Antimicrobial resistance and virulence genes in bacteria
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1 Antimicrobial resistance and virulence genes in bacteria Johanne Ahrenfeldt PhD Student BSU course - November
2 How to analyse WGS data part 2 an introduction to CGEs methods KmerFinder SpeciesFinder ResFinder VirulenceFinder MyDBFinder NDtree CSI Phylogeny BSU course - November
3 Mechanisms for anti microbial resistance Acquired resistance - Horisontal gene transfer - Mutations Intrinsic resistance BSU course - November
4 Acquired resistance genes Horizontal gene transfer via transformation, transduction or conjugation These genes can be found in the chromosome or on plasmids Staphylococcus aureus resistance to methicillin (MRSA) - Via acquisition of meca genes which is on a mobile genetic element called staphylococcal cassette chromosome (SCCmec) which codes for penicillin binding proteins (PBPs) that are not sensitive to ß-lactam inhibition BSU course - November
5 Mutations Mutations in the bacterias own genes Mycobacterium tuberculosis resistance to rifamycins - Due to a point mutation in the rifampin-binding region of rpob BSU course - November
6 Intrinsic resistance The innate ability to resist the effects of a particular drug Gram-positive bacteria are resistant to Aztreonam (a ß-lactam) - Lack of penicillin binding proteins (PBPs) that bind and are inhibited by this ß-lactam antibiotic BSU course - November
7 Unknown seq BLAST Resistant genes MLST ResFinder Resistant profile BSU course - November
8 Database BSU course - November
9 BSU course - November
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17 HSP is the length of the alignment between the best matching resistance gene and the corresponding sequence in the genome Query length is the length of the best matching resistance gene in the database. The dark green colour indicates a perfect match for a given gene. The % Identity is 100 and the sequence in the genome covers the entire length of the resistance gene in the database. The red colour indicates that no resistance gene was detected for that antimicrobial class. BSU course - November
18 The grey colour indicates a warning due to a non-perfect match, HSP length is shorter than resistance gene length, % ID < 100%. The light green colour indicates a warning due to a non-perfect match, % ID < 100%, HSP length = resistance gene length. BSU course - November
19 BSU course - November
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26 How to analyse WGS data part 2 an introduction to CGEs methods KmerFinder SpeciesFinder ResFinder VirulenceFinder MyDBFinder NDtree CSI Phylogeny BSU course - November
27 VirulenceFinder 3 databases of known virulence genes for E. coli S. Aureus Enterococcus Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. J. Clin. Micobiol (5): BSU course - November
28 Unknown seq BLAST Virulence genes MLST VirulenceFinder Virulence profile BSU course - November
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30 BSU course - November
31 The databases are maintained for E.coli and S.Aureus BSU course - November
32 What if you are working on another species or you have another database We have a solution that can help BSU course - November
33 How to analyse WGS data part 2 an introduction to CGEs methods KmerFinder SpeciesFinder ResFinder VirulenceFinder MyDBFinder NDtree CSI Phylogeny BSU course - November
34 Unknown seq BLAST Your own database MLST MyDbFinder matched genes from your own database BSU course - November
35 BSU course - November
36 - The database should be made in a text editor (for example Notepad, TextEdit, Sublime text) - The database must contain of DNA sequences in FASTA format BSU course - November
37 - MyDbFinder only shows the first word of the header for outputted genes - different genes/sequences names without spaces are recommended BSU course - November
38 - MyDbFinder only shows the first word of the header for outputted genes - different genes/sequences names without spaces are recommended BSU course - November
39 BSU course - November
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number Done by Corrected by Doctor Hamed Al Zoubi
number 8 Done by م ها أبو عجمي ة Corrected by Mamoon Alqtamin Doctor Hamed Al Zoubi The last page includes definitions for the underlined asterisked words *, You can skip Extra notes, Enjoy! A Brief Introduction