Draft Genome Sequences of 171 Listeria monocytogenes Isolates from Food-Related Listeriosis Outbreaks in California from 2007 to 2017.

This publication reports the availability of draft genome sequences of 171 Listeria monocytogenes strains isolated from various food-related sources from California between 2007 and 2017. All isolates contain at least two antimicrobial resistance genes.

ANNOUNCEMENT

Listeria monocytogenes is a Gram-positive bacterium found in various food sources and is the etiologic agent of listeriosis. In 2014, there were 675 cases of listeriosis reported in the United States and 23% resulted in death (1). Symptoms of listeriosis include fever, muscle aches, nausea, and diarrhea. Severe cases could lead to premature delivery or stillbirth in pregnant women and bacteremia and meningitis in the immunocompromised. Attenuated strains of L. monocytogenes have been used as cancer vaccine vectors (2–4).

A total of 171 L. monocytogenes strains, isolated from foods and food-related environmental swabs between 2007 and 2017, were sequenced. The strains were isolated as described in the Bacteriological Analytical Manual (BAM) (5) with modifications. For solids, semisolids, or liquids, 25 g of the sample was added to 225 ml of buffered Listeria enrichment broth (BLEB) containing pyruvate and incubated at 30°C for 4 hours. Subsequently, selective reagents were aseptically added to concentrations of 10 mg/liter acriflavine, 40 mg/liter cycloheximide, and 50 mg/liter sodium nalidixic acid. Sample incubation continued at 30°C for 40 to 48 hours. Samples were screened using real-time PCR (6), and potentially positive samples were streaked onto RAPID'L.mono agar (Bio-Rad) and CHROMagar Listeria (CHROMagar). Colonies with typical characteristics were streaked onto Trypticase soy agar with 0.6% yeast extract (TSA-YE) and incubated at 30°C for 24 to 48 hours. Isolates were confirmed by real-time PCR (6), motility test, beta-lysin disk test, catalase test, and Vitek (bioMérieux) analysis.

A single colony grown on brain heart infusion (BHI) agar was inoculated into 5 ml of BHI broth, without antibiotics, and incubated at 37°C with shaking at 200 rpm for 16 to 18 hours. Genomic DNA was extracted from the liquid culture using the DNeasy blood and tissue kit (Qiagen) and quantified using a Qubit fluorometer (ThermoFisher Scientific). DNA libraries were prepared using the Nextera XT DNA library preparation kit version 2 (Illumina), and whole-genome sequencing was performed on an Illumina MiSeq system using the MiSeq reagent kit version 2 (2 × 250-bp paired-end reads). Default parameters were used for all software unless otherwise specified. FastQC version 0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control by examining the per-base-sequence quality, per-sequence quality scores, and sequence length distributions. SPAdes version 3.8.2 (7) was used for de novo assembly of the raw sequences, and contigs with less than 200 bp were removed. The assembled contigs were deposited into NCBI GenBank and annotated through the Prokaryotic Genome Annotation Pipeline (PGAP) version 4.2 (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/).

Based on PGAP annotation results, the total numbers of genes found in the L. monocytogenes isolates range from 2,890 to 3,322. Table 1 includes detailed information for each of the isolates.

TABLE 1

List of Listeria monocytogenes strains sequenced in this study

GenBank accession no.	SRA accession no.	Sample name	Estimated genome size (bp)	GC content (%)	Total no. of reads	Genome coverage (fold)	No. of contigs	N50 (bp)	Total no. of genesa	Antimicrobial resistance genotypesb	Isolation source
NYQY00000000	SRR5666392	CDPHFDLB-F07F-672	2,838,285	37.9	2,412,924	55	20	434,456	3,018	fosX, lin	Onions
NYQX00000000	SRR5666381	CDPHFDLB-F09M01162	2,931,178	37.8	1,171,380	35	17	637,977	3,163	fosX, lin	Chicken salad sandwich
NYQW00000000	SRR5666391	CDPHFDLB-F09M01164	2,938,266	37.8	1,207,844	35	18	637977	3,161	fosX, lin	Chicken salad sandwich
NYQV00000000	SRR5666383	CDPHFDLB-F09M01172	2,899,878	37.9	1,104,456	34	13	560,951	3,013	fosX, lin	Turkey cheese sandwich
NYQU00000000	SRR5666390	CDPHFDLB-F10M00415a	2,987,803	37.8	878,056	28	22	435,148	3,175	fosX, lin	Tofu
NYSI00000000	SRR5666385	CDPHFDLB-F10M00415b	2,987,375	37.8	1,142,624	33	22	435,148	3,173	fosX, lin	Tofu
NYQT00000000	SRR5666382	CDPHFDLB-F10M00444a	2,903,564	37.9	1,329,508	38	18	581,348	3,122	fosX, lin	Burrito
NYQS00000000	SRR5666389	CDPHFDLB-F10M00444b	2,879,406	37.8	1,323,810	38	22	435,148	3,176	fosX, lin	Burrito
NYQR00000000	SRR3131140	CDPHFDLB-F11M00452	2,391,665	38.0	1,519,826	50	23	502,427	2,902	fosX, lin	Environmental swab
NYSH00000000	SRR3131133	CDPHFDLB-F12M00816	2,560,850	37.9	3,242,820	70	37	160,005	3,114	fosX, lin	Environmental swab
NYQQ00000000	SRR3131134	CDPHFDLB-F12M00817	2,802,446	37.9	3,359,908	46	19	511,221	3,016	fosX, lin	Environmental swab
NYQP00000000	SRR3309443	CDPHFDLB-F12M00821	2,529,630	37.9	5,160,586	106	19	511,221	3,016	fosX, lin	Environmental swab
NYQO00000000	SRR3131135	CDPHFDLB-F12M00823	2,374,952	37.9	2,281,430	66	23	291,526	3,113	fosX, lin	Environmental swab
NYQN00000000	SRR3131136	CDPHFDLB-F12M00826	2,113,953	37.9	2,933,926	51	24	434,832	3,115	fosX, lin	Environmental swab
NYQM00000000	SRR3131137	CDPHFDLB-F12M00827	2,155,752	37.9	4,419,384	83	22	511,221	3,112	fosX, lin	Environmental swab
NYQL00000000	SRR3131138	CDPHFDLB-F12M00828	2,486,405	37.9	3,243,252	67	23	511,221	3,114	fosX, lin	Environmental swab
NYQK00000000	SRR3131139	CDPHFDLB-F12M00829	2,824,478	38.0	2,173,802	47	56	228,901	3,144	fosX, lin	Environmental swab
NYQJ00000000	SRR3131141	CDPHFDLB-F12M00831	2,481,097	37.9	3,042,194	66	20	511,221	3,108	fosX, lin	Environmental swab
NYQI00000000	SRR2724148	CDPHFDLB-F12M00833	2,812,551	38.0	2,144,202	36	39	473,485	3,034	fosX, lin	Environmental swab
NYSG00000000	SRR2724149	CDPHFDLB-F12M00834	2,812,551	37.9	2,481,316	38	27	321,504	3,116	fosX, lin	Environmental swab
NYQH00000000	SRR2910646	CDPHFDLB-F12M00835	2,575,678	37.9	2,412,816	38	21	469,899	3,112	fosX, lin	Environmental swab
NYQG00000000	SRR2910647	CDPHFDLB-F12M00836	2,671,583	37.9	1,779,152	30	37	217,762	3,036	fosX, lin	Environmental swab
NYQF00000000	SRR2910648	CDPHFDLB-F12M00837	2,592,512	37.9	2,066,372	33	38	511,944	3,038	fosX, lin	Environmental swab
NYQE00000000	SRR2910649	CDPHFDLB-F12M00838	2,438,719	37.9	2,255,836	37	24	292,404	3,113	fosX, lin	Environmental swab
NYQD00000000	SRR2910650	CDPHFDLB-F12M00839	2,670,595	37.9	2,624,464	44	23	511,221	3,115	fosX, lin	Environmental swab
NYSF00000000	SRR2910651	CDPHFDLB-F12M00869a	2,741,167	38.0	2,305,740	38	100	217,762	3,195	fosX, lin	Environmental swab
NYSE00000000	SRR3143809	CDPHFDLB-F12M00869b	2,342,764	37.9	2,497,854	39	53	116,735	3,109	fosX, lin	Environmental swab
NYQC00000000	SRR3143810	CDPHFDLB-F12M00922	2,567,159	37.9	1,162,682	41	27	362,921	3,111	fosX, lin	Onion waste
NYQB00000000	SRR3113299	CDPHFDLB-F12M00923	2,821,790	37.9	3,141,634	90	24	511,221	3,117	fosX, lin	Onion waste
NYQA00000000	SRR3131129	CDPHFDLB-F12M00925	2,844,447	37.9	3,086,862	55	19	511,221	3,017	fosX, lin	Onion waste
NYSD00000000	SRR2148968	CDPHFDLB-F13M00450a	2,545,381	37.9	1,412,768	36	75	70,979	3,047	fosX, lin	Environmental swab
NYSC00000000	SRR2148959	CDPHFDLB-F13M00450b	2,497,313	38.0	766,148	27	121	48,379	3,045	fosX, lin	Environmental swab
NYSB00000000	SRR2148976	CDPHFDLB-F13M00450c	2,597,954	37.9	1,240,264	73	62	100,826	3,061	fosX, lin	Environmental swab
NYSA00000000	SRR2163253	CDPHFDLB-F13M00450d	2,487,289	37.9	1,705,886	56	38	359,200	3,061	fosX, lin	Environmental swab
NYRZ00000000	SRR2533614	CDPHFDLB-F13M00804a	2,630,873	37.8	2,090,608	69	70	195,813	3,286	fosX, lin	Environmental swab
NYPZ00000000	SRR2533615	CDPHFDLB-F13M00804b	2,381,747	37.8	1,356,878	43	84	81,398	3,246	fosX, lin	Environmental swab
NYRY00000000	SRR2533616	CDPHFDLB-F13M00804c	2,629,972	37.7	2,308,508	73	54	249,566	3,295	fosX, lin	Environmental swab
NYPY00000000	SRR2482354	CDPHFDLB-F14M00526a	2,502,089	37.9	2,751,352	69	18	729,315	3,108	fosX, lin	Environmental swab
NYPX00000000	SRR2482374	CDPHFDLB-F14M00526b	2,702,362	37.9	2,121,580	56	15	729,201	3,105	fosX, lin	Environmental swab
NYPW00000000	SRR2482355	CDPHFDLB-F14M01297.C1	2,248,748	37.9	1,530,602	55	23	303,494	2,961	fosX, lin	Nectarines
NYPV00000000	SRR2482356	CDPHFDLB-F14M01297.C3	2,404,839	37.9	2,425,866	65	17	309,901	2,965	fosX, lin	Nectarines
NYPU00000000	SRR2482357	CDPHFDLB-F14M01574.16-1	2,668,170	37.8	1,642,094	56	21	438,630	3,127	fosX, lin	Environmental swab
NYPT00000000	SRR2482358	CDPHFDLB-F14M01574.16-2	2,501,012	37.8	1,742,284	59	19	536,610	3,129	fosX, lin	Environmental swab
NYPS00000000	SRR2482359	CDPHFDLB-F14M01574.16-3	2,607,247	37.8	1,061,132	37	63	352,520	3,171	fosX, lin	Environmental swab
NYPR00000000	SRR2482360	CDPHFDLB-F14M01574.16-4	2,439,942	37.8	1,932,132	62	17	546,012	3,127	fosX, lin	Environmental swab
NYPQ00000000	SRR2482361	CDPHFDLB-F14M01604.46-1	2,457,396	37.8	2,074,814	66	40	508,250	3,152	fosX, lin	Environmental swab
NYPP00000000	SRR2482371	CDPHFDLB-F14M01604.46-2	2,567,840	37.8	5,198,446	111	47	476,844	3,159	fosX, lin	Environmental swab
NYPO00000000	SRR2482372	CDPHFDLB-F14M01612.54-1	2,467,087	37.8	1,856,872	63	47	482,078	3,202	fosX, lin	Environmental swab
NYPN00000000	SRR2482373	CDPHFDLB-F14M01612.54-2	1,862,185	37.8	1,402,132	47	55	226,202	3,268	fosX, lin	Environmental swab
NYRX00000000	SRR2533617	CDPHFDLB-F14M01612.54-3	2,412,958	37.9	1,432,934	45	84	95,898	3,195	fosX, lin	Environmental swab
NYPM00000000	SRR2533618	CDPHFDLB-F14M01612.54-4	2,630,508	37.8	1,676,036	55	62	181,470	3,186	fosX, lin	Environmental swab
NYPL00000000	SRR2533619	CDPHFDLB-F14M01618.60-1	2,353,669	37.8	2,327,122	80	36	476,844	3,099	fosX, lin	Environmental swab
NYRW00000000	SRR2533620	CDPHFDLB-F14M01618.60-2	2,093,299	37.9	1,406,566	43	123	48,341	3,141	fosX, lin	Environmental swab
NYRV00000000	SRR2533621	CDPHFDLB-F14M01624.66-1	2,506,467	37.9	1,381,308	48	76	77,142	3,079	fosX, lin	Environmental swab
NYRU00000000	SRR2533628	CDPHFDLB-F14M01624.66-2	2,160,671	38.1	904,870	30	136	35,238	3,141	fosX, lin	Environmental swab
NYRT00000000	SRR2533622	CDPHFDLB-F14M01626.68-2	2,263,387	37.9	2,211,410	75	22	406,132	3,089	fosX, lin	Environmental swab
NYPJ00000000	SRR2533623	CDPHFDLB-F14M01626.68-3	2,708,259	38.0	1,384,912	48	44	165,401	3,080	fosX, lin	Environmental swab
NYPI00000000	SRR2724068	CDPHFDLB-F14M01632.74-1	2,926,797	37.9	1,638,470	29	82	508,956	3,201	fosX, lin	Environmental swab
NYRS00000000	SRR2724069	CDPHFDLB-F14M01632.74-2	2,797,546	37.8	2,600,326	48	33	508,250	3,093	fosX, lin	Environmental swab
NYPH00000000	SRR2724070	CDPHFDLB-F14M01633.75-1	2,913,126	37.8	3,088,464	55	39	508,250	3,150	fosX, lin	Environmental swab
NYPF00000000	SRR2724072	CDPHFDLB-F14M01635.77-1	2,716,824	37.8	1,993,128	31	52	476,841	3,204	fosX, lin	Environmental swab
NYPE00000000	SRR2724073	CDPHFDLB-F14M01635.77-2	2,665,766	37.8	2,911,128	47	49	259,940	3,151	fosX, lin	Environmental swab
NYPD00000000	SRR2724074	CDPHFDLB-F14M01635.77-3	2,764,455	37.8	3,344,610	61	46	260,811	3,149	fosX, lin	Environmental swab
NYPC00000000	SRR2724075	CDPHFDLB-F14M01635.77-4	2,712,584	37.8	3,128,316	60	43	476,841	3,202	fosX, lin	Environmental swab
NYPB00000000	SRR2724076	CDPHFDLB-F14M01770.86-1	2,536,431	37.9	3,885,638	73	20	400,809	2,966	fosX, lin	Environmental swab
NYRR00000000	SRR2724145	CDPHFDLB-F14M01770.86-2	2,568,736	37.9	2,633,982	52	25	353,199	2,965	fosX, lin	Environmental swab
NYPA00000000	SRR2724146	CDPHFDLB-F14M01770.86-3	2,707,250	37.9	3,211,388	65	20	255,333	2,965	fosX, lin	Environmental swab
NYRQ00000000	SRR2724147	CDPHFDLB-F14M01770.86-4	2,515,057	37.9	2,264,226	44	23	255,333	2,967	fosX, lin	Environmental swab
PQHU00000000	SRR6425039	CDPHFDLB-F15M00075-1	2,928,516	37.8	1,178,072	31	37	353,695	3,188	fosX, lin	Environmental swab
NYRP00000000	SRR2148960	CDPHFDLB-F15M01605-12B	2,316,727	37.9	1,629,558	35	103	67,679	3,095	fosX, lin	Environmental swab
NYRO00000000	SRR2148951	CDPHFDLB-F15M01624-32A	2,241,646	37.9	1,841,154	58	71	69,727	3,038	fosX, lin	Environmental swab
NYRN00000000	SRR2148961	CDPHFDLB-F15M01653-61B	2,390,339	38.0	780,380	27	161	35,913	2,954	fosX, lin	Environmental swab
NYRM00000000	SRR2148969	CDPHFDLB-F15M01690-1	2,147,446	38.0	991,516	29	200	32,231	3,110	fexA, fosX, lin, tet(M)	Raw salmon
NYRL00000000	SRR2148970	CDPHFDLB-F15M01712-1	2,472,460	37.9	1,606,486	52	95	61,130	3,138	fexA, fosX, lin, tet(M)	Raw salmon
NYOZ00000000	SRR2533624	CDPHFDLB-F15M02278-2b	2,256,541	37.8	3,295,126	87	19	545,214	3,105	fosX, lin	Environmental swab
NYOY00000000	SRR2533625	CDPHFDLB-F15M02279-3b	2,040,358	37.8	1,577,710	55	23	411,869	3,109	fosX, lin	Environmental swab
NYOX00000000	SRR2533626	CDPHFDLB-F15M02284-8b	2,462,668	37.8	2,196,184	75	16	546,012	3,111	fosX, lin	Environmental swab
PQHT00000000	SRR6424984	CDPHFDLB-F15M02749	2,907,814	37.8	1,609,112	40	17	545,554	3,120	fosX, lin	Environmental swab
PQHS00000000	SRR6425034	CDPHFDLB-F15M02766	2,909,283	37.8	1,275,842	28	18	528,272	3,058	fosX, lin	Environmental swab
PQHR00000000	SRR6425041	CDPHFDLB-F15M02768	2,854,352	37.8	1,295,360	31	17	545,282	3,055	fosX, lin	Environmental swab
PQHQ00000000	SRR6425042	CDPHFDLB-F15M02769	2,871,732	37.8	1,724,844	39	20	528,672	3,129	bcrB, bcrC, fosX, lin	Environmental swab
NYOW00000000	SRR2724066	CDPHFDLB-F15M03122-1	2,491,738	37.9	3,012,598	46	17	400,811	2,965	fosX, lin	Environmental swab
NYOV00000000	SRR2724067	CDPHFDLB-F15M03122-2	2,632,405	37.9	2,062,246	39	17	400,811	2,964	fosX, lin	Environmental swab
NYOU00000000	SRR3113284	CDPHFDLB-F15M03674-2a	2,873,518	37.8	3,642,830	75	59	436,139	3,129	fosX, lin	Environmental swab
NYOT00000000	SRR3113296	CDPHFDLB-F15M03678-6b	2,294,206	37.8	2,510,196	79	37	432,779	3,096	fosX, lin	Environmental swab
NYOS00000000	SRR3113297	CDPHFDLB-F15M03680-8a	2,525,970	37.8	2,607,978	85	43	427,543	3,105	fosX, lin	Environmental swab
NYOR00000000	SRR3113285	CDPHFDLB-F15M03681-9a	2,843,017	37.8	3,631,380	97	42	436,139	3,116	fosX, lin	Environmental swab
NYRK00000000	SRR3113286	CDPHFDLB-F15M03685-13a	2,281,492	37.9	1,008,890	35	91	76,393	3,079	fosX, lin	Environmental swab
NYOQ00000000	SRR3113287	CDPHFDLB-F15M03686-14a	2,090,609	37.8	1,838,374	61	36	432,609	3,098	fosX, lin	Environmental swab
NYRJ00000000	SRR3113298	CDPHFDLB-F15M03691-19a	1,885,781	37.8	3,068,868	91	46	141,539	3,084	fosX, lin	Environmental swab
NYOP00000000	SRR3113288	CDPHFDLB-F15M03698-26a	2,327,743	37.8	1,843,592	62	25	330,002	2,982	fosX, lin	Environmental swab
NYRI00000000	SRR3113289	CDPHFDLB-F15M03699-27a	2,531,994	37.9	1,057,872	37	83	83,151	2,983	fosX, lin	Environmental swab
NYRH00000000	SRR3113290	CDPHFDLB-F15M03700-28a	2,521,964	37.8	1,689,550	56	45	207,537	2,994	fosX, lin	Environmental swab
NYOO00000000	SRR3113291	CDPHFDLB-F15M03701-29a	2,084,966	37.8	3,096,966	97	20	541,149	2,977	fosX, lin	Environmental swab
NYON00000000	SRR3113292	CDPHFDLB-F15M03704-32a	2,469,847	37.9	1,718,214	59	53	243,136	3,094	fosX, lin	Environmental swab
NYRG00000000	SRR3113293	CDPHFDLB-F15M03706-34a	2,126,573	38.0	977,516	30	155	34,234	2,957	fosX, lin	Environmental swab
NYOM00000000	SRR3113294	CDPHFDLB-F15M03710-38a	1,965,404	37.8	3,416,554	107	18	456,300	2,977	fosX, lin	Environmental swab
NYOL00000000	SRR3113295	CDPHFDLB-F15M03711-39a	2,517,843	37.8	2,926,038	90	23	541,945	2,988	fosX, lin	Environmental swab
NYOK00000000	SRR3143801	CDPHFDLB-F15M03850-P014B1	2,643,675	37.8	3,233,310	74	17	437,442	3,151	fosX, lin	Mushrooms
NYOJ00000000	SRR3143802	CDPHFDLB-F15M03850-P014B2	2,457,228	37.8	2,064,168	71	16	437,442	3,149	fosX, lin	Mushrooms
NYOI00000000	SRR3143803	CDPHFDLB-F15M04137-P015P1	2,606,534	37.8	2,299,194	71	17	437,508	3,148	fosX, lin	Mushrooms
NYOH00000000	SRR3143804	CDPHFDLB-F15M04137-P015P2	2,684,225	37.8	2,314,808	76	17	437,508	3,149	fosX, lin	Mushrooms
NYRF00000000	SRR3101600	CDPHFDLB-F15M04169-E005	2,625,724	37.9	1,223,806	31	76	68,069	3,151	fosX, lin	Environmental swab
NYRE00000000	SRR3101608	CDPHFDLB-F15M04169-E005-2	2,241,218	37.9	963,478	32	70	97,715	3,167	fosX, lin	Environmental swab
NYRD00000000	SRR3101601	CDPHFDLB-F15M04174-E010	2,210,047	37.9	2,167,702	46	71	66,099	2,945	fosX, lin	Environmental swab
NYRC00000000	SRR3101609	CDPHFDLB-F15M04174-E010-2	2,344,627	38.0	873,156	28	107	56,669	2,934	fosX, lin	Environmental swab
NYOG00000000	SRR3101602	CDPHFDLB-F15M04188-E024	2,488,076	37.9	1,217,930	38	70	74,906	3,022	fosX, lin	Environmental swab
NYRB00000000	SRR3101610	CDPHFDLB-F15M04188-E024-2	2,434,912	38.0	721,266	24	126	38,045	2,991	fosX, lin	Environmental swab
NYOF00000000	SRR5047483	CDPHFDLB-F15M04191-E027	2,996,396	37.8	554,754	60	31	368,155	3,226	fosX, lin	Environmental swab
NYOE00000000	SRR5047485	CDPHFDLB-F15M04191-E027-2	2,832,713	37.9	797,146	58	78	368,155	3,276	fosX, lin	Environmental swab
NYOD00000000	SRR3101604	CDPHFDLB-F15M04208-E044	2,355,581	37.9	1,676,582	42	71	66,254	3,145	fosX, lin	Environmental swab
NYOC00000000	SRR3101613	CDPHFDLB-F15M04208-E044-2	2,635,926	37.9	1,384,452	45	43	248,831	3,163	fosX, lin	Environmental swab
NYOB00000000	SRR3101605	CDPHFDLB-F15M04238-E074	2,033,023	37.9	1,608,936	37	45	111,041	2,937	fosX, lin	Environmental swab
NYOA00000000	SRR3101614	CDPHFDLB-F15M04238-E074-2	2,446,141	38.0	1,289,706	44	41	164,286	2,942	fosX, lin	Environmental swab
NYRA00000000	SRR3101606	CDPHFDLB-F15M04239-E075	2,046,871	38.0	1,898,044	44	93	67,061	2,943	fosX, lin	Environmental swab
NYNZ00000000	SRR3101615	CDPHFDLB-F15M04239-E075-2	2,351,033	38.0	1,034,762	34	85	71,341	2,945	fosX, lin	Environmental swab
NYQZ00000000	SRR3101607	CDPHFDLB-F15M04262-E098	2,029,810	38.1	1,370,446	41	133	38,407	2,917	fosX, lin	Environmental swab
NYNY00000000	SRR3101616	CDPHFDLB-F15M04262-E098-2	1,712,017	38.1	1,066,544	36	101	47,050	2,890	fosX, lin	Environmental swab
NYNX00000000	SRR3143805	CDPHFDLB-F1601028-021-E021A	2,548,949	37.8	2,756,150	87	17	437,442	3,151	fosX, lin	Environmental swab
NYNW00000000	SRR3143806	CDPHFDLB-F1601028-021-E021B	2,762,160	37.8	2,065,454	70	17	437,442	3,150	fosX, lin	Environmental swab
NYNV00000000	SRR3143807	CDPHFDLB-F1601030-027-E110B1	2,277,848	37.9	1,947,502	68	16	442,255	3,016	fosX, lin	Casing
NYNU00000000	SRR3143808	CDPHFDLB-F1601030-027-E110B2	2,520,124	37.9	2,262,468	79	22	263,843	3,016	fosX, lin	Casing
NYNT00000000	SRR3410223	CDPHFDLB-F1601052-016	2,763,221	37.8	689,190	25	29	479,619	3,104	fosX, lin	Environmental swab
NYNS00000000	SRR3407806	CDPHFDLB-F1601052-021	2,716,065	37.8	1,077,236	41	20	473,299	2,987	fosX, lin	Environmental swab
NYNR00000000	SRR3407805	CDPHFDLB-F1601052-022	2,768,196	37.8	1,038,656	38	21	528,599	3,010	fosX, lin	Environmental swab
NYNQ00000000	SRR3407804	CDPHFDLB-F1601052-032	2,785,026	37.8	2,159,626	83	15	541,819	2,981	fosX, lin	Environmental swab
NYNP00000000	SRR3407803	CDPHFDLB-F1601052-033	2,752,694	37.8	2,150,992	83	15	541,819	2,981	fosX, lin	Environmental swab
NYNO00000000	SRR3407802	CDPHFDLB-F1601052-034	2,787,666	37.8	960,738	37	16	541,421	2,931	fosX, lin	Environmental swab
NYNN00000000	SRR3407801	CDPHFDLB-F1601052-035	2,477,572	37.8	2,800,652	103	16	545,884	3,012	fosX, lin	Environmental swab
NYNM00000000	SRR3407800	CDPHFDLB-F1601052-069	2,391,239	37.8	3,605,914	130	24	475,392	3,076	fosX, lin	Environmental swab
NYNL00000000	SRR3407799	CDPHFDLB-F1601052-085	2,729,610	37.8	1,890,550	67	19	545,554	3,013	fosX, lin	Environmental swab
NYNK00000000	SRR3407798	CDPHFDLB-F1601052-113	2,702,545	37.8	3,214,746	117	20	507,335	3,096	fosX, lin	Environmental swab
PQHP00000000	SRR6425464	CDPHFDLB-F1603037-20a	2,911,771	37.8	1,408,438	36	19	528,620	3,129	bcrB, bcrC, fosX, lin	Environmental swab
NYNJ00000000	SRR3606921	CDPHFDLB-F1605001-001-1A1	2,857,261	37.8	753,798	22	11	1,516,333	3,025	fosX, lin	Frozen vegetables
NYNI00000000	SRR3606922	CDPHFDLB-F1605001-001-1A3	2,912,517	37.8	1,271,224	36	17	545,397	2,958	fosX, lin	Frozen vegetables
NYNH00000000	SRR3606923	CDPHFDLB-F1605001-002-1B1	2,650,705	37.9	876,702	33	28	425,267	2,960	fosX, lin	Frozen vegetables
NYNG00000000	SRR3606924	CDPHFDLB-F1605001-002-1B4	2,744,169	37.8	673,392	25	18	496,167	3,027	fosX, lin	Frozen vegetables
NYNF00000000	SRR3606925	CDPHFDLB-F1605001-003-2A1	2,797,455	37.8	721,422	27	14	1,516,336	3,028	fosX, lin	Frozen vegetables
NYNE00000000	SRR3606926	CDPHFDLB-F1605001-003-2A3	2,661,603	37.8	896,504	34	20	432,482	3,031	fosX, lin	Frozen vegetables
NYND00000000	SRR3606927	CDPHFDLB-F1605001-004-2B1	2,561,030	37.8	1,289,066	46	11	1,515,607	3,024	fosX, lin	Frozen vegetables
NYNC00000000	SRR3606928	CDPHFDLB-F1605001-004-2B2	2,726,234	37.9	886,118	34	23	545,769	2,964	fosX, lin	Frozen vegetables
NYNB00000000	SRR3606929	CDPHFDLB-F1605001-005-2C1	2,709,017	37.8	1,019,756	36	14	581,822	3,025	fosX, lin	Frozen vegetables
NYNA00000000	SRR3606930	CDPHFDLB-F1605001-005-2C2	2,540,561	37.8	1,834,788	64	12	581,822	3,024	fosX, lin	Frozen vegetables
NYMZ00000000	SRR3948512	CDPHFDLB-F1605034-061-1	2,740,674	37.9	989,200	38	12	1,489,538	3,006	fosX, lin	Environmental swab
NYMY00000000	SRR3948513	CDPHFDLB-F1605034-061-2	2,555,715	37.9	961,970	37	24	439,269	3,005	fosX, lin	Environmental swab
NYMX00000000	SRR5047487	CDPHFDLB-F1610030-049A	2,834,722	37.9	1,205,938	45	21	437,442	3,156	fosX, lin	Environmental swab
NYMW00000000	SRR5047481	CDPHFDLB-F1610030-049B	2,824,341	37.9	1,653,396	62	59	419,271	3,196	fosX, lin	Environmental swab
NYMV00000000	SRR5666388	CDPHFDLB-F1702031-086	2,783,956	37.8	1,481,524	42	40	285,485	3,150	fosX, lin	Environmental swab
PQHO00000000	SRR6367391	CDPHFDLB-F1704007-002	2,052,141	37.9	2,089,438	33	112	299,947	3,322	bcrB, bcrC, fosX, lin	Environmental swab
PQHN00000000	SRR6367394	CDPHFDLB-F1704007-008	2,458,205	37.8	2,509,740	80	31	480,705	3,223	bcrB, bcrC, fosX, lin	Environmental swab
PQHM00000000	SRR6369101	CDPHFDLB-FM17-00087	2,869,040	37.9	1,657,750	52	32	519,458	3,107	fosX, lin	Environmental swab
PQHL00000000	SRR6369100	CDPHFDLB-FM17-00088	2,558,183	37.9	1,671,218	56	23	513,398	3,118	bcrB, bcrC, fosX, lin	Environmental swab
PQHK00000000	SRR6369104	CDPHFDLB-FM17-00090	1,993,228	37.9	2,256,280	72	15	364,332	3,039	fosX, lin	Environmental swab
PQHJ00000000	SRR6369107	CDPHFDLB-FM17-00091	2,084,793	37.9	1,597,574	50	23	478,793	3,082	fosX, lin	Environmental swab
PQHI00000000	SRR6368628	CDPHFDLB-FM17-00092	2,344,827	37.8	2,134,582	75	51	259,981	3,210	fosX, lin	Environmental swab
PQHH00000000	SRR6368621	CDPHFDLB-FM17-00100	2,509,251	37.9	2,134,686	71	23	478,796	3,174	bcrB, bcrC, fosX, lin	Environmental swab
PQHG00000000	SRR6369108	CDPHFDLB-FM17-00110	2,402,221	37.8	2,662,808	93	33	508,250	3,104	bcrB, bcrC, fosX, lin	Environmental swab
PQHF00000000	SRR6369102	CDPHFDLB-FM17-00114	2,618,953	37.9	1,323,382	50	13	521,712	3,038	fosX, lin	Environmental swab
PQHE00000000	SRR6369105	CDPHFDLB-FM17-00115	2,152,539	37.9	1,680,510	56	16	346,961	3,036	fosX, lin	Environmental swab
PQHD00000000	SRR6369103	CDPHFDLB-FM17-00118	2,566,669	37.8	1,457,098	52	52	282,984	3,233	fosX, lin	Environmental swab
PQHC00000000	SRR6369097	CDPHFDLB-FM17-00120	2,567,383	37.8	1,653,280	58	52	282,982	3,236	fosX, lin	Environmental swab
PQHB00000000	SRR6369099	CDPHFDLB-FM17-00121	2,574,327	37.8	1,927,382	70	22	517,902	3,124	bcrB, bcrC, fosX, lin	Environmental swab
PQHA00000000	SRR6425463	CDPHFDLB-FM17-00123	2,964,701	37.8	1,215,572	28	19	517,859	3,123	bcrB, bcrC, fosX, lin	Environmental swab
PQGZ00000000	SRR6425473	CDPHFDLB-FM17-00125	2,871,050	37.9	1,868,244	38	16	517,776	3,088	fosX, lin	Environmental swab
PQGY00000000	SRR6425598	CDPHFDLB-FM17-00126	2,887,392	37.9	1,076,638	29	18	355,675	3,046	fosX, lin	Environmental swab
PQGX00000000	SRR6425582	CDPHFDLB-FM17-00136	2,940,641	37.9	1,537,420	39	17	517,904	3,116	bcrB, bcrC, fosX, lin	Environmental swab
PQGW00000000	SRR6425581	CDPHFDLB-FM17-00137	2,962,165	37.8	1,264,836	27	63	481,060	3,208	bcrB, bcrC, fosX, lin	Environmental swab
PQGV00000000	SRR6425603	CDPHFDLB-FM17-00149	2,887,274	37.9	1,414,758	38	14	518,313	3,090	fosX, lin	Environmental swab
PQGU00000000	SRR6425597	CDPHFDLB-FM17-00158	3,032,302	37.8	1,594,320	32	48	508,250	3,215	fosX, lin	Environmental swab
PQGT00000000	SRR6425600	CDPHFDLB-FM17-00159	3,008,320	37.8	1,245,706	31	50	508,250	3,219	fosX, lin	Environmental swab
PQGS00000000	SRR6425602	CDPHFDLB-FM17-00161	2,908,822	37.8	1,781,982	36	19	404,359	3,140	bcrB, bcrC, fosX, lin	Environmental swab

Total no. of genes obtained from NCBI PGAP analyses.

Antimicrobial resistance genotypes obtained from NCBI pathogen detection browser.

NCBI Pathogen Detection analysis (https://www.ncbi.nlm.nih.gov/pathogens) indicates that all 171 isolates contain the antimicrobial resistance genes fosX (fosfomycin resistance) and lin (lincomycin resistance), 24 (14.0%) contain bcrB and bcrC (bacitracin resistance) genes, 2 (1.1%) contain fexA genes (florfenicol/chloramphenicol resistance), and 2 (1.1%) contain tet genes (tetracycline resistance).

Data availability.

All accession numbers and assemblies are available in GenBank. Please see accession numbers listed in Table 1.