Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse


Human babesiosis caused by Babesia microti is an emerging tick-borne zoonosis of increasing importance due to its rising incidence and expanding geographic range1. Infection with this organism, an intraerythrocytic parasite of the phylum Apicomplexa, causes a febrile syndrome similar to malaria2. Relapsing disease is common among immunocompromised and asplenic individuals3,4 and drug resistance has recently been reported5. To investigate the origin and genetic diversity of this parasite, we sequenced the complete genomes of 42 B. microti samples from around the world, including deep coverage of clinical infections at endemic sites in the continental USA. Samples from the continental USA segregate into a Northeast lineage and a Midwest lineage, with subsequent divergence of subpopulations along geographic lines. We identify parasite variants that associate with relapsing disease, including amino acid substitutions in the atovaquone-binding regions of cytochrome b (cytb) and the azithromycin-binding region of ribosomal protein subunit L4 (rpl4). Our results shed light on the origin, diversity and evolution of B. microti, suggest possible mechanisms for clinical relapse, and create the foundation for further research on this emerging pathogen.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Phylogeny of global B. microti.
Figure 2: Genome-wide population genetic summary statistics.
Figure 3: Time to most recent common ancestry (TMRCA) for continental USA (CUS) samples.
Figure 4: Non-synonymous variants in relapsing cases.


  1. 1

    Vannier, E. & Krause, P. J. Human babesiosis. N. Engl. J. Med. 366, 2397–2407 (2012).

    Article  Google Scholar 

  2. 2

    Ruebush, T. K. & Spielman, A. Human babesiosis in the United States. Ann. Intern. Med. 88, 263–263 (1978).

    Article  Google Scholar 

  3. 3

    Krause, P. J. et al. Persistent and relapsing babesiosis in immunocompromised patients. Clin. Infect. Dis. 46, 370–376 (2008).

    Article  Google Scholar 

  4. 4

    Vyas, J. M., Telford, S. R. & Robbins, G. K. Treatment of refractory Babesia microti infection with atovaquone–proguanil in an HIV-infected patient: case report. Clin. Infect. Dis. 45, 1588–1590 (2007).

    Article  Google Scholar 

  5. 5

    Wormser, G. P. et al. Emergence of resistance to azithromycin–atovaquone in immunocompromised patients with Babesia microti infection. Clin. Infect. Dis. 50, 381–386 (2010).

    Article  Google Scholar 

  6. 6

    Telford, S. R., III . Babesial infections in humans and wildlife. Parasitic Protozoa 5, 1–47 (1993).

    Google Scholar 

  7. 7

    Herwaldt, B. L. et al. Transfusion-associated babesiosis in the United States: a description of cases. Ann. Intern. Med. 155, 509–519 (2011).

    Article  Google Scholar 

  8. 8

    Yager, P. H., Luginbuhl, L. M. & Dekker, J. P. Case 6-2014. N. Engl. J. Med. 370, 753–762 (2014).

    Article  Google Scholar 

  9. 9

    Clark, I. A. & Jacobson, L. S. Do babesiosis and malaria share a common disease process. Ann. Trop. Med. Parasitol. 92, 483–488 (1998).

    Article  Google Scholar 

  10. 10

    Hatcher, J. C., Greenberg, P. D., Antique, J. & Jimenez-Lucho, V. E. Severe babesiosis in Long Island: review of 34 cases and their complications. Clin. Infect. Dis. 32, 1117–1125 (2001).

    Article  Google Scholar 

  11. 11

    Meldrum, S. C., Birkhead, G. S., White, D. J., Benach, J. L. & Morse, D. L. Human babesiosis in New York state: an epidemiological description of 136 cases. Clin. Infect. Dis. 15, 1019–1023 (1992).

    Article  Google Scholar 

  12. 12

    Menis, M. et al. Babesiosis occurrence among the elderly in the United States, as recorded in large Medicare databases during 2006–2013. PLoS ONE 10, e0140332 (2015).

    Article  Google Scholar 

  13. 13

    Hildebrandt, A. et al. First confirmed autochthonous case of human Babesia microti infection in Europe. Eur. J. Clin. Microbiol. Infect. Dis. 26, 595–601 (2007).

    Article  Google Scholar 

  14. 14

    Wei, Q. et al. Human babesiosis in Japan: isolation of Babesia microti-like parasites from an asymptomatic transfusion donor and from a rodent from an area where babesiosis is endemic. J. Clin. Microbiol. 39, 2178–2183 (2001).

    Article  Google Scholar 

  15. 15

    Senanayake, S. N. et al. First report of human babesiosis in Australia. Med. J. Aust. 196, 350–352 (2012).

    Article  Google Scholar 

  16. 16

    Western, K. A., Benson, G. D., Gleason, N. N., Healy, G. R. & Schultz, M. G. Babesiosis in a Massachusetts resident. N. Engl. J. Med. 283, 854–856 (1970).

    Article  Google Scholar 

  17. 17

    Centers for Disease Control and Prevention (CDC). Babesiosis surveillance—18 states, 2011. Morb. Mortal. Wkly Rep. 61, 505–509 (2012).

    Google Scholar 

  18. 18

    Krause, P. J. et al. Increasing health burden of human babesiosis in endemic sites. Am. J. Trop. Med. Hyg. 68, 431–436 (2003).

    Article  Google Scholar 

  19. 19

    Stafford, K. C. III et al. Expansion of zoonotic babesiosis and reported human cases, Connecticut, 2001–2010. J. Med. Entomol. 51, 245–252 (2014).

    Article  Google Scholar 

  20. 20

    Goethert, H. K. & Telford, S. R. Not ‘out of Nantucket’: Babesia microti in southern New England comprises at least two major populations. Parasites Vectors 7, 546 (2014).

    Article  Google Scholar 

  21. 21

    Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).

    Article  Google Scholar 

  22. 22

    Homer, M. J. et al. A polymorphic multigene family encoding an immunodominant protein from Babesia microti. J. Clin. Microbiol. 38, 362–368 (2000).

    Google Scholar 

  23. 23

    Srivastava, I. K., Morrisey, J. M., Darrouzet, E., Daldal, F. & Vaidya, A. B. Resistance mutations reveal the atovaquone-binding domain of cytochrome b in malaria parasites. Mol. Microbiol. 33, 704–711 (1999).

    Article  Google Scholar 

  24. 24

    Korsinczky, M. et al. Mutations in Plasmodium falciparum cytochrome b that are associated with atovaquone resistance are located at a putative drug-binding site. Antimicrob. Agents Chemother. 44, 2100–2108 (2000).

    Article  Google Scholar 

  25. 25

    Matsuu, A., Miyamoto, K., Ikadai, H., Okano, S. & Higuchi, S. Short report: cloning of the Babesia gibsoni cytochrome b gene and isolation of three single nucleotide polymorphisms from parasites present after atovaquone treatment. Am. J. Trop. Med. Hyg. 74, 593–597 (2006).

    Article  Google Scholar 

  26. 26

    Sidhu, A. B. S. et al. In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin. J. Biol. Chem. 282, 2494–2504 (2007).

    Article  Google Scholar 

  27. 27

    Malbruny, B. et al. Resistance to macrolides in clinical isolates of Streptococcus pyogenes due to ribosomal mutations. J. Antimicrob. Chemother. 49, 935–939 (2002).

    Article  Google Scholar 

  28. 28

    Chittum, H. S. & Champney, W. S. Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli. J. Bacteriol. 176, 6192–6198 (1994).

    Article  Google Scholar 

  29. 29

    McFadden, D. C., Tomavo, S., Berry, E. A. & Boothroyd, J. C. Characterization of cytochrome b from Toxoplasma gondii and Q(o) domain mutations as a mechanism of atovaquone-resistance. Mol. Biochem. Parasitol. 108, 1–12 (2000).

    Article  Google Scholar 

  30. 30

    Pihlajamäki, M. et al. Ribosomal mutations in Streptococcus pneumoniae clinical isolates. Antimicrob. Agents Chemother. 46, 654–658 (2002).

    Article  Google Scholar 

  31. 31

    Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

    Article  Google Scholar 

  32. 32

    McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article  Google Scholar 

  33. 33

    Pages, H., Aboyoun, P., Gentleman, R. & DebRoy, S. Biostrings (Bioconductor);

  34. 34

    Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).

    Article  Google Scholar 

  35. 35

    Pfeifer, B., Wittelsbürger, U., Onsins, S. E. R. & Lercher, M. J. PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol. Biol. Evol. 31, 1929–1936 (2014).

    Article  Google Scholar 

  36. 36

    South, A. rworldmap: a new R package for mapping global data. The R Journal 3, 35–43 (2011).

    Article  Google Scholar 

  37. 37

    Charif, D. & Lobry, J. R. in Structural Approaches to Sequence Evolution 207–232 (Springer, 2007).

    Book  Google Scholar 

  38. 38

    Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945 (2000).

    Article  Google Scholar 

  39. 39

    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  Google Scholar 

  40. 40

    Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

    Article  Google Scholar 

  41. 41

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    Article  Google Scholar 

  42. 42

    Cornillot, E. et al. Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. Nucleic Acids Res. 40, 9102–9114 (2012).

    Article  Google Scholar 

  43. 43

    Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 (1986).

    Google Scholar 

  44. 44

    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995).

    Google Scholar 

  45. 45

    Birth, D., Kao, W.-C. & Hunte, C. Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Nature Commun. 5, 4029 (2014).

    Article  Google Scholar 

  46. 46

    Bulkley, D., Innis, C. A., Blaha, G. & Steitz, T. A. Revisiting the structures of several antibiotics bound to the bacterial ribosome. Proc. Natl Acad. Sci. USA 107, 17158–17163 (2010).

    Article  Google Scholar 

  47. 47

    Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123 (2009).

    Article  Google Scholar 

  48. 48

    Delcher, A. L. et al. Alignment of whole genomes. Nucleic Acids Res. 27, 2369–2376 (1999).

    Article  Google Scholar 

  49. 49

    Melnikov, A. et al. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 12, R73 (2011).

    Article  Google Scholar 

  50. 50

    Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnol. 27, 182–189 (2009).

    Article  Google Scholar 

Download references


The authors thank R. Tewhey, A. Piantadosi and J. Maguire for feedback and advice, and J. Robbins, J. Katz, J. Gelfand and T. Wieczorek for discussions and assistance with sample collection. The authors acknowledge members of the parasitology and haematology laboratories at Massachusetts General Hospital and Brigham and Women's Hospital for assistance with case identification. P.C.S. and this work are supported by the Broad Institute SPARC programme and the Bill and Melinda Gates Foundation and the Howard Hughes Medical Institute. This work was supported in part by an Infectious Disease Society of America Medical Scholars award, a MIT Division of Health Sciences and/MIT Division of Health Sciences and Technology Research Assistantship to J.E.L. and NIH MSTP grants T32GM007753 to J.E.L. and A.L. S.T. and H.K.G. are supported by NIH U01AI109656 and R41AI078631 and by grants from the Evelyn Lilly Lutz Foundation, the Dorothy Harrison Egan Foundation and the Bill and Melinda Gates Foundation. E.V. was supported by a grant from the National Research Fund for Tick-Borne Diseases.

Author information




J.E.L. performed experiments, analysed data and wrote the paper. A.D.T. and H.G. performed experiments and analysed data. L.F. performed experiments. K.G.A. analysed data. S.F.S., A.L., S.T., E.R., J.A.B. and P.C.S. analysed data and wrote the paper. S.B., G.M., L.S. and D.M. contributed reagents/materials. E.V. and B.P. contributed materials/reagants and wrote the paper.

Corresponding author

Correspondence to Pardis C. Sabeti.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Methods, Supplementary Text, Supplementary Tables 1-8, Supplementary Figures 1-13 and Supplementary References. (PDF 2335 kb)

Supplementary Dataset 1

Draft assembly of the AW1 strain. (TXT 5806 kb)

Supplementary Dataset 2

Draft assembly of the CR400 strain. (TXT 6077 kb)

Supplementary Dataset 3

Draft assembly of the Hobetsu strain. (TXT 5804 kb)

Supplementary Dataset 4

Sequences of tick-borne pathogens used to generate the SureSelect library. (TXT 41 kb)

Supplementary Dataset 5

Pairwise diversity between Russia and R1 samples for all genes. (XLSX 228 kb)

Supplementary Dataset 6

Full table of genetic diversity for all genes among CUS samples. (XLSX 310 kb)

Supplementary Dataset 7

Full table of dN/dS ratios for all genes. (XLSX 347 kb)

Supplementary Dataset 8

Code used to generate published results. (TXT 10360 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Lemieux, J., Tran, A., Freimark, L. et al. A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse. Nat Microbiol 1, 16079 (2016).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing