Comparative genomics of multidrug resistance in Acinetobacter baumannii

Abstract

Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics in the 1970s. It has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. Here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant A. baumannii strain AYE, which is epidemic in France, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible A. baumannii strain SDF, which is associated with human body lice. The assembly of the whole shotgun genome sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2 Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region termed a resistance island--the largest identified to date--in which 45 resistance genes are clustered. At the homologous location, the SDF strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. Such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. Sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the A. baumannii strain AYE have been recently acquired from bacteria of the genera Pseudomonas, Salmonella, or Escherichia. This study also resulted in the discovery of 19 new putative resistance genes. Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.

Figure 1. Comparison of Insertion Sites of the AbaR1 and AbaG1 Islands in an ATPase ORF

Insertion sites of the AbaR1 (A) and AbaG1 (B) islands in an interrupted ATPase-encoding ORF are compared. ORFs 1_837 and 1_434 in strain AYE, and 1_126 and 1_87 in strain SDF, retain a strong similarity to the 3′ and 5′ fragments, respectively, of the ATPase sequence encoded by Acinetobacter strain ADP1 [32]. The 5-bp direct repeats flanking the islands are underlined.

Figure 2. Layout of the Complete AbaR1 Inserted into the AYE Strain ATPase-Encoding Gene

The nomenclature of each ORF is indicated. Each ORF is identified according to EMBL entry CT025832. Colors are used to indicate ORF categories: resistance to antibiotics in red, resistance to heavy metals or antiseptics in blue, transposases in brown, integrases in yellow, and other functions in white. Genes exhibiting a best matching homolog in Pseudomonas are underlined in green, in yellow for Salmonella, in light blue for E. coli, and in turquoise for other bacteria. Complete integrons are indicated by red dashed lines. Transposons are indicated by blue dashed lines. Black dashed lines indicate a gene cluster found in Salmonella genomic island 1.

Figure 3. Layout of the Complete AbaG1 Inserted into the SDF Strain ATPase-Encoding Gene

The nomenclature of each ORF is indicated. Each ORF is identified according to EMBL entry CT025833. ORF categories are indicated by colors: transpositions in brown and other functions in white. The phylogenetic origin of genes is highlighted by color markers. Dashed lines indicate genes found in the same order in other bacteria.