Genome analysis reveals three genomospecies in Mycobacterium abscessus

Abstract

BackgroundMycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described.ResultsIn-depth analysis of 14 published M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors (including PE, PPE, LpqH, MCE, Yrbe and type VII secretion system ESX3 and ESX4) varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by β-lactam antibiotics and an Ambler class A β-lactamase for which inhibitors exist.ConclusionsOur comparative analysis indicates that M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-359) contains supplementary material, which is available to authorized users.

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.…”

“…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.…”

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

“…Although no information on MLST sequence types was available for our isolates, our VNTR clusters were grouped into large clonal complexes as well as global epidemiological clones that were consistent with MLST (Macheras et al, 2014). Furthermore, Malaysian M172 strain, one of the Cluster C strains in the VNTR analysis, was grouped to the Cluster 2B (C2B) strains isolated from Nepalese and English patients by wholegenome sequencing (Sassi & Drancourt, 2014). In contrast, M18 with the Cluster B VNTR profile belongs to the C2A Cluster A includes Mab reference strain and one clarithromycin-resistant strain on day 3 Fig.…”

“…strains from other Malaysian and French patients (Sassi & Drancourt, 2014). Our study did not consider epidemiological background or transmission routes amongst M. abscessus complex infectious patients.…”

Activity of LCB01-0371, a Novel Oxazolidinone, against Mycobacterium abscessus

“…Furthermore, the M. abscessus genome encodes MmpL proteins and ABC-type multidrug transporters that are involved in drug efflux. This intrinsic transporter system pumps drugs out of the cell and physiologically protects the bacteria against toxic molecules (9). Moreover, M. abscessus has the ability to modify or inactivate antibiotics using enzymes.…”