Mycobacterium abscessus, a taxonomic puzzle

Abstract

We read with interest the paper of Adekambi and coworkers [1] suggesting the reinstatement of Mycobacterium abscessus subsp. abscessus (A), M. abscessus subsp. 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.In the 3840 bp sequence of the rpoB gene obtained when the sequences of the type strains of A, B and M (deposited by Adekambi et al. in GenBank; AY147164, AY859692 and AY593981), have been cut to start and end at the same nucleotide positions, we obtained the following similarity values: A versus M=98.07 %; A v B=97.86 %; M v B=98.51 %; each of them corresponding to DDH>70 %.Adekambi et al. questioned our data produced, performing the wet lab DDH test with five replicates [11]. Instead they proposed results (Table 2 of [10]) inferred from rpoB similarity using the above mentioned formula. In our view, it is not valid to replace a complex assay that takes into account the whole genome (which is still considered the gold standard), with a formula based on just a single gene.Bioinformatic algorithms are available and validated in multiple studies, which can be used to infer the DDH from genomic data. The best known, in addition to Average Nucleotide Identity (ANI) [12], are the Genome to Genome Distance (GGD) [13,14] and the Genomic Signature-Delta Difference (GS-DD) [15].In our work we calculated the GGD, which is the equivalent in silico of DDH, using the software available at http://ggdc. dsmz.de/ggdc.php and obtained the following DDH-equivalent results: A v M=84.7 %; A v B=86.10 %; M v B=87.70 %; all clearly >70 % and not supportive of the status of independent species [12].We also calculated the GS-DD using the software available at www.cmbl.uga.edu/software/delta-differences.html, which again did not support the hypothesis of independent species (Table 1).We disagree, furthermore, in the assertion of Adekambi at al. (third page) in which we are said to have stated that ANI values >98.3 % are needed to support the status of subspecies. 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 %. Therefore ...

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

“…Much like Average Nucleotide Identity (ANI), the choice of a similarity method and a species cut-off for dDDH was based on mimicking traditional DDH as closely as possible, albeit without its problematic reproducibility; however, according to this criterion dDDH yielded better results than ANI and can thereby be seen as the method of choice (Meier-Kolthoff et al, 2013a ). For instance, the recent controversy regarding the subspecies of Mycobacterium abscessus (Adekambi et al, 2017 ; Tortoli et al, 2017 ) may have been avoided if dDDH had been preferred or pairwise comparison had been restricted to those involving type strains (Meier-Kolthoff et al, 2014c ).…”

Lipids of Clinically Significant Mycobacteria

“…Cattle diseases result from infection with related Mycobacterium farcinogenes and Mycobacterium senegalense (Chamoiseau 1979;Turenne 2019). The Mycobacterium abscessus complex consists of a group of rapidly growing, inherently drug-resistant, nontuberculous mycobacteria, differentiated into three subspecies, M. abscessus, M. massiliense, and M. bolleti, responsible for a wide spectrum of skin and soft-tissue diseases, central nervous system infections, bacteremia, and ocular and other infections (Medjahed et al 2010;Tortoli et al 2018). Mycobacterium abscessus is a serious pathogen for patients with cystic fibrosis (Parkins and Floto 2015;Martiniano and Nick 2015;Skolnik et al 2016;Ryan and Byrd 2018) and closely related Mycobacterium chelonae can infect heart valve transplants (Wallace 1994).…”

A novel DNA chromatography method to discriminate Mycobacterium abscessus subspecies and macrolide susceptibility

“…massiliense (M. massiliense), and M. abscessus subsp. bolletii (M. bolletii) [3,4]. MABC causes a range of clinical infections including chronic pulmonary disease even in immunocompetent persons, as well as postsurgical or traumatic infections and skin and soft tissue infections [4À8].…”