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Comparative Microbial Genomics and Forensics

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  • Author: Steven E. Massey1
  • Editors: Raúl J. Cano2, Gary A. Toranzos3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Biology Department, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; 2: California Polytechnic State University, San Luis Obispo, CA; 3: University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico
  • Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
  • Received 09 October 2013 Accepted 28 August 2014 Published 05 August 2016
  • Steven E. Massey, stevenemassey@gmail.com
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  • Abstract:

    Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

  • Citation: Massey S. 2016. Comparative Microbial Genomics and Forensics. Microbiol Spectrum 4(4):EMF-0001-2013. doi:10.1128/microbiolspec.EMF-0001-2013.

Key Concept Ranking

Simian immunodeficiency virus
0.5226997
West nile virus
0.49709752
Foot-and-mouth disease virus
0.4851125
0.5226997

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2016-08-05
2017-09-22

Abstract:

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

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Image of FIGURE 1a
FIGURE 1a

Metagenomic fingerprints and their applications. Example of a microbial meta-metabolomic network generated from human skin. Meta-metabolomic networks represent a novel way of interpreting metagenomic data, and certain microhabitats may have characteristic “fingerprints” reflected in the metabolism of the microbial community, irrespective of the particular taxonomic composition. Thus, such a profile can in principle reveal the origin of the sample, using biochemical considerations and comparison with reference datasets. The methodology for construction of the network was as follows. DNA was isolated from microbes isolated from the left retroauricular crease (behind the ear). This was then subjected to shotgun sequencing using the Illumina platform. The sequences were downloaded from the Human Microbiome Project webpage (http://www.hmpdacc.org/HMASM/; identification number SRS ID SRS013258). These were then used to query the NCBI nonredundant database using BLAST. Significant hits were mapped to KEGG K numbers ( 98 ), representing the respective biochemical reaction that each protein is involved in, and then superimposed onto a network of central metabolism using iPath2.0 ( 99 ).

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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Image of FIGURE 1b
FIGURE 1b

Metagenomic fingerprints and their applications. Comparative metagenomics of soil microbial communities. A comparative metagenomics analysis of bacterial communities present in different soil types is shown. Community profiles were generated from each sample using NGS of 16S rRNA PCR products generated from environmental DNA extracted from each habitat. Then, the different profiles were compared using principal-component analysis. Bacterial communities present in soil obtained from hot deserts, cold deserts, and forests cluster separately. Reproduced from reference 100 .

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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FIGURE 2a

Plotting the phylogenetics of an infectious outbreak. Phylogenetic network of strain O104:H4 and related genomes. A minimum spanning tree of strain O104:H4 was created using allelic profiles of the core genome, which contains 1,144 genes. Each node represents a complete genome; numbers on the lines connecting nodes represent numbers of alleles that differ between genomes. Different colors represent different pathovars (enterohemorrhagic [EHEC], enteroaggregative [EAEC], extraintestinal pathogenic [ExPEC], enteropathogenic [EPEC], enterotoxigenic [ETEC], and commensals). A hypothetical O104:H4 progenitor (green) was created by ancestral sequence reconstruction. Reproduced from reference 101 .

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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FIGURE 2b

Plotting the phylogenetics of an infectious outbreak. Phylogenetic tree of HIV gp120 using sequences from the criminal case ( 102 ). Six case individuals were included in the analysis, WA01 to WA06. WA04 (red) sequences were obtained from the defendant; WA01 to WA03, WA05, and WA06 were from the other case individuals, and black indicates outgroup sequences obtained from the GenBank database. Color gradients represent events of transmission from WA04 to other individuals. The red circle represents the most recent common ancestor of the WA04 sequences. Branch numbers represent statistical support (Bayesian posterior probability/maximum likelihood bootstrap proportion). Values of <0.5 are indicated by a dash or are not shown.

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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FIGURE 3

Genome of strain O104:H4. The nine circles show different strains of O104:H4, 559589 being the original isolate. Annotations on the outside of the circles show positions of transposons, while three plasmids, pTY1 to pTY3, are also included. pTY2 is an aggregative plasmid carrying a fimbria gene that is responsible for the enteroaggregative phenotype of the strain and has been linked to virulence. In green is a variable region, also associated with pathogenicity. Reproduced from reference 103 .

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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FIGURE 4a

Pandemics of the past: the Black Death and Spanish flu. Two microbial genomes of pathogens involved in severe historical pandemics have been recovered and sequenced. These are of the bacterial strain that caused the Black Death and the influenza virus strain that caused the Spanish flu. The severe effects of these epidemics are illustrated by these photos. () Plague pit from medieval Venice (photo reproduced with kind permission of Michel Drancourt, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Université de la Méditerranée, Marseille, France). Bodies were unceremoniously thrown into the pit, indicating the severity with which the epidemic struck the community. PCR was used to amplify sequences from ancient DNA obtained from the pit ( 68 ).

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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Image of FIGURE 4b
FIGURE 4b

Pandemics of the past: the Black Death and Spanish flu. Two microbial genomes of pathogens involved in severe historical pandemics have been recovered and sequenced. These are of the bacterial strain that caused the Black Death and the influenza virus strain that caused the Spanish flu. The severe effects of these epidemics are illustrated by these photos. Treatment center for victims of the Spanish flu in the main drill hall of the Naval Training Center, San Francisco, CA, 1918, showing the scale of the epidemic (U.S. Naval History and Heritage Command photograph).

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0001-2013
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