Characterization of the cluster MabR prophages of Mycobacterium abscessus and Mycobacterium chelonae

Abstract

Mycobacterium abscessus is an emerging pathogen of concern in cystic fibrosis and immunocompromised patients and is considered one of the most drug-resistant mycobacteria. The majority of clinical Mycobacterium abscessus isolates carry 1 or more prophages that are hypothesized to contribute to virulence and bacterial fitness. The prophage McProf was identified in the genome of the Bergey strain of Mycobacterium chelonae and is distinct from previously described prophages of Mycobacterium abscessus. The McProf genome increases intrinsic antibiotic resistance of Mycobacterium chelonae and drives expression of the intrinsic antibiotic resistance gene, whiB7, when superinfected by a second phage. The prevalence of McProf-like genomes was determined in sequenced mycobacterial genomes. Related prophage genomes were identified in the genomes of 25 clinical isolates of Mycobacterium abscessus and assigned to the novel cluster, MabR. They share less than 10% gene content with previously described prophages; however, they share features typical of prophages, including polymorphic toxin-immunity systems.

Keywords: Mycobacterium; bacteriophage; genome; prophage.

Fig. 1.

Diversity of MabR prophages. a) Dotplot comparison of MabR prophages. b) Phylogenetic network representation of cluster MabR prophages and M. abscessus prophages (Dedrick et al. 2021) based on shared gene content as described by Pope et al. (2015). Nodes represent individual prophage; circles represent prophage clusters. Scale marker indicates substitutions/site.

Fig. 2.

MabR prophage integration locations. The 3 integration schemes used by MabR prophage are shown as attB site locations (black bars) shown relative to M. abscessus ATCC 19977 genes for reference. Rightward and leftward transcribed genes are indicated by arrows with their ATCC 19977 gene number. Both tRNAs (t5022c and t5030c) are transcribed in the leftward direction. Not shown are McProf and prophiFVLQ01-1, which utilize the attB-18 site described by Dedrick et al. (2021).

Fig. 3.

Organization of MabR genomes. MabR genomes are shown with pairwise nucleotide sequence similarity displayed by colors between genomes: purple is the most similar and red is the least similar above a BLASTN E threshold of 10⁻⁵. The ruler represents the coordinates of the genome. Forward and reverse-transcribed genes are shown as boxes above and below the ruler, respectively. Maps were generated using Phamerator and the database, “Actino_Mab_Draft (version 20)” (Cresawn et al. 2011).

Fig. 4.

Genome organization of a) prophiMcProf and b) prophiFSQJ01-1. The ruler represents the coordinates of the genome. Forward and reverse-transcribed genes are shown as boxes above and below the ruler, respectively. Genes are colored according to their assigned Phamily with the Phamily number shown above each gene with the number of Phamily members in parentheses. Genome maps were generated using Phamerator and the database, “Actino_Mab_Draft (version 20)” (Cresawn et al. 2011).

Fig. 5.

Organization of MabR PT-Imm systems. MabR genomes are aligned at their PT-Imm systems beginning at the 3′ end of the predicted immunity proteins. Genomes are displayed as described in Fig. 2 but are ordered in such a way that genomes with the most similarity in this region are next to each other. Also shown are the motifs/domains found at the N- and C-termini of MabR PTs. All predicted PTs have a single WXG-100 motif at the N-terminus while the C-terminus is variable. Note that gp99 in prophiFSIL01-1 and prophiFSAT01-1 has no predicted function and is included to show the relationship of the PT systems to the genome ends.

Fig. 6.

MabR PT-Imm systems found in non-MabR prophage. Genomes are displayed as described in Figs. 2 and 5. prophiGD43-5 and prophiGD79-1 belong to clusters MabK and MabQ, respectively.