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Background  Genomic islands (GIs) play an important role in the chromosome diversity of  Enterococcus . In the current study, we aimed to investigate the spread of GIs between  Enterococcus  strains and their correlation with antibiotic resistance genes (ARGs). Bitsliced Genomic Signature Indexes (BIGSI) were used to screen the NCBI Sequence Read Archive (SRA) for multiple resistant  Enterococcus . A total of 37 pairs of raw reads were screened from 457,000 whole-genome sequences (WGS) in the SRA database, which come from 37  Enterococci  distributed in eight countries. These raw reads were assembled for the prediction and analysis of GIs, ARGs, plasmids and prophages.    Results  The results showed that GIs were universal in  Enterococcus,  with an average of 3.2 GIs in each strain. Network analysis showed that frequent genetic information exchanges mediated by GIs occurred between  Enterococcus  strains. Seven antibiotic-resistant genomic islands (ARGIs) were found to carry one to three ARGs,  mdtG ,  tetM ,  dfrG ,  lnuG ,  and fexA,  in six strains. These ARGIs were involved in the spread of antibiotic resistance in 45.9% of the 37 strains, although there was no significant positive correlation between the frequency of GI exchanges and the number of ARGs each strain harboured (r = 0. 287,  p  = 0.085). After comprehensively analysing the genome data, we found that partial GIs were associated with multiple mobile genetic elements (transposons, integrons, prophages and plasmids) and had potential natural transformation characteristics.    Conclusions  All of these results based on genomic sequencing suggest that GIs might mediate the acquisition of some ARGs and might be involved in the high genome plasticity of  Enterococcus  through transformation, transduction and conjugation, thus providing a fitness advantage for  Enterococcus  hosts under complex environmental factors.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02114-4.

bmc microbiology (online)

Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences