Clinical utility of target-based next-generation sequencing for drug-resistant TB.

BACKGROUND: In high TB burden countries, access to drug susceptibility testing is a major bottleneck. Targeted next-generation sequencing (tNGS) is a promising technology for rapid resistance detection. This study assessed the role of tNGS for the diagnosis of drug-resistant TB (DR-TB).METHODS: A total of 161 samples from bacteriologically confirmed TB cases were subjected to tNGS using the Deeplex® Myc-TB kit and sequenced using the MiSeq platform. These samples were also processed for conventional phenotypic DST (pDST) using 13 drugs on Mycobacteria Growth Indicator Tube and line-probe assays (MTBDRplus and MTBDRsl).RESULTS: There were 146 DR-TB and 15 drug-susceptible TB (DS-TB) samples. About 70% of patients with DR-TB had no previous TB treatment history. Overall, 88.2% had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB), 58.5% pre-extensively drug-resistant TB (pre-XDR-TB) and 9.2% had XDR-TB as defined by the WHO (2020). Around 8% (n = 13) of samples were non-culturable; however, identified 8 were resistant to first and second-line drugs using tNGS. Resistance frequency was similar across methods, with discordance in drugs less reliable using pDST or with limited mutational representation within databases. Sensitivities were aligned with literature reports for most drugs. We observed 10% heteroresistance, while 75% of strains were of Lineages 2 and 3.CONCLUSIONS: Programme data supported tNGS in the diagnosis of DR-TB for early treatment using individualised regimens.

Operationalising targeted next-generation sequencing for routine diagnosis of drug-resistant TB.

BACKGROUND: Phenotypic drug susceptibility testing (pDST) for Mycobacterium tuberculosis can take up to 8 weeks, while conventional molecular tests identify a limited set of resistance mutations. Targeted next-generation sequencing (tNGS) offers rapid results for predicting comprehensive drug resistance, and this study sought to explore its operational feasibility within a public health laboratory in Mumbai, India. METHODS: Pulmonary samples from consenting patients testing Xpert MTB-positive were tested for drug resistance by conventional methods and using tNGS. Laboratory operational and logistical implementation experiences from study team members are shared below. RESULTS: Of the total number of patients tested, 70% (113/161) had no history of previous TB or treatment; however, 88.2% (n = 142) had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB). There was a high concordance between resistance predictions of tNGS and pDST for most drugs, with tNGS more accurately identifying resistance overall. tNGS was integrated and adapted into the laboratory workflow; however, batching samples caused significantly longer result turnaround time, fastest at 24 days. Manual DNA extraction caused inefficiencies; thus protocol optimisations were performed. Technical expertise was required for analysis of uncharacterised mutations and interpretation of report templates. tNGS cost per sample was US$230, while for pDST this was US$119. CONCLUSIONS: Implementation of tNGS is feasible in reference laboratories. It can rapidly identify drug resistance and should be considered as a potential alternative to pDST.

CONTEXTE: Les tests phénotypiques de sensibilité aux médicaments (pDST) pour Mycobacterium tuberculosis peuvent prendre jusqu'à 8 semaines, tandis que les tests moléculaires conventionnels identifient un ensemble limité de mutations de résistance. Le séquençage ciblé de la prochaine génération (tNGS) offre des résultats rapides pour prédire la résistance globale aux médicaments, et cette étude avait pour objectif d'explorer sa faisabilité opérationnelle au sein d'un laboratoire de santé publique à Mumbai, en Inde. MÉTHODES: Des échantillons pulmonaires de patients consentants testés positifs au Xpert MTB ont été testés pour la résistance aux médicaments par des méthodes conventionnelles et en utilisant le tNGS. Les expériences des membres de l'équipe de l'étude en matière de fonctionnement du laboratoire et de mise en œuvre logistique sont présentées ci-dessous. RÉSULTATS: Sur le nombre total de patients testés, 70% (113/161) n'avaient pas d'antécédents de TB ou de traitement ; cependant, 88,2% (n = 142) présentaient une TB résistante à la rifampicine/multirésistante aux médicaments (RR/MDR-TB). La concordance entre les prédictions de résistance de la tNGS et de la pDST était élevée pour la plupart des médicaments, la tNGS identifiant globalement la résistance avec plus de précision. La tNGS a été intégrée et adaptée au flux de travail du laboratoire ; toutefois, la mise en lots des échantillons a entraîné un délai d'obtention des résultats beaucoup plus long, le plus rapide étant de 24 jours. L'extraction manuelle de l'ADN a été source d'inefficacité ; le protocole a donc été optimisé. L'analyse des mutations non caractérisées et l'interprétation des modèles de rapport ont nécessité une expertise technique. Le coût du tNGS par échantillon s'élevait à US$230, contre US$119 pour le pDST. CONCLUSIONS: La mise en œuvre de la tNGS est possible dans les laboratoires de référence. Elle permet d'identifier rapidement la résistance aux médicaments et devrait être considérée comme une alternative potentielle à la pDST.

Evaluating newly approved drugs in combination regimens for multidrug-resistant tuberculosis with fluoroquinolone resistance (endTB-Q): study protocol for a multi-country randomized controlled trial.

BACKGROUND: Treatment for fluoroquinolone-resistant multidrug-resistant/rifampicin-resistant tuberculosis (pre-XDR TB) often lasts longer than treatment for less resistant strains, yields worse efficacy results, and causes substantial toxicity. The newer anti-tuberculosis drugs, bedaquiline and delamanid, and repurposed drugs clofazimine and linezolid, show great promise for combination in shorter, less-toxic, and effective regimens. To date, there has been no randomized, internally and concurrently controlled trial of a shorter, all-oral regimen comprising these newer and repurposed drugs sufficiently powered to produce results for pre-XDR TB patients. METHODS: endTB-Q is a phase III, multi-country, randomized, controlled, parallel, open-label clinical trial evaluating the efficacy and safety of a treatment strategy for patients with pre-XDR TB. Study participants are randomized 2:1 to experimental or control arms, respectively. The experimental arm contains bedaquiline, linezolid, clofazimine, and delamanid. The control comprises the contemporaneous WHO standard of care for pre-XDR TB. Experimental arm duration is determined by a composite of smear microscopy and chest radiographic imaging at baseline and re-evaluated at 6 months using sputum culture results: participants with less extensive disease receive 6 months and participants with more extensive disease receive 9 months of treatment. Randomization is stratified by country and by participant extent-of-TB-disease phenotype defined according to screening/baseline characteristics. Study participation lasts up to 104 weeks post randomization. The primary objective is to assess whether the efficacy of experimental regimens at 73 weeks is non-inferior to that of the control. A sample size of 324 participants across 2 arms affords at least 80% power to show the non-inferiority, with a one-sided alpha of 0.025 and a non-inferiority margin of 12%, against the control in both modified intention-to-treat and per-protocol populations. DISCUSSION: This internally controlled study of shortened treatment for pre-XDR TB will provide urgently needed data and evidence for clinical and policy decision-making around the treatment of pre-XDR TB with a four-drug, all-oral, shortened regimen. TRIAL REGISTRATION: ClinicalTrials.Gov NCT03896685. Registered on 1 April 2018; the record was last updated for study protocol version 4.3 on 17 March 2023.

TB screening, prevention and treatment cascade in a Malawi prison.

BACKGROUND Incarcerated individuals, especially in high HIV and TB burden settings, are at increased risk of latent TB infection and/or TB disease. We implemented a comprehensive HIV-TB intervention in a Malawi prison and studied its feasibility.METHODS Between February and December 2019, consenting individuals underwent screening for HIV, TB infection and TB disease. HIV-positive individuals without TB disease were treated with a fixed-dose combination of isoniazid, cotrimoxazole and vitamin B6 (INH-CTX-B6). HIV-negative persons with TB infection received 12 weeks of isoniazid and rifapentine (3HP).RESULTS Of 1,546 consenting individuals, 1,498 (96.9%) were screened and 1,427 (92.3%) included in the analysis: 96.4% were male, the median age was 31 years (IQR 25-38). Twenty-nine (2.1%) participants were diagnosed with TB disease, of whom 89.7% started and 61.5% completed TB treatment. Of the 1,427 included, 341 (23.9%) were HIV-positive, of whom 98.5% on antiretroviral therapy and 95% were started on INH-CTX-B6. Among 1,086 HIV-negative participants, 1,015 (93.5%) underwent the tuberculin skin test (TST), 670 (65.9%) were TST-positive, 666 (99.4%) started 3HP and 570 (85.5%) completed 3HP treatment.CONCLUSION A comprehensive TB screening and treatment package among incarcerated individuals was acceptable and feasible, and showed high prevalence of HIV, TB disease and TB infection. Treatment uptake was excellent, but treatment completion needs to be improved. Greater investment in comprehensive HIV-TB services, including access to shorter TB regimens and follow-up upon release, is needed for incarcerated individuals.

Evaluating newly approved drugs for multidrug-resistant tuberculosis (endTB): study protocol for an adaptive, multi-country randomized controlled trial.

BACKGROUND: Treatment of multidrug- and rifampin-resistant tuberculosis (MDR/RR-TB) is expensive, labour-intensive, and associated with substantial adverse events and poor outcomes. While most MDR/RR-TB patients do not receive treatment, many who do are treated for 18 months or more. A shorter all-oral regimen is currently recommended for only a sub-set of MDR/RR-TB. Its use is only conditionally recommended because of very low-quality evidence underpinning the recommendation. Novel combinations of newer and repurposed drugs bring hope in the fight against MDR/RR-TB, but their use has not been optimized in all-oral, shorter regimens. This has greatly limited their impact on the burden of disease. There is, therefore, dire need for high-quality evidence on the performance of new, shortened, injectable-sparing regimens for MDR-TB which can be adapted to individual patients and different settings. METHODS: endTB is a phase III, pragmatic, multi-country, adaptive, randomized, controlled, parallel, open-label clinical trial evaluating the efficacy and safety of shorter treatment regimens containing new drugs for patients with fluoroquinolone-susceptible, rifampin-resistant tuberculosis. Study participants are randomized to either the control arm, based on the current standard of care for MDR/RR-TB, or to one of five 39-week multi-drug regimens containing newly approved and repurposed drugs. Study participation in all arms lasts at least 73 and up to 104 weeks post-randomization. Randomization is response-adapted using interim Bayesian analysis of efficacy endpoints. The primary objective is to assess whether the efficacy of experimental regimens at 73 weeks is non-inferior to that of the control. A sample size of 750 patients across 6 arms affords at least 80% power to detect the non-inferiority of at least 1 (and up to 3) experimental regimens, with a one-sided alpha of 0.025 and a non-inferiority margin of 12%, against the control in both modified intention-to-treat and per protocol populations. DISCUSSION: The lack of a safe and effective regimen that can be used in all patients is a major obstacle to delivering appropriate treatment to all patients with active MDR/RR-TB. Identifying multiple shorter, safe, and effective regimens has the potential to greatly reduce the burden of this deadly disease worldwide. TRIAL REGISTRATION: ClinicalTrials.gov Identifier NCT02754765. Registered on 28 April 2016; the record was last updated for study protocol version 3.3, on 27 August 2019.

New TB drugs for the treatment of children and adolescents with rifampicin-resistant TB in Mumbai, India.

SETTING: Médecins Sans Frontières (MSF) clinic in Mumbai, India.OBJECTIVE: To determine the final treatment outcomes, culture conversion and adverse events (AEs) during treatment among children and adolescents (0-19 years) with rifampicin-resistant tuberculosis (RR-TB) who received ambulatory injectable-free treatment, including bedaquiline (BDQ) and/or delamanid (DLM) during September 2014-January 2020.DESIGN: This was a retrospective cohort study based on review of routinely collected programme data.RESULTS: Twenty-four patients were included; the median age was 15.5 years (min-max 3-19) and 15 (63%) were females. None were HIV-coinfected. All had fluoroquinolone resistance. Twelve received treatment, including BDQ and DLM, 11 received DLM and one BDQ. The median exposure to BDQ (n = 13) and DLM (n = 23) was 82 (IQR 80-93) and 82 (IQR 77-96) weeks, respectively. Seventeen (94%) patients with positive culture at baseline (n = 18) had negative culture during treatment; median time for culture-conversion was 7 weeks (IQR 5-11). Twenty-three (96%) had successful treatment outcomes: cured (n = 16) or completed treatment (n = 7); one died. Eleven (46%) had 17 episodes of AEs. Two of 12 serious AEs were associated with new drugs (QTcF >500 ms).CONCLUSION: Based on one of the largest global cohorts of children and adolescents to receive new TB drugs, this study has shown that injectable-free regimens containing BDQ and/or DLM on ambulatory basis were effective and well-tolerated among children and adolescents and should be made routinely accessible to these vulnerable groups.

NK cells at the interface between innate and adaptive immunity.

In recent years a novel concept has emerged indicating that the actual role of natural killer (NK) cells is not confined to the destruction of virus-infected cells or tumors. Indeed, different NK subsets exist that display major functional differences in their cytolytic activity, cytokine production and homing capabilities. In particular, CD56(high) CD16(-) NK cells that largely predominate in lymph nodes, have little cytolytic activity but release high levels of cytokines whereas CD56(low) CD16(+) NK cells that predominate in peripheral blood and inflamed tissues, display lower cytokine production, but potent cytotoxicity. The latter is characterized by granule polarization and exocytosis of various proteins including perforin and granzymes that mediate target cell killing. The recruitment of CD56(low) CD16(+) NK cells into inflamed peripheral tissues is orchestrated by various chemochines including the newly identified Chemerin. At these sites, NK cells, upon engagement of different triggering receptors become activated and upregulate their cytokine production and cytotoxicity after interaction with myeloid dendritic cells (DCs). Importantly, during this interaction NK cells also mediate the 'editing' of DCs undergoing maturation. This process appears to play a crucial role in shaping both innate and adaptive immune responses. Indeed, only DCs undergoing this NK-mediated quality control would become fully mature and capable of inducing priming of protective Th1 responses.

Missed opportunities for earlier diagnosis of rifampicin-resistant tuberculosis despite access to Xpert® MTB/RIF.

OBJECTIVE: To assess the proportion of rifampicin-resistant tuberculosis (RR-TB) patients with potential earlier RR-TB diagnoses in Khayelitsha, South Africa. DESIGN: We conducted a retrospective analysis among RR-TB patients diagnosed from 2012 to 2014. Patients were considered to have missed opportunities for earlier diagnosis if 1) they were incorrectly screened according to the Western Cape diagnostic algorithm; 2) the first specimen was not tested using Xpert® MTB/RIF; 3) no specimen was ever tested; or 4) the initial Xpert test showed a negative result, but no subsequent specimen was sent for follow-up testing in human immunodeficiency virus-positive patients. RESULTS: Among 543 patients, 386 (71%) were diagnosed with Xpert and 112 (21%) had had at least one presentation at a health care facility within the 6 months before the presentation at which RR-TB was diagnosed. Overall, 95/543 (18%) patients were screened incorrectly at some point: 48 at diagnostic presentation only, 38 at previous presentation only, and 9 at both previous and diagnostic presentations. CONCLUSIONS: These data show that a significant proportion of RR-TB patients might have been diagnosed earlier, and suggest that case detection could be improved if diagnostic algorithms were followed more closely. Further training and monitoring is required to ensure the greatest benefit from universal Xpert implementation.

HLA class I molecule expression is up-regulated during maturation of dendritic cells, protecting them from natural killer cell-mediated lysis.

It has been widely demonstrated that natural killer (NK) cells are able to discriminate between normal and abnormal cells on the basis of the interaction of their NKRs with the MHC molecules expressed on the target cells. Recent studies showed that also normal dendritic cells are susceptible to NK cell-mediated lysis. In this work, the potential relationships between the expression of different surface molecules on both immature and mature DC and susceptibility to lysis have been investigated. The reduced density of HLA class I on the surface of immature DC resulted in the only permissive signal to NK cell mediated killing. On the contrary, the remarkable increase in HLA class I molecules detected during DC maturation was strictly related to the resistance to NK cell. Contemporary, no clear evidences of a role for other surface molecules modulated during DC maturation (CD80, CD83, CD86 and CD40), were obtained.

Morphological, phenotypic and karyotypic characterization of a novel natural-killer-cell target - evidence of involvement of MHC class-I molecules in NK cell recognition.

A new cell line from a neoplastic ascites was established. This strain, designated PAT-206, was characterized by plastic adherence and a high proliferative potential without any specific growth factor requirement. Karyotype analysis showed that the line was of human chromosomal constitution and aneuploid. Surface marker analysis showed that CD45, CD33 and CD15 were positive. In addition, the presence of human cytokeratins was detected by cytoplasmic immunofluorescence. Interestingly, the cell line did not express major hystocompatibility complex (MHC) class I and II, and was more sensitive than the 'classic' K562 cell line, to killing mediated by fresh uncultured peripheral blood lymphocytes. Following differentiation with interferon-gamma, the cell line expressed MHC class I antigens and resulted resistant to natural killing mediated lysis. This novel NK cell target seems to be suitable for further studies on NK cell specificities.

Analysis of HLA-class-I specific natural killer cell receptors expressed on T lymphocytes infiltrating non-small-cell lung cancer.

HLA-class I-specific natural killer cell receptors (HNKR) have been described to significantly interfere with both specific and non-specific functional activities of T lymphocytes. Despite the clear evidences obtained in T cells derived from peripheral blood, little is known about the activity of HNKR expressed in tumor infiltrating lymphocytes. For this reason, we have studied T lymphocytes derived from advanced non small cell lung cancers (NSCLC). The population of T cells expressing the HNKR(+) phenotype was rare both in NSCLC-associated lymphocytes and in the peripheral blood. The two populations were clearly oligoclonal, as shown by the analysis of T cell receptor repertoire. Interestingly, while HNKR(+) T cells derived from the peripheral blood belonged to the CD45R0 phenotype, the large majority of HNKR(+) T cells in TIL were CD45RA. Functionally, all HNKR(+) T cells displayed a cytolytic activity against allogeneic NSCLC. Autologous NSCLC, tested in a single patient, was lysed efficiently by HNKR(+) T cells, thus suggesting that at least in this model, the presence of HNKR did not significantly interfere with the functional capacity of effector cells.

Proliferation indices and p53-immunocytochemistry in uterine mixed mullerian tumors.

Mixed mullerian tumor (MMT) is a biphasic malignancy of elderly women. It, including both a carcinomatous and a sarcomatous component (CC and SC), is regarded as a female genital tract carcinosarcoma (FGTCS). Since current methods to grade CC and SC are not still univocal, the authors estimate mitotic index (MI) and MIB 1-immunolabeling index (MIB 1-LI) as common prognostic indices for the MMT components. They also compare above prognostic indices with p-53 immunocytochemistry, in MMTs. The present study thus points out that: (a) MI of CC and SC areas is consistent with the respective conventional tumor grades; (b) MI averages of CC are higher than those observed in the SC areas; (c) MI and MIB 1-LI of the CC-tumor cells correlate reciprocally in a very significant fashion; (d) A diffuse strong p53 nuclear immunostaining (> 50% cells) is often patent where the highest MI and MIB 1-LI are found. In conclusion, the authors propose MI and MIB 1-LI as two complementary useful indices to assess prognosis of MMTs. They also suggest p53 nuclear immunolabeling should be regarded as an independent biomarker of unfavourable MMT behaviour.

Fenestrated arterial switch operation: surgical approach to an unusual transposition of the great arteries complex.

Transposition of the great arteries with intact ventricular septum and aortopulmonary window is an extremely rare anatomic combination, having been reported just twice previously. Other authors performed a physiologic repair, because the combination was considered unsuitable for an anatomic repair. We describe the case of a 26-day-old baby with such anatomy who was successfully treated with an arterial switch operation. A 4 mm fenestration at atrial level was made for a smoother postoperative course.

Selective expansion of circulating CD8+ lymphocytes during cancer immunotherapy with interleukin-2 plus alpha-interferon but not with interleukin-2 alone.

The use of interferons in anti-cancer therapy is justified by the experimental evidence that these cytokines are able to enhance in vitro the expression of some surface molecules such as major histocompatibility complex and tumor associated lymphocytes. Furthermore, a synergism of action of interleukin-2 with alpha-interferon in the treatment of human malignancies has been described. Nevertheless, whether the in vivo role of interferons associated to interleukin-2 as anti-cancer drugs is actually related to the properties of this cytokine of modulating surface molecule expression on target cells, has never been clearly reported. In this report, we describe an immune system cell resetting, during immunotherapy with interleukin-2 plus alpha-interferon, which seems to support this hypothesis.

Treatment of superficial bladder cancer with intravesical perfusion of rIL-2: a follow-up study.

We have recently reported the results of a phase I study on the intravesical perfusion of recombinant interleukin-2 in patients with superficial bladder cancer. The treatment feasible with mild toxic effects, especially compared with the treatment using TUR and instillations of Bacillus Calmette-Guerin. The follow-up of these phase I study patients was continued for another twelve months. During this period, cytoscopy and cytological examination of cells washed from bladder were performed every four months. The results showed that three out of 9 patients relapsed, over a period ranging from 6 to 20 months after treatment. All these data clearly confirm that the intravesical perfusion of rIL-2 is feasible, safe and should be an effective and nontoxic treatment of patients with superficial bladder cancer.

Adoptive immunotherapy of advanced solid tumors: an eight year clinical experience.

BACKGROUND: Adoptive immunotherapy (AI) of cancer, based upon the injection of in vitro manipulated autologous lymphocytes is still in an experimental phase. Our group started different clinical trials of AI in early 1990, and, at present, some specific targets for this approach seem to have been identified. PATIENTS AND METHODS: 296 patients with solid tumors (melanoma, kidney carcinoma, non-small-cell lung cancer, mesothelioma, neoplastic pleural effusion, and liver cancer) were treated with either locoregional or systemic adoptive immunotherapy (AI) using both LAK and TIL cells in combination with s.c. rIL-2. RESULTS: The surgery/AI combination resulted in good clinical results, characterized by enhanced survival and long lasting disease free periods in a significant number of patients. CONCLUSIONS: AI seems to be efficacious in the treatment of melanoma, lung and hepatic cancers. Further studies will expand the application of the treatment to other malignancies.

Heterogeneity of the alpha-interferon-mediated overexpression of class-I and class-II major histocompatibility complex molecules in primary cultured cancer cells.

Human alpha- and gamma-interferons (IFNs) have the capability of enhancing the expression of major histocompatibility complex-class I and class II (MHC-I and MHC-II) as well as other surface tumor associated antigens (TAA) on cancer cell lines. This capability, associated to the anti-proliferative effect observed both in vitro and in vivo, was the basis of the extended use of IFN in cancer patients. Despite the great expectations, several solid neoplasms resulted resistant to treatment with IFNs. In order to analyze the actual effects of IFNs on cancer, we treated primary cultures of different histotypes of cancer cell, which are well known to differ significantly from established cell lines, with escalating doses of alpha-IFN. In this paper, we demonstrate that a variable proportion of culture was able to potentiate the expression of MCH-I and MCH-II molecules on the surface. This finding suggests that a clear functional heterogeneity was present in primary cultures of cancer cells, that strictly reflected the in vivo situation. In addition, it is of note that in some histotypes, "natural" lymphoblastoid alpha-IFN was more effective than recombinant human alpha-IFN in the induction of this capability.

A phase I study of intravesical continuous perfusion of recombinant interleukin-2 in patients with superficial bladder cancer.

A Phase I study was started to evaluate the locoregional and/or systemic toxic effects of the continuous perfusion of recombinant interleukin-2 (rIL-2) in superficial bladder cancer. Three different dose levels were used: 3 x 10(6) IU/day (3 patients), 9 x 10(6) IU/day (3 patients) and 27 x 10(6) IU/day (3 patients). Two patients (one treated with 3 x 10(6) and another with 27 x 10(6) IU/day of rIL-2) had hematuria after the end of the treatment, one patient had fever (grade I) and 7 of 9 patients experienced hypotension (grade I-II). All effects were not dose related. Routine laboratory tests indicated that no significant variations of biochemical parameters occurred. A phenotypic analysis of white blood cells detectable in the bladder, showed an evident locoregional activation of lymphoid cells. In particular, T lymphocytes expressed activation antigens (such as CD25 and HLA-DR) following treatment with rIL-2. A 6- to 12-month clinical follow-up, showed that all patients but one (which recurred after 5 months) are alive and disease-free. This therefore indicates that the locoregional perfusion of rIL-2 is safe and gives clinical results similar to those obtained using Calmette-Guérin bacillus locoregional instillation, in patients who underwent a transurethral resection of superficial bladder cancer.