Analysis of 16S–23S rRNA internal transcribed spacer regions in Pasteurellaceae isolated from laboratory rodents

The internal transcribed spacer (ITS) regions of members of Pasteurellaceae isolated from rodents, including the [Pasteurella] pneumotropica biotypes Jawetz and Heyl, [Actinobacillus] muris, “Hemophilus influenzaemurium” and Bisgaard taxon 17 were studied and their feasibility to discriminate these species was analyzed. The reference strains of all species analyzed showed unique species‐specific ITS patterns which were further present in 49 clinical isolates of [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris allowing their identification by comparison to the reference strains pattern. Sequence analysis of the amplified fragments revealed in all species, with exception of “H. influenzaemurium”, a larger ITSile + ala which contained the genes for tRNAIle(GAU) and tRNAAla(UGC) and a smaller ITSglu with the tRNAGlu(UUC) gene. “H. influenzaemurium” revealed two each of the larger and respectively the smaller ITS fragments. Both the length and the sequence of each ITS type were highly conserved within the [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris strains tested. On the contrary, ITS sequences revealed significant interspecies variations with identity levels ranging from 61.2 to 89.5% for ITSile + ala and 56.5 to 86.8% for ITSglu. Sequences regions with significant interspecies variation but highly conserved within the species were identified and might be used to design probes for the identification of rodent Pasteurellaceae to the species level.

► 16S rRNA diversity does not allow proper differentiation of mouse Pasteurellaceae.
► We analyze for the first time the ITS between 16S and 23S rRNAs as differentiation basis.
► The ITS number and length polymorphisms allow differentiation within this taxon.
► Two types of ITS sequences (ITSile + ala and ITSglu) were revealed.
► Sequence regions appropriate for specific identification of these bacteria are available.