Draft Genome Sequences of Three Mycobacterium chimaera Respiratory Isolates

Mycobacterium chimaera is an opportunistic human pathogen implicated in both pulmonary and cardiovascular infections. Here, we report the draft genome sequences of three strains isolated from human respiratory specimens.

(NTM) of the Mycobacterium avium complex (MAC) associated with opportunistic infections in patients with underlying lung disease (1). More recently, M. chimaera has been identified as a causative agent of postoperative cardiovascular infections in several European countries (2,3). In spite of its emerging clinical relevance, the genetics and pathophysiology of this species remain largely uncharacterized and whole-genome sequencing studies of this pathogen are yet to be described.
To gain insight into the genomics of this species, we undertook whole-genome sequencing of three clinical M. chimaera respiratory isolates, recovered from specimens at the Irish Mycobacteria Reference Laboratory (Dublin, Ireland). M. chimaera isolates were identified by sequence analysis of the 16S rRNA gene and 16S-23S rDNA spacer (ITS) region (4,5). Resultant 16S and ITS sequences shared 100% identity with M. chimaera strain FI-0169T (AJ548480.2) originally described by Tortoli and colleagues (1). Total M. chimaera genomic DNA from each isolate was sequenced using a paired-end approach on an Illumina MiSeq instrument (TrinSeq, Trinity College, Dublin, Ireland). Sequence reads were quality-trimmed using Trimmomatic and assembled using Spades version 3.6.0 (6, 7). Resultant contigs were oriented to the M. intracellulare MOTT-02 genome (CP003323.1) using ABACAS (8). Gene annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP; http://www .ncbi.nlm.nih.gov/genome/annotation_prok). The features and assembly statistics of all three M. chimaera isolates are detailed in Table 1.
Comparative analysis of M. chimaera genome assemblies revealed an average nucleotide identity (ANI) of 99.9% between strains, consistent with their assignment to a common species (9). In contrast, a lower ANI of 97.7% was obtained when assemblies were compared to M. intracellulare-a closely related yet distinct species of the MAC. The observed ANI values correlate with observed divergence in the M. chimaera 16S rRNA gene and ITS regions relative to M. intracellulare and lend credence to the use of the 16S rRNA gene and ITS sequence analysis to distinguish M. chimaera clinically (1, 2, 5).
Analysis of reciprocal BLAST hits among non-pseudogenecoding sequences revealed a set of 4,951 genes common to all three M. chimaera isolates (10). Strains MCIMRL2 and MCIMRL6 exhibited a higher degree of similarity to each other than to MCI-MRL4, sharing 5,230 genes, whereas MCIMRL4 shared 4,993 and 5,044 genes with MCIMRL2 and MCIMRL6, respectively. MCI-MRL4 divergence was also reflected in comparative analysis of the 4,951 common gene sequences; MCIMRL4 diverged from MCI-MRL2 and MCIMRL6 by 2,763 and 2,825 "core" single nucleotide variants (SNVs), respectively, whereas only 242 SNVs separated MCIMRL2 and MCIMRL6. Among the common genes shared by all three strains were putative host-interaction factors, including several conserved type-VII secretion systems and multiple PE/ PPE/PE-GRS-family proteins, which represent important virulence determinants in other pathogenic mycobacteria (11).
This report represents the first whole-genome sequencing study of M. chimaera-an emerging opportunistic pathogen of the MAC. The data will serve as a useful reference for M. chimaera crossmark genomic epidemiology and provide the first insights into the potential virulence determinants of this pathogen. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.