public health genetics
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2021 ◽  
Vol 7 (5) ◽  
pp. 4-5
Author(s):  
Louis E. Bartoshesky

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Leonor Sánchez-Busó ◽  
Corin A. Yeats ◽  
Benjamin Taylor ◽  
Richard J. Goater ◽  
Anthony Underwood ◽  
...  

Abstract Background Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance. Methods Here we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch (https://pathogen.watch/ngonorrhoeae). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization. Results AMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern. Conclusions The N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.


Bioethica ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 6
Author(s):  
Aikaterini A Aspradaki

The strong relationship between bioethics and public health has been put forward since the early 1970s. The HIV/AIDS epidemic, erupted in the 1980s, serves as a catalyst for the broadening of the bioethics frameworks by the inclusion of ethical issues faced in public health. From the beginning of the 21st century, public health ethics has been emerged as a discipline and has been established as a subfield of bioethics.Topics in public health ethics include, among others, the public health research, the ethics and infectious disease control, the ethics of health promotion and disease prevention, the ethical issues in environmental and occupational health, the public health and health system reform: allocation of resources, access, priority setting, the international collaboration for global public health, the vulnerability and marginalized populations, the public health genetics, the public health genomics. The COVID-19 pandemic seems to constitute an area of conceptual and practical overlapping of all the above-mentioned topics and gives huge boost to research interest for public health bioethics.This paper explains the relationship between bioethics and public health through two time periods and, in particular, the “early” 1970s- 1990s era and the2000s & 2010s that is the period of the emergence and establishment of public health ethics marked, at the end, by the COVID-19 pandemic.


Author(s):  
Leonor Sánchez-Busó ◽  
Corin A. Yeats ◽  
Benjamin Taylor ◽  
Richard J. Goater ◽  
Anthony Underwood ◽  
...  

AbstractBackgroundAntimicrobial resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones, transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance.MethodsHere we present a public health focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch (https://pathogen.watch/ngonorrhoeae). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization.ResultsAMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasizing the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern.ConclusionsThe N. gonorrhoeae scheme in Pathogenwatch provides customized bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.


Author(s):  
Paul Lombardo

This chapter details historical points of connection between the field of public health and the eugenics movement in the United States, and explores the ethical significance of public health genetics in light of that history. It explains how attention to both eugenics and public health grew simultaneously in the twentieth-century United States, and how both fields contributed to the growth of laws that emphasized the use of the police power to constrain reproduction and immigration among certain groups as a means to advance efficiency and social progress. The chapter suggests that an emphasis on the prevention of problematic hereditary conditions supplies a similar motive for a new public health genetics today.


Author(s):  
Debra J. H. Mathews

Public health genetics (more commonly referred to as “community genetics” in Europe) has been practiced to some degree in the West since at least the 1960s, but the development of a cohesive field took time and advances in technology. The application of genetics and genomics to prevent disease and promote public health became firmly established as a field in the late 1990s, as large-scale sequencing of the human genome as part of the Human Genome Project began. The field is now thriving, leading to both tremendous public health benefits and risks for both individuals and populations. This chapter provides an overview of the section of The Oxford Handbook of Public Health Ethics dedicated to public health genetics. The chapters roughly trace the evolution of public health genetics from its roots in eugenics, to the present challenges faced in newborn screening and biobanking, and finally to emerging questions raised by the application of genomics to infectious disease.


Healthcare ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 93 ◽  
Author(s):  
Stephen Modell ◽  
Toby Citrin ◽  
Sharon Kardia

The United States Precision Medicine Initiative (PMI) was announced by then President Barack Obama in January 2015. It is a national effort designed to take into account genetic, environmental, and lifestyle differences in the development of individually tailored forms of treatment and prevention. This goal was implemented in March 2015 with the formation of an advisory committee working group to provide a framework for the proposed national research cohort of one million or more participants. The working group further held a public workshop on participant engagement and health equity, focusing on the design of an inclusive cohort, building public trust, and identifying active participant engagement features for the national cohort. Precision techniques offer medical and public health practitioners the opportunity to personally tailor preventive and therapeutic regimens based on informatics applied to large volume genotypic and phenotypic data. The PMI’s (All of Us Research Program’s) medical and public health promise, its balanced attention to technical and ethical issues, and its nuanced advisory structure made it a natural choice for inclusion in the University of Michigan course “Issues in Public Health Genetics” (HMP 517), offered each fall by the University’s School of Public Health. In 2015, the instructors included the PMI as the recurrent case study introduced at the beginning and referred to throughout the course, and as a class exercise allowing students to translate issues into policy. In 2016, an entire class session was devoted to precision medicine and precision public health. In this article, we examine the dialogues that transpired in these three course components, evaluate session impact on student ability to formulate PMI policy, and share our vision for next-generation courses dealing with precision health. Methodology: Class materials (class notes, oral exercise transcripts, class exercise written hand-ins) from the three course components were inspected and analyzed for issues and policy content. The purpose of the analysis was to assess the extent to which course components have enabled our students to formulate policy in the precision public health area. Analysis of student comments responding to questions posed during the initial case study comprised the initial or “pre-” categories. Analysis of student responses to the class exercise assignment, which included the same set of questions, formed the “post-” categories. Categories were validated by cross-comparison among the three authors, and inspected for frequency with which they appeared in student responses. Frequencies steered the selection of illustrative quotations, revealing the extent to which students were able to convert issue areas into actual policies. Lecture content and student comments in the precision health didactic session were inspected for degree to which they reinforced and extended the derived categories. Results: The case study inspection yielded four overarching categories: (1) assurance (access, equity, disparities); (2) participation (involvement, representativeness); (3) ethics (consent, privacy, benefit sharing); and (4) treatment of people (stigmatization, discrimination). Class exercise inspection and analysis yielded three additional categories: (5) financial; (6) educational; and (7) trust-building. The first three categories exceeded the others in terms of number of student mentions (8–14 vs. 4–6 mentions). Three other categories were considered and excluded because of infrequent mention. Students suggested several means of trust-building, including PMI personnel working with community leaders, stakeholder consultation, networking, and use of social media. Student representatives prioritized participant and research institution access to PMI information over commercial access. Multiple schemes were proposed for participant consent and return of results. Both pricing policy and Medicaid coverage were touched on. During the didactic session, students commented on the importance of provider training in precision health. Course evaluation highlighted the need for clarity on the organizations involved in the PMI, and leaving time for student-student interaction. Conclusions: While some student responses during the exercise were terse, an evolution was detectable over the three course components in student ability to suggest tangible policies and steps for implementation. Students also gained surety in presenting policy positions to a peer audience. Students came up with some very creative suggestions, such as use of an electronic platform to assure participant involvement in the disposition of their biological sample and personal health information, and alternate examples of ways to manage large volumes of data. An examination of socio-ethical issues and policies can strengthen student understanding of the directions the Precision Medicine Initiative is taking, and aid in training for the application of more varied precision medicine and public health techniques, such as tier 1 genetic testing and whole genome and exome sequencing. Future course development may reflect additional features of the ongoing All of Us Research Program, and further articulate precision public health approaches applying to populations as opposed to single individuals.


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