AUTHOR=Nøhr-Meldgaard Katrine , Struve Carsten , Ingmer Hanne , Agersø Yvonne 

TITLE=The Tetracycline Resistance Gene, tet(W) in Bifidobacterium animalis subsp. lactis Follows Phylogeny and Differs From tet(W) in Other Species

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.658943

DOI=10.3389/fmicb.2021.658943

ISSN=1664-302X

ABSTRACT=<p>The tetracycline resistance gene <italic>tet</italic>(W) encodes a ribosomal protection protein that confers a low level of tetracycline resistance in the probiotic bacterium <italic>Bifidobacterium animalis</italic> subsp. <italic>lactis.</italic> With the aim of assessing its phylogenetic origin and potential mobility, we have performed phylogenetic and <italic>in silico</italic> genome analysis of <italic>tet</italic>(W) and its flanking genes. <italic>tet</italic>(W) was found in 41 out of 44 examined <italic>B. animalis</italic> subsp. <italic>lactis</italic> strains. In 38 strains, <italic>tet</italic>(W) was flanked by an IS5-like element and an open reading frame encoding a hypothetical protein, which exhibited a similar GC content (51–53%). These genes were positioned in the same genomic context within the examined genomes. Phylogenetically, the <italic>B. animalis</italic> subsp. <italic>lactis tet</italic>(W) cluster in a clade separate from <italic>tet</italic>(W) of other species and genera. This is not the case for <italic>tet</italic>(W) encoded by other bifidobacteria and other species where <italic>tet</italic>(W) is often found in association with transferable elements or in different genomic regions. An IS5-like element identical to the one flanking the <italic>B. animalis</italic> subsp. <italic>lactis tet</italic>(W) has been found in a human gut related bacterium, but it was not associated with any <italic>tet</italic>(W) genes. This suggests that the IS5-like element is not associated with genetic mobility. <italic>tet</italic>(W) and the IS5 element have previously been shown to be co-transcribed, indicating that co-localization may be associated with <italic>tet</italic>(W) expression. Here, we present a method where phylogenetic and <italic>in silico</italic> genome analysis can be used to determine whether antibiotic resistance genes should be considered innate (intrinsic) or acquired. We find that <italic>B. animalis</italic> subsp. <italic>lactis encoded tet</italic>(W) is part of the ancient resistome and thereby possess a negligible risk of transfer.</p>