High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated with PacBio Sequencing.

Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical Shigella strains that represent the four species and a variety of serotypes.

GENOME ANNOUNCEMENT

Shigellosis is an acute enteric disease; symptoms may include severe diarrhea with mucoid bloody stools, abdominal cramps, and tenesmus (1). Shigella species are endemic to most developing countries and are estimated to cause over 80 million cases of bloody diarrhea and 700,000 deaths each year, the majority of which occur among children less than 5 years of age (2). Here, we report the availability of high-quality genome sequences for 59 Shigella strains generated via PacBio sequencing.

The DNA of the isolates was extracted using the ArchivePure DNA extraction kit standard protocol (5 Prime, Gaithersburg, MD). Library construction and PacBio sequencing were conducted as previously described (3), and DNA was sheared to an approximate length of 20 kb via needle shearing. BluePippin (Sage Scientific, Beverly, MA) was used to size select the sheared DNA. Sheared DNA and standard library protocols from a DNA template preparation kit (Pacific Biosciences, Menlo Park, CA) were used to generate large SMRTbell libraries. All strains were sequenced on one single-molecule real-time (SMRT) cell. Completed libraries were then bound to proprietary P6 v2 polymerase and sequenced using C4 chemistry on a PacBio RS II sequencer for 360-min movies (3). The sequence reads underwent de novo assembly using the PacBio Hierarchical Genome Assembly Process version 3 (4). For 49 strains (designated in Table 1), the sequence order in the resulting PacBio assembly for the chromosomes was verified using restriction enzyme NcoI and AflII whole-genome mapping (OpGen, Gaithersburg, MD).

TABLE 1

Strain information and GenBank accession numbers for 59 Shigella isolates

Strain (reference no.)	Species	Serotype	GenBank accession no.	Chromosome size(s) (bp)	Associated plasmid size(s) (bp)	Optical map
65-6310	S. boydii	1	PTES00000000	2,603,357,a 2,046,275a	164,492a	No
ATCC 8700	S. boydii	2	CP026731–CP026733	4,575,738	59,816,a 51,078	Yes
NCTC 9850	S. boydii	3	CP026762 and CP026763	4,575,797	150,497	Yes
NCTC 9770	S. boydii	4	PSSU00000000	3,106,825,a 1,499,125a	202,816a	Yes
NCTC 9733	S. boydii	5	CP026844 and CP026845	4,932,934	230,094	Yes
ATCC 12027	S. boydii	6	CP026865 and CP026866	4,680,168a	135,321a	Yes
NCTC 9734	S. boydii	7	CP026874 and CP026875	5,163,976a	193,652a	Yes
NCTC 9353	S. boydii	8	CP026797 and CP026798	4,488,529	146,337	Yes
ATCC 49812	S. boydii	9	CP026836 and CP026837	5,106,737	213,410	Yes
ATCC 12030 (SH135)	S. boydii	10	CP026867–CP026870	4,607,824a	145,169, 52,696,a 36,641a	Yes
59-2708	S. boydii	11	CP026846	4,856,857	None	Yes
59-248	S. boydii	14	CP026766 and CP026767	4,678,058	209,166a	Yes
ATCC 12034	S. boydii	15	PSSP00000000	5,100,100,a 24,879,a 44,022a	251,107a	Yes
ATCC 35964	S. boydii	16	CP026876 and CP026877	5,129,092	166,502	Yes
ATCC 35965	S. boydii	17	PSSR00000000	3,275,068,a 1,127,682,a 662,313a	182,849a	Yes
ATCC 35966	S. boydii	18	PSSS00000000	4,267,999,a 342,076a	128,923a	Yes
83-578	S. boydii	19	CP026813 and CP026814	4,580,582	122,029	Yes
ATCC BAA-1247	S. boydii	20	CP026795 and CP026796	4,575,738	226,559a	Yes
54-1621 (5)	S. boydii	Provisional 54-1621	CP026810	4,531,304a	None	Yes
ATCC 13313	S. dysenteriae	1	CP026774 and CP026775	4,395,762	182,697	Yes
BU53M1b (6)	S. dysenteriae	1	CP024466–CP024469	4,409,083	54,993, 115,922, 184,894	Yes
69-3818	S. dysenteriae	1	CP026777–CP026779	4,390,268	115,128,a 202,417	Yes
07-3308	S. dysenteriae	1	CP026878 and CP026879	4,382,687	69,799	No
53-3937	S. dysenteriae	1	CP026780 and CP026781	4,382,743	67,064a	Yes
08-3380	S. dysenteriae	1	CP026782 and CP026783	4,464,195	183,210	No
80-547	S. dysenteriae	1	CP026784 and CP026785	4,391,331	204,250a	Yes
NCTC 9718	S. dysenteriae	1	CP026786 and CP026787	4,371,869	189,871a	No
ATCC 9750 (Sd44)	S. dysenteriae	2	CP026824	4,971,516	None	Yes
ATCC 9751	S. dysenteriae	3	CP026825	4,699,491	None	Yes
ATCC 9753	S. dysenteriae	4	CP026840 and CP026841	4,716,399	215,925	Yes
ATCC 9764	S. dysenteriae	5	CP026872 and CP026873	4,711,098a	166,878a	Yes
ATCC 9754	S. dysenteriae	6	CP026842 and CP026843	4,588,477	106,437	Yes
ATCC 9752	S. dysenteriae	7	CP026838 and CP026839	4,273,636	103,367	Yes
ATCC 12021 (Sd41)	S. dysenteriae	8	CP026826 and CP026827	4,558,619	224,352a	Yes
ATCC 12037	S. dysenteriae	9	CP026828 and CP026829	4,642,274	216,328	Yes
ATCC 12039	S. dysenteriae	10	CP026830 and CP026831	4,880,735	181,100	Yes
ATCC 12038	S. dysenteriae	11	PSSQ00000000	4,292,356,a 99,306,a 257,965a	165,104a	Yes
ATCC 49550	S. dysenteriae	12	PSST00000000	3,270,959,a 1,465,326a	230,788a	Yes
ATCC 49346	S. dysenteriae	14c	CP026832 and CP026833	4,619,326	224,419	Yes
ATCC 49347	S. dysenteriae	15d	CP026834 and CP026835	4,684,535	99,066	Yes
2017C-4522	S. dysenteriae	Provisional 2009C-3478	CP026805 and CP026806	4,609,265	69,966	Yes
96-3162 (7)	S. dysenteriae	Provisional 96-3162	CP026821–CP026823	4,804,763	79,586, 215,820	Yes
204/96 (8)	S. dysenteriae	Provisional 204/96	CP026807–CP026809	4,800,156	79,695, 226,481	Yes
93-119 (9)	S. dysenteriae	Provisional 93-119	CP026815–CP026817	4,799,750	79,553, 226,441	Yes
96-265e (10)	S. dysenteriae	Provisional 96-265	CP026818–CP026820	4,744,419	80,213, 195,489	Yes
E670/74 (11)	S. dysenteriae	Provisional E670/74	CP027027 and CP027028	5,036,586	149,179	Yes
73-5612	S. flexneri	1b	CP026871	4,490,153a	None	No
ATCC 29903	S. flexneri	2a	CP026788–CP026790	4,659,463	113,130, 165,702	Yes
61-4982	S. flexneri	4b	CP026791 and CP026792	4,631,337	59,834	Yes
74-1170	S. flexneri	5a	CP026793 and CP026794	4,733,503	251,323a	No
NCTC 9728	S. flexneri	5b	CP026799 and CP026800	4,511,010	135,368	Yes
64-5500	S. flexneri	6	CP026811 and CP026812	4,659,714	181,479	Yes
98-3193	S. flexneri	7f	CP026776	4,508,802	None	No
04-3145	S. flexneri	7f	CP026764 and CP026765	4,571,921	68,319	No
95-3008	S. flexneri	7f	CP026772 and CP026773	4,516,380a	52,051a	Yes
94-3007b (6)	S. flexneri	7f	CP024473–CP024476	4,533,699	69,554, 82,833, 220,282	Yes
93-3063	S. flexneri	Y	CP026768–CP026771	4,628,330	27,054,a 71,925,a 220,759	Yes
89-141 (12)	S. flexneri	Provisional 89-141	CP026803 and CP026804	4,481,548	245,004a	No
ATCC 29930	S. sonnei	NAg	CP026801 and CP026802	4,975,028	18,973a	Yes

Indicates genome/plasmid could not be circularized.

Two strains were previously sequenced but included here because they were part of the originally selected historical Shigella strain collection.

Proposed serotype designation for provisional serovar is E22383 (9).

Proposed serotype designation for provisional serovar is E23507 (9).

Frank Rogers, National Laboratory for Enteric Pathogens, Health Canada, Winnipeg, Canada, personal communication.

Proposed serotype designation for provisional serotype is 88-893 (94-3007).

NA, not applicable.

Table 1 lists the strain numbers, species, serotypes, accession numbers, genome and plasmid sizes, and the availability of an optical map that could be aligned to the PacBio genome sequence. One chromosomal sequence was obtained for all but seven genomes. The average genome coverage was 133.7×. The average G+C content was 51.1%. The assemblies of 14 isolates failed to be circularized, likely due to unresolved or collapsed repeat regions. Noncircular assemblies in Table 1 are noted.

Accession number(s).

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions described in this paper are the first versions.