An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective.
Epidemiology
Genomics
Pandemic
SARS-CoV-2
Surveillance
Journal
Infection
ISSN: 1439-0973
Titre abrégé: Infection
Pays: Germany
ID NLM: 0365307
Informations de publication
Date de publication:
Aug 2023
Aug 2023
Historique:
received:
20
01
2023
accepted:
13
04
2023
medline:
19
7
2023
pubmed:
2
5
2023
entrez:
2
5
2023
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 37129842
doi: 10.1007/s15010-023-02040-9
pii: 10.1007/s15010-023-02040-9
pmc: PMC10152431
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
805-811Subventions
Organisme : National University Medicine Research Network on COVID-19
ID : 01KX2121
Organisme : Bundesministerium für Bildung und Forschung
ID : ZMVI1-2518FSB706
Informations de copyright
© 2023. The Author(s).
Références
Abu-Raddad LJ, Chemaitelly H, Ayoub HH, et al. Severity, criticality, and fatality of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) beta variant. Clin Infect Dis. 2022;75:e1188–91.
doi: 10.1093/cid/ciab909
pubmed: 34657152
Alm E, Broberg EK, Connor T, et al. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveill. 2020. https://doi.org/10.2807/1560-7917.ES.2020.25.32.2001410 .
doi: 10.2807/1560-7917.ES.2020.25.32.2001410
pubmed: 33213683
pmcid: 7678039
Balabanova Y, Gilsdorf A, Buda S, et al. Communicable diseases prioritized for surveillance and epidemiological research: results of a standardized prioritization procedure in Germany, 2011. PLoS ONE. 2011;6: e25691.
doi: 10.1371/journal.pone.0025691
pubmed: 21991334
pmcid: 3186774
Brito AF, Semenova E, Dudas G, et al. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun. 2022;13:7003.
doi: 10.1038/s41467-022-33713-y
pubmed: 36385137
pmcid: 9667854
Da Silva FA, Shepherd JG, Williams T, et al. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nat Microbiol. 2021;6:112–22.
Davies NG, Abbott S, Barnard RC, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021. https://doi.org/10.1126/science.abg3055 .
doi: 10.1126/science.abg3055
pubmed: 34941392
pmcid: 8970537
Du Plessis L, Mccrone JT, Zarebski AE, et al. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science. 2021. https://doi.org/10.1126/science.abf2946 .
doi: 10.1126/science.abf2946
pubmed: 34301854
pmcid: 9269003
Emary KRW, Golubchik T, Aley PK, et al. 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 trial. Lancet. 2021;397:1351–62.
doi: 10.1016/S0140-6736(21)00628-0
pubmed: 33798499
pmcid: 8009612
Hansen CH, Friis NU, Bager P, et al. Risk of reinfection, vaccine protection, and severity of infection with the BA.5 omicron subvariant: a nation-wide population-based study in Denmark. Lancet Infect Dis. 2023;23:167–76.
doi: 10.1016/S1473-3099(22)00595-3
pubmed: 36270311
Houwaart T, Belhaj S, Tawalbeh E, et al. Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021. Euro Surveill. 2022;27:2101089.
Lazarus JV, Romero D, Kopka CJ, et al. A multinational Delphi consensus to end the COVID-19 public health threat. Nature. 2022;611:332–45.
doi: 10.1038/s41586-022-05398-2
pubmed: 36329272
pmcid: 9646517
Li J, Lai S, Gao GF, et al. The emergence, genomic diversity and global spread of SARS-CoV-2. Nature. 2021;600:408–18.
doi: 10.1038/s41586-021-04188-6
pubmed: 34880490
Lopez Bernal J, Andrews N, Gower C, et al. Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant. N Engl J Med. 2021;385:585–94.
doi: 10.1056/NEJMoa2108891
pubmed: 34289274
Mccrone JT, Hill V, Bajaj S, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature. 2022;610:154–60.
doi: 10.1038/s41586-022-05200-3
pubmed: 35952712
pmcid: 9534748
Mellmann A, Harmsen D, Cummings CA, et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE. 2011;6: e22751.
doi: 10.1371/journal.pone.0022751
pubmed: 21799941
pmcid: 3140518
S20 Academies Joint Statement. Pandemic preparedness and the role of science. 2021. LINCEI, Rome. https://easac.eu/fileadmin/user_upload/S20_Joint_Statement.pdf . Accessed 20 Jan 2023.
Scheithauer S, Dilthey A, Bludau A, et al. Etablierung der genomischen erreger surveillance zur stärkung des pandemie- und infektionsschutzes in Deutschland. Bundesgesundh Gesundh Gesundh. 2023;66:443–9.
doi: 10.1007/s00103-023-03680-w
The Covid-Genomics Uk Consorium. An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microb. 2020;1:e99–100.
doi: 10.1016/S2666-5247(20)30054-9
Vygen-Bonnet S, Rosner B, Wilking H, et al. Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017. Euro Surveill. 2017. https://doi.org/10.2807/1560-7917.ES.2017.22.21.30541 .
doi: 10.2807/1560-7917.ES.2017.22.21.30541
pubmed: 28597831
pmcid: 5479985
Walker A, Houwaart T, Finzer P, et al. Characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting. Clin Infect Dis. 2022;74:1039–46.
doi: 10.1093/cid/ciab588
pubmed: 34181711
WHO. Global genomicsurveillance strategy for pathogens with pandemic and epidemic potential 2022–2023. Geneva: WHO; 2022.