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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

From: SAUTE: sequence assembly using target enrichment

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