Fig. 2
Heatmap of bacterial isolates collected from meat samples and environmental surface samples during the second time sampling, March 2023. Taxonomy classification was determined based on whole-genome pairwise alignment to Genome Taxonomy Database. The sample codes are explained in more detail in online supplementary Table S2. The following taxa were detected only once and are not shown: Hafnia alvei and Moellerella sp. in loin 3mon; Methylobacterium sp. in C-work table; Neobacillus sp002559145 in C-CB3, Aerococcus viridans and Staphylococcus saprophyticus in C-wizard knife; Macrococcus sp019357535 in C-retail; Frigoribacterium sp001421165 and Psychrobacter maritimus in D-wall in cooler; Pseudochrobactrum sp. in D-Apron; Janthinobacterium sp002878455 in D-wizard knife; Pseudomonas extremaustralis in D-Shrink tunnel; Pseudomonas sp002874965 in D-pipes 1; Bacillus altitudinis, Priestia megaterium, Enterococcus viikkiensis, and Pigmentiphaga litoralis in D-wall in shipping truck; Yersinia intermedia in D-Bloody drain; Pseudoclavibacter sp. and Variovorax sp. in D-plastic curtain; Specibacter sp. and Shewanella glacialipiscicola in D-drain in cooler 2; Serratia sp. in D-side cutting board; Aeromonas salmonicida and Pseudomonas mohnii in D-ES1; Stenotrophomonas sp. in D-knife sharpener (plastic); Sphingobacterium sp000938735, Microbacterium sp002979655, and Pseudomonas sp010095445 in D-drain in cooler 1; Polaromonas sp. in water sample, Janthinobacterium sp009923995 in D-break table; Pseudomonas taetrolens in D-door, Pseudomonas cremoris in D-Trim 5 (T5); Janthinobacterium sp. in D-drain in cutting room; Paeniglutamicibacter antarcticus, Flavobacterium frigidimaris, Acinetobacter albensis, and Pseudomonas tritici in D-drain in bagging station; Pseudomonas koreensis in D-BT3 (AP); Listeria welshimeri, Morganella sp., and Buttiauxella massiliensis in D-BT3 CI; and Serratia fonticola in D-BT1 CI. Isolates are designated with sp# if a matching sequence is available in the GTDB but the species has not been formally described; taxa are designated with sp. if no sequence with ANI > 95% was available on the GTDB