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. 2022 Feb 15;10(2):441. doi: 10.3390/microorganisms10020441

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Pathogen detection tools compared: (A) KAT-SECT; (B) SRST2; (C) Kraken2; (D) Metaphlan. Culture-positive (red), culture-negative (black). x-axis displays the curated database chosen for each pathogen for KAT-SECT and SRST2 and the taxon for Metaphlan and Kraken2. Y-values plotted for KAT-SECT and SRST2 are the sum of the identified alleles from reference databases. An “allele hit” was defined by default settings in SRST2 and when k-mer coverage was greater than 10% in KAT-SECT. Values plotted for Kraken2 and MetaPhlAn are the percentage of fragments covered by the clade rooted at this taxon and the relative abundances of reads classified to species, respectively.