Letter to the editor: Suspected discrepancies due to inadequate quality of an in vitro analysis revealed by an in silico analysis

Kei Nishimori; Makoto Moriyama; Kazuaki Takehara

doi:10.1016/j.vetmic.2024.110064

Letter to the editor: Suspected discrepancies due to inadequate quality of an in vitro analysis revealed by an in silico analysis

Vet Microbiol. 2024 Mar 20:293:110064. doi: 10.1016/j.vetmic.2024.110064. Online ahead of print.

Authors

Kei Nishimori¹, Makoto Moriyama², Kazuaki Takehara³

Affiliations

¹ Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai, Fuchu, Tokyo 183-8509, Japan; Moriyama Environmental Wellness Laboratories, 3-87, Inagami, Nakamura, Nagoya, Aichi 453-0066, Japan; Department of Animal Disease Control and Prevention, National Institute of Animal Health, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan. Electronic address: gBh01652@nifty.ne.jp.
² Moriyama Environmental Wellness Laboratories, 3-87, Inagami, Nakamura, Nagoya, Aichi 453-0066, Japan.
³ Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai, Fuchu, Tokyo 183-8509, Japan.

PMID: 38636176
DOI: 10.1016/j.vetmic.2024.110064

Abstract

The author's in vitro analysis results were compared with those of an in silico structure analysis of the relevant sequences obtained from the author's entire genome sequence data. It was speculated that the in silico results together with author's phylogenetic results demonstrate problems in the authors' published in vitro data, which were presumably due to an inadequate accuracy of an in vitro assay. It was fortuitously suggested that alignment images to an excess repeat structure of the same locus provide a improved speculation of a number of repeats and that accurate in vitro assays are expected to complementarily provide reliable insights in the era of whole genome sequencing.

Keywords: Mycobacterium avium subsp. paratuberculosis; Variable numbers of tandem repeats; Whole genome sequencing.