Term/Abbreviation	Definition/Description
Antibiotic	An antibiotic is a drug used to treat bacterial infections. Such agents have no effect on viral or fungal infections. Examples of antibiotics include penicillins, tetracyclines, fluoroquinolones and polymyxins such as colistin. Antibiotic growth promoters (AGPs) have been used as additives to improve feed efficiency in food animals. Their use for this purpose has been banned in EU countries, including the UK, since the early 2000s but some AGPs are still licensed for use in some countries.
Antimicrobial	Any substance that kills or stops the growth of microorganisms, such as antibiotics, antifungals, biocides, and preservatives.
AMU	Antimicrobial use
AMR	Antimicrobial resistance. For the interpretation of AMR, the WHO definition was applied [@428769]: “Antimicrobial resistance is resistance of a microorganism to an antimicrobial drug that was originally effective for treatment of infections caused by it. Resistant microorganisms (including bacteria, fungi, viruses, and parasites) are able to withstand attack by antimicrobial drugs, such as antibacterial drugs (e.g., antibiotics, antifungals, antivirals, and antimalarials), so that standard treatments become ineffective, and infections persist, increasing the risk of spread to others.”
ARG(s)	Antimicrobial resistance gene (s). An ARG is a gene implicated in or associated with conferring phenotypic resistance to one or more antimicrobial. The resistance may result from the presence or absence of a gene, or specific mutations acquired spontaneously or accumulated through evolution over time. Although ARGs confer resistance, clinical treatment with higher doses of the antimicrobial may still be effective.
Bacteriophage	Often shortened to phage (as in this report), a bacteriophage is a virus that parasitises a bacterium by infecting it and reproducing inside it. Phages are capable of packaging part of their host’s genetic material (including ARGs) either by reproducing within the host cell before lysing the cell (lytic) or through incorporation into the host cell genome (lysogenic). Phages cannot infect human cells.
Biofilm	A community, which may consist of one or more types of bacteria and also other microorganisms. Biofilms attach to a surface (biotic or abiotic) and are covered by an extracellular substance, which may afford protection from an antimicrobial, due to lack of, or slower penetration of the biofilm. Organisms may grow slower in a biofilm and enter a hyper-mutable state and such proximity of bacterial cells may help promote Horizontal Gene Transfer.
BIOHAZ Panel	European Food Safety Authority (EFSA) Panel on Biological Hazards.
blaTEM	An ARG conferring resistance to β-lactam antibiotics located on a family of related β-lactamase plasmids.
blaCMY-2	A family of the AmpC β-lactamase genes that confer broad-spectrum resistance to β-lactam antimicrobials, including ceftriaxone and ceftiofur, as well as to β-lactamase inhibitors, such as clavulanic acid.
blaCTX-M	An ARG conferring extended spectrum β-lactamase (ESBL) resistance against a wide range of β-lactam antimicrobials by different transposons and Insertion sequences (IS).
Breakpoint	Breakpoints are the values used by clinical microbiology laboratories to interpret the results of antimicrobial susceptibility testing (AST) and classify isolates as susceptible or resistant.
CFU	Colony-forming unit A CFU is a unit which estimates the number of microbial cells (bacteria, fungi, viruses etc.) in a sample that are viable and able to multiply via binary fission under controlled conditions, i.e. the number of colonies counted on a petri dish.
CIAs	‘Critically Important Antimicrobials’ (WHO terminology). There are some differences in the categorisation of CIAs between different organisations. The WHO [@428769] categorises CIAs as meeting two criteria: Criterion 1 (C1): The antimicrobial class is the sole, or one of limited available therapies, to treat serious bacterial infections in people. Criterion 2 (C2): The antimicrobial class is used to treat infections in people caused by either: (1) bacteria that may be transmitted to humans from non-human sources, or (2) bacteria that may acquire resistance genes from non-human sources.
Commensal	An organism that co-exists in the internal or external environment of the host, without causing harm, as far as is known.
DNA	Deoxyribonucleic acid. Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.
ECOFF	Epidemiological Cut Off value (with respect to antimicrobial resistance): represents the point (breakpoint) at which bacteria have developed a higher level of resistance to an antimicrobial agent than the background level of resistance that exists naturally for that bacterial species. A ‘resistant’ (or ‘non-susceptible’) ECOFF does not necessarily imply a level of resistance which would correspond with clinical treatment failure.
EFSA	European Food Safety Authority.
ESBL(s)	Extended spectrum beta-lactamases. ESBLs are enzymes produced by bacteria such as Escherichia coli and Klebsiella species. ESBLs mediate resistance to 3rd/4th generation cephalosporins.
EUCAST	European Committee on Antimicrobial Susceptibility Testing
FAO	Food and Agriculture Organization of the United Nations.
FSA	Food Standards Agency.
Genome	The genetic information of an organism.
Gram-negative bacteria	Gram-negative bacteria are characterised by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. They do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Pathogenic Gram-negative bacteria are increasingly resistant to most available antimicrobials. They have built-in abilities to find new ways to be resistant and can pass along genetic materials that allow other bacteria to become drug resistant. Gram-negative bacteria are generally more resistant to antimicrobials than Gram-positive bacteria.
Gram-positive bacteria	Gram-positive bacteria have a thick peptidoglycan layer in the bacterial cell wall which allows for the take up the crystal violet stain used in the Gram staining method of bacterial differentiation. Gram-positive bacteria appear to be purple-coloured when seen through an optical microscope.
gyrA	Mutation in this gene can confer resistance to ciprofloxacin and nalidixic acid.
HGT	Horizontal Gene Transfer Transfer of genetic material (including ARGs), among different bacteria and species, other than by the transmission of DNA from parent to daughter cell. There are a number of different mechanisms through which HGT can occur.
Integron	A type of mobile genetic element (MGE) with the ability to capture and disseminate genes (including ARGs). These genes are located on gene cassettes (a term that is changing to integron cassette), though an integron does not necessarily include any gene cassettes. Integrons can be found in plasmids, chromosomes, and transposons.
MDR	Multidrug Resistance. Resistance of a bacterial isolate to three or more classes of antimicrobial.
Metaphylactic	Treatment of a group of animals without evidence of disease, which are in close contact with other animals that do have evidence of infectious disease.
MIC	Minimum Inhibitory Concentration. The lowest concentration of an antimicrobial that prevents visible growth of a bacteria in a liquid or agar test.
Microbiota	The assemblage of living microorganisms present in a defined environment.
Microorganisms (microbes)	Organisms that include bacteria, viruses, fungi, and parasites.
MGE(s)	Mobile Genetic Element (s). MGEs, also known as transposable elements (TEs), are fragments/sequences of DNA that can be transported between bacteria. They can encode a variety of virulence or resistance determinants (such as ARGs) that can change places on a chromosome, and can be transferred between chromosomes, between bacteria, sometimes including different species. Types of MGEs include plasmids, integron gene cassettes, and transposable elements.
NAP	National Action Plan UK Government 5-year (2024 to 2029) AMR National Action Plan (NAP) for tackling antimicrobial resistance.
PCR	Polymerase chain reaction A laboratory technique that amplifies specific DNA or RNA segments to detect and analyse genetic material.
Phylum	A grouping together of related organisms on the basis of their fundamental characteristics. It is the third most broad category of taxonomy, falling between kingdom and class.
Plasmid	A type of MGE in a cell that can replicate independently of the chromosome(s), typically a small circular double DNA strand in the cytoplasm of a bacterium. Plasmids can carry and transfer ARGs from the host to other cells, via other MGEs (integron gene cassettes and transposable elements).
Shotgun metagenomic sequencing	The untargeted ('shotgun') sequencing of all ('meta-') microbial genomes ('genomics') present in a biological sample. Shotgun sequencing can be used to profile taxonomic composition and functional potential of microbial communities and to recover whole genome sequences.
Spp.	Species.
ST	Sequence type An unambiguous procedure for characterising isolates of bacterial species using the sequences of internal fragments of (usually) seven house-keeping genes.
Tet(A)	An ARG found in Gram-positive bacteria, and which confers resistance to tetracycline group of antibiotics -chlortetracycline, doxycycline, and minocycline - by encoding a tetracycline efflux protein.
Therapeutic use	Use of antimicrobials to treat individual humans or animals (or groups of animals) suffering from a bacterial infection.
WGS	Whole-Genome Sequencing WGS reveals the complete DNA make-up of an organism, enabling an understanding of variations both within and between species.
WHO	World Health Organisation (of the United Nations).