Lakhasly

2.Category Description Scientific name Listeria monocytogenes Collection date Date the sample was collected Location Location from which the sample was collected Isolation type Clinical or environmental/other Serovar Serovar AMR genotype List of the AMR genotypes identified in sample After the data were downloaded from the NPDIB, they were formatted for subsequent analysis.Antimicrobial Resistance Data from the NCBI Pathogen Detection Isolate Browser The NCBI Pathogen Detection Isolate Browser (NPDIB) currently contains almost a million total isolates covering 34 organism groups [21].A MATLAB program was written to extract the AMR genotype data from a single column into multiple columns.Table 1.

2. Materials and Methods
   2.1. Antimicrobial Resistance Data from the NCBI Pathogen Detection Isolate Browser
   The NCBI Pathogen Detection Isolate Browser (NPDIB) currently contains almost a million total isolates covering 34 organism groups [21]. The data for this analysis were downloaded from the NPDIB on 24 February 2022, using the following search criteria:
   • Organism group = Listeria monocytogenes;
   • Collection date = from: 31 December 2009, to: 31 December 2021.
   For this analysis, the NPDIB data were downloaded into a Microsoft Excel worksheet.
   The data were then organized into a matrix where each row corresponded to a L. monocytogenes sample with the columns including the following: scientific name, collection date, location, isolation type, serovar, and AMR genotype. As for the isolation type, the clinical category represents samples isolated from human sources, while the environmental/other category represents samples isolated from all other sources including the environment, animals, and food. Table 1 shows a detailed description of each column category.
   Table 1. Description of data downloaded from NPDIB.
   Category Description
   Scientific name Listeria monocytogenes
   Collection date Date the sample was collected
   Location Location from which the sample was collected
   Isolation type Clinical or environmental/other
   Serovar Serovar
   AMR genotype List of the AMR genotypes identified in sample
   After the data were downloaded from the NPDIB, they were formatted for subsequent analysis. A MATLAB program was written to extract the AMR genotype data from a single column into multiple columns. As downloaded from NPDIB, the AMR genotype data are in the following format: “aac(60)-I = COMPLETE, abc-f = COMPLETE, fosX = COMPLETE, lin = COMPLETE, msr(C) = COMPLETE”. These data were processed to create one column per gene, populated with a 1 if the gene was found in the sample and 0 if the gene was not found. The data in the other columns were manipulated to align the formats and to replace text entries with numerical entries. Table 2 summarizes the data in the final spreadsheet that was used for analysis.