WHONET Webinars

WHONET-SaTScan and Cluster/Outbreak Detection, Part 2

Event date Event time Registration link
Monday March 4th, 2024 12:00 UTC (7am in New York, 1pm in Geneva and 8pm in Manila) Click here to register

Description:
One of the most important uses of laboratory data is the detection of (and response to) possible disease outbreaks in real time. In this session, we will discuss the integration of the free cluster detection software SaTScan (SaTScan.org) within WHONET and the SaTScan features used in WHONET for the detection of case clusters in the community and hospital settings. Statistically significant case clusters may be due to infectious disease outbreaks, but there can also be other reasons, such as contamination of samples, contamination of laboratory materials, quality of test reagents, changes in sampling or testing practices, changes in patient populations served, or random variation in the baseline data.

Agenda:
There will be a brief review of the material presented in Part 1 of this webinar followed by deeper discussion of data preparation, priority analysis parameters, and strategies for assessment and validation of statistical signals. Topics covered in this second session will include:

  • Advanced data preparation
    • Creating filtered WHONET data subsets
    • Data filters: Hospital versus community, screening isolates, organism subsets such as MRSA and CRE, etc.
  • Analysis parameters:
    • Review of parameters introduced in Part 1 of this webinar
    • "Meta-groups": Grouping of related medical units, hospitals, and communities
    • Interpretation of results
  • Strategies for assessment and validation of statistical signals
    • Retrospective data
    • Prospective data

One of the most important uses of laboratory data is the detection of (and response) to possible disease outbreaks in real time. In this session, we will discuss the integration of the free cluster detection software SaTScan (SaTScan.org) within WHONET and the SaTScan features used in WHONET for the detection of case clusters in the community and hospital settings. Statistically significant case clusters may be due to infectious disease outbreaks, but there can also be other reasons, such as contamination of samples, contamination of laboratory materials, quality of test reagents, changes in sampling or testing practices, changes in patient populations served, or random variation in the baseline data.

We will review the various analysis parameters within WHONET-SaTScan available to the data analyst, as well as show examples from the published literature where WHONET-SaTScan has been utilized for the detection of community and hospital outbreaks. This session will serve as an introduction to the topic of cluster detection with WHONET-SaTScan. Future webinars will dive more deeply into optimization of algorithms, validation of results, and other statistical models for cluster detection. Topics covered in this first session will include:

  • Data preparation
  • Analysis parameters:
    • Retrospective, prospective, and simulated prospective cluster detection
    • Statistical models, baseline historical data, scanning windows, and notification thresholds
    • Cluster detection variables, such as "patient location" and/or "multidrug resistance profile"
  • Interpretation of results
  • Examples from the literature
Webinar recording Powerpoint slides
YouTube WHONET-SaTScan CLUSTER/Outbreak Detection Presentation

The most common use of antimicrobial susceptibility test data is the presentation of statistics for individual antibiotics, for example 80% of Escherichia coli in a dataset might be resistant to ampicillin, but only 5% resistant to imipenem. But there is additional value is studying isolates from the perspective of “multidrug resistance” (MDR). There are important implications for treatment guidelines – for example, one isolate of MRSA may be resistant to penicillin and oxacillin alone, but another MRSA isolate could be resistant to penicillin, oxacillin, ciprofloxacin, erythromycin, and clindamycin. For the second isolate, there would be fewer treatment alternatives available for use by clinicians. The monitoring of multidrug resistance profiles also has important applications for the recognition, tracking, and containment of resistance threats, such as hospital, community, and foodborne outbreaks by multi-resistant pathogens.

The focus of this webinar will be exploring the therapeutic and public health importance of multidrug resistance, as well as WHONET’s features for categorizing, tracking, and alerting multidrug resistant microbial subpopulations. We will also cover analyses of MDR as a tool for data quality assessment. Topics to include:

  • Clinical and public health importance
  • Approaches for defining multidrug resistance
  • WHONET analyses
    • Antibiograms using resistance filters
    • Scatterplots
    • Resistance profiles
    • Outbreak detection
Webinar recording Powerpoint slides Additional resources
YouTube WHONET and Multidrug Resistance presentation ECDC MDR, XDR, PDR defintions (2012 paper)

WHONET macros and reports are valuable analysis features that permit the convenient repetition of previous analyses with new data files. The data analyst may wish to prepare standard Excel or Word reports on a daily, weekly, monthly, quarterly, or yearly basis. The analyst may also wish to customize specialized reports that can be shared with laboratory staff, pharmacists, infection control personnel, epidemiologists, national stakeholders, and others.

This webinar covers the following related points:

  • The purpose of macros and reports
  • How to create macros using “Data analysis”.
  • How to use "Quick Analysis" to create and interpret pre-defined epidemiology and quality reports created by the WHONET development team
  • How to use "Quick Analysis" to create and interpret user-defined reports
  • The manual creation of reports (e.g. weekly or monthly) as well as automated scheduled reports with the WHONET Automation Tool (e.g. daily).
  • Open question and answer session.
Webinar recording Powerpoint slides Additional resources
YouTube Macros and Quick Analysis presentation Epidemiology report
Test practies and quality report

The World Health Organization's (WHO) Global Antimicrobial Resistance and Use Surveillance System (GLASS) offers a number of reporting modules for antimicrobial resistance and use. In this webinar, we will discuss the WHO GLASS-AMR module for national annual aggregate statistics on antimicrobial resistance in priority pathogens and specimen types. WHONET greatly simplifies the process of generating the data files needed by national data managers for submission to the new WHO GLASS 2.0 online platform, which is based on the DHIS2 web application.

This webinar covers the following related points:

  • General background on WHONET and related tools.
  • Updates to the WHO GLASS AMR 2.0 protocol.
  • How to create a GLASS laboratory in WHONET.
  • How to create the RIS and Sample files using WHONET.
  • How to import the RIS and Sample files into the new GLASS platform.
  • Overview of the visualizations available in the web platform after importing your data.
  • Open question and answer session.

Webinar recording Powerpoint slides Additional resources
YouTube WHONET-WHO GLASS presentation
WHO GLASS-AMR presentation
WHO GLASS resources and manual