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

  1. Tetsuya Komatsu
  2. Kenji Ohya
  3. Atsushi Ota
  4. Yukiko Nishiuchi
  5. Hirokazu Yano
  6. Kayoko Matsuo
  7. Justice Opare Odoi
  8. Shota Suganuma
  9. Kotaro Sawai
  10. Akemi Hasebe
  11. Tetsuo Asai
  12. Tokuma Yanai
  13. Hideto Fukushi
  14. Takayuki Wada
  15. Shiomi Yoshida
  16. Toshihiro Ito
  17. Kentaro Arikawa
  18. Mikihiko Kawai
  19. Manabu Ato
  20. Anthony D Baughn
  21. Tomotada Iwamoto
  22. Fumito Maruyama

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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.

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  1. GigaByte

    Mycobacterium avium subsp

    **Reviewer 2. Dr. Nabeeh A. Hasan ** Is the language of sufficient quality? Yes. A few minor grammatical edits could be done.

    Are all data available and do they match the descriptions in the paper?
    No. The data are not currently accessible by the public in NCBI.

    [The curators will be in touch to make sure all the data is live - see GigaDB guidelines on the data they require http://gigadb.org/site/guide]

  2. GigaByte

    Abstract

    This article has been published open access in GigaByte Journal (https://doi.org/10.46471/gigabyte.33), which also publishes open peer reviews under a CC-BY4.0 license.

    **Reviewer 1. Dr.Astrid Lewin **

    Is there sufficient detail in the methods and data-processing steps to allow reproduction?

    Chapter „Methods, b) Bacterial isolation and DNA extraction”: Lines 139-140: There is a discrepancy between the method of DNA extraction as described in the reference (16) and the manuscript text. While according to the reference the bacterial pellet is dissolved in acetone, the manuscript text describes a treatment with chloroform and methanol. This should be clarified.

    Is there sufficient data validation and statistical analyses of data quality? Not my area of expertise

    Any Additional Overall Comments to the Author
    Chapter „Methods, b) Bacterial isolation and DNA extraction”: Chapter “Data Validation and quality control, Identification of MAH” Lines 218-220: It is true, that the isolates had the highest identity with one of the three MAH strains, but not with all of the three MAH reference strains. For example, isolate OCU468 has 98.69% identity with MAH TH135 but 98.79% identity with MAP K-10. The degree of identity seems to be highly dependent on the choice of strains. Therefore, this comparison may not be very significant. In my experience, growth at 42°C very well distinguishes MAH from the other *M. avium *subspecies.

    Recommendation: Accept

  3. Version published to 10.46471/gigabyte.33
  4. Version published to 10.1101/2021.06.15.447579v2 on bioRxiv
  5. Version published to 10.1101/2021.06.15.447579v1 on bioRxiv