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Seroincidence calculator tool





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Campylobacter and salmonellosis are the two leading gastrointestinal diseases reported in the European Union. The reported number of cases represents only a small fraction of all infections actually occurring in the human population. One way to assess the burden of Salmonella and Campylobacter infections in humans is to measure antibody levels in serum collections.

The seroincidence calculator tool for human Salmonella and Campylobacter infections utilises the combination of serum antibody levels (IgG, IgM, and IgA) at a given point in time to estimate the time since seroconversion, which in turn gives an estimate of annual ‘force of infection’ in the tested population. The relationship between the three antibody levels, and estimated time since infection (seroconversion), has been established in previous longitudinal studies where laboratory-confirmed cases were followed up for several months, and the decay of serum antibody levels were determined by indirect ELISA methods (see References).

The seroincidence calculator tool was developed through an ECDC-funded project. To make the functionalities provided as broadly available as possible, R was chosen as the computing platform, as it is free, open source, and runs on any modern operating system.



Antibody levels measured in a cross-sectional population samples can be translated into an estimate of the frequency with which seroconversions (new infections) occur. In order to interpret the measured cross-sectional antibody levels, parameters which predict the decay of antibodies must be known. In previously published reports (Simonsen et al. 2009 and Versteegh et al. 2005), this information has been obtained from longitudinal studies on subjects who had culture-confirmed Salmonella and Campylobacter infections. A Bayesian back-calculation model was used to convert antibody measurements into an estimation of time since infection. This can be used to estimate the seroincidence in the cross-sectional sample of population. For both the longitudinal and cross-sectional measurements of antibody concentrations, the indirect ELISA was used. The models are only valid for persons over 18 years. The seroincidence estimates are suitable for monitoring the effect of control programmes when representative cross-sectional serum samples are available for analyses. These provide more accurate information on the infection pressure in humans across countries.


Serological assays for human Salmonella and Campylobacter infections

Serological assays (ELISAs) for determination of specific antibodies IgG , IgM, and IgA against Salmonella and Campylobacter were established at Statens Serum Institut (SSI) and run on a daily basis, using in-house developed, validated and accredited laboratory protocols.
For Salmonella, indirect ELISA was performed on human serum using mixed LPS (lipopolysaccharide) antigens from Salmonella Typhimurium and Salmonella Enteritidis. IgA, IgM and IgG antibodies were measured individually through horseradish peroxidase (HRP)/tetramethylbenzidine (TMB) enzymatic reactions. For Campylobacter, indirect ELISA was performed on human serum using whole-cell Campylobacter jejuni antigen.

Installation guidelines

ECDC’s seroincidence tool is provided as an R package . To use an R package, R must first be installed on your computer. R is free software that can be downloaded from a CRAN mirror site, Installation guidelines for R are available in the FAQs section of the R website.

ECDC’s seroincidence package is distributed both through the CRAN network and through the ECDC website.

To install a package from ECDC, follow these detailed instructions. If you do not need the step by step tutorial, just follow the procedure below:
1. Download the package:
ECDC seroincidence package (platform-independent source version)
2. Open R.
3. Open the Packages menu.
4. Select Install package(s) from local zip files…
5. Navigate to where you have saved the ECDC Zip or tar.gz file.
6. Select filename and click Open.
The package must be downloaded to your computer before you can open it in R. DO NOT unpack the downloaded Zip file, it only needs to be saved on your computer.
To install the package from a CRAN mirror:
1. Open R. (instructions on installation of R)
2. Open the Packages menu.
3. Select Install package(s).
4. Select a CRAN mirror close to your location from the list.
5. Select seroincidence from the list of packages.
6. Select OK
Note, however, the CRAN verification process can lead to a delay in publication of the final package, and on occasions a newer package might be available on ECDC’s website.
To verify the integrity of the original zip file (version 1.0.5):
MD5 checksum

SHA1 checksum

Loading the package

Once the package is installed in R, it must then be loaded. A description of loading the seroincidence package is provided in the seroincidence package tutorial.

More information on R 

To have information about R software, consult the sections “What is R?”, “Manuals” and “FAQs” of the R project website
If you have any suggestions and comments or experience problems with downloading the documentation, please contact us at


Funding by Med-Vet-Net, a ‘Network of Excellence’ for research on the prevention and control of zoonoses, funded by the European Commission within the 6th Framework Programme (contract no. 506122), and by the European Centre for Disease Control and Prevention, project OJ/2009/06/03-PROC/2009/021.

A European sero-epidemiology project became Work-Package 32 of Med-Vet-Net: ‘Validation of Public Health Surveillance’. The study was funded by ECDC (ECDC 09/032/2009-2013) and builds upon the work of Med-Vet-Net.

Suggested citation

ECDC seroincidence R package [software application]. Version 1.0.4  Stockholm: European Centre for Disease Prevention and Control; 2015
Disclaimer: ECDC accepts no responsibility or liability whatsoever (including but not limited to any direct or consequential loss or damage it might occur to you and/or any other third party) arising out of or in connection with the installation and/or usage of this software.


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