Genomics and microbiology. Microbial forensics--"cross-examining pathogens"

[Use of microbiological data for the purposes of forensic medical examination]

The study objective was to describe the formation of forensic microbiological examination as an analysis of a new type, defined as the detection and registration of reliably measured environmental and physiological changes within the microbial community of corpse in order to substantiate the possibility of using microbiological parameters to establish the prescription of death coming. It has been determined that the knowledge of the patterns of interaction of a human and his corpse with endogenous and exogenous flora provides the basis for solving a number of traditional and new application-oriented expert tasks and the allocation of such a variety of forensic examination as forensic microbiological examination. Endogenous and exogenous human flora and its interaction with living and dead biological tissues are the objects of this kind of examination, and the dynamic patterns of such interaction are the subject of study. One of the initial relevant tasks of forensic microbiological examination consists in development of methods, adequate for the expert task to be solved, choice of the research «target», «models» for comparative analysis and medium, adequate for task in hand, as well as certification of these methods and standardization of assessment criteria for the obtained results.

Microbial forensics: what we've learned from Amerithrax and beyond

The Amerithrax investigation into anthrax letter attacks in the USA forever changed the game in microbial forensics. Here we review the techniques used, then and now, to neutralize bioterrorism threats. [Formula: see text].

Forensic Microbiology in India: A missing piece in the puzzle of criminal investigation system

BACKGROUND

Forensic Microbiology is an emerging branch of science that has great potential to assist criminal investigations. Having said that, microbial analysis is not performed routinely during forensic investigations in India. This could be attributed to lack of specific training and lack of evidence-based standard protocol.

OBJECTIVES

The authors attempt to highlight the key areas in forensic microbiology that need to be explored in a developing nation like India.

CONTENT

Forensic microbiology could help in linking a person to a crime, determining the cause of death, estimating postmortem interval (PMI), etc. Additionally, applications are being developed by forensic microbiologists across the globe to investigate the coordinated and dynamic changes in microbial activity which occur after the death of a human host. Such evidence from the human postmortem microbiome can aid in criminal investigations and administration of justice. These recent advances and developments have the potential to transform the field of forensic microbiology in a developing country.

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.

Animal models of invasive mycoses

Animal models of invasive fungal infections have been developed and are applied in a huge number of different animal species for a number of research purposes, for example, the study of pathogenesis, defense mechanisms, and therapeutic strategies. From the different models, which in most cases are based on the same fungal species and often the same strain, as in spontaneous human infections, fundamental results and knowledge of the diagnosis, progression, prophylaxis, and therapy have been achieved. However, in all models, one should be critical with respect to mimicking the disease entity of humans, which is often the focus of the research. In many of the models for instance, the time course is different to the one of humans, and in others, the propensity for localization and containment in specific organs does not parallel the situation in humans. Nevertheless, many animal models of invasive mycoses have proven valuable in a number of research areas. With regard to new generations of anti-mycotic drugs, the models play an essential role in demonstrating antifungal activity, as well as in demonstrating the absence of toxic side effects, a critical step which cannot be accomplished by in vitro studies.

A machine learning toolkit for genetic engineering attribution to facilitate biosecurity

The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed 'genetic engineering attribution', would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype data can reach 70% attribution accuracy in distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.

Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger

IMPORTANCE

Young febrile infants are at substantial risk of serious bacterial infections; however, the current culture-based diagnosis has limitations. Analysis of host expression patterns ("RNA biosignatures") in response to infections may provide an alternative diagnostic approach.

OBJECTIVE

To assess whether RNA biosignatures can distinguish febrile infants aged 60 days or younger with and without serious bacterial infections.

DESIGN, SETTING, AND PARTICIPANTS

Prospective observational study involving a convenience sample of febrile infants 60 days or younger evaluated for fever (temperature >38° C) in 22 emergency departments from December 2008 to December 2010 who underwent laboratory evaluations including blood cultures. A random sample of infants with and without bacterial infections was selected for RNA biosignature analysis. Afebrile healthy infants served as controls. Blood samples were collected for cultures and RNA biosignatures. Bioinformatics tools were applied to define RNA biosignatures to classify febrile infants by infection type.

EXPOSURE

RNA biosignatures compared with cultures for discriminating febrile infants with and without bacterial infections and infants with bacteremia from those without bacterial infections.

MAIN OUTCOMES AND MEASURES

Bacterial infection confirmed by culture. Performance of RNA biosignatures was compared with routine laboratory screening tests and Yale Observation Scale (YOS) scores.

RESULTS

Of 1883 febrile infants (median age, 37 days; 55.7% boys), RNA biosignatures were measured in 279 randomly selected infants (89 with bacterial infections-including 32 with bacteremia and 15 with urinary tract infections-and 190 without bacterial infections), and 19 afebrile healthy infants. Sixty-six classifier genes were identified that distinguished infants with and without bacterial infections in the test set with 87% (95% CI, 73%-95%) sensitivity and 89% (95% CI, 81%-93%) specificity. Ten classifier genes distinguished infants with bacteremia from those without bacterial infections in the test set with 94% (95% CI, 70%-100%) sensitivity and 95% (95% CI, 88%-98%) specificity. The incremental C statistic for the RNA biosignatures over the YOS score was 0.37 (95% CI, 0.30-0.43).

CONCLUSIONS AND RELEVANCE

In this preliminary study, RNA biosignatures were defined to distinguish febrile infants aged 60 days or younger with vs without bacterial infections. Further research with larger populations is needed to refine and validate the estimates of test accuracy and to assess the clinical utility of RNA biosignatures in practice.

Detecting specific infections in children through host responses: a paradigm shift

PURPOSE OF REVIEW

There is a need for improved diagnosis and for optimal classification of patients with infectious diseases. An alternative approach to the pathogen-detection strategy is based on a comprehensive analysis of the host response to the infection. This review focuses on the value of transcriptome analyses of blood leukocytes for the diagnosis and management of patients with infectious diseases.

RECENT FINDINGS

Initial studies showed that RNA from blood leukocytes of children with acute viral and bacterial infections carried pathogen-specific transcriptional signatures. Subsequently, transcriptional signatures for several other infections have been described and validated in humans with malaria, dengue, salmonella, melioidosis, respiratory syncytial virus, influenza, tuberculosis, and HIV. In addition, transcriptome analyses represent an invaluable tool to understand disease pathogenesis and to objectively classify patients according to the clinical severity.

SUMMARY

Microarray studies have been shown to be highly reproducible using different platforms, and in different patient populations, confirming the value of blood transcriptome analyses to study pathogen-specific host immune responses in the clinical setting. Combining the detection of the pathogen with a comprehensive assessment of the host immune response will provide a new understanding of the correlations between specific causative agents, the host response, and the clinical manifestations of the disease.

RNA transcriptional biosignature analysis for identifying febrile infants with serious bacterial infections in the emergency department: a feasibility study

OBJECTIVES

To develop the infrastructure and demonstrate the feasibility of conducting microarray-based RNA transcriptional profile analyses for the diagnosis of serious bacterial infections in febrile infants 60 days and younger in a multicenter pediatric emergency research network.

METHODS

We designed a prospective multicenter cohort study with the aim of enrolling more than 4000 febrile infants 60 days and younger. To ensure success of conducting complex genomic studies in emergency department (ED) settings, we established an infrastructure within the Pediatric Emergency Care Applied Research Network, including 21 sites, to evaluate RNA transcriptional profiles in young febrile infants. We developed a comprehensive manual of operations and trained site investigators to obtain and process blood samples for RNA extraction and genomic analyses. We created standard operating procedures for blood sample collection, processing, storage, shipping, and analyses. We planned to prospectively identify, enroll, and collect 1 mL blood samples for genomic analyses from eligible patients to identify logistical issues with study procedures. Finally, we planned to batch blood samples and determined RNA quantity and quality at the central microarray laboratory and organized data analysis with the Pediatric Emergency Care Applied Research Network data coordinating center. Below we report on establishment of the infrastructure and the feasibility success in the first year based on the enrollment of a limited number of patients.

RESULTS

We successfully established the infrastructure at 21 EDs. Over the first 5 months we enrolled 79% (74 of 94) of eligible febrile infants. We were able to obtain and ship 1 mL of blood from 74% (55 of 74) of enrolled participants, with at least 1 sample per participating ED. The 55 samples were shipped and evaluated at the microarray laboratory, and 95% (52 of 55) of blood samples were of adequate quality and contained sufficient RNA for expression analysis.

CONCLUSIONS

It is possible to create a robust infrastructure to conduct genomic studies in young febrile infants in the context of a multicenter pediatric ED research setting. The sufficient quantity and high quality of RNA obtained suggests that whole blood transcriptional profile analysis for the diagnostic evaluation of young febrile infants can be successfully performed in this setting.

Microbial Forensics☆

Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.

Genetic diversity of Bacillus anthracis in Europe: genotyping methods in forensic and epidemiologic investigations

Bacillus anthracis, the etiological agent of anthrax, a zoonosis relatively common throughout the world, can be used as an agent of bioterrorism. In naturally occurring outbreaks and in criminal release of this pathogen, a fast and accurate diagnosis is crucial to an effective response. Microbiological forensics and epidemiologic investigations increasingly rely on molecular markers, such as polymorphisms in DNA sequence, to obtain reliable information regarding the identification or source of a suspicious strain. Over the past decade, significant research efforts have been undertaken to develop genotyping methods with increased power to differentiate B. anthracis strains. A growing number of DNA signatures have been identified and used to survey B. anthracis diversity in nature, leading to rapid advances in our understanding of the global population of this pathogen. This article provides an overview of the different phylogenetic subgroups distributed across the world, with a particular focus on Europe. Updated information on the anthrax situation in Europe is reported. A brief description of some of the work in progress in the work package 5.1 of the AniBioThreat project is also presented, including (1) the development of a robust typing tool based on a suspension array technology and multiplexed single nucleotide polymorphisms scoring and (2) the typing of a collection of DNA from European isolates exchanged between the partners of the project. The know-how acquired will contribute to improving the EU's ability to react rapidly when the identity and real origin of a strain need to be established.

Transcriptional profiling in infectious diseases: ready for prime time?

Blood represents a reservoir and a migration compartment of cells of the immune system. Traditional microbiologic diagnostic tests relied on laboratory identification of the pathogen causing the infection. However, this approach is less than optimal for a variety of reasons: pathogen's slow growth, resistance to cultivation in vitro or insufficient proof to establish causality when a pathogen is identified. An alternative approach to the pathogen-detection strategy is based on a comprehensive analysis of the host response to the infection by analysis of blood leukocytes gene expression profiles. This strategy has been successfully applied to distinguish and classify children and adults with acute infections caused by different pathogens. Molecular distance to health (MDTH) is a genomic score that measures the global transcriptional perturbation in each individual patient compared to healthy controls. Studies indicate that MDTH is a promising biomarker to help classifying patients according to clinical severity.

Combining field epidemiological information and genetic data to comprehensively reconstruct the invasion history and the microevolution of the sudden oak death agent Phytophthora ramorum (Stramenopila: Oomycetes) in California

Understanding the migration patterns of invasive organisms is of paramount importance to predict and prevent their further spread. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: (1) incomplete sampling; (2) the inability to include infestations caused by a single genotype of the pathogen; (3) collapsing of non-spatially contiguous yet genetically similar samples into large meta-samples that confounded the coalescent analyses. Here, we employ an intensive sampling coverage of 832 isolates of Phytopthora ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci, to reconstruct its invasion. By using age of infestation as a constraint on coalescent analyses, by dividing genetically indistinguishable meta-populations into highly-resolved sets of spatially contiguous populations, and by using Bruvo genetic distances for most analyses, we reconstruct the entire history of the epidemic and convincingly show infected nursery plants are the original source for the entire California epidemic. Results indicate that multiple human-mediated introductions occurred in most counties and that further disease sources were represented by large wild infestations. The study also identifies minor introductions, some of them relatively recent, linked to infected ornamental plants. Finally, using archival isolates collected soon after the discovery of the pathogen in California, we corroborate that the epidemic is likely to have resulted form 3 to 4 core founder individuals evolved from a single genotype. This is probably the most complete reconstruction ever completed for an invasion by an exotic forest pathogen, and the approach here described may be useful for the reconstruction of invasions by any clonally reproducing organism with a relatively limited natural dispersal range.

Map-invariant spectral analysis for the identification of DNA periodicities

Many signal processing based methods for finding hidden periodicities in DNA sequences have primarily focused on assigning numerical values to the symbolic DNA sequence and then applying spectral analysis tools such as the short-time discrete Fourier transform (ST-DFT) to locate these repeats. The key results pertaining to this approach are however obtained using a very specific symbolic to numerical map, namely the so-called Voss representation. An important research problem is to therefore quantify the sensitivity of these results to the choice of the symbolic to numerical map. In this article, a novel algebraic approach to the periodicity detection problem is presented and provides a natural framework for studying the role of the symbolic to numerical map in finding these repeats. More specifically, we derive a new matrix-based expression of the DNA spectrum that comprises most of the widely used mappings in the literature as special cases, shows that the DNA spectrum is in fact invariable under all these mappings, and generates a necessary and sufficient condition for the invariance of the DNA spectrum to the symbolic to numerical map. Furthermore, the new algebraic framework decomposes the periodicity detection problem into several fundamental building blocks that are totally independent of each other. Sophisticated digital filters and/or alternate fast data transforms such as the discrete cosine and sine transforms can therefore be always incorporated in the periodicity detection scheme regardless of the choice of the symbolic to numerical map. Although the newly proposed framework is matrix based, identification of these periodicities can be achieved at a low computational cost.

Next-generation sequencing technologies and applications for human genetic history and forensics

Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics.

Nephele: genotyping via complete composition vectors and MapReduce

BACKGROUND

Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences.

RESULTS

Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.

CONCLUSIONS

We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.

PCR-free digital minisatellite tandem repeat genotyping

We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

A new approach to in silico SNP detection and some new SNPs in the Bacillus anthracis genome

Background

Bacillus anthracis is one of the most monomorphic pathogens known. Identification of polymorphisms in its genome is essential for taxonomic classification, for determination of recent evolutionary changes, and for evaluation of pathogenic potency.

Findings

In this work three strains of the Bacillus anthracis genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed. Moreover, it is shown that, despite the highly monomorphic nature of Bacillus anthracis, the SNPs are (1) abundant in the genome and (2) distributed relatively uniformly across the sequence.

Conclusions

The findings support the proposition that SNPs, together with indels and variable number tandem repeats (VNTRs), can be used effectively not only for the differentiation of perfect strain data, but also for the comparison of moderately incomplete, noisy and, in some cases, unknown Bacillus anthracis strains. In the case when the data is of still lower quality, a new DNA sequence fingerprinting approach based on recently introduced markers, based on combinatorial-analytic concepts and called cyclic difference sets, can be used.

Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing

Background

In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiD™) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization.

Results

To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination events. Most private SNPs (that is, a, variant found in only one strain in this set) selected for validation by Sanger sequencing were confirmed, although rare false-positive SNPs were associated with variable nucleotide tandem repeats.

Conclusions

The high-throughput, multiplexing capability, and accuracy of this system make it suitable for rapid whole-genome typing of microbial pathogens during a forensic or epidemiological investigation. By interrogating nearly every base of the genome, rare polymorphisms can be reliably discovered, thus facilitating high-resolution strain tracking and strengthening forensic attribution.

Human genomics and preparedness for infectious threats

Public health preparedness requires effective surveillance of and rapid response to infectious disease outbreaks. Inclusion of research activities within the outbreak setting provides important opportunities to maximize limited resources, to enhance gains in scientific knowledge, and ultimately to increase levels of preparedness. With rapid advances in laboratory technologies, banking and analysis of human genomic specimens can be conducted as part of public health investigations, enabling valuable research well into the future.

Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries

Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. Phytophthora ramorum is the exotic pathogen, discovered in the late 1990s, that is responsible for sudden oak death in California forests and ramorum blight of common ornamentals. The nursery trade has moved this pathogen from source populations on the West Coast to locations across the United States, thus risking introduction to other native forests. We examined the genetic diversity of P. ramorum in United States nurseries by microsatellite genotyping 279 isolates collected from 19 states between 2004 and 2007. Of the three known P. ramorum clonal lineages, the most common and genetically diverse lineage in the sample was NA1. Two eastward migration pathways were revealed in the clustering of NA1 isolates into two groups, one containing isolates from Connecticut, Oregon, and Washington and the other isolates from California and the remaining states. This finding is consistent with trace forward analyses conducted by the US Department of Agriculture's Animal and Plant Health Inspection Service. At the same time, genetic diversities in several states equaled those observed in California, Oregon, and Washington and two-thirds of multilocus genotypes exhibited limited geographic distributions, indicating that mutation was common during or subsequent to migration. Together, these data suggest that migration, rapid mutation, and genetic drift all play a role in structuring the genetic diversity of P. ramorum in US nurseries. This work demonstrates that fast-evolving genetic markers can be used to examine the evolutionary processes acting on recently introduced pathogens and to infer their putative migration patterns, thus showing promise for the application of forensics to plant pathogens.

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing

Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected approximately 98% of differences (including large insertion-deletions) between pairs of strains from three species while calling no false positives. VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives.

Animal models: an important tool in mycology

Animal models of fungal infections are, and will remain, a key tool in the advancement of the medical mycology. Many different types of animal models of fungal infection have been developed, with murine models the most frequently used, for studies of pathogenesis, virulence, immunology, diagnosis, and therapy. The ability to control numerous variables in performing the model allows us to mimic human disease states and quantitatively monitor the course of the disease. However, no single model can answer all questions and different animal species or different routes of infection can show somewhat different results. Thus, the choice of which animal model to use must be made carefully, addressing issues of the type of human disease to mimic, the parameters to follow and collection of the appropriate data to answer those questions being asked. This review addresses a variety of uses for animal models in medical mycology. It focuses on the most clinically important diseases affecting humans and cites various examples of the different types of studies that have been performed. Overall, animal models of fungal infection will continue to be valuable tools in addressing questions concerning fungal infections and contribute to our deeper understanding of how these infections occur, progress and can be controlled and eliminated.

Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem

MOTIVATION

One of the main tasks of DNA sequence analysis is identification of repetitive patterns. DNA symbol repetitions play a key role in a number of applications, including prediction of gene and exon locations, identification of diseases, reconstruction of human evolutionary history and DNA forensics.

RESULTS

A new approach towards identification of tandem repeats in DNA sequences is proposed. The approach is a refinement of previously considered method, based on the complex periodicity transform. The refinement is obtained, among others, by mapping of DNA symbols to pure quaternions. This mapping results in an enhanced, symbol-balanced sensitivity of the transform to DNA patterns, and an unambiguous threshold selection criterion. Computational efficiency of the transform is further improved, and coupling of the computation with the period value is removed, thereby facilitating parallel implementation of the algorithm. Additionally, a post-processing stage is inserted into the algorithm, enabling unambiguous display of results in a convenient graphical format. Comparison of the quaternionic periodicity transform with two well-known pattern detection techniques shows that the new approach is competitive with these two techniques in detection of exact and approximate repeats.

Plant pathogen forensics: capabilities, needs, and recommendations

A biological attack on U.S. crops, rangelands, or forests could reduce yield and quality, erode consumer confidence, affect economic health and the environment, and possibly impact human nutrition and international relations. Preparedness for a crop bioterror event requires a strong national security plan that includes steps for microbial forensics and criminal attribution. However, U.S. crop producers, consultants, and agricultural scientists have traditionally focused primarily on strategies for prevention and management of diseases introduced naturally or unintentionally rather than on responding appropriately to an intentional pathogen introduction. We assess currently available information, technologies, and resources that were developed originally to ensure plant health but also could be utilized for postintroduction plant pathogen forensics. Recommendations for prioritization of efforts and resource expenditures needed to enhance our plant pathogen forensics capabilities are presented.

The impact of comparative genomics on infectious disease research

The past decade has witnessed a revolution in infectious disease research, fuelled by the accumulation of a huge amount of DNA sequence data. The avalanche of genome sequence information has largely promoted the development of comparative genomics, which exploits available genome sequences to perform either inter- or intra-species comparisons of bacterial genome contents, or performs comparisons between the human genome and those of other organisms. This review aims to summarize how comparative genomics is being extensively used in infectious disease research, such as in the studies to identify virulence determinants, antimicrobial drug targets, vaccine candidates and new markers for diagnostics. These applications hold considerable promise for alleviating the burden of infectious diseases in the coming years.

Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays

Background

Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation.

Results

A method and SPR Opt (SNP and PCR-RFLP Optimization) software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed) are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes.

Conclusion

This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As more sequence data becomes available for multiple strains and isolates of a species, automated, computational approaches such as those described here will be essential to make sense of large amounts of information, and to guide and optimize efforts in the laboratory. The software and source code for SPR Opt is publicly available and free for non-profit use at .

Modeling of SEB-induced host gene expression to correlate in vitro to in vivo responses

Detection of exposure to biological threat agents has relied on ever more sensitive methods for pathogen identification, but that usually requires pathogen proliferation to dangerous, near untreatable levels. Recent events have demonstrated that assessing exposure to a biological threat agent well in advance of onset of illness or at various stages post-exposure is invaluable among the diagnostic options. There is an urgent need for better diagnostic tools that will be sensitive, rapid, and unambiguous. Since human clinical cases of illness induced by biothreat agents are, fortunately, rare, use of animal models that closely mimic the human illness is the only in vivo option. Such studies can be very difficult and expensive; therefore, maximizing the information obtained from in vitro exposures to peripheral blood mononuclear cells (PBMCs) provide an opportunity to investigate dose/time variability in host responses. In our quest to study staphylococcal enterotoxin B (SEB) induced host gene expression patterns, we addressed two core issues using microarray analysis and predictive modeling. Our first objective was to determine gene expression patterns in human PBMCs exposed to SEB in vitro. Second, we compared the in vitro data with host responses gene expression patterns in vivo using PBMCs from an animal model of SEB intoxication that closely replicates the progression of illness in humans. We used cDNA microarrays to study global gene expression patterns in piglets intoxicated with SEB. We applied a supervised learning method for class prediction based on the k-nearest neighbor algorithm for the data obtained in piglets exposed to SEB in vivo against a training data set. This data set included gene expression profiles derived from in vitro exposures to eight different pathogens (Bacillus anthracis, Yersinia pestis, Brucella melitensis, SEB, cholera toxin, Clostridium botulinum toxin A, Venezuelan equine encephalitis, and Dengue-2) in PBMCs. We found that despite differences in gene expression profiles between in vitro and in vivo systems, there exists a subset of genes that show correlations between in vitro and in vivo exposures, which can be used as a predictor of exposure to SEB in vivo.

Microbial forensics: the next forensic challenge

Pathogens and toxins can be converted to bioweapons and used to commit bioterrorism and biocrime. Because of the potential and relative ease of an attack using a bioweapon, forensic science needs to be prepared to assist in the investigation to bring perpetrators to justice and to deter future attacks. A new subfield of forensics--microbial forensics--has been created, which is focused on characterization of evidence from a bioterrorism act, biocrime, hoax, or an inadvertent release. Forensic microbiological investigations are essentially the same as any other forensic investigation regarding processing. They involve crime scene(s) investigation, chain of custody practices, evidence collection, handling and preservation, evidence shipping, analysis of evidence, interpretation of results, and court presentation. In addition to collecting and analyzing traditional forensic evidence, the forensic investigation will attempt to determine the etiology and identity of the causal agent, often in a similar fashion as in an epidemiologic investigation. However, for attribution, higher-resolution characterization is needed. The tools for attribution include genetic- and nongenetic-based assays and informatics to attempt to determine the unique source of a sample or at least eliminate some sources. In addition, chemical and physical assays may help determine the process used to prepare, store, or disseminate the bioweapon. An effective microbial forensics program will require development and/or validation of all aspects of the forensic investigative process, from sample collection to interpretation of results. Quality assurance (QA) and QC practices, comparable to those used by the forensic DNA science community, are being implemented. Lastly, partnerships with other laboratories will be requisite, because many of the necessary capabilities for analysis will not reside in the traditional forensic laboratory.

Microarray-based resequencing of multiple Bacillus anthracis isolates

Custom-designed resequencing arrays were used to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication and by comparison to independently generated shotgun sequence

We used custom-designed resequencing arrays to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication (discrepancy rate of 7.4 × 10^-7) and by comparison to independently generated shotgun sequence (discrepancy rate < 2.5 × 10^-6). Population genomics studies of microbial pathogens using rapid resequencing technologies such as resequencing arrays are critical for recognizing newly emerging or genetically engineered strains.

Genetics and attribution issues that confront the microbial forensics field

The commission of an act of bioterrorism or biocrime is a real concern for law enforcement and society. Efforts are underway to develop a strong microbial forensic program to assist in identifying perpetrators of acts of bioterrorism and biocrimes, as well as serve as a deterrent for those who might commit such illicit acts. Genetic analyses of microbial organisms will likely be a powerful tool for attribution of criminal acts. There are some similarities to forensic human DNA analysis practices, such as: molecular biology technology, use of population databases, qualitative conclusions of test results, and the application of QA/QC practices. Differences include: database size and composition, statistical interpretation methods, and confidence/uncertainty in the outcome of an interpretation.

Development of rationally designed nucleic acid signatures for microbial pathogens

The detection and identification of microbial pathogens are critical challenges in clinical medicine and public health surveillance. Advances in genome analysis technology are providing an unprecedented amount of information about bacterial and viral organisms, and hold great potential for pathogen detection and identification. In this paper, a rational approach to the development and application of nucleic acid signatures is described based on phylogenetically informative sequence features, especially single nucleotide polymorphisms. The computational tools that are available to enable the development of the next generation of microbial molecular signatures for clinical diagnostics and infectious disease surveillance are reviewed and the impact on public health and national security will be discussed.

Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolates recovered from wild animal species

Mycobacterial isolates were obtained by radiometric culture from 33 different species of captive or free-ranging animals (n = 106) and environmental sources (n = 3) from six geographic zones within the United States. The identities of all 109 isolates were confirmed by using mycobactin J dependence and characterization of five well-defined molecular markers, including two integration loci of IS900 (loci L1 and L9), one Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis)-specific sequence (locus 251), and one M. avium subsp. avium-specific marker (IS1245), as well as hsp65 and IS1311 restriction endonuclease analyses. Seventy-six acid-fast isolates were identified as M. paratuberculosis, 15 were identified as belonging to the M. avium-M. intracellulare complex (but not M. paratuberculosis), and the remaining 18 were identified as mycobacteria outside the M. avium-M. intracellulare complex. Fingerprinting by multiplex PCR for IS900 integration loci clustered 67 of the 76 M. paratuberculosis strains into a single clade (designated clade A18) and had a Simpson's diversity index (D) of 0.53. In contrast, sequence-based characterization of a recently identified M. paratuberculosis short sequence repeat (SSR) region enabled the differentiation of the M. paratuberculosis isolates in clade A18 into seven distinct alleles (D = 0.75). The analysis revealed eight subtypes among the 33 species of animals, suggesting the interspecies transmission of specific strains. Taken together, the results of our analyses demonstrate that SSR analysis enables the genetic characterization of M. paratuberculosis isolates from different host species and provide evidence for the host specificity of some M. paratuberculosis strains as well as sharing of strains between wild and domesticated animal species.

Biotechnology: impact on biological warfare and biodefense

Advances in biological research likely will permit development of a new class of advanced biological warfare (ABW) agents engineered to elicit novel effects. In addition, biotechnology will have applications supporting ABW weaponization, dissemination, and delivery. Such new agents and delivery systems would provide a variety of new use options, expanding the BW paradigm. Although ABW agents will not replace threats posed by traditional biological agents such as Bacillus anthracis (anthrax) and Variola (smallpox), they will necessitate novel approaches to counterproliferation, detection, medical countermeasures, and attribution.

A genomics-based approach to biodefence preparedness

Since October 2001, the United States has greatly expanded its commitment to biodefence-related research, with $1.75 billion earmarked for this activity in fiscal year 2003.

The goals of this accelerated research and development effort are to understand better the biology of potential bioterror agents and to use this information in the development of new diagnostics, antibiotics and vaccines to protect the world's population against bioterrorism.

Genomics, proteomics and bioinformatics approaches are considered to be key enabling technologies in the development of these new products.

Genome sequence data for all of the principal human pathogens, including most of the potential bioterror agents on the Center for Disease Control and Prevention (CDC) category A–C lists, are available in public databases and provide a new foundation for follow-up studies.

Comparative genomics approaches, together with large-scale methods for studying gene function, such as DNA microarrays, are providing insights into the molecular basis and evolution of pathogenicity, diversity within closely related isolates of the same pathogen and the molecular determinants of host–pathogen interactions.

Genomics-based approaches have already proven to be of great use in the identification of new targets for antimicrobial compounds and in the identification of new vaccine candidates.

Comparative genomics is also providing important information on the natural variability between closely related isolates that is aiding in the development of the new field of microbial forensics.

The anthrax letter attacks in October 2001, followed by the SARS outbreak in early 2003, dramatically illustrated our vulnerability to both deliberate and natural outbreaks of infectious disease. The availability of pathogen genome sequences and high-throughput methods for studying the biology of both pathogens and their hosts have provided new insights into the mechanisms of pathogenesis and host defence. As infectious disease research expands to include major bioterror agents, genomics-based approaches will provide one of the cornerstones of efforts to develop more accurate diagnostics, new therapeutics and vaccines, and further capabilities for microbial forensics.

Two-dimensional DNA displays for comparisons of bacterial genomes

We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD) was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE) in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus) numerous small changes (i.e. small deletions and point mutations) unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH), was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals) represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA.

Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis

The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.

NotI passporting to identify species composition of complex microbial systems

We describe here a new method for large-scale scanning of microbial genomes on a quantitative and qualitative basis. To achieve this aim we propose to create NotI passports: databases containing NotI tags. We demonstrated that these tags comprising 19 bp of sequence information could be successfully generated using DNA isolated from intestinal or fecal samples. Such NotI passports allow the discrimination between closely related bacterial species and even strains. This procedure for generating restriction site tagged sequences (RSTS) is called passporting and can be adapted to any other rare cutting restriction enzyme. A comparison of 1312 tags from available sequenced Escherichia coli genomes, generated with the NotI, PmeI and SbfI restriction enzymes, revealed only 219 tags that were not unique. None of these tags matched human or rodent sequences. Therefore the approach allows analysis of complex microbial mixtures such as in human gut and identification with high accuracy of a particular bacterial strain on a quantitative and qualitative basis.