The out-group comprised three new strains isolated in the Netherlands, two strains previously isolated in France, and the most diverse canonical strains N2 (Bristol) and CB4856 (Hawaii) [ 16, 18- 23, 23- 29, 67] (see Additional file 1, worksheet A for details).
To challenge the hypothesis that the native African tree isolates are more genetically diverse than global isolates, the global population sample was selected to include the most diverse global strains available from our previous studies (Table 2).
Lastly, the genotypically most diverse laboratory-kept strain CB4856 and the canonical strain Bristol N2 were added (see Additional file 1, worksheet A) [ 9, 18- 22]; these two strains have been used in many studies to uncover genotype-phenotype relations both by comparing strains or by using some type of quantitative trait loci approach [ 1, 18, 23- 30].
Of the three strains BM407 appears to be the most diverse: comparison of strain BM407 to P1/7 identified 977 SNPs, 201 insertions, and 122 deletions in the core chromosome (excluding ICE regions); and comparison to SC84 identified 1017 SNPs, 232 insertions, and 133 deletions, whereas a comparison of strain P1/7 to SC84 identified 85 SNPs, 10 insertions, and 15 deletions.
Overall, L. casei plant isolates showed the most diverse repertoire of strain-specific accessory genes.
Besides a few Opa protein variants that recognize cell surface expressed heparansulphate proteoglycans (OpaHSPG) [20], [21], most Opa proteins of diverse strains of Neisseria meningitidis and Neisseria gonorrhoeae recognize one or more members of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family (OpaCEA) [22], [23], [24].
Overall, fluoroquinolone resistance rates remain very low, most resistance arises in genetically diverse strains, and clonal dissemination is likely still not a major contributor to the appearance of QRSP.
But Africa, where the virus originated and where it has therefore become most diverse, is plagued by many strains.
