Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection

There is still incomplete knowledge of which Mycobacterium tuberculosis (Mtb) antigens can trigger distinct T cell responses at different stages of infection. Here, a proteome-wide screen of 20,610 Mtb-derived peptides in 21 patients mid-treatment for active tuberculosis (ATB) reveals IFNγ-specific T cell responses against 137 unique epitopes. Of these, 16% are recognized by two or more participants and predominantly derived from cell wall and cell processes antigens. There is differential recognition of antigens, including TB vaccine candidate antigens, between ATB participants and interferon-gamma release assay (IGRA + /-) individuals. We developed an ATB-specific peptide pool (ATB116) consisting of epitopes exclusively recognized by ATB participants. This pool can distinguish patients with pulmonary ATB from IGRA + /- individuals from various geographical locations, with a sensitivity of over 60% and a specificity exceeding 80%. This proteome-wide screen of T cell reactivity identified infection stage-specific epitopes and antigens for potential use in diagnostics and measuring Mtb-specific immune responses.

Identification of differentially recognized T cell epitopes in the spectrum of Mtb infection

Tuberculosis caused by Mycobacterium tuberculosis is one of the leading causes of death from a single infectious agent. Identifying dominant epitopes and comparing their reactivity in different tuberculosis (TB) infection states can help design diagnostics and vaccines. We performed a proteome-wide screen of 20,610 Mtb derived peptides in 21 Active TB (ATB) patients 3-4 months post-diagnosis of pulmonary TB (mid-treatment) using an IFNγ and IL-17 Fluorospot assay. Responses were mediated exclusively by IFNγ and identified a total of 137 unique epitopes, with each patient recognizing, on average, 8 individual epitopes and 22 epitopes (16%) recognized by 2 or more participants. Responses were predominantly directed against antigens part of the cell wall and cell processes category. Testing 517 peptides spanning TB vaccine candidates and ESAT-6 and CFP10 antigens also revealed differential recognition between ATB participants mid-treatment and healthy IGRA+ participants of several vaccine antigens. An ATB-specific peptide pool consisting of epitopes exclusively recognized by participants mid-treatment, allowed distinguishing participants with active pulmonary TB from healthy interferon-gamma release assay (IGRA)+/- participants from diverse geographical locations. Analysis of longitudinal samples indicated decreased reactivity during treatment for pulmonary TB. Together, these results show that a proteome-wide screen of T cell reactivity identifies epitopes and antigens that are differentially recognized depending on the Mtb infection stage. These have potential use in developing diagnostics and vaccine candidates and measuring correlates of protection.

1539. A Nine-Gene Blood-Based Signature Meets the World Health Organization Target Product Profiles for Diagnosis of Active Tuberculosis and Predicting Progression from Latent to Active Disease

Background

As part of its End TB strategy, the WHO has identified the need for non-sputum-based diagnostics that meet target product profiles (TPP) of 90% sensitivity and 70% specificity for diagnosis of Active TB (ATB) and 75% sensitivity and specificity for predicting progression from Latent TB (LTB) to ATB. The successful translation of a 3-gene blood-based signature, identified using diverse datasets, into a prototype point-of-care diagnostic, that meets the WHO TPPs, has demonstrated the power of integrating large amounts of heterogeneous data to identify generalizable disease signatures. We hypothesized that integration of more diverse datasets, comprising patients with ATB or other inflammatory lung diseases, would identify novel, robust signatures, for diagnosing ATB and predicting progression from LTB to ATB, that meet the WHO TPPs.

Methods

Using multi-cohort analyses, we integrated and analyzed data from 3,615 peripheral blood samples, in 49 publicly available transcriptomic datasets (discovery cohorts), from healthy controls and patients with LTB, ATB, and other diseases (COPD, viral infections, sarcoidosis, etc.). We used data from (1) 3,836 blood samples in 28 retrospective datasets and (2) 360 prospectively collected blood samples, from a household contact study in Moldova, as validation cohorts.

Results

Using the discovery cohorts we identified a 9-gene signature for diagnosing ATB patients from healthy controls, or individuals with LTB or other diseases. The signature achieved 90% sensitivity and 82% specificity in retrospective validation (Figure 1A) and 90% sensitivity and 69% specificity in the prospective cohort from Moldova (Figure 1B). In a longitudinal cohort of adolescents, the 9-gene signature predicted progression from LTB to ATB up to 1 year prior to sputum conversion with 76% sensitivity and 83% specificity (Figure 1C). Finally, the signature predicted prolonged lung inflammation post-treatment in the Catalysis Treatment Response Cohort (Figure 1D).

9-gene TB signature validates in independent retrospective and prospective cohorts.

(A) ROC curves for comparing ATB vs. all other samples (All), or individually comparing ATB vs. Healthy, LTBI or Other Disease (OD) samples in independent retrospective validation and (B) a prospective Moldova cohort. (C) ROC curves comparing progressor and non-progressor samples collected at different time points in the Adolescent Cohort Study (ACS), for the 9-gene signature in solid lines and a previous 3-gene signature in dashed lines, (D) Distribution of the 9-gene score at different time points post-treatment in the Catalysis Treatment Response Cohort Study, for individuals with persistent lung inflammation at 24 weeks compared with those who had clear lungs at 24 weeks.

Conclusion

Overall, the 9-gene signature meets the WHO TPPs required for the End TB strategy.

Disclosures

Purvesh Khatri, PhD, Cepheid, Inc.: Advisor/Consultant|Inflammatix, Inc.: Advisor/Consultant|Inflammatix, Inc.: Inflammatix is in negotiations to license the 9-gene signature discussed here.|Inflammatix, Inc.: Stocks/Bonds.

Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study

BACKGROUND

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce.

METHODS

In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS.

FINDINGS

Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations.

INTERPRETATION

The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background).

FUNDING

Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.

Knowledge, Attitude, Practices, and Vaccine Hesitancy Among the Latinx Community in Southern California Early in the COVID-19 Pandemic: Cross-sectional Survey

Background

The Latinx population in the United States has experienced high rates of infection, hospitalization, and death since the beginning of the COVID-19 pandemic. There is little data on the knowledge, attitude, and practices (KAP) specifically in Latinx communities in the United States.

Objective

We aimed to assess COVID-19 KAP and vaccine hesitancy among a Latinx cohort in the early stages of the COVID-19 pandemic (from July 2020 to October 2020), at a unique time when a vaccine was not available. 

Methods

Participants aged ≥18 years were recruited at a primary care clinic in Southern California and asked to self-report sociodemographic characteristics, KAP, and vaccine hesitancy. A subset of the participants answered the vaccine hesitancy assessment as it was added after the start of data collection. KAP items were summed to create composite scores, with higher scores reflecting increased COVID-19 knowledge, positive attitudes toward the COVID-19 pandemic, and disease prevention practices. Bivariate and multivariable regression models were fitted to test associations between sociodemographic characteristics and KAP scores. For our analysis, we only included patients who self-identified as Latinx.

Results

Our final data set included 265 participants. The participants had a mean age of 49 (IQR 38.5-59) years, and 72.1% (n=191) were female, 77% (n=204) had at most a high school degree, 34.7% (n=92) had an annual income <US $25,000, and 11.7% (n=31) had previously tested positive for COVID-19. We found high knowledge regarding transmission and spread; moderate knowledge regarding symptoms awareness; overall negative attitudes, which included high pessimism in government public health efforts and high amounts of fear, anxiety, and frustration due to COVID-19 pandemic; and moderate participation in preventive practices. A college education was positively associated with a higher knowledge score than those without a college education (β=0.14, 95% CI 0.01-1.60; P=.04) when adjusted for covariates. Male gender had a positive association with COVID-19 attitude scores compared to female gender (β=1.61, 95% CI 0.50-2.72; P=.05), and male gender was negatively associated with the COVID-19 practices score compared to female gender (β=–0.16, 95% CI –0.56 to –0.06; P=.03), when both were adjusted for covariates. Among a subset of 203 patients, 26.6% (n=54) indicated that if the vaccine was available, they would not take a COVID-19 vaccine, and 18.7% (n=38) were unsure.

Conclusions

Good knowledge and preventative practices in the population may have reflected effective public health messaging and the implementation of public health laws during the first wave of the pandemic; however, the overall fear and anxiety may have reflected the negative impact that the pandemic had on vulnerable populations such as the Latinx community. Although our data are a reflection of a previous time in the pandemic, we believe it captures a critical time that can be used to provide unique insights regarding potential avenues to better protect the Latinx communities against future vaccine-resistant COVID-19 strains.

International Registered Report Identifier (IRRID)

RR2-10.2196/25265

Distinct blood transcriptomic signature of treatment in latent tuberculosis infected individuals at risk of developing active disease

Although only a small fraction will ever develop the active form of tuberculosis (ATB) disease, chemoprophylaxis treatment in latent TB infected (LTBI) individuals is an effective strategy to control pathogen transmission. Characterizing immune responses in LTBI upon chemoprophylactic treatment is important to facilitate treatment monitoring, and thus improve TB control strategies. Here, we studied changes in the blood transcriptome in a cohort of 42 LTBI and 8 ATB participants who received anti-TB therapy. Based on the expression of previously published gene signatures of progression to ATB, we stratified the LTBI cohort in two groups and examined if individuals deemed to be at elevated risk of developing ATB before treatment (LTBI-Risk) differed from others (LTBI-Other). We found that LTBI-Risk and LTBI-Other groups were associated with two distinct transcriptomic treatment signatures, with the LTBI-Risk signature resembling that of treated ATB patients. Notably, overlapping genes between LTBI-Risk and ATB treatment signatures were associated with risk of progression to ATB and interferon (IFN) signaling, and were selectively downregulated upon treatment in the LTBI-Risk but not the LTBI-Other group. Our results suggest that transcriptomic reprogramming following treatment of LTBI is heterogeneous and can be used to distinguish LTBI-Risk individuals from the LTBI cohort at large.

Assessing COVID-19-Related Knowledge, Attitudes, and Practices Among Hispanic Primary Care Patients: Protocol for a Cross-sectional Survey Study

Background

Recent epidemiological data indicate that minority groups, especially Hispanic communities, experience higher rates of infection, hospitalization, and death due to COVID-19. It is important to understand the nature of this health disparity and the socioeconomic or behavioral factors that are placing Hispanic communities and other minority populations at higher risk for morbidity and mortality.

Objective

The purpose of this project is to assess current COVID-19–related knowledge, attitudes, and practices (KAP) among a predominantly Hispanic population from Orange County, California, and identify risk factors that may contribute to increased susceptibility and vulnerability to contracting SARS-CoV-2.

Methods

Our Orange County–wide community survey consists of quantitative survey questions in four domains: demographic information, COVID-19 knowledge questions, COVID-19 attitude questions, and COVID-19 practices questions. The survey questions are adapted from recent global KAP studies. Participants are being recruited from Amistad Medical Clinic, a private primary health clinic group in Orange County that treats a predominantly Hispanic population. Patients recruited during telehealth visits are surveyed remotely by telephone, and those recruited during in-person clinic visits are surveyed in person. Surveys are conducted by trained members of the study team who are native to the community setting.

Results

As of October 12, 2020, we had recruited and enrolled 327 participants. Data collection occurred June 26th to October 30th. Data analysis is ongoing.

Conclusions

Very few current COVID-19 studies focus on the perspective and experience of minority populations. Because Hispanic communities are disproportionately affected by COVID-19, it is important to understand the factors the contribute to this disparity and the next steps that should be taken to reduce the COVID-19 burden in this population. We believe that our study model of partnering with a local clinic system that serves our study population can be expanded to other settings to compare COVID-19 KAP and associated factors within different minority communities.

International Registered Report Identifier (IRRID)

DERR1-10.2196/25265

658. Effect of HIV Status on Tuberculosis Load as Detected by Xpert MTB/RIF in Sputum vs. Saliva Samples

Background

Tuberculosis (TB) is the most common co-infection among people living with HIV, but HIV positivity is associated with a lower Mycobacterium tuberculosis (MTB) bacillary load in sputum, making TB often difficult to diagnose with current diagnostic solutions. GeneXpert MTB/RIF (Cepheid, USA), a rapid, molecular diagnostic assay, has transformed the TB diagnostic landscape and can be used to diagnose TB and limited drug resistance in HIV patients from direct clinical samples in < 2 hours, but results can be significantly affected by sample bacterial load, which is quantified by the GeneXpert MTB/RIF (Xpert) instrument using Ct values. Our primary objective was to assess how a patient’s HIV status affected their MTB bacterial load in sputum vs. saliva samples submitted for Xpert diagnosis of TB.

Methods

We completed a retrospective analysis of >4,000 patient records from the Myanmar National TB Program captured as part of a nation-wide electronic reporting system developed with the assistance of FIND (Geneva). De-identified records included HIV status, Xpert testing results, and for a subset of patients, specimen type. With this diagnostic information, we compared the distribution of MTB load (quantified by Xpert Ct values) in sputum and saliva in HIV positive vs. HIV negative patients using STATA.

Results

Based on mean Ct value comparison independent of HIV status, saliva samples (mean Ct = 22.7) contained a significantly lower bacterial load of MTB as compared to sputum samples (mean Ct=19.2, p < .001).Within saliva samples, a lower bacterial load was also detected in HIV positive patients (mean Ct = 26.9) compared to HIV negative patients (mean Ct = 22.3, p< .05). Similarly, in sputum samples, a lower bacterial load was detected in HIV positive patients (mean Ct = 21.6) compared to HIV negative patients (mean Ct = 19.0, p < .001) (Figure 1).

Figure 1. Ct Values by HIV Status and Specimen Type

Conclusion

Sputum samples have a significantly higher bacterial load on average compared to saliva samples independent of HIV status. Additionally, when looking at both saliva and sputum as sample types, HIV positive patients have significantly lower bacterial load than individuals who are HIV negative. Based on these results, sputum is the optimal sample type for Xpert TB detection, especially in people living with HIV.

Disclosures

All Authors: No reported disclosures

Mycobacterial biomaterials and resources for researchers

There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

BACKGROUND

The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.

METHODS

We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.

RESULTS

A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.

CONCLUSIONS

Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).