Dataset Information

Complete microbial genomes for public health in Australia and the Southwest Pacific.

ABSTRACT: Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.

SUBMITTER: Baines SL

PROVIDER: S-EPMC8116684 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Complete microbial genomes for public health in Australia and the Southwest Pacific.

Baines Sarah L SL da Silva Anders Gonçalves AG Carter Glen P GP Jennison Amy A Rathnayake Irani I Graham Rikki M RM Sintchenko Vitali V Wang Qinning Q Rockett Rebecca J RJ Timms Verlaine J VJ Martinez Elena E Ballard Susan S Tomita Takehiro T Isles Nicole N Horan Kristy A KA Pitchers William W Stinear Timothy P TP Williamson Deborah A DA Howden Benjamin P BP Seemann Torsten T Communicable Diseases Genomics Network Cdgn

Microbial genomics 20201112 12

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbio ...[more]

PMID: 33180013

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Project description:BackgroundAt present, we have very limited ability to compare public health activity across jurisdictions and countries, or even to ascertain differences in what is considered to be a public health activity. Existing standardised health classifications do not capture important dimensions of public health, which include its functions, the methods and interventions used to achieve these, the health issues and determinants of health that public health activities address, the resources and infrastructure they use, and the settings in which they occur. A classification that describes these dimensions will promote consistency in collecting and reporting information about public health programs, expenditure, workforce and performance. This paper describes the development of an initial version of such a classification.MethodsWe used open-source Protégé software and published procedures to construct an ontology of public health, which forms the basis of the classification. We reviewed existing definitions of public health, descriptions of public health functions and classifications to develop the scope, domain, and multidimensional class structure of the ontology. These were then refined through a series of consultations with public health experts from across Australia, culminating in an initial classification framework.ResultsThe public health classification consists of six top-level classes: public health 'Functions'; 'Health Issues'; 'Determinants of Health'; 'Settings'; 'Methods' of intervention; and 'Resources and Infrastructure'. Existing classifications (such as the international classifications of diseases, disability and functioning and external causes of injuries) can be used to further classify large parts of the classes 'Health Issues', 'Settings' and 'Resources and Infrastructure', while new subclass structures are proposed for the classes of public health 'Functions', 'Determinants of Health' and 'Interventions'.ConclusionThe public health classification captures the important dimensions of public health activity. It will facilitate the organisation of information so that it can be used to address questions relating to any of these dimensions, either singly or in combination. The authors encourage readers to use the classification, and to suggest improvements.

Project description:BackgroundThe level of health professional work engagement affects retention, burnout, job satisfaction, patient satisfaction, and outcomes; however, there is a paucity of evidence that benefit health professional work engagement. Therefore, this study aimed to assess work engagement and associated factors among health professionals at public health facilities in the Bench-Sheko zone in southwest Ethiopia.MethodsFacility-based cross-sectional study was conducted among 605 health professionals from 29 March to 29 April 2021. A simple random sampling technique was used to select the participants. Data were collected using a self-administered questionnaire. Linear regression was fitted and those variables with p-value < 0.2 in simple linear regression were entered into multiple linear regression analysis. Unstandardized β-coefficient with 95% CI and p-value < 0.05 were used as the cut of points to determine the factors associated with work engagement.ResultsMean score percentage of work engagement was 71.8%. Health center staff (β = 0.31; 95% CI: 0.22, 0.40), married professionals (β = 0.10; 95% CI: 0.005, 0.17), co-worker support (β = 0.06; 95% CI: 0.004, 0.11), role clarity (β = 0.14; 95% CI: 0.07, 0.21), reward (β = 0.10; 95% CI: 0.05, 0.15), resilience (β = 0.14 95%; CI: 0.07, 0.21), self-efficacy (β = 0.24; 95% CI: 0.16, 0.31) and optimism (β = 0.20; 95% CI: 0.15, 0.26) were positively associated with work engagement. On the contrary, cognitive demand (β= -0.06; 95% CI: -0.11, -0.01) was negatively associated with work engagement.ConclusionIn this study, health professionals had a moderate level of work engagement. Health facilities shall improve their culture of co-worker support, role clarity, reward, resilience, self-efficacy, and optimism to enhance work engagement. Future researchers shall be done further studies to evaluate the relationship between cognitive demand and work engagement among health professionals.

Project description:Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

Dataset Information

Complete microbial genomes for public health in Australia and the Southwest Pacific.

Publications

Complete microbial genomes for public health in Australia and the Southwest Pacific.

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