Many bacteria can deliver pathogenic proteins (effectors) through type IV secretion systems (T4SSs) to eukaryotic cytoplasm, causing host diseases. The inherent property, such as sequence diversity and global scattering throughout the whole genome, makes it a big challenge to effectively identify the full set of T4SS effectors. Therefore, an effective inter-species T4SS effector prediction tool is urgently needed to help discover new effectors in a variety of bacterial species, especially those with few known effectors, e.g., Helicobacter pylori.

Background: Salmonella bongoriinfect mainly cold-blooded hosts, but infections byS. bongoriin warm-blooded hosts have been reported. We hypothesized thatS. bongorimight have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts.Results: To inspect the divergence status ofS. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequencedS. bongoristrains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to allS. bongoristrains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infectingSalmonellaSubgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among theS. bongoristrains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and otherS. bongorilineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the otherS. bongorilineages/strains analyzed in this study.Conclusions: The warm-blooded host-infectingS. bongoristrain RKS3044 has diverged with distinct genomic features from otherS. bongoristrains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.