Table 7 Species and number of read sets for the species assembled in the pathogen detection pipeline using SAUTE for antimicrobial resistance genes as of July 28, 2020
Species | Number of read sets |
|---|---|
Salmonella enterica | 278,133 |
E.coli and Shigella | 89,600 |
Campylobacter jejuni | 51,750 |
Listeria monocytogenes | 32,124 |
Klebsiella pneumoniae | 17,381 |
Enterococcus faecium | 14,072 |
Neisseria | 9308 |
Pseudomonas aeruginosa | 4594 |
Vibrio cholerae | 3556 |
Acinetobacter baumannii | 3204 |
Enterococcus faecalis | 3176 |
Legionella pneumophila | 2848 |
Clostridioides difficile | 1439 |
Enterobacter | 1319 |
Staphylococcus pseudintermedius | 1253 |
Vibrio parahaemolyticus | 1170 |
Candida auris | 744 |
Serratia marcescens | 709 |
Mycobacterium tuberculosis | 539 |
Citrobacter freundii | 494 |
Klebsiella oxytoca | 390 |
Vibrio vulnificus | 365 |
Providencia alcalifaciens | 253 |
Clostridium perfringens | 223 |
Cronobacter | 148 |
Corynebacterium striatum | 98 |
Clostridium botulinum | 95 |
Aeromonas hydrophila | 26 |
Morganella morganii | 20 |
Elizabethkingia anophelis | 19 |
Kluyvera intermedia | 1 |
Total | 519,051 |