Whole genome sequencing and comparative genomics in lactic acid bacteria

In the present thesis, the genomes of different microbial species, belonging to the lactic acid bacteria and including Lactobacillus crispatus, Streptococcus pneumoniae and Enterococcus faecalis, were obtained and analyzed using comparative genomics tools. In the first part of the thesis was described the genome of the probiotic L. crispatus strain M247, which contains a novel integrative and mobilizable element named Tn7088. Tn7088 carries a biosynthetic gene cluster coding for a class I bacteriocin which is homologous to the listeriolysin S gene cluster of Listeria monocytogenes and may confer selective advantages towards related bacterial species. Chromosomal rearrangements mediated by insertion sequences and involving two regions of 69.9- kb and 15.4-kb, were detected in the M247 strain. A L. crispatus M247 laboratory strain carried in our laboratory strain collection since 1990 and named M247_Siena, showed an unusual duplication of the 69.9-kb DNA region resulting in the generation of two long inverted repeats (LIRs) and the deletion of the 15.4-kb region. Analysis of ultra-long DNA Nanopore reads showed that the presence of LIRs in strain M247_Siena increased the intrinsic genome instability of strain M247. In the second part, a collection of 41 E. faecalis strains isolated from genital tract samples of infertile couples, was subjected to antimicrobial susceptibility testing and whole genome sequencing. Multi locus sequence typing and antimicrobial susceptibility testing results suggested clonality of infertility-associated E. faecalis isolates resistant to high-level aminoglycosides. Analysis of the genomic location of aminoglycoside modifying enzyme (AME) genes led to the identification of a family of novel composite transposons, whose reference element was denominated Tn7086. Tn7086 and Tn7086-like elements in infertility-associated E. faecalis shared the following traits: i) are flanked by two direct repeats of the IS1216E element, ii) employ the same chromosomal panE gene integration site, iii) excise from the bacterial chromosome leaving an IS1216E copy in the chromosome and form circular intermediates in which the ends are joined by the other IS1216E copy. Finally, the whole genome sequences of the L. crispatus type strain ATCC 33820 and of S. pneumoniae laboratory strains Rx1 and R36A, were obtained and analyzed.