Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Abstract

The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family Mycobacteriaceae , including the genus Mycolicibacterium , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the Mycobacteriaceae mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus Mycobacterium . To fill in the gaps in these issues, we performed a systematic in silico study of these mobile elements based on 242 available genomes of the genus Mycolicibacterium . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family Mycobacteriaceae , this study showed an abundance of these genetic elements in a dozen species of the genus Mycolicibacterium .

Mycolicibacterium fortuitum genomic epidemiology, resistome and virulome

“…In fact, a previous survey of Mycolicibacterium mobilome showed an 8 kb non-mobilisable plasmid, without association to any ARG, shared by two M. fortuitum metagenomes (SCH6189132/cluster II/ South Africa and MTB7/cluster III/Morocco). (18) The M. fortuitum virulome was accessed using ABRicate based on Virulence Factor Database. Four genes were identified in all genomes: icl, ideR, phoP, and relA (except relA in GA-0871).…”

“…Resistome and virulome analysis -M. fortuitum genomes were surveyed for antibiotic resistance and virulence genes through ABRicate (https://github.com/tseemann/abricate) based on The Comprehensive Antibiotic Resistance Database (16) and Virulence Factor Database. (17) In addition, T7SS was searched based on the identification of the T7SS core proteins (18) using HMMer package v3.1b2. (19)…”

Multidrug-resistant Mycolicibacterium fortuitum infection in a companion cat (Felis silvestris catus) in Brazil

“…Through genomic analysis, we identified several genes on the chromosome associated with antibiotic resistance, suggesting that they are inherent to this organism and not related to plasmid-mediated acquisition. Indeed, in a previous in silico study of Mycolicibacterium plasmids, no notable antibiotic resistance genes were observed in plasmids of M. fortuitum [ 23 ]. Another aspect verified in the genome of the 7G strain was the type VII, present in four loci and reported to be associated with virulence, iron uptake and conjugation in several species of the Mycobacteriaceae family [ 24 ].…”

Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids

“…Plasmids that encoded a relaxase gene and that did not encode VirB4 and/or VirD4 were considered mobilizable, while those encoding relaxase, VirB4, and VirD4 were considered conjugative. Plasmids lacking relaxases were considered incapable of self-mobilization, non-mobilizable 42 , 44 . However, it is possible that unknown origin of transfer (oriT) sequences are present in these plasmids, which would allow their mobilization only in a relaxase- in trans mechanism 46 , 47 .…”