Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus

Leao, Sylvia Cardoso; Tortoli, Enrico; Euzéby, J.; García, María Jesús García

doi:10.1099/ijs.0.023770-0

Cited by 193 publications

(129 citation statements)

References 15 publications

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“…abscessus and M. abscessus subsp. bolletii (17), although recent population and comparative genomic studies support the three previously recognized subspecies, i.e., M. abscessus subsp. abscessus, M. abscessus subsp.…”

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Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

et al. 2014

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f Nontuberculous mycobacterial infections caused by Mycobacterium abscessus are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical M. abscessus isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical M. abscessus isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M. abscessus subsp. abscessus isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977 T . Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical M. abscessus strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen. N ontuberculous mycobacteria (NTM) represent a diverse group of environmental and pathogenic bacteria that are increasing in clinical prevalence in the United States (1) and other countries (2, 3). NTM are thought to be acquired primarily through environmental exposure (4), as they reside in water, biofilms, and soil environments (5, 6), although a few recent studies provide evidence of possible person-to person transmission among individuals with cystic fibrosis (CF) (7,8). Mycobacterium abscessus is the second most clinically prevalent NTM species in pulmonary NTM infections (1, 9, 10), with Mycobacterium avium complex (MAC) being the most prevalent. M. abscessus infections are challenging to treat because they are innately resistant to many antimicrobials, including some that are effective against Mycobacterium tuberculosis and other mycobacteria (11-13). Acquired antibiotic resistance has been observed in some M. abscessus strains, with mechanisms of resistance ranging from mutational resistance to aminoglycosides (14) to mutational (15) and inducible (16) resistance to macrolides.The current taxonomy of M. abscessus recognizes two subspecies, M. abscessus subsp. abscessus and M. abscessus subsp. bolletii (17), although recent population and comparative genomic studies support the three previously recognized subspecies, i.e., M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii (18)(19)(20)(21). This delineation is important because clinical studies suggest diff...

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Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

et al. 2014

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“…bolletii into a single subspecies called M. abscessus subsp. bolletii (Leao et al, 2011). However, wholegenome sequencing supported the separation as three subspecies (Bryant et al, 2013).…”

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confidence: 99%

Investigation of the population structure of Mycobacterium abscessus complex strains using 17-locus variable number tandem repeat typing and the further distinction of Mycobacterium massiliense hsp65 genotypes

Yoshida

Arikawa²,

Tsuyuguchi

et al. 2015

Journal of Medical Microbiology

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Mycobacterium abscessus complex is a significant pathogen in patients with non-cystic fibrosis (non-CF). Nevertheless, there is little description of the genetic diversity of this species. The aims of this study were to investigate the distribution of M. abscessus complex isolated from respiratory specimens by variable number tandem repeat (VNTR) typing. The results of 104 clinical isolates from 104 non-CF patients were compared using PFGE, hsp65 genotypes and clarithromycin susceptibility. The allelic diversity (Hunter-Gaston Discriminatory Index) of the 17 loci examined by VNTR typing was high (0.977). We determined that C28 sequevar erm(41) genotypes and clarithromycin-acquired resistance isolates were scattered in the minimum spanning tree. Intriguingly, VNTR typing and PFGE were highly congruent and revealed that there were clear examples of grouping of isolates from different individuals amongst both M. abscessus and M. massiliense, and showed five clusters of distinct identical isolates. Within these clusters, M. massiliense hsp65 type I formed three different clusters. Although the distribution of M. massiliense hsp65 type II-1 was low (9.3 %), M. massiliense hsp65 type II-1 isolates separated from clusters contained hsp65 type I isolates. Thus, M. massiliense hsp65 genotypes could be discriminated by analysing VNTRs with sufficient genetic distance for intra-species-level discrimination.

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“…bolletii, and that a new subspecies, M. abscessus subsp. abscessus, should be designated (9). However, a recent whole-genome study strongly supported the hypothesis that the species can be divided into at least three subspecies: M. abscessus subsp.…”

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Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in Clinical Isolates by Multiplex PCR

et al. 2014

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The rapidly growing mycobacterium M. abscessus sensu lato is the causative agent of emerging pulmonary and skin diseases and of infections following cosmetic surgery and postsurgical procedures. M. abscessus sensu lato can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Clinical isolates of rapidly growing mycobacteria were previously identified as M. abscessus by DNA-DNA hybridization. More than 30% of these 117 clinical isolates were differentiated as M. abscessus subsp. massiliense using combinations of multilocus genotyping analyses. A much more cost-effective technique to distinguish M. abscessus subsp. massiliense from M. abscessus subsp. abscessus, a multiplex PCR assay, was developed using the whole-genome sequence of M. abscessus subsp. massiliense JCM15300 as a reference. Several primer sets were designed for single PCR to discriminate between the strains based on amplicons of different sizes. Two of these single-PCR target sites were chosen for development of the multiplex PCR assay. Multiplex PCR was successful in distinguishing clinical isolates of M. abscessus subsp. massiliense from samples previously identified as M. abscessus. This approach, which spans whole-genome sequencing and clinical diagnosis, will facilitate the acquisition of more-precise information about bacterial genomes, aid in the choice of more relevant therapies, and promote the advancement of novel discrimination and differential diagnostic assays. bolletii, and that a new subspecies, M. abscessus subsp. abscessus, should be designated (9). However, a recent whole-genome study strongly supported the hypothesis that the species can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii (10). M. abscessus subsp. massiliense was initially isolated from the sputum of a patient with pneumonia in France in 2004 (5). In 2005, an outbreak of M. abscessus subsp. massiliense infection was linked to intramuscular injections of an antimicrobial agent in South Korea (11). This bacterium was also the source of a lethal case of sepsis in Italy (12) and has been found in cystic fibrosis patients in France (13). Several cases of bacteremia and cutaneous pulmonary infections have also been reported in Japan (14-17).A novel approach is required to differentiate M. abscessus subsp. massiliense from M. abscessus subsp. abscessus and M. abscessus subsp. bolletii because conventional methods such as biochemical assays and 16S rRNA genotyping cannot make the discrimination. Moreover, the clinical profile of M. abscessus subsp. massiliense is different from those of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii. In particular, antibiotic treatment with clarithromycin is more effective against M. abscessus subsp. massiliense lung infections, with resistance developing more readily in cases of M. abscessus subsp. abscessus lung disease. Therefore, differentiating ...

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Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus

Cited by 193 publications

References 15 publications

Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

Investigation of the population structure of Mycobacterium abscessus complex strains using 17-locus variable number tandem repeat typing and the further distinction of Mycobacterium massiliense hsp65 genotypes

Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in Clinical Isolates by Multiplex PCR

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