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. Genome analysis on MAH of human isolates has been proceeding, however, those of pigs are limited despite its potential source of infection to human. In the current study, we obtained 30 draft genome sequences of MAH of pigs reared in Japan. The 30 draft genomes consisted of 4,848,678 _ 5,620,788 bp length, 4,652 _ 5,388 coding genes and 46 _ 75 (Med: 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 8.…”

“…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 8. The sequences of hsp65 gene were referred from repository related to our past study (43) with genes retrieved from genomes of representative lineages (OCU404: MahEastAsia1, TH135: MahEastAsia2, A5: SC1, 104: SC2, 100: SC3, OCU491: SC4) and were aligned with Molecular Evolutionary Genetics Analysis (MEGA) and were used for SNP analysis.…”

“…Draft genome sequence. Draft genome sequences of 30 isolates were obtained according to our past study (42).…”

“…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.…”