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Laboratory Methods in Molecular Epidemiology: Bacterial Infections *

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Author: Lee W. Riley1
  • Editor: Michael Sadowsky2
    Affiliations: 1: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720; 2: BioTechnology Institute, University of Minnesota, St. Paul, MN
  • Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018
  • Received 22 March 2018 Accepted 04 June 2018 Published 02 November 2018
  • Lee W. Riley, [email protected]
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  • Abstract:

    In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial “species” and “clones.” Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series.

    *This article is part of a curated collection.

  • Citation: Riley L. 2018. Laboratory Methods in Molecular Epidemiology: Bacterial Infections * . Microbiol Spectrum 6(6):AME-0004-2018. doi:10.1128/microbiolspec.AME-0004-2018.


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In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial “species” and “clones.” Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series.

*This article is part of a curated collection.

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Image of FIGURE 1

Repetitive element PCR (rep-PCR). The repeat double-stranded DNA sequences (light grey segments) are targeted as annealing sites for outwardly oriented complementary oligonucleotide primers, which amplify spaces located between these repeats (indicated as dark segments). Only one set of primers is needed to amplify the different segments, which generates amplicons of different sizes, shown at the end of each arrow, that can then be resolved by AGE for comparison of band patterns. (Illustrated by Paolo Harris Paz.) (Photo inset) AGE of band patterns generated by ERIC2 PCR analysis (a type of rep-PCR) of strains isolated from patients with community-acquired urinary tract infection. (Photo by Reina Yamaji.)

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018
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Image of FIGURE 2

Conventional gel electrophoresis (left) and pulsed-field gel electrophoresis (PFGE) (right). In conventional gel electrophoresis, negatively charged DNA fragments migrate in one direction towards the positively charged electrode. In PFGE, the electrical field is applied along a contour of a hexagonal array of electrodes powered to generate two alternating electric field vectors, which allows linear pieces of DNA to “snake through” the path of least resistance along its migration in the agarose gel matrix. This allows large DNA fragments to be resolved to generate band patterns. (Illustrated by Paolo Harris Paz.) (Photo inset) PFGE of extraintestinal pathogenic isolates. (Photo by Meena Ramchandani.)

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018
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Image of FIGURE 3

Multilocus sequence typing (MLST) of . A 400- to 600-bp region of housekeeping genes (, , , , , , and is amplified by PCR and the amplified products are sequenced. The sequences of the 7 loci are then concatenated, and all the concatenated sequences representing different genotypes are aligned to generate a tree, which can be used to depict strain relatedness. The analysis of similarity by comparison of concatenated sequence is called multilocus sequence analysis. The allele sequences can be uploaded onto an automated submission system (e.g., http://pubmlst.org/ or http://www.mlst.net/), which allows the database curators to provide an ST designation (ST number). Pairwise comparison of allele profiles can be performed by minimal spanning tree analysis using algorithms such as eBURST (http://eburst.mlst.net/default.asp). (Illustrated by Paolo Harris Paz.)

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018
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Phenotypic characterization of bacterial organisms

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018
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Genotyping tests used to conduct epidemiologic investigations of bacterial infections

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0004-2018

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