Draft Genome Sequences of 26 Salmonella Isolates Associated with Multiple Outbreaks in Brazil

Salmonella enterica subsp. enterica isolates are the leading cause of foodborne illness worldwide. Here, we report the draft genomes of 26 Salmonella isolates of food and clinical origin, belonging to four serovars, associated with outbreaks from 1999 to 2006 in the south of Brazil.

ABSTRACT

Salmonella enterica subsp. enterica isolates are the leading cause of foodborne illness worldwide. Here, we report the draft genomes of 26 Salmonella isolates of food and clinical origin, belonging to four serovars, associated with outbreaks from 1999 to 2006 in the south of Brazil.

ANNOUNCEMENT

Nontyphoidal Salmonella spp. are a major cause of diarrheal illness worldwide, leading to an estimated 93 million enteric infections and around 155,000 deaths annually (1). These 26 Salmonella enterica subsp. enterica strains (from serovars Infantis, n = 7; London, n = 6; Typhimurium, n = 7; or Johannesburg, n = 6) were isolated from a variety of sources, including chicken meat, turkey sausage, humans, etc., related to multiple outbreaks in the south of Brazil between 1999 and 2006 (Table 1). S. Infantis has been resistant to a variety of antibiotics and identified as an etiological agent of severe gastroenteritis, leading to hospitalized children in Brazil since 1994 (2). S. London has been reported to be resistant to colistin in strains isolated from swine in Brazil (3). S. Johannesburg, isolated in Brazil and carrying the genes qnrA1 and qnrB19, showed plasmid-mediated resistance to nalidixic acid, a first-generation quinolone (4). S. Typhimurium has been one of the top serovars causing gastroenteritis worldwide (5). Sequence type 19 (ST19) has been reported as the most prevalent ST, followed by the more invasive ST313 (5). As of 6 February 2020, without counting our submission, the Pathogen Detection isolates browser (https://www.ncbi.nlm.nih.gov/pathogens/) contained 54 S. Infantis, 1 S. London, 223 S. Typhimurium, and 0 S. Johannesburg isolates from Brazil. Besides offering genomic diversity information for isolates implicated in these outbreaks 2 decades ago, our data are also valuable for ongoing outbreak investigations and evolutionary history for these four serovars’ isolates.

TABLE 1.

Strain and genome information for the current study

Name	Sourcea	Yr	Size (bp)	GC (%)	No. of genes	No. of RNA genes	No. of reads	Coverage (×)	N50 (bp)	No. of contigs	SRA accession no.	GenBank accession no.
CFSAN077726b	Smoked turkey sausage	2001	4,604,173	52.25	4,445	102	12,387,058	369	208,947	45	SRS5956604	AANBIU000000000
CFSAN077739b	Food	2005	4,605,454	52.25	4,445	104	9,563,052	292	202,265	42	SRS5955826	AANBII000000000
CFSAN077748b	Food	2005	4,603,927	52.15	4,430	78	1,133,076	35	160,857	57	SRS5956596	AANBIP000000000
CFSAN077750b	Food	2005	4,605,811	52.15	4,432	99	7,399,642	232	202,248	42	SRS5956599	AANBIN000000000
CFSAN077779b	Clinical	2004	4,606,135	52.25	4,437	99	3,100,564	96	196,847	45	SRS5955850	AANBIQ000000000
CFSAN077742b	Food	2005	4,577,295	52.23	4,408	100	7,277,648	227	201,873	43	SRS5955824	AANBIL000000000
CFSAN077781b	Clinical	2005	4,576,346	52.23	4,410	99	8,990,252	285	202,133	42	SRS5955721	AANBIC000000000
CFSAN077751c	Food	2005	4,626,211	52.27	4,532	89	7,050,846	217	434,659	33	SRS5956607	AANBIV000000000
CFSAN077753c	Chicken meat	2002	4,625,978	52.27	4,530	92	6,396,868	198	340,103	32	SRS5955820	AANBIE000000000
CFSAN077778c	Clinical	2004	4,626,171	52.27	4,511	90	2,708,156	83	191,397	44	SRS5955822	AANBID000000000
CFSAN077786c	Clinical	2006	4,626,949	52.27	4,513	91	4,631,292	145	208,128	39	SRS5955828	AANBIT000000000
CFSAN077789c	Clinical	2006	4,626,970	52.27	4,512	92	3,295,404	103	208,100	38	SRS5955720	AANBIB000000000
CFSAN077790c	Clinical	2006	4,625,073	52.27	4,517	90	2,609,344	81	213,324	38	SRS5955827	AANBIG000000000
CFSAN077707d	Chicken meat with sauce	2000	4,580,419	52.25	4,402	93	7,708,866	245	229,086	44	SRS5955829	AANBIJ000000000
CFSAN077736d	Food	2004	4,580,327	52.26	4,398	90	8,954,394	280	237,179	38	SRS5964586	AANBIW000000000
CFSAN077743d	Food	2005	4,579,849	52.25	4,403	92	8,001,610	249	221,794	44	SRS5955848	AANBIO000000000
CFSAN077745d	Food	2005	4,669,736	52.22	4,502	91	9,316,388	283	237,179	41	SRS5955819	AANBIF000000000
CFSAN077746d	Food	2005	4,552,171	52.25	4,384	91	8,304,902	257	237,179	43	SRS5955821	AANBIH000000000
CFSAN077747d	Food	2005	4,578,138	52.25	4,400	90	2,612,096	81	226,309	42	SRS5956598	AANBIR000000000
CFSAN077701e	Morcela beef salami	1999	4,763,160	52.13	4,637	101	10,051,244	293	176,749	55	SRS5956603	AANBIX000000000
CFSAN077715e	Food	2001	4,997,643	51.78	4,904	97	6,144,112	177	171,826	67	SRS5955823	AANBIK000000000
CFSAN077727e	Roast chicken meat	2001	4,880,727	52.17	4,781	91	9,441,774	271	175,545	60	SRS5637490	AANBIA000000000
CFSAN077758e	Chicken meat	2006	4,914,580	52.14	4,829	72	991,930	29	172,267	71	SRS5964585	AANBIZ000000000
CFSAN077780e	Clinical	2005	4,877,842	52.18	4,778	88	1,231,090	36	145,178	71	SRS5956601	AANBIY000000000
CFSAN077783e	Clinical	2005	4,878,625	52.18	4,782	96	3,088,720	90	208,949	66	SRS5956600	AANBIM000000000
CFSAN077785e	Clinical	2006	4,881,092	52.18	4,782	99	9,172,298	268	246,869	61	SRS5956602	AANBIS000000000

^aAll strains were isolated from states in the south of Brazil.

^bS. Infantis.

^cS. Johannesburg.

^dS. London.

^eS. Typhimurium.

The 26 Salmonella isolates were from the Central Laboratory of Parana State and the State University of Londrina, Brazil (6–8). A DNeasy blood and tissue kit (Qiagen, Inc., Valencia, CA) was used to extract genomic DNA from the culture after a 16-h incubation period at 37°C in tryptic soy broth (TSB) (Becton, Dickinson, Franklin Lakes, NJ). A Qubit 3.0 fluorometer (Life Technologies, MD) was used to measure DNA concentrations. Library preparation was conducted following Nextera XT protocols, and paired-end reads were sequenced on the NextSeq 500 system (Illumina, San Diego, CA) using a NextSeq 500/550 high output kit v2 (300 cycles). We selected data based on the following criteria: cluster density (between 170,000 and 220,000/mm²) and percentage of clusters passing filters (greater than 80%). Trimmomatic (9) was used to trim the raw reads, and SPAdes v3.8.2 (10) was used to assemble the data using default parameters. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.10 (11) was used to conduct annotation of the assemblies, which were subsequently deposited in GenBank.

Data availability.

The genome sequences of these 26 Salmonella isolates were deposited in GenBank, and the SRA and whole-genome sequence (WGS) accession numbers are available in Table 1.