T be discriminated based on the absence/presence of specific RDs, since most RDs were universally present within cluster A isolates. Distribution of RDs among cluster B was more heterogeneous. Three isolates from cluster B3 (22083R1, 8186 and OV640) were responsible for a good deal of diversity: 9 RDs representing 45 genes were only absent in one or more of these isolates; whereas in total at least 29 RDs are missing from these isolates. Thus, these isolates are atypical within our selection of isolates. Serotype 7 and 9 isolates (in clusters B2 and B5) also lacked considerable numbers of RDs. For some RDs (RD1, RD6, RD17), GC content differed considerably from overall GC content of the genome (41 ), indicating these RDs might have been acquired from other species by horizontal gene transfer, since foreign DNA can often be recognized by its variation from the majority of the genome in base composition or codon preference. The gene content of RDs shows that these regions contain specific beneficial traits like RM systems, ABC transporters, or two-component systems, making it attractive regions to acquire. A core genome for S. suis was defined by selecting genes that were present in all S. suis isolates tested. The resulting core genome of S. suis consisted of 1492 genes (76 ) out of 1960 genes present on our array. Of those 1492 genes, 26 genes represent pseudogenes in P1/7. Composition of the core genome of S. suis was studied using the classification in clusters of orthologous groups of proteins (COG). Figure 4 displays the relative representation of each COG category in both P1/7 as well as in the core genome. Most COG categories were equally represented in both genomes. However, COG categories J (translation, ribosomal structure and biogenesis), E (amino acid transport and metabolism) and F (nucleotide transport and metabolism) were found to be overrepresented in the core genome. In conclusion, all isolates in our study share 1492 genes. The overrepresentation of the structural gene categories J, E, and F suggest this core genome suffices for growth, division and survival, whereas additional, beneficial traits are mainly encoded by RDs.Discussion Comparative genome hybridization (CGH) was used to study genetic heterogeneity among a collection of 55 S. suis isolates. S. suis isolates were assigned to two clusters (A and B). CGH data was compared with MLST and pulse field gel electrophoresis (PFGE) [6] and amplified fragmentde Greeff et al. BMC Microbiology 2011, 11:161 http://www.biomedcentral.com/1471-2180/11/Page 10 ofTable 3 Regions of difference (RDs) identified in relation to P1/RD# PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/16989806 Range in P1/7* Size (bp)* Present in GC n/55 strains (parts present in n/55) 23 (49) 47 37 (13) Dasatinib 36 (17) 29 29 (14) 30 (11) 52 30 (6) 52 42 34 (5) 50 45 35 34.1 40.8 33.7 43.0 38.8 33.6 39.3 36.0 35.6 36.7 42.5 38.8 40.1 42.1 38.6 Predicted Function*RD01 SSU0101 - SSU0111 7.537 RD02 SSU0178 - SSU0182 5.501 RD03 SSU0198 - SSU0209 14.234 RD04 SSU0300 - SSU0305 5.455 RD05 SSU0346 - SSU0350 7.680 RD06 SSU0413 - SSU0418 8.624 RD07 SSU0423 - SSU0428 8.383 RD08 SSU0449 - SSU0453 2.475 RD09 SSU0519 - SSU0556 27.705 RD10 SSU0592 - SSU0600 8.410 RD11 SSU0640 - SSU0642 5.514 RD12 SSU0651 - SSU0655 7.674 RD13 SSU0661 - SSU0670 10.283 RD14 SSU0673 - SSU0679 8.872 RD15 SSU0684 - SSU0693 7.Integrase, replication initiation factor, hypothetical proteins PTS IIB, transketolase PTS IIABC transporter, glucosamine-6-phosphate isomerase, pseudogene Dehydrogenase, flavin.