scholarly journals SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

2014 ◽  
Author(s):  
Michael Inouye ◽  
Harriet Dashnow ◽  
Lesley Raven ◽  
Mark B Schultz ◽  
Bernard J Pope ◽  
...  
Keyword(s):  
Public Health ◽  
Bacterial Pathogens ◽  
Source Code ◽  
Gene Detection ◽  
Read Mapping ◽  
The Face ◽  
Data Source ◽  
Public Health Epidemiology ◽  
Sequence Types ◽  
Allele Assignment

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. Here we have demonstrated the use of SRST2 for microbial genome surveillance in a variety of public health and hospital settings. In the face of rising threats of antimicrobial resistance and emerging virulence amongst bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/

Pandemic Disease, Public Health, and Ethics

2019 ◽  
pp. 796-811 ◽  
Author(s):  
Maxwell Smith ◽  
Ross Upshur
Keyword(s):  
Public Health ◽  
Ethical Issues ◽  
Ethical Challenges ◽  
Pandemic Preparedness ◽  
Scarce Resources ◽  
Ethical Frameworks ◽  
Health Measures ◽  
Care Workers ◽  
The Face ◽  
Conducting Research

Infectious disease pandemics raise significant and novel ethical challenges to the organization and practice of public health. This chapter provides an overview of the salient ethical issues involved in preparing for and responding to pandemic disease, including those arising from deploying restrictive public health measures to contain and curb the spread of disease (e.g., isolation and quarantine), setting priorities for the allocation of scarce resources, health care workers’ duty to care in the face of heightened risk of infection, conducting research during pandemics, and the global governance of preventing and responding to pandemic disease. It also outlines ethical guidance from prominent ethical frameworks that have been developed to address these ethical issues and concludes by discussing some pressing challenges that must be addressed if ethical reflection is to make a meaningful difference in pandemic preparedness and response.

scholarly journals Are public health measures and individualised care compatible in the face of a pandemic? A national observational study of bereaved relatives’ experiences during the COVID-19 pandemic

2021 ◽  
pp. 026921632110198
Author(s):  
Catriona R Mayland ◽  
Rosemary Hughes ◽  
Steven Lane ◽  
Tamsin McGlinchey ◽  
Warren Donnellan ◽  
...  
Keyword(s):  
Public Health ◽  
Family Support ◽  
Online Survey ◽  
Free Text ◽  
Professional Networks ◽  
Dying Patients ◽  
The Face ◽  
Individualised Care ◽  
The Impact ◽  
Informative Communication

Background: COVID-19 public health restrictions have affected end-of-life care experiences for dying patients and their families. Aim: To explore bereaved relatives’ experiences of quality of care and family support provided during the last days of life; to identify the impact of factors associated with perceived support. Design: A national, observational, open online survey was developed and disseminated via social media, public fora and professional networks (June–September 2020). Validated instruments and purposively designed questions assessed experiences. Analysis used descriptive statistics, logistic regression and thematic analysis of free-text responses. Participants: Individuals (⩾18 years) who had experienced the death of a relative/friend (all care settings) within the United Kingdome during the COVID-19 pandemic. Results: Respondents ( n = 278, mean 53.4 years) tended to be female ( n = 216, 78%); over half were ‘son/daughter’ (174, 62.6%) to the deceased. Deceased individuals (mean 81.6 years) most frequently died in their ‘usual place of care’ ( n = 192, 69.3%). Analysis established five conceptual themes affecting individualised care: (1) public health restrictions compounding the distress of ‘not knowing’; (2) disparate views about support from doctors and nurses; (3) challenges in communication and level of preparedness for the death; (4) delivery of compassionate care; (5) emotional needs and potential impact on grief. Male respondents (OR 2.9, p = 0.03) and those able to visit (OR 2.2, p = 0.04) were independently associated with good perceptions of family support. Conclusion: Despite public health restrictions, individualised care can be enabled by proactive, informative communication; recognising dying in a timely manner and facilitating the ability to be present before death.

Dilemmas of nudging in public health: an ethical analysis of a Danish pamphlet

2020 ◽  
Author(s):  
Jacob Busch ◽  
Emilie Kirstine Madsen ◽  
Antoinette Mary Fage-Butler ◽  
Marianne Kjær ◽  
Loni Ledderer
Keyword(s):  
Public Health ◽  
Ethical Issues ◽  
Screening Programme ◽  
Screening Program ◽  
Ethical Analysis ◽  
Choice Making ◽  
The Face ◽  
Information Materials ◽  
The Individual ◽  
To Receive

Summary Nudging has been discussed in the context of public health, and ethical issues raised by nudging in public health contexts have been highlighted. In this article, we first identify types of nudging approaches and techniques that have been used in screening programmes, and ethical issues that have been associated with nudging: paternalism, limited autonomy and manipulation. We then identify nudging techniques used in a pamphlet developed for the Danish National Screening Program for Colorectal Cancer. These include framing, default nudge, use of hassle bias, authority nudge and priming. The pamphlet and the very offering of a screening programme can in themselves be considered nudges. Whether nudging strategies are ethically problematic depend on whether they are categorized as educative- or non-educative nudges. Educative nudges seek to affect people’s choice making by engaging their reflective capabilities. Non-educative nudges work by circumventing people’s reflective capabilities. Information materials are, on the face of it, meant to engage citizens’ reflective capacities. Recipients are likely to receive information materials with this expectation, and thus not expect to be affected in other ways. Non-educative nudges may therefore be particularly problematic in the context of information on screening, also as participating in screening does not always benefit the individual.

scholarly journals Reconciling Epidemiology’s Aspirations and Capabilities

2020 ◽  
Author(s):  
David A Savitz
Keyword(s):  
Public Health ◽  
Epidemiologic Studies ◽  
Public Health Importance ◽  
Public Health Action ◽  
Action Current ◽  
Current Trends ◽  
The Face ◽  
Health Action ◽  
New Challenges ◽  
Health Applications

Abstract Interpreting the results of epidemiologic studies calls for objectivity and rigorous scrutiny, acknowledging the limitations that temper the applicability of the findings to public health action. Current trends have posed new challenges to balancing goal of scientific objectivity and validity with public health applications. The ongoing tension between epidemiology’s aspirations and capability has several sources: the need to overpromise in research proposals, compromising methodologic rigor because of public health importance, defending findings in the face of hostile critics, and appealing to core constituencies who have specific expectations from the research.

scholarly journals Epidemic of plague amidst COVID-19 in Madagascar: efforts, challenges, and recommendations

2021 ◽  
Vol 49 (1) ◽  
Author(s):  
Abdullahi Tunde Aborode ◽  
Ana Carla dos Santos Costa ◽  
Anmol Mohan ◽  
Samarth Goyal ◽  
Aishat Temitope Rabiu ◽  
...  
Keyword(s):  
Public Health ◽  
Health System ◽  
Public Health System ◽  
Healthcare Sector ◽  
The Face ◽  
Endemic Areas

AbstractThe plague has been wreaking havoc on people in Madagascar with the COVID-19 pandemic. Madagascar’s healthcare sector is striving to respond to COVID-19 in the face of a plague outbreak that has created a new strain on the country’s public health system. The goal and activities of the gradual epidemic of plague in Madagascar during COVID-19 are described in this research. In order to contain the plague and the COVID-19 pandemic in this country, we have suggested long-term recommendations that can help to contain the outbreak so that it may spread to non-endemic areas.

Healthcare and Terrorism: The Lebanese Experience

2021 ◽  
pp. 1-4
Author(s):  
Nooreddine Iskandar ◽  
Tatiana Rahbany ◽  
Ali Shokor
Keyword(s):  
Public Health ◽  
Qualitative Study ◽  
Thematic Analysis ◽  
Terrorist Attacks ◽  
Analysis Method ◽  
Structured Interviews ◽  
Security Issues ◽  
The Face ◽  
The Common ◽  
First Time

Abstract Background: Due to the common instability caused by political and security issues, Lebanese hospitals have experienced acts of terrorism multiple times. The most recent Beirut Explosion even forced several hospitals to cease operations for the first time in decades—but studies show the preparedness levels for such attacks in similar countries are low. Objective: The aim of this study is to explore the experience of Lebanese hospitals with terrorist attacks. Methods: This qualitative study used semi-structured interviews with various stakeholders to assess their experience with terrorist bombings. Data was analyzed using the thematic analysis method. Results: The researchers found that Lebanese hospitals vary greatly in their structures and procedures. Those differences are a function of 3 contextual factors: location, culture, and accreditation status. Hospitals found near ‘dangerous zones’ were more likely to be aware and to have better response to such events. A severe lack of communication, unity of command, and collaboration between stakeholders has made the process fragmented. Conclusion: The researchers recommend a larger role for the Ministry of Public Health (MOPH) in this process, and the creation of a platform where Lebanese organizations can share their experiences to improve preparedness and resilience of the Lebanese healthcare system in the face of terrorism.

scholarly journals Approaches to Reducing Risk of COVID-19 Infections in Prisons and Immigration Detention Centers: A Commentary

2020 ◽  
pp. 073401682095770
Author(s):  
Kate Kelly ◽  
Nai Soto ◽  
Nadi Damond Wisseh ◽  
Shaina A. Clerget
Keyword(s):  
Public Health ◽  
Public Health Policy ◽  
Well Being ◽  
The United States ◽  
Correctional Staff ◽  
Staff Members ◽  
Detention Centers ◽  
Fast Spreading ◽  
Returning Home ◽  
The Face

Although often left out of public health efforts and policy decisions, prisons, jails, and detention centers are integral to community health. With an average of 650,000 citizens returning home from prison each year in the United States, and thousands of correctional staff members returning home every night, there are millions of touchpoints between outside communities and carceral settings. For this reason, carceral communities should be central to planning and policy making in response to the spread of the COVID-19 illness. As social workers and clinicians, we are urgently concerned that efforts to prevent COVID-19 infections in prisons are underdeveloped and inadequate in the face of a fast-spreading virus. In this commentary, we outline a set of public health, policy, and clinical recommendations based upon the existing literature to mitigate various risks to the well-being of carceral communities.

scholarly journals Emerging cross-disciplinary profiles: The Geomatic Epidemiologist

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
M Recchioni ◽  
V Castello ◽  
S Del Vecchio ◽  
V Ciaccio ◽  
A M Donia ◽  
...  
Keyword(s):  
Public Health ◽  
Information System ◽  
Geographic Information System ◽  
Relevant Literature ◽  
Holistic Approach ◽  
Geographic Information ◽  
Health Study ◽  
Gis And Remote Sensing ◽  
Public Health Epidemiology ◽  
And Training

Abstract Issue Geographic information systems (GIS) and remote sensing technologies are increasingly used in Public Health epidemiology, showing a great potential in anticipating and responding to actual and future challenges for the public health system and in improving health services' excellence. According to the evidences collected within a wide meta-research carried on of relevant literature (”GIS geographic information system” and “GIS geographic information system and training” on Pubmed; “epidemiologist use of GIS and training” and “epidemiologist use of gis” on Google Scholar),GIS and new sensing technologies are mostly used to: map air and water pollution, map diseases prevalence, predict infection diseases and vector-spread diseases in big areas, study health service coverage and preparedness in emergencies, map cities and study urban health, study climate changes for decision making. Description of the Problem Specific skills and training are required to address the use of GIS and new sensing technologies.The specific aim of our study is to identify the professional profile of a new figure, called 'Geomatic Epidemiologist' and to define its professional and educational standards, as well as the relevant training programs. Results Data collection and analysis of INAPP and ESCO databases about existing professional profiles (starting from 2016) has allowed drafting a first qualification schema and profile. The profile has been defined according to the 4C model (elaborated by Univaq) distinguishing between Hard Skills (technical knowledge and skills),Soft Skills (cognitive, individual and social) and interpersonal behaviors. Conclusions Profile will be validated with relevant stakeholders and Public Health professionals in order to deepen the understanding of the main competences required to study health issues with GIS and related technologies; to this extent, a questionnaire has been elaborated to evaluate relevance, frequency and complexity of each component of the profile Key messages Developing cross-disciplinary profiles, (i.e. the Geomatic Epidemiologist) integrating clusters of competences (holistic approach). Public health research challenges and excellence.

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