Humans

This section provides resources and tools to measure the prevalence of infections in health care and in the community, and for prioritization among diseases. You can also access selected data sources and relevant reports.

Measuring health care-associated infections

Data on health care-associated infections can be used to inform health care facilities where to focus infection prevention and control measures, as well as to evaluate the effect of performed interventions. Such data can also be efficient in work to sensitize policy makers and authorities, or in benchmarking between facilities.

Point prevalence studies are useful to estimate the number of health care-associated infections. Generally, health care-associated infections are measured in combination with antibiotic consumption and/or antibiotic resistance. It should be noted that sampling of bacterial resistance in hospital patients and the observed bacterial resistance levels in health care-associated infections is often not representative of the overall resistance situation. These patients are often more severely ill and at higher risk of carrying resistant bacteria.

Measuring community infections

Data on infections obtained in the community can be used to inform authorities in decisions on prevention programs and about needed diagnostics and treatments. In combination with data on consumption and resistance levels, the diseases that drive antibiotic use can be identified, and countermeasures initiated.

Many countries have mandatory reporting of certain diseases of public health importance into national registries. Point prevalence surveys are also possible in community settings, looking at for example medical records from primary health care or statistics from work places or schools.

Mapping of key diseases

There are different methods to know which are the key diseases in the first place:

Systematic literature reviews give a good indication on what diseases are likely to be of importance in a certain setting.
Surveillance data collected at national level give an indication on occurrence of important diseases, but may not be representative of the situation within a specific healthcare facility or community.
Infection/pathogen prevalence surveys help to generate reliable data on various infections.
Knowledge, attitudes, beliefs and practices studies can complement prevalence surveys by giving insights into people’s response to infections and disease transmission pathways.

The resources have been sorted into the following tables:

Tools and guidelines
Databases and reports

Selected Resources

Tools and guidelines

Resource	Description
ECDC tool for the prioritisation of infectious disease threats	Tool: Qualitative spreadsheet (Excel workbook/Google doc) for ranking of infectious disease threats in a transparent, comparable and methodologically reproducible way. Intended as a supplement to other methods that support decisions in preparedness planning. Comes with an accompanying manual.
The AMR Package for R	Software. Free, open-source and independent package for R for easy analysis of microbial and antimicrobial data, and prediction of antimicrobial resistance (AMR). A manual on how to use the AMR package can be found here. See also The epidemiologist R handbook, a reference tool for using R code. Designed for people working in applied epidemiology, public health practice, and disease control.
Epi Info	Software for collecting, analyzing and managing epidemiological data (by the US CDC). Can be used for assessment of disease outbreaks or development of small or mid-size surveillance systems. Free of charge. Suitable in settings with limited network connectivity. Translated into 13 languages.
Infection Control Assessment Tool (ICAT) for Primary Health Care Facilities	Tool: Simple and practical approach to assess infection prevention and control practices in primary care and to highlight deficiencies in current practices. Also proposes reformatory actions to prevent health care-associated infections.
The ORION statement: guidelines for transparent reporting of Outbreak Reports and Intervention studies Of Nosocomial infection	Checklist: Provides a 22 item checklist (with example) to assist researchers to report on health care associated infections and interventions in a transparent and systematic way.
ECDC point prevalence survey of HAIs and antimicrobial use in European acute care hospitals	Protocol that provides methodology and data collection forms for performing point prevalence survey of HAIs and antimicrobial use in European hospitals. PPS survey validation protocol can be found here. ECDC also provides additional protocols/data collection forms for a number of healthcare settings and infections: HAI surveillance protocol and prevention indicators for intensive care units, version 2.2 PPS of HAIs and antimicrobial use in long-term care facilities, version 2.1 Survey validation protocol for long-term care Surveillance protocol for C. difficile infections, version 2.3 HAISSI protocol for surveillance of surgical site infections and prevention indicators
HELICSWin.Net	Software developed for the manual entry of data of the ECDC surveillance of healthcare-associated infections. Can also be used for private and professional purposes.
CDC HAI and Antibiotic use Prevalence Survey	Information on the CDC’s use of a prevalence survey to make improved estimates of the burden of health care-associate infections in the US, including technical information about the study.
Best Practices for Surveillance of Health Care-associated Infections (PDF, 2MB)	Best practices for hospitals and long-term care homes for establishment of surveillance of health care-associated infections. Section II D provides hands on practical advice on different steps of the process such as to assess the population to be surveyed, and how to calculate HAI rates. Appendices provide sample documents and tools. Developed by the Public Health Agency in Ontario, Canada.

Databases and reports

Resource	Description
Outbreak Database – Worldwide Database for Nosocomial Outbreaks	Database that collects published literature about disease outbreaks within the health care setting. The aim is to facilitate outbreak management and provide information for education and training. Includes information about setting, persons affected, type of microorganism, source, mode of transmission and prevention measures. Also links to the original article. Infection control and hospital epidemiology experts started the project in 2001 and the data is updated continuously.
ProMED-mail, the Program for Monitoring Emerging Diseases	Database. This online reporting system offers the possibility for rapid information dissemination on infectious disease outbreaks and acute exposures to toxins that affect human health, including livestock. Available for different regions and languages, including Spanish and for Francophone Africa and South Asia.
Global Burden of Disease (GBD) Data Visualizations	Database: Visualization tool of global, regional, national, and in some cases subnational estimates of the burden of diseases, injuries, and risk factors. Allows comparison of effects of different diseases, changes over time and across age groups and populations.
Report on the Burden of Endemic Health Care-Associated Infection Worldwide	Report: A 40 pages WHO review of the prevalence of health care-associated infection in high-, middle- and low-income countries and their impact. From 2011.
Burden of endemic health-care-associated infection in developing countries: systematic review and meta-analysis	Review from 2011 on the epidemiology of health care-associated infections in low- and middle-income countries (The Lancet).
Global tuberculosis report	Reports: WHO publishes yearly reports on the global tuberculosis situation, including the latest data on drug resistance.
Global burden of foodborne diseases	Report hat gives an overview on the global burden of foodborne diseases (WHO).
CDC’s Antibiotic Resistance and Patient Safety Portal	Database: Open and interactive data about healthcare-associated infections (HAIs) caused by antibiotic resistant bacteria reported to the CDC. The app provides national, regional, and state views of superbug-drug combinations showing resistance over time.
Surveillance Atlas of Infectious Diseases	Database: Interactive map developed by the European Centre for Disease Prevention and Control. Provides updated data on a number of infectious diseases. Allows searches for disease type, the number of deaths, cases associated with travel etc., year and European country.
Systematic review on the incubation and infectiousness/shedding period of communicable diseases in children	Review that provides evidence essential for public health action gathered from European Union member states in regard to controlling the spread of communicable diseases in childcare settings.

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