scholarly journals High frequency transmission, asymptomatic shedding, and airborne spread of Streptococcus pyogenes among schoolchildren exposed to scarlet fever: a longitudinal multi-cohort moleculo-epidemiological contact tracing study.

2021 ◽  
Author(s):  
Rebecca Cordery ◽  
Amrit Purba ◽  
Lipi Begum ◽  
Ewurabena Mills ◽  
Mia Mosavie ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Streptococcus Pyogenes ◽  
High Frequency ◽  
Scarlet Fever ◽  
Contact Tracing ◽  
Classroom Environments ◽  
Outbreak Strain ◽  
Recent Transmission ◽  
Hygiene Measures ◽  
The Impact

Background: Despite recommendations regarding prompt treatment of cases and enhanced hygiene measures, scarlet fever outbreaks increased in England between 2014-2018. Methods: We undertook a prospective, intensive contact tracing study in schools with consecutive scarlet fever cases to assess the impact of standard interventions on transmission of Streptococcus pyogenes between cases, classroom contacts, households, and classroom environments over 4 weeks using genome sequencing. Findings: Six classes, comprising 12 scarlet fever cases, 17 household contacts, and 278 classroom contacts were recruited. Prevalence of the outbreak strain in asymptomatic classroom contacts was high, increasing from 9.6% in week 1, to 26.9% in week 2, 23.9% in week 3, then 14.3% in week 4. Colonisation with non-outbreak strains was 0 - 7.5%. Genome sequencing showed clonality of isolates within each of six classes, confirming recent transmission accounted for high carriage. Of asymptomatic classroom contacts with S. pyogenes-positive throat swabs who were tested for transmissibility, 6/28 (21%) had positive cough plates and/or hand swabs, of whom three remained S. pyogenes-positive for 3 weeks. Only 1/60 surface swabs taken in 3 classrooms yielded S. pyogenes. In contrast, settle plates placed in elevated locations were S. pyogenes-positive in both classrooms tested. Interpretation: S. pyogenes transmission in schools is intense and may occur prior to, or in spite of reported treatment of cases, underlining a need for rapid case management. Despite guideline adherence, heavy shedding of S. pyogenes by small numbers of classroom contacts may perpetuate outbreaks, and airborne transmission has a plausible role in spread.

scholarly journals Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

2020 ◽  
Vol 148 ◽  
Author(s):  
J. L. Guthrie ◽  
L. Strudwick ◽  
B. Roberts ◽  
M. Allen ◽  
J. McFadzen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Yukon Territory ◽  
Contact Tracing ◽  
Whole Genome ◽  
Attitudes And Practices ◽  
Genomic Epidemiology ◽  
Recent Transmission

Abstract Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

scholarly journals Complete Genome Sequence of a Streptococcus pyogenes Serotype M12 Scarlet Fever Outbreak Isolate from China, Compiled Using Oxford Nanopore and Illumina Sequencing

2018 ◽  
Vol 6 (18) ◽  
pp. e00389-18 ◽  
Author(s):  
Yuanhai You ◽  
Yongjun Kou ◽  
Longfei Niu ◽  
Qiong Jia ◽  
Yahui Liu ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Sequence ◽  
Streptococcus Pyogenes ◽  
Illumina Sequencing ◽  
Complete Genome Sequence ◽  
Scarlet Fever ◽  
Complete Genome ◽  
Content Type ◽  
Oxford Nanopore ◽  
Outbreak Isolate

ABSTRACT The incidence of scarlet fever cases remains high in China. Here, we report the complete genome sequence of a Streptococcus pyogenes isolate of serotype M12, which has been confirmed as the predominant serotype in recent outbreaks. Genome sequencing was achieved by a combination of Oxford Nanopore MinION and Illumina methodologies.

scholarly journals Group A streptococcal skin infection outbreak in an abattoir: lessons for prevention

2006 ◽  
Vol 135 (2) ◽  
pp. 321-327 ◽  
Author(s):  
C. P. HUMPHREYS ◽  
S. J. MORGAN ◽  
M. WALAPU ◽  
G. A. J. HARRISON ◽  
A. P. KEEN ◽  
...  
Keyword(s):  
Skin Infection ◽  
Group A Streptococcus ◽  
Multivariate Model ◽  
Skin Infections ◽  
Outbreak Strain ◽  
Bacterial Counts ◽  
Hygiene Measures ◽  
Group A ◽  
The Impact ◽  
Abattoir Workers

During a group A streptococcus (GAS) outbreak 21 abattoir workers developed skin infections. The unusual outbreak strain (emm 108.1) was cultured from five workers and four persons in the community with links to the abattoir. The attack rate was 26% in the lamb line. Communal nailbrushes were neither routinely disinfected nor changed, and had high bacterial counts. A cohort study found a higher risk from working in the gutting area and getting cuts on hands more than weekly. Despite high bacterial counts daily nailbrush use had a lower risk, as did always wearing disposable gloves. Working in the gutting area (OR 11·44) and nailbrush use at least once a day (OR 0·04) were significant in the multivariate model. Transmission of infection is likely to have occurred on carcasses. GAS infection among abattoir workers was once common. Simple hygiene measures, such as nailbrush use, may reduce the impact of future outbreaks.

Global Algorithmic Capital Markets

2018 ◽  
Keyword(s):  
Public Policy ◽  
Capital Markets ◽  
Systemic Risk ◽  
High Frequency ◽  
Investor Protection ◽  
High Frequency Trading ◽  
Market Making ◽  
Market Governance ◽  
Policy Objectives ◽  
The Impact

This book illustrates and assesses the dramatic recent transformations in capital markets worldwide and the impact of those transformations. ‘Market making’ by humans in centralized markets has been replaced by supercomputers and algorithmic high frequency trading operating in often highly fragmented markets. How do recent market changes impact on core public policy objectives such as investor protection, reduction of systemic risk, fairness, efficiency, and transparency in markets? The operation and health of capital markets affect all of us and have profound implications for equality and justice in society. This unique set of chapters by leading scholars, industry insiders, and regulators sheds light on these and related questions and discusses ways to strengthen market governance for the benefit of society at large.

scholarly journals Crisis Management in Higher Education in the Time of Covid-19: The Case of Actor Training

2021 ◽  
Vol 11 (3) ◽  
pp. 132
Author(s):  
Anna McNamara
Keyword(s):  
Higher Education ◽  
Crisis Management ◽  
High Frequency ◽  
High Reliability ◽  
Actor Training ◽  
Management Actions ◽  
The Usa ◽  
The Uk ◽  
The Impact ◽  
High Frequency Words

The impact of Covid-19 placed Higher Education leadership in a state of crisis management, where decision making had to be swift and impactful. This research draws on ethea of mindfulness, actor training techniques, referencing high-reliability organisations (HRO). Interviews conducted by the author with three leaders of actor training conservatoires in Higher Education institutions in Australia, the UK and the USA reflect on crisis management actions taken in response to the impact of Covid-19 on their sector, from which high-frequency words are identified and grouped thematically. Reflecting on these high-frequency words and the thematic grouping, a model of mindful leadership is proposed as a positive tool that may enable those in leadership to recognise and respond efficiently to wider structural frailties within Higher Education, with reference to the capacity of leaders to operate with increased mindfulness, enabling a more resilient organisation that unlocks the locus of control.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Digital proximity tracing on empirical contact networks for pandemic control

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
G. Cencetti ◽  
G. Santin ◽  
A. Longa ◽  
E. Pigani ◽  
A. Barrat ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Outbreaks ◽  
Physical Distance ◽  
Contact Tracing ◽  
Reproductive Number ◽  
Modeling Framework ◽  
Infectious Disease Outbreaks ◽  
Contact Patterns ◽  
Contact Data ◽  
The Impact

AbstractDigital contact tracing is a relevant tool to control infectious disease outbreaks, including the COVID-19 epidemic. Early work evaluating digital contact tracing omitted important features and heterogeneities of real-world contact patterns influencing contagion dynamics. We fill this gap with a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing in the COVID-19 pandemic. We investigate how well contact tracing apps, coupled with the quarantine of identified contacts, can mitigate the spread in real environments. We find that restrictive policies are more effective in containing the epidemic but come at the cost of unnecessary large-scale quarantines. Policy evaluation through their efficiency and cost results in optimized solutions which only consider contacts longer than 15–20 minutes and closer than 2–3 meters to be at risk. Our results show that isolation and tracing can help control re-emerging outbreaks when some conditions are met: (i) a reduction of the reproductive number through masks and physical distance; (ii) a low-delay isolation of infected individuals; (iii) a high compliance. Finally, we observe the inefficacy of a less privacy-preserving tracing involving second order contacts. Our results may inform digital contact tracing efforts currently being implemented across several countries worldwide.

scholarly journals Exploring the effectiveness of a COVID-19 contact tracing app using an agent-based model

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jonatan Almagor ◽  
Stefano Picascia
Keyword(s):  
High Rate ◽  
Contact Tracing ◽  
Agent Based Model ◽  
Agent Based ◽  
The Social ◽  
Behavioural Factors ◽  
The Impact ◽  
Different Levels ◽  
User Rate

AbstractA contact-tracing strategy has been deemed necessary to contain the spread of COVID-19 following the relaxation of lockdown measures. Using an agent-based model, we explore one of the technology-based strategies proposed, a contact-tracing smartphone app. The model simulates the spread of COVID-19 in a population of agents on an urban scale. Agents are heterogeneous in their characteristics and are linked in a multi-layered network representing the social structure—including households, friendships, employment and schools. We explore the interplay of various adoption rates of the contact-tracing app, different levels of testing capacity, and behavioural factors to assess the impact on the epidemic. Results suggest that a contact tracing app can contribute substantially to reducing infection rates in the population when accompanied by a sufficient testing capacity or when the testing policy prioritises symptomatic cases. As user rate increases, prevalence of infection decreases. With that, when symptomatic cases are not prioritised for testing, a high rate of app users can generate an extensive increase in the demand for testing, which, if not met with adequate supply, may render the app counterproductive. This points to the crucial role of an efficient testing policy and the necessity to upscale testing capacity.

scholarly journals A Person-to-Person and Person-to-Place COVID-19 Contact Tracing System Based on OGC IndoorGML

2020 ◽  
Vol 10 (1) ◽  
pp. 2 ◽  
Author(s):  
Soroush Ojagh ◽  
Sara Saeedi ◽  
Steve H. L. Liang
Keyword(s):  
Data Model ◽  
Low Cost ◽  
Large Body ◽  
Contact Tracing ◽  
Trajectory Data ◽  
Sequential Order ◽  
Human Contact ◽  
Wide Availability ◽  
Data Points ◽  
The Impact

With the wide availability of low-cost proximity sensors, a large body of research focuses on digital person-to-person contact tracing applications that use proximity sensors. In most contact tracing applications, the impact of SARS-CoV-2 spread through touching contaminated surfaces in enclosed places is overlooked. This study is focused on tracing human contact within indoor places using the open OGC IndoorGML standard. This paper proposes a graph-based data model that considers the semantics of indoor locations, time, and users’ contexts in a hierarchical structure. The functionality of the proposed data model is evaluated for a COVID-19 contact tracing application with scalable system architecture. Indoor trajectory preprocessing is enabled by spatial topology to detect and remove semantically invalid real-world trajectory points. Results show that 91.18% percent of semantically invalid indoor trajectory data points are filtered out. Moreover, indoor trajectory data analysis is innovatively empowered by semantic user contexts (e.g., disinfecting activities) extracted from user profiles. In an enhanced contact tracing scenario, considering the disinfecting activities and sequential order of visiting common places outperformed contact tracing results by filtering out unnecessary potential contacts by 44.98 percent. However, the average execution time of person-to-place contact tracing is increased by 58.3%.

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