Characterising contact in disease outbreaks via a network model of spatial-temporal proximity
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Abstract
Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.
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SciScore for 10.1101/2021.04.07.21254497: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Genomics analysis of IncHI2 plasmids: WGS reads of the 85 CPEIMP isolates were processed and analysed for plasmid detection, phylogenetic reconstruction, and plasmid-lineage identification, as we have described in another study35. WGSsuggested: NoneBriefly, using IQ-Tree72, a maximum-likelihood phylogenetic tree of IncHI2 plasmids were reconstructed from whole-genome alignment of the reads against a reference plasmid genome pKA_P10 (RefSeq accession: NZ_CP044215.1)73. RefSeqsuggested: (RefSeq, RRID:SCR_003496)Then the tree was corrected for recombination using ClonalFrameML and eventually … SciScore for 10.1101/2021.04.07.21254497: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Genomics analysis of IncHI2 plasmids: WGS reads of the 85 CPEIMP isolates were processed and analysed for plasmid detection, phylogenetic reconstruction, and plasmid-lineage identification, as we have described in another study35. WGSsuggested: NoneBriefly, using IQ-Tree72, a maximum-likelihood phylogenetic tree of IncHI2 plasmids were reconstructed from whole-genome alignment of the reads against a reference plasmid genome pKA_P10 (RefSeq accession: NZ_CP044215.1)73. RefSeqsuggested: (RefSeq, RRID:SCR_003496)Then the tree was corrected for recombination using ClonalFrameML and eventually was rooted using BactDating74,75. ClonalFrameMLsuggested: (Clonalframe, RRID:SCR_016060)Plasmid lineages were identified from the rooted tree based on its topology and bootstrap values (≥65) in the output maximum-likelihood tree of IQ-Tree (Figure S2). IQ-Treesuggested: (IQ-TREE, RRID:SCR_017254)Database ResFinder (updated on 28 Oct 2020) and software ARIBA v2.14.6 were used for detecting acquired antimicrobial resistance genes from the reads of 72 isolates (out of the 85 isolates) carrying IncHI2 plasmids76,77. ARIBAsuggested: (Ariba, RRID:SCR_015976)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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