Biopython code refactoring
Here is a sample of code that should get you started.

I created a separate get_abstracts function.  Then that function get called repetitively until less than 100K ids are returned.  If you wanted to get fancy this whole process could be called as a recursive function but that seemed overly complex.

BUFFER_SIZE = 100000

def get_abstracts(start, term):
    """Get N number of records from Entrez
    :returns list: List of ids returned from search
    """
    handle_one = Entrez.esearch(db="pubmed", term=term, 
                       retmode="text", retstart=start, retmax=BUFFER_SIZE)
    record = Entrez.read(handle_one)
    idlist = record["IdList"]
    return idlist

list_of_ids = []
start_at = 0

# Iterate the search returning 100000
while true:
    ids = get_abstracts(start_at, 'e coli')

    list_of_ids.extend(ids)

    # Break if less than 100K results were returned 
    if len(ids) &lt; BUFFER_SIZE:
        break
    start_at += BUFFER_SIZE

# Do something with list_of_ids