Gröschel MI, Sayes F, Simeone R et al. ESX secretion systems: mycobacterial evolution to counter host immunity. *Nat Rev Microbiol* 2016; **14**:677–91.

Guan Q, Garbati M, Mfarrej S et al. Insights into the ancestry evolution of the *Mycobacterium tuberculosis* complex from analysis of *Mycobacterium riadhense*. *NAR Genom Bioinform* 2021; **3**:lqab070.

Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus *Mycobacterium* into an emended genus *Mycobacterium* and four novel genera. *Front Microbiol* 2018; **9**:67.

Gutierrez MC, Brisse S, Brosch R et al. Ancient origin and gene mobility of the progenitor of *Mycobacterium tuberculosis*. *PLoS Pathog* 2005; **1**:e5.

He L, Fan X, Xie J. Comparative genomic structures of *Mycobacterium CRISPR-Cas*. *J Cell Biochem* 2012; **113**:2464–73.

Hershberg R, Lipatov M, Small PM et al. High functional diversity in *Mycobacterium tuberculosis* driven by genetic drift and human demography. *PLoS Biol* 2008; **6**:e311.

Hirsh AE, Tsolaki AG, DeRiemer K et al. Stable association between strains of *Mycobacterium tuberculosis* and their human host populations. *Proc Natl Acad Sci* 2004; **101**:4871–6.

Homolka S, Niemann S, Russell DG et al. Functional genetic diversity among *Mycobacterium tuberculosis* complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. *PLoS Pathog* 2010; **6**:e1000988.

Hug LA, Baker BJ, Anantharaman K et al. A new view of the tree of life. *Nat Microbiol* 2016; **1**:16048.

Izquierdo Lafuente B, Ummels R, Kuijl C et al. *Mycobacterium tuberculosis* toxin CpnT is an ESX-5 substrate and requires three type VII secretion systems for intracellular secretion. *MBio* 2021; **12**:e02983–20.

Jagielski T. A man with a prepared mind - in commemoration of the bicentenary of the birth of Louis Pasteur 1822–2022. *Clin Microbiol Infect* 2023; **29**:138–40.

Jiang Q, Liu H-C, Liu Q-Y et al. The evolution and transmission dynamics of multidrug-resistant tuberculosis in an isolated high-plateau population of Tibet, China. *Microbiol Spectr* 2023; **11**:e0399122.

Kallmann FJ, Reisner D. Twin studies on the significance of genetic factors in tuberculosis. *Am Rev Tuberc* 1947; **47**:549–74.

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. *Mol Biol Evol* 2013; **30**:772–80.

Kay GL, Sergeant MJ, Zhou Z et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. *Nat Commun* 2015; **6**:6717.

Kerner G, Laval G, Patin E et al. Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. *Am J Hum Genet* 2021; **108**:517–24.

Kerner G, Ramirez-Alejo N, Seeleuthner Y et al. Homozygosity for TYK2 P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry. *Proc Natl Acad Sci* 2019; **116**:10430–4.

Koch R. Die Aetiologie der Tuberculose. *Berl Klin Wochenschr* 1882; **19**:221–30.

Kodaman N, Sobota RS, Mera R et al. Disrupted human-pathogen co-evolution: a model for disease. *Fronti Genet* 2014; **5**:290.

Koeck J-L, Fabre M, Simon F et al. Clinical characteristics of the smooth tubercle bacilli "Mycobacterium canettii" infection suggest the existence of an environmental reservoir. *Clin Microbiol Infect* 2011; **17**:1013–9.

Kozlov AM, Darriba D, Flouri T et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. *Bioinformatics* 2019; **35**:4453–5.

Laencina L, Dubois V, Le Moigne V et al. Identification of genes required for *Mycobacterium abscessus* growth in vivo with a prominent role of the ESX-4 locus. *Proc Natl Acad Sci* 2018; **115**:E1002–11.

Lagune M, Le Moigne V, Johansen MD et al. The ESX-4 substrates, EsxU and EsxT, modulate *Mycobacterium abscessus* fitness. *PLoS Pathog* 2022; **18**:e1010771.

Lemoine F, Domelevo Entfellner J-B, Wilkinson E et al. Renewing Felsenstein's phylogenetic bootstrap in the era of big data. *Nature* 2018; **556**:452–6.

Liu Q, Liu H, Shi L et al. Local adaptation of *Mycobacterium tuberculosis* on the Tibetan Plateau. *Proc Natl Acad Sci* 2021; **118**:e2017831118.

Madacki J, Orgeur M, Fiol GM et al. Esx-1-independent horizontal gene transfer by *Mycobacterium tuberculosis* complex strains. *MBio* 2021; **12**:e00965–21.

Magee JG, Ward AC, Family III. Mycobacteriaceae Chester 1897, 63AL. In: *Bergey's Manual of Systematic Bacteriology: Volume 5: the Actinobacteria*. New York, NY: Springer, 2012, 312.

Malaga W, Payros D, Meunier E et al. Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli. *PLoS Pathog* 2023; **19**:e1011437.

Marten B. *A New Theory of Consumptions, More Especially of a Phthisis or Consumption of the Lungs*. London: R. Knaplock, 1720.

McHenry ML, Bartlett J, Igo RP et al. Interaction between host genes and *Mycobacterium tuberculosis* lineage can affect tuberculosis severity: evidence for coevolution? *PLoS Genet* 2020; **16**:e1008728.

Meehan CJ, Barco RA, Loh YHE et al. Reconstituting the genus *Mycobacterium*. *Int J Syst Evol Microbiol* 2021; **71**:004922.

Miller SI, Kukral AM, Mekalanos JJ. A two-component regulatory system (phoP phoQ) controls *Salmonella typhimurium* virulence. *Proc Natl Acad Sci* 1989; **86**:5054–8.

Mizuguchi Y, Suga K, Tokunaga T. Multiple mating types of *Mycobacterium smegmatis*. *Jpn J Microbiol* 1976; **20**:435–43.

Mizuguchi Y, Tokunaga T. Recombination between *Mycobacterium smegmatis* strains Jucho and Lacticola. *Jpn J Microbiol* 1971; **15**:359–66.

Mortimer TD, Pepperell CS. Genomic signatures of distributive conjugal transfer among mycobacteria. *Genome Biol Evol* 2014; **6**:2489–500.

Mortimer TD, Weber AM, Pepperell CS. Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems. *Genome Biol Evol* 2017; **9**:398–413.

Mostowy S, Cousins D, Brinkman J et al. Genomic deletions suggest a phylogeny for the *Mycobacterium tuberculosis* complex. *J Infect Dis* 2002; **186**:74–80.

Namouchi A, Didelot X, Schöck U et al. After the bottleneck: genome-wide diversification of the *Mycobacterium tuberculosis* complex by mutation, recombination, and natural selection. *Genome Res* 2012; **22**:721–34.

Naranbhai V. The role of host genetics (and genomics) in tuberculosis. *Microbiol Spectr* 2016; **4**:TBTB2-0011-2016. https://doi.org/10.128/microbiolspec.TBTB2-0011-2016.

Newton-Foot M, Warren RM, Sampson SL et al. The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. *BMC Evol Biol* 2016; **16**:62.

Ngabonziza JCS, Loiseau C, Marceau M et al. A sister lineage of the *Mycobacterium tuberculosis* complex discovered in the African Great Lakes region. *Nat Commun* 2020; **11**:1–11.
Gröschel MI, Sayes F, Simeone R et al. ESX secretion systems: mycobacterial evolution to counter host immunity. *Nat Rev Microbiol* 2016; **14**:677–91.

Guan Q, Garbati M, Mfarrej S et al. Insights into the ancestry evolution of the *Mycobacterium tuberculosis* complex from analysis of *Mycobacterium riadhense*. *NAR Genom Bioinform* 2021; **3**:lqab070.

Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus *Mycobacterium* into an emended genus *Mycobacterium* and four novel genera. *Front Microbiol* 2018; **9**:67.

Gutierrez MC, Brisse S, Brosch R et al. Ancient origin and gene mobility of the progenitor of *Mycobacterium tuberculosis*. *PLoS Pathog* 2005; **1**:e5.

He L, Fan X, Xie J. Comparative genomic structures of *Mycobacterium CRISPR*-Cas. *J Cell Biochem* 2012; **113**:2464–73.

Hershberg R, Lipatov M, Small PM et al. High functional diversity in *Mycobacterium tuberculosis* driven by genetic drift and human demography. *PLoS Biol* 2008; **6**:e311.

Hirsh AE, Tsolaki AG, DeRiemer K et al. Stable association between strains of *Mycobacterium tuberculosis* and their human host populations. *Proc Natl Acad Sci* 2004; **101**:4871–6.

Homolka S, Niemann S, Russell DG et al. Functional genetic diversity among *Mycobacterium tuberculosis* complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. *PLoS Pathog* 2010; **6**:e1000988.

Hug LA, Baker BJ, Anantharaman K et al. A new view of the tree of life. *Nat Microbiol* 2016; **1**:16048.

Izquierdo Lafuente B, Ummels R, Kuijl C et al. *Mycobacterium tuberculosis* toxin CpnT is an ESX-5 substrate and requires three type VII secretion systems for intracellular secretion. *MBio* 2021; **12**:e02983–20.

Jagielski T. A man with a prepared mind - in commemoration of the bicentenary of the birth of Louis Pasteur 1822–2022. *Clin Microbiol Infect* 2023; **29**:138–40.

Jiang Q, Liu H-C, Liu Q-Y et al. The evolution and transmission dynamics of multidrug-resistant tuberculosis in an isolated high-plateau population of Tibet, China. *Microbiol Spectr* 2023; **11**:e0399122.

Kallmann FJ, Reisner D. Twin studies on the significance of genetic factors in tuberculosis. *Am Rev Tuberc* 1947; **47**:549–74.

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. *Mol Biol Evol* 2013; **30**:772–80.

Kay GL, Sergeant MJ, Zhou Z et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. *Nat Commun* 2015; **6**:6717.

Kerner G, Laval G, Patin E et al. Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. *Am J Hum Genet* 2021; **108**:517–24.

Kerner G, Ramirez-Alejo N, Seeleuthner Y et al. Homozygosity for TYK2 P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry. *Proc Natl Acad Sci* 2019; **116**:10430–4.

Koch R. Die Aetiologie der Tuberculose. *Berl Klin Wochenschr* 1882; **19**:221–30.

Kodaman N, Sobota RS, Mera R et al. Disrupted human-pathogen co-evolution: a model for disease. *Fronti Genet* 2014; **5**:290.

Koeck J-L, Fabre M, Simon F et al. Clinical characteristics of the smooth tubercle bacilli "Mycobacterium canettii" infection suggest the existence of an environmental reservoir. *Clin Microbiol Infect* 2011; **17**:1013–9.

Kozlov AM, Darriba D, Flouri T et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. *Bioinformatics* 2019; **35**:4453–5.

Laencina L, Dubois V, Le Moigne V et al. Identification of genes required for *Mycobacterium abscessus* growth in vivo with a prominent role of the ESX-4 locus. *Proc Natl Acad Sci* 2018; **115**:E1002–11.

Lagune M, Le Moigne V, Johansen MD et al. The ESX-4 substrates, EsxU and EsxT, modulate *Mycobacterium abscessus* fitness. *PLoS Pathog* 2022; **18**:e1010771.

Lemoine F, Domelevo Entfellner J-B, Wilkinson E et al. Renewing Felsenstein's phylogenetic bootstrap in the era of big data. *Nature* 2018; **556**:452–6.

Liu Q, Liu H, Shi L et al. Local adaptation of *Mycobacterium tuberculosis* on the Tibetan Plateau. *Proc Natl Acad Sci* 2021; **118**:e2017831118.

Madacki J, Orgeur M, Fiol GM et al. Esx-1-independent horizontal gene transfer by *Mycobacterium tuberculosis* complex strains. *MBio* 2021; **12**:e00965–21.

Magee JG, Ward AC, Family III. *Mycobacteriaceae* Chester 1897, 63AL. In: *Bergey's Manual of Systematic Bacteriology: Volume 5: the Actinobacteria*. New York, NY: Springer, 2012, 312.

Malaga W, Payros D, Meunier E et al. Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli. *PLoS Pathog* 2023; **19**:e1011437.

Marten B. *A New Theory of Consumptions, More Especially of a Phthisis or Consumption of the Lungs*. London: R. Knaplock, 1720.

McHenry ML, Bartlett J, Igo RP et al. Interaction between host genes and *Mycobacterium tuberculosis* lineage can affect tuberculosis severity: evidence for coevolution? *PLoS Genet* 2020; **16**:e1008728.

Meehan CJ, Barco RA, Loh YHE et al. Reconstituting the genus *Mycobacterium*. *Int J Syst Evol Microbiol* 2021; **71**:004922.

Miller SI, Kukral AM, Mekalanos JJ. A two-component regulatory system (phoP phoQ) controls *Salmonella typhimurium* virulence. *Proc Natl Acad Sci* 1989; **86**:5054–8.

Mizuguchi Y, Suga K, Tokunaga T. Multiple mating types of *Mycobacterium smegmatis*. *Jpn J Microbiol* 1976; **20**:435–43.

Mizuguchi Y, Tokunaga T. Recombination between *Mycobacterium smegmatis* strains Jucho and Lacticola. *Jpn J Microbiol* 1971; **15**:359–66.

Mortimer TD, Pepperell CS. Genomic signatures of distributive conjugal transfer among mycobacteria. *Genome Biol Evol* 2014; **6**:2489–500.

Mortimer TD, Weber AM, Pepperell CS. Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems. *Genome Biol Evol* 2017; **9**:398–413.

Mostowy S, Cousins D, Brinkman J et al. Genomic deletions suggest a phylogeny for the *Mycobacterium tuberculosis* complex. *J Infect Dis* 2002; **186**:74–80.

Namouchi A, Didelot X, Schöck U et al. After the bottleneck: genome-wide diversification of the *Mycobacterium tuberculosis* complex by mutation, recombination, and natural selection. *Genome Res* 2012; **22**:721–34.

Naranbhai V. The role of host genetics (and genomics) in tuberculosis. *Microbiol Spectr* 2016; **4**:TBTB2-0011-2016. https://doi.org/10.128/microbiolspec.TBTB2-0011-2016.

Newton-Foot M, Warren RM, Sampson SL et al. The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. *BMC Evol Biol* 2016; **16**:62.

Ngabonziza JCS, Loiseau C, Marceau M et al. A sister lineage of the *Mycobacterium tuberculosis* complex discovered in the African Great Lakes region. *Nat Commun* 2020; **11**:1–11.
Oren A, Garrity G. List of new names and new combinations previously effectively, but not validly, published. *Int J Syst Evol Microbiol* 2018;**68**:1411–7.

Orgeur M, Brosch R. Evolution of virulence in the *Mycobacterium tuberculosis* complex. *Curr Opin Microbiol* 2018;**41**:68–75.

Orgeur M, Frigui W, Pawlik A et al. Pathogenomic analyses of *Mycobacterium microti*, an ESX-1-deleted member of the *Mycobacterium tuberculosis* complex causing disease in various hosts. *Microb Genom* 2021;**7**:505.

Pajuelo D, Tak U, Zhang L et al. Toxin secretion and trafficking by *Mycobacterium tuberculosis*. *Nat Commun* 2021;**12**:6592.

Parsons LM, Jankowski CS, Derbyshire KM. Conjugal transfer of chromosomal DNA in *Mycobacterium smegmatis*. *Mol Microbiol* 1998;**28**:571–82.

Patané JSL, Martins J, Beatriz Castelão A et al. Patterns and processes of *Mycobacterium bovis* evolution revealed by phylogenomic analyses. *Genome Biol Evol* 2017;**9**:521–35.

Pérez E, Samper S, Bordas Y et al. An essential role for phoP in *Mycobacterium tuberculosis* virulence. *Mol Microbiol* 2001;**41**:179–87.

Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. *NAR Genom Bioinform* 2021;**3**:lqaa106.

Pfyffer GE, Auckenthaler R, van Embden JD et al. *Mycobacterium canettii*, the smooth variant of *M. tuberculosis*, isolated from a Swiss patient exposed in Africa. *Emerg Infect Dis* 1998;**4**:631–4.

Poweleit N, Czudnochowski N, Nakagawa R et al. The structure of the endogenous ESX-3 secretion system. *Elife* 2019;**8**:e52983.

Ramakrishnan L, Tran HT, Federspiel NA et al. A crtB homolog essential for photochromogenicity in *Mycobacterium marinum*: isolation, characterization, and gene disruption via homologous recombination. *J Bacteriol* 1997;**179**:5862–8.

Raman S, Puyang X, Cheng T-Y et al. *Mycobacterium tuberculosis* SigM positively regulates Esx secreted protein and nonribosomal peptide synthetase genes and down regulates virulence-associated surface lipid synthesis. *J Bacteriol* 2006;**188**:8460–8.

Reed MB, Pichler VK, McIntosh F et al. Major *Mycobacterium tuberculosis* lineages associate with patient country of origin. *J Clin Microbiol* 2009;**47**:1119–28.

Reis AC, Cunha MV. Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of *Mycobacterium bovis*. *Sci Rep* 2021;**11**:18789.

Riojas MA, McGough KJ, Rider-Riojas CJ et al. Phylogenomic analysis of the species of the *Mycobacterium tuberculosis* complex demonstrates that *Mycobacterium africanum*, *Mycobacterium bovis*, *Mycobacterium caprae*, *Mycobacterium microti* and *Mycobacterium pinnipedii* are later heterotypic synonyms of *Mycobacterium tuberculosis*. *Int J Syst Evol Microbiol* 2018;**68**:324–32.

Rock JM, Hopkins FF, Chavez A et al. Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. *Nat Microbiol* 2017;**2**:16274.

Rustad TR, Minch KJ, Ma S et al. Mapping and manipulating the *Mycobacterium tuberculosis* transcriptome using a transcription factor overexpression-derived regulatory network. *Genome Biol* 2014;**15**:502.

Saad MM, Alshukairi AN, Qutub MO et al. *Mycobacterium riyadhense* infections. *Saudi Med J* 2015;**36**:620–5.

Sabin S, Herbig A, Vågene ÅJ et al. A seventeenth-century *Mycobacterium tuberculosis* genome supports a Neolithic emergence of the *Mycobacterium tuberculosis* complex. *Genome Biol* 2020;**21**:201.

Saelens JW, Sweeney MI, Viswanathan G et al. An ancestral mycobacterial effector promotes dissemination of infection. *Cell* 2022;**185**:4507–4525.e18.

Saito H, Iwamoto T, Ohkusu K et al. *Mycobacterium shinjukuense* sp. nov., a slowly growing, non-chromogenic species isolated from

human clinical specimens. *Int J Syst Evol Microbiol* 2011;**61**:1927–32.

Sankey N, Merrick H, Singh P et al. Role of the *Mycobacterium tuberculosis* ESX-4 secretion system in heme iron utilization and pore formation by PPE proteins. *mSphere* 2023;**8**:e0057322.

Sapriel G, Brosch R. Shared pathogenomic patterns characterize a new phylotype, revealing transition toward host-adaptation long before speciation of *Mycobacterium tuberculosis*. *Genome Biol Evol* 2019;**11**:2420–38.

Sapriel G, Konjek J, Orgeur M et al. Genome-wide mosaicism within *Mycobacterium abscessus*: evolutionary and epidemiological implications. *BMC Genom* 2016;**17**:118.

Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. *Mol Microbiol* 2003;**48**:77–84.

Sassetti CM, Rubin EJ. Genetic requirements for mycobacterial survival during infection. *Proc Natl Acad Sci* 2003;**100**:12989–94.

Schliep KP. Phangorn: phylogenetic analysis in R. *Bioinformatics* 2011;**27**:592–3.

Schnappinger D, Ehrt S, Voskuil MI et al. Transcriptional adaptation of *Mycobacterium tuberculosis* within macrophages: insights into the phagosomal environment. *J Exp Med* 2003;**198**:693–704.

Seemann T. Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 2014;**30**:2068–9.

Simner PJ, Hyle EP, Buckwalter SP et al. Tenosynovitis caused by a novel nontuberculous *Mycobacterium* species initially misidentified as a member of the *Mycobacterium tuberculosis* complex. *J Clin Microbiol* 2014;**52**:4414–8.

Singh A, Gaur M, Sharma V et al. Comparative genomic analysis of *Mycobacteriaceae* reveals horizontal gene transfer-mediated evolution of the CRISPR–Cas system in the *Mycobacterium tuberculosis* complex. *mSystems* 2021;**6**:e00934–20.

Smith NH, Hewinson RG, Kremer K et al. Myths and misconceptions: the origin and evolution of *Mycobacterium tuberculosis*. *Nat Rev Microbiol* 2009;**7**:537–44.

Smith NH, Kremer K, Inwald J et al. Ecotypes of the *Mycobacterium tuberculosis* complex. *J Theor Biol* 2006;**239**:220–5.

Solans L, Gonzalo-Asensio J, Sala C et al. The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in *Mycobacterium tuberculosis*. *PLoS Pathog* 2014;**10**:e1004183.

Stead WW, Eisenach KD, Cave MD et al. When did *Mycobacterium tuberculosis* infection first occur in the New World? An important question with public health implications. *Am J Respir Crit Care Med* 1995;**151**:1267–8.

Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. *Nat Biotechnol* 2017;**35**:1026–8.

Stinear TP, Seemann T, Harrison PF et al. Insights from the complete genome sequence of *Mycobacterium marinum* on the evolution of *Mycobacterium tuberculosis*. *Genome Res* 2008;**18**:729–41.

Stucki D, Brites D, Jeljeli L et al. *Mycobacterium tuberculosis* lineage 4 comprises globally distributed and geographically restricted sublineages. *Nat Genet* 2016;**48**:1535–43.

Supply P, Brosch R. The biology and epidemiology of *Mycobacterium canettii*. *Adv Exp Med Biol* 2017;**1019**:27–41.

Supply P, Marceau M, Mangenot S et al. Genome analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of the etiologic agent of tuberculosis. *Nat Genet* 2013;**45**:172–9.

Tagini F, Pillonel T, Bertelli C et al. Pathogenic determinants of the *Mycobacterium kansasii* complex: an unsuspected role for distributive conjugal transfer. *Microorganisms* 2021;**9**:348.
Oren A, Garrity G. List of new names and new combinations previously effectively, but not validly, published. *Int J Syst Evol Microbiol* 2018;**68**:1411–7.

Orgeur M, Brosch R. Evolution of virulence in the *Mycobacterium tuberculosis* complex. *Curr Opin Microbiol* 2018;**41**:68–75.

Orgeur M, Frigui W, Pawlik A et al. Pathogenomic analyses of *Mycobacterium microti*, an ESX-1-deleted member of the *Mycobacterium tuberculosis* complex causing disease in various hosts. *Microb Genom* 2021;**7**:505.

Pajuelo D, Tak U, Zhang L et al. Toxin secretion and trafficking by *Mycobacterium tuberculosis*. *Nat Commun* 2021;**12**:6592.

Parsons LM, Jankowski CS, Derbyshire KM. Conjugal transfer of chromosomal DNA in *Mycobacterium smegmatis*. *Mol Microbiol* 1998;**28**:571–82.

Patané JSL, Martins J, Beatriz Castelão A et al. Patterns and processes of *Mycobacterium bovis* evolution revealed by phylogenomic analyses. *Genome Biol Evol* 2017;**9**:521–35.

Pérez E, Samper S, Bordas Y et al. An essential role for phoP in *Mycobacterium tuberculosis* virulence. *Mol Microbiol* 2001;**41**:179–87.

Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. *NAR Genom Bioinform* 2021;**3**:lqaa106.

Pfyffer GE, Auckenthaler R, van Embden JD et al. *Mycobacterium canettii*, the smooth variant of *M. tuberculosis*, isolated from a Swiss patient exposed in Africa. *Emerg Infect Dis* 1998;**4**:631–4.

Poweleit N, Czudnochowski N, Nakagawa R et al. The structure of the endogenous ESX-3 secretion system. *Elife* 2019;**8**:e52983.

Ramakrishnan L, Tran HT, Federspiel NA et al. A crtB homolog essential for photochromogenicity in *Mycobacterium marinum*: isolation, characterization, and gene disruption via homologous recombination. *J Bacteriol* 1997;**179**:5862–8.

Raman S, Puyang X, Cheng T-Y et al. *Mycobacterium tuberculosis* SigM positively regulates Esx secreted protein and nonribosomal peptide synthetase genes and down regulates virulence-associated surface lipid synthesis. *J Bacteriol* 2006;**188**:8460–8.

Reed MB, Pichler VK, McIntosh F et al. Major *Mycobacterium tuberculosis* lineages associate with patient country of origin. *J Clin Microbiol* 2009;**47**:1119–28.

Reis AC, Cunha MV. Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of *Mycobacterium bovis*. *Sci Rep* 2021;**11**:18789.

Riojas MA, McGough KJ, Rider-Riojas CJ et al. Phylogenomic analysis of the species of the *Mycobacterium tuberculosis* complex demonstrates that *Mycobacterium africanum*, *Mycobacterium bovis*, *Mycobacterium caprae*, *Mycobacterium microti* and *Mycobacterium pinnipedii* are later heterotypic synonyms of *Mycobacterium tuberculosis*. *Int J Syst Evol Microbiol* 2018;**68**:324–32.

Rock JM, Hopkins FF, Chavez A et al. Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. *Nat Microbiol* 2017;**2**:16274.

Rustad TR, Minch KJ, Ma S et al. Mapping and manipulating the *Mycobacterium tuberculosis* transcriptome using a transcription factor overexpression-derived regulatory network. *Genome Biol* 2014;**15**:502.

Saad MM, Alshukairi AN, Qutub MO et al. *Mycobacterium riyadhense* infections. *Saudi Med J* 2015;**36**:620–5.

Sabin S, Herbig A, Vågene ÅJ et al. A seventeenth-century *Mycobacterium tuberculosis* genome supports a Neolithic emergence of the *Mycobacterium tuberculosis* complex. *Genome Biol* 2020;**21**:201.

Saelens JW, Sweeney MI, Viswanathan G et al. An ancestral mycobacterial effector promotes dissemination of infection. *Cell* 2022;**185**:4507–4525.e18.

Saito H, Iwamoto T, Ohkusu K et al. *Mycobacterium shinjukuense* sp. nov., a slowly growing, non-chromogenic species isolated from

human clinical specimens. *Int J Syst Evol Microbiol* 2011;**61**:1927–32.

Sankey N, Merrick H, Singh P et al. Role of the *Mycobacterium tuberculosis* ESX-4 secretion system in heme iron utilization and pore formation by PPE proteins. *mSphere* 2023;**8**:e0057322.

Sapriel G, Brosch R. Shared pathogenomic patterns characterize a new phylotype, revealing transition toward host-adaptation long before speciation of *Mycobacterium tuberculosis*. *Genome Biol Evol* 2019;**11**:2420–38.

Sapriel G, Konjek J, Orgeur M et al. Genome-wide mosaicism within *Mycobacterium abscessus*: evolutionary and epidemiological implications. *BMC Genom* 2016;**17**:118.

Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. *Mol Microbiol* 2003;**48**:77–84.

Sassetti CM, Rubin EJ. Genetic requirements for mycobacterial survival during infection. *Proc Natl Acad Sci* 2003;**100**:12989–94.

Schliep KP. Phangorn: phylogenetic analysis in R. *Bioinformatics* 2011;**27**:592–3.

Schnappinger D, Ehrt S, Voskuil MI et al. Transcriptional adaptation of *Mycobacterium tuberculosis* within macrophages: insights into the phagosomal environment. *J Exp Med* 2003;**198**:693–704.

Seemann T. Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 2014;**30**:2068–9.

Simner PJ, Hyle EP, Buckwalter SP et al. Tenosynovitis caused by a novel nontuberculous *Mycobacterium* species initially misidentified as a member of the *Mycobacterium tuberculosis* complex. *J Clin Microbiol* 2014;**52**:4414–8.

Singh A, Gaur M, Sharma V et al. Comparative genomic analysis of *Mycobacteriaceae* reveals horizontal gene transfer-mediated evolution of the CRISPR–Cas system in the *Mycobacterium tuberculosis* complex. *mSystems* 2021;**6**:e00934–20.

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Zhang YJ, Reddy MC, Ioerger TR et al. Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. *Cell* 2013;155:1296-308.
Takeda K, Ohshima N, Nagai H et al. Six cases of pulmonary Mycobacterium shinjukuense infection at a single hospital. *Intern Med* 2016;55:787–91.

Taoka T, Shinohara T, Hatakeyama N et al. *Mycobacterium shinjukuense* pulmonary disease progressed to pleuritis after iatrogenic pneumothorax: a case report. *J Clin Tuberc Other Mycobact* Dis 2020;19:100160.

Tekaia F, Gordon SV, Garnier T et al. Analysis of the proteome of *Mycobacterium tuberculosis* in silico. *Tuberc Lung Dis* 1999;79: 329–42.

Thomson M, Liu Y, Nunta K et al. Expression of a novel mycobacterial phosphodiesterase successfully lowers cAMP levels resulting in reduced tolerance to cell wall-targeting antimicrobials. *J Biol Chem* 2022;298:102151.

Tientcheu LD, Koch A, Ndengane M et al. Immunological consequences of strain variation within the *Mycobacterium tuberculosis* complex. *Eur J Immunol* 2017;47:432–45.

Tokunaga T, Mizuguchi Y, Suga K. Genetic recombination in mycobacteria. *J Bacteriol* 1973;113:1104–11.

Tortoli E, Brown-Elliott BA, Chalmers JD et al. Same meat, different gravy: ignore the new names of mycobacteria. *Eur Respir J* 2019;54:1900795.

Tortoli E, Fedrizzi T, Meehan CJ et al. The new phylogeny of the genus *Mycobacterium*: the old and the news. *Infect Genet Evol* 2017;56:19–25.

Turenne C, Chedore P, Wolfe J et al. *Myobacterium lacus* sp. nov., a novel slowly growing, non-chromogenic clinical isolate. *Int J Syst Evol Microbiol* 2002;52:2135–40.

Vågene ÅJ, Honap TP, Harkins KM et al. Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. *Nat Commun* 2022;13:1195.

Val-Calvo J, Vázquez-Boland JA. *Mycobacteriales* taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. *mBio* 2023;14:e0220723.

Vallenet D, Calteau A, Cruveiller S et al. *MicroScope* in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. *Nucleic Acids Res* 2017;45:D517–28.

Vallenet D, Labarre L, Rouy Z et al. MaGe: a microbial genome annotation system supported by synteny results. *Nucleic Acids Res* 2006;34:53–65.

van Ingen J, Al-Haijoj SAM, Boeree M et al. *Mycobacterium riyadhense* sp. nov., a non-tuberculous species identified as *Mycobacterium tuberculosis* complex by a commercial line-probe assay. *Int J Syst Evol Microbiol* 2009;59:1049–53.

van Soolingen D, Hoogenboezem T, de Haas PE et al. A novel pathogenic taxon of the *Mycobacterium tuberculosis* complex, canetti: characterization of an exceptional isolate from Africa. *Int J Syst Bacteriol* 1997;47:1236–45.

Varghese B, Enani MA, Althawadi S et al. *Mycobacterium riyadhense* in Saudi Arabia. *Emerg Infect Dis* 2017;23:1732–4.

Veyrier FJ, Dufort A, Behr MA. The rise and fall of the *Mycobacterium tuberculosis* genome. *Trends Microbiol* 2011;19:156–61.

Villemin JA. Cause et nature de la tuberculose. *Bull Acad Med* 1865;37:211–6.

Walters SB, Dubnau E, Kolesnikova I et al. The *Mycobacterium tuberculosis* PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. *Mol Microbiol* 2006;60:312–30.

Wang J, Behr MA. Building a better bacillus: the emergence of *Mycobacterium tuberculosis*. *Front Microbiol* 2014;5:139.

Wang J, Derbyshire KM. Plasmid DNA transfer in *Mycobacterium smegmatis* involves novel DNA rearrangements in the recipient, which can be exploited for molecular genetic studies. *Mol Microbiol* 2004;53:1233–41.

Wang J, Karnati PK, Takacs CM et al. Chromosomal DNA transfer in *Mycobacterium smegmatis* is mechanistically different from classical Hfr chromosomal DNA transfer. *Mol Microbiol* 2005;58:280–8.

Wang J, McIntosh F, Radomski N et al. Insights on the emergence of *Mycobacterium tuberculosis* from the analysis of *Mycobacterium kansasii*. *Genome Biol Evol* 2015;7:856–70.

Wang J, Parsons LM, Derbyshire KM. Unconventional conjugal DNA transfer in mycobacteria. *Nat Genet* 2003;34:80–84.

Wang Y, Tang Y, Lin C et al. Crosstalk between the ancestral type VII secretion system ESX-4 and other T7SS in *Mycobacterium marinum*. *iScience* 2022;25:103585.

Watanabe S, Zimmermann M, Goodwin MB et al. Fumarate reductase activity maintains an energized membrane in anaerobic *Mycobacterium tuberculosis*. *PLoS Pathog* 2011;7:e1002287.

World Health Organization. *Global Tuberculosis Report* 2023. World Health Organization, Geneva, 2023.

Xia X. Horizontal Gene transfer and drug resistance involving *Mycobacterium tuberculosis*. *Antibiotics* 2023;12:1367.

Yang J, Jin Z-B, Chen J et al. Genetic signatures of high-altitude adaptation in Tibetans. *Proc Natl Acad Sci* 2017;114:4189–94.

Yano H, Iwamoto T, Nishiuchi Y et al. Population structure and local adaptation of MAC lung disease agent *Mycobacterium avium* subsp. hominissuis. *Genome Biol Evol* 2017;9:2403–17.

Yenew B, Ghodousi A, Diriba G et al. A smooth tubercle bacillus from Ethiopia phylogenetically close to the *Mycobacterium tuberculosis* complex. *Nat Commun* 2023;14:7519.

Yu G, Smith DK, Zhu H et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. *Methods Ecol Evol* 2017;8:28–36.

Zhang YJ, Reddy MC, Ioerger TR et al. Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. *Cell* 2013;155:1296–308.