TY - JOUR
T1 - Population Gene Introgression and High Genome Plasticity for the Zoonotic Pathogen Streptococcus agalactiae
AU - Richards, Vincent P.
AU - Velsko, Irina M.
AU - Alam, Md Tauqeer
AU - Zadoks, Ruth N.
AU - Manning, Shannon D.
AU - Pavinski Bitar, Paulina D.
AU - Hassler, Hayley B.
AU - Crestani, Chiara
AU - Springer, Garrett H.
AU - Probert, Brett M.
AU - Town, Christopher D.
AU - Stanhope, Michael J.
N1 - Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2019/11/1
Y1 - 2019/11/1
N2 - The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacterial populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here, we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated 12 major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of 11 populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation.
AB - The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacterial populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here, we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated 12 major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of 11 populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation.
KW - bacterial pathogen
KW - gene spillover
KW - genome plasticity
KW - host adaptation
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U2 - 10.1093/molbev/msz169
DO - 10.1093/molbev/msz169
M3 - Article
C2 - 31350563
AN - SCOPUS:85081631253
SN - 0737-4038
VL - 36
SP - 2572
EP - 2590
JO - Molecular biology and evolution
JF - Molecular biology and evolution
IS - 11
ER -