Evolution of the U.S. biological select agent Rathayibacter toxicus

Authors: DAVIS, EDWARD - Oregon State University; TABIMA, JAVIER - Oregon State University; WEISBERG, ALEXANDRA - Oregon State University; LOPES, LUCAS - Oregon State University; WISEMAN, MICHELE - Oregon State University; WISEMAN, MICHAEL - Oregon State University; PUPKO, TAL - Oregon State University; BELCHER, MICHAEL - Oregon State University; Sechler, Aaron; Tancos, Matthew; SCHROEDER, BRENDA - University Of Idaho; MURRAY, TIMOTHY - Washington State University; Luster, Douglas - Doug; SCHNEIDER, WILLIAM - US Department Of Agriculture (USDA); Rogers, Elizabeth; ANDREOTE, FERNANDO - Universidad De Sao Paulo; Grunwald, Niklaus - Nik; PUTMAN, MELODIE - Oregon State University; CHANG, JEFF - Oregon State University

Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/24/2018
Publication Date: 8/28/2018
Citation: Davis, E.W., Tabima, J.F., Weisberg, A.J., Lopes, L.D., Wiseman, M.S., Wiseman, M.S., Pupko, T., Belcher, M.S., Sechler, A.J., Tancos, M.A., Schroeder, B.K., Murray, T.D., Luster, D.G., Schneider, W.L., Rogers, E.E., Andreote, F., Grunwald, N.J., Putman, M.L., Chang, J.H. 2018. Bacteriophage NCPPB3778 and a type I-E CRISPR drive the evolution of the U.S. biological select agent Rathayibacter toxicus. mBio. 9:e01280-18.

Interpretive Summary: Rathayibacter toxicus is a bacterium that grows in developing grass seeds and can produce a toxin harmful to grazing livestock. So far, R. toxicus has only been found in Australia. The threat it poses to U.S. agriculture is such that the USDA Animal Plant Health Inspection Service (APHIS) has placed R. toxicus on a list of high-consequence agents with the potential to pose a severe threat to public health and safety. In culture, R. toxicus produces its toxin after infection with a specific bacteriophage (a virus that infects only bacteria). Repeated interactions with this bacteriophage, among other causes, has given R. toxicus a much smaller genome and more homogeneous population than is found in other related Rathayibacter species. This lack of genetic diversity may affect the ability of R. toxicus to adapt to new environments and may have implications for repeated interactions between other bacteria and bacteriophages.

Technical Abstract: Rathayibacter toxicus is a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution of R. toxicus to explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy of Rathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequenced Rathayibacter genomes indicated that Rathayibacter forms nine species-level groups. R. toxicus is the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover, R. toxicus has low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates. R. toxicus is the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of the R. toxicus species.