Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

Table 4 Number of CMY-gene(s) and allele(s) detected by KMA and SRST2 in beef metagenomes containing S. ser. Heidelberg isolate present at 1X genome coverage (n = 10)

CMY Template Coverage	Detected ARG Relatedness to CMY-2^a
	CMY-2			CMY-2 clade			Other CMY Alleles (Non-target)			Totals^b
	KMA	SRST2	RGI	KMA	SRST2	RGI	KMA	SRST2	RGI	KMA	SRST2	RGI
< 20	-	-	-	1: CMY-53	-	-	-	20: 4 × CMY-70, 1 × CMY-83, 1 × CMY-100, 6 × CMY-157, 8 × CMY-159	-	1	20	-
20 – 40	-	-	-	-	1: CMY-44	1: CMY-59	-	5: CMY-65, CMY-74, CMY-82, CMY-100, CMY-157	-	-	6	1
40 – 60	-	-	-	2: CMY-33, CMY-130	1: CMY-21	5: 1 × CMY-59, 2 × CMY-60, 1 × CMY-59, 1 × CMY-130	-	4: CMY-50, CMY-65, CMY-82, CMY-90	-	2	5	5
60 – 80	-	-	-	3: CMY-44, CMY-121, CMY-132	4: 2 × CMY-44, 2 × CMY-161	2: CMY-57, CMY-59	-	5: CMY-68, CMY-72, CMY-89, CMY-90, CMY-114	-	3	9	2
≥ 80	3	2	2	2: CMY-130, CMY-132	3: CMY-153, CMY-161,	2: CMY-61, CMY-130	-	1: CMY-68	-	5	6	4
Total:										11	46	12

Abbreviations: KMA k-mer alignment method, SRST2 short read sequence typer version 2, RGI resistance gene identifier (by Comprehensive Antibiotic Resistance Database)
^aAlleles detected by bioinformatic tools KMA version 1.42, SRST2, and CARD-RGI version 5.2.1 with KMA v 1.42 as the alignment method. Number in bold indicates total number of alleles detected in the 10 replicates. Enzyme-allele are listed below for each CMY-category and CMY-template coverage range
^bTotals are listed for each CMY-template coverage category (row totals), as well as the total number of gene-alleles predicted for all 10 replicates combined for each tool (bottom row, bold number)

ISSN: 1471-2180