The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of S. clinical isolate BM6001, which original host ICE Tn5253. The BM6001 organized in one circular chromosome 2,293,748 base pairs (bp) length, with average GC content 39.54%; harbors a type 19F capsule locus, two tandem copies pspC, comC1-comD1 alleles I restriction modification system SpnIII. mobilome accounts for 15.54% (356,521 bp) whole includes (i) Tn5253 composite; (ii) novel IME Tn7089; (iii) transposon Tn7090; (iv) 3 prophages 2 satellite prophages; (v) 5 genomic islands (GIs); (vi) 72 insertion sequences (ISs); (vii) 69 RUPs; (viii) 153 BOX elements; (ix) 31 SPRITEs. All MGEs, except GIs, produce excised forms attB site restoration. Tn7089 9089 bp long contains 11 ORFs, 6 were annotated code three functions: integration/excision, mobilization adaptation. Tn7090 9053 size, flanked by ISSpn7, seven ORFs as single transcriptional unit, genes encoding proteins likely involved uptake binding Mg2+ cations adhesion to cells intracellular survival. GI-BM6001.4, are variants pneumococcal TIGR4 RD5 region diversity, pathogenicity island PPI1, R6 Cluster 4 PTS island. Overall, contain predicted encode DNA replication lysogeny, addition phage structural lytic enzymes carried only prophages. ΦBM6001.3 has mosaic structure that shares IPP69 MM1 disrupts competent comGC/cglC gene after chromosomal integration. Treatment mitomycin C results 10-fold increase frequency coding restoration but does not restore competence genetic transformation. addition, phylogenetic analysis showed clusters small lineage five other historical strains, it distantly related due its unique mobilome, suggesting progressively accumulated many MGEs while losing