Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains

Abstract

We report the complete genome sequences of 17 rapidly growing nontuberculous mycobacterial (NTM) strains, including 16 Mycobacterium abscessus complex strains and one M. immunogenum strain. These sequences add value to studies of the genetic diversity of rapidly growing NTM strains recovered from human specimens.

Genomic Analysis of Mycobacterium abscessus Complex Isolates from Patients with Pulmonary Infection in China

“…CC6 involves 5 ST39 strains: 4 are M. bolletii , and 1 is M. abscessus . In CC1, 7 M. abscessus clinical isolates show a close relationship (with an average of 667 SNP differences) with published strains originating from France ( M. abscessus ATCC 19977 and V06705) and the United States ( M. abscessus FLAC013) (Table S9) ( 30 – 32 ). In addition, 7 clinical isolates (UM190121T0086 and UM190527T008, -09, -15, -20, -30, and -76) in CC3 show an average of 471 SNP differences compared to the reference strain M. massiliense FLAC008 obtained from the United States ( 30 ).…”

“…In CC1, 7 M. abscessus clinical isolates show a close relationship (with an average of 667 SNP differences) with published strains originating from France ( M. abscessus ATCC 19977 and V06705) and the United States ( M. abscessus FLAC013) (Table S9) ( 30 – 32 ). In addition, 7 clinical isolates (UM190121T0086 and UM190527T008, -09, -15, -20, -30, and -76) in CC3 show an average of 471 SNP differences compared to the reference strain M. massiliense FLAC008 obtained from the United States ( 30 ). In contrast, M. massiliense strains FLAC012 ( 30 ) and CCUG48898 ( 33 ) show a distant relationship compared to the 69 clinical isolates, with approximately 58,891 SNP variations detected (Table S9).…”

“…In addition, 7 clinical isolates (UM190121T0086 and UM190527T008, -09, -15, -20, -30, and -76) in CC3 show an average of 471 SNP differences compared to the reference strain M. massiliense FLAC008 obtained from the United States ( 30 ). In contrast, M. massiliense strains FLAC012 ( 30 ) and CCUG48898 ( 33 ) show a distant relationship compared to the 69 clinical isolates, with approximately 58,891 SNP variations detected (Table S9). Among the 69 strains sequenced in this study, 7, 11, 2, and 5 strains belong to CC1, -3, -4, and -6, respectively, and 46, 11, and 10 are grouped in clades I, II, and III, respectively.…”

Complete genome sequence of Mycobacterium immunogenum strain C14-1.MIM isolated from a hospitalized lung transplant recipient

“…Mycobacterium immunogenum is a species of rapidly growing nontuberculous mycobacteria (NTM) that can cause community ( 1 , 2 ) and healthcare-associated ( 3 – 6 ) infections and outbreaks. Knowledge regarding the genomic content of M. immunogenum is limited, and few complete genomes have been reported ( 7 , 8 ).…”

Mycobacterial infections in carcasses of ruminants slaughtered at the two slaughterhouses of Kassala, Sudan

“…Reads were trimmed with Trimmomatic version 0.35 for Q30 in a sliding window of 20 bp and nextera adapter contamination discarding all reads shorter than 100 bp (Bolger et al, 2014). Trimmed paired and unpaired reads were assembled with SPAdes version 3.6.2 using the built-in read error correction based on k-mer frequencies and the 'careful' option (Bankevich et al, 2012;Caverly et al, 2016). The 16S gene sequence was predicted by the RNAmmer Prediction Server from the assembled contigs which were filtered for containing ribosomal sequences (Lagesen et al, 2007).…”