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Bacterial Resistance
Problem Space
Ehren Bucholtz
Saint Mary-of-the-Woods College
Mark Gallo
Niagara University
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
Microbial drug resistance
Biological Principles
Next slide
Drug Resistance
Tools
Biology Workbench
NCBI
Data Sets
CDC
FDA
Drug Digest
RxList
Coevolution
Genetic
exchange
Phylogeny
Ecological
Factors
Drug
Classes
Bacteria
types
Host
interaction
Antibacterials
Antibiotics
Drug Resistance
Mutations
Cellular
level
Resistance
Mechanisms
Mechanism of
Action
Bacteriocidal
Bacteriostatic
Resources
• Centers for Disease Control
– Case studies
– Outbreak data
• Genbank
• Biology Workbench
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
• antimicrobial resistance gene is clustered on a
fragment of less than 46 kb
Task: Identify Resistance ORFs
• Students are given pieces
of nucleotide sequence of
SGi1 to identify homology
–
–
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–
beta-lactamase
Tetracycline resistance
Integrase
Transposase
• beta_lactamase
(partial sequence
shown)
NEGKLGDLRDTTTPKAIAS
TLNKFLFGSALSEMNQKKL
ESWMVNNQVTGNLLRSVLP
AGW
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.
BlastP and Clustal for beta
lactamase unknown
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30314015_3031401
216842_216843
47647_47648
151074_151076
12719011_12719033
9719055_9719057
beta_lactamase
4377727_4377728
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNKKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGW
NEGKLGDLRDTTTPKAIASTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKW
**********************::****:*** .:**********************. *
Rooted Tree from ClustalW
Other project ideas
• Use wealth of CDC case study data to fill
out project space
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
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.
Gene Function Treasure Hunt
• Clustering of
Salmonella
isolates