Two parallel processes, gene loss and acquisition, shape the Y. enterocolitica ssp. palearctica serobiotype O:3/4 genome. As expected, Y. enterocolitica ssp. palearctica strains do not carry the already defined high-pathogenicity associated features of 8081 O:8/1B (). This decreased pathogenicity may supply the O:3/4 group with a better chance to balance its interactions with the host and support further dissemination. Instead, Y. enterocolitica ssp. palearctica demonstrates an alternative pattern of putative virulence associated determinants including an RtxA-like toxin, a dual functional insecticidal toxin, beta-fimbriae and a novel ysp type 3 secretion system. Since serobiotype O:3/4 has adapted to a very narrow and specific niche, the pig tonsils, the bacteriocin cluster found in O:3/4 would also provide a serious advantage in colonisation. Likewise, the ability to utilise GalNAc of the gut mucin may represent both a virulence and fitness factor of particular importance for O:3/4 and reflects its adaptation/association with its host.
The ysp T3SS of O:3/4 that substitutes the ysa T3SS of O:8/1B is analogous to T3SS systems of high-pathogenic Y. pestis and Y. pseudotuberculosis, indicating a potential role in pathogenicity. The effectors of this T3SS have to be identified. The ysp and ysa secretion systems are known to be involved both in "cross-talk" with other bacteria and with the host and they are able to support transport of "heterologous" effector molecules [51, 52]. Thus, the ysp system might supply Y. enterocolitica ssp. palearctica with an additional advantage to subvert foreign imported effectors for its benefit even in the absence of the native ones.
Mobile genetic elements encoding multiple physiological traits play a significant role in bacterial evolution. A novel GIYep-01 genomic island that encodes a putative metallo-beta-lactamase and a protease in O:3/4 might be involved both in fitness and pathogenicity of yersiniae. For its integration, GIYep-01 utilizes a P4-like integrase like the HPI in O:8/1B. However, in contrast to the HPI that is frozen to a single tRNA-Asn site in O:8/1B, the GIYep-01 can leave its initial tRNA-Asn locus due to the activity of the functional integrase. Whether the integrase of one mobility element can affect the recombination of another one and the putative role of the GIYep-01 in Y. enterocolitica has still to be clarified.
The filamentous PhiYep-1 prophage of O:3/4 demonstrates a high similarity to Y. pestis Ypf and E. coli CUS-1 prophages. Both Ypf and CUS-1 are suspected to play a role in pathogenicity . However, due to severe sequential deletions in the sequenced O:3/4 strains, a possible impact of this prophage on O:3/4 pathogenicity and elevated ampicillin resistance remains questionable.
Two copies of the highly similar P2-like prophages are present in the Y11 genome. PhiYep-2, the one with a truncated integrase, is frozen in tRNA-Met while PhiYep-3, harbouring an active integrase, is integrated into tRNA-Leu. Anyhow, the genetically active PhiYep-3 is present only in about 40% of the O:3/4 strains tested. Thus, the PhiYep-3 prophage seems to represent a more recent Y11 acquisition and might serve as an additional epidemiological marker for Y. enterocolitica ssp. palearctica. The coexistence and immunity to superinfection of these two closely related P2-like prophages poses an additional question to be answered.
The presence of multiple IS elements tells a story of Y. enterocolitica interactions with its biotic neighbours. Indeed the spectrum of IS elements differs in Y. enterocolitica ssp. enterocolitica and Y. enterocolitica ssp. palearctica, with ISYen2A/B being the low -pathogenicity specific insertion sequence whilst a wide variety of IS families IS3, IS4 and IS200 dominates in the high-pathogenicity group. These differences can be applied both to subspecies identification and also for tracing history of interbacterial interactions.
It is remarkable that the gene clusters with potentially closely related functions tend to occupy exactly the same positions ("hot spots") in the Y. enterocolitica backbone genomes (like the T3SS, the O-antigen, an AidA adhesin and haemolysin, the OspG protein kinase gene cluster, etc.). On the other hand, divergence in these clusters might result from both vertical and horizontal evolution events.
Y. enterocolitica ssp. palearctica O:3/4 has an open genome with traces of frequent gene import and wastes. These different vectors have formed the present O:3/4 genome that combines standard yersinial determinants with putative alternative virulence and fitness associated factors. Such a patchwork seems to be a prerequisite for O:3/4 successful worldwide dissemination.