High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.

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.