Is there any software available for simulating a bacterial population which contains similar strains?
I am currently doing some simulations where I need bacterial populations at varying levels of identity to each other, so I wrote a tool to do that in the BBMap package.  For example, using E.coli:

    mutate.sh in=e_coli.fasta out=mutant.fasta id=99
    randomreads.sh ref=mutant.fasta out=reads.fq.gz reads=5m length=150 paired adderrors

That will create a mutant version of E.coli with 99% identity to the original, and then generate 5 million simulated read pairs from the new genome.  You can repeat this multiple times; each mutant will be different.