ABSTRACT
HDAC3 inhibition has been shown to improve memory and reduce amyloid-ß (Aß) in Alzheimer's disease (AD) models, but the underlying mechanisms are unclear. We investigated the molecular effects of HDAC3 inhibition on AD pathology, using in vitro and ex vivo models of AD, based on our finding that HDAC3 expression is increased in AD brains. For this purpose, N2a mouse neuroblastoma cells as well as organotypic brain cultures (OBCSs) of 5XFAD and wild-type mice were incubated with various concentrations of the HDAC3 selective inhibitor RGFP966 (0.1-10 µM) for 24 h. Treatment with RGFP966 or HDAC3 knockdown in N2a cells was associated with an increase on amyloid precursor protein (APP) and mRNA expressions, without alterations in Aß42 secretion. In vitro chromatin immunoprecipitation analysis revealed enriched HDAC3 binding at APP promoter regions. The increase in APP expression was also detected in OBCSs from 5XFAD mice incubated with 1 µM RGFP966, without changes in Aß. In addition, HDAC3 inhibition resulted in a reduction of activated Iba-1-positive microglia and astrocytes in 5XFAD slices, which was not observed in OBCSs from wild-type mice. mRNA sequencing analysis revealed that HDAC3 inhibition modulated neuronal regenerative pathways related to neurogenesis, differentiation, axonogenesis, and dendritic spine density in OBCSs. Our findings highlight the complexity and diversity of the effects of HDAC3 inhibition on AD models and suggest that HDAC3 may have multiple roles in the regulation of APP expression and processing, as well as in the modulation of neuroinflammatory and neuroprotective genes.
Subject(s)
Alzheimer Disease , Amyloid beta-Protein Precursor , Histone Deacetylases , Animals , Mice , Acrylamides , Alzheimer Disease/metabolism , Alzheimer Disease/genetics , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Amyloid beta-Protein Precursor/metabolism , Amyloid beta-Protein Precursor/genetics , Brain/metabolism , Brain/pathology , Cell Line, Tumor , Disease Models, Animal , Histone Deacetylase Inhibitors/pharmacology , Histone Deacetylases/metabolism , Histone Deacetylases/genetics , Mice, Inbred C57BL , Mice, Transgenic , Microglia/metabolism , Phenylenediamines/pharmacologyABSTRACT
The recent proliferation of point-of-care ultrasonography (POCUS) in the clinical practice of many medical specialties has exposed persistent barriers to education, training and standardisation. Specialist training curriculums are already overwhelming, having grossly insufficient time available for the specialist trainees and for the small number of available trainers alike to incorporate POCUS into postgraduate education. The logical solution to overcome these barriers could be to incorporate basic POCUS education and training into the undergraduate university curriculums, introducing longitudinal integration with other relevant medical sciences. The Australasian Society of Ultrasound in Medicine already has well-established educational programmes in POCUS with standardised assessment of competency, which could potentially offer the basis for symbiosis with the Australian and New Zealand medical schools.
ABSTRACT
BACKGROUND: In 2015, the UK government established the Fleming Fund with the aim to address critical gaps in surveillance of antimicrobial resistance (AMR) in low- and middle-income countries in Asia and Africa. Among a large portfolio of grants, the Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project was awarded with the specific objective of expanding the volume of historical data on AMR, consumption (AMC), and use (AMU) in the human healthcare sector across 12 countries in South and Southeast Asia. METHODS: Starting in early 2019, the CAPTURA consortium began working with local governments and >100 relevant data-holding facilities across the region to identify, assess for quality, prioritize, and subsequently retrieve data on AMR, AMC, and AMU. Relevant and shared data were collated and analyzed to provide local overviews for national stakeholders as well as regional context, wherever possible. RESULTS: From the vast information resource generated on current surveillance capacity and data availability, the project has highlighted gaps and areas for quality improvement and supported comprehensive capacity-building activities to optimize local data-collection and -management practices. CONCLUSIONS: The project has paved the way for expansion of surveillance networks to include both the academic and private sector in several countries and has actively engaged in discussions to promote data sharing at the local, national, and regional levels. This paper describes the overarching approach to, and emerging lessons from, the CAPTURA project, and how it contributes to other ongoing efforts to strengthen national AMR surveillance in the region and globally.
Subject(s)
Anti-Bacterial Agents , Awards and Prizes , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Drug Resistance, Bacterial , Asia/epidemiology , Africa/epidemiologyABSTRACT
Antimicrobial resistance (AMR) is a multifaceted global health problem disproportionately affecting low- and middle-income countries (LMICs). The Capturing data on Antimicrobial resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project was tasked to expand the volume of AMR and antimicrobial use data in Asia. The CAPTURA project used 2 data-collection streams: facility data and project metadata. Project metadata constituted information collected to map out data sources and assess data quality, while facility data referred to the retrospective data collected from healthcare facilities. A down-selection process, labelled "the funnel approach" by the project, was adopted to use the project metadata in prioritizing and selecting laboratories for retrospective AMR data collection. Moreover, the metadata served as a guide for understanding the AMR data once they were collected. The findings from CAPTURA's metadata add to the current discourse on the limitation of AMR data in LMICs. There is generally a low volume of AMR data generated as there is a lack of microbiology laboratories with sufficient antimicrobial susceptibility testing capacity. Many laboratories in Asia are still capturing data on paper, resulting in scattered or unused data not readily accessible or shareable for analyses. There is also a lack of clinical and epidemiological data captured, impeding interpretation and in-depth understanding of the AMR data. CAPTURA's experience in Asia suggests that there is a wide spectrum of capacity and capability of microbiology laboratories within a country and region. As local AMR surveillance is a crucial instrument to inform context-specific measures to combat AMR, it is important to understand and assess current capacity-building needs while implementing activities to enhance surveillance systems.
Subject(s)
Anti-Bacterial Agents , Developing Countries , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Retrospective Studies , Drug Resistance, Bacterial , Asia/epidemiologyABSTRACT
Hodgkin lymphoma (HL) treatment increases the risk of lung cancer. Most HL survivors are not eligible for lung cancer screening (LCS) programmes developed for the general population, and the utility of these programmes has not been tested in HL survivors. We ran a LCS pilot in HL survivors to describe screening uptake, participant characteristics, impact of a decision aid and screen findings. HL survivors treated ≥5 years ago with mustine/procarbazine and/or thoracic radiation, were identified from a follow-up database and invited to participate. Participants underwent a low-dose CT (LDCT) reported using protocols validated for the general population. Two hundred and eighteen individuals were invited, 123 were eligible, 102 were screened (58% response rate): 58% female, median age 52 years, median 22 years since HL treatment. 91.4% were deemed to have made an informed decision; participation was not influenced by age, gender, years since treatment or deprivation. Only 3/35 ever-smokers met criteria for LCS through the programme aimed at the general population. Baseline LDCT results were: 90 (88.2%) negative, 10 (9.8%) indeterminate, 2 (2.0%) positive. Two 3-month surveillance scans were positive. Of 4 positive scans, 2 patients were diagnosed with small-cell lung cancer; 1 underwent curative surgery. Coronary artery calcification was detected in 36.3%, and clinically significant incidental findings in 2.9%. LDCT protocols validated in ever-smokers can detect asymptomatic early-stage lung cancers in HL survivors. This finding, together with screening uptake and low false positive rates, supports further research to implement LCS for HL survivors.
ABSTRACT
The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
Subject(s)
Rhodopsin , Vibration , Motion , Hydrogen BondingABSTRACT
Volatile anesthetic agents are increasingly widely used for critical care sedation. There are concerns that sevoflurane presents a risk of renal injury when used in this role. RCTs comparing the use of critical care sevoflurane sedation with any control in humans were systematically identified using MEDLINE, Cochrane CENTRAL, web of Science, and CINAHL (until May 2022), if they presented comparative data on renal function or serum inorganic fluoride levels. Pooled SMDs (95% CI) were calculated where possible after assessment of quality with GRADE and risk of bias with ROB-2. Eight studies analyzing 793 patients were included. The median duration of use of critical care sevoflurane sedation was 4.8 [IQR 3.5-9.2] hours; however, most trials also included a period of prior intraoperative use. No significant difference was found in serum creatinine at 1 day (SMD 0.05, 95% CI - 0.12 to 0.21), 48 h (SMD = - 0.04; 95% Cl - 0.25 to 0.17), 72 h (SMD = - 0.15; 95% CI - 0.45 to 0.15), and at discharge (SMD = - 0.1; 95% CI - 0.3 to 0.13) between the sevoflurane group and the control groups. Creatinine clearance was measured in two studies at 48 h with no significant difference (SMD = - 0.13; 95% Cl - 0.38 to 0.11). Levels of serum inorganic fluoride were significantly elevated in patients where sevoflurane was used. Sevoflurane was not associated with renal failure when used for critical care sedation of fewer than 72-h duration, despite the elevation of serum fluoride. Longer-term studies are currently inadequate, including in patients with compromised renal function, to further evaluate the role of sevoflurane in this setting.Trial registration PROSPERO (CRD42022333099).
Subject(s)
Anesthetics , Fluorides , Humans , Sevoflurane/adverse effects , Kidney/physiology , Critical CareABSTRACT
STUDY OBJECTIVES: Narcolepsy is associated with cardiovascular risk factors; however, the risk of new-onset cardiovascular events in this population is unknown. This real-world study evaluated the excess risk of new-onset cardiovascular events in U.S. adults with narcolepsy. METHODS: A retrospective cohort study using IBM MarketScan administrative claims data (2014-2019) was conducted. A narcolepsy cohort, comprising adults (≥18 years) with at least two outpatient claims containing a narcolepsy diagnosis, of which at least one was non-diagnostic, was matched to a non-narcolepsy control cohort (1:3) based on cohort entry date, age, sex, geographic region, and insurance type. The relative risk of new-onset cardiovascular events was estimated using a multivariable Cox proportional hazards model to compute adjusted hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS: The narcolepsy and matched non-narcolepsy control cohorts included 12 816 and 38 441 individuals, respectively. At baseline, cohort demographics were generally similar; however, patients with narcolepsy had more comorbidities. In adjusted analyses, the risk of new-onset cardiovascular events was higher in the narcolepsy cohort compared with the control cohort: any stroke (HR [95% CI], 1.71 [1.24, 2.34]); heart failure (1.35 [1.03, 1.76]); ischemic stroke (1.67 [1.19, 2.34]); major adverse cardiac event (1.45 [1.20, 1.74]); grouped instances of stroke, atrial fibrillation, or edema (1.48 [1.25, 1.74]); and cardiovascular disease (1.30 [1.08, 1.56]). CONCLUSION: Individuals with narcolepsy are at increased risk of new-onset cardiovascular events compared with individuals without narcolepsy. Physicians should consider cardiovascular risk in patients with narcolepsy when weighing treatment options.
ABSTRACT
BACKGROUND: Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS: We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS: Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS: Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
Subject(s)
Klebsiella Infections , Klebsiella , Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Genome, Bacterial , Genomics , Humans , Klebsiella/genetics , Klebsiella Infections/epidemiology , Klebsiella pneumoniae , Phylogeny , Retrospective Studies , beta-Lactamases/geneticsABSTRACT
The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic's transmission lineages.
ABSTRACT
In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.
Subject(s)
Cloud Computing , Genomics/organization & administration , SARS-CoV-2/genetics , COVID-19/epidemiology , Epidemiological Monitoring , Genome, Viral , Humans , Sequence Analysis, DNA , United Kingdom , User-Computer Interface , Whole Genome SequencingABSTRACT
Wetland ecosystems are critical to the regulation of the global carbon cycle, and there is a high demand for data to improve carbon sequestration and emission models and predictions. Decomposition of plant litter is an important component of ecosystem carbon cycling, yet a lack of knowledge on decay rates in wetlands is an impediment to predicting carbon preservation. Here, we aim to fill this knowledge gap by quantifying the decomposition of standardised green and rooibos tea litter over one year within freshwater and coastal wetland soils across four climates in Australia. We also captured changes in the prokaryotic members of the tea-associated microbiome during this process. Ecosystem type drove differences in tea decay rates and prokaryotic microbiome community composition. Decomposition rates were up to 2-fold higher in mangrove and seagrass soils compared to freshwater wetlands and tidal marshes, in part due to greater leaching-related mass loss. For tidal marshes and freshwater wetlands, the warmer climates had 7-16% less mass remaining compared to temperate climates after a year of decomposition. The prokaryotic microbiome community composition was significantly different between substrate types and sampling times within and across ecosystem types. Microbial indicator analyses suggested putative metabolic pathways common across ecosystems were used to breakdown the tea litter, including increased presence of putative methylotrophs and sulphur oxidisers linked to the introduction of oxygen by root in-growth over the incubation period. Structural equation modelling analyses further highlighted the importance of incubation time on tea decomposition and prokaryotic microbiome community succession, particularly for rooibos tea that experienced a greater proportion of mass loss between three and twelve months compared to green tea. These results provide insights into ecosystem-level attributes that affect both the abiotic and biotic controls of belowground wetland carbon turnover at a continental scale, while also highlighting new decay dynamics for tea litter decomposing under longer incubations.
Subject(s)
Microbiota , Wetlands , Australia , Carbon , Ecosystem , Fresh Water , Soil , TeaABSTRACT
STUDY DESIGN: An in-vitro biomechanical study of human cadaver sacroiliac joints. OBJECTIVE: Our study aimed to develop a more comprehensive understanding of the native motion of the SIJ within the context of spinal kinematics and spinal implant evaluation. SUMMARY OF BACKGROUND DATA: Increasing attention has been given to the sacroiliac joint (SIJ) as a source of low back pain, despite its limited range of motion. We sought to characterize the rotational and translational motion in each axis utilizing standard pure moment flexion-extension (FE), lateral bending (LB), and axial rotation (AR) testing. METHODS: Sixteen sacroiliac joints were evaluated from eight lumbosacral cadaver specimens (six females, two males) from subjects aged 28 to 57 years (mean age 46.8) with body mass index (BMI) 22 to 36 (mean BMI 30). Single leg stance was modeled by clamping the blocks on one ischium in a vise and letting the contralateral ischium hang freely. Pure moment loading was applied in FE, right/left AR, and right/left LB. Relative motions were collected with infrared markers. RESULTS: The on-axis ratio was significantly lower in LB than in FE (Pâ=â0.012) and in AR (Pâ=â0.017). The rotation deviation angle measured 13.9â±â9.1° in FE, 17.1â±â8.7° in AR, and 35.7â±â25.7° in LB. In LB the rotational deviation angle is significantly higher than both FE and AR (Pâ=â0.003 and Pâ=â0.011, respectively). In-plane translation was significantly higher (Pâ=â0.005) in FE loading than in LB loading. CONCLUSION: A nontrivial amount of rotation and translation occurred out of the expected axis of motion. The largest amount of off-axis rotation was observed in lateral bending. Relative to resultant translation, in-plane translation was lowest in lateral bending. Our results indicate that rotation of the SIJ is not fully described with the in-plane metrics which are normally reported in evaluation of fusion devices. Future studies of the SIJ may need to consider including off-axis rotation measurements when describing SIJ kinematics.Level of Evidence: 5.
Subject(s)
Biomechanical Phenomena/physiology , Range of Motion, Articular/physiology , Rotation , Sacroiliac Joint/physiology , Adult , Cadaver , Female , Humans , Low Back Pain/pathology , Low Back Pain/physiopathology , Male , Middle Aged , Prostheses and Implants , Sacroiliac Joint/pathologyABSTRACT
The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10â% of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.
Subject(s)
Horse Diseases/microbiology , Horse Diseases/transmission , Streptococcal Infections/veterinary , Streptococcus equi/isolation & purification , Animals , Female , Genome, Bacterial , Horses , Male , Phylogeny , Streptococcal Infections/microbiology , Streptococcal Infections/transmission , Streptococcus equi/classification , Streptococcus equi/genetics , Streptococcus equi/physiologyABSTRACT
The twin forces of privacy law and data breaches have fundamentally challenged how we collect, store, and share sensitive information. Within this landscape, healthcare information is sacrosanct - and intimately tied to identity and data ownership. Building on prior work with UCLA Health, Genentech (a member of the Roche Group), Sanofi, Amgen, Biogen, and others, we offer this opinion piece to promote the development of a standard for decentralized Verifiable Credentials (VCs). This will empower Authorized Trading Partners (ATPs) in the pharmaceutical supply chain to trade and exchange information in compliance with the US federal law. Starting with credentialing and interoperability for the ATP community, our ultimate goal was to chart a path to a global standard for all health care VCs - providing individuals and health-care professionals control over their own data. By sharing our results and releasing essential components of the work to the public domain, we hope to align and connect with other foundational efforts, thus evolving standards within a truly open framework with broad stakeholder involvement.
ABSTRACT
Summary: In 2013, the Drug Supply Chain Security Act (DSCSA) was signed into law to address the growing threat of counterfeit drugs and to ensure prescription drugs remain safe and effective for patients. As part of this law, US pharmaceutical supply chain stakeholders are required to confirm the authorized status of trading partners for transactions and information disclosures, even when there is no prior business relationship. While larger Authorized Trading Partners (ATPs) have connectivity solutions in place, newer and smaller ATPs have not traditionally participated, including tens of thousands of dispensers. To unlock the full potential of the interoperable system mandated by the DSCSA, the authors tested eXtended ATP (XATP), a blockchain-backed framework for ATP authentication and enhanced verification in a real-world pharmacy with genuine drug packages. The objective of this research study was to prove that electronic authentication and enhanced verification can be achieved between ATPs using a mobile-based solution. Moreover, we tested accurate reading of drug and associated electronic med guides, flagging of expired and recalled drugs, and correct generation of documentation to support saleable returns. Methods: This study involved two dispensers and three participating manufacturers. Dispensers were onboarded to a mobile application and used supporting documentation to authenticate their identities, and then scanned 2D drug barcodes to submit drug verification requests to manufacturers (including 11 additional, randomly selected manufacturers). Genuine and synthetic drug package barcodes were used to test workflows against genuine and synthetic manufacturer serialization data records. Manufacturers authenticated the identity of requesting dispensers with verifiable credentials and responded to verification requests. Results: Enhanced drug verification was achieved, with 100% of requests successfully delivered to participating manufacturers and 88% of requests being delivered to other manufacturers (based on the pharmacist selection of random packages from the pharmacy). Drug verification matching against synthetic serialization data records resulted in 86% accuracy, with the 14% error rate attributed to human factors. All barcodes were successfully scanned and provided package-accurate data, and 97% of randomly selected packages successfully generated drug package inserts. All synthetic recalls and expired drugs were successfully flagged. Four of the manufacturers contacted were among the top 15 pharmaceutical manufacturers globally; all four responded. Conclusions: The XATP framework provides a secure, reliable, and seamless remote method to conduct enhanced verification as required by law. Interoperability between manufacturers and dispensers with no prior business relationship can be achieved on 'day zero' using mobile devices that enable digital authentication and rapid barcode scanning. As users retain control of their own private keys, the framework also mitigates the single-point-of-attack risks associated with centrally managed systems.
ABSTRACT
INTRODUCTION: Low-dose CT (LDCT) screening of high-risk smokers reduces lung cancer (LC) specific mortality. Determining screening eligibility using individualised risk may improve screening effectiveness and reduce harm. Here, we compare the performance of two risk prediction models (PLCOM2012 and Liverpool Lung Project model (LLPv2)) and National Lung Screening Trial (NLST) eligibility criteria in a community-based screening programme. METHODS: Ever-smokers aged 55-74, from deprived areas of Manchester, were invited to a Lung Health Check (LHC). Individuals at higher risk (PLCOM2012 score ≥1.51%) were offered annual LDCT screening over two rounds. LLPv2 score was calculated but not used for screening selection; ≥2.5% and ≥5% thresholds were used for analysis. RESULTS: PLCOM2012 ≥1.51% selected 56% (n=1429) of LHC attendees for screening. LLPv2 ≥2.5% also selected 56% (n=1430) whereas NLST (47%, n=1188) and LLPv2 ≥5% (33%, n=826) selected fewer. Over two screening rounds 62 individuals were diagnosed with LC; representing 87% (n=62/71) of 6-year incidence predicted by mean PLCOM2012 score (5.0%). 26% (n=16/62) of individuals with LC were not eligible for screening using LLPv2 ≥5%, 18% (n=11/62) with NLST criteria and 7% (n=5/62) with LLPv2 ≥2.5%. NLST eligible Manchester attendees had 2.5 times the LC detection rate than NLST participants after two annual screens (≈4.3% (n=51/1188) vs 1.7% (n=438/26 309); p<0.0001). Adverse measures of health, including airflow obstruction, respiratory symptoms and cardiovascular disease, were positively correlated with LC risk. Coronary artery calcification was predictive of LC (adjOR 2.50, 95% CI 1.11 to 5.64; p=0.028). CONCLUSION: Prospective comparisons of risk prediction tools are required to optimise screening selection in different settings. The PLCOM2012 model may underestimate risk in deprived UK populations; further research focused on model calibration is required.
Subject(s)
Early Detection of Cancer , Lung Neoplasms/diagnosis , Lung Neoplasms/etiology , Patient Selection , Aged , Female , Humans , Male , Middle Aged , Predictive Value of Tests , Risk Assessment , Smoking , Tomography, X-Ray Computed , United KingdomABSTRACT
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.