74 R.A. Skuce et al.
Glaser, L., Carstensen, M., Shaw, S., Robbe-Austerman, S., Wunschmann, A., et al. (2016) Descriptive
epidemiology and whole genome sequencing analysis for an outbreak of bovine tuberculosis in beef
cattle and white-tailed deer in Northwestern Minnesota. PLOS ONE 11(1), e0145735.
Goodchild, A.V., Watkins, G.H., Sayers, A.R., Jones, J.R. and Clifton-Hadley, R.S. (2012) Geographical
association between the genotype of bovine tuberculosis in found dead badgers and in cattle herds.
Veterinary Record 170(10), 259.
Gopal, R., Goodchild, A., Hewinson, G., de la Rua Domenech, R. and Clifton-Hadley, R. (2006) Intro-
duction of bovine tuberculosis to north-east England by bought-in cattle. Veterinary Record 159(9),
265–271.
Guthrie, J.L. and Gardy, J.L. (2015) Accelerating tuberculosis elimination in low-incidence settings: the role
of genomics. European Respiratory Journal 46(6), 1840–1841.
Gutierrez, M., Samper, S., Gavigan, J.A., García Marín, J.F. and Martin, C. (1995) Differentiation by molec-
ular typing of Mycobacterium bovis strains causing tuberculosis in cattle and goats. Journal of Clinical
Microbiology 33(11), 2953–2956.
Hauer, A., De Cruz, K., Cochard, T., Godreuil, S., Karoui, C., et al. (2015) Genetic evolution of Mycobac-
terium bovis causing tuberculosis in livestock and wildlife in France since 1978. PLOS ONE 10(2),
e0117103.
Heersma, H.F., Kremer, K. and van Embden, J.D. (1998) Computer analysis of IS6110 RFLP patterns of
Mycobacterium tuberculosis. Methods in Molecular Biology 101, 395–422.
Hershberg, R., Lipatov, M., Small, P.M., Sheffer, H., Niemann, S., et al. (2008) High functional diversity
in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biology 6(12),
e311.
Hlokwe, T.M., van Helden, P. and Michel, A. (2013) Evaluation of the discriminatory power of variable num-
ber of tandem repeat typing of Mycobacterium bovis isolates from Southern Africa. Transboundary
and Emerging Diseases 60, 111–120.
Jagielski, T., Minias, A., van Ingen, J., Rastogi, N., Brzostek, A., et al. (2016) Methodological and clinical
aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clini-
cal Microbiology Reviews 29(2), 239–290.
Jombart, T., Cori, A., Didelot, X., Cauchemez, S., Fraser, C. and Ferguson, N. (2014a) Bayesian recon-
struction of disease outbreaks by combining epidemiologic and genomic data. PLoS Computational
Biology 10(1), e1003457.
Jombart, T., Aanensen, D.M., Baguelin, M., Birrell, P., Cauchemez, S., et al. (2014b) OutbreakTools: a new
platform for disease outbreak analysis using the R software. Epidemics 7, 28–34.
Kamath, P.L., Foster, J.T., Drees, K.P., Luikart, G., Quance, C., et al. (2016) Genomics reveals historic
and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. Nature
Communications 7, 11448.
Kamerbeek, J., Schouls, L., Kolk, A., van Agterveld, M., van Soolingen, D., et al. (1997) Simultaneous
detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology.
Journal of Clinical Microbiology 35(4), 907–914.
Kao, R.R., Haydon, D.T., Lycett, S.J. and Murcia, P.R. (2014) Supersize me: how whole-genome sequenc-
ing and big data are transforming epidemiology. Trends in Microbiology 22(5), 282–291.
Kao, R.R., Price-Carter, M. and Robbe-Austerman, S. (2016) Use of genomics to track bovine tuberculosis
transmission. Revue Scientifique Et Technique 35(1), 241–268.
Katale, B.Z., Mbugi, E.V., Siame, K.K., Keyyu, J.D., Kendall, S., et al. (2015) Isolation and potential for
transmission of Mycobacterium bovis at Human-livestock-wildlife interface of the Serengeti ecosys-
tem, Northern Tanzania. Transboundary and Emerging Diseases 64(3), 815–825.
Kwong, J.C., McCallum, N., Sintchenko, V. and Howden, B.P. (2015) Whole genome sequencing in clinical
and public health microbiology. Pathology 47(3), 199–210.
Lahuerta-Marin A., Gallagher M., McBride S., Skuce R., Menzies F. et al.(2015) Should they stay, or should
they go? Relative future risk of bovine tuberculosis for interferon-gamma test-positive cattle left on
farms. Vet Research 46(90).
Lamine-Khemiri, H., Martinez, R., Garcia-Jimenez, W.L., Benitez-Medina, J.M., Cortes, M., et al. (2013)
Genotypic characterization by spoligotyping and VNTR typing of Mycobacterium bovis and Myco-
bacterium caprae isolates from cattle of Tunisia. Tropical Animal Health and Production 46(2),
305–311.
Lamoureux, B.E., Palmieri, P.A., Jackson, A.P. and Hobfoll, S.E. (2012) Child sexual abuse and adulthood
interpersonal outcomes: examining pathways for intervention. Psychological Trauma 4(6), 605–613.