Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator

Abstract

Although the bovine tuberculosis (TB) agent, Mycobacterium bovis, may infect humans and cause disease, long-term epidemiological data indicate that humans represent a spill-over host in which infection with M. bovis is not self-maintaining. Indeed, human-tohuman transmission of M. bovis strains and other members of the animal lineage of the tubercle bacilli is very rare. Here, we report on three mutations affecting the two-component virulence regulation system PhoP/PhoR (PhoPR) in M. bovis and in the closely linked Mycobacterium africanum lineage 6 (L6) that likely account for this discrepancy. Genetic transfer of these mutations into the human TB agent, Mycobacterium tuberculosis, resulted in downregulation of the PhoP regulon, with loss of biologically active lipids, reduced secretion of the 6-kDa early antigenic target (ESAT-6), and lower virulence. Remarkably, the deleterious effects of the phoPR mutations were partly compensated by a deletion, specific to the animal-adapted and M. africanum L6 lineages, that restores ESAT-6 secretion by a PhoPR-independent mechanism. Similarly, we also observed that insertion of an IS6110 element upstream of the phoPR locus may completely revert the phoPR-bovis-associated fitness loss, which is the case for an exceptional M. bovis human outbreak strain from Spain. Our findings ultimately explain the long-term epidemiological data, suggesting that M. bovis and related phoPR-mutated strains pose a lower risk for progression to overt human TB, with major impact on the evolutionary history of TB.evolution | phylogeny | adaptation | zoonosis T uberculosis (TB) is caused by bacilli from the genetically compact Mycobacterium tuberculosis complex (MTBC), which gathers eight defined phylogenetic lineages in addition to the more distantly related Mycobacterium canettii group (1-3): M. tuberculosis sensu-stricto from lineages L1-L4 and L7 form a large group of human-adapted strains responsible for the vast majority of global human TB cases, whereas Mycobacterium africanum lineages (L5, L6), which are restricted to humans from West Africa, are phylogenetically linked with the eighth lineage, comprising the various animal-adapted strains, with Mycobacterium bovis as the most downstream member in the phylogeny (Fig. 1A) (4, 5). Animal strains exhibit a wide host range that includes livestock animals in close contact with humans. Episodes of bovine TB in cattle herds have been reported in 128 of 155 countries during the period 2005-2008 (6). Although the bulk of these episodes is mainly found in developing countries (6), bovine TB remains a major problem even in some industrialized countries, best exemplified by the United Kingdom, which has experienced an important resurgence of bovine TB since the 1980s (7). Because M. bovis and other closely related animal-adapted strains are also capable of causing TB in humans, this situation raises concerns regarding the zoonotic risk. Indeed, human TB cases resulting from M. bovis are estimated to be around 2% worldwide (8), with higher incidence (...

Mycobacterium tuberculosis H37Rv has a single nucleotide polymorphism in PhoR which affects cell wall hydrophobicity and gene expression

“…In contrast, the M. tuberculosis PhoR allele was dominant over the M. bovis allele, presumably since the latter sensor appears to be defective (Gonzalo-Asensio et al, 2014). In the case of the two M. tuberculosis alleles, it may be that both proteins are functional, but possibly to different extents.…”

EspR, a regulator of the ESX-1 secretion system in Mycobacterium tuberculosis, is directly regulated by the two-component systems MprAB and PhoPR

“…In addition to H37Ra, mutations have also been detected in the phoPR regulator in Mycobacterium bovis and strains of Mycobacterium africanum lineage 6 (L6), which seem to affect the fitness of these bacilli for human-to-human transmission, and disrupt the synthesis of pathogenicity lipid factors (Gonzalo- Asensio et al, 2014). However, in contrast to H37Ra, these mutations did not have any influence on the expression of the espACD operon, and did not have an obvious effect on ESX-1 activity in M. africanum L6 (Gonzalo- Asensio et al, 2014).…”

“…However, in contrast to H37Ra, these mutations did not have any influence on the expression of the espACD operon, and did not have an obvious effect on ESX-1 activity in M. africanum L6 (Gonzalo- Asensio et al, 2014). M. africanum L6 strains have a deletion, RD8, that occurred during the evolution of tuberculosis strains (Boritsch et al, 2014), and which corresponds to the region 460 bp upstream of the espACD operon (Gordon et al, 1999).…”

Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks

“…M. tuberculosis strains deficient in PhoPR activity display defects in replication in mice and macrophages (111)(112)(113). Supporting the idea of a role in M. tuberculosis virulence, mutations in phoPR in M. bovis and Mycobacterium africanum are associated with reduced mycobacterial virulence (114). In addition, M. tuberculosis phoPR mutants have defects in cell morphology and lipid production in the absence of stress, suggesting that PhoPR is required to maintain normal cell physiology under all growth conditions (113).…”