeping genes ( cya , gdhA , argH , glpK , gnd , murC , pgm , pknA , pta , pur , rpoB , hsp65 , and secA1 ), including new primers designed as part of this study. Nucleotide sequences from each gene were concatenated for each genome and aligned by using ClustalW , and the core alignment was used for construction of a midpoint-rooted neighbor-joining phylogenetic tree by using MEGA . Strains from an outbreak of M. abscessus subsp. massiliense infections at a cystic fibrosis center in Seattle, Washington, USA, are indicated in red; strains from an outbreak of M. abscessus subsp. massiliense infections at a cystic fibrosis center in Papworth, UK, are indicated in blue (cluster 1) and purple (cluster 2); strains from Brazil are indicated in magenta; and the M. abscessus subsp. massiliense type strain is indicated in green. The longer branch length for Papworth isolate 12c was caused by low-quality nucleotides (single-nucleotide polymorphisms [SNPs]) located at the edge of Velvet contigs.

Article Snippet: To replicate data from the Papworth cystic fibrosis outbreak clusters 1 and 2 ( ) by using a similar approach, we mapped sequencing reads from the subset of 6 Papworth isolates, together with reads with from the 3 Seattle cystic fibrosis isolates and soft tissue strain CRM-0020 from Brazil , onto the M. abscessus type strain ATCC 19977 T reference genome by using BWA software ( ).

Techniques: