Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii and designation of Mycobacterium abscessus subsp. massiliense comb. nov.

Abstract

The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).

Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics

“…bolletii CCUG 50184 T , and M. abscessus subsp. massiliense CCUG 48898 T showed a GGD value higher than the proposed cutoff (0.0266 to 0.0288 distance values); this result is in agreement with the recent data found by Tortoli and co-workers (Tortoli et al, 2016) when describing the subspecies within M. abscessus . However, the calculated dDDH percentages were higher than 70%, therefore within the value expected for a single species (Supplementary Table 6).…”

“…massiliense , and M. abscessus subsp. bolletii (Leao et al, 2009, 2011; Tortoli et al, 2016), M. immunogenum (Wilson et al, 2001), M. salmoniphilum (Ross, 1960; Whipps et al, 2007), M. franklinii (Simmon et al, 2011; Nogueira et al, 2015a), and M. saopaulense (Nogueira et al, 2015b). …”

Mycobacterium abscessus, a taxonomic puzzle

“…massiliense (M) and M. abscessus subsp. bolletii (B) as independent species.This paper is in clear contradiction with our own recent work [2] published in 2016.The claim of the authors (1st page) that postgenomic analysis 'unambiguously supports the reinstatement of species' seems to us at least highly questionable; in none of the studies they cited in their paper [3][4][5][6][7][8], with the exception of one study [9] done in collaboration with the same authors, is the status of subspecies questioned.A major argument supporting the suggestion of Adekambi et al was published by him in 2008 [10]. The major conclusions of this work were that 1) an rpoB gene similarity 97.7 % correlates with a DNA-DNA Hybridization (DDH) <70 %; and 2) the DDH may be inferred by the formula: 5.98(rpoB similarity)-2516.1.…”

“…Fig. 1 of our paper [2] reports the results of our analysis of 46 genomes (43 clinical isolates+3 type strains) showing the ANI variability which, among strains belonging to the three taxa (A, B and M), ranged from 96.6 to 97.6 %. Within each single taxon (A or B or M), this variability ranged from 98.5 to 99.9 %.…”

Evaluation of the GenoType® NTM DR for Subspecies Identification and Determination of Drug Resistance in Clinical M. abscessus Isolates

“…massiliense and M. abscessus subsp. bolletii [2][3][4]. Macrolides and Amikacin are key drugs in the treatment of M. abscessus disease [1,5].…”