Characterization of integrative and conjugative elements carrying erm(B) and tet(O) resistance determinants in streptococcus uberis isolates from bovine milk in Chiba prefecture, Japan: CompArative GEne cluster analysis toolbox with ICEfinder

Objective: We aimed to characterize integrative and conjugative elements (ICEs) in antimicrobial resistant Streptococcs uberis isolates from bovine milk in Chiba, Japan, based on whole-genome sequence (WGS) data.

Results: Of the 101 isolates, we found the 36 isolates harboring erm(B)-tet(O), showing resistance to macrolides-lincosamides-tetracyclines. The 22 isolates were randomly selected and subject to WGS determination. The genomes measured 1.991-2.517 Mbp, with G + C contents of 35.8-36.9%. We used ResFinder-ICEfinder (web-based applications) to search for the antimicrobial resistant genes and ICEs. ResFinder detected combined erm(B)-tet(O)-ant(6)-Ia at the identical contig in each WGS. ICEfinder detected ICEs belonging to the same contigs, which contained erm(B)-tet(O)-ant(6)-Ia complete or partial sequences. Detection of putative ICEs using comparative genomic analysis was performed with identification of other streptococcal ICE resembling S. uberis ICEs. Using comparative genomic analysis (a reference WGS in NZ01 strain), putative ICE base size in UB37 isolate was 77,386-bp that was identical in other 13 isolates. Another similar streptococcal ICE was S. suis ICEnsui78-tet(O)-erm(B) mobile element. For ICE characterization in S. uberis with WGSs, a comparative genomic analysis is required with use of ICEfinder and other annotation tools.