VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation.
Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
Amy J
AJ
Vogler
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
Roxanne
R
Nottingham
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
Joseph D
JD
Busch
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
Jason W
JW
Sahl
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Medicine, Vanderbilt University, School of Medicine, Nashville, TN, United States.
Megan M
MM
Shuey
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.
Jeffrey T
JT
Foster
Translational Genomics Research Institute North, Flagstaff, AZ, United States.
James M
JM
Schupp
US Geological Survey, National Wildlife Health Center, Madison, WI, United States.
Susan R
SR
Smith
US Geological Survey, National Wildlife Health Center, Madison, WI, United States.
Tonie E
TE
Rocke
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Translational Genomics Research Institute North, Flagstaff, AZ, United States.
Paul
P
Keim
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States. Electronic address: Dave.Wagner@nau.edu.
David M
DM
Wagner
D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics*; D004195:Disease Models, Animal; D019143:Evolution, Molecular; D008099:Liver / Q000382:microbiology; D008168:Lung / Q000382:microbiology; D018598:Minisatellite Repeats / Q000235:genetics*; D058885:Multilocus Sequence Typing; D009154:Mutation / Q000235:genetics*; D010930:Plague / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012589:Sciuridae; D015010:Yersinia pestis / Q000235:genetics*
D004269:DNA, Bacterial
MLVA; Mutation; Prairie dog; SNP; VNTR; Yersinia pestis