Verocytotoxin producing Escherichia coli (VTEC) diagnostics

Transcription

1 Verocytotoxin producing Escherichia coli (VTEC) diagnostics Workshop on Whole Genome Sequencing and Analysis, 2-4 Oct. 2017

2 Learning objective: After this lecture and exercise, you should be able to describe how the methods from Center for Genomic Epidemiology for identifying the serotype of E. coli, and the virulence factors in E. coli, Enterococcus, Listeria, or S. aureus work use the above-mentioned methods as stand-alone services and interpret the results retrieve information about the genes in the CGE databases generate your own database in FASTA format and use it for searching for specific genes of interest

3 Verocytotoxin-producing E. coli (VTEC)/ Shiga toxin-producing E. coli (STEC) A gastrointestinal pathogen Produces verocytotoxins as well as other virulence factors May cause bloody diarrhoea and occasionally Haemolytic Uremic Syndrome (HUS) Primary sources are undercooked ground meet, raw milk, and faecal contamination of vegetables In EU, in 2013, there were 6,043 confirmed cases of VTEC and 13 deaths due to VTEC

4 Previous routine typing of VTEC by the Danish State Serum Institute Serotyping Examined for.... β-glucuronidase activity.. haemolysin production.. Verocytotoxin production.. Presence of specific virulence factors, most importantly, verotoxin 1 (vtx1), verotoxin 2 (vtx2) and intimin (eae), which were detected by DNA hybridization Further subtyping of the verocytotoxins was carried out by PCR Isolates with same serotype and toxin profile compared by PFGE

5 Serotyping In serotyping a group of closely related microorganisms are distinguished by a characteristic set of antigens by the use of antibodies E. coli SerotypeFinder O-type is based on the O-processing genes: wzx, wzy, wzm, and wzt, and wzx/wzy or wzm/wzt pairs H-type is based on the detection of flagellin genes: flic, flka, flla, flma, flna O:H serotyping of E. coli using WGS data Joensen KG. et al J.Clin.Microbiol. 53(8):

6 Evaluating the performance of SerotypeFinder Number of genomes for validation with detected genes with consistent WGS -and conventional results O-typing (~95%) 560 (~98%) H-typing (~100%) 503 (~99%)

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9 VirulenceFinder Joensen et al J. Clin. Microbiol. 52(5):

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11 Classification of E. coli causing diarrhoea, DEC Kaper et al Nature Reviews Microbiology 2,

12 Simplified categorisation that we will use during exercise Non-pathogenic: Few or no obvious virulence factors UPEC: Adhesion factors to avoid being flushed away from the urinary tract, siderophore proteins (iron). Presence of Pap (P) fimbriae (papg adhesion) can be a sign of increased virulence VTEC, STEC (EHEC): A hall-mark virulence factor is the Shiga toxin (stx2a and stx2b) EAEC: Many different virulence factors, especially aggregative adherence fimbriae (AFFs) located on a 100-kb paa plasmid, mycolycins such as those encoded by the pic gene and toxins (pet and asta). The regulator encoded by aggr also located on the paa plasmid is coordinating the virulence factors. ETEC: Production of Heat-Stabile Toxin (ST) or Heat-Labile Toxin (LT). The former can be encoded by the sta1 or stb genes and the latter by the elt or ltca genes.

13 Database content Static databases at are no longer maintained All databases are in an online repository called BitBucket BitBucket: Web-based hosting service aimed at software version control systems for teams Main advantages: It is easy to see which changes have been done since last update It is possible to roll back to previous versions

14 _db means it is a database repository Otherwise it is a software repository

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18 Content of notes.txt

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21 AU! Mouse arm SourceTree to the rescue!

22 Graphical User Interface client for Windows and Mac Databases of interest should be stored on local computer and connected to BitBucket repositories via SourceTree SourceTree makes it easy to see if changes have been made to BitBucket repository and to download (pull) those changes

23 BLAST-based CGE finder tools >Gene_1 GATAATGTAATAGAAATTGGATCAGGAAAAG GTCATTTTACCAAAGAACTTGTCAAAATGAG TCGGTGGGTGGATTCTATAGAAATTGATGAG GACTTGTGTCAAGTCACCCAAAAAGTCGTGA AGCCTTTTCAGAATATAAAAGTTATCCATAC GGATATTCTGAAATTTAACTTCCCCAAAAAC AAAGACTATAAAATATTTGGTAATATCCCCT TTAACATCAGTACTGATATTGTCAAAAAAAT TGCTTTTGAAAGCAATTCGAAATATAGTTA >Gene_2a ATGAACAAAAATATAAAATATTCTCAAAACT TTTTAACGAGTGAAAAAGTACTCAACCAAAT AATAAAACAATTGAATTTAAAAGAAACCGAT ACCGTTTACGAAATTGGAACAGGTAAAGGGC ATTTAACGACGAAACTGGCTAAAATAAGTAA ACAGGTAACGTCTATTGAATTAGACAGTCAT CTATTCAACTTATCGTCAGAAAAA Gene_2b ATGAAAAAAAATATAAAATATTCTCAAAACT TTTTAACGAATGAAAAGGTACTCAACCAAAT AATAAAACAATTGAATTTAAAAGAAACCGAT ACCGTTTACGAAATTGGAACAGGTAAAGGGC ATTTAACGACGAAACTGGCTAAAATAAGTAA ACAGGTAACGTCTATTGAATTAGACAGTCAT CTATTCAACTTATCTTCAGAAAAA Database >Contig_1 TGGATTCTATAGAAATTGATGAGGACTTGTG TCAAGTCACCCAAAAAGTCGTGAAGCCTTTT CAGAATATAAAAGTTATCCATACGGATATTC TGAAATTTAACTTCCCCAAAAACAAAGACTA TAAAATATTTGGTAATATCCCCTTTAACATC AGTACTGATATTGTCAAAAAAATTGCTTTTG AAAGCAATTCGAAATATAGTTAAATATAAAA TATTCTCAAAACTTTTTAACGAGTGAAAAAG TACTCAACCAAATAATAAAACAATTGAATTT AAAAGAAACCGATACCGTTTACGAAATTGGA ACAGGTAAAGGGCATTTAACGACGAAACTGG CTAAAATAAGTAAACAGGTAACGTCTATTGA ATTAGACAGTCATCTATTCAACTTATCGTCA GAAAAAATGAAAAAAAATATAAAATATTCTC AAAACTTTTTAACGAATGAAAAGGTACTCAA CCAAATAATAAAACAATTGAATTTAAAAGAA ACCGATACCGTTTACGAAATTGGAACAGGTA AAGGGCATTTAACGACGAAACTGGCTAAAAT AAGTAAACAGGTAACGTCTATTGAATTAGAC AGTCATCTATTCAACTTATCTTCAGAAAAA >Contig_12 AGTGTGTGCGAGAGAGCGAGCGTGCGTGCGA GAGAGTTTCGCGCGCGCTTTAGAGAGCGTGC GAGCGAGCGAGCGTGTTTGTGCCCCAGAGAA ATGGTAATATCCCCTTTAACATCAGTACTGA TATTGTCAAAAAAATTGCTTTTGAAAGCAAT TCGAAATATAGTTAAATATAAAATATTCTCA AAACTTTTTAACGAGTGAAAAAGTACTCAAC CAAATAATAAAACAATTGAATTTAAAAGAAA CCGATACCGTTTACGAAATTGGAACAGGTAA Draft assembly

24 BLAST-based CGE finder tools MLST ResFinder PlasmidFinder pmlst SerotypeFinder VirulenceFinder

25 Generating your own database Collect DNA sequences of the genes you wish to search for Save the DNA sequences in FASTA format Take care to provide each gene with a unique identifier (everything from the > to the first space) Save the FASTA file as pure text Congratulations - you have made your own database!

26 MyDBFinder Use your own database with any gene(s) of interest