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

Tortoli, Enrico; Kohl, Thomas A.; Brown‐Elliott, Barbara A.; Trovato, Alberto; Leão, Sylvia Cardoso; García, María Jesús García; Vasireddy, Sruthi; Turenne, Christine Y.; Griffith, David E.; Philley, Julie V.; Baldan, Rossella; Campana, S.; Cariani, Lisa; Colombo, Carla; Taccetti, Giovanni; Teri, Antonio; Niemann, Stefan; Wallace, Richard J.; Cirillo, Daniela María

doi:10.1099/ijsem.0.001376

Cited by 185 publications

(89 citation statements)

References 33 publications

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“…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).…”

Section: Discussionsupporting

confidence: 92%

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Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics

et al. 2017

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Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others. Based on ANI and GGD the isolates were identified as M. chelonae (14 isolates), M. franklinii (2 isolates) and M. salmoniphium (1 isolate). The remaining 9 isolates were subdivided into three novel putative genomospecies. Phenotypic analyses including drug susceptibility testing, as well as whole genome comparison by TETRA and delta differences, were not helpful in separating the groups revealed by ANI and GGD. The analysis of standard four conserved genomic regions showed that rpoB alone and the concatenated sequences clearly distinguished the taxonomic groups delimited by whole genome analyses. In conclusion, the CHII INNO-LiPa is not a homogeneous cluster; on the contrary, it is composed of closely related different species belonging to the M. chelonae-M. abscessus complex and also several unidentified isolates. The detection of these isolates, putatively novel species, indicates a wider inner variability than the presently known in this complex.

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Section: Discussionsupporting

confidence: 92%

“…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). …”

Section: Introductionmentioning

confidence: 99%

Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics

et al. 2017

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“…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.…”

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confidence: 54%

“…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 %.…”

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confidence: 99%

Mycobacterium abscessus, a taxonomic puzzle

Tortoli

Kohl

Trovato

et al. 2018

International Journal of Systematic and Evolutionary Microbiology

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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 ...

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

Section: Introductionmentioning

confidence: 99%