Small, Enigmatic Plasmids of the Nosocomial Pathogen, Acinetobacter baumannii: Good, Bad, Who Knows?

Abstract

Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants. An interesting genetic feature seen in majority of A. baumannii genomes analyzed is the presence of small plasmids that usually ranged from 2 to 10 kb in size, some of which harbor antibiotic resistance genes and homologs of plasmid mobilization genes. These plasmids are often overlooked when compared to their larger, conjugative counterparts that harbor multiple antibiotic resistance genes and transposable elements. In this mini-review, we will examine our current knowledge of these small A. baumannii plasmids and look into their genetic diversity and phylogenetic relationships. Some of these plasmids, such as the Rep-3 superfamily group and the pRAY-type, which has no recognizable replicase genes, are quite widespread among diverse A. baumannii clinical isolates worldwide, hinting at their usefulness to the lifestyle of this pathogen. Other small plasmids especially those from the Rep-1 superfamily are truly enigmatic, encoding only hypothetical proteins of unknown function, leading to the question of whether these small plasmids are "good" or "bad" to their host A. baumannii.

Keywords: Acinetobacter baumannii; Rep-1 superfamily; Rep-3 superfamily; antibiotic resistance genes; mobilizable plasmids; pRAY plasmids; small plasmids; toxin–antitoxin.

FIGURE 1

Phylogenetic tree of the small Acinetobacter plasmids of the Rep-3 superfamily based on the RepB replicase protein sequences as analyzed and drawn using MEGA7 (Kumar et al., 2016). Alignment of the RepB protein sequences was carried out using MUSCLE (Edgar, 2004) and the evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 3.32974406 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. (The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The analysis involved 50 RepB amino acid sequences with the GenBank accession numbers of the plasmids as listed in Supplementary Table S1. Each clade of the tree corresponded with the plasmid homology grouping (GR classification) as proposed by Bertini et al. (2010) and indicated by different colored boxes. Plasmid names marked with an asterisk (^∗) indicate partial plasmid sequences that covered only the oriV–repB sequences and were included in the analysis to validate the plasmid groupings as they were used by Bertini et al. (2010) in their classification scheme.)

FIGURE 2

Comparative map of the pRAY plasmid and its derivatives from various Acinetobacter spp. The mobA and mobC genes are indicated as black arrows whereas the AT-rich putative oriT sequence is indicated as a purple box. Antimicrobial resistance genes (either aadA27 for streptomycin/spectinomycin resistance or aadB for aminoglycoside resistance) are depicted as a dark yellow arrow while the Abi-like protein (identified by pfam07751) gene is indicated as a green arrow. IS element-encoded transposases are depicted in pink, the inverted repeats (IRs) for ISAba22 are shown as blue rectangles whereas the IRs for IS18 are shown as white rectangles (for pRAY^∗-v2). Hypothetical open reading frames are depicted as gray arrows. Accession numbers for the plasmids shown are in parentheses following their names.