Chapter 10 : Molecular Epidemiology of Species

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This chapter summarizes the various modern genotypic methods available for subtyping the various species, the use of genetic methods for investigating outbreaks of disease, the application and interpretation of large-scale techniques in broader epidemiological studies, and a perspective of future developments in the field. Discussions of three methods (pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and amplified fragment length polymorphism (AFLP)) used to compare relatively large numbers of strains follow in a section aimed at summarizing our knowledge of molecular epidemiology in a broader perspective. Limitations of MLST include cost and the degree of resolution that is possible with the quantity of data provided by seven highly conserved gene fragments. The molecular epidemiology of is less well studied, but more recent work offers some insights into host association. Current results suggest that the attribution of and isolates from human cases to their source will be best undertaken by means of a phylogenetic approach that uses analysis based on allele frequencies, or that follows robust definition of host associated sublineages within the main clonal groups. Molecular epidemiological studies of species have matured considerably since the early applications of plasmid profiling and restriction enzyme analysis in homogeneous electric fields.

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10
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Image of Figure 1.
Figure 1.

PFGE patterns of selected New Zealand isolates when digested with I and I. UPGMA (unweighted pair group with mathematical average) dendrograms generated by BioNumerics v4.5, with DICE coefficient, optimization of 1.0%, and tolerance of 1.5%.

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10
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Image of Figure 2.
Figure 2.

Novel AFLP method for use in conventional electrophoresis and detection systems aimed at identification and typing and species. Lanes 1 and 27 are 100-bp markers; lanes 2 to 7, strains; lanes 8 to 15, lanes 16 to 19, subsp. ; lanes 20 to 25, subsp. Lanes 9 to 11 and 21 to 22 represent well-characterized outbreak strains and are indistinguishable (E. Podivinsky, K. Thom, and S. L. W. On, unpublished data).

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10
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Image of Figure 3.
Figure 3.

Prediction of origin by using only alleles for which substantial reference information is available. Light lines indicate alleles different from ST-21 present mainly in chickens in the reference population (i.e., an allele that would predict chicken origin); dark lines indicate alleles present mainly in bovids (i.e., predicts bovid origin). Light boxes indicate STs found only in chickens, dark boxes indicate STs found only in bovids, and boxes with light and dark shading indicate STs found in bovids and chickens. Figure from .

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10
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Image of Figure 4.
Figure 4.

Dendrogram of STs. Allele sequences from each of the 66 STs were concatenated in the order ------ and aligned by ClustalX. The dendrogram was constructed by the neighbor-joining algorithm and the Kimura two-parameter distance estimation method. Bootstrap values of >75%, generated from 500 replicates, are shown at the nodes. The scale bar represents substitutions per site. Numeric labels represent STs. Geographic source of the strains was, where indicated: South Africa (solid circles), Belgium (open triangles), United States (crosses), or United Kingdom, France, and Sweden (solid triangles). STs representing strains are boxed in gray.

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10
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Table 1.

Summary of outbreaks in which the source of infection was definitively identified by use of genotyping

Citation: On S, McCarthy N, Miller W, Gilpin B. 2008. Molecular Epidemiology of Species, p 191-211. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch10

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