Multiple prophage acquisition events over the course of an outbreak drive lysogenic conversion of capsular polysaccharides produced by carbapenem-resistant <i>Acinetobacter baumannii</i> isolates

and is also the primary receptor for a number of bacteriophages and monoclonal antibodies. Hence, changes in CPS structure may influence virulence potential and substantially impact patient outcomes using novel therapies. Here, we have shown that acquired genes found in prophage can alter the structure of the CPS produced by the chromosomal CPS biosynthesis locus by supplying alternate Wzy polymerases to link the K unit oligosaccharides together. This highlights the need to examine the accessory genome, which we found to be rapidly evolving, as it differed between the two isolates that are closely related based on single-nucleotide polymorphism phylogeny. Other members of the same lineage from the same outbreak carried various prophages that included CPS-modifying genes. Detecting these acquired genes will be needed to underpin the application of alternative therapies.