ABSTRACT
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.
ACKNOWLEDGMENTS
This work was funded by federal appropriations to the Centers for Disease Control and Prevention through the Advanced Molecular Detection Initiative line item.
The findings and conclusions of this article are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention. The use of trade names is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention or by the U.S. Department of Health and Human Services.
Footnotes
Citation Kim J, Lindsey RL, Garcia-Toledo L, Loparev VN, Rowe LA, Batra D, Juieng P, Stoneburg D, Martin H, Knipe K, Smith P, Strockbine N. 2018. High-quality whole-genome sequences for 59 historical Shigella strains generated with PacBio sequencing. Genome Announc 6:e00282-18. https://doi.org/10.1128/genomeA.00282-18.
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