Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States.
Babesia microti is an emerging tick-borne apicomplexan parasite with increasing geographic range and incidence in the United States. The rapid expansion of B. microti into its current distribution in the northeastern USA has been due to the range expansion of the tick vector, Ixodes scapularis, upon which the causative agent is dependent for transmission to humans.



To reconstruct the history of B. microti in the continental USA and clarify the evolutionary origin of human strains, we used multiplexed hybrid capture of 25 B. microti isolates obtained from I. scapularis and human blood. Despite low genomic variation compared with other Apicomplexa, B. microti was strongly structured into three highly differentiated genetic clusters in the northeastern USA. Bayesian analyses of the apicoplast genomes suggest that the origin of the current diversity of B. microti in northeastern USA dates back 46 thousand years with a signature of recent population expansion in the last 1000 years. Human-derived samples belonged to two rarely intermixing clusters, raising the possibility of highly divergent infectious phenotypes in humans.



Our results validate the multiplexed hybrid capture strategy for characterizing genome-wide diversity and relatedness of B. microti from ticks and humans. We find strong population structure in B. microti samples from the Northeast indicating potential barriers to gene flow.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.|Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
Giovanna
G
Carpi
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.
Katharine S
KS
Walter
Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06520, USA.
Choukri Ben
CB
Mamoun
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.|Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06520, USA.
Peter J
PJ
Krause
Department of Anthropology, University of Iowa, Iowa City, IA, 52242, USA.
Andrew
A
Kitchen
Nantucket Cottage Hospital, Nantucket, MA, 02554, USA.
Timothy J
TJ
Lepore
Institut de Biologie Computationnelle, University de Montpellier, 34095, Montpellier, Cedex 5, France.
Ankit
A
Dwivedi
Institut de Biologie Computationnelle, University de Montpellier, 34095, Montpellier, Cedex 5, France.
Emmanuel
E
Cornillot
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
Adalgisa
A
Caccone
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA. mad2256@columbia.edu.|Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA. mad2256@columbia.edu.
Maria A
MA
Diuk-Wasser
D000818:Animals; D041001:Babesia microti / Q000145:classification / Q000235:genetics* / Q000382:microbiology; D001404:Babesiosis / Q000469:parasitology / Q000635:transmission; D025065:Borrelia burgdorferi; D014644:Genetic Variation; D005828:Genetics, Population; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014481:United States
Apicomplexan; Coalescent analysis; Hybrid capture; Population genomics; Tick-borne pathogen