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Karadayı S, Yılmaz İ, Özbek T, Karadayı B. Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study. J Forensic Leg Med 2024; 107:102757. [PMID: 39298862 DOI: 10.1016/j.jflm.2024.102757] [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: 11/14/2023] [Revised: 09/02/2024] [Accepted: 09/07/2024] [Indexed: 09/22/2024]
Abstract
New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator.
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Affiliation(s)
- Sukriye Karadayı
- Department of Medical Laboratory Techniques, Altınbaş University, Istanbul, Turkey.
| | - İlknur Yılmaz
- Department of Molecular Biology and Genetics, Graduate School of Science & Engineering, Yıldız Technical University, Istanbul, Turkey.
| | - Tülin Özbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey.
| | - Beytullah Karadayı
- Department of Forensic Sciences, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
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Zhao X, Yang F, Yang F, Nie H, Hu S, Gui P, Guo Y, Zhang C. Seasonal mouse cadaver microbial study: rupture time and postmortem interval estimation model construction. PeerJ 2024; 12:e17932. [PMID: 39285921 PMCID: PMC11404455 DOI: 10.7717/peerj.17932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/25/2024] [Indexed: 09/19/2024] Open
Abstract
The estimation of postmortem interval (PMI) has long been a focal point in the field of forensic science. Following the death of an organism, microorganisms exhibit a clock-like proliferation pattern during the course of cadaver decomposition, forming the foundation for utilizing microbiology in PMI estimation. The establishment of PMI estimation models based on datasets from different seasons is of great practical significance. In this experiment, we conducted microbiota sequencing and analysis on gravesoil and mouse intestinal contents collected during both the winter and summer seasons and constructed a PMI estimation model using the Random Forest algorithm. The results showed that the MAE of the gut microbiota model in summer was 0.47 ± 0.26 d, R2 = 0.991, and the MAE of the gravesoil model in winter was 1.04 ± 0.22 d, R2 = 0.998. We propose that, in practical applications, it is advantageous to selectively build PMI estimation models based on seasonal variations. Additionally, through a combination of morphological observations, gravesoil microbiota sequencing results, and soil physicochemical data, we identified the time of cadaveric rupture for mouse cadavers, occurring at around days 24-27 in winter and days 6-9 in summer. This study not only confirms previous research findings but also introduces novel insights, contributing to the foundational knowledge necessary to advance the utilization of microbiota for PMI estimation.
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Affiliation(s)
- Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing, China
| | - Hao Nie
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing, China
| | - Sheng Hu
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing, China
| | - Peng Gui
- College of Life Sciences,, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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3
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Franceschetti L, Lodetti G, Blandino A, Amadasi A, Bugelli V. Exploring the role of the human microbiome in forensic identification: opportunities and challenges. Int J Legal Med 2024; 138:1891-1905. [PMID: 38594499 PMCID: PMC11306296 DOI: 10.1007/s00414-024-03217-z] [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: 12/20/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.
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Affiliation(s)
- Lorenzo Franceschetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, via Luigi Mangiagalli 37, Milan, 20133, Italy.
| | - Giorgia Lodetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, via Luigi Mangiagalli 37, Milan, 20133, Italy
| | | | - Alberto Amadasi
- Institute of Legal Medicine and Forensic Sciences, University Medical Centre Charité, University of Berlin, Turmstr. 21, Building N, Berlin, 10559, Germany
| | - Valentina Bugelli
- Department of Medicine and Surgery, Section of Forensic Medicine, University of Parma, Parma, Italy
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4
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Foster M, McElhoe JA, Holland MM. A Custom qPCR Assay to Simultaneously Quantify Human and Microbial DNA. Genes (Basel) 2024; 15:1129. [PMID: 39336720 PMCID: PMC11431276 DOI: 10.3390/genes15091129] [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: 08/05/2024] [Revised: 08/18/2024] [Accepted: 08/24/2024] [Indexed: 09/30/2024] Open
Abstract
To date, studies on microbial forensics have focused mainly on sequence analysis and generally do not include information on the quantification of and comparison between the human and bacterial DNA present in forensic samples. Knowing the amount of each type of DNA can be important for determining when and how best to employ bacterial DNA analysis, especially when there is insufficient human DNA for successful short tandem repeat (STR) typing. The goal of this work was to develop a quantitative PCR (qPCR) assay that simultaneously quantifies human and bacterial DNA that would be simple and cost-effective for laboratories to implement. Through a reproducibility study and several small-scale experiments, the reliability of a custom qPCR assay was established. A reproducibility study illustrated that the multiplex assay produced data comparable to that of previously established bacterial DNA and human DNA qPCR assays. The small-scale experiments showed that common surfaces such as keyboards (6.76 pg/μL), elevator buttons (11.9 pg/μL), cleaning supplies (7.17 pg/μL), and dispensers (16.4 pg/μL) failed to produce human DNA quantities sufficient for quality STR analysis (≥250 pg). However, all tested surfaces produced bacterial DNA quantities suitable for reaching 1 ng of amplified bacterial targets necessary for sequence analysis. In fact, bacterial DNA concentrations down to 10-8 ng/uL produce enough amplified product for sequencing. The newly developed qPCR multiplex tool will allow scientists to make better decisions regarding whether human or bacterial DNA analysis methods can be pursued during forensic or other investigations.
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Affiliation(s)
- Miriam Foster
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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5
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Lontano A, Pascucci D, Pattavina F, Vincenti S, Boninti F, Grossi R, Incitti I, Bilotta M, Pastorino R, Vento G, Gigli F, Liperoti R, De Meo F, Antonelli M, Lochi S, Laurenti P. Pilot randomized experimental study evaluating isopropyl alcohol and ultraviolet-C radiation in the disinfection of healthcare workers' smartphones. J Hosp Infect 2024; 148:105-111. [PMID: 38670495 DOI: 10.1016/j.jhin.2024.03.020] [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: 02/12/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Smartphones in medical settings pose infection risks due to harbouring pathogenic bacteria. AIM This pilot study assessed the effectiveness duration of sanitization methods, focusing on 70% isopropyl alcohol wipes and ultraviolet-C (UVC) boxes, aiming to obtain preliminary data on the reduction in total bacterial load 3 h post-sanitization. METHODS A randomized monocentric trial with two intervention arms (wipes and UVC boxes) was designed. As participants, healthcare workers from three wards at Fondazione Policlinico Universitario 'A. Gemelli' IRCCS Hospital were recruited, stratified by ward, and block randomized within each ward to control confounders. FINDINGS Seventy-one healthcare workers, mostly nurses (62%) were included in the study. Initial bacterial load reduction was significant with both disinfection techniques, but after 3 h both methods showed increased bacterial levels, with wipes displaying potentially higher residual efficacy (P=0.056). To adequately size a trial (89% power, significance level 0.05) for assessing the residual efficacy of alcohol-impregnated wipes compared with UVC boxes at 3 h post-sanitization, 503 professionals per group were required. CONCLUSION This study highlights the necessity for guidelines on hospital smartphone sanitization and educational initiatives for healthcare workers and patients. Further studies, adequately sized, are necessary to determine optimal sanitization intervals and assess pathogen transmission risks.
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Affiliation(s)
- A Lontano
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - D Pascucci
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy; Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - F Pattavina
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - S Vincenti
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - F Boninti
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - R Grossi
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - I Incitti
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - M Bilotta
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - R Pastorino
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - G Vento
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - F Gigli
- Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - R Liperoti
- Department of Geriatric and Orthopaedic Sciences, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Ageing, Orthopaedic and Rheumatological Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - F De Meo
- Department of Ageing, Orthopaedic and Rheumatological Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - M Antonelli
- Department of Basic Biotechnology, Clinical Intensivology and Perioperative Sciences, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Emergency, Anaesthesiological and Resuscitation Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - S Lochi
- Department of Ageing, Orthopaedic and Rheumatological Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - P Laurenti
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Women, Child and Public Health Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [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: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe HC. Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem. Sci Rep 2024; 14:8715. [PMID: 38622248 PMCID: PMC11018758 DOI: 10.1038/s41598-024-59086-4] [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: 08/16/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.
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Affiliation(s)
- Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy.
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Theresa Rzehak
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Else Sprecher
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Filippo Colla
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Julia Seeber
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
- National Biodiversity Future Center (NBFC), S.c.a.r.l., Palermo, Italy
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Mir TUG, Manhas S, Khurshid Wani A, Akhtar N, Shukla S, Prakash A. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations. Sci Justice 2024; 64:81-94. [PMID: 38182316 DOI: 10.1016/j.scijus.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.
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Affiliation(s)
- Tahir Ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India; State Forensic Science Laboratory, Srinagar, Jammu and Kashmir 190001, India.
| | - Sakshi Manhas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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Olsen M, Demaneuf T, Singh G, Goldsworthy A, Jones P, Morgan M, Nassar R, Senok A, Ghemrawi R, Almheiri R, Marzooqi HA, Almansoori S, Albastaki A, Almansoori R, McKirdy S, Alghafri R, Tajouri L. Do mobile phone surfaces carry SARS-CoV-2 virus? A systematic review warranting the inclusion of a "6th" moment of hand hygiene in healthcare. J Infect Public Health 2023; 16:1750-1760. [PMID: 37738691 DOI: 10.1016/j.jiph.2023.08.017] [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: 06/27/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Mobile phones, used in billions throughout the world, are high-touch devices subject to a dynamic contamination of microorganisms and rarely considered as an important fomite to sanitise systematically. The emergence of SARS-CoV-2 resulted in the COVID-19 pandemic, arguably the most impactful pandemic of the 21st century with millions of deaths and disruption of all facets of modern life globally. AIM To perform a systematic review of the literature exploring SARS-CoV-2 presence as a contaminant on mobile phones. METHODS A systematic search (PubMed and Google Scholar) of literature was undertaken from December 2019 to March 2023 identifying English language studies. Studies included in this review specifically identified or tested for the contamination of the SARS-CoV-2 virus or genome on mobile phones while studies testing for SARS-COV-2 in environments and/or other fomites samples than but not mobile phones were excluded. RESULTS A total of 15 studies with reports of SARS-CoV-2 contamination on mobile phones between 2020 and 2023 were included. Amongst all studies, which encompassed ten countries, 511 mobile phones were evaluated for the presence of SARS-CoV-2 contamination and 45% (231/511) were positive for SARS-CoV-2. All studies were conducted in the hospital setting and two studies performed additional testing in residential isolation rooms and a patient's house. Four studies (3 in 2020 and one in 2021) reported 0% contamination while two other studies (in 2020 and 2022) reported 100% of mobile phone contamination with SARS-COV-2. All other studies report mobile phones positive for the virus within a range of 4-77%. CONCLUSION A total of 45% of mobile phones are contaminated with SARS-CoV-2 virus. These devices might be an important fomite vector for viral dissemination worldwide. Competent health authorities are advised/recommended to start a global implementation of mobile phone decontamination by introducing regulations and protocols in public health and health care settings such as the 6th moment of hand washing.
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Affiliation(s)
- Matthew Olsen
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia
| | | | - Gobinddeep Singh
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia
| | - Adrian Goldsworthy
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia
| | - Peter Jones
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia
| | - Mark Morgan
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia
| | - Rania Nassar
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates; School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Rose Ghemrawi
- College of Pharmacy, Al Ain University, P.O. Box 112612, Abu Dhabi, United Arab Emirates
| | - Reem Almheiri
- General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Hussain Al Marzooqi
- Dubai Police Scientists Council, Dubai Police, Dubai, United Arab Emirates; General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Sumaya Almansoori
- General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Abdullah Albastaki
- Dubai Police Scientists Council, Dubai Police, Dubai, United Arab Emirates; General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Rashid Almansoori
- Dubai Police Scientists Council, Dubai Police, Dubai, United Arab Emirates; General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Simon McKirdy
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Rashed Alghafri
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia; General Department of Forensic Sciences and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Lotti Tajouri
- Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia; Dubai Police Scientists Council, Dubai Police, Dubai, United Arab Emirates; Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia.
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Simon LM, Flocco C, Burkart F, Methner A, Henke D, Rauer L, Müller CL, Vogel J, Quaisser C, Overmann J, Simon S. Microbial fingerprints reveal interaction between museum objects, curators, and visitors. iScience 2023; 26:107578. [PMID: 37664629 PMCID: PMC10469763 DOI: 10.1016/j.isci.2023.107578] [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: 02/10/2023] [Revised: 05/30/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.
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Affiliation(s)
- Lukas M. Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cecilia Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - David Henke
- Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luise Rauer
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Munich, German Research Center for Environmental Health, 86156 Augsburg, Germany
- Institute of Computational Biology, Helmholtz Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Christian L. Müller
- Institute of Computational Biology, Helmholtz Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Johannes Vogel
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Christiane Quaisser
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Stefan Simon
- Rathgen-Forschungslabor, Staatliche Museen zu Berlin - Preußischer Kulturbesitz, 14059 Berlin, Germany
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11
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Tambuzzi S, Maciocco F, Gentile G, Boracchi M, Bailo P, Marchesi M, Zoja R. Applications of microbiology to different forensic scenarios - A narrative review. J Forensic Leg Med 2023; 98:102560. [PMID: 37451142 DOI: 10.1016/j.jflm.2023.102560] [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: 12/21/2022] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
In contrast to other forensic disciplines, forensic microbiology is still too often considered a "side activity" and is not able to make a real and concrete contribution to forensic investigations. Indeed, the various application aspects of this discipline still remain a niche activity and, as a result, microbiological investigations are often omitted or only approximated, in part due to poor report in the literature. However, in certain situations, forensic microbiology can prove to be extremely effective, if not crucial, when all other disciplines fail. Precisely because microorganisms can represent forensic evidence, in this narrative review all the major pathological forensic applications described in the literature have been presented. The goal of our review is to highlight the versatility and transversality of microbiology in forensic science and to provide a comprehensive source of literature to refer to when needed.
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Affiliation(s)
- Stefano Tambuzzi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | - Francesca Maciocco
- Azienda Ospedaliera "San Carlo Borromeo", Servizio di Immunoematologia e Medicina Trasfusionale (SIMT), Via Pio II°, n. 3, Milano, Italy
| | - Guendalina Gentile
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy.
| | - Michele Boracchi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | | | - Matteo Marchesi
- ASST Papa Giovanni XXIII, Piazza OMS 1, 24127, Bergamo, Italy
| | - Riccardo Zoja
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
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12
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Iancu L, Muslim A, Aazmi S, Jitaru V. Postmortem skin microbiome signatures associated with human cadavers within the first 12 h at the morgue. Front Microbiol 2023; 14:1234254. [PMID: 37564294 PMCID: PMC10410280 DOI: 10.3389/fmicb.2023.1234254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Forensic microbiome studies expanded during the last decade, aiming to identify putative bacterial biomarkers to be used for the postmortem interval (PMI) estimation. Bacterial diversity and dynamics during decomposition are influenced by each individual's micro and macroenvironment, ante and postmortem conditions, varying across body sites and time. The skin, the largest organ of the human body, hosts a diverse microbial diversity, representing the first line of defense of a living individual. Targeting the investigation of the postmortem skin microbiome could help understanding the role of microbes during decomposition, and association with the ante and postmortem conditions. Methods The current study aimed to identify the postmortem skin microbiome signatures associated with eight human bodies, received at the Institute of Legal Medicine Iasi, Romania, during April and May 2021. A total of 162 samples (including triplicate) representing face and hands skin microbiome were investigated via Illumina MiSeq, upon arrival at the morgue (T0) and after 12 hours (T1). Results The taxonomic characteristics of the skin microbiota varied across different body sites. However, there were no significant differences in taxonomic profiles between collection time, T0 and T1, except for some dynamic changes in the abundance of dominant bacteria. Moreover, different microbial signatures have been associated with a specific cause of death, such as cardiovascular disease, while an elevated blood alcohol level could be associated with a decrease in bacterial richness and diversity. Discussion The places where the bodies were discovered seemed to play an important role in explaining the bacterial diversity composition. This study shows promising results towards finding common postmortem bacterial signatures associated with human cadavers within the first 12h at the morgue.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Azdayanti Muslim
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Selangor, Malaysia
- Institute for Biodiversity and Sustainable Development, Universiti Teknologi MARA (UiTM), Selangor, Malaysia
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
| | - Shafiq Aazmi
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
- School of Biology, Faculty of Applied Science, Universiti Teknologi MARA, Selangor, Malaysia
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13
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De Alcaraz-Fossoul J, Wang Y, Liu R, Mancenido M, Marshall PA, Núñez C, Broatch J, Ferry L. Microbes in fingerprints: A source for dating crime evidence? Forensic Sci Int Genet 2023; 65:102883. [PMID: 37120981 DOI: 10.1016/j.fsigen.2023.102883] [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: 08/04/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.
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Affiliation(s)
- Josep De Alcaraz-Fossoul
- Forensic Science Department, Henry C. Lee College of Criminal Justice and Forensic Science, University of New Haven; West Haven, Connecticut 06516, United States.
| | - Yue Wang
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Ruoqian Liu
- School of Mathematical and Statistical Sciences, The College of Liberal Arts and Sciences, Arizona State University; Tempe, Arizona 85251, United States
| | - Michelle Mancenido
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Pamela Ann Marshall
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Celeste Núñez
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Jennifer Broatch
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Lara Ferry
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
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14
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Gómez-Gonzales W, Alvarado-Garcia A, Suárez-Mamani M, Dámaso-Mata B, Panduro-Correa V, Maguiña JL, Pecho-Silva S, Rabaan AA, Rodriguez-Morales AJ, Arteaga-Livias K. Contamination by Antibiotic-Resistant Bacteria on Cell Phones of Vendors in a Peruvian Market. Medicina (B Aires) 2023; 59:medicina59040669. [PMID: 37109628 PMCID: PMC10141064 DOI: 10.3390/medicina59040669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Background and Objectives. Multiple studies have evaluated the presence of bacterial contamination on cell phones in clinical settings; however, the presence and transmission of antibiotic-resistant bacteria on cell phones in the community have not been adequately elucidated. Material and Methods. A cross-sectional study was carried out to determine the presence of bacteria resistant to antibiotics on the cell phones of vendors in a Peruvian market and the associated factors. A sample of 127 vendors was obtained through stratified probabilistic sampling using a data collection form validated by experts. Cell phone samples were cultured using a standard technique, and antibiotic sensitivity was determined using the Kirby–Bauer technique. Chi-squared and Mann-Whitney U tests were used to determine factors associated with resistance in cell phone cultures. Results. Among the cell phones, 92.1% showed bacterial growth, predominantly Gram-positive bacteria (coagulase-negative staphylococci and Staphylococcus aureus), and 17% of the cultures showed resistance to at least three antibiotics evaluated. Two strains fell into the category of methicillin-resistant S. aureus, and three strains of E. coli had resistance to carbapenems. Conclusions. A short distance between customers and vendors, lack of a cell phone case, and having a cell phone with touchscreen are factors associated with antibiotic-resistant bacteria on cell phones.
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Affiliation(s)
- Walter Gómez-Gonzales
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11001, Peru;
| | - Anthony Alvarado-Garcia
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco 10003, Peru; (A.A.-G.); (M.S.-M.); (B.D.-M.); (V.P.-C.)
| | - Marytté Suárez-Mamani
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco 10003, Peru; (A.A.-G.); (M.S.-M.); (B.D.-M.); (V.P.-C.)
| | - Bernardo Dámaso-Mata
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco 10003, Peru; (A.A.-G.); (M.S.-M.); (B.D.-M.); (V.P.-C.)
| | - Vicky Panduro-Correa
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco 10003, Peru; (A.A.-G.); (M.S.-M.); (B.D.-M.); (V.P.-C.)
- Hospital Regional Hermilio Valdizan, Huánuco 15011, Peru
| | - Jorge L. Maguiña
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima 15067, Peru; (J.L.M.); (A.J.R.-M.)
| | | | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Alfonso J. Rodriguez-Morales
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima 15067, Peru; (J.L.M.); (A.J.R.-M.)
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas-Institución Universitaria Visión de las Américas, Pereira 660003, Colombia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
| | - Kovy Arteaga-Livias
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11001, Peru;
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco 10003, Peru; (A.A.-G.); (M.S.-M.); (B.D.-M.); (V.P.-C.)
- Hospital II EsSalud, Huánuco 10001, Peru
- Correspondence:
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15
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He J, Shen X, Zhang N, Sun C, Shao Y. Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens. Microbiol Spectr 2022; 10:e0150822. [PMID: 36040152 PMCID: PMC9603676 DOI: 10.1128/spectrum.01508-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022] Open
Abstract
Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 106 bacteria (2.24 × 104/cm2) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 106 bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Beijing, China
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16
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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17
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Kumari P, Prakash P, Yadav S, Saran V. Microbiome analysis: An emerging forensic investigative tool. Forensic Sci Int 2022; 340:111462. [PMID: 36155349 DOI: 10.1016/j.forsciint.2022.111462] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/30/2022]
Abstract
Microbial diversity's potential has been investigated in medical and therapeutic studies throughout the last few decades. However, its usage in forensics is increasing due to its effectiveness in circumstances when traditional approaches fail to provide a decisive opinion or are insufficient in forming a concrete opinion. The application of human microbiome may serve in detecting the type of stains of saliva and vaginal fluid, as well as in attributing the stains to the individual. Similarly, the microbiome makeup of a soil sample may be utilised to establish geographic origin or to associate humans, animals, or things with a specific area, additionally microorganisms influence the decay process which may be used in depicting the Time Since death. Further in detecting the traces of the amount and concentration of alcohol, narcotics, and other forensically relevant compounds in human body or visceral tissues as they also affect the microbial community within human body. Beside these, there is much more scope of microbiomes to be explored in terms of forensic investigation, this review focuses on multidimensional approaches to human microbiomes from a forensic standpoint, implying the potential of microbiomes as an emerging tool for forensic investigations such as individual variability via skin microbiomes, reconstructing crime scene, and linking evidence to individual.
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Affiliation(s)
- Pallavi Kumari
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India.
| | - Poonam Prakash
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Shubham Yadav
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Vaibhav Saran
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
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18
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Determination of drug-resistant bacteria in palmar surface and touchscreen cell phones from bystanders in an urban community. Microbiol Res 2021; 256:126958. [PMID: 34998184 DOI: 10.1016/j.micres.2021.126958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 12/05/2021] [Accepted: 12/27/2021] [Indexed: 11/22/2022]
Abstract
The dynamic microbiota of the human palmar surface (PS) is related to the various hygienic habits of humans and can be transmitted or exchanged upon contact with objects of daily use, such as the indispensable touchscreen cell phone (TCP); this interaction could allow the development of drug-resistant bacteria. The objective was to determine the drug-resistant bacterial contamination between PSs and TCPs in an urban community. Among the total bacterial colonies isolated and molecular and phylogenetically characterized based on the V4-V6 regions of the 16S rRNA gene from PSs and TCPs, the genera present in both types of samples were Staphylococcus (53.3 and 43.5 %, respectively), Bacillus (37.8, 37 %), Atlantibacter (2.2, 10.8 %) and Microbacterium (2.2, 4.3 %). The genera present in only one type of sample were Rothia, Paenibacillus, Escherichia and Micrococcus (2.2 % each). Resistance to penicillins (35.6-93.5 %) and nonsusceptibility to cephalosporins (8.9-37 %) and nitrofurantoin (13.3 and 15.2 %) were observed. The percentage of multidrug antibiotic resistance was 15.4 %. The prevalence of drug-resistant and multidrug-resistant bacteria in PSs and TCPs in the community could give rise to human health problems, and hygiene measures are recommended.
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19
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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: 17] [Impact Index Per Article: 5.7] [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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20
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Hessling M, Haag R, Sicks B. Review of microbial touchscreen contamination for the determination of reasonable ultraviolet disinfection doses. GMS HYGIENE AND INFECTION CONTROL 2021; 16:Doc30. [PMID: 34956822 PMCID: PMC8662742 DOI: 10.3205/dgkh000401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background: Touchscreens are usually microbially contaminated and can therefore act as fomites inside and outside healthcare environments. Due to the increasing use of such touchscreens and the growing awareness of infection risks, approaches that allow safe and automatic disinfection are desired. Ultraviolet (UV) irradiation, with its known antimicrobial efficacy, could achieve this goal, but should be executed with limited touchscreen degradation, disinfection duration, and energy consumption. It should also pose as little harm as possible to humans even in case of failure. Materials and methods: A literature search was performed first to identify the microorganisms most commonly found on touchscreens. Then, the 90% reduction doses (D90 doses) for the different relevant microorganisms and UV spectral ranges were determined from the literature, and irradiation doses are suggested that should reduce most of these important microorganisms by 5 log-levels. Results: The most frequent microorganisms are staphylococci, bacilli, micrococci, enterococci, pseudomonads and E. coli with small differences between hospital and community environments, if antibiotic resistance properties are ignored. The determined irradiation doses for a 5 log-reduction of the most frequent microorganisms are about 40 mJ/cm2, 80 J/cm2, 500 J/cm2 and 50 mJ/cm2 for the UV spectral ranges UVC, UVB, UVA and far-UVC, respectively. These doses are also sufficient to inactivate all nosocomial ESKAPE pathogens on touchscreens by at least 99.999%. Conclusion: Disinfection is achievable in all UV spectral ranges, with UVC being the most effective, enabling automatic disinfection within a minute or less. The much higher doses required in the UVB and UVA spectral range result in much longer disinfection durations, with the advantage of a reduced risk to humans. For all kinds of UV irradiation, the doses should be limited to reasonable values to avoid irradiating an already more or less sterile surface and to prevent degradation of touchscreen devices.
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Affiliation(s)
- Martin Hessling
- Ulm University of Applied Sciences, Institute of Medical Engineering and Mechatronics, Ulm, Germany
| | - Robin Haag
- Ulm University of Applied Sciences, Institute of Medical Engineering and Mechatronics, Ulm, Germany
| | - Ben Sicks
- Ulm University of Applied Sciences, Institute of Medical Engineering and Mechatronics, Ulm, Germany
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21
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Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions. Forensic Sci Int Genet 2021; 56:102627. [PMID: 34742094 DOI: 10.1016/j.fsigen.2021.102627] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022]
Abstract
Over the last few years, advances in massively parallel sequencing technologies (also referred to next generation sequencing) and bioinformatics analysis tools have boosted our knowledge on the human microbiome. Such insights have brought new perspectives and possibilities to apply human microbiome analysis in many areas, particularly in medicine. In the forensic field, the use of microbial DNA obtained from human materials is still in its infancy but has been suggested as a potential alternative in situations when other human (non-microbial) approaches present limitations. More specifically, DNA analysis of a wide variety of microorganisms that live in and on the human body offers promises to answer various forensically relevant questions, such as post-mortem interval estimation, individual identification, and tissue/body fluid identification, among others. However, human microbiome analysis currently faces significant challenges that need to be considered and overcome via future forensically oriented human microbiome research to provide the necessary solutions. In this perspective article, we discuss the most relevant biological, technical and data-related issues and propose future solutions that will pave the way towards the integration of human microbiome analysis in the forensic toolkit.
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22
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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: 36] [Impact Index Per Article: 12.0] [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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23
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Hespanha ACV, Minto BW, Cardozo MV, Menezes MPD, Tasso JB, Moraes PC. Contamination by antimicrobial-resistant enterobacteria isolated from cell phones and hands in a veterinary hospital. Acta Vet Hung 2021; 69:216-222. [PMID: 34546965 DOI: 10.1556/004.2021.00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022]
Abstract
Hospital infections are of great relevance in human and animal health, and fomites are important in the spread of pathogens in hospital units. The aim of this study was to investigate the frequency of enterobacteria in the operating room of a veterinary hospital, the potential cross-contamination of samples, and to characterise the susceptibility profile of the isolates to antimicrobials. Sixty-five samples were collected from five different surgical procedures. These samples came from the hands and cell phones of the surgical team and pet owners, operating tables, and patients. Species detection was performed through polymerase chain reaction, genetic diversity by pulsed-field gel electrophoresis (PFGE), and susceptibility to antimicrobials through an antibiogram. Escherichia coli and Proteus mirabilis isolates were obtained from eight samples, from the hands of the anaesthesiologist, the pet owner, and the surgeon; the surgeon's, the nurse's and the anaesthesiologist's cell phones, and two surgical tables. Furthermore, PFGE showed high genetic diversity among the isolates, which showed multidrug resistance. The identification of multidrug-resistant E. coli and P. mirabilis on cell phones of the surgical team is a major concern and, although no direct correlation was found, the isolation of these bacteria inside the clean area of the operating room shows the possibility of nosocomial transmission from cell phones to susceptible patients.
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Affiliation(s)
- Ana Carolina Valentim Hespanha
- 1 Department of Veterinary Clinic and Surgery, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Bruno Watanabe Minto
- 1 Department of Veterinary Clinic and Surgery, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Marita Vedovelli Cardozo
- 2 Department of Veterinary Pathology, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Mareliza Possa De Menezes
- 1 Department of Veterinary Clinic and Surgery, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Júlia Banhareli Tasso
- 1 Department of Veterinary Clinic and Surgery, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Paola Castro Moraes
- 1 Department of Veterinary Clinic and Surgery, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
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24
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Pistone D, Meroni G, Panelli S, D’Auria E, Acunzo M, Pasala AR, Zuccotti GV, Bandi C, Drago L. A Journey on the Skin Microbiome: Pitfalls and Opportunities. Int J Mol Sci 2021; 22:9846. [PMID: 34576010 PMCID: PMC8469928 DOI: 10.3390/ijms22189846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
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Affiliation(s)
- Dario Pistone
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Gabriele Meroni
- Department of Biomedical Surgical and Dental Sciences-One Health Unit, University of Milan, 20133 Milan, Italy;
| | - Simona Panelli
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Enza D’Auria
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Miriam Acunzo
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Ajay Ratan Pasala
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Claudio Bandi
- Pediatric Clinical Research Center “Invernizzi”, Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
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25
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The Associations between Knowledge and Behaviours Related to Touch Screens and Microbiological Threats among IT Students'. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179269. [PMID: 34501860 PMCID: PMC8431698 DOI: 10.3390/ijerph18179269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
Current issue like the COVID–19 pandemic show how elementary knowledge and hygiene behaviours are important for ordinary people. Microbiological hazards, not just viruses, can be transmitted in various ways through touch screens. For ordinary users, there is a wide range of behaviours that affect the ability to transfer microbial hazards (viruses, bacteria and fungi). The purpose of the paper is to analyse the association between knowledge and behaviour of touch screen users based on surveys. This paper presents selected results of a survey conducted at the end of 2019 (pre–COVID–19 survey). The survey was conducted on a group of 172 IT school students. The relationship between responses using a 2D linear model regression and clustering is used. Most respondents believe that bacteria were more common than viruses on touch screens. The respondents declare altruism in terms of a greater willingness to lend their smartphone, rather than to use someone else’s. An interesting result is that respondents often lend their smartphone to others, while being aware that viruses or bacteria are present on the touch screens. The results can be used in terms of changes in the education process of smartphone users in relation to microbiological hazards.
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26
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Population informative markers selected using Wright's fixation index and machine learning improves human identification using the skin microbiome. Appl Environ Microbiol 2021; 87:e0120821. [PMID: 34379455 DOI: 10.1128/aem.01208-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial DNA, shed from human skin, can be distinctive to its host and thus help individualize donors of forensic biological evidence. Previous studies have utilized single locus microbial DNA markers (e.g., 16S rRNA) to assess the presence/absence of personal microbiota to profile human hosts. However, since the taxonomic composition of the microbiome is in constant fluctuation, this approach may not be sufficiently robust for human identification (HID). Multi-marker approaches may be more powerful. Additionally, genetic differentiation, rather than taxonomic distinction, may be more individualizing. To this end, the non-dominant hands of 51 individuals were sampled in triplicate (n = 153). They were analyzed for markers in the hidSkinPlex, a multiplex panel comprising candidate markers for skin microbiome profiling. Single nucleotide polymorphisms (SNPs) with the highest Wright's fixation index (FST) estimates were then selected for predicting donor identity using a support vector machine (SVM) learning model. FST is an estimate of the genetic differences within and between populations. Three different SNP selection criteria were employed: SNPs with the highest-ranking FST estimates 1) common between any two samples regardless of markers present (termed overall); 2) each marker common between samples (termed per marker); and 3) common to all samples used to train the SVM algorithm for HID (termed selected). The SNPs chosen based on criteria for overall, per marker, and selected methods resulted in an accuracy of 92.00%, 94.77%, and 88.00%, respectively. The results support that estimates of FST, combined with SVM, can notably improve forensic HID via skin microbiome profiling. IMPORTANCE There is a need for additional genetic information to help identify the source of biological evidence found at a crime scene. The human skin microbiome is a potentially abundant source of DNA that can enable the identification of a donor of biological evidence. With microbial profiling for human identification, there will be an additional source of DNA to identify individuals as well as to exclude individuals wrongly associated with biological evidence, thereby improving the utility of forensic DNA profiling to support criminal investigations.
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27
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Sanjar F, Weaver AJ, Peacock TJ, Nguyen JQ, Brandenburg KS, Leung KP. Identification of Metagenomics Structure and Function Associated With Temporal Changes in Rat (Rattus norvegicus) Skin Microbiome During Health and Cutaneous Burn. J Burn Care Res 2021; 41:347-358. [PMID: 31665423 DOI: 10.1093/jbcr/irz165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The cutaneous skin microbiome is host to a vast ensemble of resident microbes that provide essential capabilities including protection of skin barrier integrity and modulation of the host immune response. Cutaneous burn-injury promotes alteration of cutaneous and systemic immune response that can affect both commensal and pathogenic microbes. A cross-sectional study of a limited number of burn patients revealed a difference in the bacteriome of burned versus control participants. Temporal changes of the skin microbiome during health and cutaneous burn-injury remains largely unknown. Furthermore, how this microbial shift relates to community function in the collective metagenome remain elusive. Due to cost considerations and reduced healing time, rodents are frequently used in burn research, despite inherent physiological differences between rodents and human skin. Using a rat burn model, a longitudinal study was conducted to characterize the rat skin bacterial residents and associated community functions in states of health (n = 30) (sham-burned) and when compromised by burn-injury (n = 24). To address the knowledge gap, traumatic thermal injury and disruption of cutaneous surface is associated with genus-level changes in the microbiota, reduced bacterial richness, and altered representation of bacterial genes and associated predicted functions across different skin microbial communities. These findings demonstrate that, upon burn-injury, there is a shift in diversity of the skin's organismal assemblages, yielding a core microbiome that is distinct at the genome and functional level. Moreover, deviations from the core community correlate with temporal changes post-injury and community transition from the state of cutaneous health to disease (burn-injury).
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Affiliation(s)
- Fatemeh Sanjar
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, U.S. Army Institute of Surgical Research, JBSA Fort, Sam Houston, Texas
| | - Alan J Weaver
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, U.S. Army Institute of Surgical Research, JBSA Fort, Sam Houston, Texas
| | | | - Jesse Q Nguyen
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, U.S. Army Institute of Surgical Research, JBSA Fort, Sam Houston, Texas
| | - Kenneth S Brandenburg
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, U.S. Army Institute of Surgical Research, JBSA Fort, Sam Houston, Texas
| | - Kai P Leung
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, U.S. Army Institute of Surgical Research, JBSA Fort, Sam Houston, Texas
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A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes. Sci Rep 2021; 11:14102. [PMID: 34239006 PMCID: PMC8266881 DOI: 10.1038/s41598-021-93622-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/28/2021] [Indexed: 11/28/2022] Open
Abstract
There is increasing attention focussed on the risks associated with mobile phones possibly serving as ‘Trojan Horse’ fomites for microbial transmission in healthcare settings. However, little is reported on the presence of microbes on community derived mobile phones which in 2021, numbered in the billions in circulation with majority being used on a daily basis. Identify viable microbial organisms swabbed from smartphones on a university campus. Entire surfaces of 5 mobile phones were swabbed and examined for their microbial content using pre-agar-based growths followed by downstream DNA metagenomic next-generation sequencing analysis. All phones were contaminated with viable microbes. 173 bacteria, 8 fungi, 8 protists, 53 bacteriophages, 317 virulence factor genes and 41 distinct antibiotic resistant genes were identified. While this research represents a pilot study, the snapshot metagenomic analysis of samples collected from the surface of mobile phones has revealed the presence of a large population of viable microbes and an array of antimicrobial resistant factors. With billions of phones in circulation, these devices might be responsible for the rise of community acquired infections. These pilot results highlight the importance of public health authorities considering mobile phones as ‘Trojan Horse’ devices for microbial transmission and ensure appropriate decontamination campaigns are implemented.
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29
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Kirchner M, Goulter RM, Chapman BJ, Clayton J, Jaykus LA. Cross-Contamination on Atypical Surfaces and Venues in Food Service Environments. J Food Prot 2021; 84:1239-1251. [PMID: 33545714 DOI: 10.4315/jfp-20-314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/02/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Cross-contamination of raw food to other surfaces, hands, and foods is a serious issue in food service. With individuals eating more meals away from home, contracting a foodborne illness from a food service establishment is an increasing concern. However, most studies have concentrated on hands or food contact surfaces and neglected atypical and unusual surfaces (surfaces that are not typically identified as a source of cross-contamination) and venues. This review was conducted to identify atypically cross-contaminated surfaces and atypical venues where cross-contamination could occur that have not been examined thoroughly in the literature. Most surfaces that could be at risk for cross-contamination are frequently touched, are rarely cleaned and sanitized, and can support the persistence and/or growth of foodborne pathogens. These surfaces include menus, spice and condiment containers, aprons and coveralls, mobile devices and tablets, and money. Venues that are explored, such as temporary events, mobile vendors, and markets, are usually limited in space or infrastructure, have low compliance with proper hand washing, and provide the opportunity for raw and ready-to-eat foods to come into contact with one another. These factors create an environment in which cross-contamination can occur and potentially impact food safety. A more comprehensive cleaning and sanitizing regime encompassing these surfaces and venues could help mitigate cross-contamination. This review highlights key surfaces and venues that have the potential to be cross-contaminated and have been underestimated or not fully investigated. These knowledge gaps indicate where further work is needed to fully understand the role of these surfaces and venues in cross-contamination and how it can be prevented. HIGHLIGHTS
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Affiliation(s)
- Margaret Kirchner
- Department of Food, Bioprocessing and Nutrition Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Rebecca M Goulter
- Department of Food, Bioprocessing and Nutrition Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Benjamin J Chapman
- Department of Agricultural and Human Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Lee-Ann Jaykus
- Department of Food, Bioprocessing and Nutrition Science, North Carolina State University, Raleigh, North Carolina 27695
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Wilkins D, Tong X, Leung MHY, Mason CE, Lee PKH. Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching. MICROBIOME 2021; 9:129. [PMID: 34090519 PMCID: PMC8180031 DOI: 10.1186/s40168-021-01082-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/21/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days. RESULTS Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied. CONCLUSIONS These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.
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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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Neckovic A, van Oorschot RAH, Szkuta B, Durdle A. Identifying background microbiomes in an evidence recovery laboratory: A preliminary study. Sci Justice 2021; 61:280-290. [PMID: 33985676 DOI: 10.1016/j.scijus.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/08/2020] [Accepted: 01/03/2021] [Indexed: 01/16/2023]
Abstract
16S rRNA profiling of bacterial communities may have forensic utility in the identification or association of individuals involved with criminal activities. Microbial profiling of evidence may, in the future, be performed within environments currently utilised for human DNA recovery, such as a forensic biology laboratory. It would be important to establish the background microbiome of such an environment to determine the potential presence of human or environmental microbial signatures to assist forensic scientists in the appropriate interpretation of target microbial communities. This study sampled various surfaces of an Evidence Recovery Laboratory (ERL) on three occasions including (a) before a monthly deep-clean, (b) immediately following the deep-clean, and (c) immediately after the laboratory's use by a single participant for the purposes of routine item examinations. Microbial profiles were also generated for the involved participant and researcher for comparison purposes. Additionally, human nuclear DNA was profiled for each of the samples collected, using standard forensic profiling techniques, to provide a prospective link to the presence or absence of a background microbial signature within the ERL after its use. Taxonomic distributions across ERL samples revealed no consistent signature of any of the items sampled over time, however, major phyla noted within all ERL samples across the three timepoints were consistent with those found in human skin microbiomes. PCoA plots based on the Unweighted Unifrac metric revealed some clustering between participant microbial reference samples and surfaces of the ERL after use, suggesting that despite a lack of direct contact, and adherence to standard operating procedures (SOPs) suitable for human DNA recovery, microbiomes may be deposited into a forensic setting over time. The reference samples collected from the involved participant and researcher generated full STR profiles. Human DNA was observed to varying degrees in samples taken from the ERL across each of the sampling timepoints. There was no correlation observed between samples that contained or did not contain detectable quantities of human nuclear DNA and microbial profile outputs.
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Affiliation(s)
- Ana Neckovic
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia.
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia; School of Molecular Sciences, La Trobe University, Bundoora, Australia
| | - Bianca Szkuta
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
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Ishak S, Dormontt E, Young JM. Microbiomes in forensic botany: a review. Forensic Sci Med Pathol 2021; 17:297-307. [PMID: 33830453 DOI: 10.1007/s12024-021-00362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/24/2022]
Abstract
Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.
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Affiliation(s)
- Sarah Ishak
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
| | - Eleanor Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Limon MR. Food safety practices of food handlers at home engaged in online food businesses during COVID-19 pandemic in the Philippines. Curr Res Food Sci 2021; 4:63-73. [PMID: 33665620 PMCID: PMC7903060 DOI: 10.1016/j.crfs.2021.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/31/2020] [Accepted: 01/10/2021] [Indexed: 11/28/2022] Open
Abstract
This study was conducted to assess the self-reported and observed food safety practices (FSP) of food handlers, who deliver food products that are prepared and cooked at home during the COVID-19 pandemic in the Philippines. 751 participated in the online survey who were selected using criterion sampling. A questionnaire developed by the researcher was used to gather data with Cronbach Alpha of 0.91. t-test, ANOVA, and Fleiss kappa were performed to treat data. There were no significant differences between self-reported FSP in four dimensions and demographic characteristics, except for age, where a significant difference exists between the FSP of the four age groups along food preparation (F = 4.530,ρ<0.01). The FSP in the four dimensions obtained a weighted x¯ and σ of 1.72 ± 0.69 which is interpreted as Sometimes Practiced. The food handlers at home inadequately and inappropriately practiced the protocols in keeping the food safe to eat. The observed reports showed that the food handlers at home do not meet food safety standards as indicated in the weighted x¯ and σ in the four dimensions 1.63 ± 0.11, with a description of Sometimes Practiced. Observed practices further show very poor adherence to guidelines. Test for inter-rater reliability yielded almost perfect agreement (κ = 0.81, ρ<0.05). There exists a significant difference with the FSP in personal hygiene (t = 0.964, ρ<0.05), cross-contamination prevention and sanitation (t = 0.815, ρ<0.05), food preparation (t = 0.753, ρ<0.05), and food delivery (t = 0.794, ρ<0.05). Government and non-government agencies should work together towards educating the food handlers at home on effective ways to learn about food safety concepts so they could become advocates of safer food practices. Online food business is growing due to restrictions brought about by the pandemic. Self-reported FSP of food handlers reveal compliance to food safety standards. Food handlers violate food safety protocols based on expert observations. There is significant difference between the self-reported and the observed FSP. Food safety training involving food handlers in online businesses is imperative.
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Affiliation(s)
- Mark Raguindin Limon
- Office of the Product Safety and Standards, Science and Technology Park, Mariano Marcos State University, Philippines
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Neckovic A, van Oorschot RAH, Szkuta B, Durdle A. Investigation into the presence and transfer of microbiomes within a forensic laboratory setting. Forensic Sci Int Genet 2021; 52:102492. [PMID: 33713931 DOI: 10.1016/j.fsigen.2021.102492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/21/2022]
Abstract
Microbial profiling within forensic science is an emerging field that may have applications in the identification of individuals using microbial signatures. It is important to determine if microbial transfer may occur within a forensic laboratory setting using current standard operating procedures (SOPs) for nuclear DNA recovery, to assess the suitability of such procedures for microbial profiling and establish the potential limitations of microbial profiling for forensic purposes. This preliminary study investigated the presence and potential transfer of human-associated microbiomes within a forensic laboratory. Swabs of laboratory surfaces, external surfaces of personal protective equipment (PPE) and equipment were taken before and after mock examinations of cotton swatches, which harboured microbiota transferred from direct hand-contact. Microbial profiles obtained from these samples were compared to reference profiles obtained from the participants, cotton swatches and the researcher to detect microbial transfer from the individuals and determine potential source contributions. The results revealed an apparent transfer of microbiota to the examined swatches, laboratory equipment and surfaces from the participants and/or researcher following the mock examinations, highlighting potential contamination issues regarding microbial profiling when using current laboratory SOPs for nuclear DNA recovery, and cleaning.
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Affiliation(s)
- Ana Neckovic
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia.
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia; La Trobe University, School of Molecular Sciences, Bundoora, Australia
| | - Bianca Szkuta
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
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Roy D, Tomo S, Purohit P, Setia P. Microbiome in Death and Beyond: Current Vistas and Future Trends. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.
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Abstract
Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. The highly personalized human skin microbiome may serve as a viable marker in personal identification. Amplicon sequencing resolution using 16S rRNA cannot identify bacterial communities sufficiently to discriminate between individuals. Thus, novel higher-resolution genetic markers are required for forensic purposes. The clustered regularly interspaced short palindromic repeats (CRISPRs) are prokaryotic genetic elements that can provide a history of infections encountered by the bacteria. The sequencing of CRISPR spacers may provide phylogenetic information with higher resolution than other markers. However, using spacer sequencing for discrimination of personal skin microbiome is difficult due to limited information on CRISPRs in human skin microbiomes. It remains unclear whether personal microbiome discrimination can be achieved using spacer diversity or which CRISPRs will be forensically relevant. We identified common CRISPRs in the human skin microbiome via metagenomic reconstruction and used amplicon sequencing for deep sequencing of spacers. We successfully reconstructed 24 putative CRISPR arrays using metagenomic data sets. A total of 1,223,462 reads from three CRISPR arrays revealed that spacers in the skin microbiome were highly personalized, and conserved repeats were commonly shared between individuals. These individual specificities observed using CRISPR typing were confirmed by comparing the CRISPR diversity to microbiome diversity assessed using 16S rRNA amplicon sequencing. CRISPR typing achieved 95.2% accuracy in personal classification, whereas 16S rRNA sequencing only achieved 52.6%. These results suggest that sequencing CRISPRs in the skin microbiome may be a more powerful approach for personal identification and ecological studies compared to conventional 16S rRNA sequencing. IMPORTANCE Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. In this study, we identified 24 putative CRISPR arrays using a shotgun metagenome data set of the human skin microbiome. The findings of this study expand our understanding of the nature of CRISPRs by identifying novel CRISPR candidates. We developed a method to efficiently determine the diversity of three CRISPR arrays. Our analysis revealed that the CRISPR spacer diversity in the human skin microbiome is highly personalized compared with the microbiome diversity assessed by 16S rRNA sequencing, providing a new perspective on the study of the skin microbiome.
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37
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Antimicrobial susceptibility of bacterial isolates from the conjunctiva, storage cases and mobile phones of university students using contact lenses. Cont Lens Anterior Eye 2021; 44:62-66. [DOI: 10.1016/j.clae.2019.10.139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/14/2023]
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Robinson JM, Pasternak Z, Mason CE, Elhaik E. Forensic Applications of Microbiomics: A Review. Front Microbiol 2021; 11:608101. [PMID: 33519756 PMCID: PMC7838326 DOI: 10.3389/fmicb.2020.608101] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape, University of Sheffield, Sheffield, United Kingdom.,Healthy Urban Microbiome Initiative (HUMI), Adelaide, SA, Australia
| | - Zohar Pasternak
- Quality Assurance and Evidence Unit, Division of Identification and Forensic Science (DIFS), National Headquarters of the Israel Police, Jerusalem, Israel
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
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39
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Ghemrawi M, Torres AR, Duncan G, Colwell R, Dadlani M, McCord B. The genital microbiome and its potential for detecting sexual assault. Forensic Sci Int Genet 2020; 51:102432. [PMID: 33307384 DOI: 10.1016/j.fsigen.2020.102432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/22/2022]
Abstract
Since its inception, the Human Microbiome Project (HMP) has provided key discoveries that can be applied to forensics, in addition to those of obvious medical value. Whether for postmortem interval estimation, geolocation, or human identification, there are many applications of the microbiome as an investigative lead for forensic casework. The human skin microbiome has shown great potential for use in studies of transfer and human identification, however there has been little focus on the genital microbiome, in particular penile skin which differs from other body sites. Our preliminary data on both the penile and vaginal microbiome demonstrates potential value in cases of sexual assault. In this study we describe genital microbial signatures based on the analysis of five male and five female genital samples and compare these results to those from longitudinal studies. Selected taxa, e.g., Gardnerella, Lactobacilli, Finegoldia, Peptoniphilus, and Anaerococci, are shown to be candidate constituents of the genital microbiome that merit investigation for use in sexual assault casework.
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Affiliation(s)
- Mirna Ghemrawi
- Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Fort Lauderdale-Davie, FL 33314, United States
| | - Rita Colwell
- University of Maryland, College Park, MD 20740, United States
| | | | - Bruce McCord
- Florida International University, Miami, FL 33199, United States.
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40
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Young JM, Linacre A. Massively parallel sequencing is unlocking the potential of environmental trace evidence. Forensic Sci Int Genet 2020; 50:102393. [PMID: 33157385 DOI: 10.1016/j.fsigen.2020.102393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 01/16/2023]
Abstract
Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.
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Affiliation(s)
- J M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
| | - A Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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41
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Challenges in Human Skin Microbial Profiling for Forensic Science: A Review. Genes (Basel) 2020; 11:genes11091015. [PMID: 32872386 PMCID: PMC7564248 DOI: 10.3390/genes11091015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach.
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Cicciarella Modica D, Maurici M, D’Alò GL, Mozzetti C, Messina A, Distefano A, Pica F, De Filippis P. Taking Screenshots of the Invisible: A Study on Bacterial Contamination of Mobile Phones from University Students of Healthcare Professions in Rome, Italy. Microorganisms 2020; 8:microorganisms8071075. [PMID: 32707676 PMCID: PMC7409191 DOI: 10.3390/microorganisms8071075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/07/2023] Open
Abstract
Mobile phones (MPs) are commonly used both in the personal and professional life. We assessed microbiological contamination of MPs from 108 students in healthcare professions (HPs), in relation to their demographic characteristics and MPs handling habits, collected by means of a questionnaire. Cultural and biochemical tests were performed, and statistical analyses were carried out. Staphylococci were present in 85% of MPs, Enterococci in 37%, Coliforms in 6.5%; E. coli was never detected. Staphylococcus epidermidis was the most frequently isolated staphylococcal species (72% of MPs), followed by S. capitis (14%), S. saprophyticus, S. warneri, S. xylosus (6%), and by S. aureus (4%). Heterotrophic Plate Counts (HPC) at 37 °C, ranged from 0 to 1.2 × 104 CFU/dm2 (mean = 362 CFU/dm2). In univariate analysis, the male gender only was significantly associated with higher HPCs and enterococcal contamination. Multiple linear regression models explained only 17% and 16% of the HPC 37 °C and staphylococcal load variability, respectively. Developing specific guidelines for a hygienic use of MPs in clinical settings, for preventing cross-infection risks, is advisable, as well as introducing specific training programs to HP students. MPs decontamination procedures could also be implemented in the community.
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Affiliation(s)
| | - Massimo Maurici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
- Correspondence: (M.M.); (G.L.D.); Tel.: +39-327-8218-514 (G.L.D.)
| | - Gian Loreto D’Alò
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
- Department of Epidemiology, Lazio Regional Health Service, 00154 Rome, Italy
- Correspondence: (M.M.); (G.L.D.); Tel.: +39-327-8218-514 (G.L.D.)
| | - Cinzia Mozzetti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
| | - Alessandra Messina
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
| | - Alessandra Distefano
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
| | - Francesca Pica
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Patrizia De Filippis
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy; (C.M.); (A.M.); (A.D.); (P.D.F.)
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Bhardwaj N, Khatri M, Bhardwaj SK, Sonne C, Deep A, Kim KH. A review on mobile phones as bacterial reservoirs in healthcare environments and potential device decontamination approaches. ENVIRONMENTAL RESEARCH 2020; 186:109569. [PMID: 32339954 DOI: 10.1016/j.envres.2020.109569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Mobile communication devices (MCDs), including cell phones and smart phones, have become an essential part of everyday life. Despite their frequent usage, most people, even healthcare personnel, often ignore the possibility that these devices might accumulate to carry a variety of microbial flora during and after the inspection of patients. The handling of MCDs with unwashed hands and/or their seldom cleaning can aggravate potential health risks. Many of the harbored bacteria species can be harmful to immune-suppressed patients for whom the disinfection precautions should be taken more seriously. In this review, we discuss the significance of maintaining the cleanliness of mobile devices, especially in healthcare settings, to prevent the spread of nosocomial infections in patients. Furthermore, we discuss strategies to address microbial contamination of MCDs to maintain good hand hygiene for the users of smartphones or other mobile communication devices. These techniques are capable of providing instant disinfection of the devices along with residual effects over prolonged periods.
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Affiliation(s)
- Neha Bhardwaj
- Department of Biotechnology, University Institute of Engineering Technology (UIET), Panjab University, Chandigarh, India
| | - Madhu Khatri
- Department of Biotechnology, University Institute of Engineering Technology (UIET), Panjab University, Chandigarh, India; Wellcome Trust/DBT IA Early Career Fellow, India
| | - Sanjeev K Bhardwaj
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing, Sector 81 (Knowledge City), S.A.S. Nagar, 140306, Punjab, India
| | - Christian Sonne
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark
| | - Akash Deep
- Central Scientific Instruments Organisation, Sector 30 C, Chandigarh, 160030, India.
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul, 04763, Republic of Korea.
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Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ 2020; 8:e9235. [PMID: 32551196 PMCID: PMC7292020 DOI: 10.7717/peerj.9235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
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Affiliation(s)
- David A Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Russell Y Neches
- Genome Center, University of California, Davis, CA, United States of America
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Wendy E Brown
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.,Science Cheerleaders, Inc., Philadelphia, PA, United States of America
| | - Darlene Cavalier
- Science Cheerleaders, Inc., Philadelphia, PA, United States of America.,SciStarter.org, Philadelphia, PA, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, University of Chicago, Lemont, IL, United States of America
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UC San Diego School of Medicine, San Diego, CA, United States of America
| | - Jonathan A Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
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45
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Tozzo P, D’Angiolella G, Brun P, Castagliuolo I, Gino S, Caenazzo L. Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Microorganisms 2020; 8:microorganisms8060873. [PMID: 32527009 PMCID: PMC7356928 DOI: 10.3390/microorganisms8060873] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 01/15/2023] Open
Abstract
Microbiome research is a highly transdisciplinary field with a wide range of applications and methods for studying it, involving different computational approaches and models. The fact that different people host radically different microbiota highlights forensic perspectives in understanding what leads to this variation and what regulates it, in order to effectively use microbes as forensic evidence. This narrative review provides an overview of some of the main scientific works so far produced, focusing on the potentiality of using skin microbiome profiling for human identification in forensics. This review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The examined literature clearly ascertains that skin microbial communities, although personalized, vary systematically across body sites and time, with intrapersonal differences over time smaller than interpersonal ones, showing such a high degree of spatial and temporal variability that the degree and nature of this variability can constitute in itself an important parameter useful in distinguishing individuals from one another. Even making the effort to organically synthesize all results achieved until now, it is quite evident that these results are still the pieces of a puzzle, which is not yet complete.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
- Correspondence: ; Tel.: +39-0498272234
| | - Gabriella D’Angiolella
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy;
| | - Paola Brun
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Sarah Gino
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
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Hampton-Marcell JT, Larsen P, Anton T, Cralle L, Sangwan N, Lax S, Gottel N, Salas-Garcia M, Young C, Duncan G, Lopez JV, Gilbert JA. Detecting personal microbiota signatures at artificial crime scenes. Forensic Sci Int 2020; 313:110351. [PMID: 32559614 DOI: 10.1016/j.forsciint.2020.110351] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/13/2020] [Accepted: 05/26/2020] [Indexed: 01/16/2023]
Abstract
When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real residences. We demonstrate that humans (n = 30) leave behind microbial signatures that can be used to track interaction with various surfaces within a building, but the likelihood of accurately detecting the specific burglar for a given home was between 20-25%. Also, the human microbiome contains rare microbial taxa that can be combined to create a unique microbial profile, which when compared to 600 other individuals can improve our ability to link an individual 'burglar' to a residence. In total, 5512 discriminating, non-singleton unique exact sequence variants (uESVs) were identified as unique to an individual, with a minimum of 1 and a maximum of 568, suggesting some people maintain a greater degree of unique taxa compared to our population of 600. Approximate 60-77% of the unique exact sequence variants originated from the hands of participants, and these microbial discriminators spanned 36 phyla but were dominated by the Proteobacteria (34%). A fitted regression generated to determine whether an intruder's uESVs found on door handles in an office decayed over time in the presence or absence of office workers, found no significant shift in proportion of uESVs over time irrespective of the presence of office workers. While it was possible to detect the correct burglars' microbiota as having contributed to the invaded space, the predictions were very weak in comparison to accepted forensic standards. This suggests that at this time 16S rRNA amplicon sequencing of the built environment microbiota cannot be used as a reliable trace evidence standard for criminal investigations.
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Affiliation(s)
- Jarrad T Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States; Department of Surgery, University of Chicago, Chicago, IL, United States.
| | - Peter Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Tifani Anton
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Lauren Cralle
- Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Simon Lax
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Neil Gottel
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Mariana Salas-Garcia
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Candace Young
- Department of Chemistry, Physics and Engineering Studies, Chicago State University, Chicago, IL, United States
| | - George Duncan
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jose V Lopez
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States; Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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Fritz B, Schäfer K, März M, Wahl S, Ziemssen F, Egert M. Eye-Catching Microbes-Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites. J Clin Med 2020; 9:jcm9051572. [PMID: 32455878 PMCID: PMC7290821 DOI: 10.3390/jcm9051572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
Microscopes are used in virtually every biological and medical laboratory. Previous cultivation-based studies have suggested that direct contact with microscope eyepieces increases the risk of eye infections. To obtain a deeper insight into the microbiota on oculars, we analysed 10 recently used university microscopes. Their left oculars were used for a cultivation-based approach, while the right oculars served for massive gene sequencing. After cleaning with isopropyl alcohol, the oculars were re-sampled and analysed again. All oculars were found to be contaminated with bacteria, with a maximum load of 1.7 × 103 CFU cm-2. MALDI Biotyping revealed mainly Cutibacterium (68%), Staphylococcus (14%) and Brevibacterium (10%), with the most abundant species being Cutibacterium acnes (13%) and Staphylococcus capitis (6%). Cleaning reduced the microbial load by up to 2 log scales. Within 10 uncleaned and 5 cleaned samples, 1480 ASVs were assigned to 10 phyla and 262 genera. The dominant genera before cleaning were Cutibacterium (78%), Paracoccus (13%), Pseudomonas (2%) and Acinetobacter (1%). The bacteriota composition on the cleaned oculars was similar; however, it probably largely represented dead bacteria. In summary, used oculars were significantly contaminated with skin and environmental bacteria, including potential pathogens. Regular cleaning is highly recommended to prevent eye and skin infections.
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Affiliation(s)
- Birgit Fritz
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Karin Schäfer
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Melanie März
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Siegfried Wahl
- Carl Zeiss Vision International GmbH, Turnstrasse 27, 73430 Aalen, Germany;
- Institute for Ophthalmic Research, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany
| | - Focke Ziemssen
- Center for Ophthalmology, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany;
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
- Correspondence: ; Tel.: +49-7720-307-4554
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Isolation of Gram-Positive, Antibiotic-Resistant Bacteria from Tactile Mobile Phones in a Northwestern Mexican City. J Community Health 2020; 45:1050-1060. [PMID: 32394120 DOI: 10.1007/s10900-020-00829-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The widespread use of touch-screen mobile devices renders them potential fomites for the transmission of bacterial pathogens among users of different ages. The objectives of the present research were to isolate bacteria from mobile phones, perform molecular and phylogenetic identification, and determine the antibiotic resistance profiles. The surfaces of 50 touch-screen mobile devices owned by bystanders were sampled in the city center of Culiacan, Sinaloa, Mexico. The samples were cultured on nutritive agar; 13 bacterial colonies were isolated and characterized based on their macroscopic and microscopic characteristics and then identified using PCR amplification and sequencing of the 16S rRNA gene V4 and V6 regions. Their taxonomic relationships were determined via a Bayesian inference approach. Antimicrobial resistance was evaluated via disc diffusion and broth microdilution assays. Species of the genera Staphylococcus, Bacillus, and Enterococcus were identified on 84.6, 7.7, and 7.7% of the mobile phones, respectively. A unique subgroup of Staphylococcus epidermidis was identified in strains FBOPL-23, CAEPL-28, and FREPL-28. Staphylococcus hominis novobiosepticus was also identified on mobile phones for the first time. Of the isolated bacteria, 92.3% were resistant to erythromycin, 76.9% to ampicillin and penicillin, 61.5% to dicloxacillin, 38.5% to cephalothin and 7.7% to cefotaxime and ceftriaxone. The presence of antibiotic-resistant bacteria of clinical relevance poses potential risks to users' health and the dissemination of antibiotic resistance mechanisms throughout the community; thus, we recommend regular cleaning to prevent cross-infection by multidrug-resistant bacteria when using touch-screen mobile devices.
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Assenmacher DM, Fields SD, Crupper SS. Comparison of Commercial Kits for Recovery and Analysis of Bacterial DNA From Fingerprints. J Forensic Sci 2020; 65:1310-1314. [PMID: 31985836 DOI: 10.1111/1556-4029.14280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/26/2019] [Accepted: 12/30/2019] [Indexed: 12/30/2022]
Abstract
In forensic science, fingerprints are a common source of evidentiary information. However, latent examination is not always successful and trace human DNA cannot always be obtained. Thus, examining the fingerprint microbiome may offer a suitable alternative to more traditional methods of forensic identification. The Zymo Research ZR Bacterial/Fungal DNA MicroPrep™ Kit, Qiagen QIAmp® DNA Mini Kit, Promega Wizard® Genomic DNA Purification Kit, and the MPBio FastDNA® Spin Kit were compared for their ability to yield a sufficient amount of bacterial DNA for next-generation sequencing in order to obtain a microbiome profile. Prints were deposited onto slides, allowed to sit for up to 1 month, and total DNA isolated and quantified using each kit. The kit from Zymo Research yielded the most concentrated DNA sample (0.0084 ng/µL) in the least amount of time as compared to other kits examined. Although this amount of DNA was far below the recommended DNA concentration threshold recommended for next-generation sequencing, a microbiome profile was successfully obtained. As interest in using the microbiome of an individual as a forensic tool continues to increase, there is the possibility that the microbiome of a fingerprint could complement traditional human DNA profiling in the future. This study provides evidence that trace amounts of bacterial DNA from fingerprints is quantifiable and sufficient for microbiome analysis.
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Affiliation(s)
- Daniel M Assenmacher
- Department of Biological Sciences, Masters of Science in Forensic Science Program, Emporia State University, 1 Kellogg Circle, Emporia, KS, 66856
| | - Stephen D Fields
- Department of Biological Sciences, Masters of Science in Forensic Science Program, Emporia State University, 1 Kellogg Circle, Emporia, KS, 66856
| | - Scott S Crupper
- Department of Biological Sciences, Masters of Science in Forensic Science Program, Emporia State University, 1 Kellogg Circle, Emporia, KS, 66856
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50
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Abstract
DNA sequencing technologies continue to improve, and there has been a corresponding expansion of DNA-based applications in the forensic sciences. DNA recovered from dust and environmental debris can be used to identify the organisms associated with these sample types, including bacteria, plants, fungi, and insects. Such results can then be leveraged to discern sample origin or geolocation and investigate individual identification. Here, we take a critical look at the current DNA-based technologies using microbiome and environmental sample sources that are focused on the generation of some investigative tools for use in forensic science. We discuss the pitfalls and contentions associated with the use of these techniques and highlight some of the future research required to expand the utility of these methods in the forensic sciences.
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