Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese Tao Luoa,b,Iñaki Comasc,d,1, Dan Luoe,1, Bing Luf,g,1, Jie Wuh,1, Lanhai Weii,1, Chongguang Yanga, Qingyun Liua, Mingyu Gana, Gang Suna, Xin Shenh, Feiying Liue, Sebastien Gagneuxj,2, Jian Meih,2, Rushu Lane,2, Kanglin Wanf,k,2, and Qian Gaoa,2 aKey Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; bLaboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China; cGenomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain; dCIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid 28029, Spain; eDepartment of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi 530028, China; fState Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; gBeijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Control and Prevention, Beijing 100013, China; hDepartment of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China; iMinistry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China; jDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, University of Basel, Basel CH-4003, Switzerland; and kCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China Edited by William R. Jacobs Jr., Howard Hughes Medical Institute, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, and approved May 14, 2015 (received for review December 23, 2014) The Beijing family is the most successful genotype of Mycobacterium great attentions due to its global emergence in recent decades tuberculosis and responsible for more than a quarter of the global (6, 7, 10–12), its tendency to cause disease outbreak (13–17), and tuberculosis epidemic. As the predominant genotype in East Asia, the its association with antibiotic resistance (12, 18). Experimental and Beijing family has been emerging in various areas of the world and is clinical evidences suggest a hypervirulent phenotype of Beijing often associated with disease outbreaks and antibiotic resistance. Re- strains (12, 19), and a higher mutation rate compared with other vealing the origin and historical dissemination of this strain family is strains (20). important for understanding its current global success. Here we char- According to genotyping data from previous molecular- acterized the global diversity of this family based on whole-genome epidemiology studies, most Beijing strains from widespread geo- sequences of 358 Beijing strains. We show that the Beijing strains graphic areas showed a remarkable degree of genetic similarity endemic in East Asia are genetically diverse, whereas the globally (6, 21), suggesting this strain family might have emerged from emerging strains mostly belong to a more homogenous subtype recent expansions. It was hypothesized that vaccination with “ ” known as modern Beijing. Phylogeographic and coalescent analy- Bacille Calmette Guerin (bacillus Calmette–Guérin) that has ses indicate that the Beijing family most likely emerged around been widely implemented in East Asian countries might be the 30,000 y ago in southern East Asia, and accompanied the early colo- force driving the dominance of this strain family in this area (21). nization by modern humans in this area. By combining the genomic Moreover, the global emergence of the Beijing family may have data and genotyping result of 1,793 strains from across China, we found the “modern” Beijing sublineage experienced massive expan- sions in northern China during the Neolithic era and subsequently Significance spread to other regions following the migration of Han Chinese. Our results support a parallel evolution of the Beijing family and Mycobacterium tuberculosis Beijing family is a group of glob- modern humans in East Asia. The dominance of the “modern” Beijing ally emerging bacterial strains that are responsible for more sublineage in East Asia and its recent global emergence are most than a quarter of the global tuberculosis epidemic. Here, we likely driven by its hypervirulence, which might reflect adaption to combine whole-genome sequencing and large-scale genotyp- increased human population densities linked to the agricultural tran- ing to map the temporal and spatial changes of the genetic sition in northern China. diversity within this strain family. We reveal a southern East Asia origin and a parallel evolution of this bacterial genotype MTBC Beijing family | origin | expansion | Han Chinese with modern humans in East Asia during the last 30,000 years. The recently globally emerged Beijing strains mainly belong to uberculosis has plagued human beings since ancient times and a hypervirulent subtype that most likely has initially been se- Tremains a leading cause of global morbidity and mortality. The lected for adaption to increased population densities during causative agent of human tuberculosis is the Mycobacterium tuber- the agricultural transition in northern China. culosis complex (MTBC), a group of organisms that harbor little Author contributions: T.L., F.L., S.G., J.M., R.L., K.W., and Q.G. designed research; T.L., D.L., genetic diversity compared with other bacteria (1). MTBC most B.L., J.W., C.Y., Q.L., M.G., G.S., and X.S. performed research; T.L., I.C., and L.W. analyzed likely originated in Africa, although its age is being debated (2–4). data; and T.L., I.C., L.W., S.G., and Q.G. wrote the paper. The human-adapted MTBC is highly clonal and is classified into The authors declare no conflict of interest. seven main phylogenetic groups, designated lineage 1 through This article is a PNAS Direct Submission. lineage 7 (2). These seven lineages show strong biogeographic as- Data deposition: The sequences in this paper have been deposited in the Sequence Read sociations that have been proposed to result from codiversification Archive database, www.ncbi.nlm.nih.gov/sra (accession no. SRP051093). with different human populations (2, 5). Lineage 2 that dominates 1I.C., D.L., B.L., J.W., and L.W. contributed equally to this work. in East Asia is one of the most successful MTBC variants; more 2To whom correspondence may be addressed. Email: [email protected], sebastien. than a quarter of the global tuberculosis epidemic is caused by this [email protected], [email protected], [email protected], or [email protected] lineage (6, 7). Lineage 2 contains strains that mostly belong to the This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. so-called Beijing family (8, 9). This strain family has attracted 1073/pnas.1424063112/-/DCSupplemental. 8136–8141 | PNAS | June 30, 2015 | vol. 112 | no. 26 www.pnas.org/cgi/doi/10.1073/pnas.1424063112 Downloaded by guest on September 28, 2021 been due to its hypervirulence and association with drug re- A East sistance (7, 18). However, there were discrepant results regarding Europe 1 the relative protective effect of bacillus Calmette–Guérin vaccina- tion against Beijing strains from animal infection experiments (19), East Europe 2 and many epidemiological studies failed to find any association between bacillus Calmette–Guérin vaccination and Beijing strains (22–25). The link between drug resistance and the Beijing family has Bj-MG3 primarily been observed in regions where this family has emerged Lineage 2.2 recently (e.g., Cuba, South Africa, countries of the former Soviet (Beijing) Union) but not in East Asian, where the Beijing family has been endemic for a long time (18, 26). Furthermore, more recent studies 7.8 kya (7.1-8.6) indicate that the expansion of the Beijing family may have started NTF::IS6110 long before the introduction of vaccination and antibiotic treatment B (2, 3, 27). 11.3 kya (10.1-12.4) With the increased availability of genotyping data, the Beijing Bj-MG2 strains were proved more heterogeneous than initially estimated, RD181 18.5 kya – (16.4-20.6) and several Beijing sublineages have been identified (28 31). 12.2 kya 27.8 kya RD207 (10.7-13.6) Bj-MG1 (24.8-30.8) However, a full understanding of the genetic diversity of Beijing (Beijing) RD105 Extended RD105 Lineage 2.1 family is constrained by the low amount of nucleotide variation (Lineage 2) (Proto-Beijing) (8, 32). Whole-genome sequencing provides an ideal tool to 1.0E8 NDT Ne study the genetic diversity of MTBC, and new insights into the expansion 1.0E7 – (6.5 kya) per generation origin and evolution of MTBC have been gained (2, 4, 20, 33 C Pre-NDT 1.0E6 expansion 35). The genomic diversity of Beijing family was initially studied (10 kya) in a most recent study, in which a general East Asian origin and 1.0E5 recent expansions of this strain family were suggested (36). However, 1.0E4 1.0E3 the details about the origin and primary dissemination of Beijing 25 20 15 10 5 0 family remain unclear. Answering of these questions is important to Time (Kya) better understand the virulence of this lineage and its global success. Fig. 1. Genetic and geographic structure and population dynamics of Here, we combined whole-genome sequencing of key strains with global MTBC lineage 2 strains. (A) Places of origin for the 358 MTBC lineage detailed single nucleotide polymorphism (SNP) typing of a large 2 strains. The size of dot corresponds to the number of strains in each place.