An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective
Open Access
- 2 May 2023
- journal article
- research article
- Published by Springer Science and Business Media LLC in Infection
- Vol. 51 (4), 805-811
- https://doi.org/10.1007/s15010-023-02040-9
Abstract
The SARS-CoV-2 pandemic has highlighted the importance of viable infection surveillance and the relevant infrastructure. From a German perspective, an integral part of this infrastructure, genomic pathogen sequencing, was at best fragmentary and stretched to its limits due to the lack or inefficient use of equipment, human resources, data management and coordination. The experience in other countries has shown that the rate of sequenced positive samples and linkage of genomic and epidemiological data (person, place, time) represent important factors for a successful application of genomic pathogen surveillance. Planning, establishing and consistently supporting adequate structures for genomic pathogen surveillance will be crucial to identify and combat future pandemics as well as other challenges in infectious diseases such as multi-drug resistant bacteria and healthcare-associated infections. Therefore, the authors propose a multifaceted and coordinated process for the definition of procedural, legal and technical standards for comprehensive genomic pathogen surveillance in Germany, covering the areas of genomic sequencing, data collection and data linkage, as well as target pathogens. A comparative analysis of the structures established in Germany and in other countries is applied. This proposal aims to better tackle epi- and pandemics to come and take action from the “lessons learned” from the SARS-CoV-2 pandemic.Keywords
Funding Information
- National University Medicine Research Network on Covid-19 (01KX2121, 01KX2121, 01KX2121, 01KX2121, 01KX2121, 01KX2121)
- Bundesministerium für Bildung und Forschung (ZMVI1-2518FSB706, ZMVI1-2518FSB706, ZMVI1-2518FSB706)
- Universitätsklinikum Regensburg
This publication has 21 references indexed in Scilit:
- Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in EnglandScience, 2021
- Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trialThe Lancet, 2021
- Science, 2021
- Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into ScotlandNature Microbiology, 2020
- Virological surveillance of influenza viruses in the WHO European Region in 2019/20 – impact of the COVID-19 pandemicEurosurveillance, 2020
- Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020Eurosurveillance, 2020
- An integrated national scale SARS-CoV-2 genomic surveillance networkThe Lancet Microbe, 2020
- Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017Eurosurveillance, 2017
- Communicable Diseases Prioritized for Surveillance and Epidemiological Research: Results of a Standardized Prioritization Procedure in Germany, 2011PLOS ONE, 2011
- Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing TechnologyPLOS ONE, 2011