TABLE 1.

Prevalence of serotype predictions that lack an O antigen call by the microassembly workflow of SeqSero2 using Salmonella genomes from different public health laboratories

Data set	Total no.	Library prepn	No. of predictions that lack an O antigen call	% of predictions that lack an O antigen call
BfRa	578	Nextera XT	71	12.3
U.S. FDAb	3,929	Nextera XT	33	0.8
U.S. PulseNetc	196	Nextera XT	5	2.6
PHEd	202	Nextera XT	0	0
U.S. NARMSe	2,280	TrueSeq	5	0.2

^aGenomes (n = 1,263) from animal production, food, and the environment in Germany under BioProject no. PRJEB31846 were analyzed. Out of the 1,263 genomes, 578 were prepared by Nextera XT kits, of which 71 were missing an O antigen call. Another 685 were prepared by Nextera Flex kits, of which 3 were missing an O antigen call. NCBI accession numbers can be found at http://denglab.info/static/AEM_letter_datasets.xlsx.

^bGenomes (n = 3,929) used by FDA for an evaluation study of SeqSero2 (unpublished data). NCBI accession numbers can be found at http://denglab.info/static/AEM_letter_datasets.xlsx.

^cGenomes (n = 196) sequenced by state and local health departments in the United States for national surveillance of Salmonella. Genomes were randomly selected from BioProject no. PRJNA230403 to represent 16 major serotypes, including Braenderup, Infantis, Montevideo, Thompson, Agona, Heidelberg, Saintpaul, Typhimurium, Hadar, Kentucky, Muenchen, Newport, Berta, Enteritidis, Javiana, and Panama. NCBI accession numbers can be found at http://denglab.info/static/AEM_letter_datasets.xlsx.

^dGenomes (n = 202) were randomly selected from the Public Health England BioProject PRJNA248792 to represent 16 major serotypes as aforementioned. NCBI accession numbers can be found at http://denglab.info/static/AEM_letter_datasets.xlsx. Genomes were prepared by Nextera XT kits according to the annotation of WGS data in the depository.

^eGenomes (n = 2,280) from human clinical isolates submitted to the U.S. NARMS in 2015 (1). NARMS performs surveillance for antimicrobial resistance in Salmonella (https://www.cdc.gov/narms/index.html); every 20th isolate, along with serotype information, is submitted by state and local health departments in the United States. NCBI accession numbers can be found at http://denglab.info/static/AEM_letter_datasets.xlsx.