| Common strings | Topic | Specific strings/number of hitsa for each specific production sector | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Plants‐based | Bovine | Pigs | Poultry | Aquaculture | ||||||||||||
| PubMed ( https://pubmed.ncbi.nlm.nih.gov/) (Status up to 01 March 2021) | (Germany OR Italy OR France OR UK OR Britain OR Netherlands OR Spain OR Sweden OR Norway OR finland OR Greece OR Portugal OR Belgium OR Poland OR hungary OR Ireland OR Scotland OR Luxembourg OR malta OR Latvia OR Lithuania OR Estonia OR Czech OR Croatia OR Austria OR Slovakia OR Slovenia OR Europe* OR EU) | AND | 1) (ctx‐m OR SHV OR ESBL OR ‘extended spectrum’ OR TEM)2) (carbapenem OR carbapenemase) 3) (‘Enterococcus faecium’ OR ‘Acinetobacter baumannii’ OR ‘Pseudomonas aeruginosa’ OR ‘Klebsiella pneumoniae’ OR ‘Staphylococus aureus’). 4) (salmonella OR campylobacter) 5) E. coli | AND | – – –a) – b) (‘antimicrobial resistan*’ OR ‘antibiotic resistan*’) a) (mcr OR fluoroquinolone OR colistin OR ‘antimicrobial resistan*’ OR ‘antibiotic resistan*’) (mcr OR fluoroquinolone OR colistin OR ‘antimicrobial resistan*’ OR ‘antibiotic resistan*’) | AND | (manure OR sludge OR irrigation) (manure OR sludge OR irrigation OR dust) | 192 79 419 67 43 181 | (cattle OR dairy OR veal OR beef) | 382 46 345 55 205 393 | (pig OR swine OR sow OR wild boar) | 344 75 360 62 259 387 | (poultry OR chicken OR turkey) | 615 214 554 152 516 554 | (aquaculture OR fish OR shellfish OR bivalve* OR mussel* OR oyster* OR salmon OR shrimp* OR prawn*) | 323 28 194 22 30 76 |
| (antibiotic) | (dust OR airborne) | (agriculture OR farm OR poultry OR swine OR slaughterhouse OR dairy)/56 hits | – | – | ||||||||||||
a
When large number of hits were obtained, they were skimmed briefly for titles which lead to rejection of a fraction of hits, then, after screening the abstract and affiliation and only a small fraction from these was selected based on expected contents for full text reading. In several cases, only a handful from the publications screened were of interest. For Tables F.1 and F.2 (Appendix F), a hierarchical search strategy was used. In a first search, bacteria co‐existing with various fish species (i.e. Atlantic salmon, rainbow trout, European whitefish, carp, sea bass, European eel) were identified. Then in a second search keywords were used to identify the resistances of the bacteria identified in the first search.