Supplementary Figure 1: Lineage and geographic distribution of M. tuberculosis isolates.

(a) Geographic distribution of M. tuberculosis isolates by lineage. This plot shows the sampling frequency within our data set of 5,310 strains and is not necessarily indicative of overall global incidence. The pie charts illustrate the relative proportions of M. tuberculosis lineages isolated within each of 11 UN subregions (http://unstats.un.org/unsd/methods/m49/m49regin.htm). The map is colored by UN geographic subregion. There were no strains in our data set from geographic regions colored gray. UN geographic subregions with fewer than 30 strains were excluded from this figure. This map was modified from a blank map of UN geographical subregions (Pusch, T.; licensed under CC BY-SA 3.0 via Wikimedia Commons; https://commons.wikimedia.org/wiki/File:Geografiaj_subregionoj_la%C5%AD_Unui%C4%9Dintaj_Nacioj_malplene.svg). (b) Global prevalence for each of six WHO global subregions as a percentage of total global TB burden (black bars), side by side with the percentage of our data set from each of these regions. We used different geographic subdivisions (WHO rather than UN) for this panel to present our data side by side with WHO data. Note that our data set is under-represented in strains from Southeast Asia (which includes India) and over-represented in strains from Africa and Europe (which includes Russia). WHO global subregions are defined as follows. AFR (Africa): Algeria, Angola, Benin, Burkina Faso, Cameroon, Cape Verde, Chad, Comoros, Equatorial Guinea, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Liberia, Madagascar, Mali, Mauritania, Mauritius, Niger, Nigeria, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Togo, Botswana, Burundi, Central African Republic, Congo, Côte d'Ivoire, Democratic Republic of the Congo, Eritrea, Ethiopia, Kenya, Lesotho, Malawi, Mozambique, Namibia, Rwanda, South Africa, Swaziland, Uganda, United Republic of Tanzania, Zambia, Zimbabwe; AMR (Americas): Canada, Cuba, United States of America, Antigua and Barbuda, Argentina, Bahamas, Barbados, Belize, Brazil, Chile, Colombia, Costa Rica, Dominica, Dominican Republic, El Salvador, Grenada, Guyana, Honduras, Jamaica, Mexico, Panama, Paraguay, Saint Kitts and Nevis, Saint Lucia, Saint Vincent and the Grenadines, Suriname, Trinidad and Tobago, Uruguay, Venezuela, Bolivia, Ecuador, Guatemala, Haiti, Nicaragua, Peru; EMR (Eastern Mediterranean): Bahrain, Cyprus, Iran (Islamic Republic of), Jordan, Kuwait, Lebanon, Libyan Arab Jamahiriya, Oman, Qatar, Saudi Arabia, Syrian Arab Republic, Tunisia, United Arab Emirates, Afghanistan, Djibouti, Egypt, Iraq, Morocco, Pakistan, Somalia, Sudan, Yemen; EUR (Europe): Andorra, Austria, Belgium, Croatia, Czech Republic, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, Malta, Monaco, Netherlands, Norway, Portugal, San Marino, Slovenia, Spain, Sweden, Switzerland, United Kingdom, Albania, Armenia, Azerbaijan, Bosnia and Herzegovina, Bulgaria, Georgia, Kyrgyzstan, Poland, Romania, Slovakia, Tajikistan, The Former Yugoslav Republic of Macedonia, Turkey, Turkmenistan, Uzbekistan, Yugoslavia, Belarus, Estonia, Hungary, Kazakhstan, Latvia, Lithuania, Republic of Moldova, Russian Federation, Ukraine; SEAR (Southeast Asia): Indonesia, Sri Lanka, Thailand, Bangladesh, Bhutan, Democratic People's Republic of Korea, India, Maldives, Myanmar, Nepal, Timor Leste; WPR (Western Pacific): Cambodia, China, Cook Islands, Fiji, Kiribati, Lao People's Democratic Republic, Malaysia, Marshall Islands, Micronesia (Federated States of), Mongolia, Nauru, Niue, Palau, Papua New Guinea, Philippines, Republic of Korea, Samoa, Solomon Islands, Tonga, Tuvalu, Vanuatu, Viet Nam, Australia, Brunei Darussalam, Japan, New Zealand, Singapore.