Abstract
Acinetobacter baumannii is of major clinical importance as the bacterial pathogen often causes hospital acquired infections, further complicated by the high prevalence of antibiotic resistant strains. Aside from natural tolerance to certain antibiotic classes, resistance is often acquired by the exchange of genetic information via conjugation but also by the high natural competence exhibited by A. baumannii. In addition, bacteriophages are able to introduce resistance genes but also toxins and virulence factors via phage mediated transduction. In this work, we analyzed the complete genomes of 177 A. baumannii strains for the occurrence of prophages, and analyzed their taxonomy, size and positions of insertion. Among all the prophages that were detected, Siphoviridae and Myoviridae were the two most commonly found families, while the average genome size was determined to be approximately 4 Mbp. Our data shows the wide variation in the number of prophages in A. baumannii genomes and the prevalence of certain prophages within strains that are most “successful” or potentially beneficial to the host. Our study also revealed that only two specific sites of insertion within the genome of the host bacterium are being used, with few exceptions only. Lastly, we analyzed the existence of genes that are encoded in the prophages, which may confer antimicrobial resistance (AMR). Several phages carry AMR genes, including OXA-23 and NDM-1, illustrating the importance of lysogenic phages in the acquisition of resistance genes.
Highlights
The opportunistic pathogen Acinetobacter baumannii is the causative agent for bloodstream infections, meningitis and urinary tract infections, and is responsible for 2–10% of all Gramnegative hospital-acquired infections (Joly-Guillou, 2005)
Our first aim was to analyze how frequently prophages occur in the genomes of A. baumannii strains
The average length of the genomes was 3,981,579 bp with a median value of 4,001,318 bp; the smallest genome had a length of 3,072,399 bp (22.9% shorter than average), and the largest genome displayed a size of 4,389,990 bp (10.25% larger than average) (Figure 1A)
Summary
The opportunistic pathogen Acinetobacter baumannii is the causative agent for bloodstream infections, meningitis and urinary tract infections, and is responsible for 2–10% of all Gramnegative hospital-acquired infections (Joly-Guillou, 2005) Such infections include ventilatorassociated pneumonia and bacteremia with a mortality rate of 35–52% (Dijkshoorn et al, 2007; Kempf et al, 2013; Antunes et al, 2014). While A. baumannii acquires genetic material by conjugation, natural transformation is widespread as many strains are highly naturally competent (Hu et al, 2019) Such mechanisms give rise to an increasing number of strains that display high levels of antimicrobial resistance (AMR), against which antibiotics show little or no effect. Phages play an important role in the development of AMR
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