- Low-quality bases & read-pairs, together with Illumina adaptor sequences, were trimmed from the raw reads using Trimmomatic v0.36 (Bolger et al., 2014) (settings: LEADING:10 TRAILING:10 MINLEN:50 HEADCROP:10).
- The average sequence coverage depth was estimated from mapping reads to the complete chromosome of E. coli ST131 strain EC958 using SPANDx v3.2 (Sarovich & Price, 2014).
- Quality-trimmed paired-end reads were de novo assembled using the Microbial Genome Assembler Pipeline (MGAP).
- MGAP implements:
- Velvet v1.2.10 (Zerbino & Birney, 2008)
- VelvetOptimiser (https://github.com/tseemann/VelvetOptimiser)
- GapFiller v1.10 (Boetzer & Pirovano, 2012)
- ABACAS v1.3.1 (Assefa et al., 2009) (scaffolds against the chromosome of EC958)
- IMAGE v2.4 (Tsai et al., 2010)
- SSPACE v2.0 (Boetzer et al., 2011)
- Pilon v1.22 (Walker et al., 2014)
- MIRA v4 (Chevreux et al., 2004)
- QUAST v4.5 (Gurevich et al., 2013) assessed the assembly statistics generated from MGAP by comparing each isolate to EC958.
Table. Quality control & assembly metrics for 142 Welsh isolates sequenced to coverage ≥20-fold:
| Strain | Estimated coverage (-fold) | No. contigs ≥1kbp | Total length (bp) | GC (%) | N50 |
|---|---|---|---|---|---|
| BA16 | 40.7 | 88 | 5,297,485 | 50.80 | 225,953 |
| BA42 | 120.8 | 64 | 5,269,659 | 50.69 | 268,007 |
| BA43 | 35.2 | 63 | 5,236,807 | 50.69 | 226,190 |
| BA44 | 59.6 | 66 | 5,203,917 | 50.74 | 234,062 |
| BA47 | 78.1 | 67 | 5,271,594 | 50.69 | 235,977 |
| BA68 | 87.4 | 39 | 5,197,813 | 50.61 | 360,017 |
| BA70 | 48.0 | 52 | 5,175,026 | 50.76 | 426,957 |
| BA108 | 85.6 | 59 | 5,228,742 | 50.73 | 375,014 |
| BA115 | 57.0 | 60 | 5,252,089 | 50.66 | 225,814 |
| BA116 | 46.1 | 62 | 5,137,252 | 50.80 | 225,914 |
| BA130 | 72.8 | 57 | 4,995,114 | 50.73 | 272,278 |
| BA133 | 80.2 | 71 | 5,290,074 | 50.66 | 224,811 |
| BA155 | 33.0 | 79 | 5,364,310 | 50.61 | 222,489 |
| BA156 | 96.3 | 65 | 5,317,485 | 50.76 | 379,052 |
| BA164 | 40.7 | 61 | 5,066,840 | 50.69 | 221,693 |
| BA166 | 68.2 | 50 | 5,152,183 | 50.79 | 316,585 |
| BA167 | 50.8 | 78 | 5,269,782 | 50.70 | 230,427 |
| BA176 | 27.7 | 72 | 5,260,991 | 50.77 | 224,289 |
| BA177 | 88.3 | 63 | 5,253,232 | 50.69 | 234,398 |
| BA178 | 52.5 | 51 | 5,152,555 | 50.75 | 276,193 |
| BA187 | 58.1 | 76 | 5,262,949 | 50.69 | 228,314 |
| BA203 | 58.8 | 59 | 5,189,327 | 50.76 | 249,934 |
| BA210 | 66.8 | 60 | 5,265,740 | 50.75 | 191,296 |
| BA264 | 31.3 | 81 | 5,324,397 | 50.66 | 185,396 |
| BA306 | 33.3 | 64 | 5,019,437 | 50.72 | 354,032 |
| BA307 | 59.2 | 72 | 5,145,503 | 50.71 | 203,341 |
| BA337 | 76.5 | 53 | 5,082,765 | 50.79 | 499,502 |
| BA352 | 81.2 | 68 | 5,213,560 | 50.78 | 212,265 |
| BA377 | 50.3 | 70 | 5,308,726 | 50.69 | 282,618 |
| BA389 | 80.6 | 79 | 5,293,796 | 50.62 | 236,197 |
| BA392 | 60.0 | 54 | 5,193,784 | 50.74 | 411,196 |
| BA394 | 63.2 | 91 | 5,248,955 | 50.59 | 174,506 |
| BA397 | 53.4 | 71 | 5,088,782 | 50.79 | 222,638 |
| BA408 | 59.5 | 70 | 5,267,864 | 50.69 | 320,063 |
| BA412 | 84.8 | 67 | 5,286,319 | 50.73 | 227,535 |
| BA417 | 43.0 | 47 | 5,161,880 | 50.69 | 369,769 |
| BA418 | 95.3 | 56 | 5,235,387 | 50.80 | 199,587 |
| BA434 | 120.6 | 61 | 5,257,449 | 50.70 | 236,650 |
| BA435 | 64.6 | 60 | 5,202,902 | 50.84 | 320,127 |
| BA437 | 103.2 | 73 | 5,249,371 | 50.71 | 279,150 |
| BA440 | 52.0 | 73 | 5,385,925 | 50.66 | 212,854 |
| BA445 | 79.9 | 82 | 5,428,585 | 50.66 | 246,504 |
| BA446 | 91.6 | 66 | 5,293,370 | 50.78 | 194,929 |
| BA461 | 121.4 | 52 | 5,016,793 | 50.72 | 380,654 |
| BA464 | 108.5 | 82 | 5,304,798 | 50.68 | 269,078 |
| BA487 | 61.5 | 83 | 5,011,352 | 50.71 | 292,786 |
| BA490 | 114.5 | 92 | 5,356,585 | 50.70 | 218,672 |
| BA494 | 79.1 | 86 | 5,252,933 | 50.68 | 378,887 |
| BA496 | 90.5 | 47 | 5,119,322 | 50.74 | 365,000 |
| BA497 | 60.5 | 68 | 5,267,488 | 50.69 | 344,882 |
| BA515 | 71.6 | 63 | 5,260,506 | 50.69 | 231,546 |
| BA517 | 91.9 | 63 | 5,267,804 | 50.69 | 231,364 |
| BA523 | 67.7 | 69 | 5,119,854 | 50.71 | 293,747 |
| BA575 | 37.7 | 36 | 5,084,062 | 50.73 | 329,326 |
| BA655 | 68.1 | 68 | 5,089,797 | 50.66 | 224,226 |
| BA669 | 68.0 | 45 | 5,187,105 | 50.81 | 277,022 |
| BA694 | 29.1 | 341 | 5,154,547 | 50.92 | 28,518 |
| BA730 | 22.0 | 380 | 5,114,774 | 51.09 | 23,071 |
| BA810 | 38.5 | 233 | 5,168,786 | 50.87 | 39,344 |
| BA829 | 25.1 | 364 | 5,054,941 | 51.01 | 23,620 |
| BA871 | 29.4 | 312 | 5,148,625 | 50.90 | 30,061 |
| BA876 | 25.3 | 378 | 5,175,205 | 50.98 | 23,411 |
| BA901 | 31.2 | 261 | 5,038,995 | 50.72 | 34,848 |
| BA909 | 30.3 | 275 | 5,157,958 | 50.92 | 33,840 |
| BA910 | 32.8 | 276 | 5,211,662 | 50.88 | 34,907 |
| BA942 | 25.6 | 313 | 4,778,961 | 50.92 | 26,138 |
| BA1110 | 31.0 | 289 | 5,163,895 | 50.94 | 37,542 |
| BA1112 | 21.8 | 373 | 5,133,034 | 50.88 | 26,288 |
| BA1165 | 28.8 | 283 | 5,163,615 | 50.89 | 37,638 |
| BA1243 | 13.5 | 897 | 4,747,308 | 51.27 | 7,502 |
| BA1275 | 15.8 | 461 | 5,000,323 | 50.98 | 16,543 |
| BA1279 | 12.9 | 668 | 4,958,370 | 51.00 | 10,998 |
| BA1287 | 10.9 | 993 | 4,772,761 | 51.10 | 6,422 |
| BA1293 | 29.9 | 260 | 5,334,146 | 50.85 | 43,134 |
| BA1295 | 35.6 | 345 | 5,215,129 | 51.01 | 27,698 |
| BA1344 | 13.5 | 523 | 4,987,869 | 50.94 | 14,544 |
| BA1347 | 59.0 | 119 | 5,095,120 | 50.77 | 89,952 |
| BA1353 | 45.3 | 66 | 5,110,261 | 50.72 | 192,060 |
| BA1355 | 50.2 | 62 | 5,130,152 | 50.80 | 253,431 |
| BA1368 | 61.5 | 79 | 5,281,069 | 50.68 | 229,569 |
| BA1387 | 56.4 | 84 | 5,233,184 | 50.67 | 182,110 |
| BA1390 | 47.7 | 100 | 5,080,851 | 50.66 | 221,214 |
| BA1391 | 42.0 | 63 | 5,149,818 | 50.75 | 210,310 |
| BA1393 | 52.4 | 79 | 5,015,343 | 50.67 | 349,741 |
| BA1397 | 39.5 | 88 | 5,220,217 | 50.80 | 197,411 |
| BA1404 | 48.2 | 90 | 5,279,705 | 50.67 | 157,134 |
| BA1408 | 32.6 | 34 | 4,785,837 | 50.67 | 284,015 |
| BA1413 | 49.7 | 127 | 5,290,467 | 50.61 | 238,152 |
| BA1418 | 33.3 | 116 | 5,055,916 | 50.67 | 190,563 |
| BA1422 | 32.1 | 110 | 5,262,004 | 50.71 | 142,864 |
| BA1431 | 41.4 | 88 | 5,052,865 | 50.70 | 188,140 |
| BA1435 | 39.9 | 108 | 5,476,377 | 50.66 | 159,076 |
| BA1441 | 57.8 | 89 | 5,110,031 | 50.74 | 145,320 |
| BA1442 | 43.4 | 94 | 5,209,293 | 50.49 | 156,584 |
| BA1446 | 44.7 | 75 | 5,199,739 | 50.65 | 226,804 |
| BA1447 | 49.5 | 102 | 5,303,113 | 50.67 | 173,701 |
| BA1458 | 41.7 | 85 | 5,140,634 | 50.79 | 182,682 |
| BA1482 | 32.5 | 77 | 5,077,900 | 50.69 | 203,840 |
| BA1490 | 36.9 | 95 | 5,279,717 | 50.65 | 191,129 |
| BA1496 | 45.5 | 98 | 5,254,168 | 50.76 | 162,946 |
| BA1507 | 47.5 | 130 | 5,166,617 | 50.76 | 108,396 |
| BA1509 | 31.7 | 65 | 5,094,575 | 50.61 | 262,514 |
| BA1511 | 53.8 | 76 | 5,246,319 | 50.69 | 317,362 |
| BA1512 | 38.0 | 82 | 5,213,355 | 50.68 | 192,513 |
| BA1517 | 44.1 | 47 | 5,093,734 | 50.65 | 333,756 |
| BA1542 | 39.2 | 140 | 5,472,702 | 50.72 | 169,994 |
| BA1543 | 36.9 | 118 | 5,303,188 | 50.77 | 133,596 |
| BA1553 | 24.7 | 97 | 5,396,040 | 50.68 | 186,201 |
| BA1561 | 43.8 | 80 | 5,256,720 | 50.66 | 182,291 |
| BA1570 | 32.4 | 61 | 5,096,028 | 50.73 | 242,888 |
| BA1575 | 41.6 | 103 | 5,389,527 | 50.64 | 274,731 |
| BA1581 | 41.5 | 89 | 5,383,614 | 50.59 | 229,543 |
| BA1585 | 56.0 | 52 | 5,152,731 | 50.74 | 341,715 |
| BA1588 | 61.4 | 167 | 5,212,376 | 50.65 | 88,958 |
| BA1593 | 48.8 | 141 | 5,239,260 | 50.67 | 109,455 |
| BA1606 | 52.1 | 58 | 5,073,770 | 50.78 | 311,341 |
| BA1637 | 47.7 | 395 | 5,190,213 | 50.69 | 26,377 |
| BA1688 | 56.6 | 180 | 5,091,922 | 50.68 | 84,605 |
| BA1843 | 46.4 | 93 | 5,029,987 | 50.73 | 199,596 |
| BA2000 | 52.5 | 158 | 5,246,115 | 50.69 | 123,898 |
| BA2055 | 64.2 | 95 | 5,241,788 | 50.84 | 172,175 |
| BA2056 | 58.8 | 100 | 5,071,449 | 50.71 | 139,739 |
| BA2065 | 32.0 | 103 | 4,968,736 | 50.71 | 131,344 |
| BA2075 | 88.8 | 115 | 5,331,739 | 50.71 | 163,065 |
| BA2078 | 37.0 | 200 | 5,203,752 | 50.68 | 51,504 |
| BA2079 | 45.2 | 115 | 5,124,900 | 50.70 | 81,753 |
| BA2080 | 72.5 | 85 | 5,346,277 | 50.73 | 191,817 |
| BA2081 | 48.6 | 386 | 4,993,499 | 50.80 | 23,688 |
| BA2082 | 95.8 | 139 | 5,198,516 | 50.65 | 100,389 |
| BA2088 | 41.5 | 209 | 5,155,144 | 50.89 | 51,890 |
| BA2090 | 46.7 | 151 | 5,320,517 | 50.78 | 116,475 |
| BA2091 | 36.2 | 272 | 5,306,670 | 50.83 | 53,526 |
| BA2097 | 79.1 | 90 | 5,130,019 | 50.73 | 174,248 |
| BA2098 | 93.8 | 150 | 4,805,145 | 50.72 | 78,155 |
| BA2102 | 47.1 | 291 | 5,326,101 | 50.68 | 38,600 |
| BA2105 | 51.9 | 89 | 5,062,533 | 50.63 | 234,016 |
| BA2112 | 49.8 | 140 | 5,101,446 | 50.74 | 88,767 |
| BA2113 | 38.0 | 356 | 5,306,832 | 50.94 | 36,104 |
| BA2121 | 76.2 | 63 | 5,167,987 | 50.74 | 229,717 |
| BA2123 | 53.6 | 164 | 5,141,008 | 50.55 | 86,260 |
| BA2133 | 105.5 | 91 | 4,937,313 | 50.80 | 159,529 |
| BA2134 | 52.3 | 219 | 5,159,253 | 50.73 | 76,686 |