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Live genomics for pathogen monitoring in public health.

ABSTRACT: Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the "local" level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a "streaming approach" (pipeline). Such pipeline would NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted "comprehensible" results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences.

SUBMITTER: D'Auria G

PROVIDER: S-EPMC4235738 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Live genomics for pathogen monitoring in public health.

D'Auria Giuseppe G Schneider Maria Victoria MV Moya Andrés A

Pathogens (Basel, Switzerland) 20140121 1

Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, viru ...[more]

PMID: 25437609

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Project description:BACKGROUND: Public health genomics is an emerging multidisciplinary approach, which aims to integrate genome-based knowledge in a responsible and effective way into public health. Despite several surveys performed to evaluate knowledge, attitudes and professional behaviors of physicians towards predictive genetic testing, similar surveys have not been carried out for public health practitioners. This study is the first to assess knowledge, attitudes and training needs of public health professionals in the field of predictive genetic testing for chronic diseases. METHODS: A self-administered questionnaire was used to carry out a cross-sectional survey of a random sample of Italian public health professionals. RESULTS: A response rate of 67.4% (797 questionnaires) was achieved. Italian public health professionals have the necessary attitudinal background to contribute to the proper use of predictive genetic testing for chronic diseases, but they need additional training to increase their methodological knowledge. Knowledge significantly increases with exposure to predictive genetic testing during postgraduate training (odds ratio (OR)?=?1.74, 95% confidence interval (CI)?=?1.05-2.88), time dedicated to continuing medical education (OR?=?1.53, 95% CI?=?1.14-2.04) and level of English language knowledge (OR?=?1.36, 95% CI?=?1.07-1.72). Adequate knowledge is the strongest predictor of positive attitudes from a public health perspective (OR?=?3.98, 95% CI?=?2.44-6.50). Physicians show a lower level of knowledge and more public health attitudes than other public health professionals do. About 80% of public health professionals considered their knowledge inadequate and 86.0% believed that it should be improved through specific postgraduate training courses. CONCLUSIONS: Specific and targeted training initiatives are needed to develop a skilled public health workforce competent in identifying genomic technology that is ready for use in population health and in modeling public health genomic programs and primary care services that need to be developed, implemented and evaluated.

Project description:BackgroundPathogen genomics is increasingly being translated from the research setting into the activities of public health professionals operating at different levels. This survey aims to appraise the literacy level and gather the opinions of public health experts and allied professionals working in the field of infectious diseases in Belgium concerning the implementation of next-generation sequencing (NGS) in public health practice.MethodsIn May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic analysis was used to analyze free text responses. A multivariable logistic regression model was constructed to identify important predictors for a positive attitude towards the implementation of pathogen genomics in public health practice.Results146 out of the 753 invited public health professionals completed the survey. 63% of respondents indicated that public health agencies should be using genomics to understand and control infectious diseases. Having a high level of expertise in the field of pathogen genomics was the strongest predictor of a positive attitude (OR = 4.04, 95% CI = 1.11 - 17.23). A significantly higher proportion of data providers indicated to have followed training in the field of pathogen genomics compared to data end-users (p < 0.001). Overall, 79% of participants expressed interest in receiving further training. Main concerns were related to the cost of sequencing technologies, data sharing, data integration, interdisciplinary working, and bioinformatics expertise.ConclusionsBelgian health professionals expressed favorable views about implementation of pathogen genomics in their work activities related to infectious disease surveillance and control. They expressed the need for suitable training initiatives to strengthen their competences in the field. Their perception of the utility and feasibility of pathogen genomics for public health purposes will be a key driver for its further implementation.

Project description:The health systems in developing countries face challenges because of deficient monitoring and evaluation (M&E) capacity with respect to their knowledge, skills, and practices. Strengthening M&E training in public health education can help overcome the gaps in M&E capacity. There is a need to advance the teaching of M&E as a core element of public health education.To review M&E teaching across Masters of Public Health programs and to identify core competencies for M&E teaching in South Asian context.We undertook two activities to understand the M&E teaching across masters level programs: (1) desk review of M&E curriculum and teaching in masters programs globally and (2) review of M&E teaching across 10 institutions representing 4 South Asian countries. Subsequently, we used the findings of these two activities as inputs to identify core competencies for an M&E module through a consultative meeting with the 10 South Asian universities.Masters programs are being offered globally in 321 universities of which 88 offered a Masters in Public Health, and M&E was taught in 95 universities. M&E was taught as a part of another module in 49 institutions. The most common duration of M&E teaching was 4-5 weeks. From the 70 institutes where information on electives was available, M&E was a core module/part of a core module at 42 universities and an elective at 28 universities. The consultative meeting identified 10 core competencies and draft learning objectives for M&E teaching in masters programs in South Asia.The desk review showed similarities in M&E course content but variations in course structure and delivery. The core competencies identified during the consultation included basic M&E concepts. The results of the review and the core competencies identified at the consultation are useful resources for institutions interested in refining/updating M&E curricula in their postgraduate degree programs. Our approach for curriculum development as well as the consensus building experience could also be adapted for use in other situations.

Project description:BACKGROUND:Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS:In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS:Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS:For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.

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Live genomics for pathogen monitoring in public health.

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Live genomics for pathogen monitoring in public health.

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