MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
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ABSTRACT:
SUBMITTER: Campbell EM
PROVIDER: S-EPMC8491948 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Objectives: To summarize current research in the field of Public Health and Epidemiology Informatics. Methods: The complete 2016 literature concerning public health and epidemiology informatics has been searched in PubMed and Web of Science, and the returned references were reviewed by the two section editors to select 14 candidate best papers. These papers were then peer-reviewed by external reviewers to allow the editorial team an enlightened selection of the best papers. Results: Among the 829 references retrieved from PubMed and Web of Science, three were finally selected as best papers. The first one compares Google, Twitter, and Wikipedia as tools for Influenza surveillance. The second paper presents a Geographic Knowledge-Based Model for mapping suitable areas for Rift Valley fever transmission in Eastern Africa. The last paper evaluates the factors associated with the visit of Facebook pages devoted to Public Health Communication. Conclusions: Surveillance is still a productive topic in public health informatics but other very important topics in public health are appearing.
| S-EPMC6239244 | biostudies-other
Project description:ObjectiveThis study focuses on the epidemiology of COVID-19 in Europe and investigates public health response in severely hit countries.MethodsEuropean Centre for Disease Prevention and Control, Oxford COVID-19 Government Response Tracker and Health System Response Monitor were referred. The relationship between stringency index and COVID-19 cases, and between speed of stringency implementation and growth of cases was examined using linear regression.ResultsThe case-fatality ratio (CFR) of Europe (2.35%) was higher than the global CFR (2.2%). United Kingdom, Russia, France, Italy, Spain, and Germany together, accounted for 61.15% of cases and 65.62% of deaths in Europe. Significant relationship was observed between growth of COVID-19 cases and late substantive stringency imposed by countries. Population aged 65 and above (r = 0.9037, p < 0.01) and male population (r = 0.8701, p < 0.01) were significantly and positively correlated with COVID-19 deaths. The public health system of even big European countries encountered roadblocks, such as shortages of healthcare resources and deferral of non-COVID-19 treatments while dealing with the unprecedented pandemic.ConclusionEven big and richest European countries delayed the implementation of non-pharmaceutical interventions which led to rapid virus transmission. The pandemic has posed a reminder to make the public health system more resilient, as epidemics and pandemics of this nature will continue to threaten in future as well.
| S-EPMC8556869 | biostudies-literature
Project description:BackgroundEstimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies.MethodsPortuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups.ResultsWe identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively.ConclusionsThe estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
| S-EPMC6581889 | biostudies-literature
Project description:ObjectivesThe COVID-19 pandemic threatens to widen existing gender inequities worldwide. A growing body of literature assesses the harmful consequences of public health emergencies (PHEs) for women and girls; however, evidence of what works to alleviate such impacts is limited. To inform viable mitigation strategies, we reviewed the evidence on gender-based interventions implemented in PHEs, including disease outbreaks and natural disasters.MethodsWe conducted a rapid scoping review to identify eligible studies by systematically searching the databases MEDLINE, Global Health and Web of Science with the latest search update on 28 May 2021. We used the Sustainable Development Goals as a guiding framework to identify eligible outcomes of gender (in)equality.ResultsOut of 13 920 records, 16 studies met our eligibility criteria. These included experimental (3), cohort (2), case-control (3) and cross-sectional (9) studies conducted in the context of natural disasters (earthquakes, droughts and storms) or epidemics (Zika, Ebola and COVID-19). Six studies were implemented in Asia, seven in North/Central America and three in Africa. Interventions included economic empowerment programmes (5); health promotion, largely focused on reproductive health (10); and a postearthquake resettlement programme (1). Included studies assessed gender-based outcomes in the domains of sexual and reproductive health, equal opportunities, access to economic resources, violence and health. There was a dearth of evidence for other outcome domains relevant to gender equity such as harmful practices, sanitation and hygiene practices, workplace discrimination and unpaid work. Economic empowerment interventions showed promise in promoting women's and girls' economic and educational opportunities as well as their sexual and reproductive health during PHEs. However, some programme beneficiaries may be at risk of experiencing unintended harms such as an increase in domestic violence. Focused reproductive health promotion may also be an effective strategy for supporting women's sexual and reproductive health, although additional experimental evidence is needed.ConclusionsThis study identified critical evidence gaps to guide future research on approaches to alleviating gender inequities during PHEs. We further highlight that interventions to promote gender equity in PHEs should take into account possible harmful side effects such as increased gender-based violence.Review registrationDOI 10.17605/OSF.IO/8HKFD.
| S-EPMC8361708 | biostudies-literature
Project description:BackgroundEnvironmental transmission of the zoonotic parasite Toxoplasma gondii, which is shed only by felids, poses risks to human and animal health in temperate and tropical ecosystems. Atypical T. gondii genotypes have been linked to severe disease in people and the threatened population of California sea otters. To investigate land-to-sea parasite transmission, we screened 373 carnivores (feral domestic cats, mountain lions, bobcats, foxes, and coyotes) for T. gondii infection and examined the distribution of genotypes in 85 infected animals sampled near the sea otter range.Methodology/principal findingsNested PCR-RFLP analyses and direct DNA sequencing at six independent polymorphic genetic loci (B1, SAG1, SAG3, GRA6, L358, and Apico) were used to characterize T. gondii strains in infected animals. Strains consistent with Type X, a novel genotype previously identified in over 70% of infected sea otters and four terrestrial wild carnivores along the California coast, were detected in all sampled species, including domestic cats. However, odds of Type X infection were 14 times higher (95% CI: 1.3-148.6) for wild felids than feral domestic cats. Type X infection was also linked to undeveloped lands (OR = 22, 95% CI: 2.3-250.7). A spatial cluster of terrestrial Type II infection (P = 0.04) was identified in developed lands bordering an area of increased risk for sea otter Type II infection. Two spatial clusters of animals infected with strains consistent with Type X (P ? 0.01) were detected in less developed landscapes.ConclusionsDifferences in T. gondii genotype prevalence among domestic and wild felids, as well as the spatial distribution of genotypes, suggest co-existing domestic and wild T. gondii transmission cycles that likely overlap at the interface of developed and undeveloped lands. Anthropogenic development driving contact between these cycles may increase atypical T. gondii genotypes in domestic cats and facilitate transmission of potentially more pathogenic genotypes to humans, domestic animals, and wildlife.
| S-EPMC4038486 | biostudies-literature
Project description:IntroductionThe changing epidemiology of Clostridioides difficile reflects a well-established and intricate community transmission network. With rising numbers of reported community-acquired infections, recent studies tried to identify the role played by non-human reservoirs in the pathogen's transmission chain. This study aimed at describing the C. difficile strains circulating in canine and feline populations, and to evaluate their genetic overlap with human strains to assess the possibility of interspecies transmission.MethodsFecal samples from dogs (n = 335) and cats (n = 140) were collected from two populations (group A and group B) in Portugal. C. difficile isolates were characterized for toxigenic profile and PCR-ribotyping. The presence of genetic determinants of antimicrobial resistance was assessed in all phenotypically resistant isolates. To evaluate the genetic overlap between companion animals and human isolates from Portugal, RT106 (n = 42) and RT014/020 (n = 41) strains from both sources were subjected to whole genome sequencing and integrated with previously sequenced RT106 (n = 43) and RT014/020 (n = 142) genomes from different countries. The genetic overlap was assessed based on core-single nucleotide polymorphism (SNP) using a threshold of 2 SNP.ResultsThe overall positivity rate for C. difficile was 26% (76/292) in group A and 18.6% (34/183) in group B. Toxigenic strains accounted for 50% (38/76) and 52.9% (18/34) of animal carriage rates, respectively. The most prevalent ribotypes (RT) were the toxigenic RT106 and RT014/020, and the non-toxigenic RT010 and RT009. Antimicrobial resistance was found for clindamycin (27.9%), metronidazole (17.1%) and moxifloxacin (12.4%), associated with the presence of the ermB gene, the pCD-METRO plasmid and point mutations in the gyrA gene, respectively. Both RT106 and RT014/020 genetic analysis revealed several clusters integrating isolates from animal and human sources, supporting the possibility of clonal interspecies transmission or a shared environmental contamination source.DiscussionThis study shows that companion animals may constitute a source of infection of toxigenic and antimicrobial resistant human associated C. difficile isolates. Additionally, it contributes with important data on the genetic proximity between C. difficile isolates from both sources, adding new information to guide future work on the role of animal reservoirs in the establishment of community associated transmission networks and alerting for potential public health risk.
| S-EPMC9853383 | biostudies-literature
Project description:SARS CoV-2 WGS (Georgia Department of Public Health)
| PRJNA713775 | ENA
Project description:IntroductionCommunity pharmacists and their teams have remained accessible to the public providing essential services despite immense pressures during the COVID-19 pandemic. They have successfully expanded the influenza vaccination programme and are now supporting the delivery of the COVID-19 vaccination roll-out.AimThis rapid realist review aims to understand how community pharmacy can most effectively deliver essential and advanced services, with a focus on vaccination, during the pandemic and in the future.MethodAn embryonic programme theory was generated using four diverse and complementary documents along with the expertise of the project team. Academic databases, preprint services and grey literature were searched and screened for documents meeting our inclusion criteria. The data were extracted from 103 documents to develop and refine a programme theory using a realist logic of analysis. Our analysis generated 13 context-mechanism-outcome configurations explaining when, why and how community pharmacy can support public health vaccination campaigns, maintain essential services during pandemics and capitalise on opportunities for expanded, sustainable public health service roles. The views of stakeholders including pharmacy users, pharmacists, pharmacy teams and other healthcare professionals were sought throughout to refine the 13 explanatory configurations.ResultsThe 13 context-mechanism-outcome configurations are organised according to decision makers, community pharmacy teams and community pharmacy users as key actors. Review findings include: supporting a clear role for community pharmacies in public health; clarifying pharmacists' legal and professional liabilities; involving pharmacy teams in service specification design; providing suitable guidance, adequate compensation and resources; and leveraging accessible, convenient locations of community pharmacy.DiscussionCommunity pharmacy has been able to offer key services during the pandemic. Decision makers must endorse, articulate and support a clear public health role for community pharmacy. We provide key recommendations for decision makers to optimise such a role during these unprecedented times and in the future.
| S-EPMC8210681 | biostudies-literature
Project description:Although Mycoplasma genitalium is increasingly recognized as a sexually transmitted pathogen, at present there is no defined public health response to this relatively newly identified sexually transmitted infection. Currently available data are insufficient to justify routinely screening any defined population for M. genitalium infection. More effective therapies, data on acceptability of screening and its impact on clinical outcomes, and better information on the natural history of infection will likely be required before the value of potential screening programs can be adequately assessed. Insofar as diagnostic tests are available or become available in the near future, clinicians and public health agencies should consider integrating M. genitalium testing into the management of persons with sexually transmitted infection (STI) syndromes associated with the infection (ie urethritis, cervicitis, and pelvic inflammatory disease) and their sex partners. Antimicrobial-resistant M. genitalium is a significant problem and may require clinicians and public health authorities to reconsider the management of STI syndromes in an effort to prevent the emergence of ever more resistant M. genitalium infections.
| S-EPMC5853686 | biostudies-other
Project description:Advances in laboratory and information technologies are transforming public health microbiology. High-throughput genome sequencing and bioinformatics are enhancing our ability to investigate and control outbreaks, detect emerging infectious diseases, develop vaccines, and combat antimicrobial resistance, all with increased accuracy, timeliness, and efficiency. The Advanced Molecular Detection (AMD) initiative has allowed the Centers for Disease Control and Prevention (CDC) to provide leadership and coordination in integrating new technologies into routine practice throughout the U.S. public health laboratory system. Collaboration and partnerships are the key to navigating this transition and to leveraging the next generation of methods and tools most effectively for public health.
| S-EPMC5328438 | biostudies-literature