Dataset Information

Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.

ABSTRACT: Pockets of susceptibility resulting from spatial or social heterogeneity in vaccine coverage can drive measles outbreaks, as cases imported into such pockets are likely to cause further transmission and lead to large transmission clusters. Characterizing the dynamics of transmission is essential for identifying which individuals and regions might be most at risk. As data from detailed contact-tracing investigations are not available in many settings, we developed an R package called o2geosocial to reconstruct the transmission clusters and the importation status of the cases from their age, location, genotype and onset date. We compared our inferred cluster size distributions to 737 transmission clusters identified through detailed contact-tracing in the USA between 2001 and 2016. We were able to reconstruct the importation status of the cases and found good agreement between the inferred and reference clusters. The results were improved when the contact-tracing investigations were used to set the importation status before running the model. Spatial heterogeneity in vaccine coverage is difficult to measure directly. Our approach was able to highlight areas with potential for local transmission using a minimal number of variables and could be applied to assess the intensity of ongoing transmission in a region.

SUBMITTER: Robert A

PROVIDER: S-EPMC7423430 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.

Robert Alexis A Kucharski Adam J AJ Gastañaduy Paul A PA Paul Prabasaj P Funk Sebastian S

Journal of the Royal Society, Interface 20200701 168

Pockets of susceptibility resulting from spatial or social heterogeneity in vaccine coverage can drive measles outbreaks, as cases imported into such pockets are likely to cause further transmission and lead to large transmission clusters. Characterizing the dynamics of transmission is essential for identifying which individuals and regions might be most at risk. As data from detailed contact-tracing investigations are not available in many settings, we developed an R package called <i>o2geosoci ...[more]

PMID: 32603651

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Project description:BackgroundMolecular epidemiological approaches provide opportunities to characterize HIV transmission dynamics. We analyzed HIV sequences and virus load (VL) results obtained during routine clinical care, and individual's zip-code location to determine utility of this approach.MethodsHIV-1 pol sequences aligned using ClustalW were subtyped using REGA. A maximum likelihood (ML) tree was generated using IQTree. Transmission clusters with ≤3% genetic distance (GD) and ≥90% bootstrap support were identified using ClusterPicker. We conducted Bayesian analysis using BEAST to confirm transmission clusters. The proportion of nucleotides with ambiguity ≤0.5% was considered indicative of early infection. Descriptive statistics were applied to characterize clusters and group comparisons were performed using chi-square or t-test.ResultsAmong 2775 adults with data from 2014-2015, 2589 (93%) had subtype B HIV-1, mean age was 44 years (SD 12.7), 66.4% were male, and 25% had nucleotide ambiguity ≤0.5. There were 456 individuals in 193 clusters: 149 dyads, 32 triads, and 12 groups with ≥ four individuals per cluster. More commonly in clusters were males than females, 349 (76.5%) vs. 107 (23.5%), p < 0.0001; younger individuals, 35.3 years (SD 12.1) vs. 44.7 (SD 12.3), p < 0.0001; and those with early HIV-1 infection by nucleotide ambiguity, 202/456 (44.3%) vs. 442/2133 (20.7%), p < 0.0001. Members of 43/193 (22.3%) of clusters included individuals in different jurisdictions. Clusters ≥ four individuals were similarly found using BEAST. HIV-1 viral load (VL) ≥3.0 log10 c/mL was most common among individuals in clusters ≥ four, 18/21, (85.7%) compared to 137/208 (65.8%) in clusters sized 2-3, and 927/1169 (79.3%) who were not in a cluster (p < 0.0001).DiscussionHIV sequence data obtained for HIV clinical management provide insights into regional transmission dynamics. Our findings demonstrate the additional utility of HIV-1 VL data in combination with phylogenetic inferences as an enhanced contact tracing tool to direct HIV treatment and prevention services. Trans-jurisdictional approaches are needed to optimize efforts to end the HIV epidemic.

Project description:ObjectiveAntipsychotics are licensed for psychosis and are also prescribed for behavior control. This study aims to examine characteristics and outcomes of children prescribed antipsychotics.MethodsA cohort study using general practice and hospital records linked with education records for 1,488,936 children living in Wales between 1999 and 2015. The characteristics of the children who were prescribed antipsychotics are presented using descriptive statistics and outcomes such as respiratory illness, diabetes, and injury were analyzed using multilevel logistic regression and the prior event rate ratio (PERR).ResultsChildren with intellectual difficulty/autism were more likely to be prescribed antipsychotics (2.8% have been prescribed an antipsychotic [75% with autism] compared with 0.15% of children without intellectual difficulty). Those with intellectual disabilities/autism were prescribed antipsychotics at a younger age and for a longer period. Antipsychotic use was associated with a higher rate of respiratory illness for all (PERR of hospital admission: 1.55 [95% CI: 1.51-1.598] or increase in rate of 2 per 100 per year in those treated), and for those with intellectual difficulty/autism, there was a higher rate of injury and hospitalized depression. However, among those without intellectual difficulty/autism, there were lower rates of depression (PERR: 0.55 [95% CI: 0.51-0.59]).ConclusionsThis work shows real-world use of antipsychotics and provides information on the rate of possible adverse events in children treated. Antipsychotics are predominantly used for those with intellectual difficulty/autism rather than those with a psychotic diagnosis. There is evidence that rates of respiratory disease, epilepsy, and diabetes are also higher postantipsychotic use for all. In those with intellectual difficulty/autism, hospital-admitted depression and injury are higher postantipsychotic use. The use of antipsychotics for behavioral management is likely to have increased cost implications to the healthcare system.

Dataset Information

Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.

Publications

Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.

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