Complete genome analysis of three Acinetobacter baumannii clinical isolates in China for insight into the diversification of drug resistance elements

Abstract

Background: The emergence and rapid spreading of multidrug-resistant Acinetobacter baumannii strains has become a major health threat worldwide. To better understand the genetic recombination related with the acquisition of drug-resistant elements during bacterial infection, we performed complete genome analysis on three newly isolated multidrug-resistant A. baumannii strains from Beijing using next-generation sequencing technology.

Methodologies/principal findings: Whole genome comparison revealed that all 3 strains share some common drug resistant elements including carbapenem-resistant bla OXA-23 and tetracycline (tet) resistance islands, but the genome structures are diversified among strains. Various genomic islands intersperse on the genome with transposons and insertions, reflecting the recombination flexibility during the acquisition of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated BJAB0868 exhibit high similarity on their genome structure with most of the global clone II strains, suggesting these two strains belong to the dominant outbreak strains prevalent worldwide. A large resistance island (RI) of about 121-kb, carrying a cluster of resistance-related genes, was inserted into the ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying tra-locus and bla OXA-23 island, can be either inserted into one of the tniB gene in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the two BJAB strains. The third strains of this study, BJAB0715, which was isolated from spinal fluid, exhibit much more divergence compared with above two strains. It harbors multiple drug-resistance elements including a truncated AbaR-22-like RI on its genome. One of the unique features of this strain is that it carries both bla OXA-23 and bla OXA-58 genes on its genome. Besides, an Acinetobacter lwoffii adeABC efflux element was found inserted into the ATPase position in BJAB0715.

Conclusions: Our comparative analysis on currently completed Acinetobacter baumannii genomes revealed extensive and dynamic genome organizations, which may facilitate the bacteria to acquire drug-resistance elements into their genomes.

Figure 1. Circular representation of genomes of threeAcinetobacter baumannii strains.

(a) BJAB07104. (b) BJAB0868. (c) BJAB0715. Circles display (from outside in order of) (i) coding regions in the clockwise direction; (ii-iii) open reading frames (>100 codons) in the clockwise and counterclockwise direction respectively; (iv) coding regions in the counterclockwise direction; (v-vi) comparison with three selected genomes by BLAST (BJAB0868, BJAB0715 and SDF for BJAB07104, BJAB07104, BJAB0715 and SDF for BJAB0868, BJAB07104, BJAB0868 and ATCC17978 for BJAB0715); (vii) GC content; and (viii) G-C skew. The plot was produced by CGView server (http://stothard.afns.ualberta.ca/cgview_server/index.html) . The locus of AbaR-like resistance islands were marked beside the circular genomes.

Figure 2. The structures of representative plasmids containing drug resistance genes.

(a) pBJAB0715 contains bla _OXA-58 flanked by two ISAba3 elements, and aphA6 flanked by two ISAba125 elements. (b) pBJAB07104 and p2BJAB0868 containing aphA1 in transposon Tn6210 (in red) and genes of class I integron (in blue).

Figure 3. Sequence comparison of BJAB strains with otherA. baumannii strains.

(a) Phylogenetic analysis of 13 A. baumannii strains with Acinetobacter baylyi ADP1 as outgroup. 1,119 orthologous proteins identified from 14 genomes were aligned by CLUSTALW and PHYLIP software package was used to construct the tree. 1000 replicates were used in bootstrap analysis. (b) An insert region in the genome of BJAB0715, was found in all three genomes of GC I strains but not in GC II strains.

Figure 4. Transposons containing drug resistance genebla _OXA-23 in different A. baumannii strains

(a) Truncated Tn2006 in TCDC0715 and complete Tn2006 in AbaR4 reported in AB0057 strain; (b) Tn6206 found in three BJAB strains and Tn2009 in MDR-ZJ06 and MDR-TJ strains. (c) 9-bp target site direct repeat sequences (DR sequences) of ISAba1 elements (in bold font).

Figure 5. Structure of resistance islands AbaR25-27 containing drug resistant genetetA.

(a) AbaR25 in BJAB07104 and AbaR26 in BJAB0868 are both inserted into the ATPase gene. Transposons Tn6206-6209 are showed in dashed rectangles. While Tn6208 (in BJAB07104) is flanked by two ISAba1 elements, Tn6209 (in BJAB0868) only has the left flanking ISAba1 element. When being present in chromosome, Tn6206 and tra system are inserted into the gene tniB, while this region can also form free plasmids. (b) AbaR27 in BJAB0715 is inserted into gene EJP43116, which produces a protein 100% identical to a hypothetical protein found in A. baumannii OIFC032 strain.

Figure 6. The alignment of a 800-kb inversion region in BJAB07104 genome with the genomes of other 11A. baumannii strains.