Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy

Therapeutic antibodies have become one of the most influential therapeutics in modern medicine to fight against infectious pathogens, cancer, and many other diseases. However, experimental screening for highly efficacious targeting antibodies is labor-intensive and of high cost, which is exacerbated by evolving antigen targets under selective pressure such as fast-mutating viral variants. As a proof-of-concept, we developed a machine learning-assisted antibody generation pipeline that greatly accelerates the screening and re-design of immunoglobulins G (IgGs) against a broad spectrum of SARS-CoV-2 coronavirus variant strains. These viruses infect human host cells via the viral spike protein binding to the host cell receptor angiotensin-converting enzyme 2 (ACE2). Using over 1300 IgG sequences derived from convalescent patient B cells that bind with spike's receptor binding domain (RBD), we first established protein structural docking models in assessing the RBD-IgG-ACE2 interaction interfaces and predicting the virus-neutralizing activity of each IgG with a confidence score. Additionally, employing Gaussian process regression (also known as Kriging) in a latent space of an antibody language model, we predicted the landscape of IgGs' activity profiles against individual coronaviral variants of concern. With functional analyses and experimental validations, we efficiently prioritized IgG candidates for neutralizing a broad spectrum of viral variants (wildtype, Delta, and Omicron) to prevent the infection of host cells in vitro and hACE2 transgenic mice in vivo. Furthermore, the computational analyses enabled rational redesigns of selective IgG clones with single amino acid substitutions at the RBD-binding interface to improve the IgG blockade efficacy for one of the severe, therapy-resistant strains - Delta (B.1.617). Our work expedites applications of artificial intelligence in antibody screening and re-design even in low-data regimes combining protein language models and Kriging for antibody sequence analysis, activity prediction, and efficacy improvement, in synergy with physics-driven protein docking models for antibody-antigen interface structure analyses and functional optimization.

Tissue-Resident Alveolar Macrophages Reduce Ozone-induced Inflammation via MerTK Mediated Efferocytosis

Lung inflammation, caused by acute exposure to ozone (O3) - one of the six criteria air pollutants - is a significant source of morbidity in susceptible individuals. Alveolar macrophages (AMØs) are the most abundant immune cells in the normal lung and their number increases following O3 exposure. However, the role of AMØs in promoting or limiting O3-induced lung inflammation has not been clearly defined. Here, we used a mouse model of acute O3 exposure, lineage tracing, genetic knockouts, and data from O3-exposed human volunteers to define the role and ontogeny of AMØs during acute O3 exposure. Lineage tracing experiments showed that 12, 24, and 72 h after exposure to O3 (2 ppm) for 3h all AMØs were tissue-resident origin. Similarly, in humans exposed to FA and O3 (200 ppb) for 135 minutes, we did not observe ~21h post-exposure an increase in monocyte-derived AMØs by flow cytometry. Highlighting a role for tissue-resident AMØs, we demonstrate that depletion of tissue-resident AMØs with clodronate-loaded liposomes led to persistence of neutrophils in the alveolar space after O3 exposure, suggesting that impaired neutrophil clearance (i.e., efferocytosis) leads to prolonged lung inflammation. Moreover, depletion of tissue-resident AMØ demonstrated reduced clearance of intratracheally instilled apoptotic Jurkat cells, consistent with reduced efferocytosis. Genetic ablation of MerTK - a key receptor involved in efferocytosis - also resulted in impaired clearance of apoptotic neutrophils followed O3 exposure. Overall, these findings underscore the pivotal role of tissue-resident AMØs in resolving O3-induced inflammation via MerTK-mediated efferocytosis.

A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

Pathogen clearance and resolution of inflammation in patients with pneumonia require an effective local T cell response. Nevertheless, local T cell activation may drive lung injury, particularly during prolonged episodes of respiratory failure characteristic of severe SARS-CoV-2 pneumonia. While T cell responses in the peripheral blood are well described, the evolution of T cell phenotypes and molecular signatures in the distal lung of patients with severe pneumonia caused by SARS-CoV-2 or other pathogens is understudied. Accordingly, we serially obtained 432 bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia and respiratory failure, including 74 unvaccinated patients with COVID-19, and performed flow cytometry, transcriptional, and T cell receptor profiling on sorted CD8+ and CD4+ T cell subsets. In patients with COVID-19 but not pneumonia secondary to other pathogens, we found that early and persistent enrichment in CD8+ and CD4+ T cell subsets correlated with survival to hospital discharge. Activation of interferon signaling pathways early after intubation for COVID-19 was associated with favorable outcomes, while activation of NF-κB-driven programs late in disease was associated with poor outcomes. Patients with SARS-CoV-2 pneumonia whose alveolar T cells preferentially targeted the Spike and Nucleocapsid proteins tended to experience more favorable outcomes than patients whose T cells predominantly targeted the ORF1ab polyprotein complex. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize patients who recover, yet these responses progress to NF-κB activation against non-structural proteins in patients who go on to experience poor clinical outcomes.

Tissue-resident alveolar macrophages reduce O3-induced inflammation via MerTK mediated efferocytosis

Lung inflammation, caused by acute exposure to ozone (O3) - one of the six criteria air pollutants - is a significant source of morbidity in susceptible individuals. Alveolar macrophages (AMØs) are the most abundant immune cells in the normal lung and their number increases following O3 exposure. However, the role of AMØs in promoting or limiting O3-induced lung inflammation has not been clearly defined. Here, we used a mouse model of acute O3 exposure, lineage tracing, genetic knockouts, and data from O3-exposed human volunteers to define the role and ontogeny of AMØs during acute O3 exposure. Lineage tracing experiments showed that 12, 24, and 72 h after exposure to O3 (2 ppm) for 3h all AMØs were tissue-resident origin. Similarly, in humans exposed to FA and O3 (200 ppb) for 135 minutes, we did not observe ~21h post-exposure an increase in monocyte-derived AMØs by flow cytometry. Highlighting a role for tissue-resident AMØs, we demonstrate that depletion of tissue-resident AMØs with clodronate-loaded liposomes led to persistence of neutrophils in the alveolar space after O3 exposure, suggesting that impaired neutrophil clearance (i.e., efferocytosis) leads to prolonged lung inflammation. Moreover, depletion of tissue-resident AMØ demonstrated reduced clearance of intratracheally instilled apoptotic Jurkat cells, consistent with reduced efferocytosis. Genetic ablation of MerTK - a key receptor involved in efferocytosis - also resulted in impaired clearance of apoptotic neutrophils followed O3 exposure. Overall, these findings underscore the pivotal role of tissue-resident AMØs in resolving O3-induced inflammation via MerTK-mediated efferocytosis.

Development of a novel humanized mouse model to study bronchopulmonary dysplasia

Rationale

The role of circulating fetal monocytes in bronchopulmonary dysplasia is not known. We utilized a humanized mouse model that supports human progenitor cell engraftment (MISTRG) to test the hypothesis that prenatal monocyte programming alters early lung development and response to hyperoxia.

Methods

Cord blood-derived monocytes from 10 human infants were adoptively transferred into newborn MISTRG mice at p0 (1 × 106 cells/mouse, intrahepatic injection) followed by normoxia versus hyperoxia (85% oxygen × 14 days). Lungs were harvested at p14 for alveolar histology (alveolar count, perimeter and area) and vascular parameters (vWF staining for microvessel density, Fulton's index). Human CD45 staining was conducted to compare presence of hematopoietic cells. Murine lung parameters were compared among placebo and monocyte-injected groups. The individual profiles of the 10 patients were further considered, including gestational age (GA; n = 2 term, n = 3 moderate/late preterm, and n = 5 very preterm infants) and preeclampsia (n = 4 patients). To explore the monocyte microenvironment of these patients, 30 cytokines/chemokines were measured in corresponding human plasma by multiplex immunoassay.

Results

Across the majority of patients and corresponding mice, MISTRG alveolarization was simplified and microvessel density was decreased following hyperoxia. Hyperoxia-induced changes were seen in both placebo (PBS) and monocyte-injected mice. Under normoxic conditions, alveolar development was altered modestly by monocytes as compared with placebo (P < 0.05). Monocyte injection was associated with increased microvessel density at P14 as compared with placebo (26.7 ± 0.73 vs. 18.8 ± 1.7 vessels per lung field; P < 0.001). Pooled analysis of patients revealed that injection of monocytes from births complicated by lower GA and preeclampsia was associated with changes in alveolarization and vascularization under normoxic conditions. These differences were modified by hyperoxia. CD45+ cell count was positively correlated with plasma monocyte chemoattractant protein-1 (P < 0.001) and macrophage inflammatory protein-1β (P < 0.01). Immunohistochemical staining for human CD206 and mouse F4/80 confirmed absence of macrophages in MISTRG lungs at P14.

Conclusions

Despite the inherent absence of macrophages in early stages of lung development, immunodeficient MISTRG mice revealed changes in alveolar and microvascular development induced by human monocytes. MISTRG mice exposed to neonatal hyperoxia may serve as a novel model to study isolated effects of human monocytes on alveolar and pulmonary vascular development.

Unique molecular signatures sustained in circulating monocytes and regulatory T cells in convalescent COVID-19 patients

Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including convalescent COVID-19 and sero-negative controls. Flow cytometry analyses revealed reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells within the patients who have recovered from severe COVID-19. sc-RNA seq analysis identifies seven heterogeneous clusters of monocytes and nine Treg clusters featuring distinct molecular signatures in association with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocytes and Tregs expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters featuring S100 family genes: one monocyte cluster of S100A8 & A9 coupled with high HLA-I and another cluster of S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, as well as a unique TGF-β high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-lived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (≥ 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.

SBT-272 improves TDP-43 pathology in ALS upper motor neurons by modulating mitochondrial integrity, motility, and function

Mitochondrial defects are one of the common underlying causes of neuronal vulnerability in neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), and TDP-43 pathology is the most commonly observed proteinopathy. Disrupted inner mitochondrial membrane (IMM) reported in the upper motor neurons (UMNs) of ALS patients with TDP-43 pathology is recapitulated in the UMNs of well-characterized hTDP-43 mouse model of ALS. The construct validity, such as shared and common cellular pathology in mice and human, offers a unique opportunity to test treatment strategies that may translate to patients. SBT-272 is a well-tolerated brain-penetrant small molecule that stabilizes cardiolipin, a phospholipid found in IMM, thereby restoring mitochondrial structure and respiratory function. We investigated whether SBT-272 can improve IMM structure and health in UMNs diseased with TDP-43 pathology in our well-characterized UMN reporter line for ALS. We found that SBT-272 significantly improved mitochondrial structural integrity and restored mitochondrial motility and function. This led to improved health of diseased UMNs in vitro. In comparison to edaravone and AMX0035, SBT-272 appeared more effective in restoring health of diseased UMNs. Chronic treatment of SBT-272 for sixty days starting at an early symptomatic stage of the disease in vivo led to a significant reduction in astrogliosis, microgliosis, and TDP-43 pathology in the ALS motor cortex. Our results underscore the therapeutic potential of SBT-272, especially within the context of TDP-43 pathology and mitochondrial dysfunction.

Inflammatory Cell Dynamics after Murine Femoral Artery Wire Injury: A Multi-Parameter Flow Cytometry-Based Analysis

An acute inflammatory response following arterial surgery for atherosclerosis, such as balloon angioplasty, stenting, and surgical bypass, is an important driver of neointimal hyperplasia after arterial injury, which leads to recurrent ischemia. However, a comprehensive understanding of the dynamics of the inflammatory infiltrate in the remodeling artery is difficult to attain due to the shortcomings of conventional methods such as immunofluorescence. We developed a 15-parameter flow cytometry method to quantitate leukocytes and 13 leukocyte subtypes in murine arteries at 4 time points after femoral artery wire injury. Live leukocyte numbers peaked at 7 days, which preceded the peak neointimal hyperplasia lesion at 28 days. Neutrophils were the most abundant early infiltrate, followed by monocytes and macrophages. Eosinophils were elevated after 1 day, while natural killer and dendritic cells gradually infiltrated over the first 7 days; all decreased between 7 and 14 days. Lymphocytes began accumulating at 3 days and peaked at 7 days. Immunofluorescence of arterial sections demonstrated similar temporal trends of CD45+ and F4/80+ cells. This method allows for the simultaneous quantitation of multiple leukocyte subtypes from small tissue samples of injured murine arteries and identifies the CD64+Tim4+ macrophage phenotype as being potentially important in the first 7 days post-injury.

First-in-human Intravesical Delivery of Pembrolizumab Identifies Immune Activation in Bladder Cancer Unresponsive to Bacillus Calmette-Guérin

BACKGROUND

Intravenous immune checkpoint inhibition is an effective anticancer strategy for bacillus Calmette-Guérin (BCG)-unresponsive non-muscle-invasive bladder cancer (NMIBC) but may be associated with greater systemic toxicity compared with localized therapies.

OBJECTIVE

We assessed the safety and antitumor activity of intravesical pembrolizumab combined with BCG.

DESIGN, SETTING, AND PARTICIPANTS

A 3 + 3 phase 1 trial of pembrolizumab + BCG was conducted in patients with BCG-unresponsive NMIBC (NCT02808143).

INTERVENTION

Pembrolizumab was given intravesically (1-5 mg/kg for 2 h) beginning 2 weeks prior to BCG induction until recurrence. Urine profiling during treatment and spatial transcriptomic profiling of pre- and post-treatment tumors were conducted to identify biomarkers that correlated with response.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Safety and tolerability of immune checkpoint inhibition were assessed, and Kaplan-Meier survival analysis was performed.

RESULTS AND LIMITATIONS

Nine patients completed therapy. Median follow-up was 35 months for five patients still alive at the end of the trial. The trial was closed due to the COVID-19 pandemic. Grade 1-2 urinary symptoms were common. The maximum tolerated dose was not reached; however, one dose-limiting toxicity was reported (grade 2 diarrhea) in the only patient who reached 52 weeks without recurrence. One death occurred from myasthenia gravis that was deemed potentially related to treatment. The 6-mo and 1-yr recurrence-free rates were 67% (95% confidence interval [CI]: 42-100%) and 22% (95% CI: 6.5-75%), respectively. Pembrolizumab was detected in the urine and not in blood. CD4⁺ T cells were significantly increased in the urine after treatment, and a transcriptomic analysis identified decreased expression of T-cell exhaustion markers in late recurrences.

CONCLUSIONS

We demonstrate that intravesical pembrolizumab is safe, feasible, and capable of eliciting strong immune responses in a clinical setting and should be investigated further.

PATIENT SUMMARY

Direct application of pembrolizumab to the bladder is a promising alternative for non-muscle-invasive bladder cancer unresponsive to Bacillus Calmette-Guérin and should be investigated further.

Feeding mode influences dynamic gut microbiota signatures and affects susceptibility to anti-CD3 mAb-induced intestinal injury in neonatal mice

Feeding modes influence the gut microbiome, immune system, and intestinal barrier homeostasis in neonates; how feeding modes impact susceptibility to neonatal gastrointestinal (GI) diseases is still uncertain. Here, we investigated the impact of dam feeding (DF) and formula feeding (FF) on features of the gut microbiome and physiological inflammation during the first 2 days of postnatal development and on the susceptibility to intestinal injury related to the inflammatory state in neonatal mouse pups. 16S rRNA sequencing data revealed microbiome changes, lower α-diversity, and a distinct pattern of β-diversity including expansion of f_Enterobacteriaceae and f_Enterococcaceae in the ileum of FF pups compared with DF pups by postnatal day (P)2. Together with gut dysbiosis, the FF cohort also had greater ileal mucosa physiological inflammatory activity compared with DF pups by P2 but maintained normal histological features. Interestingly, FF but not DF mouse pups developed necrotizing enterocolitis (NEC)-like intestinal injury within 24 h after anti-CD3 mAb treatment, suggesting that FF influences the susceptibility to intestinal injury in neonates. We further found that NEC-like incidence in anti-CD3 mAb-treated FF neonatal pups was attenuated by antibiotic treatment. Collectively, our data suggest that FF predisposes mouse pups to anti-CD3 mAb-induced intestinal injury due to abnormal f_Enterobacteriaceae and f_Enterococcaceae colonization. These findings advance our understanding of FF-associated microbial colonization and intestinal inflammation, which may help inform the development of new therapeutic approaches to GI diseases like NEC in infants.NEW & NOTEWORTHY This report shows that a feeding mode profoundly affects gut colonization in neonatal mice. Furthermore, our results demonstrate that formula feeding predisposes mouse pups to anti-CD3 mAb-induced necrotizing enterocolitis (NEC)-like intestinal injury upon inadequate microbial colonization. The study suggests the role of the combined presence of formula feeding-associated dysbiosis and mucosal inflammation in the pathogenesis of NEC and provides a new mouse model to study this disease.

Design of digital image encryption based on elliptic curve cryptography (ECC) algorithm and Radix-64 conversion

The billions of bits of information are transferred each second through the internet every day. The information may be text, image, audio or video etc, accordingly, we need some protection mechanism while sharing confidential data. Generally, RSA algorithm is used for encrypting the Secret images. However, the security provided by Elliptic Curve Cryptography (ECC) is higher with lower sized key than the RSA algorithm. So, this article proposes an extended Elliptic Curve encryption approach for encrypting the secret images. In this system, the secret image is partitioned into three color image planes such as Red, Green and Blue. By applying Radix-64 encoding and Mapping table, these planes are converted into elliptic curve points and then these points are encrypted using ECC algorithm. Again, these points are applied to the Radix-64 decoding and the mapping table to get ciphered-image. At last, the key parameters such as a, b, p and Generator point (G) are embedded in the last four pixel positions of the ciphered-image. In order to get the original secret image, the recipient must extract these key parameters from the encrypted image and then apply the remaining processes to the encrypted image in the opposite order. Experimental results tested using MATLAB R2021b and it shows that the NPCR and UACI values are 99.54% and 28.73 % and better quality feature is attained since the entropy value is almost closer to eight. So, the proposed image encryption has robust capacity to fight against the differential attack.

Placental dysfunction influences fetal monocyte subpopulation gene expression in preterm birth

The placenta is the primary organ for immune regulation, nutrient delivery, gas exchange, protection against environmental toxins, and physiologic perturbations during pregnancy. Placental inflammation and vascular dysfunction during pregnancy are associated with a growing list of prematurity-related complications. The goal of this study was to identify differences in gene expression profiles in fetal monocytes - cells that persist and differentiate postnatally - according to distinct placental histologic domains. Here, by using bulk RNA-Seq, we report that placental lesions are associated with gene expression changes in fetal monocyte subsets. Specifically, we found that fetal monocytes exposed to acute placental inflammation upregulate biological processes related to monocyte activation, monocyte chemotaxis, and platelet function, while monocytes exposed to maternal vascular malperfusion lesions downregulate these processes. Additionally, we show that intermediate monocytes might be a source of mitogens, such as HBEGF, NRG1, and VEGFA, implicated in different outcomes related to prematurity. This is the first study to our knowledge to show that placental lesions are associated with unique changes in fetal monocytes and monocyte subsets. As fetal monocytes persist and differentiate into various phagocytic cells following birth, our study may provide insight into morbidity related to prematurity and ultimately potential therapeutic targets.

Concomitant pulmonary disease is common among patients with extrapulmonary TB

BACKGROUND :

Microbiologic screening of extrapulmonary TB (EPTB) patients could inform recommendations for aerosol precautions and close contact prophylaxis. However, this is currently not routinely recommended in India. Therefore, we estimated the proportion of Indian patients with EPTB with microbiologic evidence of pulmonary TB (PTB).

METHODS :

We characterized baseline clinical, radiological and sputum microbiologic data of 885 adult and pediatric TB patients in Chennai and Pune, India, between March 2014 and November 2018.

RESULTS :

Of 277 patients with EPTB, enhanced screening led to the identification of 124 (45%) with concomitant PTB, including 53 (19%) who reported a cough >2 weeks; 158 (63%) had an abnormal CXR and 51 (19%) had a positive sputum for TB. Of 70 participants with a normal CXR and without any cough, 14 (20%) had a positive sputum for TB. Overall, the incremental yield of enhanced screening of patients with EPTB to identify concomitant PTB disease was 14% (95% CI 12–16).

CONCLUSIONS :

A high proportion of patients classified as EPTB in India have concomitant PTB. Our results support the need for improved symptom and CXR screening, and recommends routine sputum TB microbiology screening of all Indian patients with EPTB.

Unique molecular signatures sustained in circulating monocytes and regulatory T cells in Convalescent COVID-19 patients

Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized multi-omic single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including covenlesent COVID-19 and sero-negative controls. The reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells are significantly associated with the patients recovered from severe COVID-19. Consistently, sc-RNA seq analysis reveals seven heterogeneous clusters of monocytes (M0-M6) and ten Treg clusters (T0-T9) featuring distinct molecular signatures and associated with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocyte and Treg expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters with S100 family genes: S100A8 & A9 with high HLA-I whereas S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, and a unique TGF-β high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-ived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (>= 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.

Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of the coronavirus induced disease 2019 (COVID-19) with evolving variants of concern. It remains urgent to identify novel approaches against broad strains of SARS-CoV-2, which infect host cells via the entry receptor angiotensin-converting enzyme 2 (ACE2). Herein, we report an increase in circulating extracellular vesicles (EVs) that express ACE2 (evACE2) in plasma of COVID-19 patients, which levels are associated with severe pathogenesis. Importantly, evACE2 isolated from human plasma or cells neutralizes SARS-CoV-2 infection by competing with cellular ACE2. Compared to vesicle-free recombinant human ACE2 (rhACE2), evACE2 shows a 135-fold higher potency in blocking the binding of the viral spike protein RBD, and a 60- to 80-fold higher efficacy in preventing infections by both pseudotyped and authentic SARS-CoV-2. Consistently, evACE2 protects the hACE2 transgenic mice from SARS-CoV-2-induced lung injury and mortality. Furthermore, evACE2 inhibits the infection of SARS-CoV-2 variants (α, β, and δ) with equal or higher potency than for the wildtype strain, supporting a broad-spectrum antiviral mechanism of evACE2 for therapeutic development to block the infection of existing and future coronaviruses that use the ACE2 receptor.

The effect of radiological imaging on treatment delay and hospitalisation in patients with peritoneal dialysis-related peritonitis: A secondary analysis of the PROMPT study

BACKGROUND

In peritoneal dialysis-related peritonitis (peritonitis), delayed antibiotic therapy is associated with adverse outcomes. Identifying barriers to timely treatment may improve outcomes.

AIM

To determine the impact of radiological investigations on treatment delay and predictors of hospitalisation and length of stay (LOS).

METHODS

Retrospective review of patients with presumed peritonitis in Western Australia.

RESULTS

In 153 episodes of peritonitis, 79 (51.6%) resulted in admission with a median LOS of 3 days (Q1, Q3: 1, 6). In a multivariable model, significant predictors of admission were abnormal exit-site (odds ration (OR) 5.7; 95% confidence interval (CI): 1.4, 23.6; p = 0.02), failure to detect a cloudy bag (OR 11.9; 95%CI: 3.2, 44.7; p < 0.001), female sex (OR 3.3; 95% CI: 1.4, 9.7; p = 0.027), radiological imaging within 24 h (OR 8.8; 95% CI: 2.2, 34.8; p = 0.002) and contact with ambulant care facility (OR 0.32, 95% CI: 0.11, 0.98; p = 0.04). Imaging within 24 h of presentation occurred in 41 (27%) episodes of peritonitis, mostly plain X-rays (91%), of which 83% were clinically irrelevant. Imaging performed within 24 h of presentation increased the median time to antibiotic treatment (2.9 h (Q1, Q3: 1.6, 6.4) vs 2.0 h (Q1, Q3: 1, 3.8; p = 0.046)). Imaging performed prior to administering antibiotics significantly increased the median time to treatment (4.7 h (Q1, Q3: 2.9, 25) vs 1.5 h (Q1, Q3: 0.75, 2.5; p < 0.001)) in those where imaging followed antibiotic treatment.

CONCLUSIONS

Half of all presentations with peritonitis result in hospital admission. Radiological imaging was associated with an increased risk of hospitalisation, potentially contributes to treatment delay, and was mostly clinically unnecessary. When required, imaging should follow antibiotic therapy.

Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells

Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation. This manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/.

ONE SENTENCE SUMMARY

SARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19.

A novel murine model of differentiation-mediated cytomegalovirus reactivation from latently infected bone marrow haematopoietic cells

CD34+ myeloid lineage progenitor cells are an important reservoir of latent human cytomegalovirus (HCMV), and differentiation to macrophages or dendritic cells (DCs) is known to cause reactivation of latent virus. Due to its species-specificity, murine models have been used to study mouse CMV (MCMV) latency and reactivation in vivo. While previous studies have shown that MCMV genomic DNA can be detected in the bone marrow (BM) of latently infected mice, the identity of these cells has not been defined. Therefore, we sought to identify and enrich for cellular sites of MCMV latency in the BM haematopoietic system, and to explore the potential for establishing an in vitro model for reactivation of latent MCMV. We studied the kinetics and cellular characteristics of acute infection and establishment of latency in the BM of mice. We found that while MCMV can infect a broad range of haematopoietic BM cells (BMCs), latent virus is only detectable in haematopoietic stem cells (HSCs), myeloid progenitor cells, monocytes and DC-enriched cell subsets. Using three separate approaches, MCMV reactivation was detected in association with differentiation into DC-enriched BMCs cultured in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 4 (IL-4) followed by lipopolysaccharide (LPS) treatment. In summary, we have defined the kinetics and cellular profile of MCMV infection followed by the natural establishment of latency in vivo in the mouse BM haematopoietic system, including the haematopoietic phenotypes of cells that are permissive to acute infection, establish and harbour detectable latent virus, and can be stimulated to reactivate following DC enrichment and differentiation, followed by treatment with LPS.

FRI0011 DEVELOPMENT OF A HIGH-DIMENSIONAL FLOW CYTOMETRY PANEL TO ANALYSE NATURAL KILLER CELLS IN SLE

Background:

Natural Killer (NK) cells are an innate immune cell type that has somewhat been overlooked in the context of systemic lupus erythematosus (SLE). SLE patients display a reduced number of NK cells with an activated phenotype and increased capacity to produce IFN-γ, decreased antibody-dependent cellular cytotoxicity (ADCC), and altered natural cytotoxicity (1). NK cell activation is determined by the integration of input from a myriad of activating and inhibitory receptors. Previously, using Nanostring® gene expression technologies, we found our SLE cohort showed decreased gene expression of a number of these receptors (KLRC2, KLRC1, KLRB1, KLRF1, KLRG1, PRF1 and IL2RB) leading us to explore NK cells in SLE in more depth.

Objectives:

Our aim was to develop a high-dimensional flow cytometry panel to characterise dysregulation of NK cell in SLE, with particular reference to the activating and inhibitory receptors found to be dysregulated in SLE at the gene expression level.

Methods:

Markers for NK panel were selected to include canonical phenotyping/functional molecules of NK cells with a particular emphasis on receptors found to be lower in our SLE cohort’s gene expression findings. NK panel was designed to minimise spectral overlap, expression and co-expression of markers was taken into consideration. Antibodies were titrated, and voltages optimised to achieve the best separation index for each of the antibodies. The 24-marker panel was run on 52 SLE patients of various disease manifestations, treatments and disease severity. 20 healthy controls were also run for comparison.

Results:

A 24-marker flow cytometry panel including 19 NK cell antigens was optimised, including basic phenotype (CD3/CD56/CD16/NKp46) and NK differentiation markers (CD57/CD94), activating and inhibitory receptors (NKG2A/NKG2C/NKG2D), costimulatory receptors (CD244/CD226), transcription factors (Eomes/Tbet) and effector molecules (granzyme/perforin). Immunophenotypic high-parameter analysis of SLE and control samples is in progress and results will be presented.

Conclusion:

Our development of a high-dimensional immunophenotypic panel allows identification of changes in NK cells in SLE including antigen expression levels, subset percentages and potentially of novel subsets. This panel will be used to investigate NK cell changes with disease course/activity, therapeutic response, and to discover potential drug targets for SLE.

References:

[1]Spada R, Rojas JM, Barber DF. Recent findings on the role of natural killer cells in the pathogenesis of systemic lupus erythematosus. J Leukocyte Biol. 2015;98(4):479-487. doi:10.1189/jlb.4ru0315-081rr

Acknowledgments:

Westmead Institute for Medical Research Genomics Facility

Westmead Institute for Medical Research Flow Cytometry Facility

Staff Specialists’ TESL and Trust Fund Committee

Disclosure of Interests:

None declared

Safety and tolerability of injectable Rilpivirine LA in HPTN 076: A phase 2 HIV pre-exposure prophylaxis study in women

BACKGROUND

Daily oral TDF/FTC is protective against HIV infection when used for pre-exposure prophylaxis (PrEP). However, daily adherence to oral PrEP is difficult for many; therefore, finding alternative PrEP strategies remains a priority. HPTN 076 evaluated the long-acting injectable form of rilpivirine (RPV), known as RPV LA for safety, pharmacokinetics and acceptability.

METHODS

HPTN 076 (NTC 02165202) was a phase 2, double-blind, 2:1 randomized trial comparing the safety of 1200mg RPV LA (LA) to placebo (P). The study included a 28-day oral run-in phase of daily, self- administered oral RPV (25 mg), with directly observed oral dosing about six times. Of 136 enrolled sexually active, HIV-uninfected, low HIV-risk African (100) and US (36) adult women, injectable product was administered in two gluteal, intramuscular (IM) injections once every eight weeks to 122 participants following the oral run-in phase. A maximum of six injection time points occurred over a 48-week period. Acceptability, safety, tolerability and pharmacokinetic (PK) data were collected throughout the study. This paper includes primary endpoint data collected up to the week 52 post enrollment.

FINDINGS

The median age of the enrolled population was 31 years (IQR: 25,38), median weight 75 kg (IQR: 64, 89), median body mass index (BMI) 30 (IQR: 27, 35), 46% married, 94% Black and 60% unemployed. A total of 122 (80 LA, 42 P) women received at least one injection and 98 (64 LA, 34 P) received all six injections. During the injection phase, three women withdrew from the study (2 LA, 1 P) and 16 women discontinued study product (10 LA, 6 P). Fourteen women (11 LA and 3 P) discontinued oral study product and did not enter the injection phase. Study product discontinuations were not significantly different between the two arms throughout. Of the product discontinuations in the injection phase, 8% in LA and 5% in P arm were due to adverse events (AEs), including one randomized to the P arm with prolonged QTc interval on EKG. The proportion of women who experienced Grade 2 or higher AEs during the injection phase as the primary outcome was not significantly different between the two arms [73.8%, 95% CI: (63.2%, 82.1%) for LA and 73.8%, 95% CI: (58.9%, 84.7%), p>0.99]. Transient Grade ≥2 liver abnormalities occurred in 14% of women in the LA arm compared with 12% in P arm. Three LA women (4%) developed Grade 3 injection site reactions compared with none in P arm. In participants who received at least 1 injection, the geometric mean of overall RPV trough concentrations (Ctrough) was 62.2 ng/mL. In participants who received all six injections, the geometric mean of CTrough through the injection phase and after the last injection were 72.8 ng/mL and 100.9 ng/mL, respectively. At week 52 (eight weeks after last injection), the geometric mean of RPV Ctrough was 75.0 ng/mL. At the last injection visit (Week 44), 80 % of women who answered acceptability questions strongly agreed that they would think about using- and 68% that they would definitely use a PrEP injectable in the future.

INTERPRETATION

RPV LA IM injections every eight weeks in African and US women were safe and acceptable. Overall, despite more injection site reactions and pain in the participants receiving RPV LA the injections were well tolerated. Data from this study support the further development of injectable PrEP agents.

Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes

Histone posttranslational modifications (PTMs) are essential for regulating chromatin and maintaining gene expression throughout cell differentiation. Despite the deep level of understanding of immunophenotypic differentiation pathways in hematopoietic cells, few studies have investigated global levels of histone PTMs required for differentiation and maintenance of these distinct cell types. Here, we describe an approach to couple fluorescence-activated cell sorting (FACS) with targeted mass spectrometry to define global "epi-proteomic" signatures for primary leukocytes. FACS was used to sort closely and distantly related leukocytes from normal human peripheral blood for quantitation of histone PTMs with a multiple reaction monitoring LC-MS/MS method measuring histone PTMs on histones H3 and H4. We validate cell sorting directly into H₂SO₄ for immediate histone extraction to decrease time and number of steps after FACS to analyze histone PTMs. Relative histone PTM levels vary in T cells across healthy donors, and the majority of PTMs remain stable up to 2 days following initial blood draw. Large differences in the levels of histone PTMs are observed across the mature lymphoid and myeloid lineages, as well as between different types within the same lineage, though no differences are observed in closely related T cell subtypes. The results show a streamlined approach for quantifying global changes in histone PTMs in cell types separated by FACS that is poised for clinical deployment.

Pharmacokinetics of rifampicin in adult TB patients and healthy volunteers: a systematic review and meta-analysis

Objectives

The objectives of this study were to explore inter-study heterogeneity in the pharmacokinetics (PK) of orally administered rifampicin, to derive summary estimates of rifampicin PK parameters at standard dosages and to compare these with summary estimates for higher dosages.

Methods

A systematic search was performed for studies of rifampicin PK published in the English language up to May 2017. Data describing the C_max and AUC were extracted. Meta-analysis provided summary estimates for PK parameter estimates at standard rifampicin dosages. Heterogeneity was assessed by estimation of the I² statistic and visual inspection of forest plots. Summary AUC estimates at standard and higher dosages were compared graphically and contextualized using preclinical pharmacodynamic (PD) data.

Results

Substantial heterogeneity in PK parameters was evident and upheld in meta-regression. Treatment duration had a significant impact on the summary estimates for rifampicin PK parameters, with C_max 8.98 mg/L (SEM 2.19) after a single dose and 5.79 mg/L (SEM 2.14) at steady-state dosing, and AUC 72.56 mg·h/L (SEM 2.60) and 38.73 mg·h/L (SEM 4.33) after single and steady-state dosing, respectively. Rifampicin dosages of at least 25 mg/kg are required to achieve plasma PK/PD targets defined in preclinical studies.

Conclusions

Vast inter-study heterogeneity exists in rifampicin PK parameter estimates. This is not explained by the available modifying variables. The recommended dosage of rifampicin should be increased to improve efficacy. This study provides an important point of reference for understanding rifampicin PK at standard dosages as efforts to explore higher dosing strategies continue in this field.

Improving the Quality and Reproducibility of Flow Cytometry in the Lung. An Official American Thoracic Society Workshop Report

Defining responses of the structural and immune cells in biologic systems is critically important to understanding disease states and responses to injury. This requires accurate and sensitive methods to define cell types in organ systems. The principal method to delineate the cell populations involved in these processes is flow cytometry. Although researchers increasingly use flow cytometry, technical challenges can affect its accuracy and reproducibility, thus significantly limiting scientific advancements. This challenge is particularly critical to lung immunology, as the lung is readily accessible and therefore used in preclinical and clinical studies to define potential therapeutics. Given the importance of flow cytometry in pulmonary research, the American Thoracic Society convened a working group to highlight issues and technical challenges to the performance of high-quality pulmonary flow cytometry, with a goal of improving its quality and reproducibility.

Diabetes and pre-diabetes among household contacts of tuberculosis patients in India: is it time to screen them all?

SETTING

Pre-diabetes mellitus (pre-DM) and DM increase the risk of developing tuberculosis (TB). Screening contacts of TB patients for pre-DM/DM and linking them to care may mitigate the risk of developing TB and improve DM management.

OBJECTIVE

To measure the prevalence of pre-DM/DM and associated factors among the adult household contacts (HHCs) of pulmonary TB patients.

METHODS

Between August 2014 and May 2017, adult HHCs of newly diagnosed adult PTB patients in Pune and Chennai, India, had single blood samples tested for glycosylated haemoglobin (HbA1c) at enrolment. DM was defined as previously diagnosed, self-reported DM or HbA1c 6.5%, and pre-DM as HbA1c between 5.7% and 6.4%. Latent tuberculous infection (LTBI) was defined as a positive tuberculin skin test (5 mm induration) or QuantiFERON® Gold In-Tube (0.35 international units/ml).

RESULTS

Of 652 adult HHCs, 175 (27%) had pre-DM and 64 (10%) had DM. Forty (64%) HHCs were newly diagnosed with DM and 48 (75%) had poor glycaemic control (HbA1c 7.0%). Sixty-eight (22%) pre-DM cases were aged 18-34 years. Age 35 years, body mass index 25 kg/m2, chronic disease and current tobacco smoking were significantly associated with DM among HHCs.

CONCLUSIONS

Adult HHCs of TB patients in India have a high prevalence of undiagnosed DM, pre-DM and LTBI, putting them at high risk for developing TB. Routine DM screening should be considered among all adult HHCs of TB.

Alcohol intervention strategy among tuberculosis patients: a pilot study from South India

BACKGROUND

Alcohol dependence has been a major cause of treatment non-adherence in tuberculosis (TB) management. There is an urgent need to develop a feasible, acceptable alcohol intervention programme to ensure treatment completion.

METHODOLOGY

Four of the 10 Chennai Corporation zones in Chennai, South India, were randomly selected: two each for the experimental and control arms of the study. TB patients registered from August 2013 to January 2014 with the Revised National Tuberculosis Control Programme were assessed using the Alcohol Use Disorder Identification Test (AUDIT) scale. The intervention consisted of four individual counselling sessions at months 0, 2, 4 and 6 conducted by highly trained interventionists.

RESULTS

Of 872 TB patients, 298 (31%) were found to have alcohol use disorders. The numbers of TB patients in the experimental and control arms were respectively 113 (38%) and 185 (62%). The proportion of patients with favourable treatment outcomes was higher in the intervention than in the control group (87% vs. 62%, P = 0.04). Overall adherence to anti-tuberculosis treatment was significantly higher in the intervention group (P = 0.02).

CONCLUSION

Study findings suggest that alcohol interventions could be effective in ensuring favourable TB treatment outcomes and adherence. This calls for a large cluster randomised trial for greater generalisability. Tested alcohol-intervention strategies should be recommended to promote treatment adherence among TB patients who consume alcohol.

Factors associated with sputum culture conversion in multidrug-resistant pulmonary tuberculosis

INTRODUCTION

Sputum culture conversion in pulmonary multidrug-resistant tuberculosis (MDR-TB) is important to make treatment-related decisions and prevent transmission of disease.

OBJECTIVE

To identify factors associated with sputum culture conversion, and to determine time to culture conversion and the impact of culture conversion on successful treatment outcomes in MDR-/rifampicin (RMP) resistant TB.

METHOD

Retrospective analysis of data from treatment cards and registers of MDR-/RMP-resistant patients initiated on treatment under India's Revised National TB Control Programme in Delhi, West Bengal and Kerala from January 2009 to December 2011. Proportions were calculated and logistic regression analysis was performed.

RESULTS

Of 836 patients, 787 were analysed, 651 (83%) of whom experienced culture conversion: respectively 57%, 73% and 79% culture converted by month 3, 4 and 6 of treatment. The median time to culture conversion was 91.3 days. Patients with body mass index (BMI) 16 kg/m2 (OR 0.403, P = 0.001) and 1618 kg/m2 (OR 0.519, P = 0.039) were less likely to have culture conversion. High rates of culture conversion were observed in patients with successful treatment outcomes compared to those without treatment success (462/469, 99% vs. 183/311, 59%; P 0.0001).

CONCLUSION

Low BMI is associated with poor sputum culture conversion in MDR-/RMP-resistant TB patients. Lack of culture conversion can impact successful treatment outcomes.

Pharmacokinetics of thrice-weekly rifampicin, isoniazid and pyrazinamide in adult tuberculosis patients in India

OBJECTIVE

To study the pharmacokinetics of rifampicin (RMP), isoniazid (INH) and pyrazinamide (PZA) in adult tuberculosis (TB) patients and examine factors that influence drug pharmacokinetics.

METHODS

Adult TB patients (n = 101) receiving thrice-weekly anti-tuberculosis treatment in the Revised National TB Control Programme (RNTCP) were studied. The study was conducted at steady state after directly observed drug administration. RMP, INH and PZA concentrations were estimated using high-performance liquid chromatography and NAT2 genotyping by real-time polymerase chain reaction.

RESULTS

RMP peak concentration (Cmax) was sub-therapeutic (<8 μg/ml) in 88% of the patients. The Cmax of RMP, INH and PZA at 2 h was observed in respectively 83.2%, 97.0% and 92.1% of the patients. The Cmax and area under the curve from 0 to 8 h (AUC0-8) of PZA was lower in TB patients with diabetes mellitus than in non-diabetics. Significant associations were observed between the Cmax and the AUC0-8 of RMP, INH and PZA with drug doses; RMP with category of treatment; INH with smoking, body mass index and N-acetyl transferase 2 genotype; and PZA with sex and smoking.

CONCLUSIONS

Several risk factors for drug concentration variations were identified. Two-hour post-dosing drug concentrations mimicked Cmax. A high proportion of TB patients had RMP Cmax below the expected range, which is a matter of concern.

Treatment outcomes of daily anti-tuberculosis treatment in HIV-infected patients seeking care at a private clinic in India

SETTING

Little is known about outcomes of patients co-infected with human immunodeficiency virus (HIV) and tuberculosis (TB) who are treated in the private sector in India.

OBJECTIVE

To describe the treatment outcomes of daily anti-tuberculosis treatment (ATT) and their determinants among HIV-TB co-infected patients treated at a private clinic in Pune, India.

DESIGN

Data on adult HIV-TB co-infected patients treated with daily ATT were analysed using logistic regression and Cox model to assess risk factors for default and death.

RESULTS

Of 769 cases, 78% were aged <45 years, 71% were males, 64% had CD4 < 200 cells/mm³, 67% were antiretroviral treatment (ART) naïve at TB diagnosis, 53% had extra-pulmonary TB, and 12% had a past history of TB. ATT was successfully completed by 58.5%, 34.3% defaulted (i.e., discontinued ATT for >2 months) and 3.9% died during ATT. The risk of default was higher among males (aOR 1.67, 95%CI 1.17-2.39), ART-naïve patients (aOR 1.91, 95%CI 1.34-2.73) and those with a past history of TB (aOR 1.86, 95%CI 1.15-3.01). Survival probability at 365 days was 95% (95%CI 93-97). The risk of death was higher among patients with CD4 < 50 cells/mm³ (aHR 4.63, 95%CI 1.47-14.65) than in those with CD4 > 200 cells/mm³.

CONCLUSIONS

Low overall mortality was seen with daily ATT in HIV-TB co-infected patients. High default rates in private facilities warrant urgent attention.

Comprehensive T-cell immunophenotyping and next-generation sequencing of human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinomas

The success of programmed cell death 1 (PD-1) inhibition in achieving a clinical response in a subset of head and neck squamous cell carcinoma (HNSCC) patients emphasizes the need to better understand the immunobiology of HNSCC. Immunophenotyping was performed for 30 HCSCC patients [16 human papillomavirus (HPV)-positive; 14 HPV-negative] on matched tissue from the primary tumour site, locally metastatic cervical lymph nodes (LNs), uninvolved local cervical LNs, and peripheral blood. CD4⁺ and CD8⁺ T-cell lymphocytes obtained from tissue were analysed for expression levels of the inhibitory receptors PD-1, TIM-3 and CTLA-4. Next-generation sequencing of the T-cell receptor (TCR) β chain was performed on patients (n = 9) to determine receptor repertoire diversity and for clonality analysis. HPV-negative HNSCC patients, particularly those with stage IV disease, had significantly higher proportions of CD8⁺ T cells expressing CTLA-4 in tumour tissue (P = 0.0013) and in peripheral blood (P = 0.0344) than HPV-positive patients, as well as higher expression levels of TIM-3⁺ PD-1⁺ CD8⁺ T cells (P = 0.0072) than controls. For all patients, PD-1 expression on CD8⁺ T cells - particularly in HPV-negative HNSCC cases - strongly correlated (r = 0.63, P = 0.013) with tumour size at the primary site. The top CD8⁺ TCR clones from tumour tissue significantly overlapped with circulating peripheral blood TCR clones (r = 0.946), and HPV-positive patients had frequently expanded TCR clones that were more hydrophobic - and potentially more immunogenic - than those from HPV-negative patients. Collectively, our findings demonstrate, for the first time, that high-stage HPV-negative HNSCC patients with primary tumours at different sites in the head and neck have elevated peripheral CTLA-4⁺ CD8⁺ T-cell levels, that tumour-familiar CD8⁺ T cells are detectable in peripheral blood from HNSCC patients, and that TCRs from HPV-positive HNSCC patients potentially recognize distinctly immunogenic cognate antigens. However, our findings are preliminary, and need to be further confirmed in a larger patient cohort; also, how these factors affect patient response to immunotherapy needs to be determined. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

TB-HIV co-infection: a catastrophic comradeship

The symbiotic association of tuberculosis (TB) and HIV poses a challenge to human survival. HIV complicates every aspect of TB including presentation, diagnosis and treatment. HIV-TB patients encounter unique problems like drug-drug interactions, cumulative toxicity, immune reconstitution inflammatory syndrome (IRIS), lower plasma drug levels and emergence of drug resistance during treatment despite adherence. TB may also be overdiagnosed in HIV due to a number of diseases that closely resemble TB. Notable among them are non-tuberculous mycobacteria, Pneumocystis Jirovecii and Nocardia. Even though diagnostic procedures have improved over the years, patients in developing countries usually seek health care at later stage of the disease. Research data ascertains the duration of therapy for TB to be 6 months with rifampicin and isoniazid, reinforced with ethambutol and pyrazinamide in the first 2 months. The schedule of therapy is still debatable with daily regimens being preferred in the context of HIV. Many reasons exist for persistence of Mycobacterium Tuberculosis (M.TB) in sputum, or delayed-clearance of TB from sputum smears in HIV, apart from emergence of drug resistance and non-compliance. Acquired rifampicin resistance (ARR) is a unique phenomenon complicating HIV-associated TB when an intermittent regimen of antituberculosis therapy (ATT) is used without timely initiation of highly active antiretroviral therapy (HAART), especially in patients harbouring isoniazid-resistant strains Immune restoration is often incomplete ('swiss cheese' pattern) even with effective HAART if not started early. Immune reconstitution inflammatory syndrome (IRIS) is the paradoxical worsening of the patient's condition often with radiological deterioration, due to an enhanced immune response with HAART. IRIS occurs despite an effective virological suppression and a favourable response to ATT. The incidence of IRIS in HIV has reached up to 54%, requiring utilization of experts and tertiary care which forms an obstacle to the decentralization of patients in the ART programme. Research in HIV-TB immunology and management needs further exploration in order to understand the diseases and offer appropriate treatment. The following paragraphs provide scientific evidences generated through research that could potentially guide management.

Loss to follow-up among children in pre-ART care under the National AIDS Programme, Tamil Nadu, South India

Setting: Children aged <15 years constitute 7% of all people living with the human immunodeficiency virus (HIV) in India. A previous study from an antiretroviral therapy (ART) centre in south India reported 82% loss to follow-up (LTFU) among children in pre-ART care (2006-2011). Objective: To assess the proportion of LTFU within 1 year of registration among HIV-infected children (aged < 15 years) registered in all 43 ART centres in the state of Tamil Nadu, India, during the year 2012. Design: This was a retrospective cohort study involving a review of programme records. Results: Of 656 children registered for HIV care, 20 (3%) were not assessed for ART eligibility. Of those remaining, 226 (36%) were not ART eligible and entered pre-ART care. Among these, at 1 year of registration, 50 (22%) were LTFU, 40 (18%) were transferred out and 136 (60%) were retained in care at the same centre. The child's age, sex, World Health Organization stage or occurrence of opportunistic infection were not associated with LTFU. Conclusion: One in five children registered under pre-ART care were lost to follow-up. Stronger measures to prevent LTFU and reinforce retrieval actions are necessary in the existing National HIV Programme.

Role of bacille Calmette-Guérin in preventing tuberculous infection

SETTING

Rural community in South India.

OBJECTIVE

To determine the role of bacille Calmette-Guérin (BCG) in preventing tuberculous infection in children.

DESIGN

A prevalence survey was undertaken in 1999-2001 in a representative rural population in Tiruvallur District in South India using cluster sampling. Tuberculin testing was performed among all children aged <15 years, and all adults aged 15 years were questioned about chest symptoms and underwent radiography, followed by sputum examinations, if indicated.

RESULTS

In children living in households with a tuberculosis case, the proportion with evidence of tuberculous infection was 35.5% of 200 in the absence of a BCG scar and 27.0% of 100 in its presence, a reduction of 24% (P = 0.14). In very young children (age <5 years), the corresponding proportions were 29.1% of 55 and 11.9% of 42, a reduction of 59%; the difference was statistically significant (P = 0.048).

CONCLUSION

There is a possible role for BCG in preventing tuberculous infection in very young children.

Predictors of unfavourable treatment outcome in patients with multidrug-resistant tuberculosis in India

Setting: India has one of the highest global rates of multidrug-resistant tuberculosis (MDR-TB), which is associated with poor treatment outcomes. A better understanding of the risk factors for unfavourable outcomes is needed. Objectives: To describe 1) the demographic and clinical characteristics of MDR-TB patients registered in three states of India during 2009-2011, 2) treatment outcomes, and 3) factors associated with unfavourable outcomes. Design: A retrospective cohort study involving a record review of registered MDR-TB patients. Results: Of 788 patients, 68% were male, 70% were aged 15-44 years, 90% had failed previous anti-tuberculosis treatment or were retreatment smear-positive, 60% had a body mass index < 18.5 kg/m² and 72% had additional resistance to streptomycin and/or ethambutol. The median time from sputum collection to the start of MDR-TB treatment was 128 days (IQR 103-173). Unfavourable outcomes occurred in 40% of the patients, mostly from death or loss to follow-up. Factors significantly associated with unfavourable outcomes included male sex, age ⩾ 45 years, being underweight and infection with the human immunodeficiency virus. Adverse drug reactions were reported in 24% of patients, with gastrointestinal disturbance, psychiatric morbidity and ototoxicity the most common. Conclusion: Long delays from sputum collection to treatment initiation using conventional methods, along with poor treatment outcomes, suggest the need to scale up rapid diagnostic tests and shorter regimens for MDR-TB.

Physician's advice on quitting smoking in HIV and TB patients in south India: a randomised clinical trial

Setting: National Institute for Research in Tuberculosis, Madurai, India. Objective: To determine the efficacy of physician's advice on quitting smoking compared with standard counselling in patients with tuberculosis (TB) and patients with human immunodeficiency virus (HIV) infection. Design/Methods: This was a clinical trial conducted in Madurai, south India, among 160 male patients (80 with TB and 80 with HIV), randomised and stratified by nicotine dependence (low/high according to the Fagerström scale), who received physician's advice with standard counselling or standard counselling alone for smoking cessation. Abstinence at 1 month was assessed by self-report and carbon monoxide breath analysis. Results: The patients' mean age was 39.4 years (SD 8.5). Overall, 35% of the patients had high nicotine dependence. Most patients (41%) smoked both cigarettes and bidis. In a combined analysis including both the HIV and the TB groups, quit rates were 41% of the 68 patients in the physician group and 35% of the 68 patients in the standard counselling arm. Conclusions: Physician's advice to quit smoking delivered to patients with TB or HIV is feasible and acceptable. Smoking cessation could easily be initiated in TB patients in programme settings. Future studies should assess long-term abstinence rates with a larger sample size to demonstrate the efficacy of physician's advice.

Pancreatic Tuberculosis: A Puzzle for Physicians. A Rare Case and Review of Literature

Pancreatic Tuberculosis is an uncommon form of extra pulmonary tuberculosis that resembles malignancy of pancreas and serve as a diagnostic challenge for physicians. Conservative management with Anti Tuberculosis Therapy (ATT) will suffice for pancreatic tuberculosis whereas a malignancy may require major surgeries which may lead to significant morbidity. Here, we discuss the case of a female patient who presented with abdominal pain and vomiting and is a known case of chronic calcific pancreatitis. Radiological findings were that of malignancy of the pancreas. Enteroscopy showed pus flowing out from the duodenum. Endoscopic Ultrasound (EUS) guided Fine Needle Aspiration Cytology (FNAC) of the pancreas revealed acid fast bacilli. The patient was treated successfully with ATT. Timely diagnosis of this rare form of extra pulmonary tuberculosis can thus help avoid unwanted resections done for presumed malignancy, for which a high index of suspicion is needed.

Treatment of childhood tuberculosis in India

With a quarter of the global burden of tuberculosis (TB) occurring in India, children in this country are at high risk of tuberculous infection and TB disease. India's Revised National Tuberculosis Control Programme provides free diagnosis and treatment for children with TB using quality assured, weight-based individual drug boxes. Guidelines have recently been revised, updating both the diagnostic algorithm and shifting to a daily regimen with World Health Organization recommended dosages using child-friendly, fixed-dose combination pills. Active case finding is practised in households of TB patients as well as among human immunodeficiency virus infected and malnourished children. More attention needs to be paid to the provision of preventive therapy for household contacts aged <6 years as well as to the detection of multidrug-resistant TB among children. Case notification and the use of the Standards of TB Care in India are being strengthened in the private sector.

Tuberculosis mortality in a rural population from South India

BACKGROUND

General mortality rate (GMR) is an essential indicator for assessing the health status of a community. Tuberculosis (TB) mortality is an indicator for the Millennium Development Goal for 2015.

METHODS

This community-based retrospective survey was conducted in 2007-2008 on a sample of 114,605 rural populations living in 56 villages randomly selected from 218 villages in Tiruvallur district, South India, where the DOTS strategy was implemented in 1999. All the permanent residents of the households were registered and information on occurrence of death was recorded. All the deaths were investigated by verbal autopsy (VA) using standardized methods.

RESULTS

A total of 719 deaths were registered. The GMR and tuberculosis mortality rate (TMR) were 648 (95% CI: 568-727) and 39 (95% CI: 25-52) per 100,000 p-yrs, respectively. The GMR increased with age, and was higher in males than females at all ages. The TMR was higher in males than females and the overall male:female ratio was 5:1.

CONCLUSION

TB was the 6th leading cause of death overall and the 2nd leading cause among men in this area. Strategies to reduce TB death should be implemented and the impact should be monitored by repeat VA studies.

General and tuberculosis mortality in two states of India: A population-based survey

BACKGROUND

General and cause-specific mortality data for causes of death are not available for the states of Andhra Pradesh (AP) and Orissa in India.

OBJECTIVES

To estimate general mortality rate (GMR) and the tuberculosis mortality rate (TMR) among the general population in the two states.

METHODS

All permanent residents in households of selected districts of AP and Orissa states were registered in the survey in 2005-2006. A sample size of 380,000 persons was selected from each state. Health workers carried out house-to-house enumeration. Demographic and occurrence of death data were collected. The cause of death was determined using the instrument of verbal autopsy.

RESULTS

The GMR for AP and Orissa was 636 (95% CI: 610-662) and 616 (95% CI: 588-643) per 100,000 person years (p-ys) respectively. The TMR for AP and Orissa was 76 (95% CI: 67-85) and 41 (95% CI: 34-48) per 100,000 p-ys respectively. The difference in TMR between the states was statistically significant (P<0.0001).

CONCLUSION

The GMRs are similar in AP and Orissa states. Tuberculosis accounted for 12% and 7% of deaths in AP and Orissa respectively. Focused strategies are needed to reduce mortality due to tuberculosis.