Nanopore sequencing for malaria molecular surveillance: opportunities and challenges

Nanopore-based sequencing platforms offer the potential for affordable malaria molecular surveillance (MMS) in resource-limited settings to track and ultimately counteract emerging threats, such as drug resistance and diagnostic escape. Here, we discuss opportunities and challenges to implementing MMS using nanopore sequencing, highlighting priority areas for technical development and innovation.

Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana

Malaria results in over 600,000 deaths annually, with the highest burden of deaths in young children living in sub-Saharan Africa. Molecular surveillance can provide important information for malaria control policies, including detection of antimalarial drug resistance. However, genome sequencing capacity in malaria-endemic countries is limited. We designed and implemented an end-to-end workflow to detect Plasmodium falciparum antimalarial resistance markers and diversity in the vaccine target circumsporozoite protein (csp) using nanopore sequencing in Ghana. We analysed 196 clinical samples and showed that our method is rapid, robust, accurate and straightforward to implement. Importantly, our method could be applied to dried blood spot samples, which are readily collected in endemic settings. We report that P. falciparum parasites in Ghana are mostly susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single nucleotide polymorphisms were identified in csp, but their significance is uncertain. Our study demonstrates the feasibility of nanopore sequencing for malaria genomic surveillance in endemic countries.

The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom

Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300 E. coli isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of E. coli bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR E. coli populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.

A review of biomedical datasets relating to drug discovery: a knowledge graph perspective

Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritization. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, while relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data are required. In this review, we detail publicly available sources suitable for use in constructing drug discovery focused KGs. We aim to help guide machine learning and KG practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. The datasets are selected via strict criteria, categorized according to the primary type of information contained within and are considered based upon what information could be extracted to build a KG. We then present a comparative analysis of existing public drug discovery KGs and an evaluation of selected motivating case studies from the literature. Additionally, we raise numerous and unique challenges and issues associated with the domain and its datasets, while also highlighting key future research directions. We hope this review will motivate KGs use in solving key and emerging questions in the drug discovery domain.

Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers

Breakthrough infections with SARS-CoV-2 Delta variant have been reported in doubly-vaccinated recipients and as re-infections. Studies of viral spread within hospital settings have highlighted the potential for transmission between doubly-vaccinated patients and health care workers and have highlighted the benefits of high-grade respiratory protection for health care workers. However the extent to which vaccination is preventative of viral spread in health care settings is less well studied. Here, we analysed data from 118 vaccinated health care workers (HCW) across two hospitals in India, constructing two probable transmission networks involving six HCWs in Hospital A and eight HCWs in Hospital B from epidemiological and virus genome sequence data, using a suite of computational approaches. A maximum likelihood reconstruction of transmission involving known cases of infection suggests a high probability that doubly vaccinated HCWs transmitted SARS-CoV-2 between each other and highlights potential cases of virus transmission between individuals who had received two doses of vaccine. Our findings show firstly that vaccination may reduce rates of transmission, supporting the need for ongoing infection control measures even in highly vaccinated populations, and secondly we have described a novel approach to identifying transmissions that is scalable and rapid, without the need for an infection control infrastructure.

RNAglib: a python package for RNA 2.5 D graphs

SUMMARY

RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent progresses in machine learning techniques. RNAglib is a library that eases the use of this representation, by providing clean data, methods to load it in machine learning pipelines and graph-based deep learning models suited for this representation. RNAglib also offers other utilities to model RNA with 2.5 D graphs, such as drawing tools, comparison functions or baseline performances on RNA applications.

AVAILABILITY AND IMPLEMENTATION

The method is distributed as a pip package, RNAglib. Data are available in a repository and can be accessed on rnaglib's web page. The source code, data and documentation are available at https://rnaglib.cs.mcgill.ca.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events

Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.

Vernal: a tool for mining fuzzy network motifs in RNA

MOTIVATION

RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space.

RESULTS

Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs.

AVAILABILITY AND IMPLEMENTATION

The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)¹. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.

Patterns of within-host genetic diversity in SARS-CoV-2

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed.  Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed.  Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions

Motivation

RNA-protein interactions are key effectors of post-transcriptional regulation. Significant experimental and bioinformatics efforts have been expended on characterizing protein binding mechanisms on the molecular level, and on highlighting the sequence and structural traits of RNA that impact the binding specificity for different proteins. Yet our ability to predict these interactions in silico remains relatively poor.

Results

In this study, we introduce RPI-Net, a graph neural network approach for RNA-protein interaction prediction. RPI-Net learns and exploits a graph representation of RNA molecules, yielding significant performance gains over existing state-of-the-art approaches. We also introduce an approach to rectify an important type of sequence bias caused by the RNase T1 enzyme used in many CLIP-Seq experiments, and we show that correcting this bias is essential in order to learn meaningful predictors and properly evaluate their accuracy. Finally, we provide new approaches to interpret the trained models and extract simple, biologically interpretable representations of the learned sequence and structural motifs.

Availability and implementation

Source code can be accessed at https://www.github.com/HarveyYan/RNAonGraph.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genomic epidemiology of COVID-19 in care homes in the east of England

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report

The response to the coronavirus disease 2019 (COVID-19) pandemic has been hampered by lack of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral therapy. Here we report the use of remdesivir in a patient with COVID-19 and the prototypic genetic antibody deficiency X-linked agammaglobulinaemia (XLA). Despite evidence of complement activation and a robust T cell response, the patient developed persistent SARS-CoV-2 pneumonitis, without progressing to multi-organ involvement. This unusual clinical course is consistent with a contribution of antibodies to both viral clearance and progression to severe disease. In the absence of these confounders, we take an experimental medicine approach to examine the in vivo utility of remdesivir. Over two independent courses of treatment, we observe a temporally correlated clinical and virological response, leading to clinical resolution and viral clearance, with no evidence of acquired drug resistance. We therefore provide evidence for the antiviral efficacy of remdesivir in vivo, and its potential benefit in selected patients.

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

BACKGROUND

The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures.

METHODS

In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases.

FINDINGS

Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting.

INTERPRETATION

We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings.

FUNDING

COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.

Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

The impact of diagnostic microbiology on de-escalation of antimicrobial therapy in hospitalised adults

Background

Minimising antimicrobial overuse is needed to limit antimicrobial resistance. There is little evidence on how often microbiological testing informs antimicrobial de-escalation (e.g. stopping, shortening duration, switching to narrower spectrum or intravenous to oral switch) at 48–72 h “review and revise”. We performed a patient level analysis of diagnostic microbiology and antimicrobial prescribing to determine the impact of microbiology results on antimicrobial review outcomes.

Methods

Antimicrobial prescribing data were collected for hospitalised adults from across Brighton and Sussex University Hospitals NHS Trust using routine monthly audits of prescribing practice from July 2016 to April 2017. Microbiology testing data for cultures of blood, urine, sputum and cerebrospinal fluid (CSF) were gathered from the hospital pathology database and linked to prescriptions with matching patient identification codes. Antimicrobial prescriptions were grouped into “prescription episodes” (PEs), defined as one or more antimicrobials prescribed to the same patient for the same indication. Medical records were reviewed for all PEs with positive microbiology and a randomised sample of those with negative results to assess the impact of the microbiology result on the antimicrobial prescription(s).

Results

After excluding topical and prophylactic prescriptions, data were available for 382 inpatient antimicrobial prescriptions grouped into 276 prescription episodes. 162/276 (59%) had contemporaneous microbiology sent. After filtering likely contaminants, 33/276 (12%) returned relevant positive results, of which 20/33 (61%) had antimicrobials changed from empiric therapy as a result with 6/33 (18%) prompting de-escalation. Positive blood and CSF tended to have greater impact than urine or sputum cultures. 124/276 (45%) PEs returned only negative microbiology, and this was documented in the medical notes less often (9/40, 23%) than positive results (28/33, 85%). Out of 40 reviewed PEs with negative microbiology, we identified just one (~ 3%) in which antimicrobials were unambiguously de-escalated following the negative result.

Conclusions

The majority of diagnostic microbiology tests sent to inform clinical management yielded negative results. However, negative microbiology contributed little to clinical decision making about antimicrobial de-escalation, perhaps reflecting a lack of trust in negative results by treating clinicians. Improving the negative predictive value of currently available diagnostic microbiology could help hospital prescribers in de-escalating antimicrobial therapy.

Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study

BACKGROUND

A multidrug-resistant co-lineage of Plasmodium falciparum malaria, named KEL1/PLA1, spread across Cambodia in 2008-13, causing high rates of treatment failure with the frontline combination therapy dihydroartemisinin-piperaquine. Here, we report on the evolution and spread of KEL1/PLA1 in subsequent years.

METHODS

For this genomic epidemiology study, we analysed whole genome sequencing data from P falciparum clinical samples collected from patients with malaria between 2007 and 2018 from Cambodia, Laos, northeastern Thailand, and Vietnam, through the MalariaGEN P falciparum Community Project. Previously unpublished samples were provided by two large-scale multisite projects: the Tracking Artemisinin Resistance Collaboration II (TRAC2) and the Genetic Reconnaissance in the Greater Mekong Subregion (GenRe-Mekong) project. By investigating genome-wide relatedness between parasites, we inferred patterns of shared ancestry in the KEL1/PLA1 population.

FINDINGS

We analysed 1673 whole genome sequences that passed quality filters, and determined KEL1/PLA1 status in 1615. Before 2009, KEL1/PLA1 was only found in western Cambodia; by 2016-17 its prevalence had risen to higher than 50% in all of the surveyed countries except for Laos. In northeastern Thailand and Vietnam, KEL1/PLA1 exceeded 80% of the most recent P falciparum parasites. KEL1/PLA1 parasites maintained high genetic relatedness and low diversity, reflecting a recent common origin. Several subgroups of highly related parasites have recently emerged within this co-lineage, with diverse geographical distributions. The three largest of these subgroups (n=84, n=79, and n=47) mostly emerged since 2016 and were all present in Cambodia, Laos, and Vietnam. These expanding subgroups carried new mutations in the crt gene, which arose on a specific genetic background comprising multiple genomic regions. Four newly emerging crt mutations were rare in the early period and became more prevalent by 2016-17 (Thr93Ser, rising to 19·8%; His97Tyr to 11·2%; Phe145Ile to 5·5%; and Ile218Phe to 11·1%).

INTERPRETATION

After emerging and circulating for several years within Cambodia, the P falciparum KEL1/PLA1 co-lineage diversified into multiple subgroups and acquired new genetic features, including novel crt mutations. These subgroups have rapidly spread into neighbouring countries, suggesting enhanced fitness. These findings highlight the urgent need for elimination of this increasingly drug-resistant parasite co-lineage, and the importance of genetic surveillance in accelerating malaria elimination efforts.

FUNDING

Wellcome Trust, Bill & Melinda Gates Foundation, UK Medical Research Council, and UK Department for International Development.

Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study

BACKGROUND

The emergence and spread of resistance in Plasmodium falciparum malaria to artemisinin combination therapies in the Greater Mekong subregion poses a major threat to malaria control and elimination. The current study is part of a multi-country, open-label, randomised clinical trial (TRACII, 2015-18) evaluating the efficacy, safety, and tolerability of triple artemisinin combination therapies. A very high rate of treatment failure after treatment with dihydroartemisinin-piperaquine was observed in Thailand, Cambodia, and Vietnam. The immediate public health importance of our findings prompted us to report the efficacy data on dihydroartemisinin-piperaquine and its determinants ahead of the results of the overall trial, which will be published later this year.

METHODS

Patients aged between 2 and 65 years presenting with uncomplicated P falciparum or mixed species malaria at seven sites in Thailand, Cambodia, and Vietnam were randomly assigned to receive dihydroartemisinin-piperaquine with or without mefloquine, as part of the TRACII trial. The primary outcome was the PCR-corrected efficacy at day 42. Next-generation sequencing was used to assess the prevalence of molecular markers associated with artemisinin resistance (kelch13 mutations, in particular Cys580Tyr) and piperaquine resistance (plasmepsin-2 and plasmepsin-3 amplifications and crt mutations). This study is registered with ClinicalTrials.gov, number NCT02453308.

FINDINGS

Between Sept 28, 2015, and Jan 18, 2018, 539 patients with acute P falciparum malaria were screened for eligibility, 292 were enrolled, and 140 received dihydroartemisinin-piperaquine. The overall Kaplan-Meier estimate of PCR-corrected efficacy of dihydroartemisinin-piperaquine at day 42 was 50·0% (95% CI 41·1-58·3). PCR-corrected efficacies for individual sites were 12·7% (2·2-33·0) in northeastern Thailand, 38·2% (15·9-60·5) in western Cambodia, 73·4% (57·0-84·3) in Ratanakiri (northeastern Cambodia), and 47·1% (33·5-59·6) in Binh Phuoc (southwestern Vietnam). Treatment failure was associated independently with plasmepsin2/3 amplification status and four mutations in the crt gene (Thr93Ser, His97Tyr, Phe145Ile, and Ile218Phe). Compared with the results of our previous TRACI trial in 2011-13, the prevalence of molecular markers of artemisinin resistance (kelch13 Cys580Tyr mutations) and piperaquine resistance (plasmepsin2/3 amplifications and crt mutations) has increased substantially in the Greater Mekong subregion in the past decade.

INTERPRETATION

Dihydroartemisinin-piperaquine is not treating malaria effectively across the eastern Greater Mekong subregion. A highly drug-resistant P falciparum co-lineage is evolving, acquiring new resistance mechanisms, and spreading. Accelerated elimination of P falciparum malaria in this region is needed urgently, to prevent further spread and avoid a potential global health emergency.

FUNDING

UK Department for International Development, Wellcome Trust, Bill & Melinda Gates Foundation, Medical Research Council, and National Institutes of Health.

Weisfeiler and Leman Go Neural: Higher-Order Graph Neural Networks

In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically—showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the 1-dimensional Weisfeiler-Leman graph isomorphism heuristic (1-WL). We show that GNNs have the same expressiveness as the 1-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcomings. Based on this, we propose a generalization of GNNs, so-called k-dimensional GNNs (k-GNNs), which can take higher-order graph structures at multiple scales into account. These higher-order structures play an essential role in the characterization of social networks and molecule graphs. Our experimental evaluation confirms our theoretical findings as well as confirms that higher-order information is useful in the task of graph classification and regression.

Clinical predictors of specialist treatment requirements in pelvic fracture: A retrospective cohort study

Objectives and background

To describe the pelvic fracture population presenting to a district hospital in New Zealand and investigate whether clinical measurements can predict subsequent transfer to specialist tertiary care units. Early transfer to tertiary care is associated with improved surgical outcomes and cost-effectiveness, but there has as yet been little research into predictive markers for referral.

Methods

Retrospective cohort study of all patients admitted with pelvic fracture to the intensive care unit of Hastings Memorial Hospital, New Zealand from 2005 to 2014. The primary outcome was transfer to specialist tertiary care. Secondary outcomes were total duration of hospitalisation and conservative vs. surgical management. Clinical variables including age, sex, observations and comorbidities were analysed against these outcomes using logistic regression.

Results

Data from 40 patients were collected (24 male, 16 female; median age: 44 years). Median distance from the hospital was 22.6 km, with 27 (67.5%) patients transported by land and 13 (32.5%) arriving by helicopter. Median time from receipt of emergency call to arrival at hospital was 60 min. Three patients died and 14/40 (35%) required transfer to tertiary centres. Damage to intra-abdominal structures such as spleen, liver and bladder lacerations were associated with transfer to tertiary care, unadjusted relative risk 3.34 (95% confidence intervals: 1.39–8.05).

Conclusion

Despite a 10-year recruitment window, only 40 patients were included in this study, limiting its statistical power. Nonetheless, our data suggest that pelvic fracture patients with injuries to intra-abdominal viscera are more likely to require tertiary care transfer.

Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres

Background: Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions.

Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal var genes clusters.

  Results: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates.  We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa.

Conclusions: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.

Imported gnathostomiasis manifesting as cutaneous larva migrans and Löffler's syndrome

Here, we report an unusual case of invasive gnathostomiasis in a returning traveller, with a shifting pattern of relapsing cutaneous disease. The previously fit and well 32-year-old man first presented with serpiginous, pruriginous erythematous tracks characteristic of cutaneous larva migrans shortly after returning from South-East Asia. He was systemically well with no other symptoms. After ivermectin therapy, he re-presented with respiratory symptoms, peripheral eosinophilia and transient pulmonary infiltrates; the classic triad of Löffler's syndrome associated with invasive helminth infection. Gnathostoma spinigerum immunoblot was positive. After a second round of ivermectin therapy his respiratory symptoms resolved, but the patient's cutaneous disease relapsed repeatedly over months, with migratory erythematous swellings appearing and settling after a few days. He was treated with a 21-day course of albendazole and is lesion free at 40 weeks post initial presentation.

Extreme mutation bias and high AT content in Plasmodium falciparum

For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution.

Community Identity and User Engagement in a Multi-Community Landscape

A community's identity defines and shapes its internal dynamics. Our current understanding of this interplay is mostly limited to glimpses gathered from isolated studies of individual communities. In this work we provide a systematic exploration of the nature of this relation across a wide variety of online communities. To this end we introduce a quantitative, language-based typology reflecting two key aspects of a community's identity: how distinctive, and how temporally dynamic it is. By mapping almost 300 Reddit communities into the landscape induced by this typology, we reveal regularities in how patterns of user engagement vary with the characteristics of a community. Our results suggest that the way new and existing users engage with a community depends strongly and systematically on the nature of the collective identity it fosters, in ways that are highly consequential to community maintainers. For example, communities with distinctive and highly dynamic identities are more likely to retain their users. However, such niche communities also exhibit much larger acculturation gaps between existing users and newcomers, which potentially hinder the integration of the latter. More generally, our methodology reveals differences in how various social phenomena manifest across communities, and shows that structuring the multi-community landscape can lead to a better understanding of the systematic nature of this diversity.

Loyalty in Online Communities

Loyalty is an essential component of multi-community engagement. When users have the choice to engage with a variety of different communities, they often become loyal to just one, focusing on that community at the expense of others. However, it is unclear how loyalty is manifested in user behavior, or whether certain community characteristics encourage loyalty. In this paper we operationalize loyalty as a user-community relation: users loyal to a community consistently prefer it over all others; loyal communities retain their loyal users over time. By exploring a large set of Reddit communities, we reveal that loyalty is manifested in remarkably consistent behaviors. Loyal users employ language that signals collective identity and engage with more esoteric, less popular content, indicating that they may play a curational role in surfacing new material. Loyal communities have denser user-user interaction networks and lower rates of triadic closure, suggesting that community-level loyalty is associated with more cohesive interactions and less fragmentation into subgroups. We exploit these general patterns to predict future rates of loyalty. Our results show that a user's propensity to become loyal is apparent from their initial interactions with a community, suggesting that some users are intrinsically loyal from the very beginning.

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Background

Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB.

Methods

Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8–12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes.

Results

Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls.

Conclusion

The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1641-7) contains supplementary material, which is available to authorized users.

Inducing Domain-Specific Sentiment Lexicons from Unlabeled Corpora

A word's sentiment depends on the domain in which it is used. Computational social science research thus requires sentiment lexicons that are specific to the domains being studied. We combine domain-specific word embeddings with a label propagation framework to induce accurate domain-specific sentiment lexicons using small sets of seed words. We show that our approach achieves state-of-the-art performance on inducing sentiment lexicons from domain-specific corpora and that our purely corpus-based approach outperforms methods that rely on hand-curated resources (e.g., WordNet). Using our framework, we induce and release historical sentiment lexicons for 150 years of English and community-specific sentiment lexicons for 250 online communities from the social media forum Reddit. The historical lexicons we induce show that more than 5% of sentiment-bearing (non-neutral) English words completely switched polarity during the last 150 years, and the community-specific lexicons highlight how sentiment varies drastically between different communities.

Public health interventions to protect against falsified medicines: a systematic review of international, national and local policies

BACKGROUND

Falsified medicines are deliberately fraudulent drugs that pose a direct risk to patient health and undermine healthcare systems, causing global morbidity and mortality.

OBJECTIVE

To produce an overview of anti-falsifying public health interventions deployed at international, national and local scales in low and middle income countries (LMIC).

DATA SOURCES

We conducted a systematic search of the PubMed, Web of Science, Embase and Cochrane Central Register of Controlled Trials databases for healthcare or pharmaceutical policies relevant to reducing the burden of falsified medicines in LMIC.

RESULTS

Our initial search identified 660 unique studies, of which 203 met title/abstract inclusion criteria and were categorised according to their primary focus: international; national; local pharmacy; internet pharmacy; drug analysis tools. Eighty-four were included in the qualitative synthesis, along with 108 articles and website links retrieved through secondary searches.

DISCUSSION

On the international stage, we discuss the need for accessible pharmacovigilance (PV) global reporting systems, international leadership and funding incorporating multiple stakeholders (healthcare, pharmaceutical, law enforcement) and multilateral trade agreements that emphasise public health. On the national level, we explore the importance of establishing adequate medicine regulatory authorities and PV capacity, with drug screening along the supply chain. This requires interdepartmental coordination, drug certification and criminal justice legislation and enforcement that recognise the severity of medicine falsification. Local healthcare professionals can receive training on medicine quality assessments, drug registration and pharmacological testing equipment. Finally, we discuss novel technologies for drug analysis which allow rapid identification of fake medicines in low-resource settings. Innovative point-of-purchase systems like mobile phone verification allow consumers to check the authenticity of their medicines.

CONCLUSIONS

Combining anti-falsifying strategies targeting different levels of the pharmaceutical supply chain provides multiple barriers of protection from falsified medicines. This requires the political will to drive policy implementation; otherwise, people around the world remain at risk.

Shiga Toxin-Producing Escherichia coli Infection, Antibiotics, and Risk of Developing Hemolytic Uremic Syndrome: A Meta-analysis

BACKGROUND

Antibiotic administration to individuals with Shiga toxin-producing Escherichia coli (STEC) infection remains controversial. We assessed if antibiotic administration to individuals with STEC infection is associated with development of hemolytic uremic syndrome (HUS).

METHODS

The analysis included studies published up to 29 April 2015, that provided data from patients (1) with STEC infection, (2) who received antibiotics, (3) who developed HUS, and (4) for whom data reported timing of antibiotic administration in relation to HUS. Risk of bias was assessed; strength of evidence was adjudicated. HUS was the primary outcome. Secondary outcomes restricted the analysis to low-risk-of-bias studies employing commonly used HUS criteria. Pooled estimates of the odds ratio (OR) were obtained using random-effects models.

RESULTS

Seventeen reports and 1896 patients met eligibility; 8 (47%) studies were retrospective, 5 (29%) were prospective cohort, 3 (18%) were case-control, and 1 was a trial. The pooled OR, including all studies, associating antibiotic administration and development of HUS was 1.33 (95% confidence interval [CI], .89-1.99; I(2) = 42%). The repeat analysis including only studies with a low risk of bias and those employing an appropriate definition of HUS yielded an OR of 2.24 (95% CI, 1.45-3.46; I(2) = 0%).

CONCLUSIONS

Overall, use of antibiotics was not associated with an increased risk of developing HUS; however, after excluding studies at high risk of bias and those that did not employ an acceptable definition of HUS, there was a significant association. Consequently, the use of antibiotics in individuals with STEC infections is not recommended.

Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis

The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs) were scattered across the genome, structural variants (deletions, duplications, translocations) were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7–72.4%) yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

Malaria kills >600,000 people each year, with most deaths caused by Plasmodium falciparum. A family of proteins known as P. falciparum erythrocyte membrane protein 1, PfEMP1, is expressed on the surface of infected erythrocytes and plays an important role in pathogenesis. Each P. falciparum genome contains approximately 60 highly polymorphic var genes encoding the PfEMP1 proteins, and monoallelic expression with periodic switching results in immune evasion. Var gene polymorphism is thus critical to this survival strategy. We investigated how var gene diversity is generated by performing an in vitro evolution experiment, tracking var gene mutation in ‘real-time’ with whole genome sequencing. We found that genome structural variation is focused in and around var genes. These genetic rearrangements created new ‘chimeric’ var gene sequences during the mitotic part of the life cycle, and were consistent with processes of mitotic non-allelic homologous recombination. The recombinant var genes were always in frame and with conserved overall var gene architecture, and the recombination rate implies that many millions of rearranged var gene sequences are produced every 48-hour life cycle within infected individuals. In conclusion, we provide a detailed description of how new var gene sequences are continuously generated in the parasite genome, helping to explain long-term parasite survival within infected human hosts.

Optimized whole-genome amplification strategy for extremely AT-biased template

Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.

TRIM15 is a focal adhesion protein that regulates focal adhesion disassembly

Focal adhesions are macromolecular complexes that connect the actin cytoskeleton to the extracellular matrix. Dynamic turnover of focal adhesions is crucial for cell migration. Paxillin is a multi-adaptor protein that plays an important role in regulating focal adhesion dynamics. Here, we identify TRIM15, a member of the tripartite motif protein family, as a paxillin-interacting factor and a component of focal adhesions. TRIM15 localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. Unlike other focal adhesion proteins, TRIM15 is a stable focal adhesion component with restricted mobility due to its ability to form oligomers. TRIM15-depleted cells display impaired cell migration and reduced focal adhesion disassembly rates, in addition to enlarged focal adhesions. Thus, our studies demonstrate a cellular function for TRIM15 as a regulatory component of focal adhesion turnover and cell migration.

Individual, social-normative, and policy predictors of smoking cessation: a multilevel longitudinal analysis

OBJECTIVES

We assessed the prospective impact of individual, social-normative, and policy predictors of quit attempts and smoking cessation among Massachusetts adults.

METHODS

We interviewed a representative sample of current and recent smokers in Massachusetts by telephone in 2001 through 2002 and then again twice at 2-year intervals. The unit of analysis was the 2-year transition from wave 1 to wave 2 and from wave 2 to wave 3. Predictors of quit attempts and abstinence of longer than 3 months were analyzed using multilevel analysis. Predictors included individual, social-normative, and policy factors.

RESULTS

Multivariate analyses of 2-year transitions showed that perceptions of strong antismoking town norms were predictive of abstinence (odds ratio = 2.06; P < .01). Household smoking bans were the only policy associated with abstinence, but smoking bans at one's worksite were significant predictors of quit attempts.

CONCLUSIONS

Although previous research showed a strong relation between local policy and norms, we found no observable, prospective impact of local policy on smoking cessation over 2 years. Our findings provide clear support for the importance of strong antismoking social norms as a facilitator of smoking cessation.

Do local tobacco regulations influence perceived smoking norms? Evidence from adult and youth surveys in Massachusetts

Smoking behavior has been shown to be influenced by individuals' perceptions of social norms about smoking. This study examines whether local regulations regarding clean indoor air and youth access to tobacco are associated with residents' subsequent perceptions of smoking norms. Data came from Massachusetts surveys of adults and youths and from records of local tobacco control policies. Indices of perceived smoking norms were based on perceived smoking prevalence and perceived community acceptance of smoking. Multilevel models tested the association between perceived norms and the presence of strong local regulations in four policy domains (restaurant smoking bans, smoking restrictions in other venues, enforcement of laws prohibiting sales to youths and youth-oriented marketing restrictions). The model controlled for town voting results on a tobacco tax referendum, which served as a measure of antismoking sentiment pre-dating the regulations. Results showed that youths perceived community norms to be significantly more 'antismoking' if they lived in a town that had strong regulations in at least three of the four domains. For adults, having strong regulations in as few as one to two domains was associated with perceiving community norms to be significantly more antismoking. Implementing and publicizing local regulations may help shape perceptions of community smoking norms.

Local restaurant smoking regulations and the adolescent smoking initiation process: results of a multilevel contextual analysis among Massachusetts youth

OBJECTIVE

To assess whether smoke-free restaurant laws influence the progression from (1) never smoking to early experimentation and (2) early experimentation to established smoking.

DESIGN

A longitudinal, 4-year, 3-wave study of a representative sample of Massachusetts youth.

SETTING

A total of 301 Massachusetts communities.

PARTICIPANTS

Study participants were 3834 Massachusetts youths aged 12 to 17 years at baseline, from January 2, 2001, to June 18, 2002, of whom 2791 (72.8%) were reinterviewed after 2 years (from January 30, 2003, to July 31, 2004) and 2217 (57.8%) were reinterviewed after 4 years (from February 16, 2005, to March 26, 2006). Wave 3 respondents were recruited from both those who responded at wave 2 and those who did not.

MAIN EXPOSURE

The primary predictor of interest is the strength of the local restaurant smoking regulation in the respondents' town of residence at the baseline of each transition period.

MAIN OUTCOME MEASURES

(1) Overall progression to established smoking (having smoked > or =100 cigarettes in one's lifetime), (2) transition from nonsmoking (never having puffed a cigarette) to experimentation, and (3) transition from experimentation to established smoking.

RESULTS

Youths living in towns with a strong restaurant smoking regulation at baseline had significantly lower odds of progressing to established smoking (odds ratio, 0.60; 95% confidence interval, 0.42-0.85) compared with those living in towns with weak regulations. The observed association between strong restaurant smoking regulations and impeded progression to established smoking was entirely due to an effect on the transition from experimentation to established smoking (odds ratio, 0.53; 95% confidence interval, 0.33-0.86).

CONCLUSION

Local smoke-free restaurant laws may significantly lower youth smoking initiation by impeding the progression from cigarette experimentation to established smoking.

Effect of local youth-access regulations on progression to established smoking among youths in Massachusetts

OBJECTIVE

To test whether community-level restrictions on youth access to tobacco (including both ordinances and enforcement) are associated with less smoking initiation or less progression to established smoking among adolescents.

DESIGN

Prospective cohort study of a random sample of adolescents in Massachusetts whose smoking status was assessed by telephone interviews at baseline and 2-year follow-up, and linked to a state-wide database of town-level youth-access ordinances and enforcement practices.

PARTICIPANTS

A random sample of 2623 adolescents aged 12-17 years who lived in 295 towns in Massachusetts in 2001-2 and were followed in 2003-4.

MAIN OUTCOME MEASURES

The relationship between the strength of local youth access restrictions (including both ordinances and level of enforcement) and (1) never-smokers' smoking initiation rates and (2) experimenters' rate of progression to established smoking was tested in a multilevel analysis that accounted for town-level clustering and adjusted for potential individual, household and town-level confounders.

RESULTS

Over 2 years, 21% of 1986 never-smokers initiated smoking and 25% of 518 experimenters became established smokers. The adjusted odds ratio (OR) for smoking initiation was 0.89 (95% CI 0.61 to 1.31) for strong versus weak youth-access policies and 0.93 (95% CI 0.67 to 1.29) for medium versus weak policies. The adjusted OR for progression to established smoking among adolescents who had experimented with smoking was 0.79 (95% CI 0.45 to 1.39) for strong versus weak local smoking restrictions and 0.85 (95% CI 0.50 to 1.45) for medium versus weak restrictions.

CONCLUSIONS

This prospective cohort study found no association between community-level youth-access restrictions and adolescents' rate of smoking initiation or progression to established smoking over 2 years.

Who supports tobacco excise taxes? Factors associated with towns' and individuals' support in Massachusetts

OBJECTIVES

The authors examined factors related to public support for cigarette taxes: smoking behavior, attitudes about other tobacco control policies, and sociodemographic factors.

METHODS

The authors regressed referendum voting outcomes on sociodemographic characteristics of Massachusetts' 351 towns. Logistic regressions on the surveys of Massachusetts adults (N = 14,000+) showed support for hypothetical tax increases to be related to respondents' smoking status, support for other tobacco control policies, and sociodemographic characteristics.

RESULTS

Average educational attainment, probably acting as a proxy for nonsmoking prevalence, strongly predicted town-level support for Massachusetts' 1992 cigarette tax referendum. Survey respondents' support for hypothetical further increases was strongest if tax proceeds were earmarked for tobacco control or health purposes and if the individual was a nonsmoker and favored other tobacco control policies. For an earmarked tax, support was stronger among younger persons, females, persons with higher education, racial/ethnic minorities, and smokers with children.

CONCLUSIONS

The high nationwide proportion of nonsmokers means that tobacco tax proposals can obtain strong voter support, but only if tax revenues are clearly earmarked for tobacco control and similar uses. Individual- and town-level characteristics can identify likely concentrations of support. Because attitudes toward tobacco control are only partly linked to smoking status, education campaigns may make a difference.

Smokers' responses to advertisements for regular and light cigarettes and potential reduced-exposure tobacco products

This study examines smokers' responses to advertisements for potentially reduced exposure tobacco products (PREP), light cigarettes, and regular cigarettes. A convenience sample of 600 adult smokers reviewed one actual advertisement for each type of product. Smokers ranked the products on health risk, amount of tar, and carcinogenicity, and identified the messages they perceived the advertisements to convey. Smokers perceived PREP products as having lower health risks (mean = 5.4 on a scale of 1-10) and carcinogens (6.6) than light cigarettes (5.8 and 6.9, respectively, p < .001), and lights as having lower health risks and carcinogen levels than regular cigarettes (8.2 and 8.8, respectively, p <.001). The average PREP rating for level of tar (5.3) was not significantly less than the light mean of 5.4, but both were significantly less than the regular mean of 8.4 (p <.001). Although no advertisements explicitly said that the products were healthy or safe, advertisements for PREP products and light cigarettes were interpreted as conveying positive messages about health and safety. Most smokers believed that claims made in cigarette advertisements must be approved by a government agency. The results indicate that advertisements can and do leave consumers with perceptions of the health and safety of tobacco products that are contrary to the scientific evidence. Explicit and implicit advertising messages may be strengthened by the perceived government endorsement. This supports the Institute of Medicine's recommendation to regulate the promotion, advertising, and labeling of PREP tobacco products and light cigarettes. Effective regulation may need to focus on consumer perceptions resulting from advertisements rather than the explicit content of advertising text.

Town-level characteristics and smoking policy adoption in Massachusetts: are local restaurant smoking regulations fostering disparities in health protection?

OBJECTIVES

We identified and quantified differences in sociodemographic characteristics of communities relative to the strength of local restaurant smoking regulations in Massachusetts.

METHODS

We examined the relationship between the strength of the 351 local restaurant smoking regulations in Massachusetts and a number of town-level characteristics, using a multinomial logistic regression model.

RESULTS

Characteristics important to the adoption of stronger restaurant smoking regulations included higher education and per capita income, geographic region, voter support for a state cigarette tax initiative, board of health funding to promote clean indoor air policy making, and the presence of a bordering town with a strong regulation.

CONCLUSIONS

The current pattern of smoke-free restaurant policy enactment fosters socioeconomic and geographic disparities in health protection, undermining an important national health goal.

Cigarette advertising in magazines: the tobacco industry response to the Master Settlement Agreement and to public pressure

OBJECTIVE

The Master Settlement Agreement (MSA) of November 1998 prohibited participating tobacco companies from directly or indirectly targeting youth in marketing. Widely publicised information in May 2000 showed increased cigarette advertising in magazines with substantial youth readership and companies were pressed to change their practices. The responses of the tobacco industry to the MSA and to the public pressure are examined.

DESIGN

Expenditures on cigarette advertisements in national magazines in the USA are compared for three periods: January to November 1998, December 1998 to June 2000, and July 2000 to November 2001. Magazines in which at least 15% of readers are youth under age 18 are focused upon. Regression models test for the significance of period differences after controlling for seasonal and long term patterns.

DATA SOURCES

Commercially maintained data on advertising in US magazines and on magazine readership by age.

KEY MEASURES

Monthly cigarette ad expenditures in magazines with 15%+ youth readership, and monthly proportion of ad expenditures in 15%+ youth magazines.

RESULTS

Cigarette advertising expenditures in magazines with 15%+ youth readership increased dramatically after MSA implementation and fell dramatically after public pressure. The percentage allocation of expenditures to 15%+ magazines fell significantly in both periods. Results differ somewhat by company.

CONCLUSIONS

The tobacco industry response to the MSA was at best modest, reducing proportional allocations of advertising to youth magazines but increasing the absolute amount of such advertising. The value of public pressure was seen in substantial reductions in both absolute and proportional spending on youth magazines, although not by all companies.

Recall of health warnings in smokeless tobacco ads

OBJECTIVE

To determine the effects of health warning characteristics in smokeless tobacco magazine print ads on warning recall, and the implications for current US Federal regulations.

DESIGN

Subjects examined two distracter ads and one of nine randomly assigned smokeless tobacco ads varying in health warning presence, size (8 to 18 point font), and contrast (low versus high)-including no health warning. They were then interviewed about ad content using recall and recognition questions.

SUBJECTS

A convenience sample of 895 English speaking males aged 16-24 years old who were intercepted at seven shopping malls throughout Massachusetts during May 2000.

MAIN OUTCOME MEASURES

Proven aided recall, or recall of a health warning and correct recognition of the warning message among distracters, and false recall.

RESULTS

Controlling for covariates such as education, employment/student status, and Hispanic background, proven aided recall increased significantly with font size; doubling size from 10 to 20 point font would increase recall from 63% to 76%. Although not statistically significant, recall was somewhat better for high contrast warnings. Ten per cent of the sample mistakenly recalled the warning where none existed.

CONCLUSIONS

As demonstrated by substantially greater recall among ads that included health warnings over ads that had none, health warnings retained their value to consumers despite years of exposure (that can produce false recall). Larger health warnings would enhance recall, and the proposed model can be used to estimate potential recall that affects communication, perceived health risk, and behaviour modification.

Trends in prevalence of current smoking, Massachusetts and states without tobacco control programmes, 1990 to 1999

OBJECTIVE

To assess the effect of a comprehensive tobacco control programme initiated in Massachusetts in 1993, and to compare the 1990 to 1999 trend in smoking prevalence to that in 41 states without tobacco control programmes, controlling for demographic shifts over time.

DESIGN

Data from the Behavioral Risk Factor Surveillance System for the years 1990 to 1999 were used to examine changes and trends in prevalence of smoking using multivariate logistic regression models.

MAIN OUTCOME MEASURES

Trend in prevalence of current smoking for the years 1990 to 1999.

RESULTS

In 1990, the prevalence of current smoking in Massachusetts was 23.5% (95% confidence interval (CI) 21.0% to 26.1%), and 24.2% in the rest of the USA (95% CI 23.7% to 24.7%). By 1999, the prevalence had declined in Massachusetts to 19.4%, and to 23.3% in 41 other US states. Controlling for sex, age, race, and education, there was a greater decline in current smoking between 1990 and 1999 among Massachusetts men than among Massachusetts women, and the decline was greater in Massachusetts than in the rest of the USA for men and for both sexes combined.

CONCLUSIONS

These results suggest that the Massachusetts Tobacco Control Program is having a beneficial impact, but suggest a need for additional targeted efforts to achieve similar declines among Massachusetts women.

The effectiveness of a short form of the Household Food Security Scale

OBJECTIVES

On the basis of an 18-item Household Food Security Scale, a short form was developed to assess financially based food insecurity and hunger in surveys of households with and without children.

METHODS

To maximize the probability that households would be correctly classified with respect to food insecurity and hunger, 6 items from the full scale were selected on the basis of April 1995 Current Population Survey data.

RESULTS

The short form classified 97.7% of households correctly and underestimated the prevalence of overall food insecurity and of hunger by 0.3 percentage points.

CONCLUSIONS

The short form of the Household Food Security Scale is a brief but potentially useful tool for national surveys and some state/local applications.

Hybrid bioartificial liver in hepatic failure: preliminary clinical report

A hybrid bioartificial liver has been developed on the principle of hemodialysis against a suspension of functioning hepatocytes. The new chimeric device of synthetics and living parts was used successfully to treat a patient in hepatic failure due to an inoperable bile duct carcinoma that involved the bifurcation of the common duct.