ABSTRACT
Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here the high-quality whole-genome sequences of 21 ETEC strains isolated from patients in the United States, international diarrheal surveillance studies, and cruise ship outbreaks.
GENOME ANNOUNCEMENT
Enterotoxigenic Escherichia coli (ETEC) infections are the leading cause of travelers’ diarrhea and the most common cause of diarrhea among children in developing countries (1). ETEC causes approximately 210 million infections and 380,000 deaths per year (2). ETEC infections in humans are characterized by the production of either or both heat-stable (ST) and heat-labile (LT) enterotoxins (3). Here, we report the availability of high-quality genome sequences for 21 ETEC strains generated by PacBio sequencing. Each of the 21 genomes contained one chromosomal sequence, and 17 of these were determined to be circular with overlapping ends that were trimmed from one end.
ETEC genomic DNA was extracted using Archive Pure according to the manufacturer’s protocol (5 Prime, Gaithersburg, MD, USA). The genomic DNA was sheared to 20 kb using needle shearing. These libraries were further size selected using BluePippin (Sage Scientific, Beverly, MA, USA). The sheared DNA was used to generate large SMRTbell libraries using the standard library protocols of the Pacific Biosciences DNA template preparation kit (Pacific Biosciences, Menlo Park, CA, USA). All strains were sequenced using one single-molecule real-time (SMRT) cell, except strain 9276-90, which used two. The finished libraries were bound to proprietary P6 v2 polymerase and sequenced on a PacBio RSII system using C4 chemistry for 360-min movies. Sequence reads were filtered and assembled de novo utilizing the PacBio Hierarchical Genome Assembly Process version 3 (4).
Table 1 lists the accession numbers, detected serotype (genotypic), assembly metrics, and reference (if available) for each ETEC whole-genome sequence. A single chromosomal sequence was obtained for all genomes with an average coverage of 102.6× (range, 42.3× to 188.6×). The average G+C content for each chromosomal sequence was 50.68%, ranging from 50.37% to 50.82%. The chromosomal sequences are circular with overlapping ends for all but four genomes. The single chromosomal sequences for isolates 90-9276, 90-9269, F5176C6, and 00-3279 could not be circularized because of unresolved or collapsed repeats. Each ETEC genome contained between one and five plasmids. Table 1 notes whether overlap was found to form circular chromosomal or plasmid contigs.
TABLE 1 .
Accession numbers and assembly metrics of 21 ETEC whole-genome sequences
|
E. coli strain no. (reference) |
Serotype | Chromosomal GenBank accession no. |
Average coverage (×) |
Chromosome size (bp) |
Associated plasmid size (bp) (GenBank accession no.) |
|---|---|---|---|---|---|
| 2014EL-1345-2 | O169:H41 | CP024223 | 92.3 | 4,943,397a | 145,086a (CP024227) |
| 85,864 (CP024226) | |||||
| 27,947 (CP024225) | |||||
| 20,005 (CP024224) | |||||
| ATCC 43886 or E2539C1 (5, 6) | O25:H16 | CP024256 | 148.1 | 4,914,654a | 95,515a (CP024255) |
| 107,732a (CP024254) | |||||
| D181 (7) | O182:H21 | CP024252 | 101.6 | 4,891,230a | 46,427 (CP024253) |
| 99,099a (CP024250) | |||||
| 167,230a (CP024249) | |||||
| 35,752 (CP024251) | |||||
| 90-9281 (8) | O128:H27 | CP024243 | 117.5 | 4,978,613a | 152,012a (CP024244) |
| 90-9276 (8) | O114:H49 | CP024299 | 79.8 | 5,004,571 | 167,764 (CP024297) |
| 110,577 (CP024298) | |||||
| 90-9280 (8) | O114:H49 | CP024240 | 188.6 | 4,966,338a | 74,644a (CP024242) |
| 104,674 (CP024241) | |||||
| 90-9269 (8) | OUND:H4 | CP024661 | 150.6 | 4,759,941 | 160,351a (CP024662) |
| 12,610 (CP024663) | |||||
| 52,270a (CP024664) | |||||
| 96,720 (CP024665) | |||||
| 20,753 (CP024666) | |||||
| 90-9272 (8) | O15:H11 | CP024239 | 48.3 | 4,906,680a | 274,465 (CP024238) |
| ATCC 43896 (or TX1) (9, 10) | O78:H12 | CP024278 | 107.7 | 5,088,038a | 84,894a (CP024281) |
| 52,655 (CP024280) | |||||
| 28,860 (CP024279) | |||||
| M9682-C1 (11) | O6:H16 | CP024275 | 156.6 | 4,778,550a | 100,184a (CP024277) |
| 38,177 (CP024276) | |||||
| B4103-1 (12) | O27:H7 | CP024245 | 83.1 | 4,708,118a | 138,289a (CP024248) |
| 68,864 (CP024247) | |||||
| 36,948 (CP024246) | |||||
| F6326-C1 | O169:H41 | CP024263 | 78.1 | 4,934,701a | 150,389a (CP024265) |
| 72,060 (CP024264) | |||||
| F5176C6 (13) | O167:H5 | CP024667 | 86.4 | 5,069,317 | 167,071a (CP024668) |
| 110,612a (CP024669) | |||||
| 46,919a (CP024670) | |||||
| 31,494 (CP024671) | |||||
| 2014EL-1343-2 | O25:H16 (genotypic), O25:NM (phenotypic) |
CP024228 | 91.4 | 4,848,034a | 82,510a (CP024231) |
| 73,915 (CP024230) | |||||
| 38,467 (CP024229) | |||||
| F5656C1 (14) | O6:H16 | CP024260 | 63.8 | 4,733,683a | 119,846a (CP024262) |
| 45,056a (CP024261) | |||||
| 2014EL-1346-6 | O6:H16 | CP024232 | 98.8 | 4,872,840a | 152,713a (CP024237) |
| 226,119a (CP024236) | |||||
| 62,188a (CP024235) | |||||
| 40,223 (CP024234) | |||||
| 30,162 (CP024233) | |||||
| F9792 (14, 15) | O169:H41 | CP024273 | 92.2 | 4,875,605a | 145,089a (CP024274) |
| F5505-C1 | O25:H16 | CP024257 | 94.3 | 4,886,938a | 94,817a (CP024259) |
| 96,607a (CP024258) | |||||
| F6699 | O6:H16 | CP024266 | 42.3 | 4,881,899a | 95,350 (CP024268) |
| 34,042 (CP024267) | |||||
| F8111-1SC3 (14) | O169:H41 | CP024269 | 78.6 | 4,905,023a | 147,766a (CP024272) |
| 103,618 (CP024271) | |||||
| 35,769 (CP024270) | |||||
| 00-3279 | O78:H12 | CP024293 | 155.0 | 5,116,480 | 101,907a (CP024294) |
| 103,995a (CP024295) | |||||
| 97,297a (CP024296) |
A sequence that is circular with overlapping ends.
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. 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 Smith P, Lindsey RL, Rowe LA, Batra D, Stripling D, Garcia-Toledo L, Drapeau D, Knipe K, Strockbine N. 2018. High-quality whole-genome sequences for 21 enterotoxigenic Escherichia coli strains generated with PacBio sequencing. Genome Announc 6:e01311-17. https://doi.org/10.1128/genomeA.01311-17.
REFERENCES
- 1.Isidean SD, Riddle MS, Savarino SJ, Porter CK. 2011. A systematic review of ETEC epidemiology focusing on colonization factor and toxin expression. Vaccine 29:6167–6178. doi: 10.1016/j.vaccine.2011.06.084. [DOI] [PubMed] [Google Scholar]
- 2.Wennerås C, Erling V. 2004. Prevalence of enterotoxigenic Escherichia coli-associated diarrhoea and carrier state in the developing world. J Health Popul Nutr 22:370–382. [PubMed] [Google Scholar]
- 3.Sack RB. 1975. Human diarrheal disease caused by enterotoxigenic Escherichia coli. Annu Rev Microbiol 29:333–353. doi: 10.1146/annurev.mi.29.100175.002001. [DOI] [PubMed] [Google Scholar]
- 4.Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 5.Wachsmuth K, Wells J, Shipley P, Ryder R. 1979. Heat-labile enterotoxin production in isolates from a shipboard outbreak of human diarrheal illness. Infect Immun 24:793–797. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Centers for Disease Control and Prevention (CDC) 1976. Diarrheal illness on a cruise ship caused by enterotoxigenic Escherichia coli. MMWR Morbid Mortal Wkly Rep 25:229–230. [Google Scholar]
- 7.Youssef M, Shurman A, Bougnoux M, Rawashdeh M, Bretagne S, Strockbine N. 2000. Bacterial, viral and parasitic enteric pathogens associated with acute diarrhea in hospitalized children from northern Jordan. FEMS Immunol Med Microbiol 28:257–263. doi: 10.1111/j.1574-695X.2000.tb01485.x. [DOI] [PubMed] [Google Scholar]
- 8.Strockbine NA, Faruque SM, Kay BA, Haider K, Alam K, Alam AN, Tzipori S, Wachsmuth IK. 1992. DNA probe analysis of diarrhoeagenic Escherichia coli: detection of EAF-positive isolates of traditional enteropathogenic E. coli serotypes among Bangladeshi paediatric diarrhoea patients. Mol Cell Probes 6:93–99. doi: 10.1016/0890-8508(92)90052-Y. [DOI] [PubMed] [Google Scholar]
- 9.Ryder RW, Wachsmuth IK, Buxton AE, Evans DG, DuPont HL, Mason E, Barrett FF. 1976. Infantile diarrhea produced by heat-stable enterotoxigenic Escherichia coli. N Engl J Med 295:849–853. doi: 10.1056/NEJM197610142951601. [DOI] [PubMed] [Google Scholar]
- 10.Wachsmuth IK, Falkow S, Ryder RW. 1976. Plasmid-mediated properties of a heat-stable enterotoxin-producing Escherichia coli associated with infantile diarrhea. Infect Immun 14:403–407. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Rosenberg ML, Koplan JP, Wachsmuth IK, Wells JG, Gangarosa EJ, Guerrant RL, Sack DA. 1977. Epidemic diarrhea at Crater Lake from enterotoxigenic Escherichia coli: a large waterborne outbreak. Ann Intern Med 86:714–718. doi: 10.7326/0003-4819-86-6-714. [DOI] [PubMed] [Google Scholar]
- 12.Dalton CB, Mintz ED, Wells JG, Bopp CA, Tauxe RV. 1999. Outbreaks of enterotoxigenic Escherichia coli infection in American adults: a clinical and epidemiologic profile. Epidemiol Infect 123:9–16. doi: 10.1017/S0950268899002526. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Daniels NA, Neimann J, Karpati A, Parashar UD, Greene KD, Wells JG, Srivastava A, Tauxe RV, Mintz ED, Quick R. 2000. Traveler’s diarrhea at sea: three outbreaks of waterborne enterotoxigenic Escherichia coli on cruise ships. J Infect Dis 181:1491–1495. doi: 10.1086/315397. [DOI] [PubMed] [Google Scholar]
- 14.Beatty ME, Bopp CA, Wells JG, Greene KD, Puhr ND, Mintz ED. 2004. Enterotoxin-producing Escherichia coli O169:H41, United States. Emerg Infect Dis 10:518–521. doi: 10.3201/eid1003.030268. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Devasia RA, Jones TF, Ward J, Stafford L, Hardin H, Bopp C, Beatty M, Mintz E, Schaffner W. 2006. Endemically acquired foodborne outbreak of enterotoxin-producing Escherichia coli serotype O169:H41. Am J Med 119:168.e7–168.e10. doi: 10.1016/j.amjmed.2005.07.063. [DOI] [PubMed] [Google Scholar]