1. Bacterial Resistance Problem Space Ehren Bucholtz Saint Mary-of-the-Woods College Mark Gallo Niagara University

2. Background Microbial drug resistance (DR) is a growing concern among health professionals and others around the world. DR Issues that can be studied in a problem space environment include –Types of Drug classes –Types of Bacteria –Mechanism of Action –Mechanisms of DR

3. Microbial drug resistance Biological Principles Next slide Tools Biology Workbench NCBI Data Sets CDC FDA Drug Digest RxList Drug Resistance

4. Bacteria types Drug Classes Mechanism of Action Resistance Mechanisms Cellular level Mutations Antibacterials Antibiotics Phylogeny Genetic exchange Host interaction Bacteriostatic Bacteriocidal Coevolution Ecological Factors

5. Resources Centers for Disease Control –Case studies –Outbreak data Genbank Biology Workbench

6. Multidrug Resistance Region of Salmonella enterica Serovar Typhimurium DT104 Outbreaks of MDR Typhimurium DT104 have also been reported in poultry, beef, cheese, and swine in numerous countries Resistant to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline however, isolates have been identified which are also resistant to fluoroquinolones, trimethoprim, and kanamycin

7. antimicrobial resistance gene is clustered on a fragment of less than 46 kb

8. Task: Identify Resistance ORFs Students are given pieces of nucleotide sequence of SGi1 to identify homology –beta-lactamase –Tetracycline resistance –Integrase –Transposase beta_lactamase (partial sequence shown) NEGKLGDLRDTTTPKAIAS TLNKFLFGSALSEMNQKKL ESWMVNNQVTGNLLRSVLP AGW

9. Find results for 4377727_4377728Vibrio cholerae non O1, non O139 plasmid class A beta-lactamase 216842_216843Proteus mirabilis plasmid pCS229 blaP gene for bata-lactamase, 30314015_30314018Pasteurella multocida plasmid pJR2, complete sequence. 9719055_9719057Vibrio cholerae class 1 integron integrase (intI1) gene,partial 12719011_12719033Salmonella enterica subsp. enterica serovar Typhimurium genomic 151074_151076P.aeruginosa beta-lactamase (PSE-1) gene, complete cds 47647_47648S.typhimurium beta-lactamase gene.

10. BlastP and Clustal for beta lactamase unknown 30314015_3031401 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW 216842_216843 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNKKKLESWMVNNQVTGNLLRSVLPAGW 47647_47648 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW 151074_151076 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW 12719011_12719033 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW 9719055_9719057 NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW beta_lactamase NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW 4377727_4377728 NEGKLGDLRDTTTPKAIASTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKW **********************::****:***.:**********************. *

11. Rooted Tree from ClustalW

12. Other project ideas Use wealth of CDC case study data to fill out project space

13. CDC Case Study Variant Salmonella Genomic Island 1 Antibiotic Resistance Gene Cluster in Salmonella enterica Serovar Albany –Benoît Doublet et.al. Emerg Infect Dis 2003 May Available from: URL: http://www.cdc.gov/ncidod/EID/vol9no5/02-0609.htm

14. Something’s fishy A variant SGI1, Salmonella genomic island 1, was identified as an antibiotic-resistance gene cluster in a multidrug-resistant strain of S. enterica serovar Albany isolated from food fish from Thailand and imported to France. In this strain, the streptomycin resistance aadA2 gene cassette in one of the SGI1 integrons was replaced by a dfrA1 gene cassette, conferring resistance to trimethoprim and an open reading frame of unknown function.

15. Gene Function Treasure Hunt

16. Clustering of Salmonella isolates