Genomic epidemiology reveals geographical clustering of multi-drug-resistant Escherichia coli sequence type (ST)131 associated with bacteraemia in Wales, United Kingdom
This repository provides de novo assemblies of paired-end short-read sequencing data for our phylogenomic study of E. coli sequence type (ST)131 in an accessible format. If you use this data in your publications please cite:
White RT, Bull MJ, Barker CR, Arnott JM, Wootton M, Jones LS, Howe RA, Morgan M, Ashcroft MM,
Forde BM, Connor TR^, Beatson SA^. Genomic epidemiology reveals geographical clustering of
multidrug-resistant Escherichia coli sequence type (ST)131 associated with bacteraemia in
Wales, United Kingdom. medRxiv:21257487v1 [Preprint]. 2021. Available from:
https://www.medrxiv.org/content/10.1101/2021.05.21.21257487v1 doi: 10.1101/2021.05.21.21257487
^CORRESPONDING AUTHORS
The Illumina sequence read data have been submitted to the National Center for Biotechnology Information (NCBI) sequence read archive (SRA) under Bioproject number PRJNA729115 (157 paired reads).
Contains:
- Assemblies/ - the assembled contigs from Velvet that have been ordered against E. coli ST131 strain EC958 (GenBank: HG941718.1) described by Forde et al. (2014).
- Contigs from the draft assemblies were ordered against the complete chromosome of EC958 using Mauve by Darling, et al. (2004).
- The assembly statistics are provided.
The following table facilitates this:
| Strain | BioSample accession | SRA Accession |
|---|---|---|
| BA16 | SAMN19110938 | SRR14519463 |
| BA42 | SAMN19110990 | SRR14519440 |
| BA43 | SAMN19110991 | SRR14519439 |
| BA44 | SAMN19110995 | SRR14519435 |
| BA47 | SAMN19111001 | SRR14519428 |
| BA68 | SAMN19111013 | SRR14519415 |
| BA70 | SAMN19111015 | SRR14519414 |
| BA108 | SAMN19110868 | SRR14519482 |
| BA115 | SAMN19110873 | SRR14519481 |
| BA116 | SAMN19110874 | SRR14519480 |
| BA130 | SAMN19110889 | SRR14519479 |
| BA133 | SAMN19110892 | SRR14519478 |
| BA155 | SAMN19110928 | SRR14519506 |
| BA156 | SAMN19110930 | SRR14519504 |
| BA164 | SAMN19110941 | SRR14519460 |
| BA166 | SAMN19110942 | SRR14519459 |
| BA167 | SAMN19110943 | SRR14519458 |
| BA176 | SAMN19110945 | SRR14519456 |
| BA177 | SAMN19110946 | SRR14519455 |
| BA178 | SAMN19110947 | SRR14519454 |
| BA187 | SAMN19110949 | SRR14519451 |
| BA203 | SAMN19110951 | SRR14519449 |
| BA210 | SAMN19110967 | SRR14519555 |
| BA264 | SAMN19110976 | SRR14519545 |
| BA306 | SAMN19110977 | SRR14519544 |
| BA307 | SAMN19110978 | SRR14519542 |
| BA337 | SAMN19110979 | SRR14519541 |
| BA352 | SAMN19110980 | SRR14519540 |
| BA377 | SAMN19110981 | SRR14519539 |
| BA389 | SAMN19110982 | SRR14519538 |
| BA392 | SAMN19110983 | SRR14519537 |
| BA394 | SAMN19110984 | SRR14519536 |
| BA397 | SAMN19110985 | SRR14519535 |
| BA408 | SAMN19110986 | SRR14519534 |
| BA412 | SAMN19110987 | SRR14519533 |
| BA417 | SAMN19110988 | SRR14519442 |
| BA418 | SAMN19110989 | SRR14519441 |
| BA434 | SAMN19110992 | SRR14519438 |
| BA435 | SAMN19110993 | SRR14519437 |
| BA437 | SAMN19110994 | SRR14519436 |
| BA440 | SAMN19110996 | SRR14519434 |
| BA445 | SAMN19110997 | SRR14519433 |
| BA446 | SAMN19110998 | SRR14519431 |
| BA461 | SAMN19110999 | SRR14519430 |
| BA464 | SAMN19111000 | SRR14519429 |
| BA487 | SAMN19111002 | SRR14519427 |
| BA490 | SAMN19111003 | SRR14519426 |
| BA494 | SAMN19111004 | SRR14519425 |
| BA496 | SAMN19111005 | SRR14519424 |
| BA497 | SAMN19111006 | SRR14519423 |
| BA515 | SAMN19111007 | SRR14519422 |
| BA517 | SAMN19111008 | SRR14519420 |
| BA523 | SAMN19111009 | SRR14519419 |
| BA575 | SAMN19111010 | SRR14519418 |
| BA655 | SAMN19111011 | SRR14519417 |
| BA669 | SAMN19111012 | SRR14519416 |
| BA694 | SAMN19111014 | SRR14519493 |
| BA730 | SAMN19111016 | SRR14519492 |
| BA810 | SAMN19111017 | SRR14519491 |
| BA829 | SAMN19111018 | SRR14519490 |
| BA871 | SAMN19111019 | SRR14519489 |
| BA876 | SAMN19111020 | SRR14519488 |
| BA901 | SAMN19111021 | SRR14519486 |
| BA909 | SAMN19111022 | SRR14519485 |
| BA910 | SAMN19111023 | SRR14519484 |
| BA942 | SAMN19111024 | SRR14519483 |
| BA1110 | SAMN19110869 | SRR14519567 |
| BA1112 | SAMN19110870 | SRR14519566 |
| BA1123 | SAMN19110871 | SRR14519498 |
| BA1128 | SAMN19110872 | SRR14519487 |
| BA1165 | SAMN19110875 | SRR14519476 |
| BA1170 | SAMN19110876 | SRR14519529 |
| BA1214 | SAMN19110877 | SRR14519518 |
| BA1215 | SAMN19110878 | SRR14519507 |
| BA1243 | SAMN19110879 | SRR14519464 |
| BA1256 | SAMN19110880 | SRR14519453 |
| BA1257 | SAMN19110881 | SRR14519565 |
| BA1274 | SAMN19110882 | SRR14519554 |
| BA1275 | SAMN19110883 | SRR14519543 |
| BA1279 | SAMN19110884 | SRR14519532 |
| BA1287 | SAMN19110885 | SRR14519432 |
| BA1292 | SAMN19110886 | SRR14519421 |
| BA1293 | SAMN19110887 | SRR14519413 |
| BA1295 | SAMN19110888 | SRR14519412 |
| BA1320 | SAMN19110890 | SRR14519411 |
| BA1327 | SAMN19110891 | SRR14519499 |
| BA1341 | SAMN19110893 | SRR14519497 |
| BA1344 | SAMN19110894 | SRR14519496 |
| BA1345 | SAMN19110895 | SRR14519495 |
| BA1347 | SAMN19110896 | SRR14519494 |
| BA1353 | SAMN19110897 | SRR14519477 |
| BA1355 | SAMN19110898 | SRR14519475 |
| BA1368 | SAMN19110899 | SRR14519474 |
| BA1387 | SAMN19110900 | SRR14519473 |
| BA1390 | SAMN19110901 | SRR14519472 |
| BA1391 | SAMN19110902 | SRR14519471 |
| BA1393 | SAMN19110903 | SRR14519470 |
| BA1397 | SAMN19110904 | SRR14519469 |
| BA1404 | SAMN19110905 | SRR14519468 |
| BA1408 | SAMN19110906 | SRR14519531 |
| BA1413 | SAMN19110907 | SRR14519530 |
| BA1418 | SAMN19110908 | SRR14519528 |
| BA1422 | SAMN19110909 | SRR14519527 |
| BA1431 | SAMN19110910 | SRR14519526 |
| BA1435 | SAMN19110911 | SRR14519525 |
| BA1441 | SAMN19110912 | SRR14519524 |
| BA1442 | SAMN19110913 | SRR14519523 |
| BA1446 | SAMN19110914 | SRR14519522 |
| BA1447 | SAMN19110915 | SRR14519521 |
| BA1458 | SAMN19110916 | SRR14519520 |
| BA1477 | SAMN19110917 | SRR14519519 |
| BA1482 | SAMN19110918 | SRR14519517 |
| BA1490 | SAMN19110919 | SRR14519516 |
| BA1496 | SAMN19110920 | SRR14519515 |
| BA1507 | SAMN19110921 | SRR14519514 |
| BA1509 | SAMN19110922 | SRR14519513 |
| BA1511 | SAMN19110923 | SRR14519512 |
| BA1512 | SAMN19110924 | SRR14519511 |
| BA1517 | SAMN19110925 | SRR14519510 |
| BA1542 | SAMN19110926 | SRR14519509 |
| BA1543 | SAMN19110927 | SRR14519508 |
| BA1553 | SAMN19110929 | SRR14519505 |
| BA1561 | SAMN19110931 | SRR14519503 |
| BA1570 | SAMN19110932 | SRR14519502 |
| BA1575 | SAMN19110933 | SRR14519501 |
| BA1581 | SAMN19110934 | SRR14519500 |
| BA1585 | SAMN19110935 | SRR14519467 |
| BA1588 | SAMN19110936 | SRR14519466 |
| BA1593 | SAMN19110937 | SRR14519465 |
| BA1606 | SAMN19110939 | SRR14519462 |
| BA1637 | SAMN19110940 | SRR14519461 |
| BA1688 | SAMN19110944 | SRR14519457 |
| BA1843 | SAMN19110948 | SRR14519452 |
| BA2000 | SAMN19110950 | SRR14519450 |
| BA2055 | SAMN19110952 | SRR14519448 |
| BA2056 | SAMN19110953 | SRR14519447 |
| BA2057 | SAMN19110954 | SRR14519446 |
| BA2065 | SAMN19110955 | SRR14519445 |
| BA2075 | SAMN19110956 | SRR14519444 |
| BA2078 | SAMN19110957 | SRR14519443 |
| BA2079 | SAMN19110958 | SRR14519564 |
| BA2080 | SAMN19110959 | SRR14519563 |
| BA2081 | SAMN19110960 | SRR14519562 |
| BA2082 | SAMN19110961 | SRR14519561 |
| BA2088 | SAMN19110962 | SRR14519560 |
| BA2090 | SAMN19110963 | SRR14519559 |
| BA2091 | SAMN19110964 | SRR14519558 |
| BA2097 | SAMN19110965 | SRR14519557 |
| BA2098 | SAMN19110966 | SRR14519556 |
| BA2102 | SAMN19110968 | SRR14519553 |
| BA2105 | SAMN19110969 | SRR14519552 |
| BA2112 | SAMN19110970 | SRR14519551 |
| BA2113 | SAMN19110971 | SRR14519550 |
| BA2121 | SAMN19110972 | SRR14519549 |
| BA2123 | SAMN19110973 | SRR14519548 |
| BA2133 | SAMN19110974 | SRR14519547 |
| BA2134 | SAMN19110975 | SRR14519546 |
Note: The data is ~825 MB
Option 1) Download the current release as an archive:
$ wget https://github.com/RhysWhite/ST131_157_Blood_WLS/archive/master.zip -O ST131_157_Blood_WLS_v1.tar.gz
$ unzip ST131_157_Blood_WLS_v1.tar.gz
Option 2) Clone the current master branch in this repository:
Please ensure you have git installed. git can be really useful for scientists. See here for some discussion.
With git:
$ git clone --recursive https://github.com/RhysWhite/ST131_157_Blood_WLS.git
# The --recursive option is used to pull down all the smaller repositories