Search

DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, method for recovery, transport and storage routines of the objects before the objects arrive in the laboratory. The present study evaluated the effect of four storage conditions on the DNA retrieved from bloodstains, touch DNA, fingerprints and hairs, initially deposited on knives, smartphones, packing tapes, duct tapes and garbage bags, and submerged in lake water for three time periods. After retrieval, the objects were stored either through air-drying at room temperature, freezing at -30 degrees C, in nitrogen gas or in lake water. The results showed that the submersion time strongly influenced the amount and degradation of DNA, especially after the longest submersion time (21 days). A significant variation was observed in success for STR profiling, while mtDNA profiling was less affected by the submersion time interval and storage conditions. This study illustrates that retrieval from water as soon as possible and immediate storage through air-drying or freezing before DNA analysis is beneficial for the outcome of DNA profiling in crime scene investigations.

The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.

Touch DNA recovery techniques can have limitations, as their effectiveness depends on the substrate on which the DNA of a person of interest can be found. In this study, an in-house dry-vacuuming device, the DNA-Buster, was compared to traditional methods for its DNA recovery performance from items typically examined in forensic casework. The aim was to evaluate whether this dry-vacuuming approach can recover DNA efficiently, potentially complementing the well-established recovery strategies. For this, the performances of swabbing, taping, wet-(M-Vac & REG;) and dry-vacuuming (DNA-Buster) were investigated quantitatively and qualitatively for touch DNA deposited on carpet, cotton sweater, stone, tile and wood. For the sweater, both vacuuming methods outperformed the other collection tools quantitatively. While the highest DNA amounts for the carpet were yielded by swabbing and taping, dry-vacuuming was equally good in reaching full DNA profiles, whereas less complete profiles were observed for the M-Vac & REG;. For stone and tile, swabbing was optimal, whereas dry-vacuuming clearly underperformed for these substrates. Taping was the best recovery method for wood. Despite applying single donor DNA after thoroughly cleaning the items, undesired DNA mixtures were detected for all recovery techniques and all substrates. The overall research findings show first that the novel dry-vacuuming method is suited for DNA recovery from textiles. Secondly, they indicate that more attention should be paid to the substrate-collection dependency to ensure best practices in recovering genetic material in a precise, confident and targeted manner from the variety of forensic casework material.

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene(R), for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon(R) for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells.

Clostridium perfringens est une bactérie pathogène causant diverses infections chez l'homme et l'animal. L'entérite nécrotique (EN) chez la volaille causée par C. perfringens entraîne des pertes économiques importantes au niveau mondial. Le développement d'alternatives pour limiter les infections à C. perfringens est nécessaire car l'utilisation d'antibiotiques comme promoteurs de croissance a été restreinte. Les bactériophages représentent une alternative intéressante et notre objectif dans le présent travail était d'isoler des phages lytiques afin de tester leur potentiel thérapeutique contre C. perfringens. Quatre phages ont été isolés de fientes de poulet provenant de fermes du Québec. Le spectre d'hôtes a été réalisé sur 50 souches de C. perfringens collectées lors d'une éclosion d’EN dans des élevages avicoles. Les phages vB_CpeS-1185 (phiCp-A) et vB_CpeS-1192 (phiCp-D) ont un spectre étroit, alors qu'il est plus large pour vB_CpeS-1153 (phiCp-B) et vB_CpeS-1181 (phiCp-E), qui étaient également capables d’infecter des isolats humains de C. perfringens. Tous les phages appartiennent à la famille des Siphoviridae, et le séquençage de leur génome a révélé qu'ils sont tous tempérés, avec des génomes allant de 33 985 pb (phiCp-B) à 54 735 pb (phiCp-D). Les phages phiCp-A et phiCp-B partagent une homologie de séquence avec des phages connus, à savoir vB_CpeS-CP51 et phi3626, respectivement, tandis que phiCpD est unique. Il convient de noter que phiCp-E est presque identique (100% sur 94% de sa longueur) à pDle1_3, une séquence annotée comme un plasmide dans la souche Del1 de C. perfringens. De plus, nous avons montré que les nouveaux lysogènes porteurs de phiCpE sont instables, conduisant à un phénomène de pseudolysogénie. Ces quatre phages étant tempérés, ils ne conviennent pas pour des applications thérapeutiques, mais leur caractérisation s'ajoute aux données disponibles pour les phages de C. perfringens, qui sont encore limitées., Clostridium perfringens is a pathogenic bacterium causing various infections in humans and animals. Necrotic enteritis (NE) in poultry caused by C. perfringens leads to significant economic losses worldwide. The development of alternatives to limit C. perfringens infections is needed since the use of antibiotics as growth promoters has been restricted. Bacteriophages represent an interesting alternative and our goal in the present work was to isolate lytic phages in order to test their therapeutic potential against C. perfringens. Four phages were isolated from chicken droppings from farms of Québec. Host range was assessed on 50 strains of C. perfringens collected during an outbreak of NE in poultry farms. Phages vB_CpeS-1185 (phiCp-A) and vB_CpeS-1192 (phiCp-D) have a narrow range, while it is broader for vB_CpeS-1153 (phiCp-B) and vB_CpeS-1181 (phiCpE), which were also able to infect human C. perfringens isolates. All phages belong to the Siphoviridae family, and whole genome sequencing revealed that they are all temperate, with genomes ranging in size from 33,985 bp (phiCp-B) to 54,735 bp (phiCp-D). Phages phiCpA and phiCp-B share sequence homology with known phages, namely vB_CpeS-CP51 and phi-3626, respectively, while phiCp-D is unique. Of note, phiCp-E is almost identical (100% over 94% of its length) to pDle1_3, a sequence annotated as a plasmid in C. perfringens strain Del1. Also, we showed that new lysogens carrying phiCp-E were unstable, leading to pseudolysogeny. Since these four phages are temperate, they are unsuitable for therapeutic applications, but their characterization adds to the available data on C. perfringens phages, which is still limited.