Complete microbial genomes for public health in Australia and the Southwest Pacific.
Ontology highlight
ABSTRACT:
SUBMITTER: Baines SL
PROVIDER: S-EPMC8116684 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recently in Australia concerns have been raised regarding the contamination of municipal drinking water supplies with lead. This is of particular concern to children due to the impact of lead exposure on cognitive development and as such these findings have received much media attention. The response from legislators has been swift, and The Victorian School Building Authority has announced that all new schools and school upgrade works will only use lead-free tapware and piping systems. However, while the immediate replacement of lead-containing brass fittings may seem a logical and obvious response, it does not consider the potential implications on microbial contamination. This is particularly concerning given the increasing public health threat posed by opportunistic premise plumbing pathogens (OPPPs). This commentary explores this public health risk of lead exposure from plumbing materials compared to the potential public health risks from OPPPs. Non-tuberculous mycobacterium was chosen as the example OPPP, and the influence on plumbing material and its public health burden in Australia is explored. This commentary highlights the need for future research into the influence of plumbing material on OPPPs prior to any changes in legislation regarding plumbing material.
| S-EPMC6843933 | biostudies-literature
Project description:BACKGROUND:At 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. METHODS:We 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. RESULTS:The 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'. CONCLUSION:The 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.
| S-EPMC2674448 | biostudies-literature
Project description:We report the unprecedented Lapita exploitation and subsequent extinction of large megafauna tortoises (?Meiolania damelipi) on tropical islands during the late Holocene over a 281,000?km2 region of the southwest Pacific spanning from the Vanuatu archipelago to Viti Levu in Fiji. Zooarchaeological analyses have identified seven early archaeological sites with the remains of this distinctive hornless tortoise, unlike the Gondwanan horned meiolaniid radiation to the southwest. These large tortoise radiations in the Pacific may have contributed to the rapid dispersal of early mobile Neolithic hunters throughout southwest Melanesia and on to western Polynesia. Subsequent rapid extinctions of these terrestrial herbivorous megafauna are likely to have led to significant changes in ecosystems that help explain changes in current archaeological patterns from Post-Lapita contexts in the region.
| S-EPMC5138842 | biostudies-other
Project description:Genomic analyses of VRE at an Australian public hospital
| PRJEB25449 | ENA
Project description:Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-?m size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.
| S-EPMC4410273 | biostudies-literature
Project description:BackgroundEqualizing basic public health services (BPHS) for all has been one goal of the health system reform in China since 2009. At the end of the 12th five-year plan, we conducted a series of surveys to understand BPHS implementation in Southwest China, and firstly reported implementation of health education (HE) and explore the barriers to HE delivery.MethodsMixed research methods were used to investigate achievement in and barriers to HE in Southwest China. SPSS 22.0 was used for data analysis.ResultsNine hundred and eighty-nine residents were surveyed by questionnaire. 16 health care workers (HCWs) and 16 directors from 16 PHC sectors were included in the in-depth interviews. Less than 50% of residents who knew or utilized some item of HE. Age, residence, region (Chongqing or Guizhou), marital status, education, occupation, type and quality of primary health care (PHC) sectors to deliver BPHS, self-reported health and status of chronic diseases were associated with knowledge or utilization of HE. Distance to PHC sectors was associated with the knowledge of HE, gender and health insurance were associated with utilization of HE. Age, marital status, occupation region and self-reported health were associated with satisfaction regarding HE. Barriers to HE delivery included defects in HE design, weak capacity in PHC sectors to provide HE, residents' poor cooperation, lack of multi-sector cooperation, poor equipment and weak health system.ConclusionsSouthwest China delivered HE in all PHC sectors. However, our study underlined many barriers to equalization of HE. To address those barriers and achieve HE quality improvement, comprehensive measures to improve capacity of PHC sectors, enhance multi-sector cooperation and strengthen health information systems are all urgent needs.
| S-EPMC7092608 | biostudies-literature
Project description:Roundworms (Ascaridida: Nematoda), one of the most common soil-transmitted helminths (STHs), can cause ascariasis in various hosts worldwide, ranging from wild to domestic animals and humans. Despite the veterinary and health importance of the Ascaridida species, little or no attention has been paid to roundworms infecting wild animals including non-human primates due to the current taxon sampling and survey bias in this order. Importantly, there has been considerable controversy over the years as to whether Ascaris species infecting non-human primates are the same as or distinct from Ascaris lumbricoides infecting humans. Herein, we first characterized the complete mitochondrial genomes of two representative Ascaris isolates derived from two non-human primates, namely, chimpanzees (Pan troglodytes) and gibbons (Hylobates hoolock), in a zoological garden of southwest China and compared them with those of A. lumbricoides and the congeneric Ascaris suum as well as other related species in the same order, and then used comparative mitogenomics, genome-wide nucleotide sequence identity analysis, and phylogeny to determine whether the parasites from chimpanzees and gibbons represent a single species and share genetic similarity with A. lumbricoides. Taken together, our results yielded strong statistical support for the hypothesis that the chimpanzee- and gibbon-derived Ascaris represent a single species that is genetically similar to A. lumbricoides, consistent with the results of previous morphological and molecular studies. Our finding should enhance public alertness to roundworms originating from chimpanzees and gibbons and the mtDNA data presented here also serves to enrich the resource of markers that can be used in molecular diagnostic, systematic, population genetic, and evolutionary biological studies of parasitic nematodes from either wild or domestic hosts.
| S-EPMC3866200 | biostudies-literature
Project description:SARS CoV-2 WGS (Georgia Department of Public Health)
| PRJNA713775 | ENA
Project description:BackgroundProviding universal basic public health services (BPHS) for residents is the main goal of the new health reform in China. Lay health workers (LHWs) in primary health care (PHC) sectors play key roles in BPHS delivery. The competency of LHWs is critical to quality BPHS. This study assessed LHWs' competency to deliver BPHS and related training in resource-limited Southwest China.MethodsA mixed research method combining in-depth interviews with secondary data collection was used to collect data in this cross-sectional study. Fifty-four LHWs and 16 leaders in 16 PHC sectors were recruited for in-depth interviews. Secondary data on 198 LHWs were collected through standard forms.ResultsBoth the interviews and secondary data suggested that all PHC sectors did not have sufficient LHWs and lacked qualified LHWs to deliver BPHS overall, particularly in relatively low economic rural areas in Guizhou province. Furthermore, PHC sectors had difficulties retaining existing LHWs due to low incomes and fewer opportunities for self-development. In-depth interviews discovered that, although numerous training opportunities have been provided for LHWs since 2009, the trainings did not achieve the expected outcome in LHW competency building, as LHWs actually did not have access to the trainings and the training design was unresponsive to the actual needs of LHWs. Both LHWs and leaders expressed an urgent need for effective training for LHWs based on systematic needs assessments and the use of qualified trainers and materials.ConclusionsThe shortage of qualified LHWs in PHC sectors became the bottleneck for BPHS delivery in Southwest China. Recent trainings for LHWs were less effective with regard to LHW competency building. A need-based professional training programme for LHWs by qualified trainers was expected by both LHWs and leaders in PHC sectors.
| S-EPMC6708187 | biostudies-literature
Project description:Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.
| S-EPMC1201611 | biostudies-literature