# Hybrid Assembly from 75 E. coli Genomes Isolated from French Bovine Food Products between 1995 and 2016

Sandra Jaudou, Mai-Lan Tran, Fabien Vorimore, Patrick Fach, Sabine Delannoy

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Sandra Jaudou, Mai-Lan Tran, Fabien Vorimore, Patrick Fach, Sabine Delannoy. Hybrid Assem-
bly from 75 E. coli Genomes Isolated from French Bovine Food Products between 1995 and 2016.
Microbiology Resource Announcements, 2023, 12 (3), 10.1128/mra.01095-22. anses-04206828

HAL Id: anses-04206828

https://anses.hal.science/anses-04206828

Submitted on 14 Sep 2023

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# Hybrid Assembly from 75 *E. coli* Genomes Isolated from French Bovine Food Products between 1995 and 2016

Sandra Jaudou,ª Mai-Lan Tran,ª,b Fabien Vorimore,ᵇ Patrick Fach,ª,b Sabine Delannoyª,b

**ABSTRACT** Here, we report the complete (or near-complete) genome sequences of 75 *Escherichia coli* isolates, including 71 stx-positive *E. coli* isolates, isolated in France between 1995 and 2016 from food of bovine origin. Genomes were assembled using a combination of long- and short-read sequencing.

Shiga toxin-producing *Escherichia coli* (STEC) food contamination can lead to severe human symptoms (1). Here, we assembled 75 *E. coli* genomes, including 31 *eae*-positive STEC and 39 *eae*-negative STEC genomes, isolated from food of bovine origin within a 21-year period in France.

*E. coli* strains were originally isolated on Trypticase soy broth with yeast extract (TSYE) plates overnight at 37°C. Isolates were revived from 20 to 30% glycerol stock on TSYE plates and incubated overnight at 37°C. One colony was cultured overnight at 37°C in brain heart infusion broth (BHI) with rotation. Genomic DNA was extracted from BHI culture (1 mL) using different extraction methods and sequenced using both MiSeq (Illumina, Inc., San Diego, CA, USA) and MinION (Nanopore, Oxford Science Park, Oxford, UK) technologies (2). Default parameters were used for all software unless otherwise specified. Illumina libraries were constructed using Nextera XT kit and sequenced on v2 micro or standard flow cells (2 × 150 bp or 2 × 250 bp). MinION libraries were constructed from unsheared and non-size-selected DNA using the SQK-LSK109 ligation kit and EXP-NBD104 or EXP-NBD114 barcoding kit and sequenced on FLO-MIN106 flow cells using an Mk1B device.

Illumina reads were trimmed and quality checked using the CLC Genomics Workbench v21 (Qiagen). We generated 299,212 to 3,972,904 reads (mean, 1,368,471 ± 720,963.42) with an average read length of 198.08 (±37.99) bases per sample, representing 12 to 174× (mean, 51 ± 22.65) (Table 1). MinION FAST5 files were basecalled and demultiplexed using guppy_basename and guppy_barcoder v3.4.5+fb1fbfb or v5.0.11+2b6dbff using "-compress-fastq" and "-trim-barcodes" parameters (3). Statistics on raw reads were performed using NanoPlot v1.29.0 (4). Between 14,450 and 1,992,878 reads (mean, 239,919 ± 341,570.565) were generated with N₅₀ values ranging from 2,565 bp to 29,351 bp (mean, 16,330 ± 7,056.38). Assemblies were generated using Unicycler v0.4.8 (-min_fasta_length 1,000), Flye v2.6 or v2.8.1-b1676 (-genome-size 5m), and Raven v1.2.2 (5-7). Assembly quality and contiguity were assessed using QUAST v5.0.2 (8) and manual inspection of the assemblies (stx-phage and large plasmids integrity). Either the Unicycler-generated assembly was conserved or the Flye and/or Raven assemblies were further polished with short reads using racon v1.4.13, medaka v0.12.1 (optional), and pilon v1.24 polishing tools (3 to 5 rounds) (9, 10; https://github.com/nanoporetech/medaka). If none of these strategies produced satisfying assemblies, Canu v1.8 or v2.1.1 (genomeSize 5m) or Unicycler based on Flye or Raven assembly (-existing_long-read_assembly) was generated (11). Because assemblers have different performances regarding plasmid or phage reconstruction, several assemblies

**Editor** David Rasko, University of Maryland
School of Medicine

**Copyright** © 2023 Jaudou et al. This is an open-access article distributed under the terms of the [Creative Commons Attribution 4.0 International license](https://creativecommons.org/licenses/by/4.0/).

Address correspondence to Sabine Delannoy, Sabine.Delannoy@anses.fr.
The authors declare no conflict of interest.

**Received** 12 March 2022

**Accepted** 16 January 2023

**Published** 1 February 2023

<footnote>ªPathogenic *E. coli* Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France</footnote>

<footnote>ᵇIdentityPath Genomics Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France</footnote>
<table><caption>TABLE 1 Assembly metrics of *Escherichia coli* draft genomes and NCBI accession numbers for each isolate sequenced</caption><thead><tr><th>NCBI accession no. (ONT, Illumina)</th><th>DNA extraction method(s)</th><th>Strain</th><th>Serotype<sup>a</sup></th><th>stx subtype(s)</th><th>oea</th><th>Hybrid assembly</th><th>MINION read length (N<sub>50</sub> [bp])</th><th>No. of contigs</th><th>Genome size (bp)</th><th>Assembly N<sub>50</sub> (bp)</th><th>GC content (%)</th><th>Genome coverage (X)</th><th>GenBank accession no.</th></tr></thead><tbody><tr><td>SRR18191646, SRR18191606</td><td>Bead based</td><td>1429</td><td>O76:H19</td><td>1c</td><td>—</td><td>Unicycler</td><td>10,334</td><td>3</td><td>5,316,065</td><td>5,183,674</td><td>50.64</td><td>107</td><td>JAOQM00000000</td></tr><tr><td>SRR18191539, SRR18191528</td><td>Salting out</td><td>2206</td><td>O79:H48</td><td>1a, 2a</td><td>—</td><td>Canu<sup>b</sup></td><td>14,002</td><td>16</td><td>5,228,843</td><td>5,270,995</td><td>50.64</td><td>107</td><td>JAOWP00000000</td></tr><tr><td>SRR18191517, SRR18191506</td><td>Salting out</td><td>06QMA126.1</td><td>O153/O178:H19</td><td>1a, 2a, 2d</td><td>—</td><td>Flye<sup>c</sup></td><td>17,384</td><td>6</td><td>5,258,581</td><td>1,387,201</td><td>50.73</td><td>184</td><td>JAOQM00000000</td></tr><tr><td>SRR18191495, SRR18191580</td><td>Salting out</td><td>06QMA140.2</td><td>O149:H1</td><td>1d</td><td>—</td><td>Flye<sup>d</sup></td><td>7,397</td><td>4</td><td>5,368,292</td><td>4,589,384</td><td>50.59</td><td>179</td><td>JAOWP00000000</td></tr><tr><td>SRR18191569, SRR18191644</td><td>Bead based, salting out</td><td>06QMA181.1a</td><td>O91:H14</td><td>1a, 2b, 2b</td><td>—</td><td>Unicycler</td><td>28,527</td><td>13</td><td>5,618,742</td><td>5,174,383</td><td>50.74</td><td>242</td><td>JAOQM00000000</td></tr><tr><td>SRR18191633, SRR18191566</td><td>Salting out</td><td>06QMA227.3</td><td>O116:H48</td><td>2a</td><td>—</td><td>Raven<sup>d</sup></td><td>13,538</td><td>5</td><td>5,602,836</td><td>5,378,985</td><td>50.76</td><td>242</td><td>JAOWN00000000</td></tr><tr><td>SRR18191555, SRR18191544</td><td>Salting out</td><td>07HMPA386</td><td>O46/O134:H38</td><td>1a, 2a</td><td>—</td><td>Unicycler</td><td>18,809</td><td>5</td><td>4,943,051</td><td>4,790,646</td><td>50.57</td><td>150</td><td>JAOQMC00000000</td></tr><tr><td>SRR18191613, SRR18191609</td><td>Salting out</td><td>07HMPA903</td><td>O113:H21</td><td>2a, 2a</td><td>—</td><td>Flye<sup>d</sup></td><td>22,124</td><td>6</td><td>4,965,900</td><td>4,764,076</td><td>50.63</td><td>150</td><td>JAOWP00000000</td></tr><tr><td>SRR18191608, SRR18191607</td><td>Salting out</td><td>09QMA299.3B</td><td>O175:H16</td><td>2a</td><td>—</td><td>Unicycler</td><td>7,440</td><td>10</td><td>5,144,288</td><td>4,966,076</td><td>50.73</td><td>230</td><td>JAOQMD00000000</td></tr><tr><td>SRR18191605, SRR18191604</td><td>Salting out</td><td>09QMA303.1</td><td>O8:H19</td><td>2g</td><td>—</td><td>Unicycler</td><td>20,236</td><td>3</td><td>5,132,730</td><td>5,022,134</td><td>50.76</td><td>168</td><td>JAOQL00000000</td></tr><tr><td>SRR18191603, SRR18191602</td><td>Salting out</td><td>09QMA311.2.3</td><td>O175:H16</td><td>2d</td><td>—</td><td>Unicycler</td><td>23,479</td><td>4</td><td>5,179,346</td><td>5,125,959</td><td>50.77</td><td>149</td><td>JAOQLY00000000</td></tr><tr><td>SRR18191601, SRR18191600, SRR18191599</td><td>Salting out</td><td>09QMA33.1</td><td>O2:H27</td><td>2a</td><td>—</td><td>Unicycler</td><td>20,366</td><td>11</td><td>5,335,100</td><td>5,226,378</td><td>50.61</td><td>223</td><td>JAOQL00000000</td></tr><tr><td>SRR18191542, SRR18191541</td><td>Salting out</td><td>09QMA47.1</td><td>O6:H10</td><td>1c</td><td>—</td><td>Flye<sup>d</sup></td><td>17,841</td><td>2</td><td>5,283,406</td><td>4,794,423</td><td>50.53</td><td>215</td><td>JAOQL00000000</td></tr><tr><td>SRR18191540, SRR18191538</td><td>Salting out</td><td>1890-4</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>d</sup></td><td>22,209</td><td>17</td><td>5,268,782</td><td>4,794,913</td><td>50.54</td><td>215</td><td>JAOWPA00000000</td></tr><tr><td>SRR18191537, SRR18191536</td><td>Salting out</td><td>2011-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Raven<sup>d</sup></td><td>17,173</td><td>2</td><td>5,801,088</td><td>4,709,082</td><td>50.64</td><td>272</td><td>JAOQLY00000000</td></tr><tr><td>SRR18191535, SRR18191534</td><td>Salting out</td><td>2026-O145</td><td>O145:H28</td><td>2c</td><td>+</td><td>Flye<sup>d</sup></td><td>23,580</td><td>9</td><td>5,834,018</td><td>5,743,918</td><td>50.68</td><td>272</td><td>JAOWNH00000000</td></tr><tr><td>SRR18191533, SRR18191532</td><td>Salting out</td><td>2039-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Raven</td><td>9,087</td><td>3</td><td>5,891,761</td><td>2,948,002</td><td>50.45</td><td>262</td><td>JAOQL00000000</td></tr><tr><td>SRR18191531, SRR18191530</td><td>Salting out</td><td>2048-O145</td><td>O145:H28</td><td>2c</td><td>+</td><td>Unicycler</td><td>18,920</td><td>15</td><td>5,226,494</td><td>5,203,884</td><td>50.57</td><td>250</td><td>JAOQLR00000000</td></tr><tr><td>SRR18191529, SRR18191527</td><td>Salting out</td><td>2142-O103</td><td>O103:H25</td><td>—<sup>m</sup></td><td>+</td><td>Flye<sup>d</sup></td><td>22,773</td><td>10</td><td>5,628,166</td><td>5,402,071</td><td>50.59</td><td>250</td><td>JAOWY00000000</td></tr><tr><td>SRR18191526, SRR18191525</td><td>Salting out</td><td>2149-O103</td><td>O103:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>14,099</td><td>27</td><td>5,661,007</td><td>5,368,150</td><td>50.51</td><td>174</td><td>JAOWNE00000000</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td></td><td>Unicycler</td><td></td><td>12</td><td>5,844,869</td><td>5,519,265</td><td>50.69</td><td>153</td><td>JAOQLQ00000000</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>5,758,941</td><td>5,122,111</td><td>50.69</td><td>153</td><td>JAOWNX00000000</td></tr></tbody></table>

(Continued on next page)
<table><caption>TABLE 1 (Continued)</caption><thead><tr><th>NCBI accession no. (ONT, Illumina)</th><th>DNA extraction method(s)</th><th>Strain</th><th>Serotype<sup>k</sup></th><th>stx subtype(s)</th><th>eo<sup>e</sup></th><th>Hybrid assembly</th><th>MinION read length (N<sub>50</sub> (bp))</th><th>No. of contigs</th><th>Genome size (bp)</th><th>Assembly N<sub>50</sub> (bp)</th><th>GC content (%)</th><th>Genome coverage (X)</th><th>GenBank accession no.</th></tr></thead><tbody><tr><td>SRR18191524</td><td>Salting out</td><td>2236-3b</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>16,957</td><td>23</td><td>5,997,576</td><td>5,003,748</td><td>50.63</td><td>154</td><td>JAOOWOX00000000</td></tr><tr><td>SRR18191523</td><td>Bead based</td><td>2918-O145</td><td>O145:H28</td><td>2a</td><td>+</td><td>Raven<sup>o</sup></td><td>6,716</td><td>7</td><td>6,044,444</td><td>5,011,133</td><td>50.61</td><td>154</td><td>JAOOWN00000000</td></tr><tr><td>SRR18191522</td><td>Bead based</td><td>2918-O145</td><td>O145:H28</td><td>2a</td><td>+</td><td>Unicycler</td><td>20,998</td><td>28</td><td>5,553,909</td><td>3,535,429</td><td>50.63</td><td>72</td><td>JAOOWN00000000</td></tr><tr><td>SRR18191521</td><td>Salting out</td><td>3273-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>20,998</td><td>22</td><td>5,492,229</td><td>1,347,297</td><td>50.54</td><td>72</td><td>JAOQLP00000000</td></tr><tr><td>SRR18191520</td><td>Salting out</td><td>3273-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>20,998</td><td>22</td><td>5,769,060</td><td>5,373,151</td><td>50.72</td><td>238</td><td>JAOOW00000000</td></tr><tr><td>SRR18191519</td><td>Bead based, salting out</td><td>3313-O111</td><td>O111:H8</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>4,229</td><td>7</td><td>5,570,495</td><td>5,272,882</td><td>50.63</td><td>90</td><td>JAOOW00000000</td></tr><tr><td>SRR21721513</td><td>SRR18191516</td><td>3313-O111</td><td>O111:H8</td><td>1a</td><td>+</td><td>Unicycler</td><td>10,277</td><td>17</td><td>5,489,297</td><td>3,617,166</td><td>50.55</td><td>90</td><td>JAOQLP00000000</td></tr><tr><td>SRR21721512</td><td>Bead based, salting out</td><td>3313-O111</td><td>O111:H8</td><td>1a</td><td>+</td><td>Unicycler</td><td>21,079</td><td>19</td><td>5,488,508</td><td>1,232,028</td><td>50.55</td><td>398</td><td>JAOOWN00000000</td></tr><tr><td>SRR18191518</td><td>Salting out</td><td>3313-O111</td><td>O111:H8</td><td>1a</td><td>+</td><td>Unicycler</td><td>21,079</td><td>19</td><td>5,488,508</td><td>1,232,028</td><td>50.55</td><td>398</td><td>JAOOWN00000000</td></tr><tr><td>SRR18191516</td><td>Salting out</td><td>3382-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>13,920</td><td>18</td><td>5,719,857</td><td>4,395,063</td><td>50.65</td><td>128</td><td>JAOOWU00000000</td></tr><tr><td>SRR18191515</td><td>Bead based</td><td>3383-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Unicycler</td><td>5,882</td><td>18</td><td>5,719,857</td><td>4,395,063</td><td>50.65</td><td>128</td><td>JAOOWNL00000000</td></tr><tr><td>SRR18191514</td><td>Bead based</td><td>3383-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>5,882</td><td>18</td><td>5,719,857</td><td>4,395,063</td><td>50.65</td><td>671</td><td>JAOOWNU00000000</td></tr><tr><td>SRR18191513</td><td>Bead based</td><td>3383-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>5,882</td><td>18</td><td>5,719,857</td><td>4,395,063</td><td>50.65</td><td>671</td><td>JAOWOT00000000</td></tr><tr><td>SRR18191512</td><td>Bead based</td><td>3383-O26b</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>6,945</td><td>6</td><td>5,838,831</td><td>5,709,619</td><td>50.59</td><td>778</td><td>JAOWNT00000000</td></tr><tr><td>SRR18191511</td><td>Bead based</td><td>3383-O26b</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>6,945</td><td>9</td><td>5,822,451</td><td>5,697,780</td><td>50.62</td><td>778</td><td>JAOWOS00000000</td></tr><tr><td>SRR18191510</td><td>Bead based</td><td>3430-O103</td><td>O103:H2</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>8,683</td><td>5</td><td>5,557,311</td><td>4,743,383</td><td>50.73</td><td>259</td><td>JAOWOR00000000</td></tr><tr><td>SRR18191508</td><td>Bead based, salting out</td><td>429-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>12,758</td><td>37</td><td>5,558,675</td><td>4,744,103</td><td>50.72</td><td>259</td><td>JAOWNS00000000</td></tr><tr><td>SRR18191507</td><td>Bead based, salting out</td><td>429-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>12,758</td><td>37</td><td>5,728,320</td><td>1,975,710</td><td>50.56</td><td>270</td><td>JAOQLN00000000</td></tr><tr><td>SRR21721511</td><td>Salting out</td><td>429-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>12,758</td><td>12</td><td>5,605,978</td><td>3,820,369</td><td>50.73</td><td>148</td><td>JAOWOC00000000</td></tr><tr><td>SRR18191507</td><td>Bead based, salting out</td><td>429-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>12,758</td><td>28</td><td>5,659,566</td><td>1,082,226</td><td>50.60</td><td>148</td><td>JAOOWNR00000000</td></tr><tr><td>SRR18191505</td><td>Bead based, salting out</td><td>4712-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Flye<sup>e</sup></td><td>25,662</td><td>4</td><td>5,972,468</td><td>5,737,945</td><td>50.75</td><td>71</td><td>JAOWOP00000000</td></tr><tr><td>SRR18191504</td><td>Bead based, salting out</td><td>4712-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>12,482</td><td>39</td><td>5,664,587</td><td>2,049,284</td><td>50.56</td><td>148</td><td>JAOQLM00000000</td></tr><tr><td>SRR18191503</td><td>Bead based, salting out</td><td>4747-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Unicycler</td><td>12,482</td><td>6</td><td>5,856,627</td><td>5,621,430</td><td>50.64</td><td>148</td><td>JAOOWNP00000000</td></tr><tr><td>SRR18191502</td><td>Bead based, salting out</td><td>4747-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Canu<sup>o</sup></td><td>6</td><td>6</td><td>5,714,135</td><td>5,609,626</td><td>50.62</td><td>148</td><td>JAOWOO00000000</td></tr><tr><td>SRR18191501</td><td>Bead based, salting out</td><td>6423-O26</td><td>O26:H11</td><td>1a</td><td>+</td><td>Canu<sup>o</sup></td><td>19,317</td><td>5</td><td>5,992,428</td><td>5,821,752</td><td>50.66</td><td>264</td><td>JAOWPM00000000</td></tr><tr><td>SRR18191500</td><td>Bead based</td><td>97HMPL449</td><td>O3:H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>5,941</td><td>6</td><td>5,371,299</td><td>5,104,752</td><td>50.51</td><td>334</td><td>JAOQLL00000000</td></tr><tr><td>SRR18191498</td><td>Bead based</td><td>97HMPL449</td><td>O3:H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>5,941</td><td>6</td><td>5,472,012</td><td>3,671,848</td><td>50.47</td><td>334</td><td>JAOWPL00000000</td></tr><tr><td>SRR18191497</td><td>Bead based</td><td>97HMPL473</td><td>O3:H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>15,334</td><td>6</td><td>5,309,043</td><td>5,043,017</td><td>50.54</td><td>185</td><td>JAOQLK00000000</td></tr><tr><td>SRR18191496</td><td>Bead based, salting out</td><td>97HMPL473</td><td>O3:H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>15,334</td><td>6</td><td>4,862,109</td><td>4,701,590</td><td>50.71</td><td>141</td><td>JAOQLL00000000</td></tr><tr><td>SRR18191509</td><td>Bead based, salting out</td><td>97HMPL650</td><td>O110:H9</td><td>1c</td><td>—</td><td>Unicycler</td><td>28,759</td><td>4</td><td>4,849,707</td><td>4,849,707</td><td>50.71</td><td>141</td><td>JAOWNCO00000000</td></tr><tr><td>SRR18191589</td><td>Bead based, salting out</td><td>97HMPL650</td><td>O110:H9</td><td>1c</td><td>—</td><td>Unicycler</td><td>28,759</td><td>4</td><td>4,864,116</td><td>4,850,996</td><td>50.71</td><td>238</td><td>JAOQLI00000000</td></tr><tr><td>SRR18191588</td><td>Bead based, salting out</td><td>97HMPL652</td><td>O110:H9</td><td>1c</td><td>—</td><td>Unicycler</td><td>22,595</td><td>3</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td></tr><tr><td>SRR18191587</td><td>Bead based, salting out</td><td>97HMPL652</td><td>O110:H9</td><td>1c</td><td>—</td><td>Unicycler</td><td>22,595</td><td>3</td><td>—</td><td>—</td><td>—</td><td>—</td><td>—</td></tr><tr><td>SRR18191586</td><td>Bead based, salting out</td><td>97HMPL657</td><td>O136:H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>21,241</td><td>9</td><td>5,439,851</td><td>5,167,313</td><td>50.67</td><td>175</td><td>JAOWNQ00000000</td></tr><tr><td>SRR18191585</td><td>Bead based, salting out</td><td>97HMPL657</td><td>O136:H12</td><td>1a</td><td>—</td><td>Flye<sup>e</sup></td><td>21,241</td><td>44</td><td>5,655,428</td><td>5,156,955</td><td>50.68</td><td>125</td><td>JAOWON00000000</td></tr><tr><td>SRR21721510</td><td>Bead based, salting out</td><td>97HMPL657</td><td>O136:H12</td><td>1a</td><td>—</td><td>Flye<sup>e</sup></td><td>21,241</td><td>44</td><td>5,655,428</td><td>5,156,955</td><td>50.68</td><td>125</td><td>JAOWON00000000</td></tr><tr><td>SRR18191585</td><td>Bead based</td><td>97HMPL657</td><td>O136:H12</td><td>1a</td><td>—</td><td>Flye<sup>e</sup></td><td>21,241</td><td>44</td><td>5,655,428</td><td>5,156,955</td><td>50.68</td><td>125</td><td>JAOWON00000000</td></tr><tr><td>SRR18191584</td><td>Bead based</td><td>97HMPL657</td><td>O136:H12</td><td>2c</td><td>—</td><td>Unicycler</td><td>8,149</td><td>2</td><td>5,247,946</td><td>5,142,912</td><td>50.78</td><td>805</td><td>JAOQLH00000000</td></tr><tr><td>SRR18191583</td><td>Bead based</td><td>97HMPL657</td><td>O136:H12</td><td>2c</td><td>—</td><td>Unicycler</td><td>8,149</td><td>2</td><td>5,247,946</td><td>5,142,912</td><td>50.78</td><td>805</td><td>JAOQLH00000000</td></tr><tr><td>SRR18191582</td><td>Bead based</td><td>97HMPL657</td><td>O136:H12</td><td>2c</td><td>—</td><td>Unicycler</td><td>8,149</td><td>2</td><td>5,247,946</td><td>5,142,912</td><td>50.78</td><td>805</td><td>JAOQLH00000000</td></tr></tbody></table>

(Continued on next page)
<table><caption>TABLE 1 (Continued)</caption><thead><tr><th>NCBI accession no. (ONT, Illumina)</th><th>DNA extraction method(s)</th><th>Strain</th><th>Serotype<sup>k</sup></th><th>stx subtype(s)</th><th>eo<sup>e</sup></th><th>Hybrid assembly</th><th>MinION read length (N<sub>50</sub> (bp))</th><th>No. of contigs</th><th>Genome size (bp)</th><th>Assembly N<sub>50</sub> (bp)</th><th>GC content (%)</th><th>Genome coverage (X)</th><th>GenBank accession no.</th></tr></thead><tbody><tr><td>SRR18191581</td><td>Bead based</td><td>98HMPL324</td><td>O174H21</td><td>2c</td><td>—</td><td>Raven<sup>d</sup></td><td>5,263</td><td>4</td><td>5,714,333</td><td>5,042,330</td><td>50.76</td><td>908</td><td>JAOWNB000000000</td></tr><tr><td>SRR18191579</td><td></td><td></td><td></td><td></td><td></td><td>Canu</td><td></td><td>8</td><td>5,317,997</td><td>5,045,734</td><td>50.79</td><td>908</td><td>JAOWPK000000000</td></tr><tr><td>SRR18191578</td><td>Salting out</td><td>98HMPL325</td><td>O17/044/077:H18</td><td>2d</td><td>—</td><td>Unicycler</td><td>14,916</td><td>6</td><td>5,373,540</td><td>5,090,743</td><td>50.71</td><td>199</td><td>JAOQLG000000000</td></tr><tr><td>SRR18191577</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191576</td><td>Bead based</td><td>98HMPL475</td><td>O110H9</td><td>1c</td><td>—</td><td>Unicycler</td><td>4,854</td><td>6</td><td>5,010,608</td><td>4,847,085</td><td>50.59</td><td>1148</td><td>JAOQLF000000000</td></tr><tr><td>SRR18191575</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191574</td><td>Salting out</td><td>98HMPL479</td><td>O91:H14</td><td>1a, 2b, 2b</td><td>—</td><td>Unicycler</td><td>8,894</td><td>13</td><td>5,831,137</td><td>5,558,854</td><td>50.68</td><td>152</td><td>JAOQLE000000000</td></tr><tr><td>SRR18191573</td><td></td><td></td><td></td><td></td><td></td><td>Canu<sup>e</sup></td><td></td><td>11</td><td>6,118,277</td><td>5,606,901</td><td>50.72</td><td>152</td><td>JAOWP000000000</td></tr><tr><td>SRR18191572</td><td>Salting out</td><td>98HMPL487</td><td>O136H12</td><td>1a</td><td>—</td><td>Unicycler</td><td>20,281</td><td>2</td><td>5,430,616</td><td>5,174,002</td><td>50.58</td><td>191</td><td>JAOQLD000000000</td></tr><tr><td>SRR18191571</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191570</td><td>Salting out</td><td>CrI54393</td><td>O157:H7</td><td>2a, 2c</td><td>+</td><td>Unicycler</td><td>21,282</td><td>11</td><td>5,744,891</td><td>5,126,924</td><td>50.47</td><td>134</td><td>JAOQLC000000000</td></tr><tr><td>SRR18191568</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>3</td><td>5,807,355</td><td>5,666,998</td><td>50.47</td><td>134</td><td>JAOWOM000000000</td></tr><tr><td>SRR18191567</td><td>Salting out</td><td>CrI54395</td><td>O157:H7</td><td>2c</td><td>+</td><td>Unicycler</td><td>21,865</td><td>17</td><td>5,780,274</td><td>5,273,188</td><td>50.49</td><td>134</td><td>JAOWNA000000000</td></tr><tr><td>SRR18191598</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>2</td><td>5,720,557</td><td>4,991,949</td><td>50.39</td><td>129</td><td>JAOQLB000000000</td></tr><tr><td>SRR18191597</td><td>Salting out</td><td>CrI54393</td><td>O157:H7</td><td>2c, 2c</td><td>+</td><td>Unicycler</td><td>20,389</td><td>19</td><td>5,644,625</td><td>5,555,517</td><td>50.48</td><td>129</td><td>JAOWOL000000000</td></tr><tr><td>SRR18191596</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>5,749,327</td><td>5,423,006</td><td>50.49</td><td>240</td><td>JAOQLA000000000</td></tr><tr><td>SRR18191595</td><td>Salting out</td><td>CrI69922</td><td>O82:H8</td><td></td><td>—</td><td>Unicycler</td><td>20,244</td><td>6</td><td>4,868,876</td><td>2,456,854</td><td>50.78</td><td>225</td><td>JAOQKZ000000000</td></tr><tr><td>SRR18191594</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>9</td><td>4,976,199</td><td>4,761,119</td><td>50.80</td><td>225</td><td>JAOWOK000000000</td></tr><tr><td>SRR18191593</td><td>Salting out</td><td>CrI6593</td><td>O51:H41</td><td></td><td>—</td><td>Unicycler</td><td>13,654</td><td>4</td><td>4,958,903</td><td>4,892,016</td><td>50.63</td><td>95</td><td>JAOKY000000000</td></tr><tr><td>SRR18191592</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191591</td><td>Salting out</td><td>CrIO103</td><td>O103:H2</td><td></td><td>—</td><td>Unicycler</td><td>16,776</td><td>4</td><td>5,090,231</td><td>4,969,612</td><td>50.57</td><td>144</td><td>JAOQKX000000000</td></tr><tr><td>SRR18191643</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191642</td><td>Salting out</td><td>CrIO157</td><td>O157:H7</td><td>2c</td><td>+</td><td>Unicycler</td><td>22,759</td><td>19</td><td>5,624,392</td><td>4,232,969</td><td>50.43</td><td>278</td><td>JAOQKW000000000</td></tr><tr><td>SRR18191641</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>10</td><td>5,642,849</td><td>5,231,425</td><td>50.52</td><td>278</td><td>JAOWIO000000000</td></tr><tr><td>SRR18191640</td><td>Bead based, salting out</td><td>E. coli/12-1</td><td>O157:H7</td><td>2a, 2c</td><td>+</td><td>Canu<sup>e</sup></td><td>25,609</td><td>3</td><td>5,009,043</td><td>5,747,499</td><td>50.44</td><td>284</td><td>JAOWP000000000</td></tr><tr><td>SRR18191639</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>4</td><td>5,807,203</td><td>5,669,286</td><td>50.50</td><td>284</td><td>JAOWOI000000000</td></tr><tr><td>SRR18191638</td><td>Salting out</td><td>EC14</td><td>O174:H21</td><td>2c</td><td>—</td><td>Unicycler</td><td>20,105</td><td>4</td><td>5,082,783</td><td>4,945,157</td><td>50.83</td><td>219</td><td>JAOQKV000000000</td></tr><tr><td>SRR18191637</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>12</td><td>5,155,830</td><td>4,911,711</td><td>50.83</td><td>219</td><td>JAOWOH000000000</td></tr><tr><td>SRR18191636</td><td>Salting out, bead based</td><td>ECA135</td><td>O22:H16</td><td>2b, 2c, 2d</td><td>—</td><td>Canu<sup>e</sup></td><td>29,351</td><td>5</td><td>5,459,604</td><td>5,386,935</td><td>50.63</td><td>276</td><td>JAOWPH000000000</td></tr><tr><td>SRR18191635</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>1</td><td>5,313,712</td><td>5,313,712</td><td>50.70</td><td>276</td><td>JAOWOG000000000</td></tr><tr><td>SRR18191634</td><td>Bead based, salting out</td><td>ECA15</td><td>O79:H48</td><td>1a, 2a</td><td>—</td><td>Raven<sup>b</sup></td><td>19,793</td><td>5</td><td>5,326,335</td><td>4,303,608</td><td>50.71</td><td>58</td><td>JAOWMZ000000000</td></tr><tr><td>SRR18191632</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191631</td><td>Salting out</td><td>ECA193</td><td>O8:H21</td><td>1a, 2c</td><td>—</td><td>Unicycler</td><td>20,554</td><td>9</td><td>5,596,707</td><td>5,158,603</td><td>50.69</td><td>222</td><td>JAOQKU000000000</td></tr><tr><td>SRR18191630</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191629</td><td>Bead based</td><td>ECA194</td><td>O179:H8</td><td>1a, 2a</td><td>—</td><td>Unicycler</td><td>15,826</td><td>3</td><td>5,094,287</td><td>4,913,760</td><td>50.72</td><td>154</td><td>JAOQKT000000000</td></tr><tr><td>SRR18191628</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191627</td><td>Bead based</td><td>ECA279</td><td>O174:H2</td><td>1a, 2d</td><td>—</td><td>Unicycler</td><td>2,565</td><td>7</td><td>5,126,030</td><td>2,145,451</td><td>50.72</td><td>199</td><td>JAOQKS000000000</td></tr><tr><td>SRR18191626</td><td></td><td></td><td></td><td></td><td></td><td>Flye<sup>a</sup></td><td></td><td>4</td><td>5,167,400</td><td>5,037,956</td><td>50.76</td><td>199</td><td>JAOWOF000000000</td></tr><tr><td>SRR18191625</td><td>Bead based, salting out</td><td>ECA329</td><td>O91:H21</td><td>2a, 2d</td><td>—</td><td>Unicycler</td><td>15,119</td><td>5</td><td>5,167,518</td><td>5,016,862</td><td>50.71</td><td>235</td><td>JAOWNP000000000</td></tr><tr><td>SRR18191624</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191625</td><td>Salting out</td><td>ECA329</td><td>O91:H21</td><td>2a, 2d</td><td>—</td><td>Flye<sup>a</sup></td><td>15,119</td><td>25</td><td>5,342,559</td><td>4,901,208</td><td>50.76</td><td>167</td><td>JAOWOE000000000</td></tr><tr><td>SRR21748932</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>SRR18191565</td><td>Salting out</td><td>ECA34</td><td>O5:H9</td><td>1a</td><td>+</td><td>Flye<sup>a</sup></td><td>6,208</td><td>14</td><td>5,341,159</td><td>4,796,583</td><td>50.64</td><td>86</td><td>JAOWOD000000000</td></tr><tr><td>SRR18191564</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr></tbody></table>

(Continued on next page)
<table><caption>TABLE 1 (Continued)</caption><thead><tr><th>NCBI accession no. (ONT, Illumina)</th><th>DNA extraction method(s)</th><th>Strain</th><th>Serotype<sup>k</sup></th><th>stx subtype(s)</th><th>oeo</th><th>Hybrid assembly</th><th>MinION read length (N<sub>50</sub> [bp])</th><th>No. of contigs</th><th>Genome size (bp)</th><th>Assembly N<sub>50</sub> (bp)</th><th>GC content (%)</th><th>Genome coverage (X)</th><th>GenBank accession no.</th></tr></thead><tbody><tr><td>SRR18191623</td><td>Salting out</td><td>EC434</td><td>O5H9</td><td>1a</td><td>+</td><td>Raven<sup>d</sup></td><td>24,947</td><td>4</td><td>5,414,456</td><td>4,637,316</td><td>50.68</td><td>115</td><td>JAOWMY00000000</td></tr><tr><td>SRR18191564</td><td>Bead based, salting out</td><td>EC436</td><td>O5H9</td><td>1a, 1a</td><td>+</td><td>Unicycler</td><td>22,228</td><td>14</td><td>5,418,653</td><td>4,566,021</td><td>50.66</td><td>100</td><td>JAOWIN00000000</td></tr><tr><td>SRR18191562</td><td>Bead based, salting out</td><td>EC437</td><td>O5H9</td><td>1a, 1a</td><td>+</td><td>Flye<sup>e</sup></td><td>24,413</td><td>11</td><td>5,403,523</td><td>5,306,942</td><td>50.69</td><td>112</td><td>JAOWOC00000000</td></tr><tr><td>SRR18191561</td><td>Bead based</td><td>EC439</td><td>O174H21</td><td>2c</td><td>-</td><td>Unicycler</td><td>3,390</td><td>5</td><td>5,141,946</td><td>3,448,145</td><td>50.78</td><td>479</td><td>JAQKR00000000</td></tr><tr><td>SRR18191558</td><td>Bead based</td><td>EC439</td><td>O174H21</td><td>2c</td><td>-</td><td>Canu<sup>o</sup></td><td>24,727</td><td>2</td><td>5,061,078</td><td>5,053,258</td><td>50.68</td><td>200</td><td>JAOWPG00000000</td></tr><tr><td>SRR18191557</td><td>Salting out</td><td>EC440</td><td>O6H10</td><td>2d</td><td>-</td><td>Canu<sup>o</sup></td><td>24,727</td><td>2</td><td>5,061,078</td><td>5,053,258</td><td>50.68</td><td>200</td><td>JAOWPG00000000</td></tr><tr><td>SRR18191556</td><td>Bead based</td><td>EC447</td><td>O22H16</td><td>1a, 2b, 2d</td><td>-</td><td>Unicycler</td><td>6,419</td><td>5</td><td>5,351,044</td><td>5,298,558</td><td>50.63</td><td>121</td><td>JAQKQ00000000</td></tr><tr><td>SRR18191553</td><td>Salting out</td><td>EC489</td><td>OgN-RKI2H16</td><td>1c</td><td>-</td><td>Raven<sup>d</sup></td><td>18,224</td><td>52</td><td>5,345,303</td><td>3,529,088</td><td>50.64</td><td>121</td><td>JAOWMX00000000</td></tr><tr><td>SRR18191552</td><td>Salting out</td><td>EC489</td><td>OgN-RKI2H16</td><td>1c</td><td>-</td><td>Flye</td><td>18,224</td><td>52</td><td>5,336,292</td><td>4,922,938</td><td>50.72</td><td>180</td><td>JAOWNY00000000</td></tr><tr><td>SRR18191551</td><td>Salting out</td><td>EC497</td><td>O113H4</td><td>2d</td><td>-</td><td>Unicycler</td><td>17,597</td><td>3</td><td>5,163,781</td><td>4,943,802</td><td>50.76</td><td>180</td><td>JAOWNK00000000</td></tr><tr><td>SRR18191550</td><td>Salting out</td><td>EC497</td><td>O113H4</td><td>2d</td><td>-</td><td>Unicycler</td><td>17,597</td><td>4</td><td>5,626,159</td><td>5,257,847</td><td>50.55</td><td>149</td><td>JAQKP00000000</td></tr><tr><td>SRR18191549</td><td>Salting out</td><td>HSVR03</td><td>O157H7</td><td>2c</td><td>+</td><td>Raven<sup>d</sup></td><td>22,885</td><td>40</td><td>5,585,011</td><td>1,473,641</td><td>50.49</td><td>67</td><td>JAOWMW00000000</td></tr><tr><td>SRR18191548</td><td>Salting out</td><td>HSVR03</td><td>O157H7</td><td>2c</td><td>+</td><td>Flye<sup>e</sup></td><td>22,926</td><td>11</td><td>5,843,094</td><td>5,515,994</td><td>50.43</td><td>113</td><td>JAOWOB00000000</td></tr><tr><td>SRR18191547</td><td>Salting out</td><td>HSVR04</td><td>O157H7</td><td>2c</td><td>+</td><td>Flye<sup>e</sup></td><td>22,926</td><td>11</td><td>5,843,094</td><td>5,515,994</td><td>50.43</td><td>113</td><td>JAOWOB00000000</td></tr><tr><td>SRR18191546</td><td>Salting out</td><td>HSVR04</td><td>O157H7</td><td>2c</td><td>+</td><td>Flye<sup>e</sup></td><td>22,926</td><td>11</td><td>5,843,094</td><td>5,515,994</td><td>50.43</td><td>113</td><td>JAOWOB00000000</td></tr><tr><td>SRR18191545</td><td>Bead based</td><td>NC672mucus</td><td>O13H2</td><td>2c</td><td>-</td><td>Flye<sup>e</sup></td><td>6,632</td><td>3</td><td>5,323,626</td><td>5,187,741</td><td>50.66</td><td>381</td><td>JAOWOA00000000</td></tr><tr><td>SRR18191622</td><td>Salting out</td><td>NC809</td><td>O41H7</td><td>2c</td><td>-</td><td>Unicycler</td><td>19,581</td><td>8</td><td>5,227,833</td><td>4,891,608</td><td>50.51</td><td>230</td><td>JAQKQ00000000</td></tr><tr><td>SRR18191620</td><td>Bead based</td><td>NV34</td><td>O168H8</td><td>2d</td><td>-</td><td>Unicycler</td><td>6,450</td><td>6</td><td>5,269,996</td><td>4,249,978</td><td>50.77</td><td>402</td><td>JAQKQ00000000</td></tr><tr><td>SRR18191619</td><td>Bead based</td><td>NV34</td><td>O168H8</td><td>2d</td><td>-</td><td>Raven<sup>d</sup></td><td>6,450</td><td>3</td><td>5,314,568</td><td>5,184,508</td><td>50.81</td><td>402</td><td>JAOWMY00000000</td></tr><tr><td>SRR18191618</td><td>Bead based</td><td>NV36</td><td>O75H8</td><td>1c, 2b</td><td>-</td><td>Unicycler</td><td>6,484</td><td>8</td><td>5,575,909</td><td>5,306,095</td><td>50.65</td><td>468</td><td>JAQKM00000000</td></tr><tr><td>SRR18191617</td><td>Bead based</td><td>NV36</td><td>O75H8</td><td>1c, 2b</td><td>-</td><td>Unicycler</td><td>6,484</td><td>11</td><td>5,577,269</td><td>5,301,141</td><td>50.65</td><td>113</td><td>JAOWIN00000000</td></tr><tr><td>SRR18191616</td><td>Salting out</td><td>Sik8430761</td><td>O177H25</td><td>2c, 2d</td><td>+</td><td>Flye<sup>e</sup></td><td>20,113</td><td>28</td><td>5,639,340</td><td>5,231,455</td><td>50.58</td><td>180</td><td>JAOWNO00000000</td></tr><tr><td>SRR18191615</td><td>Salting out</td><td>Sik8430761</td><td>O177H25</td><td>2c, 2d</td><td>+</td><td>Flye<sup>e</sup></td><td>20,113</td><td>28</td><td>5,658,335</td><td>5,248,496</td><td>50.58</td><td>180</td><td>JAOWNZ00000000</td></tr><tr><td>SRR18191614</td><td>Salting out</td><td>Sik8430767</td><td>O177H25</td><td>2c, 2d</td><td>+</td><td>Unicycler</td><td>17,583</td><td>12</td><td>5,420,630</td><td>5,017,089</td><td>50.54</td><td>150</td><td>JAQKL00000000</td></tr><tr><td>SRR18191612</td><td>Salting out</td><td>Sik8430767</td><td>O177H25</td><td>2c, 2d</td><td>+</td><td>Raven<sup>d</sup></td><td>17,583</td><td>3</td><td>5,458,939</td><td>5,276,849</td><td>50.57</td><td>150</td><td>JAOWML00000000</td></tr><tr><td>SRR18191611</td><td>Salting out</td><td>Sik8430767</td><td>O177H25</td><td>2c, 2d</td><td>+</td><td>Raven<sup>d</sup></td><td>17,583</td><td>3</td><td>5,458,939</td><td>5,276,849</td><td>50.57</td><td>150</td><td>JAOWML00000000</td></tr></tbody></table>

<footnote>a Long-read assembly polished with pilon.</footnote>

<footnote>b Long-read assembly polished with conron and medaka.</footnote>

<footnote>c Long-read assembly polished with conron (2 rounds) and medaka.</footnote>

<footnote>d Long-read assembly polished with conron, medaka, and pilon, and contigs <1 kb were removed.</footnote>

<footnote>e Long-read assembly polished with conron, medaka, and pilon, and contigs <1 kb were removed.</footnote>

<footnote>f Long-read assembly polished with conron (3 rounds), medaka, and pilon, and contigs <1 kb were removed.</footnote>

<footnote>g Long-read assembly polished with conron (4 rounds), medaka, and pilon, and contigs <1 kb were removed.</footnote>

<footnote>h Long-read assembly polished with conron (3 rounds) and pilon.</footnote>

<footnote>i Long-read assembly polished with conron (3 rounds), pilon, and contigs <1 kb were removed.</footnote>

<footnote>j If two methods were used for DNA extraction, the first one corresponds to the DNA extraction method used for sequencing using Illumina and the second for MinION sequencing.</footnote>

<footnote>k Serotypes were determined using *in silico* analysis.</footnote>

<footnote>l 50× subsampling.</footnote>

<footnote>m - are used to describe bash arguments/options.</footnote>
were retained for some of the samples. Whenever possible, Unicycler performed the circu-
larization of the replicons (5).

Assemblies from 1 to 52 contigs (mean, 10.33 ± 9.73) with a total assembly length between 4,849,707 and 6,118,277 bp (mean, 5,468,530.42 ± 292,599.77 bp) and mean GC content of 50.64% (±0.13) were generated. N₅₀ values ranged from 1,082,226 to 5,821,752 bp (mean, 4,759,454.32 ± 1,018,105.98 bp). The main sample characteristics, including serotype, stx and eae gene presence (determined using abricate [-min-cov 60 -min-id 80]), genome coverage, and accession numbers are reported in Table 1. All genomes were annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) v6.3 at http://www.ncbi.nlm.nih.gov/genome/annotation_prok (12).

**Data availability.** Short and long raw reads were deposited in the NCBI SRA database under BioProject accession number PRJNA808207. Additionally, assembled genomes were deposited in GenBank under accession numbers as referred to in Table 1 within BioProject accession numbers PRJNA808207, PRJNA885284, PRJNA884285, PRJNA884276, and PRJNA883638.

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