AMR	Antimicrobial resistance
AST	Antimicrobial susceptibility testing
CAESAR	Central Asian and European Surveillance of Antimicrobial Resistance
CDC	Centre for Disease Control and Prevention
cgMLST	Core genome multilocus sequence typing
ddNTPs	Dideoxynucleotides
dNTPs	Deoxynucleotides
E. coli	Escherichia coli
EARS-Net	European Antimicrobial Resistance Surveillance Network
ECDC	European Centre for Disease Prevention and Control
EISN	European Influenza Surveillance Network
EUCAST	European Committee on Antimicrobial Susceptibility Testing
GWAS	Genome-wide association studies
IPC	Infection prevention and control
IPSN	Pathogen Surveillance Network
ISS	Italian National Institute of Health
K. pneumoniae	Klebsiella pneumoniae
LRS	Long-read sequencing
M. tuberculosis	Mycobacterium tuberculosis
MIC	Minimal inhibitory concentration
MLST	Multilocus sequence typing
mNGS	Metagenomics next-generation sequencing
NGS	Next-generation sequencing
OECD	Organization for Economic Cooperation and Development
ONT	Oxford nanopore technologies
P. aeruginosa	Pseudomonas aeruginosa
PPi	Pyrophosphate
REDI-NET	Remote Emerging Disease Intelligence—NETwork
RT	Real-time
RVI	Respiratory Virus and Microbiome Initiative
S. aureus	Staphylococcus aureus
S. pneumoniae	Streptococcus pneumoniae
SBS	Sequencing-by-synthesis
SM	Single molecule
SMRT	Single molecule real time
SNPs	Single nucleotide polymorphisms
SPSP	Swiss Pathogen Surveillance Platform
tNGS	Targeted next-generation sequencing
WGS	Whole genome sequencing
WHO	World Health Organization
ZMWs	Zero-mode wavelengths