The capsular polysaccharide (CPS) on the bacterial cell-surface is a key virulence determinant of Acinetobacter baumannii, and novel therapies including monoclonal antibodies and bacteriophage that target the capsule show promise as a means to curb the high mortality rate associated with extensively resistant strains. However, these therapies rely on specificity to a particular capsule type. Members of the dominant clonal complexes of A. baumannii can carry one of many different capsule loci (KL), so understanding the variability of the KL within and between clonal complexes underpins the development and application of these therapies.
We examined a collection of 86 clinical global clone 2 (GC2) isolates recovered from five Singapore hospitals between 2000 and 2011 to determine the capsule variation. Available short reads were assembled into draft assemblies using SPAdes. The CPS type for each isolate was deduced from the whole genome sequence using Kaptive with the A. baumannii K locus reference sequence database. A total of 13 different capsule types were detected, including KL2, KL3, KL6, KL9, KL14, KL32, KL49b, KL52, KL70, KL72, KL73 and KL76. KL2 with 28 isolates was the most prevalent KL, followed by KL7 (19 isolates) and KL3 (18 isolates). Five capsule types were represented by just a single isolate.
A SNP-based phylogeny was constructed using Snippy and Gubbins, with A320, the earliest available GC2 strain, as the reference sequence. The phylogeny revealed five examples of a KL replacement within a GC2 sub-lineage. Regions of high SNP density were indicative of homologous recombination occurring in the chromosome on either side of the K locus, resulting in replacement of one KL with another from an exogenous source. The recombination patches ranged in size from 35kb to 133kb, and additional recombination patches were detected elsewhere in the genomes examined. Low SNP density throughout the remainder of the genome indicated that these switches were relatively recent evolutionary events.
Homologous recombination has previously been shown to be an important, underappreciated route for acquiring antibiotic resistance genes in A. baumannii. This work highlights the importance of this phenomenon in capsule variability within a single clonal complex.