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:BackgroundYersinia enterocolitica has been sporadically recovered from animals, foods, and human clinical samples in various regions of Ningxia, China. However, the ecological and molecular characteristics of Y. enterocolitica, as well as public health concerns about infection in the Ningxia Hui Autonomous Region, remain unclear. This study aims to analyze the ecological and molecular epidemiological characteristics of Y. enterocolitis in order to inform the public health intervention strategies for the contains of related diseases.MethodsA total of 270 samples were collected for isolation [animals (n = 208), food (n = 49), and patients (n = 13)], then suspect colonies were isolated and identified by the API20E biochemical identification system, serological tests, biotyping tests, and 16S rRNA-PCR. Then, we used an ecological epidemiological approach combined with machine learning algorithms (general linear model, random forest model, and eXtreme Gradient Boosting) to explore the associations between ecological factors and the pathogenicity of Y. enterocolitis. Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. The statistical test used single-factor analysis, Chi-square tests, t-tests/ANOVA-tests, Wilcoxon rank-sum tests, and Kruskal-Wallis tests.ResultsA total of 270 isolates of Yersinia were identified from poultry and livestock (n = 191), food (n = 49), diarrhoea patients (n = 13), rats (n = 15), and hamsters (n = 2). The detection rates of samples from different hosts were statistically different (χ2 = 22.636, P < 0.001). According to the relatedness clustering results, 270 isolates were divided into 12 species, and Y. enterocolitica (n = 187) is a predominated species. Pathogenic isolates made up 52.4% (98/187), while non-pathogenic isolates made up 47.6% (89/187). Temperature and precipitation were strongly associated with the pathogenicity of the isolates (P < 0.001). The random forest (RF) prediction model showed the best performance. The prediction result shows a high risk of pathogenicity Y. enterocolitica was located in the northern, northwestern, and southern of the Ningxia Hui Autonomous Region. The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571, respectively.ConclusionsThe data indicated geographical variations in the distribution of STs and CTs of Y. enterocolitica isolates in Ningxia. Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment. CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. Therefore, strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.
| S-EPMC10120104 | 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: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:Wastewater-based epidemiology (WBE) is an environmental approach to monitor community health through the analysis of sewage. The COVID-19 pandemic catalyzed scientists and public health professionals to revisit WBE as a tool to optimize resource allocation to mitigate disease spread and prevent outbreaks. Some studies have highlighted the value of WBE programs that coordinate with public health professionals; however, the details necessary for implementation are not well-characterized. To respond to this knowledge gap, this article documents the framework of a successful WBE program in Arizona, titled Wastewater Analysis for Tactical Epidemiological Response Systems (WATERS), detailing the developed structure and methods of communication that enabled public health preparedness and response actions. This communication illustrates how program operations were employed to reduce outbreak severity. The structure outlined here is customizable and may guide other programs in the implementation of WBE as a public health tool.
| S-EPMC11312382 | biostudies-literature
Project description:SARS CoV-2 WGS (Georgia Department of Public Health)
| PRJNA713775 | ENA
Project description:On September 21, 2019, the Shenzhen and Dongguan Centers for Disease Control and Prevention received notification of a large cluster of suspected gastroenteritis involving primarily children who sought medical care at hospitals throughout two adjacent cities in China, Shenzhen, and Dongguan. A joint outbreak response was promptly initiated across jurisdictions in a concerted effort between clinical microbiologists, epidemiologists, and public health scientists. Concurrently, multiplex PCRs were used for rapid laboratory diagnosis of suspected cases; epidemiological investigations were conducted to identify the outbreak source, complemented by near real-time multicenter whole-genome analyses completed within 34 h. Epidemiological evidence indicated that all patients had consumed egg sandwiches served on September 20 as snacks to children and staff at a nursery in Dongguan, located near Shenzhen. Salmonella Enteritidis was isolated from case-patients, food handlers, kitchenware, and sandwiches with kitchen-made mayonnaise. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis demonstrated a well-supported cluster with pairwise distances of ≤1 SNP between genomes for outbreak-associated isolates, providing the definitive link between all samples. In comparison with historical isolates from the same geographical region, the minimum pairwise distance was >14 SNPs, suggesting a non-local outbreak source. Genomic source tracing revealed the possible transmission dynamics of a S. Enteritidis clone throughout a multi-provincial egg distribution network. The efficiency and scale with which multidisciplinary and integrated approaches were coordinated in this foodborne disease outbreak response was unprecedented in China, leading to the timely intervention of a large cross-jurisdiction Salmonella outbreak.
| S-EPMC9117964 | 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