A specialised SKI complex assists the cytoplasmic RNA exosome in the absence of direct association with ribosomes.

The Ski2-Ski3-Ski8 (SKI) complex assists the RNA exosome during the 3' to 5' degradation of cytoplasmic transcripts. Previous reports showed that the SKI complex is involved in the 3' to 5' degradation of mRNAs, including 3' untranslated regions (UTRs) and devoid of ribosomes. Paradoxically, we recently showed that the SKI complex directly interacts with ribosomes during the co-translational mRNA decay and that this interaction is necessary for its RNA degradation promoting activity. Here, we characterised a new SKI-associated factor, Ska1, that associates with a subpopulation of the SKI complex. We showed that Ska1 is specifically involved in the degradation of long 3'UTR-containing mRNAs, poorly translated mRNAs as well as other RNA regions not associated with ribosomes, such as cytoplasmic lncRNAs. We further show that the overexpression of SKA1 antagonises the SKI-ribosome association. We propose that the Ska1-SKI complex assists the cytoplasmic exosome in the absence of direct association of the SKI complex with ribosomes.

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε.

BACKGROUND: (-)-Balanol is an ATP-mimicking inhibitor that non-selectively targets protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA). While PKA constantly shows tumor promoting activities, PKC isozymes can ambiguously be tumor promoters or suppressors. In particular, PKCε is frequently implicated in tumorigenesis and a potential target for anticancer drugs. We recently reported that the C5(S)-fluorinated balanol analogue (balanoid 1c) had improved binding affinity and selectivity for PKCε but not to the other novel PKC isozymes, which share a highly similar ATP site. The underlying basis for this fluorine-based selectivity is not entirely comprehended and needs to be investigated further for the development of ATP mimic inhibitors specific for PKCε. RESULTS: Using molecular dynamics (MD) simulations assisted by homology modelling and sequence analysis, we have studied the fluorine-based selectivity in the highly similar ATP sites of novel PKC (nPKC) isozymes. The study suggests that every nPKC isozyme has different dynamics behaviour in both apo and 1c-bound forms. Interestingly, the apo form of PKCε, where 1c binds strongly, shows the highest degree of flexibility which dramatically decreases after binding 1c. CONCLUSIONS: For the first time to the best of our knowledge, we found that the origin of 1c selectivity for PKCε comes from the unique dynamics feature of each PKC isozyme. Fluorine conformational control in 1c can synergize with and lock down the dynamics of PKCε, which optimize binding interactions with the ATP site residues of the enzyme, particularly the invariant Lys437. This finding has implications for further rational design of balanol-based PKCε inhibitors for cancer drug development.

Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria.

Horizontal gene transfer (HGT) is a major driving force of bacterial diversification and evolution. For tuberculosis-causing mycobacteria, the impact of HGT in the emergence and distribution of dominant lineages remains a matter of debate. Here, by using fluorescence-assisted mating assays and whole genome sequencing, we present unique experimental evidence of chromosomal DNA transfer between tubercle bacilli of the early-branching Mycobacterium canettii clade. We found that the obtained recombinants had received multiple donor-derived DNA fragments in the size range of 100 bp to 118 kbp, fragments large enough to contain whole operons. Although the transfer frequency between M. canettii strains was low and no transfer could be observed among classical Mycobacterium tuberculosis complex (MTBC) strains, our study provides the proof of concept for genetic exchange in tubercle bacilli. This outstanding, now experimentally validated phenomenon presumably played a key role in the early evolution of the MTBC toward pathogenicity. Moreover, our findings also provide important information for the risk evaluation of potential transfer of drug resistance and fitness mutations among clinically relevant mycobacterial strains.

Resistance to Thiacetazone Derivatives Active against Mycobacterium abscessus Involves Mutations in the MmpL5 Transcriptional Repressor MAB_4384.

Available chemotherapeutic options are very limited against Mycobacterium abscessus, which imparts a particular challenge in the treatment of cystic fibrosis (CF) patients infected with this rapidly growing mycobacterium. New drugs are urgently needed against this emerging pathogen, but the discovery of active chemotypes has not been performed intensively. Interestingly, however, the repurposing of thiacetazone (TAC), a drug once used to treat tuberculosis, has increased following the deciphering of its mechanism of action and the detection of significantly more potent analogues. We therefore report studies performed on a library of 38 TAC-related derivatives previously evaluated for their antitubercular activity. Several compounds, including D6, D15, and D17, were found to exhibit potent activity in vitro against M. abscessus, Mycobacterium massiliense, and Mycobacterium bolletii clinical isolates from CF and non-CF patients. Similar to TAC in Mycobacterium tuberculosis, the three analogues act as prodrugs in M. abscessus, requiring bioactivation by the EthA enzyme, MAB_0985. Importantly, mutations in the transcriptional TetR repressor MAB_4384, with concomitant upregulation of the divergently oriented adjacent genes encoding an MmpS5/MmpL5 efflux pump system, accounted for high cross-resistance levels among all three compounds. Overall, this study uncovered a new mechanism of drug resistance in M. abscessus and demonstrated that simple structural optimization of the TAC scaffold can lead to the development of new drug candidates against M. abscessus infections.

Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4 Escherichia coli clonal complex.

OBJECTIVES: Amongst the highly diverse Escherichia coli population, the ST131-O25b:H4 clonal complex is particularly worrisome as it is associated with a high level of antibiotic resistance. The lack of new antibiotics, the worldwide continuous increase of infections caused by MDR bacteria and the need for narrow-spectrum antimicrobial agents have revived interest in phage therapy. In this article, we describe a virulent bacteriophage, LM33_P1, which specifically infects O25b strains, and provide data related to its therapeutic potential. METHODS: A large panel of E. coli strains (n = 283) was used to assess both the specificity and the activity of bacteriophage LM33_P1. Immunology, biochemistry and genetics-based methods confirmed this specificity. Virology methods and sequencing were used to characterize this bacteriophage in vitro, while three relevant mouse models were employed to show its in vivo efficacy. RESULTS: Bacteriophage LM33_P1 exclusively infects O25b E. coli strains with a 70% coverage on sequence types associated with high antibiotic resistance (ST131 and ST69). This specificity is due to an interaction with the LPS mediated by an original tail fibre. LM33_P1 also has exceptional intrinsic properties with a high adsorption constant and produces over 300 virions per cell in <10 min. Using animal pneumonia, septicaemia and urinary tract infection models, we showed the in vivo efficacy of LM33_P1 to reduce the bacterial load in several organs. CONCLUSIONS: Bacteriophage LM33_P1 represents the first weapon that specifically and quickly kills O25b E. coli strains. Therapeutic approaches derived from this bacteriophage could be developed to stop or slow down the spread of the ST131-O25b:H4 drug-resistant clonal complex in humans.

Novel mutations in the glucocerebrosidase gene of Indian patients with Gaucher disease.

Gaucher disease (GD) is the most common glycolipid storage disorder resulting from glucocerebrosidase deficiency due to mutations in the GBA gene. Study was performed in 33 unrelated patients with low ß-glucosidase activity in leukocytes and/or fibroblasts. The exons and exon-intron boundaries of the GBA gene were bidirectionally sequenced using an automated sequencer. Mutations were confirmed in parents and were looked up in public databases, and in silico analysis was carried for novel mutations. We identified two novel missense mutations G289A (c.866G>C) and I466S (c.1397T>G) in exons 7 and 10, respectively, in two (6.06%) patients that destabilize the protein structure. L444P (c.1448T>C) was the most common mutation identified in 20/33 (60.60%) non-neuronopathic and 1/33 (3.03%) sub-acute neuronopathic form based on clinical presentation at the time of investigation. Other nine rare mutations were: R463C (c.1504C>T), R395C (c.1300C>T), R359Q (c.1193G>A), G355D (c.1181G>A), V352M (c.1171G>A) and S356F (c.1184C>T) found in each patient (18.18%). Compound heterozygous mutation L444P (c.1448T>C)/R496C (c.1603C>T) in exon 10/11 and L444P (c.1448T>C)/R329C (c.1102C>T) were observed in exon 10/8 in one each patient (6.06%). Two patients (6.06%) from Sri Lanka showed E326K (c.1093G>A) mutation in exon 8. We conclude that L444P is the most common mutant allele with exons 8 and 10 as the hot spot region of GBA gene observed in Indian GD patients.

YLR419W is the homolog of the mammalian translation initiation factor DHX29.

27 years after the yeast genome sequencing, the function of many ORFs remain unknown. Despite the evolutionary distance between human and yeast, homology with the conserved DEAH/DExH-box helicase domains allowed us to list DHX29, DHX36 and DHX57 as three putative homologs of the yeast Ylr419wp. Functional studies first linked the Ylr419w protein to the translating ribosome and cross-linking and analysis of cDNA (CRAC) experiments determined the precise region of Ylr419wp in contact with the ribosome. It corresponds to the loop of the h16 helix in the 18S rRNA designing the translation initiation factor DHX29, as the functional homolog of Ylr419wp.

Influence of Preoperative Sagittal Alignment on Functional Recovery in Operated Cases of Cervical Spondylotic Myelopathy.

Objective We examine the influence of preoperative cervical sagittal curvature (lordotic or nonlordotic) on the functional recovery of surgically managed cases of cervical spondylotic myelopathy (CSM). The impact of sagittal alignment on the functional improvement of operated CSM cases has not been thoroughly investigated. Materials and Methods We did retrospective analysis of consecutively operated cases of CSM from March 2019 to April 2021. Patients were grouped into two categories: lordotic curvature (with Cobb angle > 10 degrees) and nonlordotic curvature (including neutral [Cobb angle 0-10 degrees] and kyphotic [Cobb angle < 0 degrees]). Demographic data, and preoperative and postoperative functional outcome scores (modified Japanese Orthopaedic Association [mJOA] and Nurick grade) were analyzed for dependency on preoperative curvature, and correlations between outcomes and sagittal parameters were assessed. Results In the analysis of 124 cases, 63.1% (78 cases) were lordotic (mean Cobb angle of 23.57 ± 9.1 degrees; 11-50 degrees) and 36.9% (46 cases) were nonlordotic (mean Cobb angle of 0.89 ± 6.5 degrees; -11 to 10 degrees), 32 cases (24.6%) had neutral alignment, and 14 cases (12.3%) had kyphotic alignment. At the final follow-up, the mean change in mJOA score, Nurick grade, and functional recovery rate (mJOArr) were not significantly different between the lordotic and nonlordotic group. In the nonlordotic group, cases with anterior surgery had a significantly better mJOArr than those with posterior surgery ( p = 0.04), whereas there was similar improvement with either approach in lordotic cases. In the nonlordotic group, patients who gained lordosis (78.1%) had better recovery rates than those who had lost lordosis (21.9%). However, this difference was not statistically significant. Conclusion We report noninferiority of the functional outcome in the cases with preoperative nonlordotic alignment when compared with those with lordotic alignment. Further, nonlordotic patients who were approached anteriorly fared better than those approached posteriorly. Although increasing sagittal imbalance in nonlordotic spines portend toward higher preoperative disability, gain in lordosis in such cases may improve results. We recommend further studies with larger nonlordotic subjects to elucidate the impact of sagittal alignment on functional outcome.

Clinicoradiological Risk Factors Associated with Inability to Achieve Minimum Clinically Important Difference in Operated Cases of Cervical Spondylotic Myelopathy.

STUDY DESIGN: This is a retrospective cohort study. PURPOSE: This study aimed to identify the clinicoradiological risk factors associated with the inability to achieve minimum clinically important difference (MCID) on the modified Japanese Orthopaedic Association (mJOA) Scale in operated cases of cervical spondylotic myelopathy (CSM). OVERVIEW OF LITERATURE: Only a few studies have evaluated the outcomes of surgery performed for CSM using MCID on the mJOA scale. METHODS: We analyzed 124 operated CSM cases from March 2019 to April 2021 for preoperative clinical features, cervical sagittal radiographic parameters, and magnetic resonance imaging (MRI) signal intensities (SI). The risk factors associated with missing the MCID (poor outcome) on mJOA at the final follow-up were identified using binary logistic regression. Multivariate analysis was used to find significant risk factors, and odds ratios (OR) were computed. RESULTS: A total of 110 men (89.2%) and 14 women (10.8%) with an average age of 53.5±13.2 years were included in the analysis. During the last follow-up, 89 cases (72.1%) achieved MCID (meaningful gains following surgery) while 35 (27.9%) could not. The final model identified the following parameters as significant risk factors for poor outcome: increased duration of symptoms (OR, 6.77; p=0.001), lower preoperative mJOA scale (OR, 0.75; p=0.029), the presence of multilevel T2-weighted (T2W) MRI SI (OR, 4.79; p=0.004), and larger change in cervical sagittal vertical axis (ΔcSVA) (OR, 1.06; p=0.013). Also, an increase in cSVA postoperatively correlated with a reduced functional recovery rate (r=-0.4, p<0.001). CONCLUSIONS: Surgery for CSM leads to significant functional benefits. However, poorer outcomes are observed in cases of greater duration of symptoms, higher preoperative severity with multilevel T2W MRI SI, and a larger increase in the postoperative cSVA (sagittal imbalance).

In Silico Structure-Based Vaccine Design.

Structure-based vaccine design (SBVD) is an important technique in computational vaccine design that uses structural information on a targeted protein to design novel vaccine candidates. This increasing ability to rapidly model structural information on proteins and antibodies has provided the scientific community with many new vaccine targets and novel opportunities for future vaccine discovery. This chapter provides a comprehensive overview of the status of in silico SBVD and discusses the current challenges and limitations. Key strategies in the field of SBVD are exemplified by a case study on design of COVID-19 vaccines targeting SARS-CoV-2 spike protein.

Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae.

It is unclear how gene order within the chromosome influences genome evolution. Bacteria cluster transcription and translation genes close to the replication origin (oriC). In Vibrio cholerae, relocation of s10-spc-α locus (S10), the major locus of ribosomal protein genes, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction in growth rate, fitness, and infectivity. To test the long-term impact of this trait, we evolved 12 populations of V. cholerae strains bearing S10 at an oriC-proximal or an oriC-distal location for 1,000 generations. During the first 250 generations, positive selection was the main force driving mutation. After 1,000 generations, we observed more nonadaptative mutations and hypermutator genotypes. Populations fixed inactivating mutations at many genes linked to virulence: flagellum, chemotaxis, biofilm, and quorum sensing. Throughout the experiment, all populations increased their growth rates. However, those bearing S10 close to oriC remained the fittest, indicating that suppressor mutations cannot compensate for the genomic position of the main ribosomal protein locus. Selection and sequencing of the fastest-growing clones allowed us to characterize mutations inactivating, among other sites, flagellum master regulators. Reintroduction of these mutations into the wild-type context led to a ≈10% growth improvement. In conclusion, the genomic location of ribosomal protein genes conditions the evolutionary trajectory of V. cholerae. While genomic content is highly plastic in prokaryotes, gene order is an underestimated factor that conditions cellular physiology and evolution. A lack of suppression enables artificial gene relocation as a tool for genetic circuit reprogramming. IMPORTANCE The bacterial chromosome harbors several entangled processes such as replication, transcription, DNA repair, and segregation. Replication begins bidirectionally at the replication origin (oriC) until the terminal region (ter) organizing the genome along the ori-ter axis gene order along this axis could link genome structure to cell physiology. Fast-growing bacteria cluster translation genes near oriC. In Vibrio cholerae, moving them away was feasible but at the cost of losing fitness and infectivity. Here, we evolved strains harboring ribosomal genes close or far from oriC. Growth rate differences persisted after 1,000 generations. No mutation was able to compensate for the growth defect, showing that ribosomal gene location conditions their evolutionary trajectory. Despite the high plasticity of bacterial genomes, evolution has sculpted gene order to optimize the ecological strategy of the microorganism. We observed growth rate improvement throughout the evolution experiment that occurred at expense of energetically costly processes such the flagellum biosynthesis and virulence-related functions. From the biotechnological point of view, manipulation of gene order enables altering bacterial growth with no escape events.

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance.

BACKGROUND: Infections due to parasitic nematodes are common causes of morbidity and fatality around the world especially in developing nations. At present however, there are only three major classes of drugs for treating human nematode infections. Additionally the scientific knowledge on the mechanism of action and the reason for the resistance to these drugs is poorly understood. Commercial incentives to design drugs that are endemic to developing countries are limited therefore, virtual screening in academic settings can play a vital role is discovering novel drugs useful against neglected diseases. In this study we propose to build robust machine learning model to classify and screen compounds active against parasitic nematodes. RESULTS: A set of compounds active against parasitic nematodes were collated from various literature sources including PubChem while the inactive set was derived from DrugBank database. The support vector machine (SVM) algorithm was used for model development, and stratified ten-fold cross validation was used to evaluate the performance of each classifier. The best results were obtained using the radial basis function kernel. The SVM method achieved an accuracy of 81.79% on an independent test set. Using the model developed above, we were able to indentify novel compounds with potential anthelmintic activity. CONCLUSION: In this study, we successfully present the SVM approach for predicting compounds active against parasitic nematodes which suggests the effectiveness of computational approaches for antiparasitic drug discovery. Although, the accuracy obtained is lower than the previously reported in a similar study but we believe that our model is more robust because we intentionally employed stringent criteria to select inactive dataset thus making it difficult for the model to classify compounds. The method presents an alternative approach to the existing traditional methods and may be useful for predicting hitherto novel anthelmintic compounds.

The Formation of Neochromosomes during Experimental Evolution in the Yeast Saccharomyces cerevisiae.

Novel, large-scale structural mutations were previously discovered during the cultivation of engineered Saccharomyces cerevisiae strains in which essential tRNA synthetase genes were replaced by their orthologs from the distantly related yeast Yarrowia lipolytica. Among those were internal segmental amplifications forming giant chromosomes as well as complex segmental rearrangements associated with massive amplifications at an unselected short locus. The formation of such novel structures, whose stability is high enough to propagate over multiple generations, involved short repeated sequences dispersed in the genome (as expected), but also novel junctions between unrelated sequences likely triggered by accidental template switching within replication forks. Using the same evolutionary protocol, we now describe yet another type of major structural mutation in the yeast genome, the formation of neochromosomes, with functional centromeres and telomeres, made of extra copies of very long chromosomal segments ligated together in novel arrangements. The novel junctions occurred between short repeated sequences dispersed in the genome. They first resulted in the formation of an instable neochromosome present in a single copy in the diploid cells, followed by its replacement by a shorter, partially palindromic neochromosome present in two copies, whose stability eventually increased the chromosome number of the diploid strains harboring it.

Impending spontaneous head neck dissociation caused by anteverted cup: A case report on reverse bottle opener effect and review of literature.

Modularity in total hip arthroplasty (THA) not only allows adjustments of leg length and offset but also simplifies the revision. It allows limited revision of various components and decreases surgical morbidity of complete revision. Despite benefits, modularity is associated with risks like corrosion and component dissociation. Dissociation between head and neck taper is rare and the cause is attributed to taper corrosion, revision, stem subsidence, pumping phenomenon, injury and closed reduction of dislocated THA. We report a case of late-onset impending head-neck dissociation in a THA caused by a well-fixed anteverted cup with polyethylene liner wear by "reverse bottle opener effect." To our knowledge, this is the most late-onset reported case of head-neck dissociation, occurring after 13yrs of index surgery.

Impact of Covid-19 pandemic on arthroplasty services and early experience after resuming surgeries at a 'non Covid' center.

BACKGROUND: The aim of this study is to assess the impact of Covid-19 crisis on hip and knee joint replacement surgeries at a high volume tertiary care hospital in the Indian National Capital Region and to evaluate the early experience of resumption of arthroplasty services. METHODS: Institutional records of the arthroplasty cases, operated between 1st March to 31 August of 2019 (Group A, pre-Covid) and 2020 (Group B, pandemic year) were compared retrospectively over numerous parameters including the complications within six weeks of surgery. RESULTS: There was a significant drop (by 82.53 %) in the total number of arthroplasty surgeries in Group B (62) as compared with Group A (355). Average number of arthroplasties per month were 59.17 ± 12.93 and 10.67 ± 13.29 in Group A and Group B respectively (p < 0.001). There was a significant increase in postoperative complication rate 7/355 (1.97 %) in Group A vs 7/62 (11.29 %) in Group B during pandemic (p < 0.002), along with a higher 30-days mortality rate 2/355 (3.22 %) vs 2/62 (0.56 %). Pandemic year also saw an increased readmission rate (4.83 %) vs (0.56 %) and postoperative ICU transfer rate (1.61 %) vs (0.56 %) in comparison with pre-Covid year. CONCLUSION: In the pandemic, arthroplasty services got severely affected at our center. With nearly six fold increase in complication rates, higher 30-days mortality and increased readmission rates, caution is advised in resuming arthroplasty surgeries without robust evaluation of cases. Whether undetected Covid-19 infection or poor pre-existing disease control due to lockdown can be linked to these results is a matter of further research with larger multicenter studies.

Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex.

Previously, we have identified a putative novel rapidly growing Mycobacterium species, referred to as TNTM28, recovered from the sputum of an apparently immunocompetent young man with an underlying pulmonary disease. Here we provide a thorough characterization of TNTM28 genome sequence, which consists of one chromosome of 5,526,191 bp with a 67.3% G + C content, and a total of 5193 predicted coding sequences. Phylogenomic analyses revealed a deep-rooting relationship to the Mycobacterium fortuitum complex, thus suggesting a new taxonomic entity. TNTM28 was predicted to be a human pathogen with a probability of 0.804, reflecting the identification of several virulence factors, including export systems (Sec, Tat, and ESX), a nearly complete set of Mce proteins, toxin-antitoxins systems, and an extended range of other genes involved in intramacrophage replication and persistence (hspX, ahpC, sodA, sodC, katG, mgtC, ClpR, virS, etc.), some of which had likely been acquired through horizontal gene transfer. Such an arsenal of potential virulence factors, along with an almost intact ESX-1 locus, might have significantly contributed to TNTM28 pathogenicity, as witnessed by its ability to replicate efficiently in macrophages. Overall, the identification of this new species as a potential human pathogen will help to broaden our understanding of mycobacterial pathogenesis.

Rare Asymptomatic Posterior Dislocation of Mobile Bearing Insert in Unicondylar Knee Arthroplasty: A Case Report.

Dislocation of polyethylene insert is a common complication of mobile bearing uniconylar knee arthroplasty (UKA). Dislocation, when occurs is common in anterior, lateral or medial direction. The authors report a case of posterior dislocation in which patient remained asymptomatic and the dislocation was detected in a routine follow-up radiograph done at 18 months after surgery. UKA was subsequently converted into total knee arthroplasty and patient had a stable knee at two years follow-up with no signs of loosening or instability. Posterior meniscal bearing dislocation may remain asymptomatic and continued examination with high index of suspicion is needed to disclose such complications in the absence of symptoms.

BBIQ, a pure TLR7 agonist, is an effective influenza vaccine adjuvant.

Better adjuvants are needed for vaccines against seasonal influenza. TLR7 agonists are potent activators of innate immune responses and thereby may be promising adjuvants. Among the imidazoquinoline compounds, 1-benzyl-2-butyl-1H-imidazo[4,5-c]quinolin-4-amine (BBIQ) was reported to be a highly active TLR7 agonist but has remained relatively unexplored because of its commercial unavailability. Indeed, in silico molecular modeling studies predicted that BBIQ had a higher TLR7 docking score and binding free energy than imiquimod, the gold standard TLR7 agonist. To circumvent the availability issue, we developed an improved and higher yield method to synthesize BBIQ. Testing BBIQ on human and mouse TLR7 reporter cell lines confirmed it to be TLR7 specific with significantly higher potency than imiquimod. To test its adjuvant potential, BBIQ or imiquimod were admixed with recombinant influenza hemagglutinin protein and administered to mice as two intramuscular immunizations 2 weeks apart. Serum anti-influenza IgG responses assessed by ELISA 2 weeks after the second immunization confirmed that the mice that received vaccine admixed with BBIQ had significantly higher anti-influenza IgG1 and IgG2c responses than mice immunized with antigen alone or admixed with imiquimod. This confirmed BBIQ to be a TLR7-specific adjuvant able to enhance humoral immune responses.

TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages.

Mycobacterium tuberculosis (Mtb) strains are classified into different phylogenetic lineages (L), three of which (L2/L3/L4) emerged from a common progenitor after the loss of the MmpS6/MmpL6-encoding Mtb-specific deletion 1 region (TbD1). These TbD1-deleted "modern" lineages are responsible for globally-spread tuberculosis epidemics, whereas TbD1-intact "ancestral" lineages tend to be restricted to specific geographical areas, such as South India and South East Asia (L1) or East Africa (L7). By constructing and characterizing a panel of recombinant TbD1-knock-in and knock-out strains and comparison with clinical isolates, here we show that deletion of TbD1 confers to Mtb a significant increase in resistance to oxidative stress and hypoxia, which correlates with enhanced virulence in selected cellular, guinea pig and C3HeB/FeJ mouse infection models, the latter two mirroring in part the development of hypoxic granulomas in human disease progression. Our results suggest that loss of TbD1 at the origin of the L2/L3/L4 Mtb lineages was a key driver for their global epidemic spread and outstanding evolutionary success.