Abstract
BackgroundSalmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts.ResultsTo inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. 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 all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study.ConclusionsThe warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, 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.
Highlights
Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported
Whereas we cannot conclude that the additional T6SS might be involved in the warmblooded host invasion by RKS3044, our results show that S. bongori bacteria can be circumscribed into discrete phylogenetic clusters, each having a distinct set of genomic characteristics
We found that the CTAG sequence had different genomic distributions among the S. bongori lineages and the divergence patterns were consistent with the phylogenetic clustering of the bacteria, suggesting that the lineages have diverged into different phylogenetic and ecological positions for long evolutionary times, so they do not have much chances to freely exchange their genetic materials (Additional file 10: Table S8)
Summary
Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts. Genome structure analysis may provide objective and reliable parameters for differentiating bacteria based on their evolutionary relationships rather than according to any arbitrary standards. To prove this postulation, we recently profiled genomic characteristics among representative human-infecting Salmonella pathogens and demonstrated the existence of genetic boundaries that can be used to divide the Salmonella bacteria into clearcut phylogenetic clusters [16,17,18,19,20,21]
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