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.

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.

Temperature and luminosity outputs of endoscopes used in transcanal endoscopic ear surgery: an experimental study.

OBJECTIVE: To establish the relationship between endoscope temperatures and luminosity with a variety of light source types, endoscope ages, endoscope sizes, angles and operative distance in transcanal endoscopic ear surgery. METHODS: Transcanal endoscopic ear surgery was simulated in an operating theatre using 7 mm plastic suction tubing coated in insulating tape. An ATP ET-959 thermometer was used to record temperatures, and a Trotec BF06 lux meter was used to measure luminosity. Luminosity and temperature recordings were taken at 0 mm and 5 mm from the endoscope tip. RESULTS: Thermal energy transfer from operating endoscopes is greatest when: the light intensity is high, there is a light-emitting diode light source and the endoscope is touching the surface. Additionally, larger-diameter endoscopes, angled endoscopes and new endoscopes generated greater heat. CONCLUSION: It is recommended that operative light intensity is maintained at the lowest level possible, and that the surgeon avoids contact between patient tissues and the endoscope tip.

Transcriptomic changes during stage progression of mycosis fungoides.

BACKGROUND: Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma, which in the early patch/plaque stages runs an indolent course. However, ~25% of patients with MF develop skin tumours, a hallmark of progression to the advanced stage, which is associated with high mortality. The mechanisms involved in stage progression are poorly elucidated. OBJECTIVES: We sought to address the hypothesis of MF cell trafficking between skin lesions by comparing transcriptomic profiles of skin samples in different clinical stages of MF. METHODS: We performed whole-transcriptome and whole-exome sequencing of malignant MF cells from skin biopsies obtained by laser-capture microdissection. We compared three types of MF lesions: early-stage plaques (ESP, n = 12) as well as plaques and tumours from patients in late-stage disease [late-stage plaques (LSP, n = 10) and tumours (TMR, n = 15)]. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to determine pathway changes specific for different lesions which were linked to the recurrent somatic mutations overrepresented in MF tumours. RESULTS: The key upregulated pathways during stage progression were those related to cell proliferation and survival (MEK/ERK, Akt-mTOR), T helper cell (Th)2/Th9 signalling [interleukin (IL)4, STAT3, STAT5, STAT6], meiomitosis (CT45A1, CT45A3, STAG3, GTSF1, REC8) and DNA repair (PARP1, MYCN, OGG1). Principal coordinate clustering of the transcriptome revealed extensive gene expression differences between early (ESP) and advanced-stage lesions (LSP and TMR). LSP and TMR showed remarkable similarities at the level of the transcriptome, which we interpreted as evidence of cell percolation between lesions via haematogenous self-seeding. CONCLUSIONS: Stage progression in MF is associated with Th2/Th9 polarization of malignant cells, activation of proliferation, survival, as well as increased genomic instability. Global transcriptomic changes in multiple lesions may be caused by haematogenous cell percolation between discrete skin lesions.

Aortic Valve Replacement and Penicillin Desensitization in a Patient with Abiotrophia defectiva Aortic Valve Endocarditis.

Abiotrophia defectiva is an uncommon and insidious yet destructive cause of infective endocarditis preferentially treated with penicillin/gentamicin and often requiring surgical treatment. A 60-year-old man with penicillin anaphylaxis history presented with fevers and a nonspecific constellation of symptoms. He was ultimately diagnosed with bicuspid aortic valve infective endocarditis based on blood cultures growing A.defectiva and echocardiographic evidence of bicuspid aortic valve, severe valvular regurgitation, and 5 × 7 mm vegetation. Aortic valve replacement and culture yielded penicillin-sensitive A.defectiva. After successful penicillin desensitization, antibiotic therapy was switched from vancomycin/gentamicin to benzylpenicillin. This is the first published case of penicillin desensitization in a patient with A.defectiva-associated infection. Penicillin desensitization, optimal antibiotic therapy, prompt aortic valve replacement, and close collaboration between cardiology and various other specialties were essential in achieving a positive outcome.

Providing more balanced information on the harms and benefits of cervical cancer screening: A randomized survey among US and Norwegian women.

We aimed to identify how additional information about benefits and harms of cervical cancer (CC) screening impacted intention to participate in screening, what type of information on harms women preferred receiving, from whom, and whether it differed between two national healthcare settings. We conducted a survey that randomized screen-eligible women in the United States (n = 1084) and Norway (n = 1060) into four groups according to the timing of introducing additional information. We found that additional information did not significantly impact stated intentions-to-participate in screening or follow-up testing in either country; however, the proportion of Norwegian women stating uncertainty about seeking precancer treatment increased from 7.9% to 14.3% (p = 0.012). Women reported strong system-specific preferences for sources of information: Norwegians (59%) preferred it come from a national public health agency while Americans (59%) preferred it come from a specialist care provider. Regression models revealed having a prior Pap-test was the most important predictor of intentions-to-participate in both countries, while having lower income reduced the probabilities of intentions-to-follow-up and seek precancer treatment among U.S. women. These results suggest that additional information on harms is unlikely to reduce participation in CC screening but could increase decision uncertainty to seek treatment. Providing unbiased information would improve on the ethical principle of respect for autonomy and self-determination. However, the clinical impact of additional information on women's understanding of the trade-offs involved with CC screening should be investigated. Future studies should also consider country-specific socioeconomic barriers to screening if communication re-design initiatives aim to improve CC screening participation.

Reducing potential aerosol generation in flexible nasolaryngoscopy: a novel method.

BACKGROUND: Fibre-optic nasoendoscopy and fibre-optic laryngoscopy are high-risk procedures in the coronavirus disease 2019 era, as they are potential aerosol-generating procedures. Barrier protection remains key to preventing transmission. METHODS: A device was developed that patients can wear to reduce potential aerosol contamination of the surroundings. CONCLUSION: This device is simple, reproducible, easy to use, economical and well-tolerated. Full personal protection equipment should additionally be worn by the operator.

Feasibility of ovine and synthetic temporal bone models for simulation training in endoscopic ear surgery.

OBJECTIVE: Comparing the feasibility of ovine and synthetic temporal bones for simulating endoscopic ear surgery against the 'gold standard' of human cadaveric tissue. METHODS: A total of 10 candidates (5 trainees and 5 experts) performed endoscopic tympanoplasty on 3 models: Pettigrew temporal bones, ovine temporal bones and cadaveric temporal bones. Candidates completed a questionnaire assessing the face validity, global content validity and task-specific content validity of each model. RESULTS: Regarding ovine temporal bone validity, the median values were 4 (interquartile range = 4-4) for face validity, 4 (interquartile range = 4-4) for global content validity and 4 (interquartile range = 4-4) for task-specific content validity. For the Pettigrew temporal bone, the median values were 3.5 (interquartile range = 2.25-4) for face validity, 3 (interquartile range = 2.75-3) for global content validity and 3 (interquartile range = 2.5-3) for task-specific content validity. The ovine temporal bone was considered significantly superior to the Pettigrew temporal bone for the majority of validity categories assessed. CONCLUSION: Tympanoplasty is feasible in both the ovine temporal bone and the Pettigrew temporal bone. However, the ovine model was a significantly more realistic simulation tool.

Toward personalized dose-prescription in locally advanced non-small cell lung cancer: Validation of published normal tissue complication probability models.

PURPOSE: To identify published normal tissue complication probability (NTCP) models suitable for patient-specific dose-prescription in locally advanced non-small cell lung cancer (LA-NSCLC) through in-house validation. MATERIAL AND METHODS: From eight previously published candidate NTCP models (≥grade 2 acute esophagitis and radiation pneumonitis; AE2, RP2), patient-specific dose-responses were calculated using model variables and fractionation-corrected doses for 241 LA-NSCLC patients treated with chemo-IMRT to 50-80 Gy@1.8-2.0 Gy between 2004 and 2014 (AE2/RP2 rate: 50%/12%). A model was judged final if it significantly predicted AE2 or RP2 (p ≤ 0.05), was discriminative and well calibrated (AUC > 0.60; Hosmer-Lemeshow test pHL > 0.05), which were assessed as the median over 1000 bootstrap samples. RESULTS: Models for AE2 had superior discrimination to RP2 models (AUC = 0.63-0.65 vs. 0.51-0.65). The final AE2 model included mean esophageal dose and concurrent chemotherapy (AUC = 0.65; p < 0.0001). The final RP2 model was a slightly adjusted version of the RP2 model with the best discrimination, and included age, mean lung dose, and pulmonary comorbidity (AUC = 0.73; p < 0.0001). CONCLUSION: Of the eight investigated and published NTCP models, one model successfully described AE2 and one slightly adjusted model successfully described RP2 in the independent cohort. Estimates from these two NTCP models will, therefore, be considered internally when prescribing patient-specific doses in LA-NSCLC patients.

Preliminary outcomes of endoscopic middle-ear surgery in 103 cases: a UK experience.

BACKGROUND: Totally endoscopic ear surgery and endoscope-assisted microsurgery are still new concepts, with relatively few centres in the UK performing them. Advantages include better visualisation of difficult to reach areas, such as the sinus tympani, and limited external incisions. This paper reports our short-term outcomes for endoscopic middle-ear surgery. METHODS: A prospective review was conducted of the first 103 consecutive patients undergoing totally endoscopic ear surgery or endoscope-assisted microsurgery in 1 centre performed by 1 operator. The outcomes assessed were: tympanic membrane healing, audiological data and complications. RESULTS: Twenty-five patients underwent endoscope-assisted microsurgery, while 78 had totally endoscopic ear surgery. There were no reported cases of dead ear or permanent facial nerve palsy. The average air-bone gap following stapedectomy was 7.38 dB. The tympanic membrane healing rate was 89 per cent. CONCLUSION: Our results confirm that endoscopic middle-ear surgery is safe, and the short-term outcomes are comparable with conventional surgery.

The effect of light intensity on image quality in endoscopic ear surgery.

OBJECTIVES: Endoscopic ear surgery is a rapidly developing field with many advantages. But endoscopes can reach temperatures of over 110°C at the tip, raising safety concerns. Reducing the intensity of the light source reduces temperatures produced. However, quality of images at lower light intensities has not yet been studied. We set out to study the effect of light intensity on image quality in EES. DESIGN: Prospective study of patients undergoing EES from April to October 2016. Consecutive images of the same operative field at 10%, 30%, 50% and 100% light intensities were taken. Eight international experts were asked to each evaluate 100 anonymised, randomised images. SETTING: District General Hospital. PARTICIPANTS: Twenty patients. MAIN OUTCOME MEASURES: Images were evaluated on a 5-point Likert scale (1 = significantly worse than average; 5 = significantly better than average) for detail of anatomy; colour contrast; overall quality; and suitability for operating. RESULTS: Mean scores for photographs at 10%, 30%, 50% and 100% light intensity were 3.22 (SD 0.93), 3.15 (SD 0.84), 3.08 (SD 0.88) and 3.10 (SD 0.86), respectively. In ANOVA models for the scores on each of the scales (anatomy, colour contrast, overall quality and suitability for operating), the effects of rater and patient were highly significant (P < .0005) but light intensity was non-significant (P = .34, .32, .21, .15, respectively). CONCLUSION: Images taken during surgery by our endoscope and operative camera have no loss of quality when taken at lower light intensities. We recommend the surgeon considers use of lower light intensities in endoscopic ear surgery.

The physiological phosphorylation of tau is critically changed in fetal brains of individuals with Down syndrome.

AIMS: Down syndrome (DS) is a common cause of mental retardation accompanied by cognitive impairment. Comprehensive studies suggested a link between development and ageing, as nearly all individuals with DS develop Alzheimer disease (AD)-like pathology. However, there is still a paucity of data on tau in early DS to support this notion. METHODS: Using morphometric immunohistochemistry we compared tau phosphorylation in normal brains and in brains of individuals with DS from early development until early postnatal life. RESULTS: We observed in DS a critical loss of physiological phosphorylation of tau. Rhombencephalic structures showed prominent differences between controls and DS using antibodies AT8 (Ser-202/Thr-205) and AT180 (Thr-231). In contrast, in the subiculum only a small portion of controls deviated from DS using antibodies AT100 (Thr-212/Ser-214) and AT270 (Thr-181). With exception of the subiculum, phosphorylation-independent tau did not differ between groups, as confirmed by immunostaining for the HT-7 antibody (epitope between 159 and 163 of the human tau) as well. DISCUSSION: Our observations suggest functional tau disturbance in DS brains during development, rather than axonal loss. This supports the role of tau as a further important player in the pathophysiology of cognitive impairment in DS and related AD.

Developmental Expression and Dysregulation of miR-146a and miR-155 in Down's Syndrome and Mouse Models of Down's Syndrome and Alzheimer's Disease.

BACKGROUND: miR-146a and miR-155 are key regulators of the innate immune response. We hypothesized that an inflammation-mediated dysregulation of these miRNAs may occur in patients with Down syndrome (DS) and Alzheimer's disease (AD). METHODS: The miRNA expression patterns were investigated by in situ hybridization in developing hippocampus from controls, patients with DS and in adults with AD pathology (DS and sporadic AD; sAD). Quantitative real-time PCR was employed to evaluate the miRNA levels in the hippocampus of sAD and in mouse models of DS and AD. Both miRNAs were expressed in prenatal human hippocampus. In DS we detected increased miR-146a expression in reactive astrocytes. Increased expression of miR-146a was found in the hippocampus of sAD and negatively correlated with its target IRAK-1. APP/PS1 mice showed a significant increase in the expression of both miRNAs at 11-13 months of age as compared to WT and mice at 3 months. A negative correlation between miR-146a levels and its target TRAF6 was observed in both Ts65Dn and APP/PS1 mice. CONCLUSION: These findings suggest a possible involvement of miR-146a and miR-155 in brain development and neurodegeneration. In particular, we provide evidence of a dysregulation of these two immunomodulatory miRNAs in AD with a potential therapeutical implication, deserving further investigation.

Successful Comparison of US Food and Drug Administration Sentinel Analysis Tools to Traditional Approaches in Quantifying a Known Drug-Adverse Event Association.

The US Food and Drug Administration's Sentinel system has developed the capability to conduct active safety surveillance of marketed medical products in a large network of electronic healthcare databases. We assessed the extent to which the newly developed, semiautomated Sentinel Propensity Score Matching (PSM) tool could produce the same results as a customized protocol-driven assessment, which found an adjusted hazard ratio (HR) of 3.04 (95% confidence interval [CI], 2.81-3.27) comparing angioedema in patients initiating angiotensin-converting enzyme (ACE) inhibitors vs. beta-blockers. Using data from 13 Data Partners between 1 January 2008, and 30 September 2013, the PSM tool identified 2,211,215 eligible ACE inhibitor and 1,673,682 eligible beta-blocker initiators. The tool produced an HR of 3.14 (95% CI, 2.86-3.44). This comparison provides initial evidence that Sentinel analytic tools can produce findings similar to those produced by a highly customized protocol-driven assessment.

Promoter-Specific Hypomethylation Correlates with IL-1ß Overexpression in Tuberous Sclerosis Complex (TSC).

In tuberous sclerosis complex (TSC), overexpression of numerous genes associated with inflammation has been observed. Among different proinflammatory cytokines, interleukin-1ß (IL-1ß) has been shown to be significantly involved in epileptogenesis and maintenance of seizures. Recent evidence indicates that IL-1ß gene expression can be regulated by DNA methylation of its promoter. In the present study, we hypothesized that hypomethylation in the promoter region of the IL-1ß gene may underlie its overexpression observed in TSC brain tissue. Bisulfite sequencing was used to study the methylation status of the promoter region of the IL-1ß gene in TSC and control samples. We identified hypomethylation in the promoter region of the IL-1ß gene in TSC samples. IL-1ß is overexpressed in tubers, and gene expression is correlated with promoter hypomethylation at CpG and non-CpG sites. Our results provide the first evidence of epigenetic modulation of the IL-1ß signaling in TSC. Thus, strategies that target epigenetic alterations could offer new therapeutic avenues to control the persistent activation of interleukin-1ß-mediated inflammatory signaling in TSC brain.

Acquired torticollis due to primary pyomyositis of the paraspinal muscles in an 11-year-old boy.

Torticollis is characterised by tilting and rotation of the cervical spine in opposite directions. Causes can be congenital or acquired. Primary pyomyositis is a rare subacute deep bacterial infection of skeletal muscles that typically affects individuals under 20 years of age from tropical countries. Infrequently, pyomyositis occurs in individuals from temperate regions, usually in immunocompromised adults, and this is defined as secondary pyomyositis. We report a case of acquired torticollis due to primary pyomyositis of the paraspinal muscles in a previously healthy boy from the UK. A prolonged course of antibiotics and physiotherapy led to a complete resolution of his illness. We review how to differentiate pyomyositis from focal myositis, a more common inflammatory muscular cause of acquired torticollis.

Expression of microRNAs miR21, miR146a, and miR155 in tuberous sclerosis complex cortical tubers and their regulation in human astrocytes and SEGA-derived cell cultures.

Tuberous sclerosis complex (TSC) is a genetic disease presenting with multiple neurological symptoms including epilepsy, mental retardation, and autism. Abnormal activation of various inflammatory pathways has been observed in astrocytes in brain lesions associated with TSC. Increasing evidence supports the involvement of microRNAs in the regulation of astrocyte-mediated inflammatory response. To study the role of inflammation-related microRNAs in TSC, we employed real-time PCR and in situ hybridization to characterize the expression of miR21, miR146a, and miR155 in TSC lesions (cortical tubers and subependymal giant cell astrocytomas, SEGAs). We observed an increased expression of miR21, miR146a, and miR155 in TSC tubers compared with control and perituberal brain tissue. Expression was localized in dysmorphic neurons, giant cells, and reactive astrocytes and positively correlated with IL-1ß expression. In addition, cultured human astrocytes and SEGA-derived cell cultures were used to study the regulation of the expression of these miRNAs in response to the proinflammatory cytokine IL-1ß and to evaluate the effects of overexpression or knockdown of miR21, miR146a, and miR155 on inflammatory signaling. IL-1ß stimulation of cultured glial cells strongly induced intracellular miR21, miR146a, and miR155 expression, as well as miR146a extracellular release. IL-1ß signaling was differentially modulated by overexpression of miR155 or miR146a, which resulted in pro- or anti-inflammatory effects, respectively. This study provides supportive evidence that inflammation-related microRNAs play a role in TSC. In particular, miR146a and miR155 appear to be key players in the regulation of astrocyte-mediated inflammatory response, with miR146a as most interesting anti-inflammatory therapeutic candidate.

Role of apoptosis-related miRNAs in resveratrol-induced breast cancer cell death.

Breast cancer is the most frequently diagnosed cancer in women, and one of the leading causes of cancer-related deaths worldwide. Recent evidences indicate that dietary agents such as resveratrol may inhibit cancer progression through modulation of microRNAs (miRNAs). We demonstrate that resveratrol regulates apoptotic and cell cycle machinery in breast cancer cells by modulating key tumor-suppressive miRNAs including miR-125b-5p, miR-200c-3p, miR-409-3p, miR-122-5p and miR-542-3p. Resveratrol-mediated miRNA modulation regulates key anti-apoptotic and cell cycle proteins including Bcl-2, X-linked inhibitor of apoptosis protein and CDKs, which are critical for its activity. Modulating miRNAs with mimics or inhibitors further validated a key role for miR-542-3p in MCF-7 and miR-122-5p in MDA-MB-231 breast cancer cell death in response to resveratrol. In conclusion, this study reveals novel miRNAs modulated by resveratrol that have a key role in breast cancer cell death.