Extensive variation in the ddl gene of penicillin-resistant Streptococcus pneumoniae results from a hitchhiking effect driven by the penicillin binding protein 2b gene

An internal fragment of the ddl gene, encoding the cytoplasmic enzyme D-ala nyl-D-alanine ligase, was sequenced from 566 isolates of Streptococcus pneu moniae and single isolates of Streptococcus mitis and Streptococcus oralis. The 52 alleles found among the S. pneumoniae isolates fell into two groups . Group A alleles were very uniform in sequence and were present in both pe nicillin-susceptible and penicillin-resistant pneumococci. Group B alleles were much more diverse and were found only in penicillin-resistant isolates . The Streptococcus oralis and Streptococcus mitis alleles were less diverg ed from group A alleles than some of the group B pneumococcal alleles, sugg esting that the latter alleles contain interspecies recombinational replace ments. The ddl gene was located 783 bp downstream of the penicillin-binding protein 2b gene (pbp2b). Sequencing of the pbp2b-recR-ddl-murF region of t hree penicillin-resistant pneumococci that had diverged ddl alleles showed that the whole region from pbp2b to ddl (or beyond) was highly diverged (ab out 8%) compared with the sequences from three penicillin-susceptible isola tes. The high levels of diversity in the group B ddl alleles from penicilli n-resistant isolates were ascribed to a hitchhiking effect whereby interspe cies recombinational exchanges at pbp2b, selected by penicillin usage, ofte n extend into, or through, the ddl gene. The data allow the average size of the interspecies recombinational replacements to be estimated at about 6 k b.