Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan

Abstract

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. There have been advances in genome analysis of MAH from human isolates, but studies of isolates from pigs are limited despite its potential source of infection to human. Here, we obtained 30 draft genome sequences of MAH from pigs reared in Japan. The 30 draft genomes were 4,848,678–5,620,788 bp in length, comprising 4652–5388 coding genes and 46–75 (median: 47) tRNAs. All isolates had restriction modification-associated genes and 185–222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.

Unique genomic sequences in a novelMycobacterium aviumsubsp.hominissuislineage enable fine scale transmission route tracing during pig movement

“…Bacterial isolation and identification of MAH isolates of 30 isolates (GM5, GM10, GM12, GM16, GM17, GM21, GM32, GM44, OCU467 – OCU486 and Toy194 – Toy195) were referred in our past study (42). 20 isolates used for VNTR analysis (gifu-1 – gifu-92, GM6, GM11, GM23 – GM25) were isolates from mesenteric lymph nodes, feces, sawdust and farm soil (Table S1).…”

“…20 isolates used for VNTR analysis (gifu-1 – gifu-92, GM6, GM11, GM23 – GM25) were isolates from mesenteric lymph nodes, feces, sawdust and farm soil (Table S1). Isolation and identification of these isolates including determination of IS profiles and hsp code were conducted by our study (42). All of them were isolated from pigs or environment in Tokai area (Gifu, Aichi and Shiga Prefecture) and Hokuriku area (Toyama and Ishikawa Prefecture), whose geographical relationship was showed in Figure 6.…”

“…Genome phylogenetic tree analysis based on 30 MAH isolates in this study and 20 reference strains were performed via online tool CSI Phylogeny version 1.4 (https://cge.cbs.dtu.dk/services/CSIPhylogeny/) with default parameters (26) and IQ-TREE (27). Obtained newick file was visualized by MEGA according to our past study (42). Alignment file generated by CSI Phylogeny was used for phylogenetic analysis by NJ method with p-distance method via MEGA.…”

“…The sequence of two marker genes, cinA (product name: cytochrome P-450) and sugA (product name: trehalose ABC transporter) of 30 MAH located in recombination cold region, which are offered to be able to distinguish major six MAH lineages (25), were retrieved from draft genome sequences. These sequences in this study and the reference strains shown in the past report (25) were aligned and used for the phylogenetic tree analysis by ML method via MEGA according to our past study (42).…”

“…The draft genome sequence data used in this study have been submitted to the NCBI and all of accession number was available in our past study (42).…”