Table 1.
Epidemiological data on the 74 Acinetobacter baumannii isolates included in this study.
Fig 1.
Genetic structure of the CRISPR-cas subtype I-Fb locus in Acinetobacter baumannii.
A) The CRISPR-cas subtype I-Fb locus in A. baumannii strain AYE (GenBank accession number: CU459141, located at position 1,057,691 to 1,069,768). The locus consisted of two CRISPR–associated genes (cas1 and cas3/cas2), four Cas system-associated genes (csy1, csy2, csy3, and csy4), and an array of spacers. The map was created using Artemis (http://www.sanger.ac.uk/resources/software/artemis/). B) Nucleotide sequence of the array of spacers in A. baumannii strain AYE. The array included 59 spacers surrounded by 60 direct repeats (marked in green). Some repeats, mainly at the trailer end of the array, included degenerated nucleotides (marked in yellow). C) Comparative analysis of the genetic surroundings. The comparison was performed between the locus-positive strain AYE which belonged to sequence type (ST1) and the locus-negative strains TYTH-1, AB4857, and OIFC099 which belonged to ST2, ST3, and ST32, respectively. Homologous sequences shared by all the isolates were indicated by gray zones.
Fig 2.
Schematic comparison of the trailer end of the arrays of spacers in Acinetobacter baumannii AYE and A. baumannii ab299505.
The region carrying spacers Ab-1 to Ab-4 in A. baumannii AYE was missing in A. baumannii ab299505, most likely due to an internal deletion caused by a recombination event between the two direct repeats (highlighted by a black frame) surrounding the deleted region. This created a unique direct repeat (highlighted by a black frame and vertical lines) characterized by a novel mosaic sequence derived from the recombined direct repeats. Sequence of the direct repeats involved in the recombination was presented in adjacent black boxes.
Fig 3.
Phylogenetic trees of cas1, csy1, csy4 and the concatenated MLST sequences.
The phylogenetic trees were based on aligned nucleotide sequences of (A) 920 bp of cas1 from 69 isolates of Acinetobacter baumannii, (B) 1251 bp of csy-1 from 68 isolates of A. baumannii since csy1 was lacking in isolate Naval-82, (C) 615 bp of csy4 from 69 isolates of A. baumannii, and (D) 2976 bp of concatenated MLST sequences of 69 isolates of A. baumannii. MUSCLE, Gblocks, PhyML, and TreeDyn were used for nucleotide alignment and tree construction. One hundred bootstraps were used for bootstrap analysis. Branch support values were displayed in %. Isolates of the CRISPR-cas subtype I-Fb pathways of evolution 1, 2, 3, and 4 were highlighted in gray, blue, green, and yellow, respectively. The corresponding sequence type (ST) was presented next to the name of each isolate in (D).
Fig 4.
Graphic representation of the arrays of spacers in the CRISPR-cas subtype I-Fb locus of Acinetobacter baumannii.
The figure demonstrated the assortment of 74 A. baumannii isolates into 40 CRISPR sequence types (CST) based on the spacer content of their CRISPR arrays. Spacers were represented by red rectangles. Each unique spacer was assigned a number (1–876). Spacers were sequentially aligned in order to facilitate comparison among the CSTs.