Tracking genetics - Researchers study brucellosis genomeWritten by Saige Albert
Bozeman, Mont. – During a two-day public meeting of the Committee on Revisiting Brucellosis in the Greater Yellowstone Area, the National Academy of Sciences (NAS) reviewed a variety of topics related to brucellosis, ranging from livestock activities to the latest science on brucellosis.
On the second day of the meeting, Pauline Kamath of the U.S. Geological Survey discussed the preliminary results of a study using genomics to assess transmission of the disease.
“This project makes use of recent advancements in genomic sequencing to obtain whole genome sequences from the bacteria Brucella abortus,” says Kamath. “We have obtained isolates from elk, bison and cattle over a 30-year time period in the Greater Yellowstone Ecosystem.”
The goal of the project is to better understand cross-species transmission dynamics of the disease.
Looking at genetics
NAS began looking at the genomics of brucellosis because of the low genetic diversity and low mutation rate of the bacteria B. abortus, explains Kamath.
“In the past, genetic studies have been done based on genetic markers that have high mutation rates,” she says. “They represent a very small portion of the genome, and they can be unstable. Across larger scales, they may be misleading. Whole genome sequencing is the most comprehensive data we could obtain in assessing Brucella abortus.”
The study also looked at incorporating time sampling within their analysis to attempt to pinpoint directionality of transmission.
As the basis of the study, NAS utilized phylogenetic trees, which compare current genomic sequences and their differences to determine a common ancestor.
Sequences that are very similar are more closely related. The more differences in a sequence indicate a more distant relationship. By creating a tree that depicts these relationships, cross-species transmission can be determined.
“Our study objectives were to examine the history of brucellosis introduction into the Greater Yellowstone Ecosystem, to determine the lineages associated with hosts in those locations, to estimate the relative rates of cross-species transmission and to identify historical and recent infection sources,” Kamath said.
Inside the data
Kamath and her team looked at 245 Brucella genomes. Close to 1,500 single nucleotide polymorphisms, or variable DNA sites, were identified and use in the analysis.
Samples were connected to year, host and location.
“We found a common ancestor in the late 1700s, which represents the most likely time of introduction of Brucella into North America,” Kamath said. “We also identified five very distinct lineages that are not closely related to one another. They are more related to an isolate outside the Greater Yellowstone Ecosystem.”
The five lineages are also largely localized in a specific area.
“Two lineages are found primarily in the feedgrounds. The Yellowstone lineage is only found in Yellowstone into the Paradise Valley in Montana,” Kamath said. “We also have two lineages that are widely distributed throughout the ecosystem.”
After lineages were identified, Kamath noted that the isolates were correlated back to the hosts through time and sequenced to obtain relative rates of transmission, as well as ancestral host states.
“There are multiple species per lineage,” she explained. “No lineage is associated with just one species, but the Yellowstone lineage is primarily dominated by bison.”
“At the tips of our tree is a clustering of species, suggesting that most transmission is within each species,” Kamath said. “The main transmission source is primarily elk, except in Yellowstone, which is bison.”
The trees also allowed the research team to assess transmission between species over time, as well as to estimate a transmission rate.
“Over evolutionary time, we are showing the most supported host transmission is from elk to livestock, then bison to elk and elk to bison,” Kamath said.
Kamath mentioned that even if brucellosis was eradicated completely in bison, it is likely that they would be re-infected by elk.
The results were also analyzed chronologically. In looking at 1993, 2003 and 2013, the spatial distribution was analyzed.
“If we look at the spread, it seems to be originating primarily from the Wyoming feedgrounds in four of the five lineages,” Kamath said. “However, the northern feedgrounds, which encompasses the National Elk Refuge, was the source of multiple long-distance linkages.”
While this evidence may seem to suggest that feedgrounds are the problem, Kamath also noted, “Once brucellosis is in a new location, it seems to maintained in the local wildlife, outside of the feedgrounds. We no longer need elk in the feedgrounds for Brucella to be maintained.”
Kamath noted that several conclusions were reached from the analysis, commenting, “We found evidences for five introduction of B. abortus into the Greater Yellowstone Ecosystem.”
Most transmission of brucellosis occurs within species, but the highest transmission rates occur from elk to livestock. There is not support for transmission from bison to livestock.
“While Wyoming feedgrounds seem to be the source on long-distance movement, that long distance transmission is rare and more in the past, suggesting that elk are now a reservoir outside the feedgrounds,” she continued.
As a result of information from the study, Kamath noted that several management recommendations could result when the data is finalized.
“Targeting Yellowstone bison may be unlikely to affect B. abortus in regions outside the Greater Yellowstone Ecosystem with the exception of Paradise Valley,” she said. “Removal of the feedgrounds may not reduce seroprevalence in other areas, mainly because Brucella is being maintained outside the feedgrounds.”
She also noted that evidence supports current management focuses on minimizing elk to livestock contact to reduce brucellosis transmission.
The data Kamath presented is preliminary data from their analysis, and it will be available in final form at a later date.