Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae

Richards, V. P. et al. (2019) Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. Molecular Biology and Evolution, 36(11), pp. 2572-2590. (doi: 10.1093/molbev/msz169) (PMID:31350563) (PMCID:PMC6805230)

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The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacteria 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 twelve 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 eleven 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.

Item Type:Articles
Additional Information:This work was supported by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, [contract number HHSN272200900007C and grant number AI073368 to MJS]; and by the USDA National Institute of Food and Agriculture Research Initiative Postdoctoral Fellowship [grant no. 2013-67012-21020 to VPR].
Glasgow Author(s) Enlighten ID:Zadoks, Professor Ruth
Authors: Richards, V. P., Velsko, I. M., Alam, T., Zadoks, R. N., Manning, S. D., Pavinski Bitar, P. D., Hasler, H. B., Crestani, C., Springer, G., Probert, B., Town, C. D., and Stanhope, M. J.
College/School:College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Molecular Biology and Evolution
Publisher:Oxford University Press (OUP)
ISSN (Online):1537-1719
Published Online:27 July 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Molecular Biology and Evolution 36(11):2572–2590
Publisher Policy:Reproduced under a Creative Commons license

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