Medical Abstracts

Keyword: tuberculosis

1. Acc Chem Res. 2019 Aug 20;52(8):2340-2348. doi: 10.1021/acs.accounts.9b00275.

Epub 2019 Jul 30.

Harnessing Biological Insight to Accelerate Tuberculosis Drug Discovery.

de Wet TJ(1)(2), Warner DF(1)(3), Mizrahi V(1)(3).

Author information:

(1)SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit and DST/NRF Centre of

Excellence for Biomedical TB Research, Department of Pathology and Institute of

Infectious Disease and Molecular Medicine , University of Cape Town ,

Observatory, Cape Town 7925 , South Africa.

(2)Department of Integrative Biomedical Sciences , University of Cape Town ,

Observatory, Cape Town 7925 , South Africa.

(3)Wellcome Centre for Infectious Disease Research in Africa , University of Cape

Town , Observatory, Cape Town 7925 , South Africa.

Tuberculosis (TB) is the leading cause of mortality globally resulting from an

infectious disease, killing almost 1.6 million people annually and accounting for

approximately 30% of deaths attributed to antimicrobial resistance (AMR). This

despite the widespread administration of a neonatal vaccine, and the availability

of an effective combination drug therapy against the causative agent,

Mycobacterium tuberculosis (Mtb). Instead, TB prevalence worldwide is

characterized by high-burden regions in which co-epidemics, such as HIV, and

social and economic factors, undermine efforts to control TB. These elements

additionally ensure conditions that favor the emergence of drug-resistant Mtb

strains, which further threaten prospects for future TB control. To address this

challenge, significant resources have been invested in developing a TB drug

pipeline, an initiative given impetus by the recent regulatory approval of two

new anti-TB drugs. However, both drugs have been reserved for drug-resistant

disease, and the seeming inevitability of new resistance plus the recognized need

to shorten the duration of chemotherapy demands continual replenishment of the

pipeline with high-quality "hits" with novel mechanisms of action. This

represents a massive challenge, which has been undermined by key gaps in our

understanding of Mtb physiology and metabolism, especially during host infection.

Whereas drug discovery for other bacterial infections can rely on predictive in

vitro assays and animal models, for Mtb, inherent metabolic flexibility and

uncertainties about the nutrients available to infecting bacilli in different

host (micro)environments instead requires educated predictions or demonstrations

of efficacy in animal models of arguable relevance to human disease. Even

microbiological methods for enumeration of viable mycobacterial cells are fraught

with complication. Our research has focused on elucidating those aspects of

mycobacterial metabolism that contribute to the robustness of the bacillus to

host immunological defenses and applied antibiotics and that, possibly, drive the

emergence of drug resistance. This work has identified a handful of metabolic

pathways that appear vulnerable to antibiotic targeting. Those highlighted, here,

include the inter-related functions of pantothenate and coenzyme A biosynthesis

and recycling and nucleotide metabolism-the last of which reinforces our view

that DNA metabolism constitutes an under-explored area for new TB drug

development. Although nonessential functions have traditionally been

deprioritized for antibiotic development, a common theme emerging from this work

is that these very functions might represent attractive targets because of the

potential to cripple mechanisms critical to bacillary survival under stress (for

example, the RelMtb-dependent stringent response) or to adaptability under

unfavorable, potentially lethal, conditions including antibiotic therapy (for

example, DnaE2-dependent SOS mutagenesis). The bar, however, is high:

demonstrating convincingly the likely efficacy of this strategy will require

innovative models of human TB disease. In the concluding section, we focus on the

need for improved techniques to elucidate mycobacterial metabolism during

infection and its impact on disease outcomes. Here, we argue that developments in

other fields suggest the potential to break through this barrier by harnessing

chemical-biology approaches in tandem with the most advanced technologies. As

researchers based in a high-burden country, we are impelled to continue

participating in this important endeavor.

DOI: 10.1021/acs.accounts.9b00275

PMCID: PMC6704484

PMID: 31361123

2. Lancet Infect Dis. 2019 Aug 22. pii: S1473-3099(19)30420-7. doi:

10.1016/S1473-3099(19)30420-7. [Epub ahead of print]

Improving the cascade of global tuberculosis care: moving from the "what" to the

"how" of quality improvement.

Agins BD(1), Ikeda DJ(2), Reid MJA(3), Goosby E(3), Pai M(4), Cattamanchi A(5).

Author information:

(1)HEALTHQUAL, Institute for Global Health Sciences, University of California,

San Francisco, CA, USA; Division of Global Epidemiology, University of

California, San Francisco, CA, USA; Institute for Implementation Science in

Population Health, City University of New York, NY, USA. Electronic address:

bruce.agins@ucsf.edu.

(2)HEALTHQUAL, Institute for Global Health Sciences, University of California,

San Francisco, CA, USA; Harvard Medical School, Boston, MA, USA.

(3)Division of HIV, Infectious Diseases and Global Medicine, University of

California, San Francisco, CA, USA.

(4)McGill International TB Centre, McGill University, Montreal, Canada.

(5)Division of Pulmonary and Critical Care Medicine, University of California,

San Francisco, CA, USA.

Tuberculosis is preventable, treatable, and curable, yet it has the highest

mortality rate of infectious diseases worldwide. Over the past decade, services

to prevent, screen, diagnose, and treat tuberculosis have been developed and

scaled up globally, but progress to end the disease as a public health threat has

been slow, particularly in low-income and middle-income countries. In these

settings, low-quality tuberculosis prevention, diagnostic, and treatment services

frustrate efforts to translate use of existing tools, approaches, and treatment

regimens into improved individual and public health outcomes. Increasingly

sophisticated methods have been used to identify gaps in quality of tuberculosis

care, but inadequate work has been done to apply these findings to activities

that generate population-level improvements. In this Personal View, we contend

that shifting the focus from the "what" to the "how" of quality improvement will

require National Tuberculosis Programmes to change the way they organise, use

data, implement, and respond to the needs and preferences of people with

tuberculosis and at-risk communities.

Copyright © 2019 Elsevier Ltd. All rights reserved.

DOI: 10.1016/S1473-3099(19)30420-7

PMID: 31447305

3. Nat Chem Biol. 2019 Sep;15(9):889-899. doi: 10.1038/s41589-019-0336-0. Epub 2019

Aug 19.

Mycobacterium tuberculosis releases an antacid that remodels phagosomes.

Buter J(1), Cheng TY(1), Ghanem M(2), Grootemaat AE(3), Raman S(1), Feng X(4),

Plantijn AR(5), Ennis T(1), Wang J(2), Cotton RN(1), Layre E(1), Ramnarine AK(1),

Mayfield JA(1), Young DC(1), Jezek Martinot A(6), Siddiqi N(6), Wakabayashi S(6),

Botella H(7), Calderon R(8), Murray M(9), Ehrt S(7), Snider BB(10), Reed MB(2),

Oldfield E(4), Tan S(11), Rubin EJ(6), Behr MA(2), van der Wel NN(3), Minnaard

AJ(5), Moody DB(12).

Author information:

(1)Division of Rheumatology, Immunology and Allergy, Brigham and Women's

Hospital, Harvard Medical School, Boston, MA, USA.

(2)Infectious Diseases and Immunity in Global Health, McGill University Health

Centre Research Institute, McGill International TB Centre, Montreal, Canada.

(3)Electron Microscopy Center Amsterdam, Department of Medical Biology, Amsterdam

UMC, Amsterdam, the Netherlands.

...

Mycobacterium tuberculosis (Mtb) is the world's most deadly pathogen. Unlike less

virulent mycobacteria, Mtb produces 1-tuberculosinyladenosine (1-TbAd), an

unusual terpene nucleoside of unknown function. In the present study 1-TbAd has

been shown to be a naturally evolved phagolysosome disruptor. 1-TbAd is highly

prevalent among patient-derived Mtb strains, where it is among the most abundant

lipids produced. Synthesis of TbAd analogs and their testing in cells demonstrate

that their biological action is dependent on lipid linkage to the 1-position of

adenosine, which creates a strong conjugate base. Furthermore, C20 lipid moieties

confer passage through membranes. 1-TbAd selectively accumulates in acidic

compartments, where it neutralizes the pH and swells lysosomes, obliterating

their multilamellar structure. During macrophage infection, a 1-TbAd biosynthesis

gene (Rv3378c) confers marked phagosomal swelling and intraphagosomal inclusions,

demonstrating an essential role in regulating the Mtb cellular microenvironment.

Although macrophages kill intracellular bacteria through phagosome acidification,

Mtb coats itself abundantly with antacid.

DOI: 10.1038/s41589-019-0336-0

PMID: 31427817

4. Am J Respir Crit Care Med. 2019 Aug 5. doi: 10.1164/rccm.201904-0772OC. [Epub

ahead of print]

Tuberculosis Diagnosis in Children Using Xpert Ultra on Different Respiratory

Specimens.

Zar HJ(1)(2), Workman LJ(3)(4), Prins M(5), Bateman LJ(1), Mbhele SP(1), Whitman

CB(1), Denkinger CM(6), Nicol MP(1).

Author information:

(1)University of Capetown, Pediatrics & Child Health, Cape Town, South Africa.

(2)MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town,

South Africa; Heather.Zar@uct.ac.za.

(3)University of Cape Town Faculty of Health Sciences, 63726, Paediatrics and

Child Health, Observatory, South Africa.

...

RATIONALE: Microbiological confirmation of pulmonary tuberculosis in children is

desirable.

OBJECTIVES: To investigate the diagnostic accuracy and incremental yield of

Xpert-Ultra, a new rapid test, on repeated induced sputum, nasopharyngeal

aspirates and combinations of specimens.

METHODS: Consecutive South African children hospitalized with suspected pulmonary

tuberculosis were enrolled.

MEASUREMENTS: Induced sputum and nasopharyngeal aspirates were obtained.

Nasopharyngeal aspirates were frozen; induced sputum underwent liquid culture, an

aliquot was frozen. Ultra was performed on thawed nasopharyngeal aspirates and

induced sputum specimens individually. Children were categorised as confirmed,

unconfirmed or unlikely tuberculosis according to NIH consensus case definitions.

The diagnostic accuracy of Ultra was compared with liquid culture on induced

sputum.

MAIN RESULTS: 195 children [median age 23·3 months, 32(16·4%) HIV-infected] had

one induced sputum and nasopharyngeal aspirate; 130 had two nasopharyngeal

aspirates. There were 40(20·5%) culture confirmed cases. Ultra was positive on

nasopharyngeal aspirates in 26(13·3%) and on induced sputum in 31(15·9%).

Sensitivity and specificity of Ultra on one nasopharyngeal-aspirate were 46% and

98% respectively, similar by HIV status. Sensitivity and specificity of Ultra on

one induced sputum were 74·3% and 96·9% respectively. Combining one

nasopharyngeal aspirate and one induced sputum increased sensitivity to 80%.

Sensitivity using Ultra on two nasopharyngeal aspirates was 54.2%, increasing to

87.5% with an induced sputum Ultra.

CONCLUSIONS: Induced sputum provides a better specimen than repeated

nasopharyngeal aspirate for rapid diagnosis using Ultra. However, Ultra testing

of combinations of specimens provides a novel strategy that can be adapted to

identify most children with confirmed pulmonary tuberculosis.

DOI: 10.1164/rccm.201904-0772OC

PMID: 31381861

5. Lancet Infect Dis. 2019 Aug;19(8):903-912. doi: 10.1016/S1473-3099(19)30307-X.

Epub 2019 Jul 4.

Global burden of latent multidrug-resistant tuberculosis: trends and estimates

based on mathematical modelling.

Knight GM(1), McQuaid CF(2), Dodd PJ(3), Houben RMGJ(2).

Author information:

(1)Department of Infectious Disease Epidemiology, London School of Hygiene &

Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious

Diseases, London School of Hygiene & Tropical Medicine, London, UK; TB Modelling

Group, TB Centre, London School of Hygiene & Tropical Medicine, London, UK.

Electronic address: gwen.knight@lshtm.ac.uk.

(2)Department of Infectious Disease Epidemiology, London School of Hygiene &

Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious

Diseases, London School of Hygiene & Tropical Medicine, London, UK; TB Modelling

Group, TB Centre, London School of Hygiene & Tropical Medicine, London, UK.

(3)School of Health and Related Research, University of Sheffield, Sheffield, UK.

BACKGROUND: To end the global tuberculosis epidemic, latent tuberculosis

infection needs to be addressed. All standard treatments for latent tuberculosis

contain drugs to which multidrug-resistant (MDR) Mycobacterium tuberculosis is

resistant. We aimed to estimate the global burden of multidrug-resistant latent

tuberculosis infection to inform tuberculosis elimination policy.

METHODS: By fitting a flexible statistical model to tuberculosis drug resistance

surveillance and survey data collated by WHO, we estimated national trends in the

proportion of new tuberculosis cases that were caused by MDR strains. We used

these data as a proxy for the proportion of new infections caused by MDR M

tuberculosis and multiplied trends in annual risk of infection from previous

estimates of the burden of latent tuberculosis to generate trends in the annual

risk of infection with MDR M tuberculosis. These estimates were used in a cohort

model to estimate changes in the global and national prevalence of latent

infection with MDR M tuberculosis. We also estimated recent infection levels (ie,

in 2013 and 2014) and made predictions for the future burden of MDR tuberculosis

in 2035 and 2050.

FINDINGS: 19·1 million (95% uncertainty interval [UI] 16·4 million-21·7 million)

people were latently infected with MDR tuberculosis in 2014-a global prevalence

of 0·3% (95% UI 0·2-0·3). MDR strains accounted for 1·2% (95% UI 1·0-1·4) of the

total latent tuberculosis burden overall, but for 2·9% (95% UI 2·6-3·1) of the

burden among children younger than 15 years (risk ratio for those younger than 15

years vs those aged 15 years or older 2·65 [95% UI 2·11-3·25]). Recent latent

infection with MDR M tuberculosis meant that 1·9 million (95% UI 1·7 million-2·3

million) people globally were at high risk of active MDR tuberculosis in 2015.

INTERPRETATION: We estimate that three in every 1000 people globally carry latent

MDR tuberculosis infection, and prevalence is around ten times higher among those

younger than 15 years. If current trends continue, the proportion of latent

tuberculosis caused by MDR strains will increase, which will pose serious

challenges for management of latent tuberculosis-a cornerstone of tuberculosis

elimination strategies.

FUNDING: UK Medical Research Council, Bill & Melinda Gates Foundation, and

European Research Council.

Copyright © 2019 The Author(s). Published by Elsevier Ltd. This is an Open Access

article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights

reserved.

DOI: 10.1016/S1473-3099(19)30307-X

PMCID: PMC6656782

PMID: 31281059

6. Am J Respir Crit Care Med. 2019 Aug 1;200(3):370-380. doi:

10.1164/rccm.201807-1361OC.

Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities

Using RNA Sequencing.

Dheda K(1)(2), Lenders L(1), Srivastava S(3)(4), Magombedze G(3), Wainwright

H(5), Raj P(4), Bush SJ(3), Pollara G(6), Steyn R(7), Davids M(1), Pooran A(1),

Pennel T(8), Linegar A(8), McNerney R(1), Moodley L(8), Pasipanodya JG(3), Turner

CT(6), Noursadeghi M(6), Warren RM(9), Wakeland E(4), Gumbo T(1)(3).

Author information:

(1)1Centre for Lung Infection and Immunity, Division of Pulmonology, Department

of Medicine and UCT Lung Institute and South African MRC/UCT Centre for the Study

of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.

(2)2Faculty of Infectious and Tropical Diseases, Department of Immunology and

Infection, London School of Hygiene and Tropical Medicine, London, United

Kingdom.

(3)3Center for Infectious Diseases Research and Experimental Therapeutics, Baylor

Research Institute, Baylor University Medical Center, Dallas, Texas.

...

Rationale: There is poor understanding about protective immunity and the

pathogenesis of cavitation in patients with tuberculosis.Objectives: To map

pathophysiological pathways at anatomically distinct positions within the human

tuberculosis cavity.Methods: Biopsies were obtained from eight predetermined

locations within lung cavities of patients with multidrug-resistant tuberculosis

undergoing therapeutic surgical resection (n = 14) and healthy lung tissue from

control subjects without tuberculosis (n = 10). RNA sequencing,

immunohistochemistry, and bacterial load determination were performed at each

cavity position. Differentially expressed genes were normalized to control

subjects without tuberculosis, and ontologically mapped to identify a spatially

compartmentalized pathophysiological map of the cavity. In silico perturbation

using a novel distance-dependent dynamical sink model was used to investigate

interactions between immune networks and bacterial burden, and to integrate these

identified pathways.Measurements and Main Results: The median (range) lung cavity

volume on positron emission tomography/computed tomography scans was 50 cm3

(15-389 cm3). RNA sequence reads (31% splice variants) mapped to 19,049 annotated

human genes. Multiple proinflammatory pathways were upregulated in the cavity

wall, whereas a downregulation "sink" in the central caseum-fluid interface

characterized 53% of pathways including neuroendocrine signaling, calcium

signaling, triggering receptor expressed on myeloid cells-1, reactive oxygen and

nitrogen species production, retinoic acid-mediated apoptosis, and RIG-I-like

receptor signaling. The mathematical model demonstrated that neuroendocrine,

protein kinase C-θ, and triggering receptor expressed on myeloid cells-1

pathways, and macrophage and neutrophil numbers, had the highest correlation with

bacterial burden (r > 0.6), whereas T-helper effector systems did

not.Conclusions: These data provide novel insights into host immunity to

Mycobacterium tuberculosis-related cavitation. The pathways defined may serve as

useful targets for the design of host-directed therapies, and transmission

prevention interventions.

DOI: 10.1164/rccm.201807-1361OC

PMCID: PMC6680310

PMID: 30694692

7. Cell. 2019 Sep 5;178(6):1344-1361.e11. doi: 10.1016/j.cell.2019.08.004. Epub 2019

Aug 29.

TNF Induces Pathogenic Programmed Macrophage Necrosis in Tuberculosis through a

Mitochondrial-Lysosomal-Endoplasmic Reticulum Circuit.

Roca FJ(1), Whitworth LJ(2), Redmond S(3), Jones AA(2), Ramakrishnan L(4).

Author information:

(1)Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC

Laboratory of Molecular Biology, Cambridge CB2 OQH, UK. Electronic address:

froca@mrc-lmb.cam.ac.uk.

...

Necrosis of infected macrophages constitutes a critical pathogenetic event in

tuberculosis by releasing mycobacteria into the growth-permissive extracellular

environment. In zebrafish infected with Mycobacterium marinum or Mycobacterium

tuberculosis, excess tumor necrosis factor triggers programmed necrosis of

infected macrophages through the production of mitochondrial reactive oxygen

species (ROS) and the participation of cyclophilin D, a component of the

mitochondrial permeability transition pore. Here, we show that this necrosis

pathway is not mitochondrion-intrinsic but results from an inter-organellar

circuit initiating and culminating in the mitochondrion. Mitochondrial ROS induce

production of lysosomal ceramide that ultimately activates the cytosolic protein

BAX. BAX promotes calcium flow from the endoplasmic reticulum into the

mitochondrion through ryanodine receptors, and the resultant mitochondrial

calcium overload triggers cyclophilin-D-mediated necrosis. We identify ryanodine

receptors and plasma membrane L-type calcium channels as druggable targets to

intercept mitochondrial calcium overload and necrosis of mycobacterium-infected

zebrafish and human macrophages.

Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.

DOI: 10.1016/j.cell.2019.08.004

PMCID: PMC6736209

PMID: 31474371

8. Bioinformatics. 2019 Aug 26. pii: btz658. doi: 10.1093/bioinformatics/btz658.

[Epub ahead of print]

COMBAT-TB-NeoDB: fostering Tuberculosis research through integrative analysis

using graph database technologies.

Lose T(1), van Heusden P(1), Christoffels A(1).

Author information:

(1)South African National Bioinformatics Institute, South African MRC

Bioinformatics Unit, University of the Western Cape, Bellville, South Africa.

MOTIVATION: Recent advancements in genomic technologies have enabled high

throughput cost-effective generation of 'omics' data from M.tuberculosis (M.tb)

isolates, which then gets shared via a number of heterogeneous publicly available

biological data resources. Albeit useful, fragmented curation negatively impacts

the researcher's ability to leverage the data via federated queries.

RESULTS: We present Combat-TB-NeoDB, an integrated M.tuberculosis 'omics'

knowledge-base. Combat-TB-NeoDB is based on Neo4j and was created by binding the

labeled property graph model to a suitable ontology namely Chado. Combat-TB-NeoDB

enables researchers to execute complex federated queries by linking prominent

biological databases, and supplementary M.tb variants data from published

literature.

AVAILABILITY AND IMPLEMENTATION: The Combat-TB-NeoDB (https://neodb.sanbi.ac.za)

repository and all tools mentioned in this manuscript are freely available at

https://github.com/COMBAT-TB.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics

online and https://combattb.org/combat-tb-neodb.

© The Author(s) 2019. Published by Oxford University Press.

DOI: 10.1093/bioinformatics/btz658

PMID: 31504165

9. Clin Infect Dis. 2019 Aug 15. pii: ciz785. doi: 10.1093/cid/ciz785. [Epub ahead

of print]

Changes in transcript, metabolite and antibody reactivity during the early

protective immune response in humans to Mycobacterium tuberculosis infection.

Weiner J(1), Domaszewska T(1), Donkor S(2), Kaufmann SHE(1)(3), Hill PC(2)(4),

Sutherland JS(2).

Author information:

(1)Max Planck Institute for Infection Biology, Berlin, Germany.

(2)Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at

London School of Hygiene and Tropical Medicine, Banjul, The Gambia.

(3)Hagler Institute for Advanced Study, Texas A&M University, College Station,

TX, United States.

(4)Otago University, Otago, New Zealand.

BACKGROUND: Strategies to prevent Mycobacterium tuberculosis (Mtb) infection are

urgently required. This study aimed to identify correlates of protection against

early Mtb infection.

METHODS: Two groups of Mtb-exposed contacts of TB patients were recruited and

classified according to their Mtb infection status using Tuberculin skin test

(TST; cohort 1) or QuantiFERON (QFT; cohort 2. A negative reading at baseline

with a positive reading at follow-up classified TST or QFT converters and a

negative reading at both time-points classified TST or QFT non-converters.

RNA-sequencing, Mtb proteome arrays (IgG and IgA) and metabolic profiling was

performed.

RESULTS: Several genes were found to be differentially expressed at baseline

between converters and non-converters prior to any signs of infection by current

tests. Gene set enrichment analysis revealed a distinct B cell gene signature in

TST non-converters compared to converters. When infection status was defined by

QFT, enrichment of Type I IFN and antiviral gene signatures was observed. A

remarkable AUC of 1.0 was observed for IgA reactivity to Rv0134 and an AUC of

0.98 for IgA reactivity to both Rv0629c and Rv2188c. IgG reactivity to Rv3223c

resulted in an AUC of 0.96 and was markedly higher compared to TST

non-converters. We also identified several differences in metabolite profiles,

including changes in biomarkers of inflammation, fatty acid metabolism, and bile

acids. Pantothenate (Vitamin B5) was significantly increased in TST

non-converters compared to converters at baseline (q=0.0060).

CONCLUSIONS: These data provide new insights into the early protective response

to Mtb infection and possible avenues to interfere with Mtb infection including

Vitamin B5 supplementation.

© The Author(s) 2019. Published by Oxford University Press for the Infectious

Diseases Society of America.

DOI: 10.1093/cid/ciz785

PMID: 31412355

10. Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16326-16331. doi:

10.1073/pnas.1820683116. Epub 2019 Jul 31.

Phase separation and clustering of an ABC transporter in Mycobacterium

tuberculosis.

Heinkel F(1)(2), Abraham L(3), Ko M(4), Chao J(3)(4), Bach H(4), Hui LT(2), Li

H(1)(2), Zhu M(1)(2), Ling YM(2), Rogalski JC(1), Scurll J(5), Bui JM(1)(2),

Mayor T(1)(2), Gold MR(3), Chou KC(6), Av-Gay Y(3)(4), McIntosh LP(7)(2)(6),

Gsponer J(7)(2).

Author information:

(1)Michael Smith Laboratories, University of British Columbia, Vancouver, BC,

Canada V6T 1Z4.

(2)Department of Biochemistry and Molecular Biology, University of British

Columbia, Vancouver, BC, Canada V6T 1Z3.

(3)Department of Microbiology and Immunology, University of British Columbia,

Vancouver, BC, Canada V6T 1Z3.

...

Phase separation drives numerous cellular processes, ranging from the formation

of membrane-less organelles to the cooperative assembly of signaling proteins.

Features such as multivalency and intrinsic disorder that enable condensate

formation are found not only in cytosolic and nuclear proteins, but also in

membrane-associated proteins. The ABC transporter Rv1747, which is important for

Mycobacterium tuberculosis (Mtb) growth in infected hosts, has a cytoplasmic

regulatory module consisting of 2 phosphothreonine-binding Forkhead-associated

domains joined by an intrinsically disordered linker with multiple

phospho-acceptor threonines. Here we demonstrate that the regulatory modules of

Rv1747 and its homolog in Mycobacterium smegmatis form liquid-like condensates as

a function of concentration and phosphorylation. The serine/threonine kinases and

sole phosphatase of Mtb tune phosphorylation-enhanced phase separation and

differentially colocalize with the resulting condensates. The Rv1747 regulatory

module also phase-separates on supported lipid bilayers and forms dynamic foci

when expressed heterologously in live yeast and M. smegmatis cells. Consistent

with these observations, single-molecule localization microscopy reveals that the

endogenous Mtb transporter forms higher-order clusters within the Mycobacterium

membrane. Collectively, these data suggest a key role for phase separation in the

function of these mycobacterial ABC transporters and their regulation via

intracellular signaling.

DOI: 10.1073/pnas.1820683116

PMCID: PMC6697873 [Available on 2020-01-31]

PMID: 31366629

Conflict of interest statement: The authors declare no conflict of interest.

11. Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):15907-15913. doi:

10.1073/pnas.1906606116. Epub 2019 Jul 18.

An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate

dissimilation and leucine catabolism.

Wang H(1), Fedorov AA(2), Fedorov EV(2), Hunt DM(1), Rodgers A(1), Douglas HL(1),

Garza-Garcia A(1), Bonanno JB(2), Almo SC(2), de Carvalho LPS(3).

Author information:

(1)Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick

Institute, London NW1 1AT, United Kingdom.

(2)Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY

10461.

(3)Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick

Institute, London NW1 1AT, United Kingdom; luiz.carvalho@crick.ac.uk.

Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis.

One-fourth of the global population is estimated to be infected with Mtb,

accounting for ∼1.3 million deaths in 2017. As part of the immune response to Mtb

infection, macrophages produce metabolites with the purpose of inhibiting or

killing the bacterial cell. Itaconate is an abundant host metabolite thought to

be both an antimicrobial agent and a modulator of the host inflammatory response.

However, the exact mode of action of itaconate remains unclear. Here, we show

that Mtb has an itaconate dissimilation pathway and that the last enzyme in this

pathway, Rv2498c, also participates in l-leucine catabolism. Our results from

phylogenetic analysis, in vitro enzymatic assays, X-ray crystallography, and in

vivo Mtb experiments, identified Mtb Rv2498c as a bifunctional β-hydroxyacyl-CoA

lyase and that deletion of the rv2498c gene from the Mtb genome resulted in

attenuation in a mouse infection model. Altogether, this report describes an

itaconate resistance mechanism in Mtb and an l-leucine catabolic pathway that

proceeds via an unprecedented (R)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA)

stereospecific route in nature.

Copyright © 2019 the Author(s). Published by PNAS.

DOI: 10.1073/pnas.1906606116

PMCID: PMC6689899

PMID: 31320588

Conflict of interest statement: The authors declare no conflict of interest.

12. J Immunol. 2019 Aug 15;203(4):972-980. doi: 10.4049/jimmunol.1900209. Epub 2019

Jun 28.

A Subset of Mycobacteria-Specific CD4+ IFN-γ+ T Cell Expressing Naive Phenotype

Confers Protection against Tuberculosis Infection in the Lung.

Yuan J(1), Tenant J(1), Pacatte T(1), Eickhoff C(1), Blazevic A(1), Hoft DF(1),

Chatterjee S(2).

Author information:

(1)Division of Infectious Diseases, Allergy and Immunology, Department of

Internal Medicine, Saint Louis University, St. Louis, MO 63104.

(2)Division of Infectious Diseases, Allergy and Immunology, Department of

Internal Medicine, Saint Louis University, St. Louis, MO 63104

soumyadoc@gmail.com.

Failure of the most recent tuberculosis (TB) vaccine trial to boost bacillus

Calmette-Guérin-mediated anti-TB immunity despite the induction of Th1-specific

central memory cell and effector memory cell responses highlights the importance

of identifying optimal T cell targets for protective vaccines. In this study, we

describe a novel, Mycobacterium tuberculosis-specific IFN-γ+CD4+ T cell

population expressing surface markers characteristic of naive-like memory T cells

(TNLM), which were induced in both human (CD45RA+CCR7+CD27+CD95-) and murine

(CD62L+CD44-Sca-1+CD122-) systems in response to mycobacteria. In bacillus

Calmette-Guérin-vaccinated subjects and those with latent TB infection, TNLM were

marked by the production of IFN-γ but not TNF-α and identified by the absence of

CD95 expression and increased surface expression CCR7, CD27, the activation

markers T-bet, CD69, and the survival marker CD74. Increased tetramer-positive

TNLM frequencies were noted in the lung and spleen of ESAT-61-20-specific TCR

transgenic mice at 2 wk postinfection with M. tuberculosis and progressively

decreased at later time points, a pattern not seen with TNF-α+CD4+ T cells

expressing naive cell surface markers. Importantly, adoptive transfer of highly

purified TNLM alone, from vaccinated ESAT-61-20-specific TCR transgenic mice,

conferred equivalent protection against M. tuberculosis infection in the lungs of

Rag-/- mice when compared with total memory populations (central and effector

memory cells). Thus, TNLM may represent a memory T cell population that, if

optimally targeted, may significantly improve future TB vaccine responses.

Copyright © 2019 by The American Association of Immunologists, Inc.

DOI: 10.4049/jimmunol.1900209

PMID: 31253726

13. J Immunol. 2019 Aug 15;203(4):922-935. doi: 10.4049/jimmunol.1900169. Epub 2019

Jun 24.

IL-36γ Promotes Killing of Mycobacterium tuberculosis by Macrophages via

WNT5A-Induced Noncanonical WNT Signaling.

Gao Y(1), Wen Q(1), Hu S(1), Zhou X(1), Xiong W(1), Du X(1), Zhang L(1), Fu Y(1),

Yang J(1), Zhou C(1), Zhang Z(1), Li Y(1), Liu H(1), Huang Y(1), Ma L(2).

Author information:

(1)Institute of Molecular Immunology, School of Laboratory Medicine and

Biotechnology, Southern Medical University, Guangzhou 510515, China.

(2)Institute of Molecular Immunology, School of Laboratory Medicine and

Biotechnology, Southern Medical University, Guangzhou 510515, China

maryhmz@126.com.

Mycobacterium tuberculosis, which primarily infects mononuclear phagocytes,

remains the leading bacterial cause of enormous morbidity and mortality because

of bacterial infections in humans throughout the world. The IL-1 family of

cytokines is critical for host resistance to M. tuberculosis As a newly

discovered subgroup of the IL-1 family, although IL-36 cytokines have been proven

to play roles in protection against M. tuberculosis infection, the antibacterial

mechanisms are poorly understood. In this study, we demonstrated that IL-36γ

conferred to human monocyte-derived macrophages bacterial resistance through

activation of autophagy as well as induction of WNT5A, a reported downstream

effector of IL-1 involved in several inflammatory diseases. Further studies

showed that WNT5A could enhance autophagy of monocyte-derived macrophages by

inducing cyclooxygenase-2 (COX-2) expression and in turn decrease phosphorylation

of AKT/mTOR via noncanonical WNT signaling. Consistently, the underlying

molecular mechanisms of IL-36γ function are also mediated by the COX-2/AKT/mTOR

signaling axis. Altogether, our findings reveal a novel activity for IL-36γ as an

inducer of autophagy, which represents a critical inflammatory cytokine that

control the outcome of M. tuberculosis infection in human macrophages.

Copyright © 2019 by The American Association of Immunologists, Inc.

DOI: 10.4049/jimmunol.1900169

PMCID: PMC6680068

PMID: 31235551

14. Biosens Bioelectron. 2019 Aug 1;138:111322. doi: 10.1016/j.bios.2019.111322. Epub

2019 May 14.

The construction of Mycobacterium tuberculosis 16S rDNA MSPQC sensor based on

Exonuclease III-assisted cyclic signal amplification.

Zhang J(1), Huang J(1), He F(2).

Author information:

(1)State Key Laboratory of Chemo/Biosensing and Chemometrics, College of

Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.

(2)State Key Laboratory of Chemo/Biosensing and Chemometrics, College of

Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.

Electronic address: fengjiao87799232@hotmail.com.

Tuberculosis caused by Mycobacterium tuberculosis (M. tuberculosis) remains one

of the most serious infectious diseases all over the world. The key to reduce the

spread and mortality rate of tuberculosis is to develop faster and more sensitive

approaches for detection of M. tuberculosis. However, current detection methods

can not meet the requirements of rapid clinical M. tuberculosis detection in

terms of detection time. Herein, a new 16S rDNA multichannel series piezoelectric

quartz crystal (MSPQC) sensor based on Exonuclease III (Exo III)-aided target

recycling has been developed for rapid detection of M. tuberculosis. The specific

16S rDNA fragment of M. tuberculosis was used as biomarker, DNA capture probes

complementary to the biomarker were designed and modified on the surface of

AuNPs. The Exo III which could recognise hybrid duplexes and selectively digest

DNA capture probe was used to assist digestion cycle by digesting DNA capture

probe and releasing the intact target fragment. After all DNA probes loading on

the surface of AuNPs were removed, the surface of AuNPs was exposed and

conductive connection was formed between the nanogap network electrode by

self-catalytic growth of exposed AuNPs in the glucose and HAuCl4 solution. This

resulted in sensitive response of M. tuberculosis sensor and M. tuberculosis was

detected by recording this response. The limit of detection (LOD) of the method

was 20?CFU/mL and the detection time was less than 3?h. It was expected to be

widely used in detection methods of M. tuberculosis.

Copyright © 2019 Elsevier B.V. All rights reserved.

DOI: 10.1016/j.bios.2019.111322

PMID: 31112916 [Indexed for MEDLINE]

15. Eur Respir J. 2019 Aug 8;54(2). pii: 1802242. doi: 10.1183/13993003.02242-2018.

Print 2019 Aug.

IL-4 subverts mycobacterial containment in Mycobacterium tuberculosis-infected

human macrophages.

Pooran A(1), Davids M(1), Nel A(2), Shoko A(3), Blackburn J(2), Dheda K(4)(5).

Author information:

(1)Centre for Lung Infection and Immunity, Division of Pulmonology, Dept of

Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of

Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.

(2)Dept of Integrative Biomedical Sciences, Institute for Infectious Disease and

Molecular Medicine, University of Cape Town, Cape Town, South Africa.

(3)Centre for Proteomics and Genomics Research, Cape Town, South Africa.

(4)Centre for Lung Infection and Immunity, Division of Pulmonology, Dept of

Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of

Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa

keertan.dheda@uct.ac.za.

(5)Faculty of Infectious and Tropical Diseases, Dept of Immunology and Infection,

London School of Hygiene and Tropical Medicine, London, UK.

Protective immunity against Mycobacterium tuberculosis is poorly understood. The

role of interleukin (IL)-4, the archetypal T-helper type 2 (Th2) cytokine, in the

immunopathogenesis of human tuberculosis remains unclear.Blood and/or

bronchoalveolar lavage fluid (BAL) were obtained from participants with pulmonary

tuberculosis (TB) (n=23) and presumed latent TB infection (LTBI) (n=22).

Messenger RNA expression levels of interferon (IFN)-γ, IL-4 and its splice

variant IL-4δ2 were determined by real-time PCR. The effect of human recombinant

(hr)IL-4 on mycobacterial survival/containment (CFU·mL-1) was evaluated in M.

tuberculosis-infected macrophages co-cultured with mycobacterial antigen-primed

effector T-cells. Regulatory T-cell (Treg) and Th1 cytokine levels were evaluated

using flow cytometry.In blood, but not BAL, IL-4 mRNA levels (p=0.02) and the

IL-4/IFN-γ ratio (p=0.01) was higher in TB versus LTBI. hrIL-4 reduced

mycobacterial containment in infected macrophages (p<0.008) in a dose-dependent

manner and was associated with an increase in Tregs (p<0.001), but decreased

CD4+Th1 cytokine levels (CD4+IFN-γ+ p<0.001; CD4+TNFα+ p=0.01). Blocking IL-4

significantly neutralised mycobacterial containment (p=0.03), CD4+IFNγ+ levels

(p=0.03) and Treg expression (p=0.03).IL-4 can subvert mycobacterial containment

in human macrophages, probably via perturbations in Treg and Th1-linked pathways.

These data may have implications for the design of effective TB vaccines and

host-directed therapies.

Copyright ©ERS 2019.

DOI: 10.1183/13993003.02242-2018

PMID: 31097521

16. Clin Infect Dis. 2019 Aug 16;69(5):739-747. doi: 10.1093/cid/ciy967.

Development and Validation of a Deep Learning-based Automatic Detection Algorithm

for Active Pulmonary Tuberculosis on Chest Radiographs.

Hwang EJ(1), Park S(2), Jin KN(3), Kim JI(4), Choi SY(5), Lee JH(1), Goo JM(1),

Aum J(2), Yim JJ(6), Park CM(1); Deep Learning-Based Automatic Detection

Algorithm Development and Evaluation Group.

Collaborators: Kim DH, Woo W, Choi C, Hwang IP, Song YS, Lim L, Kim K, Wi JY, Oh

SS, Kang MJ.

Author information:

(1)Department of Radiology, Seoul National University College of Medicine, Seoul.

(2)Lunit Inc, Seoul National University Boramae Medical Center, Seoul.

(3)Department of Radiology, Seoul National University Boramae Medical Center,

Seoul.

...

Medicine, Seoul National University College of Medicine, Korea.

BACKGROUND: Detection of active pulmonary tuberculosis on chest radiographs (CRs)

is critical for the diagnosis and screening of tuberculosis. An automated system

may help streamline the tuberculosis screening process and improve diagnostic

performance.

METHODS: We developed a deep learning-based automatic detection (DLAD) algorithm

using 54c221 normal CRs and 6768 CRs with active pulmonary tuberculosis that were

labeled and annotated by 13 board-certified radiologists. The performance of DLAD

was validated using 6 external multicenter, multinational datasets. To compare

the performances of DLAD with physicians, an observer performance test was

conducted by 15 physicians including nonradiology physicians, board-certified

radiologists, and thoracic radiologists. Image-wise classification and

lesion-wise localization performances were measured using area under the receiver

operating characteristic (ROC) curves and area under the alternative

free-response ROC curves, respectively. Sensitivities and specificities of DLAD

were calculated using 2 cutoffs (high sensitivity [98%] and high specificity

[98%]) obtained through in-house validation.

RESULTS: DLAD demonstrated classification performance of 0.977-1.000 and

localization performance of 0.973-1.000. Sensitivities and specificities for

classification were 94.3%-100% and 91.1%-100% using the high-sensitivity cutoff

and 84.1%-99.0% and 99.1%-100% using the high-specificity cutoff. DLAD showed

significantly higher performance in both classification (0.993 vs 0.746-0.971)

and localization (0.993 vs 0.664-0.925) compared to all groups of physicians.

CONCLUSIONS: Our DLAD demonstrated excellent and consistent performance in the

detection of active pulmonary tuberculosis on CR, outperforming physicians,

including thoracic radiologists.

© The Author(s) 2018. Published by Oxford University Press for the Infectious

Diseases Society of America.

DOI: 10.1093/cid/ciy967

PMCID: PMC6695514

PMID: 30418527