Table 11.
Distribution of antimicrobial‐resistant bacteria and resistance genes in potential environmental sources of contamination of aquaculture and processing facilities: examples based on European literature
| Main sources (risk factors) | Bacteria [antimicrobial resistance profiles and genes]a | Detection of highest relevant ARB pathogens/ARGd , e/comments | Factors influencing persistence and occurrence | Supporting referencesf |
|---|---|---|---|---|
| Primary production | In some cases the source of specific organisms in water and sediment can be attributed to either human faecal waste (where isolates are known to be human adapted or ARGs are associated with clinical isolates) or from livestock waste (where strains are animal adapted sequence types or genes are predominantly associated with animal strains). Other species such as Aeromonas spp. and Vibrio spp. are indigenous environmental organisms. Microbial source tracking methodologies are used, and are being further developed, to identify aquatic microbial pollution sources. | |||
| Freshwater | S. Abony [COL, STR]] S. Newport [STR, KAN] E. coli [FQ; qnrS1; bla TEM] E. coli [3rd‐GCs; bla SHV‐12; strA/strB, tet b] E. coli [AMX, AZT, CAZ, 3rd‐GCs, TET, bla SHV‐12 , strA‐strB, tet b] | +/? ?/? ST118 ?/+ ?/+ ?/+ Samples taken upstream, in trout farm or downstream. | Low FQ and TET concentrations in water of aquaculture facility. | Antunes et al. (2018) |
| E. faecalis [MDR; tet(M), tet(L), erm b, aadE, cat_pC221]b E. faecium [MDR; tet(M), tet(L), erm b , aadE]b | ?/? ?/? | Low FQ and TET concentrations in water of aquaculture facility | Novais et al. (2018) | |
| Seawater | E. casseliflavus; [TET, AMP; tet(L), tet(M), blaZ] E. durans [AMP; blaZ] E. faecalis [AMP, TET; tet(M), tet(K), blaZ] E. faecium [MDR; tet(M), tet(K), blaZ)] Enterococcus spp. [AMP, TET; tet(L), tet(K), blaZ] | ?/? ?/? ?/? ?/? ?/? Mediterranean aquaculture sites | Di Cesare et al. (2012) | |
| Freshwater sediment | E. coli [AMX, FQ; KAN, STR, TET/bla TEM, qnrS3, aphA1, aadA, tet b] Citrobacter gillenii [KAN, STR, TET; qnrS3, strA/strB] Klebsiella pneumoniae [CHL, FQ, STR, SUL, TET, TMP/catA, aadA, sul1, dfrA1, qnrB7, oqxA, oqxB] | ?/? ?/+ +/+ Trout farm | Antunes et al. (2018) | |
| Marine sediment | E. casseliflavus; [AMP; blaZ] E. faecalis [AMP; blaZ] E. faecium [MDR; tet(M), tet(L)] E. gallinarum [TET; tet(M)] Enterococcus spp. [AMP, TET; tet(M), tet(L), blaZ] | ?/? ?/? ?/? ?/? ?/? Mediterranean aquaculture sites | Di Cesare et al. (2012) | |
| Feed | E. hirae [MDR; tet(M), tet(L), erm b] | ?/? tcrB, cueO present | Novais et al. (2018) | |
| K. pneumoniae [FQ; oqxAB ; cmlA, aphA1, aadA, sul3, tet b , dfrA12] | +/+ | Antunes et al. (2018) | ||
| Fish and bivalve molluscs (g) | ||||
| Bivalve molluscs | Salmonella serovars [MDR] Salmonella Rissen aac(6’)‐Iaa, aadA1, aadA2, bla TEM‐1B , cmlA1, sul1, sul3, tet(a, dfrA1 and mcr‐1 | +/+ +/+ farmed mussels | Lozano‐León et al. (2019) | |
| E. coli [3rd‐GCs; blaCTX-M‐15, blaCTX-M‐14] | ?/+ farmed and wild mussels | Grevskott et al. (2017) | ||
| Fish in freshwater | Aeromonas hydrophila complex and A. veronii [cphA] | ?/– cphA is an intrinsic ARG conferring resistance to carbapenems when induced by carbapenem exposure. Aeromonas spp. are fish and opportunistic human pathogens | Smyrli et al. (2019) | |
MIC below clinical breakpoints.
Multidrug (MDR) and resistance phenotypes in capital letters; acquired resistance genes italicised; genes conferring resistance to last resort antibiotics are underlined.
Diverse phenotypes and/or different resistance determinant combinations.
Group 1 ARB (according to definition in Table 6) were present (+), absent (–) or no information provided to indicate their presence (?)/ARG of highest relevance (according to definition in Section 3.2.2) were present (+), absent (–) or no information provided to indicate their presence (?).
Horizontal transferability of resistance is assumed for resistance phenotypes or genes usually acquired by this process (e.g. bla CTX‐M and mcr genes).
Source of the data presented in ‘Bacteria [antimicrobial resistance profiles and genes]’ column and in the categorisation as Group 1 ARB/highest relevant ARG.
Fish and bivalve molluscs contamination by relevant ARB are indicators of AMR contaminated sources at preharvest or post‐harvest processes.
Antimicrobials: AMX – amoxicillin; AMP – ampicillin; AZT – aztreonam; CARBA – carbapenem; CHL – chloramphenicol; COL – colistin; 3rd‐GCs – third‐generation cephalosporins; FQ – fluoroquinolone; KAN – kanamycin; STR – streptomycin; SUL – sulfonamide; TET – tetracyclines; TMP – Trimethoprim. Other acronyms: ST: multi‐locus sequence type; ND – not determined.