The theme of this year’s World TB Day is ‘Unite to End TB’. Part of advocating for greater attention to TB is celebrating the scientific advances we have made in understanding Mycobacterium tuberculosis infection biology and the new avenues we have opened up for eradicating the disease. Supporting this message, we have assembled a ‘Further Reading’ list highlighting such pioneering research from across the Nature journals within the last year or so:

A. The Background:

For those unfamiliar with TB (or even TB researchers who are focused on a specific line of investigation), reviews are a great way to approach and interpret the complexity of the bacterium and its interaction with the host.

• A Nature Reviews Disease Primer on tuberculosis from Pai and colleagues provides a broad overview of tuberculosis pathogenesis, diagnosis and treatment. This work, as part of the Nature's Antimicrobial Resistance collection is free until July 17. See also the Primeview infographic overview that accompanies this work. And a related correspondence from Laughton and Nacy updates further developments in drug development.

• Since ESX-1 was identified as a major virulence locus (its deletion largely accounts for the attenuation of the BCG vaccine), the five Type VII ESX secretion systems have been a major area of interest for those hoping to understand how M. tuberculosis communicates with and subverts the host. Last year, Brosch and colleagues published a review in Nature Reviews Microbiology on the function of these secretion systems and their roles in infection.

B. TB pathogenesis and host response:

M. tuberculosis has evolved alongside the immune system. Understanding the molecular bases of the interactions between the bacterium and host is a prerequisite for unraveling the complicated crosstalk involved in causing persistent infection.

1. Avoiding autophagy: work from Stallings and colleagues in 2015 in Nature found that xenophagy (degradation of pathogens through autophagy pathways) surprisingly did not appear to mediate TB control (in contrast to other intracellular pathogens). That, then logically left us with the major question of how TB avoids this innate immune defense.

• In Nature Microbiology, Porcelli and colleagues investigated the bacterial side of the equation and identified a gene, rv2741 (encoding PE_PGRS47), that was required to inhibit autophagy in macrophages and reduce MHC-II antigen presentation. This gene was also required for full virulence in mice at late stages of infection.

• On the host side, Phillips, Moore and colleagues in Nature Immunology showed that TB induced the miR-33 pathway to inhibit autophagy and support bacterial replication. Silencing the pathway enhanced xenophagy and TB clearance in mice, representing a potential avenue for host-directed therapy.

2. Inhibiting immune responses: natural TB infection generally does not elicit effective long-term immunity. Understanding the reason for this reduced immunogenicity will aid in the design of a long sought-after efficacious vaccine.

• In their Nature Microbiology paper, Jacobs, Philips and colleagues demonstrated that the ESX-3 secretion substrate EsxH inhibits ESCRT trafficking, leading to decreased TB antigen presentation in phagocytes and enhanced bacterial replication in mice.

• Sintim, Bishai and colleagues in Nature Chemical Biology define a cyclic dinucleotide-based axis of immune activation. While infection releases both bacterial c-di-AMP and induces host production of cGAMP, TB encodes a phosphodiesterase CdnP to hydrolyse these signals and block inflammatory cytokine induction. Disruption of cdnP leads to bacterial attenuation and enhanced mouse survival during infection.

C. Human TB infection:

Animal models of TB vary in their ability to reproduce the spectrum of pathology and disease progression seen in human infections. Thus, it remains critical to understand the host response in natural human infections and define clinical parameters that can affect patient cure and relapse rates.

• In their Nature Medicine study, Cohen, Kishony and colleagues investigate TB disease progression in HIV-positive individuals, a group particularly susceptible to symptomatic disease and death. From autopsy samples, they observed that multiple lineages evolved in parallel and persisted for years in patients, with evidence of equal dissemination rates between lung regions and to extrapulmonary sites.

• While the above work captured TB diversity within individuals, the M. tuberculosis species comprises of distinct lineages with varying geographical ranges. Gagneux and colleagues in Nature Genetics carried out phylogenetic reconstruction of diverse TB strains, which suggested that the global Lineage 4 originated in Europe and disseminated via human migration. Analysis of immune epitopes in these global strains showed more diversity compared to more geographically restricted lineages, suggesting these changes may be driven by adaptation to different immune pressures across diverse human populations.

• Esmail, Wilkinson and colleagues in Nature Medicine, describe how FDG positron emission coupled with computed tomography (PET-CT) can identify individuals with pulmonary changes reminiscent of active disease despite being clinically consistent with latent infection. These individuals had greater likelihood of disease progression, challenging the binary view of active vs. latent disease as a discriminatory clinical diagnosis.

• Malherbe and colleagues in Nature Medicine also used PET-CT to assess lung inflammation during and after curative antibiotic treatment. They found that only a minority of individuals had inert lesions despite clinical cure. Some of these individuals also had detectable M. tuberculosis mRNA in sputum or bronchial alveolar lavage samples, suggesting clinical cure may not necessarily mean microbial sterilization and that ongoing immunological control even after treatment is likely a key factor in preventing relapse.

• But how do these host-pathogen forces molecularly play out in human infections? In Nature Medicine, Dartois, Rubin and colleagues utilized proteomics to create a spatial map of immune responses in human TB granulomas. This map showed a physical segregation of pro- and anti-inflammatory signals—while central necrotic regions were rich with antimicrobial peptides, reactive oxygen species and pro-inflammatory cytokines, an anti-inflammatory signature was seen in the peripheral regions. This immunological split was reproduced in the rabbit infection model, suggesting that spatial effects are a common lens through which net TB immune responses can be interpreted in the future.

D. Resistance:

With around half a million multidrug resistant TB infections in 2015, antibiotic resistance is a threat to the clinical efficacy of our first line antibiotics. Greater surveillance and characterization of resistance mutations have provided a broader view of global drug resistance emergence and has enabled better prediction of clinical resistance from genome sequences.

• In a Nature Genetics article, Earl and colleagues analyzed 5,310 TB genome sequences and showed that regardless of geography, similar drug resistance mutations were globally observed. In particular, a katG S315T mutation arose before rifampicin resistance mutations in diverse regions, suggesting this represents a common route for multidrug resistance emergence and offers new markers for better assessing likelihoods of MDR-TB evolution.

• Javid and colleagues in Nature Microbiology found that clinically relevant mutations in the glutamine amidotransferase subunit GatA leads to increased mistranslation rates and enhanced phenotypic rifampicin tolerance.

• Iqbal and colleagues in Nature Communications analysed whole genome sequences to create de Bruijn representations of known resistance alleles. This approach allowed them to produce resistance reports for clinicians with good sensitivity and specificity when compared with gold standard clinical resistance testing.

E. Drug development:

After decades of quiescence, several new anti-TB compounds have been licensed, including Bedaquiline in 2012 and Delamanid in 2014 (which is specifically geared towards treating multidrug resistant TB). Work still remains on improving our understanding of how promising pre-clinical candidates can kill TB, developing new compounds with improved potency and identifying synergistic combinations of existing drugs to shorten treatment times.

• Futterer, Ballell, Besra and colleagues in Nature Microbiology showed that the anti-tubercular compound tetrahydropyrazo[1,5-a]pyrimidine-3-carboxamide (THPP) inhibits EchA6 to block mycolic acid synthesis. This is in contrast to previously observed resistance mutations in MmpL3, suggesting MmpL3 may act as a drug importer for this compound instead.

• Baliga and colleagues in Nature Microbiology found that bedaquiline treatment induced a transcriptional response associated with drug tolerance and required two transcription factors, Rv0324 and Rv0880. Systems analysis of expression data showed that pretonamid induced similar changes to the deletion of Rv0880, and thus was able to synergize with bedaquiline.

• In Nature Chemical Biology, Lamichhane and colleagues found that carbapenem antibiotics can target the 3->3 L,D peptidoglycan transpeptidases in addition to the canonical 4->3 D,D transpeptidases. Using structural modeling, they developed new carbapenems that had improved L,D transpeptidase inhibition, which increased their potency against TB (as well as against other major human pathogens).

• In their Nature Communications work, Horwitz and colleagues used a computational approach to screen billions of potential drug interactions to identify combinations with better killing kinetics. They found several regimens that offered up to 75% faster TB clearance in mice compared to current gold-standard treatment.

F. Tools:

In trying to unravel the complexity of TB infection, researchers have had to develop new tools with better resolution and greater functionality. Further methodological innovation will certainly be required to dig even deeper and answer ever more difficult questions.

• From bacteria to eukaryotes and back again, CRISPR-Cas tools are now being used for genome engineering in TB. Fortune and colleagues in Nature Microbiology identified a Streptococcus thermophilus Cas9 variant that offered a programmable CRISPRi system for M. tuberculosis with improved transcriptional knockdown over other methods.

• Love, Shalek and colleagues in Nature Methods advanced single cell RNA-seq by developing a low-cost platform that integrates mRNA capture and barcoding and reduces cross contamination, while being portable enough for isolation of TB infected cells in a BSL3 facility. RNA-seq analysis of TB infected cells showed 3 distinct macrophages expression profiles suggesting TB infection is heterogeneous.

• While not specific to TB, in Nature Reviews Genetics, Power, Parkhill and de Oliveira review methods for conducting microbial genome-wide association studies to define genetic markers associated with disease and resistance. Also, see work in Nature Microbiology from Wilson and colleagues on how to control for lineage affects that can bias microbial GWAS studies. And also a News and Views on this work from Falush.

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