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Oliveira M, Azevedo L, Ballard D, Branicki W, Amorim A. Using plants in forensics: State-of-the-art and prospects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111860. [PMID: 37683985 DOI: 10.1016/j.plantsci.2023.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
The increasing use of plant evidence in forensic investigations gave rise to a powerful new discipline - Forensic Botany - that analyses micro- or macroscopic plant materials, such as the totality or fragments of an organ (i.e., leaves, stems, seeds, fruits, roots) and tissue (i.e., pollen grains, spores, fibers, cork) or its chemical composition (i. e., secondary metabolites, isotopes, DNA, starch grains). Forensic botanists frequently use microscopy, chemical analysis, and botanical expertise to identify and interpret evidence crucial to solving civil and criminal issues, collaborating in enforcing laws or regulations, and ensuring public health safeguards. The present work comprehensively examines the current state and future potential of Forensic Botany. The first section conveys the critical steps of plant evidence collection, documentation, and preservation, emphasizing the importance of these initial steps in maintaining the integrity of the items. It explores the different molecular analyses, covering the identification of plant species and varieties or cultivars, and discusses the limitations and challenges of these techniques in forensics. The subsequent section covers the diversity of Forensic Botany approaches, examining how plant evidence exposes food and pharmaceutical frauds, uncovers insufficient or erroneous labeling, traces illegal drug trafficking routes, and combats the illegal collection or trade of protected species and derivatives. National and global security issues, including the implications of biological warfare, bioterrorism, and biocrime are addressed, and a review of the contributions of plant evidence in crime scene investigations is provided, synthesizing a comprehensive overview of the diverse facets of Forensic Botany.
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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.
| | - Luísa Azevedo
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland; Institute of Forensic Research, Kraków, Poland
| | - Antonio 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; FCUP - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Scoffone VC, Chiarelli LR, Trespidi G, Mentasti M, Riccardi G, Buroni S. Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches. Front Microbiol 2017; 8:1592. [PMID: 28878751 PMCID: PMC5572248 DOI: 10.3389/fmicb.2017.01592] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen particularly dangerous for cystic fibrosis (CF) patients. It can cause a severe decline in CF lung function possibly developing into a life-threatening systemic infection known as cepacia syndrome. Antibiotic resistance and presence of numerous virulence determinants in the genome make B. cenocepacia extremely difficult to treat. Better understanding of its resistance profiles and mechanisms is crucial to improve management of these infections. Here, we present the clinical distribution of B. cenocepacia described in the last 6 years and methods for identification and classification of epidemic strains. We also detail new antibiotics, clinical trials, and alternative approaches reported in the literature in the last 5 years to tackle B. cenocepacia resistance issue. All together these findings point out the urgent need of new and alternative therapies to improve CF patients’ life expectancy.
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Affiliation(s)
- Viola C Scoffone
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | | | - Gabriele Trespidi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Massimo Mentasti
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health EnglandLondon, United Kingdom.,Department of Microbiology, Royal Cornwall HospitalTruro, United Kingdom
| | - Giovanna Riccardi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
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Guo FB, Xiong L, Zhang KY, Dong C, Zhang FZ, Woo PCY. Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands. BMC Microbiol 2017; 17:73. [PMID: 28347342 PMCID: PMC5369199 DOI: 10.1186/s12866-017-0986-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium's adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline. RESULTS In this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection. CONCLUSIONS This approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.
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Affiliation(s)
- Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Lifeng Xiong
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Kai-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Fa-Zhan Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
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Pauletto M, Carraro L, Babbucci M, Lucchini R, Bargelloni L, Cardazzo B. Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b-RAD to investigate Listeria monocytogenes genetic structure. Mol Ecol Resour 2015; 16:823-35. [PMID: 26613186 DOI: 10.1111/1755-0998.12495] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/14/2015] [Accepted: 11/23/2015] [Indexed: 12/24/2022]
Abstract
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Rosaria Lucchini
- Istituto Zooprofilattico delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
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SNaPBceBcon: a Practical Tool for Identification and Genotyping of Burkholderia cepacia and Burkholderia contaminans. J Clin Microbiol 2015; 54:483-8. [PMID: 26659211 DOI: 10.1128/jcm.02476-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/24/2015] [Indexed: 12/20/2022] Open
Abstract
We propose an optimized protocol for an extensive population analysis of Burkholderia cepacia and Burkholderia contaminans. Seven new polymorphisms were added to the recently proposed SNaPBcen assay, and a total of 18 markers ensured the clear identification and distinction of B. cepacia and B. contaminans isolates and high genotypic discrimination (Simpson index of 0.94) compared to those for multilocus sequence typing.
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Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses. Appl Microbiol Biotechnol 2015; 99:2513-21. [DOI: 10.1007/s00253-015-6427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
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Eusebio N, Amorim AA, Gamboa F, Araujo R. Molecular identification and genotyping of Pseudomonas aeruginosa isolated from cystic fibrosis and non-cystic fibrosis patients with bronchiectasis. Pathog Dis 2014; 73:1-7. [DOI: 10.1093/femspd/ftu014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Oliveira M, Lackner M, Amorim A, Araujo R. Feasibility of mitochondrial single nucleotide polymorphisms to detect and identify Aspergillus fumigatus in clinical samples. Diagn Microbiol Infect Dis 2014; 80:53-8. [DOI: 10.1016/j.diagmicrobio.2014.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 05/05/2014] [Accepted: 05/10/2014] [Indexed: 01/02/2023]
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Soares I, Araujo R. MLST@SNaP: user-friendly software for simplification of multilocus sequence typing and dissemination of microbial population analyses. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Inês Soares
- IPATIMUP; Institute of Molecular Pathology and Immunology of the University of Porto; Rua Dr. Roberto Frias s/n Porto 4200-465 Portugal
- Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
- Center of Mathematics of the University of Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - Ricardo Araujo
- IPATIMUP; Institute of Molecular Pathology and Immunology of the University of Porto; Rua Dr. Roberto Frias s/n Porto 4200-465 Portugal
- Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
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