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Bacterial ResistanceProblem Space
Ehren BucholtzSaint Mary-of-the-Woods College
Mark GalloNiagara University
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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
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Microbial drug resistance
Biological PrinciplesNext slide
ToolsBiology Workbench
NCBI
Data SetsCDCFDA
Drug DigestRxList
Drug Resistance
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Drug Resistance
Bacteriatypes
DrugClasses
Mechanism of Action
ResistanceMechanisms
Cellularlevel
Mutations
Antibacterials
Antibiotics
Phylogeny
Geneticexchange
Hostinteraction
Bacteriostatic
Bacteriocidal
Coevolution
EcologicalFactors
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Resources
• Centers for Disease Control– Case studies– Outbreak data
• Genbank
• Biology Workbench
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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
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• antimicrobial resistance gene is clustered on a fragment of less than 46 kb
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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) NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
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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.
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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 • **********************::****:*** .:**********************. *
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Rooted Tree from ClustalW
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Other project ideas
• Use wealth of CDC case study data to fill out project space
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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
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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.
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Gene Function Treasure Hunt
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• Clustering of Salmonella isolates