1.  Staphylococcus aureus CC398: Host Adaption and Emergence of Methicillin Resistance in Livestock Price et al., 2012 Jourdan Meltzer November 4, 2013

2. Background: S. aureus  bacteria frequently found in human respiratory tract & skin.  not always pathogenic: 20% long-term carriers  disease-associated strains: potent protein toxins & cell-surface proteins that inactivate antibodies  Methicillin Resistant Staphylococcus aureus : strain of S. aureus bacteria resistant to most β -lactam antibiotics  not always so: 1943-- antibacterial activity of Penicillium fungus demonstrated against S. aureus  Rates of resistance rising

3. Background: MRSA and MSSA  Types based on sources:  health care-associated  community-associated  health care-associated w/ community onset  livestock-associated  Differentiating from methicillin-susceptible S. aureus (MSSA): MSSA unable to resist β -lactam antibiotics   MRSA not more virulent, simply harder to treat

4. Background: Risks, Diagnosis, & Treatment  Hospital patients, prisoners, homeless, athletes, people in contact w/ live food-producing animals, & children  Grow tissue sample in presence of antibiotic & check for bacterial growth  developing DNA methods  Draining of superficial abscesses in certain cases; bactrim & vancomycin most common antibiotics  Exciting research: bacteriophage

5. Clonal Complex 398  new strain of MRSA discovered June 2011  responsible for livestock-associated MRSA (LA-MRSA)  found primarily in food-producing animals (e.g. pig, bovine, and turkey)  dangerous to humans; often asymptomatic in animals

6. Question What are the origins and evolution of MRSA CC398?

7. Methods: Sample Selection  48 MRSA & 40 MSSA CC398 isolates  25 human strains & 63 livestock strains (live animals, meat samples, & environmental contamination)  referenced against ST398 strain, SO385 (2,872,582 bps)

8. Methods Overview  whole-genome sequence typing (WGST)  + multilocus sequence typing (MLST)  + spa typing  Identifying SNPs & building phylogenetic tree using maximum parsimony  SCC mec typing  Detection of antimicrobial resistance & host adaption genes

9. Methods Background: Next Generation Sequencing  Sequencing avg. of 2,651,848 bases: previously major endeavor

10. Methods: Building Tree from Data  w/ Burrows-Wheeler Aligner software, aligned data sequences against ST398 reference genome  analyzed w/ SolSNP: excluding SNP loci  w/ coverage <10X  w/ variants present in <90% of base calls for given position  in duplicated regions on reference genome  Tree built w/ maximum parsimony method in PAUP

11. Methods: “Enriching” the Tree  MLST: sequence-based genotyping of 7 housekeeping genes  allelic profiles (sequence type: ST) associated with known clonal complexes (CCs) via computer program eBURST  spa typing: sequence-based analysis of VNTRs in gene encoding Protein A ( spa )  use primers targeting specific locus  enter sequence results into BioNumerics software  SCC mec typing: genomic island containing antibiotic resistance gene mec A  Detection of antimicrobial resistance genes

12. Results  In building tree took major care: making adjustments post initial analysis  Rooted first using ST36 as out-group  revealed 4 isolates of t899 spa type 1 st to diverge  Similarity between cluster & ST36 single 123,000bp region, which comparative genetic analysis revealed was acquired horizontally  SNP’s from region excluded: clade of human MSSA isolates from France, French Guiana, & U.S. 1 st to diverge  4,238 SNPs ID’d, 1,102 parsimony informative w/ CI=0.951  Lack of homeoplasy demonstrated w/out need for addt’l measured

14. Results: Most Ancestral Lineage

15. Results: spa types & SCC mec  limited # of spa types: 15 ID’d among 89 isolates  two most common represented 67%  spa types inconsistent w/ overall CC398 phylogeny  30/49 CC398 MRSA isolates had cadmium zinc resistance gene

16. Key Conclusions  CC398 lineage originated in humans as MSSA  then spread to livestock where acquired SCC mec cassette & methicillin resistance  Potential power of WGST for epidemiological investigations: revealing common ancestors & avoiding homeoplasy w/in spa gene

17. Implications  Potential public health risk in using broad-spectrum cephalosporins in food animal production selects  select for MRSA  Presence of zinc in feed  select for MRSA CC398 strains with zinc r gene  WGST as most reliable method

18. Further Directions  Categorizing bi-directional nature: jump from humans to animals truly assoc. w/  capacity for human colonization, transmission, & virulence?  Further examining genetic changes in shift  Surveillance to predict public health impact

19. References  http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/phage/phage-virulence.html http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/phage/phage-virulence.html  http://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics) http://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics  http://www.mayoclinic.org/mrsa/index.html http://www.mayoclinic.org/mrsa/index.html  http://en.wikipedia.org/wiki/Methicillin-resistant_Staphylococcus_aureus#Strains http://en.wikipedia.org/wiki/Methicillin-resistant_Staphylococcus_aureus#Strains  http://www.webmd.com/skin-problems-and-treatments/understanding-mrsa-detection-treatment http://www.webmd.com/skin-problems-and-treatments/understanding-mrsa-detection-treatment  http://www.st398.com http://www.st398.com  http://res.illumina.com/documents/products/illumina_sequencing_introduction.pdf http://res.illumina.com/documents/products/illumina_sequencing_introduction.pdf  http://www.premierbiosoft.com/tech_notes/multiplex-pcr.html http://www.premierbiosoft.com/tech_notes/multiplex-pcr.html  http://en.wikipedia.org/wiki/Dna_sequencing#Next-generation_methods http://en.wikipedia.org/wiki/Dna_sequencing#Next-generation_methods  http://phylo.bio.ku.edu/slides/BIOL848-lec9-Distances.pdf http://phylo.bio.ku.edu/slides/BIOL848-lec9-Distances.pdf

20. Papers Consulted  Kondo Y, Ito T, Ma XX, Watanabe S, Kreiswirth BN, Etienne J, Hiramatsu K. Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: rapid identification system for mec, ccr, and major differences in junkyard regions. Antimicrob Agents Chemother. 2007 Jan;51(1):264-74. Epub 2006 Oct 16.  J. Ross Fitzgerald. Livestock-associated Staphylococcus aureus: origin, evolution and public health threat. Trends in Microbiology. 2012 April;20(4):192–98.  B. Strommenger, C. Kettlitz, Weniger,D. Harmsen, W. Friedrich, and W. Witte1. Assignment of Staphylococcus Isolates to Groups by spa Typing, SmaI Macrorestriction Analysis, and Multilocus Sequence Typing. J Clin Microbiol. 2006 July; 44(7): 2533–2540.  Chambers HF and DeLeo FR. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nature. 2009 Sep; 7:629-641.

21. Thank You!