1. ©2011 Elsevier, Inc. Molecular Tools and Infectious Disease Epidemiology Betsy Foxman Chapter 7 Omics Analyses in Molecular Epidemiologic Studies

2. ©2011 Elsevier, Inc. DNA, antibody, and small molecular microarrays. The microarrays differ in the substrate bound to the surface and the detection principle. DNA microarrays are based on hybridization, antibody on antigen–antibody reactions, and small molecular arrays on antigen–antibody reaction and other binding reactions. Source: Reproduced, with permission, from Uttamchandani et al. (2009). FIGURE 7.1

3. ©2011 Elsevier, Inc. Nomenclature of a dendrogram. Source: Reproduced, with permission, from the National Center for Biotechnology. FIGURE 7.2

4. ©2011 Elsevier, Inc. Examples of dendrograms with unscaled and scaled branches, and rooted and unrooted trees. Source: Reproduced, with permission, from Vierstraete (1999). FIGURE 7.3

5. ©2011 Elsevier, Inc. Phylogenic analysis of pulsed-field gel electrophoresis (PFGE) patterns from Salmonella enterica serotype Montevideo strains from an outbreak in France, 2006. Twelve case-patients and three isolates from cheese or raw milk processed in the incriminated plant (AFSSA SMVDXB0038-39-40) identified from epidemiologic analyses as the putative source shared the identical PFGE pattern (only patient strain XMON-1 is shown on the figure because all others were identical). Isolates from other case-patients (XMON-11-12-13-14) and non-outbreak-associated patients (XMON-2 to XMON-10) were quite heterogeneous. Similarity calculated using DICE. Source: Reproduced, with permission, from Dominguez et al. (2009). FIGURE 7.4

6. ©2011 Elsevier, Inc. The relationship of HIV to representative simian immunodeficiency viruses using the viral polymerase gene (Pol) amino acid sequence. Crosses represent possible transmission between species. The length of the distance bar is ~1 amino acid replacement per 10 sites. Horizontal lines represent the degree of genetic distance, vertical lines have no meaning. The tree is rooted using Sykes monkeys. Source: Reproduced, with permission, from Hungnes et al. (2000). FIGURE 7.5

7. ©2011 Elsevier, Inc. A, Measles phylogeny: the measles virus nucleocapsid gene (63 sequences, 1575 base pairs [bp]). B, Influenza phylogeny: the human influenza A virus (subtype H3N2) hemagglutinin (HA1) gene longitudinally sampled over a period of 32 years (50 sequences, 1080 bp). C, Dengue phylogeny: the dengue virus envelope gene from all four serotypes (DENV-1 to DENV-4, 120 sequences, 1485 bp). D, HIV-1 population phylogeny: the subtype B envelope (E) gene sampled from different patients (39 sequences, 2979 bp). E, HCV population phylogeny: the virus genotype 1b E1E2 gene sampled from different patients (65 sequences, 1677 bp). F, HIV-1 within-host phylogeny: the partial envelope (E) gene longitudinally sampled from a single patient over 5.8 years (58 sequences, 627 bp). All sequences were collected from GenBank and trees were constructed with maximum likelihood in phylogenetic analysis using parsimony (PAUP). Horizontal branch lengths are proportional to substitutions per site. Source: Adapted, with permission, from Grenfell et al. (2004). FIGURE 7.6 AB C D EF

8. ©2011 Elsevier, Inc. Rarefaction curves for pyrosequencing reads of the V4 and V6 regions of 16S rDNA from fecal samples from individuals A, B, C, and D. Phylotypes assigned using 97% (dotted lines) and 98% levels (solid lines, except for ALL-V4, which has single dots) of similarity. The inset shows curves for half the A-V6-1.0 reads and the three constituent parts of the C-V4-0.5 reads. Source: Reproduced, with permission, from Claesson et al. (2009). FIGURE 7.7