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. 2018 Oct 11;7(14):e01133-18. doi: 10.1128/MRA.01133-18

Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection

Isha R Patel a, Jayanthi Gangiredla a, Mark K Mammel a, Keith A Lampel a, Christopher A Elkins a, David W Lacher a,✉
Editor: Irene L G Newtonb
PMCID: PMC6256646  PMID: 30533715

Here, we report the genomes of all 72 isolates belonging to the Escherichia coli reference (ECOR) collection. Strains in this collection were isolated from diverse hosts and geographic locations and have been used for more than 30 years to represent the phylogenetic diversity of E. coli.

ABSTRACT

Here, we report the genomes of all 72 isolates belonging to the Escherichia coli reference (ECOR) collection. Strains in this collection were isolated from diverse hosts and geographic locations and have been used for more than 30 years to represent the phylogenetic diversity of E. coli.

ANNOUNCEMENT

Escherichia coli has been used as a model species to analyze the processes involved in bacterial genome evolution. More than 30 years ago, a set of strains known as the E. coli reference (ECOR) collection was assembled to represent the known genetic diversity of the species (1). Subsequent phylogenetic studies have shown that pathogenic and nonpathogenic strains of E. coli are randomly distributed when classified into the ECOR phylogroups (2, 3). PCR-based methods were used later to reassign strains ECOR 35, 36, 38, 39, 40, and 41 from phylogroup D to the newly described phylogroup F (4, 5). This finding was also supported by whole-genome-based microarray data (6). Since its creation, the ECOR collection has been widely used by scientists around the world. Unfortunately, during this time, several discrepancies from the original collection have been reported (7). Other researchers have made genome sequence data available for the entire ECOR collection (8). However, we caution against use of these data since nearly half of the strains appear to be contaminated, as evidenced by the presence of multiple molecular serotyping loci within the affected assemblies. For example, the assembly for strain ECOR 46 (GenBank accession number LYCC00000000) contains the wzxO1, wzxO7, wzyO1, wzyO7, fliCH6 and fliCH45 alleles. Here, we report our version of the ECOR collection so that others may use the data to better understand the nature of their differences with the original collection (Table 1).

TABLE 1.

Accession numbers and assembly metrics for the 72 ECOR strains

ECOR
strain		 SRA run no. No. of reads GenBank
accession no.		 Average
coverage (×)		 No. of
contigs		 Genome
size (bp)		 N50 values
(bp)		 G+C
content (%)		 Messerer et al. (8)
GenBank accession no.
1 SRR3989531 2,464,522 QOWM00000000 32.5 79 4,715,492 430,669 50.6 LYBJ00000000a
2 SRR7819145 6,102,266 QOWN00000000 78.9 234 5,239,177 104,055 50.7 LYBI00000000a
3 SRR3951465 6,911,676 QOWO00000000 81.7 143 4,926,647 124,670 50.7 LYBH00000000
4 SRR3951466 5,536,830 QOWP00000000 72.0 121 4,587,238 129,060 50.8 LYBG00000000a
5 SRR3951467 4,299,776 QOWQ00000000 50.8 246 5,065,618 121,007 50.7 LYBF00000000a
6 SRR3951468 8,044,114 QOWR00000000 125.0 144 4,556,862 69,692 50.9 LYBE00000000a
7 SRR3951469 6,530,276 QOWS00000000 80.2 90 4,896,746 169,935 50.7 LYBD00000000
8 SRR3951470 10,733,010 QOWT00000000 130.6 150 4,896,359 146,113 50.5 LYBC00000000a
9 SRR3951471 6,022,232 QOWU00000000 68.6 287 5,177,520 67,394 50.9 LYBB00000000
10 SRR3951472 5,570,968 QOWV00000000 68.6 98 4,751,057 230,922 50.6 LYBA00000000a
11 SRR3951473 12,657,330 QOWW00000000 145.5 280 5,182,586 144,669 50.7 LYAZ00000000
12 SRR3951474 9,606,228 QOWX00000000 114.4 218 5,078,970 128,904 50.7 LYAY00000000a
13 SRR3951475 9,627,106 QOWY00000000 127.8 165 4,619,031 70,958 50.8 LYAX00000000
14 SRR3951476 6,464,928 QOWZ00000000 79.1 150 4,941,866 112,447 50.7 LYAW00000000a
15 SRR3951517 4,867,598 QOXA00000000 60.5 128 4,911,383 121,074 50.7 LYAV00000000
16 SRR3951477 4,046,036 QOXB00000000 52.9 126 4,636,981 93,940 50.8 LYAU00000000
17 SRR3951478 4,786,784 QOXC00000000 66.1 110 4,506,698 88,853 50.7 LYAT00000000
18 SRR3951479 9,042,146 QOXD00000000 121.2 112 4,634,531 104,351 50.8 LYAS00000000
19 SRR3951480 9,318,330 QOXE00000000 142.7 164 4,535,554 82,278 50.8 LYAR00000000
20 SRR3951481 10,805,000 QOXF00000000 155.2 154 4,595,721 84,141 50.8 LYAQ00000000
21 SRR3951482 6,045,112 QOXG00000000 85.1 159 4,568,662 85,429 50.9 LYAP00000000
22 SRR3951484 9,380,404 QOXH00000000 118.8 84 4,514,994 211,903 50.8 LYAO00000000
23 SRR3951485 4,819,930 QOXI00000000 56.6 161 5,093,876 233,304 50.4 LYAN00000000
24 SRR3951486 10,917,604 QOXJ00000000 119.9 146 5,227,547 157,129 50.7 LYAM00000000
25 SRR3951488 7,017,374 QOXK00000000 86.9 125 4,752,894 184,763 50.5 LYAL00000000
26 SRR3951489 12,549,182 QOXL00000000 153.3 93 4,678,648 236,086 50.7 LYAK00000000
27 SRR3951490 10,793,212 QOXM00000000 128.6 109 4,867,073 190,031 50.5 LYAJ00000000
28 SRR3951491 6,645,234 QOXN00000000 81.3 109 4,925,046 187,237 50.7 LYAI00000000
29 SRR3951492 6,383,664 QOXO00000000 79.1 112 4,928,564 177,525 50.6 LYAH00000000
30 SRR3951493 6,835,550 QOXP00000000 85.1 120 4,825,526 193,320 50.6 LYAG00000000a
31 SRR3951494 11,223,998 QOXQ00000000 126.0 120 5,302,667 135,887 50.7 LYAF00000000
32 SRR3951518 10,348,842 QOXR00000000 129.2 129 4,794,190 185,245 50.7 LYAE00000000
33 SRR3951496 11,691,094 QOXS00000000 152.7 129 4,795,454 185,228 50.7 LYAD00000000a
34 SRR3951497 12,857,174 QOXT00000000 165.3 128 4,908,743 154,834 50.7 LYAC00000000a
35 SRR3951498 9,789,342 QOXU00000000 132.4 220 5,104,518 79,466 50.6 LYAB00000000
36 SRR3951499 10,108,776 QOXV00000000 134.8 279 5,231,499 58,260 50.5 LYBO00000000
37 SRR3951500 14,011,950 QOXW00000000 149.3 313 5,589,959 97,745 50.3 LYAA00000000
38 SRR3951501 19,252,412 QOXX00000000 211.7 206 5,240,321 109,902 50.5 LXZZ00000000a
39 SRR3951503 16,096,112 QOXY00000000 170.4 211 5,284,758 109,902 50.4 LYCJ00000000a
40 SRR3951504 5,498,306 QOXZ00000000 62.4 190 5,201,125 109,345 50.5 LYCI00000000a
41 SRR3951505 12,179,258 QOYA00000000 131.7 204 5,242,084 105,640 50.4 LYCH00000000
42 SRR3951506 10,293,022 QOYB00000000 114.7 111 5,189,763 467,104 50.5 LYCG00000000a
43 SRR3951508 10,938,788 QOYC00000000 127.3 226 5,272,828 107,735 50.6 LYCF00000000a
44 SRR3951509 9,842,910 QOYD00000000 112.4 171 5,240,115 179,757 50.6 LYCE00000000a
45 SRR3951510 17,558,230 QOYE00000000 226.1 95 4,726,888 210,969 50.7 LYCD00000000a
46 SRR3987677 2,932,548 QOYF00000000 107.7 151 5,259,340 90,485 50.5 LYCC00000000a
47 SRR3951512 18,191,986 QOYG00000000 228.5 77 4,920,788 214,558 50.6 LYCB00000000a
48 SRR3951513 18,794,936 QOYH00000000 218.1 131 5,333,881 171,963 50.5 LYCA00000000a
49 SRR3989514 4,399,522 QOYI00000000 187.7 277 5,278,098 118,118 50.6 LYBZ00000000
50 SRR3989532 1,990,960 QOYJ00000000 22.7 354 5,591,744 82,352 50.5 LYBY00000000
51 SRR3989533 3,562,062 QOYK00000000 44.5 135 5,169,898 234,505 50.5 LYYB00000000a
52 SRR7819144 5,273,668 QOYL00000000 72.6 172 5,097,032 219,132 50.4 LYCT00000000
53 SRR7819143 3,163,954 QOYM00000000 43.3 141 5,131,093 244,875 50.4 LYCU00000000
54 SRR3989534 5,331,188 QOYN00000000 70.4 113 5,035,502 332,014 50.4 LYCV00000000
55 SRR3989535 4,680,452 QOYO00000000 60.0 122 5,049,489 284,057 50.6 LYCW00000000
56 SRR7819142 2,047,664 QOYP00000000 28.8 110 4,956,973 196,112 50.5 LYDK00000000
57 SRR3989515 3,149,298 QOYQ00000000 137.2 128 5,277,375 185,269 50.5 LYCX00000000a
58 SRR3989521 1,955,120 QOYR00000000 91.7 103 4,902,658 120,850 50.6 LYCY00000000a
59 SRR3989507 2,122,200 QOZF00000000 99.6 84 4,764,104 194,584 50.4 LYCZ00000000a
60 SRR3989522 1,995,476 QOYS00000000 90.8 135 5,068,027 305,372 50.7 LYDA00000000a
61 SRR3987678 2,362,538 QOYT00000000 99.1 118 4,885,105 129,207 50.6 LYDB00000000a
62 SRR3989523 2,518,590 QOYU00000000 114.4 115 5,155,092 161,545 50.4 LYDL00000000a
63 SRR3989529 1,790,086 QOYV00000000 78.0 162 5,113,907 113,045 50.5 LYDM00000000
64 SRR7819148 10,979,330 QOYW00000000 143.2 169 5,105,087 196,230 50.8 LYDC00000000
65 SRR3989537 3,338,208 QOYX00000000 42.2 102 4,946,845 237,525 50.7 LYDD00000000
66 SRR3989538 2,878,266 QOYY00000000 39.5 47 4,739,108 239,490 50.9 LYDE00000000a
67 SRR3989530 1,916,842 QOYZ00000000 170.2 82 4,725,509 198,152 50.7 LYDN00000000
68 SRR7819147 7,341,922 QOZA00000000 99.6 156 5,037,255 191,327 50.7 LYDF00000000
69 SRR3989539 2,363,422 QOZB00000000 33.7 74 4,641,530 141,371 50.6 LYDG00000000
70 SRR3989540 4,864,768 QOZC00000000 61.8 135 5,123,298 225,733 50.8 LYDH00000000a
71 SRR3989541 4,321,280 QOZD00000000 56.8 138 4,875,196 113,172 50.8 LYDI00000000a
72 SRR7819146 2,653,970 QOZE00000000 39.2 75 4,725,669 288,629 50.6 LYDJ00000000a
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a

Possible contamination identified by the presence of multiple O and/or H molecular serotyping loci.

Pure cultures for each strain were grown aerobically overnight in Luria-Bertani broth at 37°C. Total genomic DNA was extracted from 1 ml of overnight culture using the DNeasy blood and tissue kit (Qiagen, Hilden, Germany). DNA extractions were performed with the Qiagen QIAcube instrument using the manufacturer’s protocol for Gram-negative bacteria. Sequencing libraries were prepared with 1 ng of DNA using the Nextera XT DNA sample prep kit (Illumina, San Diego, CA, USA) and sequenced on either the Illumina MiSeq or NextSeq platform. The resulting paired-end reads (2 × 250 bp for MiSeq, 2 × 150 bp for NextSeq) were quality controlled using FastQC (Q score, >30) and de novo assembled using SPAdes 3.8.2 (9) or CLC Genomics Workbench 8.2.1 (CLC bio, Aarhus, Denmark).

Depth of coverage for the draft genomes ranged from 23× to 229×, with the genome sizes ranging from 4,506,698 to 5,591,744 bp. The number of contigs ranged from 47 to 354, while the N50 values ranged from 58,260 to 467,104 bp. Preliminary phylogenetic analysis utilizing polymorphisms present within conserved core genes identified two strains as belonging to a phylogroup inconsistent with their expected ECOR designation. Phylogroup A strains ECOR 7 and ECOR 23 were found to cluster within phylogroups B1 and B2, respectively. The phylogroup F status of strains ECOR 35, 36, 38, 39, 40, and 41 was confirmed by our phylogenetic analysis.

Data availability.

The draft genome assemblies were deposited at DDBJ/ENA/GenBank under the accession numbers QOWM00000000 to QOZF00000000 and under BioProject accession number PRJNA230969. The versions described in this announcement are the first versions.

ACKNOWLEDGMENTS

We thank Shannon Manning at Michigan State University for providing replacements for some of the ECOR strains.

The views expressed in this article are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration (FDA), or the U.S. Government. Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the FDA.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The draft genome assemblies were deposited at DDBJ/ENA/GenBank under the accession numbers QOWM00000000 to QOZF00000000 and under BioProject accession number PRJNA230969. The versions described in this announcement are the first versions.

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