Table 1.
Antimicrobial agents tested, their concentrations and clinical break points of the zone diameter used in the AST.
Fig 1.
AMR profile of 77 Salmonella isolates from bovine Lymph Nodes (LN) and Ground Beef (GB).
Within each antibiotic class, AMR phenotypes are first indicated, followed by AMR genes. Non-susceptible phenotypes are indicated with “R” (resistance) and “I” (intermediate resistance), while blank cells correspond to susceptible isolates. For AMR genotypes, cells filled with the corresponding antibiotic class color indicate the gene is present. AMR genes in gray are not associated with any antibiotic class included in the AST panel. Point mutations and MDR phenotypes are presented on the rightmost columns. Isolates with black cells have mutations/MDR phenotypes and those with blank cells lack these features. Antibiotic abbreviations are as follows: amikacin (AMK), gentamycin (GEN), carbenicillin (CB), amoxicillin-clavulanic acid (AMC), cefotaxime (CTX), ceftriaxone (CRO), cefepime (FEP), meropenem (MEM), ertapenem (ETP), imipenem (IMP), chloramphenicol (CHL), trimethoprim-sulfamethoxazole (SXT), ciprofloxacin (CIP), tetracycline (TET).
Fig 2.
Schematic representation of the overall correlation between predicted AMR genotypes and observed AMR phenotypes of 77 Salmonella isolates.
The figure shows the number of genotypically and phenotypically non-susceptible isolates to each tested antibiotic. Antibiotic abbreviations: ciprofloxacin (CIP), tetracycline (TET), carbenicillin (CB), amoxicillin-clavulanic acid (AMC), chloramphenicol (CHL), trimethoprim-sulfamethoxazole (SXT), imipenem (IMP), ceftriaxone (CRO), cefotaxime (CTX), gentamycin (GEN), amikacin (AMK), cefepime (FEP), meropenem (MEM), ertapenem (ETP).
Fig 3.
Heatmap showing the AMR profile of public NTS isolated from major sources in Mexico.
AMR genes and the antibiotic class affected by them are indicated on the bottom. Refer to S2 File for accessions and metadata of isolates included in this analysis.
Fig 4.
BLAST atlas analysis of SGI1 of 10 serovar Typhimurium isolates and one monophasic Typhimurium.
The black slot corresponds to the backbone and the brown inner ring to the reference sequence. The most inner ring shows gene annotation, with AMR genes highlighted in bold text. The outer rings correspond to the serovars and isolate names indicated. Regions with shared synteny between genomes and reference sequence are filled with intense color while blank spaces indicate a lack of synteny. Refer to S1 File for accession numbers and metadata of isolates.
Table 2.
General features of the plasmids predicted per Salmonella serovar.