Medical Abstracts

Keyword: tuberculosis

1. PLoS Med. 2019 Apr 30;16(4):e1002790. doi: 10.1371/journal.pmed.1002790.

eCollection 2019 Apr.

Alternate aerosol and systemic immunisation with a recombinant viral vector for

tuberculosis, MVA85A: A phase I randomised controlled trial.

Manjaly Thomas ZR(1), Satti I(1), Marshall JL(1), Harris SA(1), Lopez Ramon R(1),

Hamidi A(1), Minhinnick A(1), Riste M(1), Stockdale L(1), Lawrie AM(1), Vermaak

S(1), Wilkie M(1), Bettinson H(2), McShane H(1).

Author information:

(1)Jenner Institute, Nuffield Department of Clinical Medicine, University of

Oxford, Oxford, United Kingdom.

(2)Oxford Centre for Respiratory Medicine, Nuffield Department of Clinical

Medicine, University of Oxford, Oxford, United Kingdom.

BACKGROUND: There is an urgent need for an effective tuberculosis (TB) vaccine.

Heterologous prime-boost regimens induce potent cellular immunity. MVA85A is a

candidate TB vaccine. This phase I clinical trial was designed to evaluate

whether alternating aerosol and intradermal vaccination routes would boost

cellular immunity to the Mycobacterium tuberculosis antigen 85A (Ag85A).

METHODS AND FINDINGS: Between December 2013 and January 2016, 36 bacille

Calmette-Guérin-vaccinated, healthy UK adults were randomised equally between 3

groups to receive 2 MVA85A vaccinations 1 month apart using either heterologous

(Group 1, aerosol-intradermal; Group 2, intradermal-aerosol) or homologous (Group

3, intradermal-intradermal) immunisation. Bronchoscopy and bronchoalveolar lavage

(BAL) were performed 7 days post-vaccination. Adverse events (AEs) and peripheral

blood were collected for 6 months post-vaccination. The laboratory and

bronchoscopy teams were blinded to treatment allocation. One participant was

withdrawn and was replaced. Participants were aged 21-42 years, and 28/37 were

female. In a per protocol analysis, aerosol delivery of MVA85A as a priming

immunisation was well tolerated and highly immunogenic. Most AEs were mild local

injection site reactions following intradermal vaccination. Transient systemic

AEs occurred following vaccination by both routes and were most frequently mild.

All respiratory AEs following primary aerosol MVA85A (Group 1) were mild.

Boosting an intradermal MVA85A prime with an aerosolised MVA85A boost 1 month

later (Group 2) resulted in transient moderate/severe respiratory and systemic

AEs. There were no serious adverse events and no bronchoscopy-related

complications. Only the intradermal-aerosol vaccination regimen (Group 2)

resulted in modest, significant boosting of the cell-mediated immune response to

Ag85A (p = 0.027; 95% CI: 28 to 630 spot forming cells per 1 × 106 peripheral

blood mononuclear cells). All 3 regimens induced systemic cellular immune

responses to the modified vaccinia virus Ankara (MVA) vector. Serum antibodies to

Ag85A and MVA were only induced after intradermal vaccination. Aerosolised MVA85A

induced significantly higher levels of Ag85A lung mucosal CD4+ and CD8+ T cell

cytokines compared to intradermal vaccination. Boosting with aerosol-inhaled

MVA85A enhanced the intradermal primed responses in Group 2. The magnitude of BAL

MVA-specific CD4+ T cell responses was lower than the Ag85A-specific responses. A

limitation of the study is that while the intradermal-aerosol regimen induced the

most potent cellular Ag85A immune responses, we did not boost the last 3

participants in this group because of the AE profile. Timing of bronchoscopies

aimed to capture peak mucosal response; however, peak responses may have occurred

outside of this time frame.

CONCLUSIONS: To our knowledge, this is the first human randomised clinical trial

to explore heterologous prime-boost regimes using aerosol and systemic routes of

administration of a virally vectored vaccine. In this trial, the aerosol

prime-intradermal boost regime was well tolerated, but intradermal prime-aerosol

boost resulted in transient but significant respiratory AEs. Aerosol vaccination

induced potent cellular Ag85A-specific mucosal and systemic immune responses.

Whilst the implications of inducing potent mucosal and systemic immunity for

protection are unclear, these findings are of relevance for the development of

aerosolised vaccines for TB and other respiratory and mucosal pathogens.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01954563.

DOI: 10.1371/journal.pmed.1002790

PMCID: PMC6490884

PMID: 31039172

2. PLoS Med. 2019 Apr 30;16(4):e1002794. doi: 10.1371/journal.pmed.1002794.

eCollection 2019 Apr.

Whole-genome and targeted sequencing of drug-resistant Mycobacterium tuberculosis

on the iSeq100 and MiSeq: A performance, ease-of-use, and cost evaluation.

Colman RE(1)(2), Mace A(1), Seifert M(2), Hetzel J(3), Mshaiel H(2), Suresh A(1),

Lemmer D(4), Engelthaler DM(4), Catanzaro DG(5), Young AG(3), Denkinger CM(1),

Rodwell TC(1)(2).

Author information:

(1)Foundation for Innovative New Diagnostics, Campus Biotech, Geneva,

Switzerland.

(2)Department of Medicine, University of California, San Diego, San Diego,

California, United States of America.

(3)Illumina Inc., San Diego, California, United States of America.

…

BACKGROUND: Accurate, comprehensive, and timely detection of drug-resistant

tuberculosis (TB) is essential to inform patient treatment and enable public

health surveillance. This is crucial for effective control of TB globally.

Whole-genome sequencing (WGS) and targeted next-generation sequencing (NGS)

approaches have potential as rapid in vitro diagnostics (IVDs), but the

complexity of workflows, interpretation of results, high costs, and vulnerability

of instrumentation have been barriers to broad uptake outside of reference

laboratories, especially in low- and middle-income countries. A new, solid-state,

tabletop sequencing instrument, Illumina iSeq100, has the potential to

decentralize NGS for individual patient care.

METHODS AND FINDINGS: In this study, we evaluated WGS and targeted NGS for TB on

both the new iSeq100 and the widely used MiSeq (both manufactured by Illumina)

and compared sequencing performance, costs, and usability. We utilized DNA

libraries produced from Mycobacterium tuberculosis clinical isolates for the

evaluation. We conducted WGS on three strains and observed equivalent uniform

genome coverage with both platforms and found the depth of coverage obtained was

consistent with the expected data output. Utilizing the standardized, cloud-based

ReSeqTB bioinformatics pipeline for variant analysis, we found the two platforms

to have 94.0% (CI 93.1%-94.8%) agreement, in comparison to 97.6% (CI 97%-98.1%)

agreement for the same libraries on two MiSeq instruments. For the targeted NGS

approach, 46 M. tuberculosis-specific amplicon libraries had 99.6% (CI

98.0%-99.9%) agreement between the iSeq100 and MiSeq data sets in drug

resistance-associated SNPs. The upfront capital costs are almost 5-fold lower for

the iSeq100 ($19,900 USD) platform in comparison to the MiSeq ($99,000 USD);

however, because of difference in the batching capabilities, the price per sample

for WGS was higher on the iSeq100. For WGS of M. tuberculosis at the minimum

depth of coverage of 30x, the cost per sample on the iSeq100 was $69.44 USD

versus $28.21 USD on the MiSeq, assuming a 2 × 150 bp run on a v3 kit. In terms

of ease of use, the sequencing workflow of iSeq100 has been optimized to only

require 27 minutes total of hands-on time pre- and post-run, and the maintenance

is simplified by a single-use cartridge-based fluidic system. As these are the

first sequencing attempts on the iSeq100 for M. tuberculosis, the sequencing pool

loading concentration still needs optimization, which will affect sequencing

error and depth of coverage. Additionally, the costs are based on current

equipment and reagent costs, which are subject to change.

CONCLUSIONS: The iSeq100 instrument is capable of running existing TB WGS and

targeted NGS library preparations with comparable accuracy to the MiSeq. The

iSeq100 has reduced sequencing workflow hands-on time and is able to deliver

sequencing results in <24 hours. Reduced capital and maintenance costs and

lower-throughput capabilities also give the iSeq100 an advantage over MiSeq in

settings of individualized care but not in high-throughput settings such as

reference laboratories, where sample batching can be optimized to minimize cost

at the expense of workflow complexity and time.

DOI: 10.1371/journal.pmed.1002794

PMCID: PMC6490892

PMID: 31039166

3. PLoS Med. 2019 Apr 30;16(4):e1002788. doi: 10.1371/journal.pmed.1002788.

eCollection 2019 Apr.

Evaluation of a social protection policy on tuberculosis treatment outcomes: A

prospective cohort study.

Klein K(1), Bernachea MP(1), Irribarren S(2), Gibbons L(1), Chirico C(3),

Rubinstein F(1).

Author information:

(1)Institute for Clinical Effectiveness and Health Policy (IECS), Buenos Aires,

Argentina.

(2)Biobehavioral Nursing and Health Informatics, University of Washington, School

of Nursing HSB, Seattle, Washington, United States of America.

(3)Tuberculosis Control Program of the 5th Health Region, Ministry of Health of

the Province of Buenos Aires, Hospital Cetrángolo, Buenos Aires, Argentina.

Erratum in

PLoS Med. 2019 May 31;16(5):e1002826.

BACKGROUND: Tuberculosis (TB) still represents a major public health problem in

Latin America, with low success and high default rates. Poor adherence represents

a major threat for TB control and promotes emergence of drug-resistant TB.

Expanding social protection programs could have a substantial effect on the

global burden of TB; however, there is little evidence to evaluate the outcomes

of socioeconomic support interventions. This study evaluated the effect of a

conditional cash transfer (CCT) policy on treatment success and default rates in

a prospective cohort of socioeconomically disadvantaged patients.

METHODS AND FINDINGS: Data were collected on adult patients with first diagnosis

of pulmonary TB starting treatment in public healthcare facilities (HCFs) from 16

health departments with high TB burden in Buenos Aires who were followed until

treatment completion or abandonment. The main exposure of interest was the

registration to receive the CCT. Other covariates, such as sociodemographic and

clinical variables and HCFs' characteristics usually associated with treatment

adherence and outcomes, were also considered in the analysis. We used

hierarchical models, propensity score (PS) matching, and inverse probability

weighting (IPW) to estimate treatment effects, adjusting for individual and

health system confounders. Of 941 patients with known CCT status, 377 registered

for the program showed significantly higher success rates (82% versus 69%) and

lower default rates (11% versus 20%). After controlling for individual and system

characteristics and modality of treatment, odds ratio (OR) for success was 2.9

(95% CI 2, 4.3, P < 0.001) and default was 0.36 (95% CI 0.23, 0.57, P < 0.001).

As this is an observational study evaluating an intervention not randomly

assigned, there might be some unmeasured residual confounding. Although it is

possible that a small number of patients was not registered into the program

because they were deemed not eligible, the majority of patients fulfilled the

requirements and were not registered because of different reasons. Since the

information on the CCT was collected at the end of the study, we do not know the

exact timing for when each patient was registered for the program.

CONCLUSIONS: The CCT appears to be a valuable health policy intervention to

improve TB treatment outcomes. Incorporating these interventions as established

policies may have a considerable effect on the control of TB in similar

high-burden areas.

DOI: 10.1371/journal.pmed.1002788

PMCID: PMC6490910

PMID: 31039158

Conflict of interest statement: The authors have declared that no competing

interests exist.

4. PLoS Med. 2019 Apr 30;16(4):e1002789. doi: 10.1371/journal.pmed.1002789.

eCollection 2019 Apr.

Pharmacokinetics, optimal dosing, and safety of linezolid in children with

multidrug-resistant tuberculosis: Combined data from two prospective

observational studies.

Garcia-Prats AJ(1), Schaaf HS(1), Draper HR(1), Garcia-Cremades M(2), Winckler

J(1), Wiesner L(3), Hesseling AC(1), Savic RM(2).

Author information:

(1)Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of

Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.

(2)Department of Bioengineering and Therapeutic Sciences, University of

California, San Francisco, San Francisco, California, United States of America.

(3)Division of Clinical Pharmacology, Department of Medicine, University of Cape

Town, Cape Town, South Africa.

BACKGROUND: Linezolid is increasingly important for multidrug-resistant

tuberculosis (MDR-TB) treatment. However, among children with MDR-TB, there are

no linezolid pharmacokinetic data, and its adverse effects have not yet been

prospectively described. We characterised the pharmacokinetics, safety, and

optimal dose of linezolid in children treated for MDR-TB.

METHODS AND FINDINGS: Children routinely treated for MDR-TB in 2 observational

studies (2011-2015, 2016-2018) conducted at a single site in Cape Town, South

Africa, underwent intensive pharmacokinetic sampling after either a single dose

or multiple doses of linezolid (at steady state). Linezolid pharmacokinetic

parameters, and their relationships with covariates of interest, were described

using nonlinear mixed-effects modelling. Children receiving long-term linezolid

as a component of their routine treatment had regular clinical and laboratory

monitoring. Adverse events were assessed for severity and attribution to

linezolid. The final population pharmacokinetic model was used to derive optimal

weight-banded doses resulting in exposures in children approximating those in

adults receiving once-daily linezolid 600 mg. Forty-eight children were included

(mean age 5.9 years; range 0.6 to 15.3); 31 received a single dose of linezolid,

and 17 received multiple doses. The final pharmacokinetic model consisted of a

one-compartment model characterised by clearance (CL) and volume (V) parameters

that included allometric scaling to account for weight; no other evaluated

covariates contributed to the model. Linezolid exposures in this population were

higher compared to exposures in adults who had received a 600 mg once-daily dose.

Consequently simulated, weight-banded once-daily optimal doses for children were

lower than those currently used for most weight bands. Ten of 17 children who

were followed long term had a linezolid-related adverse event, including 5 with a

grade 3 or 4 event, all anaemia. Adverse events resulted in linezolid dose

reductions in 4, temporary interruptions in 5, and permanent discontinuation in 4

children. Limitations of the study include the lack of very young children (none

below 6 months of age), the limited number who were HIV infected, and the modest

number of children contributing to long-term safety data.

CONCLUSIONS: Linezolid-related adverse effects were frequent and occasionally

severe. Careful linezolid safety monitoring is required. Compared to doses

currently used in children in many settings for MDR-TB treatment, lower doses may

approximate current adult target exposures, might result in fewer adverse events,

and should therefore be evaluated.

DOI: 10.1371/journal.pmed.1002789

PMCID: PMC6490911

PMID: 31039153

Conflict of interest statement: The authors have declared that no competing

interests exist.

5. Nat Commun. 2019 Apr 29;10(1):1973. doi: 10.1038/s41467-019-09955-8.

A Mycobacterium tuberculosis surface protein recruits ubiquitin to trigger host

xenophagy.

Chai Q(1)(2), Wang X(1)(3), Qiang L(1)(2), Zhang Y(1)(2), Ge P(1)(2), Lu Z(1)(2),

Zhong Y(1)(2), Li B(1), Wang J(1), Zhang L(4), Zhou D(5), Li W(6), Dong W(7),

Pang Y(7), Gao GF(1)(2), Liu CH(8)(9).

Author information:

(1)Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and

Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing,

100101, China.

(2)Savaid Medical School, University of Chinese Academy of Sciences, Beijing,

101408, China.

(3)College of Life Sciences, University of Chinese Academy of Sciences, Beijing,

100049, China.

…

Ubiquitin-mediated xenophagy, a type of selective autophagy, plays crucial roles

in host defense against intracellular pathogens including Mycobacterium

tuberculosis (Mtb). However, the exact mechanism by which host ubiquitin targets

invaded microbes to trigger xenophagy remains obscure. Here we show that

ubiquitin could recognize Mtb surface protein Rv1468c, a previously unidentified

ubiquitin-binding protein containing a eukaryotic-like ubiquitin-associated (UBA)

domain. The UBA-mediated direct binding of ubiquitin to, but not E3 ubiquitin

ligases-mediated ubiquitination of, Rv1468c recruits autophagy receptor p62 to

deliver mycobacteria into LC3-associated autophagosomes. Disruption of

Rv1468c-ubiquitin interaction attenuates xenophagic clearance of Mtb in

macrophages, and increases bacterial loads in mice with elevated inflammatory

responses. Together, our findings reveal a unique mechanism of host xenophagy

triggered by direct binding of ubiquitin to the pathogen surface protein, and

indicate a diplomatic strategy adopted by Mtb to benefit its persistent

intracellular infection through controlling intracellular bacterial loads and

restricting host inflammatory responses.

DOI: 10.1038/s41467-019-09955-8

PMCID: PMC6488588

PMID: 31036822 [Indexed for MEDLINE]

6. Nat Commun. 2019 Apr 23;10(1):1823. doi: 10.1038/s41467-019-09816-4.

Spatial and temporal localization of immune transcripts defines hallmarks and

diversity in the tuberculosis granuloma.

Carow B(1), Hauling T(2), Qian X(2), Kramnik I(3), Nilsson M(2), Rottenberg

ME(4).

Author information:

(1)Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171

77, Stockholm, Sweden.

(2)Science for Life Laboratory, Department of Biochemistry and Biophysics,

Stockholm University, 171 65, Solna, Sweden.

(3)Department of Medicine, Boston University School of Medicine, Boston,

Massachusetts, 02118, USA.

(4)Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171

77, Stockholm, Sweden. Martin.Rottenberg@ki.se.

Granulomas are the pathological hallmark of tuberculosis (TB) and the niche where

bacilli can grow and disseminate or the immunological microenvironment in which

host cells interact to prevent bacterial dissemination. Here we show 34 immune

transcripts align to the morphology of lung sections from Mycobacterium

tuberculosis-infected mice at cellular resolution. Colocalizing transcript

networks at <10 μm in C57BL/6 mouse granulomas increase complexity with time

after infection. B-cell clusters develop late after infection. Transcripts from

activated macrophages are enriched at subcellular distances from M. tuberculosis.

Encapsulated C3HeB/FeJ granulomas show necrotic centers with transcripts

associated with immunosuppression (Foxp3, Il10), whereas those in the granuloma

rims associate with activated T cells and macrophages. We see highly diverse

networks with common interactors in similar lesions. Different immune landscapes

of M. tuberculosis granulomas depending on the time after infection, the

histopathological features of the lesion, and the proximity to bacteria are here

defined.

DOI: 10.1038/s41467-019-09816-4

PMCID: PMC6479067

PMID: 31015452

7. PLoS Med. 2019 Apr 23;16(4):e1002786. doi: 10.1371/journal.pmed.1002786.

eCollection 2019 Apr.

Host-response-based gene signatures for tuberculosis diagnosis: A systematic

comparison of 16 signatures.

Warsinske H(1)(2), Vashisht R(1)(2), Khatri P(1)(2).

Author information:

(1)Institute for Immunity, Transplantation and Infection, Stanford University,

Stanford, California, United States of America.

(2)Center for Biomedical Informatics, Department of Medicine, Stanford

University, Stanford, California, United States of America.

BACKGROUND: The World Health Organization (WHO) and Foundation for Innovative New

Diagnostics (FIND) have published target product profiles (TPPs) calling for

non-sputum-based diagnostic tests for the diagnosis of active tuberculosis (ATB)

disease and for predicting the progression from latent tuberculosis infection

(LTBI) to ATB. A large number of host-derived blood-based gene-expression

biomarkers for diagnosis of patients with ATB have been proposed to date, but

none have been implemented in clinical settings. The focus of this study is to

directly compare published gene signatures for diagnosis of patients with ATB

across a large, diverse list of publicly available gene expression datasets, and

evaluate their performance against the WHO/FIND TPPs.

METHODS AND FINDINGS: We searched PubMed, Gene Expression Omnibus (GEO), and

ArrayExpress in June 2018. We included all studies irrespective of study design

and enrollment criteria. We found 16 gene signatures for the diagnosis of ATB

compared to other clinical conditions in PubMed. For each signature, we

implemented a classification model as described in the corresponding original

publication of the signature. We identified 24 datasets containing 3,083

transcriptome profiles from whole blood or peripheral blood mononuclear cell

samples of healthy controls or patients with ATB, LTBI, or other diseases from 14

countries in GEO. Using these datasets, we calculated weighted mean area under

the receiver operating characteristic curve (AUROC), specificity at 90%

sensitivity, and negative predictive value (NPV) for each gene signature across

all datasets. We also compared the diagnostic odds ratio (DOR), heterogeneity in

DOR, and false positive rate (FPR) for each signature using bivariate

meta-analysis. Across 9 datasets of patients with culture-confirmed diagnosis of

ATB, 11 signatures had weighted mean AUROC > 0.8, and 2 signatures had weighted

mean AUROC ≤ 0.6. All but 2 signatures had high NPV (>98% at 2% prevalence). Two

gene signatures achieved the minimal WHO TPP for a non-sputum-based triage test.

When including datasets with clinical diagnosis of ATB, there was minimal

reduction in the weighted mean AUROC and specificity of all but 3 signatures

compared to when using only culture-confirmed ATB data. Only 4 signatures had

homogeneous DOR and lower FPR when datasets with clinical diagnosis of ATB were

included; other signatures either had heterogeneous DOR or higher FPR or both.

Finally, 7 of 16 gene signatures predicted progression from LTBI to ATB 6 months

prior to sputum conversion with positive predictive value > 6% at 2% prevalence.

Our analyses may have under- or overestimated the performance of certain ATB

diagnostic signatures because our implementation may be different from the

published models for those signatures. We re-implemented published models because

the exact models were not publicly available.

CONCLUSIONS: We found that host-response-based diagnostics could accurately

identify patients with ATB and predict individuals with high risk of progression

from LTBI to ATB prior to sputum conversion. We found that a higher number of

genes in a signature did not increase the accuracy of the signature. Overall, the

Sweeney3 signature performed robustly across all comparisons. Our results provide

strong evidence for the potential of host-response-based diagnostics in achieving

the WHO goal of ending tuberculosis by 2035, and host-response-based diagnostics

should be pursued for clinical implementation.

DOI: 10.1371/journal.pmed.1002786

PMCID: PMC6478271

PMID: 31013272

8. PLoS Med. 2019 Apr 16;16(4):e1002781. doi: 10.1371/journal.pmed.1002781.

eCollection 2019 Apr.

Discovery and validation of a prognostic proteomic signature for tuberculosis

progression: A prospective cohort study.

Penn-Nicholson A(1), Hraha T(2), Thompson EG(3), Sterling D(2), Mbandi SK(1),

Wall KM(2), Fisher M(1), Suliman S(1), Shankar S(3), Hanekom WA(1), Janjic N(2),

Hatherill M(1), Kaufmann SHE(4), Sutherland J(5), Walzl G(6), De Groote MA(2),

Ochsner U(2), Zak DE(3), Scriba TJ(1); ACS and GC6–74 cohort study groups.

Author information:

(1)South African Tuberculosis Vaccine Initiative, Division of Immunology,

Department of Pathology and Institute of Infectious Disease and Molecular

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

(2)SomaLogic, Inc., Boulder, Colorado, United States of America.

(3)Center for Infectious Disease Research, Seattle, Washington, United States of

America.

…

BACKGROUND: A nonsputum blood test capable of predicting progression of healthy

individuals to active tuberculosis (TB) before clinical symptoms manifest would

allow targeted treatment to curb transmission. We aimed to develop a proteomic

biomarker of risk of TB progression for ultimate translation into a point-of-care

diagnostic.

METHODS AND FINDINGS: Proteomic TB risk signatures were discovered in a

longitudinal cohort of 6,363 Mycobacterium tuberculosis-infected, HIV-negative

South African adolescents aged 12-18 years (68% female) who participated in the

Adolescent Cohort Study (ACS) between July 6, 2005 and April 23, 2007, through

either active (every 6 months) or passive follow-up over 2 years. Forty-six

individuals developed microbiologically confirmed TB disease within 2 years of

follow-up and were selected as progressors; 106 nonprogressors, who remained

healthy, were matched to progressors. Over 3,000 human proteins were quantified

in plasma with a highly multiplexed proteomic assay (SOMAscan). Three hundred

sixty-one proteins of differential abundance between progressors and

nonprogressors were identified. A 5-protein signature, TB Risk Model 5 (TRM5),

was discovered in the ACS training set and verified by blind prediction in the

ACS test set. Poor performance on samples 13-24 months before TB diagnosis

motivated discovery of a second 3-protein signature, 3-protein pair-ratio (3PR)

developed using an orthogonal strategy on the full ACS subcohort. Prognostic

performance of both signatures was validated in an independent cohort of 1,948

HIV-negative household TB contacts from The Gambia (aged 15-60 years, 66%

female), longitudinally followed up for 2 years between March 5, 2007 and October

21, 2010, sampled at baseline, month 6, and month 18. Amongst these contacts, 34

individuals progressed to microbiologically confirmed TB disease and were

included as progressors, and 115 nonprogressors were included as controls.

Prognostic performance of the TRM5 signature in the ACS training set was

excellent within 6 months of TB diagnosis (area under the receiver operating

characteristic curve [AUC] 0.96 [95% confidence interval, 0.93-0.99]) and 6-12

months (AUC 0.76 [0.65-0.87]) before TB diagnosis. TRM5 validated with an AUC of

0.66 (0.56-0.75) within 1 year of TB diagnosis in the Gambian validation cohort.

The 3PR signature yielded an AUC of 0.89 (0.84-0.95) within 6 months of TB

diagnosis and 0.72 (0.64-0.81) 7-12 months before TB diagnosis in the entire

South African discovery cohort and validated with an AUC of 0.65 (0.55-0.75)

within 1 year of TB diagnosis in the Gambian validation cohort. Signature

validation may have been limited by a systematic shift in signal magnitudes

generated by differences between the validation assay when compared to the

discovery assay. Further validation, especially in cohorts from non-African

countries, is necessary to determine how generalizable signature performance is.

CONCLUSIONS: Both proteomic TB risk signatures predicted progression to incident

TB within a year of diagnosis. To our knowledge, these are the first validated

prognostic proteomic signatures. Neither meet the minimum criteria as defined in

the WHO Target Product Profile for a progression test. More work is required to

develop such a test for practical identification of individuals for investigation

of incipient, subclinical, or active TB disease for appropriate treatment and

care.

DOI: 10.1371/journal.pmed.1002781

PMCID: PMC6467365

PMID: 30990820

9. PLoS Med. 2019 Apr 12;16(4):e1002780. doi: 10.1371/journal.pmed.1002780.

eCollection 2019 Apr.

Lipoarabinomannan in sputum to detect bacterial load and treatment response in

patients with pulmonary tuberculosis: Analytic validation and evaluation in two

cohorts.

Kawasaki M(1), Echiverri C(2), Raymond L(3), Cadena E(4), Reside E(5), Gler

MT(6), Oda T(1), Ito R(1), Higashiyama R(1), Katsuragi K(1), Liu Y(7).

Author information:

(1)Otsuka Pharmaceutical Company, Tokyo, Japan.

(2)Tropical Disease Foundation, Makati City, Metro Manila, Philippines.

(3)Lung Center of the Philippines, Quezon City, Metro Manila, Philippines.

…

BACKGROUND: Lipoarabinomannan (LAM) is a major antigen of Mycobacterium

tuberculosis (MTB). In this report, we evaluated the ability of a novel

immunoassay to measure concentrations of LAM in sputum as a biomarker of

bacterial load prior to and during treatment in pulmonary tuberculosis (TB)

patients.

METHODS AND FINDINGS: Phage display technology was used to isolate monoclonal

antibodies binding to epitopes unique in LAM from MTB and slow-growing

nontuberculous mycobacteria (NTM). Using these antibodies, a sandwich

enzyme-linked immunosorbent assay (LAM-ELISA) was developed to quantitate LAM

concentration. The LAM-ELISA had a lower limit of quantification of 15 pg/mL LAM,

corresponding to 121 colony-forming units (CFUs)/mL of MTB strain H37Rv. It

detected slow-growing NTMs but without cross-reacting to common oral bacteria.

Two clinical studies were performed between the years 2013 and 2016 in Manila,

Philippines, in patients without known human immunodeficiency virus (HIV)

coinfection. In a case-control cohort diagnostic study, sputum specimens were

collected from 308 patients (aged 17-69 years; 62% male) diagnosed as having

pulmonary TB diseases or non-TB diseases, but who could expectorate sputum, and

were then evaluated by smear microscopy, BACTEC MGIT 960 Mycobacterial Detection

System (MGIT) and Lowenstein-Jensen (LJ) culture, and LAM-ELISA. Some sputum

specimens were also examined by Xpert MTB/RIF. The LAM-ELISA detected all smear-

and MTB-culture-positive samples (n = 70) and 50% (n = 29) of smear-negative but

culture-positive samples (n = 58) (versus 79.3%; 46 positive cases by the Xpert

MTB/RIF), but none from non-TB patients (n = 56). Among both LAM and MGIT

MTB-culture-positive samples, log10-transformed LAM concentration and MGIT time

to detection (TTD) showed a good inverse relationship (r = -0.803, p < 0.0001).

In a prospective longitudinal cohort study, 40 drug-susceptible pulmonary TB

patients (aged 18-69 years; 60% male) were enrolled during the first 56 days of

the standard 4-drug therapy. Declines in sputum LAM concentrations correlated

with increases of MGIT TTD in individual patients. There was a 1.29 log10

decrease of sputum LAM concentration, corresponding to an increase of 221 hours

for MGIT TTD during the first 14 days of treatment, a treatment duration often

used in early bactericidal activity (EBA) trials. Major limitations of this study

include a relatively small number of patients, treatment duration up to only 56

days, lack of quantitative sputum culture CFU count data, and no examination of

the correlation of sputum LAM to clinical cure.

CONCLUSIONS: These results indicate that the LAM-ELISA can determine LAM

concentration in sputum, and sputum LAM measured by the assay may be used as a

biomarker of bacterial load prior to and during TB treatment. Additional studies

are needed to examine the predictive value of this novel biomarker on treatment

outcomes.

DOI: 10.1371/journal.pmed.1002780

PMCID: PMC6461223

PMID: 30978194

10. PLoS Med. 2019 Apr 2;16(4):e1002773. doi: 10.1371/journal.pmed.1002773.

eCollection 2019 Apr.

Tuberculosis drugs' distribution and emergence of resistance in patient's lung

lesions: A mechanistic model and tool for regimen and dose optimization.

Strydom N(1), Gupta SV(1), Fox WS(1), Via LE(2), Bang H(2), Lee M(3), Eum S(3),

Shim T(4), Barry CE 3rd(2), Zimmerman M(5), Dartois V(5), Savic RM(1).

Author information:

(1)Department of Bioengineering and Therapeutic Sciences, University of

California, San Francisco, San Francisco, California, United States of America.

(2)Tuberculosis Research Section, Laboratory of Clinical Immunology and

Microbiology, NIAID, NIH, Bethesda, Maryland, United States of America.

(3)International Tuberculosis Research Center, Changwon, Republic of Korea.

(4)Asan Medical Center, Seoul, Republic of Korea.

(5)Public Health Research Institute and New Jersey Medical School, Rutgers, The

State University of New Jersey, Newark, New Jersey, United States of America.

BACKGROUND: The sites of mycobacterial infection in the lungs of tuberculosis

(TB) patients have complex structures and poor vascularization, which obstructs

drug distribution to these hard-to-reach and hard-to-treat disease sites, further

leading to suboptimal drug concentrations, resulting in compromised TB treatment

response and resistance development. Quantifying lesion-specific drug uptake and

pharmacokinetics (PKs) in TB patients is necessary to optimize treatment regimens

at all infection sites, to identify patients at risk, to improve existing

regimens, and to advance development of novel regimens. Using drug-level data in

plasma and from 9 distinct pulmonary lesion types (vascular, avascular, and

mixed) obtained from 15 hard-to-treat TB patients who failed TB treatments and

therefore underwent lung resection surgery, we quantified the distribution and

the penetration of 7 major TB drugs at these sites, and we provide novel tools

for treatment optimization.

METHODS AND FINDINGS: A total of 329 plasma- and 1,362 tissue-specific drug

concentrations from 9 distinct lung lesion types were obtained according to

optimal PK sampling schema from 15 patients (10 men, 5 women, aged 23 to 58)

undergoing lung resection surgery (clinical study NCT00816426 performed in South

Korea between 9 June 2010 and 24 June 2014). Seven major TB drugs (rifampin

[RIF], isoniazid [INH], linezolid [LZD], moxifloxacin [MFX], clofazimine [CFZ],

pyrazinamide [PZA], and kanamycin [KAN]) were quantified. We developed and

evaluated a site-of-action mechanistic PK model using nonlinear mixed effects

methodology. We quantified population- and patient-specific lesion/plasma ratios

(RPLs), dynamics, and variability of drug uptake into each lesion for each drug.

CFZ and MFX had higher drug exposures in lesions compared to plasma (median RPL

2.37, range across lesions 1.26-22.03); RIF, PZA, and LZD showed moderate yet

suboptimal lesion penetration (median RPL 0.61, range 0.21-2.4), while INH and

KAN showed poor tissue penetration (median RPL 0.4, range 0.03-0.73). Stochastic

PK/pharmacodynamic (PD) simulations were carried out to evaluate current regimen

combinations and dosing guidelines in distinct patient strata. Patients receiving

standard doses of RIF and INH, who are of the lower range of exposure

distribution, spent substantial periods (>12 h/d) below effective concentrations

in hard-to-treat lesions, such as caseous lesions and cavities. Standard doses of

INH (300 mg) and KAN (1,000 mg) did not reach therapeutic thresholds in most

lesions for a majority of the population. Drugs and doses that did reach target

exposure in most subjects include 400 mg MFX and 100 mg CFZ. Patients with

cavitary lesions, irrespective of drug choice, have an increased likelihood of

subtherapeutic concentrations, leading to a higher risk of resistance acquisition

while on treatment. A limitation of this study was the small sample size of 15

patients, performed in a unique study population of TB patients who failed

treatment and underwent lung resection surgery. These results still need further

exploration and validation in larger and more diverse cohorts.

CONCLUSIONS: Our results suggest that the ability to reach and maintain

therapeutic concentrations is both lesion and drug specific, indicating that

stratifying patients based on disease extent, lesion types, and individual

drug-susceptibility profiles may eventually be useful for guiding the selection

of patient-tailored drug regimens and may lead to improved TB treatment outcomes.

We provide a web-based tool to further explore this model and results at

http://saviclab.org/tb-lesion/.

DOI: 10.1371/journal.pmed.1002773

PMCID: PMC6445413

PMID: 30939136

Conflict of interest statement: The authors have declared that no competing

interests exist.

11. Clin Pharmacokinet. 2019 Apr 17. doi: 10.1007/s40262-019-00763-3. [Epub ahead of print]

Optimal Sampling Strategies for Therapeutic Drug Monitoring of First-Line

Tuberculosis Drugs in Patients with Tuberculosis.

Saktiawati AMI(1)(2)(3), Harkema M(4), Setyawan A(5), Subronto YW(1)(3),

Sumardi(1), Stienstra Y(6), Aarnoutse RE(7), Magis-Escurra C(8), Kosterink

JGW(9)(10), van der Werf TS(2)(6), Alffenaar JC(9)(11), Sturkenboom MGG(12).

Author information:

(1)Department of Internal Medicine, Faculty of Medicine, Public Health and

Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.

(2)Department of Pulmonary Diseases and Tuberculosis, University Medical Center

Groningen, University of Groningen, Groningen, The Netherlands.

(3)Center for Tropical Medicine, Faculty of Medicine, Public Health and Nursing,

Universitas Gadjah Mada, Yogyakarta, Indonesia.

…

BACKGROUND: The 24-h area under the concentration-time curve (AUC24)/minimal

inhibitory concentration ratio is the best predictive

pharmacokinetic/pharmacodynamic (PK/PD) parameter of the efficacy of first-line

anti-tuberculosis (TB) drugs. An optimal sampling strategy (OSS) is useful for

accurately estimating AUC24; however, OSS has not been developed in the fed state

or in the early phase of treatment for first-line anti-TB drugs.

METHODS: An OSS for the prediction of AUC24 of isoniazid, rifampicin, ethambutol

and pyrazinamide was developed for TB patients starting treatment. A prospective,

randomized, crossover trial was performed during the first 3 days of treatment in

which first-line anti-TB drugs were administered either intravenously or in

fasting or fed conditions. The PK data were used to develop OSS with best subset

selection multiple linear regression. The OSS was internally validated using a

jackknife analysis and externally validated with other patients from different

ethnicities and in a steady state of treatment.

RESULTS: OSS using time points of 2, 4 and 8 h post-dose performed best. Bias

was < 5% and imprecision was < 15% for all drugs except ethambutol in the fed

condition. External validation showed that OSS2-4-8 cannot be used for rifampicin

in steady state conditions.

CONCLUSION: OSS at 2, 4 and 8 h post-dose enabled an accurate and precise

prediction of AUC24 values of first-line anti-TB drugs in this population.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT02121314).

DOI: 10.1007/s40262-019-00763-3

PMID: 30997650

12. Clin Infect Dis. 2019 Apr 4. pii: ciz263. doi: 10.1093/cid/ciz263. [Epub ahead of print]

Eligibility for a Shorter Treatment Regimen for Multidrug-resistant Tuberculosis

in the United States, 2011-2016.

Tsang CA(1), Shah N(1), Armstrong LR(1), Marks SM(1).

Author information:

(1)Division of Tuberculosis Elimination, Centers for Disease Control and

Prevention, Atlanta, Georgia, United States of America.

BACKGROUND: In 2016, the World Health Organization (WHO) recommended a shorter

(9-12 month) multidrug-resistant tuberculosis (MDR-TB) treatment regimen (as

compared to the conventional 18-24 month regimen) for patients without

extrapulmonary TB, pregnancy, previous second-line TB medication exposure, or

drug resistance to pyrazinamide, ethambutol, kanamycin, moxifloxacin,

ethionamide, or clofazimine. The recommendation was based on successful clinical

trials conducted in Asia and Africa, but studies, using mainly European data,

have shown few patients in higher resource settings would meet WHO eligibility

criteria.

METHODS: We assessed eligibility for the shorter regimen among U.S. MDR-TB cases

that had full drug susceptibility testing (DST) results and were reported during

2011-2016 to the U.S. National TB Surveillance System. We estimated costs by

applying the eligibility criteria for the shorter regimen, and proportional

inpatient/outpatient costs from a previous population-based study to all MDR-TB

patients reported to NTSS.

RESULTS: Of 586 reported MDR cases, 10% (59) were eligible for the shorter

regimen. Of 527 ineligible patients, 386 had full DST, of which 246 were

resistant to ethambutol and 217 resistant to pyrazinamide. Compared with

conventional MDR-TB treatment, implementing the shorter regimen would reduce the

U.S. annual societal MDR-TB cost burden by 4%, but the cost burden for eligible

individuals would be reduced by 37-46%.

CONCLUSIONS: Relying on full DST use, our analysis found a minority of U.S.

MDR-TB patients would be eligible for the shorter regimen. Cost reductions would

be minimal for society, but large for eligible individuals.

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

Diseases Society of America. All rights reserved. For permissions, e-mail:

journals.permissions@oup.com.

DOI: 10.1093/cid/ciz263

PMID: 30944927

13. J Infect Dis. 2019 Apr 19;219(10):1554-1558. doi: 10.1093/infdis/jiy710.

Diverse Clinical Isolates of Mycobacterium tuberculosis Develop

Macrophage-Induced Rifampin Tolerance.

Adams KN(1), Verma AK(2), Gopalaswamy R(3), Adikesavalu H(3), Singhal DK(3),

Tripathy S(3), Ranganathan UD(3), Sherman DR(1), Urdahl KB(1), Ramakrishnan L(2),

Hernandez RE(1)(4).

Author information:

(1)Center for Global Infectious Diseases Research, Seattle Children's Research

Institute, Center for Infectious Diseases Research, Seattle, Washington.

(2)Molecular Immunity Unit, Department of Medicine, University of Cambridge,

United Kingdom.

(3)National Institute for Research in Tuberculosis, Chennai, India.

(4)Department of Pediatrics, University of Washington, Seattle, Washington.

The Mycobacterium tuberculosis lineage 4 strains CDC1551 and H37Rv develop

tolerance to multiple antibiotics upon macrophage residence. To determine whether

macrophage-induced tolerance is a general feature of clinical M. tuberculosis

isolates, we assessed macrophage-induced drug tolerance in strains from lineages

1-3, representing the other predominant M. tuberculosis strains responsible for

tuberculosis globally. All 3 lineages developed isoniazid tolerance. While

lineage 1, 3, and 4 strains developed rifampin tolerance, lineage 2 Beijing

strains did not. Their failure to develop tolerance may be explained by their

harboring of a loss-of-function mutation in the Rv1258c efflux pump that is

linked to macrophage-induced rifampicin tolerance.

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

Diseases Society of America.

DOI: 10.1093/infdis/jiy710

PMCID: PMC6473171

PMID: 30753612

14. J Infect Dis. 2019 Apr 19;219(10):1662-1670. doi: 10.1093/infdis/jiy709.

Role of Glutamine Metabolism in Host Defense Against Mycobacterium tuberculosis

Infection.

Koeken VACM(1)(2), Lachmandas E(1)(2), Riza A(3), Matzaraki V(4), Li Y(4), Kumar

V(1)(2)(4), Oosting M(1)(2), Joosten LAB(1)(2), Netea MG(1)(2)(3), van Crevel

R(1)(2).

Author information:

(1)Department of Internal Medicine, Radboud University Medical Center, Nijmegen.

(2)Center for Infectious Diseases, Radboud University Medical Center, Nijmegen.

(3)Human Genomics Laboratory, Craiova University of Medicine and Pharmacy,

Romania.

(4)Department of Genetics, University Medical Center Groningen, University of

Groningen, Groningen, the Netherlands.

BACKGROUND: Rewiring cellular metabolism is important for activation of immune

cells during host defense against Mycobacterium tuberculosis. Glutamine has been

implicated as an immunomodulatory nutrient, but its role in the response to M.

tuberculosis is unknown.

METHODS: We assessed expression of glutamine pathway genes in M.

tuberculosis-infected macrophages and blood transcriptomic profiles of

individuals with latent M. tuberculosis infection or tuberculosis. Subsequently,

we studied the effect of blocking glutaminolysis on M. tuberculosis-induced

cytokines. Finally, we examined whether polymorphisms in genes involved in the

glutamine pathway influence M. tuberculosis-induced cytokines in a cohort of 500

individuals.

RESULTS: Glutamine pathway genes were differentially expressed in infected

macrophages and patients with tuberculosis. Human peripheral blood mononuclear

cells stimulated with M. tuberculosis displayed decreased cytokine (ie,

interleukin 1β, interferon γ, and interleukin 17) responses when medium was

devoid of glutamine. Specific inhibitors of the glutamine pathway led to

decreased cytokine responses, especially T-cell cytokines (ie, interferon γ,

interleukin 17, and interleukin 22). Finally, genetic polymorphisms in glutamine

metabolism genes (including GLS2, SLC1A5, and SLC7A5) influenced ex vivo cytokine

responses to M. tuberculosis, especially for T-cell cytokines.

CONCLUSIONS: Cellular glutamine metabolism is implicated in effective host

responses against M. tuberculosis. Targeting immunometabolism may represent new

strategies for tuberculosis prevention and/or treatment.

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

Diseases Society of America. All rights reserved. For permissions, e-mail:

journals.permissions@oup.com.

DOI: 10.1093/infdis/jiy709

PMID: 30541099