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To determine whether ITS sequences in the  rrn  operon are suitable for identifying individual  Acinetobacter  Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between  A. nosocomialis  BCRC15417 T  (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of  A. calcoaceticus,  all 639 bp long, and the 628 bp ITS of  Acinetobacter  strain BENAB127. Four additional indels (13i/2–13i/5) were detected in  Acinetobacter  strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other  Acinetobacter  species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in  Acinetobacter  strains b/n1&3,  A. pittii  (10 strains),  A. calcoaceticus  and  A. oleivorans  (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate  Acinetobacter  species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in  A. pitti.  The presence of indel 13i/5 in the ITS of  Acinetobacter  strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.

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Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members