Ressources: Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae - DrAnneJ/DrAnneJ.github.io GitHub Wiki

Front Cell Infect Microbiol. 2018; 8: 4. Published online 2018 Jan 22. doi: 10.3389/fcimb.2018.00004

The accessory genome

Within a bacterial species, there is typically a set of genes that is conserved amongst all members. This set of genes is considered the core genome. In K. pneumoniae the core genome, defined as present in >95% of isolates, is currently estimated to be comprised of ~2,000 genes (Holt et al., 2015). Genes that vary between isolates are referred to as the accessory genome. This includes chromosomally encoded genes and genes on plasmids. Since K. pneumoniae genomes are typically between 5,000 and 6,000 genes, this means that the majority of the genome is comprised of accessory genes. Genes in the accessory genome can aid in specific processes, such as nitrogen fixation (Fouts et al., 2008). They can also encode specific virulence factors, as discussed below. The accessory genome also carries genes encoding various antibiotic-resistant enzymes and mechanisms (Bi et al., 2015). Accessory genes can be acquired due to horizontal gene transfer among bacterial species, as evidenced by the presence of genomic islands and mobile genetic elements in many isolates. The genes encoded in genomic islands can help isolates adapt to specific sites of infection or colonization (Chen et al., 2010; Zhang et al., 2011; van Aartsen et al., 2012). Elements of the accessory genome can be identified or predicted using various in silico applications, including computation of GC content and comparative genomic analysis (Ou et al., 2007; Zhang et al., 2014). A recent study of 328 Klebsiella isolates identified almost 30,000 unique protein-coding sequences (Holt et al., 2015), estimating the current known Klebsiella “pangenome.” The authors further demonstrated that the pangenome is open, indicating that there are more accessory genes yet to be identified and characterized.

In addition to fim and mrk pili, a number of additional usher-type pili have been identified in K. pneumoniae, with an average of ~8 pili clusters per strain (Wu et al., 2010; Khater et al., 2015). Based on varying gene frequencies, some of these appear to be part of the accessory genome.

Bioinformatic analysis of K. pneumoniae genomes has identified the presence of putative T6SS gene clusters, with up to 3 loci per strain, although the number and gene content vary (Sarris et al., 2011).