Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample

GENOME ANNOUNCEMENT

Mycobacterium avium subsp. hominissuis (MAH) is one of the four subspecies of M. avium within the M. avium complex (MAC) (1). MAH is widely present in soil and water, and it is an opportunistic pathogen of humans and swine (1). Susceptible humans, particularly those with T-cell deficiencies, are thought to acquire infection through exposure to drinking water or household aerosols, and infected individuals may develop pulmonary and soft tissue infections, lymphadenitis, or disseminated disease (1, 2). The incidence of human MAH disease specifically is unknown, though there is increasing global incidence of disease caused by nontuberculous mycobacteria (NTM), which constitute mycobacteria other than Mycobacterium leprae or those in the M. tuberculosis complex (3). Here, we report the complete genome sequence of MAH H87, a strain isolated from tap water of an indoor sink faucet (4). H87 exhibits the ability to infect and survive within multiple species of free-living amoebae, especially Acanthamoeba lenticulata (4).

DNA of MAH strain H87 was sequenced using Pacific Biosciences (PacBio) RSII single-molecular real-time technology at a depth of 278×, and de novo genome assembly was performed using the Hierarchical Genome Assembly Process (5). The genome was also sequenced with the Illumina MiSeq platform, resulting in 741,051 paired-end reads that were used to correct PacBio sequencing errors using Pilon version 1.20 (6). The finished H87 chromosome was compared to four additional MAC genomes, including M. avium 104 (GenBank accession no. CP000479.1), M. avium subsp. hominissuis TH135 (GenBank accession no. AP012555.1), M. intracellulare ATCC 13950 (GenBank accession no. CP003322.1), and M. chimaera AH16 (GenBank accession no. CP012885.2) using Mauve version 2.4.0 and the average nucleotide identity (ANI) calculator (7, 8). Gene prediction and annotation were conducted by the NCBI Prokaryotic Genome Annotation Pipeline.

The genome of H87 is a circular chromosome of 5,626,623 bp with a G+C content of 68.8%. The genome has 5,293 predicted genes, including 5,240 predicted coding sequences (CDSs) and 53 RNAs. Among the CDSs, 3,899 have functional annotations that could be assigned and 1,341 are annotated as hypothetical proteins. RNA genes include one rRNA operon with the 16S, 23S, and 5S rRNA subunits, 47 tRNAs, two ncRNAs, and one tmRNA. The H87 genome was aligned to four additional MAC genomes, and a total of 537,860 single nucleotide polymorphisms (SNPs) were identified. Relative to MAH H87, there are 37,506 SNPs in M. avium 104; 58,709 SNPs in MAH TH135; 381,471 SNPs in M. intracellulare ATCC 13950; and 377,485 SNPs in M. chimaera AH16. ANIs relative to the MAH H87 genome are 99.19% for M. avium 104, 98.74% for MAH TH135, 86.10% for M. intracellulare ATCC 13950, and 85.96% for M. chimaera AH16. Therefore, of the four genome comparisons, environmental strain H87 is most closely related to M. avium 104 [a strain isolated from an AIDS patient that is known to cause lung infections in a murine model (9, 10)] and MAH TH135 [a strain isolated from an HIV-negative patient with pulmonary MAC disease (11)].