Fig. 1.

Comparison of the average number of reads classified as Listeria monocytogenes in artificially contaminated ready-to-eat (RTE) turkey deli meat. RTE turkey deli meat was artificially contaminated with L. monocytogenes colony forming units (CFU) at three levels (high:10⁴ CFU/ml; medium:10³ CFU/ml; low:10² CFU/ml). Genomic DNA was extracted in duplicate with the Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit. The number of reads classified as L. monocytogenes was averaged across reference databases and classifiers for each set of replicates. Raw = raw datasets classified with default settings (no host sequence removal); Filtered = low-quality read filtered datasets (fastp) classified with default settings; Filtered + HR = low-quality read filtered (fastp) and in silico host removed (Bowtie 2) datasets classified with default settings; Filtered + HR + OL = low-quality read filtered (fastp) and in silico host removed (Bowtie 2) datasets classified using Centrifuge with the sequence threshold label adjusted to one (k = 1) to mimic the classification algorithm of Kraken 2 and KrakenUniq; Filtered + HR + OL + Min31 = low-quality read filtered (fastp) and in silico host removed (Bowtie 2) datasets classified using Centrifuge with the sequence threshold label adjusted to one (k = 1) to mimic the classification algorithm of Kraken 2 and KrakenUniq and minimum length of partial hits adjusted to 31 (–min-hitlen = 31); Raw + OL = raw datasets classified with one taxonomic label (k = 1); Raw + OL + Min31 = raw datasets classified using Centrifuge with the sequence threshold label adjusted to one (k = 1) to mimic the classification algorithm of Kraken 2 and KrakenUniq and minimum length of partial hits adjusted to 31 (–min-hitlen = 31); Filtered + HR + CS = low-quality read filtered (fastp) and in silico host removed (Bowtie 2) datasets classified with Kraken 2 or KrakenUniq and a confidence score threshold of 0.1 (–confidence = 0.1); Raw + CS = raw datasets classified with Kraken 2 or KrakenUniq and a confidence score threshold of 0.1 (–confidence = 0.1). UNIVERSAL = universal (taxon-agnostic) reference database; FBP = foodborne pathogen-specific (taxon-specific) reference database. *No TP reads were detected