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Yu D, Zhang J, Gao N, Huo Y, Li W, Wang T, Zhang X, Simayijiang H, Yan J. Rapid and visual detection of specific bacteria for saliva and vaginal fluid identification with the lateral flow dipstick strategy. Int J Legal Med 2023; 137:1853-1863. [PMID: 37358650 DOI: 10.1007/s00414-023-03051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
Identification of body fluids is critical for crime scene reconstruction, and a source of investigation source of investigative leads. In recent years, microbial DNA analysis using sequencing and quantitative real-time polymerase chain reaction have been used to identify body fluids. However, these techniques are time-consuming, expensive, and require complex workflows. In this study, a new method for simultaneous detection of Streptococcus salivarius and Lactobacillus crispatus using polymerase chain reaction (PCR) in combination with a lateral flow dipstick (LFD) was developed to identify saliva and vaginal fluid in forensic samples. LFD results can be observed with the naked eye within 3 min with a sensitivity of 0.001 ng/µL DNA. The PCR-LFD assay was successfully used to detect S. salivarius and L. crispatus in saliva and vaginal fluid respectively, and showed negative results in blood, semen, nasal fluid, and skin. Moreover, saliva and vaginal fluid were detectable even at an extremely high mixing ratio of sample DNA (1:999). Saliva and vaginal fluid were identified in various mock forensic samples. These results indicate that saliva and vaginal fluid can be effectively detected by identifying S. salivarius and L. crispatus, respectively. Furthermore, we have shown that DNA samples used to identify saliva and vaginal fluid can also provide a complete short tandem repeat (STR) profile when used as source material for forensic STR profiling. In summary, our results suggest that PCR-LFD is a promising assay for rapid, simple, reliable, and efficient identification of body fluids.
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Affiliation(s)
- Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China.
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Toyomane K, Akutsu T, Watanabe K, Yamagishi T, Kubota S. Potential application of Staphylococcus species detection in the specific identification of saliva. Leg Med (Tokyo) 2023; 65:102320. [PMID: 37657351 DOI: 10.1016/j.legalmed.2023.102320] [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: 08/01/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
When found at crime scenes, saliva constitutes forensically relevant evidence. Although several tests have been developed to effectively identify saliva in such circumstances, most cannot discriminate between saliva and nasal secretion. Recently, studies have developed saliva tests involving oral bacteria as salivary markers. Although the specificity of such tests has been evaluated on most biological specimens, their specificity for nasal secretion samples remains to be tested. Herein, to improve the specificity of the saliva detection tests for nasal secretion samples, we reanalyzed a public microbiome dataset and conducted inhouse 16S rRNA sequencing to identify a new marker to distinguish between saliva and nasal secretions. The sequencing data indicated the existence of oral bacteria such as Streptococcus in nasal secretion samples, which may be responsible for the false positives in the saliva tests. Furthermore, we found that including the 16S rRNA gene of the genus Staphylococcus as a nasal secretion marker may improve the specificity of PCR-based saliva tests for nasal secretion samples. In addition, we assessed the specificity of previously developed salivary bacteria detection tests for nasal secretion samples and oral bacterial markers were detected in two of eight nasal secretion samples, which led to the false positive results for saliva detection. Thus, the specificity of such tests can be improved by adding Staphylococcus as a nasal marker, as revealed by our sequencing analysis.
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Affiliation(s)
- Kochi Toyomane
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Tomoko Akutsu
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Ken Watanabe
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takayuki Yamagishi
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Satoshi Kubota
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Cláudia-Ferreira A, Barbosa DJ, Saegeman V, Fernández-Rodríguez A, Dinis-Oliveira RJ, Freitas AR. The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms 2023; 11:2509. [PMID: 37894167 PMCID: PMC10608847 DOI: 10.3390/microorganisms11102509] [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: 07/24/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.
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Affiliation(s)
- Ana Cláudia-Ferreira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
| | - Daniel José Barbosa
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Veroniek Saegeman
- Department of Infection Control and Prevention, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Amparo Fernández-Rodríguez
- Microbiology Laboratory, Biology Service, Institute of Toxicology and Forensic Sciences, 28232 Madrid, Spain;
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Dass M, Singh Y, Ghai M. A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans. Curr Microbiol 2023; 80:299. [PMID: 37491404 PMCID: PMC10368579 DOI: 10.1007/s00284-023-03413-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 07/27/2023]
Abstract
Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.
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Affiliation(s)
- Mishka Dass
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Yashna Singh
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
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Ding R, Liu L, Zhang J, Lv P, Zhou L, Zhang T, Li S, Zhao R, Yang Z, Xiong P, Chen H, Wang W, Wang H, Tian Z, Liu B, Chen C. Accurate quantification of DNA using on-site PCR (osPCR) by characterizing DNA amplification at single-molecule resolution. Nucleic Acids Res 2023; 51:e65. [PMID: 37194709 PMCID: PMC10287937 DOI: 10.1093/nar/gkad388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/04/2023] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Despite the need in various applications, accurate quantification of nucleic acids still remains a challenge. The widely-used qPCR has reduced accuracy at ultralow template concentration and is susceptible to nonspecific amplifications. The more recently developed dPCR is costly and cannot handle high-concentration samples. We combine the strengths of qPCR and dPCR by performing PCR in silicon-based microfluidic chips and demonstrate high quantification accuracy in a large concentration range. Importantly, at low template concentration, we observe on-site PCR (osPCR), where only certain sites of the channel show amplification. The sites have almost identical ct values, showing osPCR is a quasi-single molecule phenomenon. Using osPCR, we can measure both the ct values and the absolute concentration of templates in the same reaction. Additionally, osPCR enables identification of each template molecule, allowing removal of nonspecific amplification during quantification and greatly improving quantification accuracy. We develop sectioning algorithm that improves the signal amplitude and demonstrate improved detection of COVID in patient samples.
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Affiliation(s)
- Ruihua Ding
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Liying Liu
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Jiali Zhang
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Pengxiao Lv
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Lin Zhou
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Tinglu Zhang
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Ran Zhao
- Shanghai Center for Clinical Laboratory, Shanghai200126, China
| | - Zhuo Yang
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Peng Xiong
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Hu Chen
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Wei Wang
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Hualiang Wang
- Shanghai Center for Clinical Laboratory, Shanghai200126, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Bo Liu
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Chang Chen
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
- School of Microelectronics, Shanghai University, Shanghai201800, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai200050, China
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6
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Wang Y, Xu H, Wei M, Wang Y, Wang W, Ju J, Liu Y, Wang X. Identification of Putative Bacterial Pathogens for Orofacial Granulomatosis Based on 16S rRNA Metagenomic Analysis. Microbiol Spectr 2023; 11:e0226622. [PMID: 37227290 PMCID: PMC10269498 DOI: 10.1128/spectrum.02266-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 05/15/2023] [Indexed: 05/26/2023] Open
Abstract
Orofacial granulomatosis (OFG) is a chronic inflammatory disease characterized by nontender swelling of the orofacial tissues, the underlying cause of which remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) is involved in the development of OFG. To characterize the AP bacterial signatures of OFG patients and identify possible pathogenic bacteria that cause OFG, the compositions of the AP microbiotas in OFG patients and controls were compared using 16S rRNA gene sequencing. Pure cultures of putative bacterial pathogens were established by growing bacteria as colonies followed by purification, identification, and enrichment and then were injected into animal models to determine the causative bacteria contributing to OFG. A specific AP microbiota signature in the OFG patients was shown, characterized by the predominance of phyla Firmicutes and Proteobacteria, notably members of the genera Streptococcus, Lactobacillus, and Neisseria, were found. Streptococcus spp., Lactobacillus casei, Neisseria subflava, Veillonella parvula, and Actinomyces spp. from OFG patients were isolated and successfully cultured in vitro and then injected into mice. Ultimately, footpad injection with N. subflava elicited granulomatous inflammation. IMPORTANCE Infectious agents have long been considered to play a role in the initiation of OFG; however, a direct causal relationship between microbes and OFG has not yet been established. In this study, a unique AP microbiota signature was identified in OFG patients. Moreover, we successfully isolated candidate bacteria from AP lesions of OFG patients and assessed their pathogenicity in laboratory mice. Findings from this study may help provide in-depth insights into the role of microbes in OFG development, providing the basis for targeted therapeutic approaches for OFG.
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Affiliation(s)
- Yuanyuan Wang
- Department of Oral Medicine, School of Stomatology, the Fourth Military Medical University, Xi’an, China
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
| | - Hao Xu
- Shaanxi Key Laboratory of Brain Disorders & School of Basic Medical Sciences, Xi'an Medical University, Xi’an, China
| | - Minghui Wei
- Department of Oral Medicine, School of Stomatology, the Fourth Military Medical University, Xi’an, China
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
| | - Yuhong Wang
- Department of Oral Medicine, School of Stomatology, the Fourth Military Medical University, Xi’an, China
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
| | - Wenzhe Wang
- Department of Oral Medicine, School of Stomatology, the Fourth Military Medical University, Xi’an, China
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
| | - Jia Ju
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
- Department of Pharmacy, School of Stomatology, the Fourth Military Medical University, Xi’an, China
| | - Yuan Liu
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
- Department of Oral Histology and Pathology, School of Stomatology, the Fourth Military Medical University, Xi’an, China
| | - Xinwen Wang
- Department of Oral Medicine, School of Stomatology, the Fourth Military Medical University, Xi’an, China
- Shaanxi Clinical Research Center for Oral Diseases, the National Clinical Research Center for Oral Disease of China, State Key Laboratory of Military Stomatology, Xi’an, China
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Ohta J, Minegishi S, Noda N, Sakurada K. Estimating the way of deposition of saliva stains using quantitative analysis of forensic salivary biomarkers. Leg Med (Tokyo) 2023; 64:102277. [PMID: 37300921 DOI: 10.1016/j.legalmed.2023.102277] [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: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Analyzing the way of deposition of saliva stains contributes to appropriate interpretation of saliva as evidence in court, particularly in sexual assault cases. In this proof-of-concept study, we aimed to confirm the difference between drooling-derived (non-contact) saliva and licking-derived (contact) saliva and clarify whether objectively distinguishing between the two saliva is possible. To allow discrimination between these two samples, an indicator was devised where the relative Streptococcus salivarius DNA quantity was calculated by dividing the S. salivarius DNA copies by the amount of stained saliva from the same saliva sample using quantitative polymerase chain reaction and salivary α-amylase activity assays. The study findings reveal that the value of the proposed indicator of licking-derived saliva was 100-fold significantly greater than that of drooling-derived saliva (P < 0.05, Welch's t-test). However, theoretical and technical challenges preclude the application of this indicator as a practical method. We believe that this saliva-specific bacterial DNA-based approach could allow estimation of the saliva stain deposition method.
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Affiliation(s)
- Jun Ohta
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Forensic Biology Unit, Scientific Crime Laboratory, Kanagawa Prefectural Police, 155-1 Yamashita-cho, Naka-ku, Yokohama, Kanagawa 231-0023, Japan.
| | - Saki Minegishi
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Nanaka Noda
- Forensic Biology Unit, Scientific Crime Laboratory, Kanagawa Prefectural Police, 155-1 Yamashita-cho, Naka-ku, Yokohama, Kanagawa 231-0023, Japan
| | - Koichi Sakurada
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Liang X, Liu X, Ye L, Du W, Huang L, Liu C, Xiao G, Huang M, Zheng Y, Shi M, Liu C, Chen L. Development and application of a multiplex PCR system for forensic salivary identification. Int J Legal Med 2023:10.1007/s00414-023-03004-2. [PMID: 37127761 DOI: 10.1007/s00414-023-03004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensics, accurate identification of the origin of body fluids is essential for reconstructing a crime scene or presenting strong evidence in court. Microorganisms have demonstrated great potential in body fluid identification. We developed a multiplex PCR system for forensic salivary identification, which contains five types of bacteria:Streptococcus salivarius, Neisseria subflava, Streptococcus. mutans, Bacteroides thetaiotaomicron, and Bacteroides. uniformis. And the validated studies were carried out following the validation guidelines for DNA analysis methods developed by the Scientific Working Group on DNA Analysis Methods (SWGDAM), which included tests for sensitivity, species specificity, repeatability, stability, and mixed samples, trace samples, case samples, and a population study. Our result depicted that the lowest detection limit of the system was 0.01 ng template DNA. Moreover, the corresponding bacteria can still be detected when the amount of saliva input is low to 0.1 μL for DNA extraction. In addition, the target bacteria were not detected in the DNA of human, seven common animals, and seven bacteria DNA and in nine other body fluid samples (skin, semen, blood, menstrual blood, nasal mucus, sweat, tears, urine, and vaginal secretions). Six common inhibitors such as indigo, EDTA, hemoglobin, calcium ions, alcohol and humic acid were well tolerated by the system. What is more, the salivary identification system recognized the saliva component in all mixed samples and simulated case samples. Among 400 unrelated individuals from the Chinese Han population analyzed by this novel system, the detection rates of N. subflava, S. salivarius, and S. mutans were 97.75%, 70.75%, and 19.75%, respectively, with 100% identification of saliva. In conclusion, the salivary identification system has good sensitivity, specificity, stability, and accuracy, which can be a new effective tool for saliva identification.
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Affiliation(s)
- Xiaomin Liang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Weian Du
- Guangdong Homy Genetics Ltd, Foshan, 528000, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Changhui Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China
| | - Guichao Xiao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Manling Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | | | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, 100088, People's Republic of China.
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China.
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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Li Z, Wang Y, Gao Z, Sekine S, You Q, Zhuang S, Zhang D, Feng S, Yamaguchi Y. Lower fluidic resistance of double-layer droplet continuous flow PCR microfluidic chip for rapid detection of bacteria. Anal Chim Acta 2023; 1251:340995. [PMID: 36925286 DOI: 10.1016/j.aca.2023.340995] [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: 01/09/2023] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Rapid diagnosis of harmful microorganisms demonstrated its great importance for social health. Continuous flow PCR (CF-PCR) can realize rapid amplification of target genes by placing the microfluidic chip on heaters with different temperature. However, bubbles and evaporation always arise from heating, which makes the amplification not stable. Water-in-oil droplets running in CF-PCR microfluidic chip with uniform height takes long time because of the high resistance induced by long meandering microchannel. To overcome those drawbacks, we proposed a double-layer droplet CF-PCR microfluidic chip to reduce the fluidic resistance, and meanwhile nanoliter droplets were generated to minimize the bubbles and evaporation. RESULTS Experiments showed that (1) fluidic resistance could be reduced with the increase of the height of the serpentine microchannel if the height of the T-junction part was certain. (2) Running speed, the size and the number of generated droplets were positively correlated with the cross-sectional area of the T-junction and water pressure. (3) Droplet fusion happened at higher water pressure if other experimental conditions were the same. (4) 0.032 nL droplet was created if the cross-sectional area of T-junction and water pressure were 1600 μm2 (40 × 40 μm) and 7 kPa, respectively. Finally, we successfully amplified the target genes of Porphyromonas gingivalis within 11'16″ and observed the fluorescence from droplets. SIGNIFICANCE AND NOVELTY Such a microfluidic chip can effectively reduce the high resistance induced by long meandering microchannel, and greatly save time required for droplets CF-PCR. It offers a new way for the rapid detection of bacterial.
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Affiliation(s)
- Zhenqing Li
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yifei Wang
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Zehang Gao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangdong, 510150, China
| | - Shinichi Sekine
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Qingxiang You
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Songlin Zhuang
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Yoshinori Yamaguchi
- Engineering Research Center of Optical Instrument and System, Key Lab of Optical Instruments and Equipment for Medical Engineering, Ministry of Education, Shanghai Key Lab of Modern Optical System, Shanghai Environmental Biosafety Instruments and Equipment Engineering Technology Research Center, University of Shanghai for Science and Technology, Shanghai, 200093, China; Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.
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10
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Role of Nanomaterials in COVID-19 Prevention, Diagnostics, Therapeutics, and Vaccine Development. JOURNAL OF NANOTHERANOSTICS 2022. [DOI: 10.3390/jnt3040011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Facing the deadly pandemic caused by the SARS-CoV-2 virus all over the globe, it is crucial to devote efforts to fighting and preventing this infectious virus. Nanomaterials have gained much attention after the approval of lipid nanoparticle-based COVID-19 vaccines by the United States Food and Drug Administration (USFDA). In light of increasing demands for utilizing nanomaterials in the management of COVID-19, this comprehensive review focuses on the role of nanomaterials in the prevention, diagnostics, therapeutics, and vaccine development of COVID-19. First, we highlight the variety of nanomaterials usage in the prevention of COVID-19. We discuss the advantages of nanomaterials as well as their uses in the production of diagnostic tools and treatment methods. Finally, we review the role of nanomaterials in COVID-19 vaccine development. This review offers direction for creating products based on nanomaterials to combat COVID-19.
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11
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Al Tuma RR, Yassir YA. Effect of calcium fluoride nanoparticles in prevention of demineralization during orthodontic fixed appliance treatment: a randomized clinical trial. Eur J Orthod 2022; 45:122-132. [PMID: 36049047 DOI: 10.1093/ejo/cjac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND White spot lesions (WSLs) are the most common complications of fixed appliance orthodontic treatment. OBJECTIVES To evaluate the effectiveness of calcium fluoride nanoparticles-containing orthodontic primer (nCaF2-primer) in preventing the incidence of WSLs during orthodontic treatment. TRIAL DESIGN Single-centre, double-blinded, split-mouth, randomized clinical trial. METHODS The sample involved 31 orthodontic patients (≥12 years). Participants were recruited using a simple nonstratified randomization. Data collection, measurements, and analysis were performed blindly. Outcome measures included comparing the effect of nCaF2-primer with control primer (Transbond) regarding the degree of demineralization (DIAGNOdent pen), Streptococcus mutans (S. mutans) bacterial counting [real-time polymerase chain reaction device (PCR)], and WSLs incidence (pre- and post-operative photographs). The measurements were performed before bonding, 1, 3, and 6 months after bonding and after appliance removal. A two-way repeated measure analysis of variance test (for DIAGNOdent pen scores), and Wilcoxon signed-rank test (for the difference between bacterial counting and WSLs incidence) were used (P < 0.05). RESULTS Thirty-one patients were recruited and randomized (mean age 17.9 ± 2.45 years). For the primary outcome (DIAGNOdent pen scores) and secondary outcome of S. mutans counting: 31 patients (310 teeth for each group) were included in scoring at T1 and T3, and 30 patients (300 teeth) were included at T6. While for the photographic scores, 26 patients were included after bracket bonding. The demineralization scores showed significant differences at all-time intervals within the 6 months after bracket bonding which was more noticeable after the first month. There was a significant difference in bacterial count between the two primer groups at the T1 only. Regarding photographic scores, there were no significant differences in the WSLs incidence between the two primers groups after brackets removal. No harm was detected during treatment, except the usual pain/gingival irritation. CONCLUSIONS nCaF2-primer effectively decreased demineralization scores within the 6 months after bracket bonding. Moreover, it significantly reduced S. mutans colonization after the first month. However, the tested primer did not have an extra advantage in preventing WSLs development at the clinical level after appliance removal. TRIAL REGISTRATION The trial was registered with ClinicalTrials.gov on 8 May 2021 (registration number: NCT04994314).
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Affiliation(s)
- Rawof R Al Tuma
- Orthodontic Department, College of Dentistry, University of Karbala, Kerbala, Iraq
| | - Yassir A Yassir
- Orthodontic Department, College of Dentistry, University of Baghdad, Baghdad, Iraq
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12
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Nanfack CDV, Yang J, Yuan X, Sun J, Sun X, Ji J. 3, 4-Dihydroxy-l-phenylalanine Biopolymer Cellulose DNA Adhesive Card as an Enhanced Solid-Phase One-Step DNA Extraction Method from Foodborne Pathogens in Food Samples. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Lewis C, Seashols-Williams SJ. Design and optimization of a 16S microbial qPCR multiplex for the presumptive identification of feces, saliva, vaginal and menstrual secretions. J Forensic Sci 2022; 67:1660-1667. [PMID: 35352345 PMCID: PMC9310585 DOI: 10.1111/1556-4029.15029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 11/26/2022]
Abstract
Molecular methods for body fluid identification have been extensively researched in the forensic community over the last decade, mostly focusing on RNA‐based methods. Microbial DNA analysis has long been used for forensic applications, such as postmortem interval estimations, but only recently has it been applied to body fluid identification. High‐throughput sequencing of the 16S ribosomal RNA gene by previous research groups revealed that microbial signatures and abundances vary across human body fluids at the genus and/or species taxonomic level. Since quantitative PCR is still the current technique used in forensic DNA analysis, the purpose of this study was to design a qPCR multiplex targeting the 16S gene of Bacteroides uniformis, Streptococcus salivarius, and Lactobacillus crispatus that can distinguish between feces, saliva, and vaginal/menstrual secretions, respectively. Primers and probes were designed at the species level because these bacteria are highly abundant within their respective fluid. The validated 16S triplex was evaluated in DNA extracts from thirty donors of each body fluid. A classification regression tree model resulted in 96.5% classification accuracy of the population data, which demonstrates the ability of this 16S triplex to presumptively identify these fluids with high confidence at the quantification step of the forensic workflow using minimal input volume of DNA extracted from evidentiary samples.
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Affiliation(s)
- Carolyn Lewis
- Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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14
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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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15
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Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
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Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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16
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Solis-Marcano NE, Morales-Cruz M, Vega-Hernández G, Gómez-Moreno R, Binder C, Baerga-Ortiz A, Priest C, Cabrera CR. PCR-assisted impedimetric biosensor for colibactin-encoding pks genomic island detection in E. coli samples. Anal Bioanal Chem 2021; 413:4673-4680. [PMID: 34046698 PMCID: PMC8159250 DOI: 10.1007/s00216-021-03404-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
A fast PCR-assisted impedimetric biosensor was developed for the selective detection of the clbN gene from the polyketide synthase (pks) genomic island in real Escherichia coli samples. This genomic island is responsible for the production of colibactin, a harmful genotoxin that has been associated with colorectal cancer. The experimental protocol consisted of immobilizing the designated forward primer onto an Au electrode surface to create the sensing probe, followed by PCR temperature cycling in blank, positive, and negative DNA controls. Target DNA identification was possible by monitoring changes in the system’s charge transfer resistance values (Rct) before and after PCR treatment through electrochemical impedance spectroscopy (EIS) analysis. Custom-made, flexible gold electrodes were fabricated using chemical etching optical lithography. A PCR cycle study determined the optimum conditions to be at 6 cycles providing fast results while maintaining a good sensitivity. EIS data for the DNA recognition process demonstrated the successful distinction between target interaction resulting in an increase in resistance to charge transfer (Rct) percentage change of 176% for the positive DNA control vs. 21% and 20% for the negative and non-DNA-containing controls, respectively. Results showed effective fabrication of a fast, PCR-based electrochemical biosensor for the detection of pks genomic island with a calculated limit of detection of 17 ng/μL.
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Affiliation(s)
- Nadja E Solis-Marcano
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Myreisa Morales-Cruz
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Gabriela Vega-Hernández
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Ramón Gómez-Moreno
- Department of Biochemistry, Molecular Sciences Research Center, University of Puerto Rico, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Claudia Binder
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Abel Baerga-Ortiz
- Department of Biochemistry, Molecular Sciences Research Center, University of Puerto Rico, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Craig Priest
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Carlos R Cabrera
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico.
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Montagut E, Martin-Gomez MT, Marco MP. An Immunochemical Approach to Quantify and Assess the Potential Value of the Pseudomonas Quinolone Signal as a Biomarker of Infection. Anal Chem 2021; 93:4859-4866. [PMID: 33691411 PMCID: PMC8479725 DOI: 10.1021/acs.analchem.0c04731] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/04/2021] [Indexed: 01/20/2023]
Abstract
Quorum sensing (QS) is a bacterial cell density-based communication system using low molecular weight signals called autoinducers (AIs). Identification and quantification of these molecules could provide valuable information related to the stage of colonization or infection as well as the stage of the disease. With this scenario, we report here for the first time the development of antibodies against the PQS (pseudomonas quinolone signal), the main signaling molecule from the pqs QS system of Pseudomonas aeruginosa, and the development of a microplate-based enzyme-linked immunosorbent assay (ELISA) able of quantifying this molecule in complex biological media in the low nanometer range (LOD, 0.36 ± 0.14 nM in culture broth media). Moreover, the PQS ELISA here reported has been found to be robust and reliable, providing accurate results in culture media. The technique allowed us to follow up the PQS profile of the release of bacterial clinical isolates obtained from patients of different disease status. A clear correlation was found between the PQS immunoreactivity equivalents and the chronic or acute infection conditions, which supports the reported differences on virulence and behavior of these bacterial strains due to their adaptation capability to the host environment. The results obtained point to the potential of the PQS as a biomarker of infection and to the value of the antibodies and the technology developed for improving diagnosis and management of P. aeruginosa infections based on the precise identification of the pathogen, appropriate stratification of the patients according to their disease status, and knowledge of the disease progression.
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Affiliation(s)
- Enrique
J. Montagut
- Nanobiotechnology
for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC)
of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - M. Teresa Martin-Gomez
- Microbiology
Department, Vall d’Hebron University
Hospital (VHUH), 08035 Barcelona, Spain
- Genetics
and Microbiology Department, Universitat
Autònoma de Barcelona (UAB), 08193 Barcelona, Spain
| | - M. Pilar Marco
- Nanobiotechnology
for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC)
of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
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18
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Jiang Y, Jiang S, Wu Y, Zhou B, Wang K, Jiang L, Long Y, Chen G, Zeng D. Multiplex and on-site PCR detection of swine diseases based on the microfluidic chip system. BMC Vet Res 2021; 17:117. [PMID: 33712000 PMCID: PMC7953195 DOI: 10.1186/s12917-021-02825-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/02/2021] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND At present, the process of inspection and quarantine starts with sampling at the customs port, continues with transporting the samples to the central laboratory for inspection experiments, and ends with the inspected results being fed back to the port. This process had the risks of degradation of biological samples and generation of pathogenic microorganisms and did not meet the rapid on-site detection demand because it took a rather long time. Therefore, it is urgently needed to develop a rapid and high-throughput detection assay of pathogenic microorganisms at the customs port. The aim of this study was to develop a microfluidic chip to rapidly detect swine pathogenic microorganisms with high-throughput and higher accuracy. Moreover, this chip will decrease the risk of spreading infection during transportation. RESULTS A series of experiments were performed to establish a microfluidic chip. The resulting data showed that the positive nucleic acid of four swine viruses were detected by using a portable and rapid microfluidic PCR system, which could achieve a on-site real-time quantitative PCR detection. Furthermore, the detection results of eight clinical samples were obtained within an hour. The lowest concentration that amplified of this microfluidic PCR detection system was as low as 1 copies/μL. The results showed that the high specificity of this chip system in disease detection played an important role in customs inspection and quarantine during customs clearance. CONCLUSION The microfluidic PCR detection system established in this study could meet the requirement for rapid detection of samples at the customs port. This chip could avoid the risky process of transporting the samples from the sampling site to the testing lab, and drastically reduce the inspection cycle. Moreover, it would enable parallel inspections on one chip, which greatly raised the efficiency of inspection.
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Affiliation(s)
- Yan Jiang
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
| | - Shan Jiang
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
| | - Yue Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaimin Wang
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
| | - Luyan Jiang
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
| | - Yunfeng Long
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
| | - Gan Chen
- Jinggangshan Agricultural Science and Technology Park Management Committee, Jian, 343000 China
| | - Dexin Zeng
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, 210019 China
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Liu J, Cheng X, Liu F, Hao T, Wang J, Guo J, Li J, Liu Z, Li W, Shi J, Zhang X, Li J, Yan J, Zhang G. Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture. Forensic Sci Int Genet 2021; 52:102483. [PMID: 33610949 DOI: 10.1016/j.fsigen.2021.102483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
mRNA markers provide a very promising method for the identification of human body fluids or tissues in the context of forensic investigations. Previous studies have shown that different body fluids can be distinguished from each other according to their specific mRNA biomarkers. In this study, we evaluated eight semen-specific mRNA markers (KLK3, NKX3-1, CKB, KLK2, PRAC1, SEMG1, TGM4, and SORD) that encompass 12 coding single nucleotide polymorphisms (cSNPs) to identify the semen contributor in a mixed stain. Five highly specific and sensitive mRNA markers for blood, menstrual blood, saliva, vaginal secretions, and skin were also incorporated into the PCR system as body fluid-positive controls. Reverse transcription polymerase chain reaction (RT-PCR), multiplex PCR and SNaPshot mini-sequencing assays were established for the identification of semen-specific mRNA. The amplicon size ranged from 133 to 337 bp. The semen-specific system was examined against blood, menstrual blood, saliva, vaginal secretions, and skin swabs. The eight mRNA biomarkers were semen-specific and could be successfully typed in laboratory-generated mixtures composed of different body fluids supplemented with 1 ng of semen cDNA. This system possessed a high sensitivity that ranged from 1:10-1:100 for detecting trace amounts of semen in semen-containing body fluid mixtures. Additionally, our results demonstrated that the cSNPs polymorphisms included in the mRNA markers were concordant with genomic DNA (gDNA). Despite the presence of other body fluids, the system exhibited high sensitivity and specificity to the semen in the mixture. In future studies, we will add other cSNPs from the semen-specific genes using massively parallel sequencing to further improve our system.
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Affiliation(s)
- Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Ting Hao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangling Guo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Wenyan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jie Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiuying Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jing Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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Kartsova L, Makeeva D, Kravchenko A, Moskvichev D, Polikarpova D. Capillary electrophoresis as a powerful tool for the analyses of bacterial samples. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116110] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Li Z, Bai Y, You M, Hu J, Yao C, Cao L, Xu F. Fully integrated microfluidic devices for qualitative, quantitative and digital nucleic acids testing at point of care. Biosens Bioelectron 2020; 177:112952. [PMID: 33453463 PMCID: PMC7774487 DOI: 10.1016/j.bios.2020.112952] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Benefiting from emerging miniaturized and equipment-free nucleic acid testing (NAT) technologies, fully integrated NAT devices at point of care (POC) with the capability of "sample-in-answer-out" are proceeding at a break-neck speed to eliminate complex operations and reduce the risk of contamination. Like the development of polymerase chain reaction (PCR) technology (the standard technique for NAT), the detection signal of fully integrated NAT devices has evolved from qualitative to quantitative and recently to digital readout, aiming at expanding their extensive applications through gradually improving detection sensitivity and accuracy. This review firstly introduces the existing commercial products, and then illustrates recent fully integrated microfluidic devices for NAT at POC from the aspect of detection signals (i.e., qualitative, quantitative and digital). Importantly, the key issues of existing commercial products and the main challenges between scientific research and product development are discussed. On this basis, we envision that the MARCHED (miniaturized, automatic, reagent-preloaded, commercializable, high-throughput, environment-independent and disposable) NAT devices are expected to be realized in the near future.
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Affiliation(s)
- Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Yuemeng Bai
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Co., Ltd, Suzhou, 215010, PR China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
| | - Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
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22
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Montagut EJ, Vilaplana L, Martin-Gomez MT, Marco MP. High-Throughput Immunochemical Method to Assess the 2-Heptyl-4-quinolone Quorum Sensing Molecule as a Potential Biomarker of Pseudomonas aeruginosa Infections. ACS Infect Dis 2020; 6:3237-3246. [PMID: 33210530 DOI: 10.1021/acsinfecdis.0c00604] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacterial quorum sensing (QS) is being contemplated as a promising target for developing innovative diagnostic and therapeutic strategies. Here we report for the first time the development of antibodies against 2-heptyl-4-quinolone (HHQ), a signaling molecule from the pqs QS system of Pseudomonas aeruginosa, involved in the production of important virulent factors and biofilm formation. The antibodies produced were used to develop an immunochemical diagnostic approach to assess the potential of this molecule as a biomarker of P. aeruginosa infection. The ELISA developed is able to reach a detectability in the low nM range (IC50 = 4.59 ± 0.29 nM and LOD = 0.34 ± 0.13 nM), even in complex biological samples such as Müeller Hinton (MH) culture media. The ELISA developed is robust and reproducible and has been found to be specific to HHQ, with little interference from other related alkylquinolones from the pqs QS system. The ELISA has been used to analyze the HHQ production kinetics of P. aeruginosa clinical isolates grown in MH media, pointing to its potential as a biomarker of infection and at the possibility to use the technology developed to obtain additional information about the disease stage.
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Affiliation(s)
- Enrique J. Montagut
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Lluisa Vilaplana
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - M. Teresa Martin-Gomez
- Microbiology Department, Vall d’Hebron University Hospital (VHUH), 08035 Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona (UAB), 08193, Barcelona, Spain
| | - M. Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
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23
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Li X, Nguyen LV, Hill K, Ebendorff-Heidepriem H, Schartner EP, Zhao Y, Zhou X, Zhang Y, Warren-Smith SC. All-fiber all-optical quantitative polymerase chain reaction (qPCR). SENSORS AND ACTUATORS. B, CHEMICAL 2020; 323:128681. [PMID: 32834504 PMCID: PMC7415342 DOI: 10.1016/j.snb.2020.128681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/19/2020] [Accepted: 07/30/2020] [Indexed: 05/22/2023]
Abstract
Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system. By using an all-optical approach, we achieve ultra-fast temperature response with real-time temperature feedback using nanoliter scale reaction volumes. The system uses a microcavity to act as a nanoliter scale reaction vessel with a laser-driven and optically monitored temperature cycling system for ultrafast thermal cycling and incorporates an all-fiber fluorescence excitation/detection system to achieve real-time, high sensitivity fluorescence monitoring of the qPCR process. Further, we demonstrate the potential of the system to operate as a label-free qPCR system through direct optical measurement of the sample refractive index. Due to advantages in portability and fabrication simplicity, we anticipate that this platform technology will offer a new strategy for fundamental techniques in biochemistry applications, such as point-of-care and remote diagnostics.
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Affiliation(s)
- Xuegang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning, 110819, China
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Linh V Nguyen
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Kelly Hill
- South Australian Research and Development Institute, Urrbrae, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Heike Ebendorff-Heidepriem
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Erik P Schartner
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning, 110819, China
| | - Xue Zhou
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning, 110819, China
| | - Yanan Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning, 110819, China
| | - Stephen C Warren-Smith
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, SA, 5005, Australia
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24
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Abstract
Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18-25 years and investigated if diversity is associated with gender (male and female).Method. The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.Results. Microbiota of navel skin is dominated by Corynebacterium and Staphylococcus and includes opportunistic pathogens like Clostridium and Pseudomonas. Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as Acinetobacter, Campylobacter, Klebsiella and organisms from the Enterobacteriaceae and Moraxellaceae families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (P>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of Klebsiella and Enterobacter in females.Conclusion. Our findings indicate that the navel skin microbiota of young adults has a core microbiota of Corynebacterium and Staphylococcus. We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.
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Affiliation(s)
- Shreya Shah
- College of the Sciences and Mathematics, West Chester University, West Chester, PA, USA
| | | | - Vishal Shah
- College of the Sciences and Mathematics, West Chester University, West Chester, PA, USA
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25
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Lehel J, Yaucat-Guendi R, Darnay L, Palotás P, Laczay P. Possible food safety hazards of ready-to-eat raw fish containing product (sushi, sashimi). Crit Rev Food Sci Nutr 2020; 61:867-888. [PMID: 32270692 DOI: 10.1080/10408398.2020.1749024] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
It is undeniable that with the popularity of sushi and sashimi over the last decade the consumption of raw fish has extremely increased. Raw fish is very appreciated worldwide and has become a major component of human diet because of its fine taste and nutritional properties. Possible hazards concerning fish safety and quality are classified as biological and chemical hazards. They are contaminants that often accumulate in edible tissue of fish and transmit to humans via the food chain affecting the consumer's health. Although their concentration in fish and fishery products are found at non-alarming level of a daily basis period, they induce hazardous outcome on human health due to long and continuous consumption of raw fish. Regular sushi and sashimi eaters have to be aware of the contaminants found in the other components of their dish that often add up to acceptable residue limits found in fish. Hence, there is the urge for effective analytical methods to be developed as well as stricter regulations to be put in force between countries to monitor the safety and quality of fish for the interest of public health.
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Affiliation(s)
- József Lehel
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Lívia Darnay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Péter Laczay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
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26
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Li X, Ding Y, Ling J, Yao W, Zha L, Li N, Chang Y, Wang Y, Cai J. Bacteria-targeting BSA-stabilized SiC nanoparticles as a fluorescent nanoprobe for forensic identification of saliva. Mikrochim Acta 2019; 186:756. [DOI: 10.1007/s00604-019-3890-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/01/2019] [Indexed: 01/16/2023]
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27
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Jung JY, Ryu GH, Kim DH, Kim JY, Hwang IK, Kang PW, Chun BW, Yoo SY. Simplified Direct PCR Method for Reference Buccal Samples Using a Non-FTA Card by Omitting the Pretreatment Step. J Forensic Sci 2019; 65:209-213. [PMID: 31433497 DOI: 10.1111/1556-4029.14147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
When using non-FTA cards in commercial multiplex STR kits for direct PCR, pretreatment steps with specific buffers are recommended. Here, we designed a rapid direct PCR method utilizing a non-FTA card, Oral Cell Sampling Kit, by omitting the pretreatment step involving Prep-n-Go™ Buffer, and it showed compatibility with the GlobalFiler™ Express PCR Amplification Kit, GlobalFiler™ PCR Amplification Kit, and PowerPlex® Fusion system. To optimize the PCR conditions, we tested the method with different final PCR volumes and cycles. Finally, we conducted a performance test using 50 Korean buccal samples and confirmed the high performance of the method, detecting more than 90% of the samples with full profiles when using GlobalFiler™ PCR Amplification Kit and PowerPlex® Fusion system at 29 cycles in a 10 μL final PCR volume. Thus, we report a simple direct PCR set-up to analyze reference samples collected using a non-FTA card manufactured in Korea.
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Affiliation(s)
- Ju Yeon Jung
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Ga Hee Ryu
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Da-Hye Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - In Kwan Hwang
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Pil-Won Kang
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Byung Won Chun
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
| | - Seong Yeon Yoo
- Forensic DNA Division, National Forensic Service, Wonju, 26460, South Korea
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28
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Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations. Int J Legal Med 2019; 133:1711-1719. [DOI: 10.1007/s00414-019-02129-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 07/26/2019] [Indexed: 01/28/2023]
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29
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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