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Inglis TJJ. A systematic approach to microbial forensics. J Med Microbiol 2024; 73. [PMID: 38305344 DOI: 10.1099/jmm.0.001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The coronavirus disease 2019 pandemic accelerated developments in biotechnology that underpin infection science. These advances present an opportunity to refresh the microbial forensic toolkit. Integration of novel analytical techniques with established forensic methods will speed up acquisition of evidence and better support lines of enquiry. A critical part of any such investigation is demonstration of a robust causal relationship and attribution of responsibility for an incident. In the wider context of a formal investigation into agency, motivation and intent, the quick and efficient assembly of microbiological evidence sets the tone and tempo of the entire investigation. Integration of established and novel analytical techniques from infection science into a systematic approach to microbial forensics will therefore ensure that major perspectives are correctly used to frame and shape the evidence into a clear narrative, while recognizing that forensic hypothesis generation, testing and refinement comprise an iterative process. Development of multidisciplinary training exercises that use this approach will enable translation into practice and efficient implementation when the need arises.
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Affiliation(s)
- T J J Inglis
- Pathology and Laboratory Medicine, School of Medicine, University of Western Australia, Crawley, WA 6009, Australia
- PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA 6009, Australia
- Western Australian Country Health Service, Perth, WA 6000, Australia
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2
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Frégeau CJ, Laurin N. Processing biological samples from simulated radiological terrorist events using Rapid DNA instruments. Forensic Sci Int 2024; 354:111887. [PMID: 38007870 DOI: 10.1016/j.forsciint.2023.111887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
Two commercially available portable Rapid DNA instruments were evaluated for their ability to process 1 µL and 10 µL saliva samples deposited on metal and plastic surfaces and contaminated with surrogates of cesium (Cs)-137, strontium (Sr)-90 and cobalt (Co)-60; radioactive materials potentially released during a nuclear weapon accident or a radiological dispersal device detonation. A comparable success rate was noted for both Rapid DNA instruments when considering the number of complete and balanced DNA profiles, the number of profiles with a minimum of 10 autosomal STR loci (out of 23 [FlexPlex™ 27] or 21 [GlobalFiler™ Express]), and the possibility to search a national DNA database in Canada and the United States. Cobalt had an adverse impact on the quality of the megaplex short tandem repeat (STR) DNA profiles derived on each instrument for two of the three contamination levels tested in this study, i.e., 0.05 M and 0.1 M as reflected by a reduced number of detected alleles and decreased profile peak heights. Strontium exhibited some adverse effect on the Rapid DNA results when used at the highest contamination level (0.1 M) whereas cesium had none. No new artifacts were observed in the Rapid DNA profiles of samples spiked with the non-radiogenic surrogates. Importantly, in the context of a radiological/nuclear (RN) event, the ANDE™ 6C offers the possibility to dispose of all radioactive materials associated with contaminated samples quickly using a chip on which all steps of the Rapid DNA process are performed whereas the RapidHIT™ ID accumulates radioactive materials for many days before disposal. An individual handling 25 samples in a week (5 per day) on the RapidHIT™ ID at a 30.5 cm distance with a 5 min exposure to the radioactive source estimated at every run would exceed the 0.042 µSv/5 min limit with gamma dose rates for Cs at 0.13 mSv and for Co at 3.8 mSv. Beta dose rates calculated for the surrogate isotopes at the three concentrations tested were also above the recommended radiation exposure limit of 1 mSv/yr (0.042 µSv/5 min). Various potential mechanisms of action behind the interference noted for Sr and Co at high concentrations are presented. These elements may play a role in the steps prior to PCR (at the DNA molecule by binding to bases or to phosphate groups), during PCR (at the DNA polymerase as cofactors for catalytic sites), or even during amplified DNA fragment detection (as fluorescence quenchers).
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, National Forensic Laboratory Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
| | - Nancy Laurin
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Science & Strategic Policy, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada
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The Chain of Custody in the Era of Modern Forensics: From the Classic Procedures for Gathering Evidence to the New Challenges Related to Digital Data. Healthcare (Basel) 2023; 11:healthcare11050634. [PMID: 36900637 PMCID: PMC10000967 DOI: 10.3390/healthcare11050634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
The purpose of this work is to renew the interest and attention for the chain of custody in forensic medicine, its establishment and maintenance, protecting the integrity and validity of evidence as well as to analyze how over time the establishment of the chain of custody and the collection of evidence has evolved also in function of the advent of technology and the use of electronic devices connected to the network. The analysis of the various aspects of the chain of custody demonstrates how necessary it is for the professional figures involved in the phases of the investigation (especially those who manage the evidence and who have, therefore, designated the assignment) to know the procedures to follow, trace the movement and the handling of objects subjected to seizure, also for the purposes of toxicological and/or histological investigations. The knowledge of interferences or complications helps to reduce errors and safeguard the validity of the evidence, assuring the proceeding judicial authority that the evidence is authentic and that it is, in other words, the same evidence seized at the scene of the crime. Furthermore, the issue is particularly felt today, with the recent need to guarantee the originality of digital data. Following a careful review and analysis of the literature currently available in this regard, it is worth adding that further efforts are needed to formulate internationally validated guidelines, harmonizing the different reference criteria in forensic science and medical areas, given the current absence of good international practices valid in the field and applicable both in the case of physical evidence and in the case of seizure of digital evidence.
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Affiliation(s)
- David Gisselsson
- David Gisselsson, MD, PhD, is a Senior Consultant and Professor, Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Picciotti U, Lahbib N, Sefa V, Porcelli F, Garganese F. Aphrophoridae Role in Xylella fastidiosa subsp. pauca ST53 Invasion in Southern Italy. Pathogens 2021; 10:1035. [PMID: 34451499 PMCID: PMC8399165 DOI: 10.3390/pathogens10081035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/03/2022] Open
Abstract
The Philaenus spumarius L. (Hemiptera Aphrophoridae) is a xylem-sap feeder vector that acquires Xylella fastidiosa subsp. pauca ST53 during feeding on infected plants. The bacterium is the plant pathogen responsible for olive quick decline syndrome that has decimated olive trees in Southern Italy. Damage originates mainly from the insect vector attitude that multiplies the pathogen potentialities propagating Xf in time and space. The principal action to manage insect-borne pathogens and to contain the disease spread consists in vector and transmission control. The analysis of an innovative and sustainable integrated pest management quantitative strategy that targets the vector and the infection by combining chemical and physical control means demonstrates that it is possible to stop the Xylella invasion. This review updates the available topics addressing vectors' identification, bionomics, infection management, and induced disease by Xylella invasion to discuss major available tools to mitigate the damage consequent to the disease.
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Affiliation(s)
- Ugo Picciotti
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy; (U.P.); (N.L.); (V.S.); (F.G.)
- Department of Marine Science and Applied Biology, Laboratory of Plant Pathology, University of Alicante, 03080 Alicante, Spain
| | - Nada Lahbib
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy; (U.P.); (N.L.); (V.S.); (F.G.)
- Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis 1068, Tunisia
- INRAT—National Institute of Agronomic Research of Tunisia, Laboratory of Plant Protection, Rue Hédi Karray, Ariana 2049, Tunisia
| | - Valdete Sefa
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy; (U.P.); (N.L.); (V.S.); (F.G.)
| | - Francesco Porcelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy; (U.P.); (N.L.); (V.S.); (F.G.)
- CIHEAM—Centre International de Hautes Etudes Agronomiques Méditerranéennes, Mediterranean Agronomic Institute of Bari, 70010 Valenzano, BA, Italy
| | - Francesca Garganese
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy; (U.P.); (N.L.); (V.S.); (F.G.)
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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Oliveira M, Mason-Buck G, Ballard D, Branicki W, Amorim A. Biowarfare, bioterrorism and biocrime: A historical overview on microbial harmful applications. Forensic Sci Int 2020; 314:110366. [PMID: 32683271 PMCID: PMC7305902 DOI: 10.1016/j.forsciint.2020.110366] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022]
Abstract
Microbial Forensics is a field that continues to grow in interest and application among the forensic community. This review, divided into two sections, covers several topics associated with this new field. The first section presents a historic overview concerning the use of microorganisms (or its product, i.e. toxins) as harmful biological agents in the context of biological warfare (biowarfare), bioterrorism, and biocrime. Each case is illustrated with the examination of case reports that span from prehistory to the present day. The second part of the manuscript is devoted to the role of MF and highlights the necessity to prepare for the pressing threat of the harmful use of biological agents as weapons. Preventative actions, developments within the field to ensure a timely and effective response and are discussed herein.
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MESH Headings
- Bacterial Infections
- Biological Warfare/history
- Bioterrorism/history
- Crime/history
- Forensic Sciences
- HIV Infections
- High-Throughput Screening Assays
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Machine Learning
- Microbiological Techniques
- Toxins, Biological/adverse effects
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
| | | | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Dwibedi C, Larsson P, Ahlinder J, Lindgren P, Myrtennäs K, Granberg M, Larsson E, Öhrman C, Sjödin A, Stenberg P, Forsman M, Johansson A. Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis. Forensic Sci Int Genet 2020; 45:102230. [PMID: 31924594 DOI: 10.1016/j.fsigen.2019.102230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/22/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample. We used parallel serial passage experiments and high-throughput sequencing of F. tularensis to explore the genetic variation. We found that during early laboratory culture passages of F. tularensis, gene duplications emerged in the pathogen genome followed by single-nucleotide polymorphisms in genes for bacterial capsule synthesis. Based on a biological enrichment scheme and the use of high-throughput sequencing, we identified genetic variation that likely pre-existed in a source sample. The results support that capsule synthesis gene mutations are common during laboratory culture, and that a biological amplification strategy is useful for linking a F. tularensis sample to a specific laboratory variant among many highly similar variants.
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Affiliation(s)
- Chinmay Dwibedi
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 85 Umeå, Sweden; Swedish Defense Research Agency, Umeå, Sweden.
| | - Pär Larsson
- Swedish Defense Research Agency, Umeå, Sweden
| | | | | | | | | | - Eva Larsson
- Swedish Defense Research Agency, Umeå, Sweden
| | | | | | - Per Stenberg
- Swedish Defense Research Agency, Umeå, Sweden; Department of Ecology and Environmental Science (EMG), Umeå University, Umeå, Sweden
| | | | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 85 Umeå, Sweden
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case. Forensic Sci Int Genet 2019; 42:141-146. [PMID: 31319352 DOI: 10.1016/j.fsigen.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022]
Abstract
Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission episode in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods. We obtained genomes of Neisseria gonorrhoeae from the victim, the suspect, and 29 unrelated controls. The analysis of the genomes revealed that the victim and suspect isolates had identical sequences in both the bacterial chromosome and the single plasmid present in them. One of the local controls was very similar (differing in only 2 SNPs) to the case sequences, but the remaining controls were very divergent. Additional cases of identity and very high similarity among controls were observed occasionally, pointing at recent transmission cases. These results were more discriminative than the previous molecular epidemiology analyses performed at the hospital's Microbiology Service, as Multi-Locus Sequence Typing (MLST) could not distinguish between the suspect/victim and the controls isolates, and Pulse Field Gel Electrophoresis (PFGE) was not able to distinguish between the suspect/victim and one of the local controls. These results lead us to conclude that complete bacterial genome sequences obtained with HTS technologies may be a valuable tool for establishing recent transmission cases and, although more studies are needed, they have a great potential for being used in forensic analyses.
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Hosokawa-Muto J, Sakai H, Sassa Y, Fujinami Y, Kishimoto M, Nakahara H. Rapid detection of pathogenic virus genome sequence from throat and nasal swab samples using an exhaustive gene amplification method. Forensic Sci Med Pathol 2019; 15:399-403. [PMID: 31250258 DOI: 10.1007/s12024-019-00128-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 12/01/2022]
Abstract
Rapid identification of pathogenic agents is important in response to the emergence of biocrime and bioterrorism, to facilitate appropriate confinement and treatment. As the rapid determination system of viral genome sequences (RDV method) using exhaustive gene amplification is useful for rapid identification, we examined whether this method could be applied to forensic samples. To detect pathogenic virus in a cat with suspected viral infections, fluid swab samples were applied to the RDV method. The following steps were performed: viral propagation, extraction of the viral genome, amplification of the first library, fragmentation of the library, amplification of the second library using non-specific primer sets, and direct sequencing of the amplicon. To confirm the viruses detected by this method, we performed conventional PCR using virus-specific primers. We detected pathogenic virus genome sequences from the swab samples and confirmed infection with these viruses. In addition, we directly detected a viral genome sequence from the nasal swab sample without the viral propagation step. The RDV method is infrequently used in forensic analysis. This method is practicable with equipment existing in a normal laboratory and is useful for rapid detection and identification of pathogenic viruses in forensic samples. This method would also be applicable to the detection of bacteria and fungi.
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Affiliation(s)
- Junji Hosokawa-Muto
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
| | - Hiroki Sakai
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yukiko Sassa
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Yoshihito Fujinami
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Mai Kishimoto
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Hiroaki Nakahara
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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Retrieving forensic information about the donor through bacterial profiling. Int J Legal Med 2019; 134:21-29. [DOI: 10.1007/s00414-019-02069-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/15/2019] [Indexed: 02/06/2023]
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Future Technologies. Microbiol Spectr 2018. [PMID: 29521257 DOI: 10.1128/microbiolspec.emf-0015-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbiome analysis of environmental samples may represent the next frontier in environmental microbial forensics. Next-generation sequencing technologies significantly increased the available genetic data that could be used as evidentiary material. It is not clear, however, whether the microbiome can scale across institutions using forensic-based evidence due to the data resource requirements and the associated costs of maintaining these databases. A successful microbiome study is impacted by the quality of the information gathered and the steps in sample processing and data analysis. To ascertain the validity of methods and the results obtained, there needs to be a stringent procedure to validate the methods and ensure that the results are comparable and reproducible, not only within the laboratory but also between laboratories conducting similar research. Of primary importance for meaningful microbiome studies is an experimental design that leads to carefully executed, controlled, and reproducible studies. The microbiome literature contains a fair share of anecdotal descriptions of microbial community composition and "diagnostic" relative abundance of the taxa therein. These studies are now being supplemented by experimental designs that feature repeated measurements, error estimates, correlations of microbiota with covariates, and increasingly sophisticated statistical tests that enhance the robustness of data analysis and study conclusions. It is imperative to be careful, especially when carrying out attribution studies, to be fully aware of the possible biases included in a specific sample being analyzed.
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Abstract
Environmental forensics is a tool that uses chemical, physical, and statistical techniques to investigate contaminants in the environment as a means to determine attribution for legal purposes. Environmental microbiology is a branch of science that has benefited from the use of metagenomics. The term microbial forensics, which includes nucleic acid sequencing methods, is now used to investigate the sources of microorganisms for attribution purposes as well. Environmental microbial forensics can fully address the questions that must be answered for attribution of causation and subsequent remedial actions within a reasonably short time frame. Although sensu stricto forensics refers to obtaining scientific evidence to be presented during legal proceedings, the term sensu lato is used as a description of the procedures used to reconstruct previous events, such as contamination. The term microbial forensics was first used to describe a forensic science approach for attribution purposes, specifically for bioterror as a purposeful release of pathogen microorganisms, but it also especially refers to investigations on the inadvertent or accidental release of pathogenic agents. However, microbial forensics can be used to determine the source of a microorganism or a group of microorganisms, regardless of whether they are pathogenic or not. Microbial forensics has limitations, but it should be used as part of a toolbox of methods to be relied upon when doing forensic studies. Environmental microbial forensics can only benefit from the development of new methods, and we already are experiencing a paradigm change in terms of approaches to the forensic sciences.
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Frégeau CJ, Dalpé C. Simulated radioactive decontamination of biological samples using a portable DNA extraction instrument for rapid DNA profiling. Forensic Sci Int 2016; 259:161-78. [DOI: 10.1016/j.forsciint.2015.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 12/09/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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D'Amelio E, Gentile B, Lista F, D'Amelio R. Historical evolution of human anthrax from occupational disease to potentially global threat as bioweapon. ENVIRONMENT INTERNATIONAL 2015; 85:133-146. [PMID: 26386727 DOI: 10.1016/j.envint.2015.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
PURPOSE Anthrax is caused by Bacillus anthracis, which can naturally infect livestock, wildlife and occupationally exposed humans. However, for its resistance due to spore formation, ease of dissemination, persistence in the environment and high virulence, B. anthracis has been considered the most serious bioterrorism agent for a long time. During the last century anthrax evolved from limited natural disease to potentially global threat if used as bioweapon. Several factors may mitigate the consequences of an anthrax attack, including 1. the capability to promptly recognize and manage the illness and its public health consequences; 2. the limitation of secondary contamination risk through an appropriate decontamination; and 3. the evolution of genotyping methods (for microbes characterization at high resolution level) that can influence the course and/or focus of investigations, impacting the response of the government to an attack. METHODS A PubMed search has been done using the key words “bioterrorism anthrax”. RESULTS Over one thousand papers have been screened and the most significant examined to present a comprehensive literature review in order to discuss the current knowledge and strategies in preparedness for a possible deliberate release of B. anthracis spores and to indicate the most current and complete documents in which to deepen. CONCLUSIONS The comprehensive analysis of the two most relevant unnatural anthrax release events, Sverdlovsk in the former Soviet Union (1979) and the contaminated letters in the USA (2001), shows that inhalational anthrax may easily and cheaply be spread resulting in serious consequences. The damage caused by an anthrax attack can be limited if public health organization, first responders, researchers and investigators will be able to promptly manage anthrax cases and use new technologies for decontamination methods and in forensic microbiology.
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Affiliation(s)
| | - Bernardina Gentile
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Florigio Lista
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Raffaele D'Amelio
- Sapienza University of Rome, Department of Clinical and Molecular Medicine, S. Andrea University Hospital, Via di Grottarossa 1039, 00189 Rome, Italy.
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Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials. Appl Environ Microbiol 2015; 82:596-607. [PMID: 26567301 DOI: 10.1128/aem.02231-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
Effective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.
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Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics. J Forensic Leg Med 2015; 34:29-33. [PMID: 26165655 DOI: 10.1016/j.jflm.2015.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/05/2015] [Accepted: 04/30/2015] [Indexed: 11/20/2022]
Abstract
Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens.
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Fernández-Rodríguez A, Cohen MC, Lucena J, Van de Voorde W, Angelini A, Ziyade N, Saegeman V. How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation. Eur J Clin Microbiol Infect Dis 2015; 34:1045-57. [PMID: 25680317 DOI: 10.1007/s10096-015-2317-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/07/2015] [Indexed: 11/25/2022]
Abstract
Post-mortem microbiology (PMM) is an important tool in forensic pathology, helping to determine the cause and manner of death, especially in difficult scenarios such as sudden unexpected death (SD). Currently, there is a lack of standardization of PMM sampling throughout Europe. We present recommendations elaborated by a panel of European experts aimed to standardize microbiological sampling in the most frequent forensic and clinical post-mortem situations. A network of forensic microbiologists, pathologists and physicians from Spain, England, Belgium, Italy and Turkey shaped a flexible protocol providing minimal requirements for PMM sampling at four practical scenarios: SD, bioterrorism, tissue and cell transplantation (TCT) and paleomicrobiology. Biosafety recommendations were also included. SD was categorized into four subgroups according to the age of the deceased and circumstances at autopsy: (1) included SD in infancy and childhood (0-16 years); (2) corresponded to SD in the young (17-35 years); (3) comprised SD at any age with clinical symptoms; and (4) included traumatic/iatrogenic SD. For each subgroup, a minimum set of samples and general recommendations for microbiological analyses were established. Sampling recommendations for main bioterrorism scenarios were provided. In the TCT setting, the Belgian sampling protocol was presented as an example. Finally, regarding paleomicrobiology, the sampling selection for different types of human remains was reviewed. This proposal for standardization in the sampling constitutes the first step towards a consensus in PMM procedures. In addition, the protocol flexibility to adapt the sampling to the clinical scenario and specific forensic findings adds a cost-benefit value.
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Affiliation(s)
- A Fernández-Rodríguez
- Forensic Microbiology Laboratory, Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain,
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21
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Abstract
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.
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22
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Development of a candidate method for forensic microbial genotyping using multiplex pyrosequencing combined with a universal biotinylated primer. Forensic Sci Int 2014; 246:e1-6. [PMID: 25440080 DOI: 10.1016/j.forsciint.2014.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 10/23/2014] [Accepted: 11/08/2014] [Indexed: 11/22/2022]
Abstract
Bacterial genotyping can be used for crime scene investigations and contribute to the attribution of biological attacks for microbial forensics. PyroMark ID Pyrosequencer as an accurate detection platform for single nucleotide polymorphisms (SNPs) has been applied to identify and resolve microorganisms involved in closely Escherichia coli O157:H7 (E. coli O157:H7). To explore more applications and improve the efficiency for pyrosequencing in this field, we developed a method integrated multiplex pyrosequencing with a universal primer. Two multiplex pyrosequencing assays with a universal biotinylated primer were designed to analyze five SNPs located in four gene of E. coli O157:H7 strain. The accuracy of the established assays was validated by genotyping reference strain E. coli O157:H7 EDL933 and E. coli K-12. We also demonstrated that two multiplex pyrosequencing assays were specific and sensitive for genotyping closely related E. coli O157 strains. Reproducibility of results and multiplexing capability were evaluated by a comparison of this method with the monoplex pyrosequencing. Furthermore, these two multiplex pyrosequencing assays have been successfully applied to detect 11 E. coli O157 strains isolated from 1504 Chinese livestock samples. This method reduces costs and time consumption in the process of pyrosequencing analysis, and potentially serves as a rapid tool and reliable candidate strategy for the microbial identification and other genotyping application.
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23
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Designing an effective microbial forensics program for law enforcement and national security purposes. Arch Immunol Ther Exp (Warsz) 2014; 62:179-85. [PMID: 24781710 DOI: 10.1007/s00005-014-0289-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
Abstract
Forensic capabilities that provide lead information, and investigative, intelligence, prosecution and policy decision support can be invaluable for responding to and resolving bioterrorism events. Attributing biological attacks through scientific and other resources and processes is an important goal, for which science can be instrumental. Some even believe that having effective microbial forensics capabilities along with others can even deter adversaries from using biological weapons. For those nations that do not have such or wish to integrate or upgrade capabilities, thoughtful analysis and consideration of certain design principles will increase the likelihood that success will be attained.
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Nelson M, Roffey P, McNevin D, Lennard C, Gahan ME. An overview of biosecurity in Australia. AUST J FORENSIC SCI 2014. [DOI: 10.1080/00450618.2014.882986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Yan Y, Wang H, Li D, Yang X, Wang Z, Qi Z, Zhang Q, Cui B, Guo Z, Yu C, Wang J, Wang J, Liu G, Song Y, Li Y, Cui Y, Yang R. Two-step source tracing strategy of Yersinia pestis and its historical epidemiology in a specific region. PLoS One 2014; 9:e85374. [PMID: 24416399 PMCID: PMC3887043 DOI: 10.1371/journal.pone.0085374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/26/2013] [Indexed: 11/24/2022] Open
Abstract
Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by Y. pestis that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information.
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Affiliation(s)
- Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Hu Wang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | | | - Xianwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuyun Wang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Qingwen Zhang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Baizhong Cui
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Zhaobiao Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | | | | | - Guangming Liu
- School of Computer Science, National University of Defense Technology, Changsha, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (RY); (YC)
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (RY); (YC)
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Wunschel D, Tulman E, Engelmann H, Clowers BH, Geary S, Robinson A, Liao X. Forensic proteomics of poxvirus production. Analyst 2013; 138:6385-97. [PMID: 23979794 DOI: 10.1039/c3an00711a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of microbial forensics has recently sought to develop methods to discern biological signatures to indicate production methods for biological agents. Viral agents have received less attention to date. Their obligate propagation in living cells makes purification from cellular material a challenge. This leads to potential carryover of protein-rich signatures of their production system. Here we have explored a proteomic analysis of vaccinia virus as a model poxvirus system in which to compare samples of virus propagated in different cell lines and subjected to different purification schemes. The proteomic data sets indicated viral, host cell and culture medium proteins. Several layers of data analysis were applied to build confidence in the peptide identification and capture information on the taxonomic utility of each. The analysis showed clear shifts in protein profiles with virus purification, with successive gradient purification steps showing different levels of viral protein enrichment. Peptides from cellular proteins, including those present in purified virus preparations, provided signatures which enabled discrimination of cell line substrates, including distinguishing between cells derived from different primate species. The ability to discern multiple aspects of viral production demonstrates the potential value of proteomic analysis as tool for microbial forensics.
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Affiliation(s)
- David Wunschel
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA.
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27
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Assessment of viable bacteria and bacterial DNA in blood and bloodstain specimens stored under various conditions. J Forensic Leg Med 2013; 20:1035-40. [PMID: 24237815 DOI: 10.1016/j.jflm.2013.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 11/24/2022]
Abstract
Microbial forensic specimens that are collected at biocrime and bioterrorism scenes include blood, tissue, cloths containing biological fluids, swabs, water, soil, and aerosols. It is preferable that pathogens in such specimens are alive and kept in a steady state. Specimens may be stored for a prolonged period before analysis; therefore, it is important to understand the effect of the storage conditions on the pathogens contained within the specimens. In this study, we prepared blood and bloodstain specimens containing Gram-negative or -positive bacteria, stored the samples for 482 days under various conditions, and measured viable bacterial counts and total bacterial contents in the samples. Viable bacteria were preserved well in the samples stored at -30 and -80 °C, but were diminished or undetectable in the samples stored at 4 °C and room temperature. The total bacterial content was maintained in the blood samples stored at -30 and -80 °C and in the bloodstain samples stored under all temperature conditions, but decreased in the blood samples stored at 4 °C and room temperature. This study showed that the storage conditions affected viable bacteria and bacterial DNA and that freezing and drying were significant for their long-term storage. We provide important information for the storage of microbial forensic specimens.
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Sjödin A, Broman T, Melefors Ö, Andersson G, Rasmusson B, Knutsson R, Forsman M. The Need for High-Quality Whole-Genome Sequence Databases in Microbial Forensics. Biosecur Bioterror 2013; 11 Suppl 1:S78-86. [DOI: 10.1089/bsp.2013.0007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Multiplex-direct PCR assay for foodborne pathogen identification: An application in forensic investigation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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References. Parasitology 2012. [DOI: 10.1002/9781119968986.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Duarte A, Slutsky M, Hanrahan G, Mello CM, Bazan GC. Supramolecular Electrostatic Nanoassemblies for Bacterial Forensics. Chemistry 2011; 18:756-9. [DOI: 10.1002/chem.201103237] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Indexed: 11/06/2022]
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32
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Utility of multilocus variable number tandem repeat analysis as a microbial forensic tool for subtyping Chinese Escherichia coli O157:H7 strains. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Abstract
The threat posed by terrorism remains many years ahead. Bioterrorism remains a real threat, but because actual incidents remain at a low level, complacency is a constant enemy; hence the continuing background of false alarms may indeed be beneficial, encouraging responding agencies to keep practiced and alert. The Australian Federal Police (AFP) model of an integrated intelligence and forensic approach is a useful model for other nations of similar size or maturity to consider as a measured contribution to a whole of government approach to threats posed by bioterrorism. The Australian microbial forensic capability is reliant on the combined and coordinated efforts of numerous government facilities, departments, and agencies within law enforcement and public health at the state, territory, and commonwealth levels, as well as the private sector. It is a shining example of how a coordinated effort can provide a comprehensive capability that does well to protect the Australian community. The AFP and Australian Chemical, Biological, Radiological and Nuclear Data Center also work closely with international law enforcement partners in the United Kingdom, Canada, and the United States. The contribution of these and other international partners can be understated in the ongoing united effort to protect the citizens and assets of Australia and other countries against bioterrorism.
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Wahl KL, Colburn HA, Wunschel DS, Petersen CE, Jarman KH, Valentine NB. Residual agar determination in bacterial spores by electrospray ionization mass spectrometry. Anal Chem 2010; 82:1200-6. [PMID: 20073479 DOI: 10.1021/ac901491c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Presented here is an analytical method to detect residual agar from a bacterial spore sample as an indication of culturing on an agar plate. This method is based on the resolubilization of agar polysaccharide from a bacterial spore sample, enzymatic digestion, followed by electrospray ionization tandem mass spectrometry (ESI-MS(n)) analysis for detection of a specific agar fragment ion. A range of Bacillus species and strains were selected to demonstrate the effectiveness of this approach. The characteristic agar fragment ion was detected in the spores grown on agar that were washed from 1 to 5 times, irradiated or nonirradiated, and not in the spores grown in broth. A sample containing approximately 10(8) spores is currently needed for confident detection of residual agar from culture on agar plates in the presence of bacterial spores with a limit of detection of approximately 1 ppm agar spiked into a broth-grown spore sample. The results of a proficiency test with 42 blinded samples are presented demonstrating the utility of this method with no false positives and only three false negatives for samples that were below the detection level of the method as documented.
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Affiliation(s)
- Karen L Wahl
- Pacific Northwest National Laboratory, P.O. Box 999, MS P7-50, Richland, Washington 99352, USA.
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35
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Araujo R, Amorim A, Gusmão L. Microbial forensics: Do Aspergillus fumigatus strains present local or regional differentiation? FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Microbial DNA fingerprinting of human fingerprints: dynamic colonization of fingertip microflora challenges human host inferences for forensic purposes. Int J Legal Med 2009; 124:477-81. [PMID: 19551400 PMCID: PMC2955242 DOI: 10.1007/s00414-009-0352-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 05/12/2009] [Indexed: 01/30/2023]
Abstract
Human fingertip microflora is transferred to touched objects and may provide forensically relevant information on individual hosts, such as on geographic origins, if endogenous microbial skin species/strains would be retrievable from physical fingerprints and would carry geographically restricted DNA diversity. We tested the suitability of physical fingerprints for revealing human host information, with geographic inference as example, via microbial DNA fingerprinting. We showed that the transient exogenous fingertip microflora is frequently different from the resident endogenous bacteria of the same individuals. In only 54% of the experiments, the DNA analysis of the transient fingertip microflora allowed the detection of defined, but often not the major, elements of the resident microflora. Although we found microbial persistency in certain individuals, time-wise variation of transient and resident microflora within individuals was also observed when resampling fingerprints after 3 weeks. While microbial species differed considerably in their frequency spectrum between fingerprint samples from volunteers in Europe and southern Asia, there was no clear geographic distinction between Staphylococcus strains in a cluster analysis, although bacterial genotypes did not overlap between both continental regions. Our results, though limited in quantity, clearly demonstrate that the dynamic fingerprint microflora challenges human host inferences for forensic purposes including geographic ones. Overall, our results suggest that human fingerprint microflora is too dynamic to allow for forensic marker developments for retrieving human information.
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37
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Hari KL, Goates AT, Jain R, Towers A, Harpin VS, Robertson JM, Wilson MR, Samant VS, Ecker DJ, McNeil JA, Budowle B. The Microbial Rosetta Stone: a database system for tracking infectious microorganisms. Int J Legal Med 2008; 123:65-9. [DOI: 10.1007/s00414-008-0247-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 03/18/2008] [Indexed: 11/28/2022]
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Fletcher J, Bender C, Budowle B, Cobb WT, Gold SE, Ishimaru CA, Luster D, Melcher U, Murch R, Scherm H, Seem RC, Sherwood JL, Sobral BW, Tolin SA. Plant pathogen forensics: capabilities, needs, and recommendations. Microbiol Mol Biol Rev 2006; 70:450-71. [PMID: 16760310 PMCID: PMC1489535 DOI: 10.1128/mmbr.00022-05] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- J Fletcher
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA.
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Abstract
Schutzer and colleagues give guidance for physicians who believe that one of their patients has been a victim of an act of bioterror or another biocrime.
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Affiliation(s)
- Steven E Schutzer
- Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America.
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