2671 research outputs found
Sort by
superspreading: Understand Individual-Level Variation in Infectious Disease Transmission
No full textEstimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions (Kremer et al. (2021) ), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct (Kucharski et al. (2020) ), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission (Lloyd-Smith et al. (2005) )
ckim0509/amr_cost
No full textData and code to support systematic review and meta-analysis, titled "Length of hospital stay and associated treatment costs for patients with susceptible and antibiotic-resistant Salmonella infections
esnightingale/vl-spatial-diagnosis-delay
No full textVisceral leishmaniasis (VL) is a debilitating and - without treatment – fatal parasitic disease which burdens the most impoverished communities in northeastern India. Control and ultimately, elimination of VL depends heavily on prompt case detection. However, a proportion of VL cases remain undiagnosed many months after symptom onset. Delay to diagnosis increases the chance of onward transmission, and poses a risk of resurgence in populations with waning immunity. We checked the spatial variation of delayed diagnosis of VL in Bihar, India and aimed to understand the potential driving factors of delayed diagnosis.
The spatial distribution of time to diagnosis was explored using a Bayesian hierarchical model fit to 4,270 geo-located cases notified between January 2018 and July 2019 through routine surveillance. Days between symptoms meeting clinical criteria (14 days’ fever) and diagnosis were assumed to be Poisson-distributed, adjusting for individual- and village-level characteristics. Residual variance was modelled with an explicit spatial structure. Cumulative delays were estimated under different scenarios of active case detection coverage. This repository contains the code used to produce the result of "Spatial variation in time to diagnosis of visceral leishmaniasis in Bihar, India"
Does cytomegalovirus infection increase the risk of tuberculosis in UK children?
No full textThere is a hypothesised association between pre-existing cytomegalovirus (CMV) infection and risk of acquiring tuberculosis (TB). We aimed to explore if CMV seroprevalence and CMV IgG levels in children were associated with TB disease or Mycobacterium tuberculosis (Mtb) infection compared to children who were exposed to TB but remained well. In this cross-sectional analysis from an observational cohort study of children exposed to TB in their household in the United Kingdom, we examined samples from seventy-five participants, of whom 40 (53%) were male. Median age of the cohort was 6 years (interquartile range: 3-11 years). Twenty-one (28%) children had TB disease, 27 (36%) had Mtb infection, and 27 (36%) had TB exposure only. There was no increased risk of TB in children who were CMV-seropositive (OR 2.18 (0.75-6.48)), and there were no differences in CMV IgG quantification by TB category. There was no detectable CMV viraemia in any of the children in our study. We found higher levels of CMV seroprevalence (49%) than previously described in the United Kingdom. In this small study of children exposed to TB, in a low TB burden setting, we found no association between CMV serostatus or CMV IgG titre and TB status
TOAST - a new amplicon designing tool for bacteria, specialised for TB
No full textAmplicon sequencing (Amp-Seq) of Mycobacterium tuberculosis genes associated with drug resistance and strain typing offers a cost-effective approach for profiling infections and tailoring the clinical management of tuberculosis. However, Amp-Seq assays require continual updates to incorporate new loci and mutations linked to drug resistance. We introduce TOAST (Tuberculosis Optimised Amplicon Sequencing Tool), a customisable software tool that optimises amplicon design across any loci and sequencing platforms (e.g., Illumina, Oxford Nanopore Technology (ONT)), informed by an integrated and expanding database of mutations from >50K M. tuberculosis isolates. TOAST software allows users to define parameters such as melting temperature, amplicon length, and GC content, while accounting for potential primer interactions like homodimer formation and non-specific binding. To demonstrate its robustness, we designed 33 amplicons in a single multiplex group, prioritising coverage of resistance-associated mutations in the form of insertions, deletions and single nucleotide polymorphisms (SNPs) for 13 different drugs. An efficient experimental protocol was established, resulting in a minimum depth coverage exceeding 50-fold for each amplicon region as validated by ONT sequencing of a clinical sample with multi-drug resistance. TOAST software enables the development of Amp-Seq assays for the rapid detection of drug-resistant TB, enhancing treatment strategies, improving outcomes, and curbing resistant infections. The cost-effectiveness and adaptability of Amp-Seq approaches make it crucial for managing TB in resource-limited settings, advancing global control efforts
linfeng-wang/TOAST
No full textWe present TOAST, a software tool designed to streamline and optimize amplicon primer design for Mycobacterium tuberculosis sequencing. TOAST integrates the robust primer design capabilities of Primer3—accounting for Tm, homopolymers, hairpins, and homodimers—with an in-house pipeline that rigorously filters for heterodimer formation and unintended alternative binding. What sets TOAST apart is its automation and intelligence: it leverages a curated database of over 50 M. tuberculosis genomes to inform amplicon placement, ensuring robust primer performance across strain diversity. Users can prioritize SNPs for coverage, focus on specific resistance genes, and tailor designs to spoligotype backgrounds. The tool outputs primer sequences along with detailed thermodynamic profiles and genomic coordinates, making it an end-to-end solution for targeted TB panel design
zmhesketh/2023_TBVaccine_Confidence
No full textThe analytic code for both the main analysis and the sex- and age group-disaggregated analysis In this repository, you will find two files: (1) Main analysis of 2023 VCP data: This includes analytical code to obtain individual confidence scores, for the 18 high TB burden countries in the dataset, for each of the three statements of interest (vaccines are important for everyone to have, vaccines are safe, vaccines are effective). It also includes the calculation of the overall combined confidence scored based on these individual scores. (2) Sex- and age-group-disaggregated analysis of 2023 VCP data: This includes the analytical code to obtain confidence scores by sex and age group for each of the 18 high TB burden countries in the dataset
Reproduction Package for "Food system transformation pathway reconciles 1.5° global warming with improved health, environment and social inclusion"
No full textA reproduction package for "Food system transformation pathway reconciles 1.5° global warming with improved health, environment and social inclusion" as published in Nature Food. This package contains the MAgPIE model version used in the article, required input data, and the latest raw model results. For details see BodirskyEtAl_2025_FSDP-reproduction-package.tar.xz/README.md (replicated next to the archive file). Extracted archive requires 170 GB of storage
Additional file 1 of Translational framework for implementation evaluation and research: implementation strategies derived from normalization process theory
No full textDataset for "Translational framework for implementation evaluation and research: implementation strategies derived from normalization process theory"