DNA Analysis Research Articles

P-533 Impact on clinical outcomes of day-6 extended culture and reduced culture media volume applied to non-invasive PGT-A

Abstract Study question Impact on clinical outcomes of day-6 extended culture and reduced culture media volume applied to non-invasive PGT-A Summary answer The implementation of changes in culture conditions to accommodate niPGT-A has no impact on blastocysts viability or pregnancy outcomes. What is known already The recent identification of embryo cell-free DNA (cfDNA) in the culture media has created the possibility of a non-invasive approach for aneuploidy testing in blastocysts. Concerns have however arisen at two levels. Firstly, the concordance rates that cfDNA results have with the full blastocyst or a trophectoderm (TE) biopsy and secondly, the impact on clinical outcomes of the changes in the embryo culture protocol that are required to implement niPGT-A in the IVF laboratory. Concordance rates of niPGT-A to invasive PGT-A have gradually improved, however the impact of culture protocol changes is not as well understood. Study design, size, duration Six IVF clinics participating in a trial examining concordance rates for invasive and non-invasive PGT-A on day-6/7 blastocysts were involved (Rubio et al., 2020). Patients were recruited from April 2018 to December 2020. In the study group, 428 PGT-A cases following the niPGT-A protocol for embryo culture were included. The control group consisted of 1,392 regular PGT-A cases that did not participate in the study and underwent the standard PGT-A culture protocol. Participants/materials, setting, methods In the control group, embryos were biopsied and vitrified on day 5, 6 or 7. In the study group, niPGT-A culture conditions started on day 4, when embryos were washed and cultured individually in 10μl of fresh media. On day 6/7 blastocysts were biopsied, vitrified and media collected for niPGT-A analysis. Clinic A cultured all embryos up to day 6/7, whereas in clinics B-F a minority of day-5 blastocysts were biopsied and transferred. Main results and the role of chance Statistical comparisons were performed between the study and the control groups. Mean female age, number of oocytes, fertilization rates and number of blastocysts biopsied were not significantly different for the study and the control group. Overall, the niPGT-A protocol did not have any detrimental effect on blastocyst quality, euploidy rates or informativity rates. Deferred single embryo transfers (SET) were performed in both groups. Regarding the overall pregnancy outcomes, no significant effect was observed on clinical pregnancy rate, miscarriage rate or ongoing pregnancy rate (OPR, ≥12 weeks) in the study group compared to the control group when stratified by day of biopsy. Clinic A showed no difference in OPR per transfer regardless of culture protocol (62.3% in control group day 5/6/7; 60.8% in control group day 6/7; and 65.6% in study group day 6/7). For the remaining clinics (B-F), a comparison was made separately between day-5 and day-6 blastocysts that were transferred and cultured according to the standard and to the niPGT-A protocol. No significant differences in OPR were observed, neither between control group day 5 (60.6%) and study group day 5 (58.7%), nor between control group day 6 (44.7%) and study group day 6 (41.9%). Limitations, reasons for caution The limitations are intrinsic to the retrospective nature of the study, and also to the fact that the study was conducted in invasive PGT-A patients and not in niPGT-A cases alone. Wider implications of the findings This study shows that changing current IVF laboratory practice to adopt niPGT-A protocols has no impact on the number of blastocysts available for transfer and overall clinical outcomes. Whether removal of the actual invasive biopsy step leads to further improvements in pregnancy rates awaits further studies. Trial registration number ClinicalTrials.gov (NCT03520933)

A project‐based learning mode for science students: Fluorescent protein expression in trypanosomes

AbstractAn effective, practical approach for incorporating molecular biology tools to biology and biochemistry students is described. For 6 weeks, students are exposed to bacterial transformation, plasmid DNA purification and analysis, parasite transfection, ectopic expression of fluorescent proteins, fluorescence microscopy, and flow cytometry analysis. This research‐oriented laboratory course delves into theoretical and practical concepts of basic techniques in molecular biology to emphasize the logical connections between the obtained results and the resolution of problems that arise daily in a research laboratory, training the students in planning, conducting, discussing, and presenting their own experiments and results.

O-117 Advances in PGT diagnostics - technologies beyond copy number

Abstract Genetic abnormalities are well recognised as the main factor contributing to the high rate of infertility, pregnancy loss and congenital abnormalities in humans. A prime example of this can be seen from recent studies showing that embryos identified as uniformly aneuploid following PGT-A have little to no reproductive potential. However, embryos shown to have no gross chromosomal abnormalities after PGT are not a guarantee of healthy pregnancy and many other undetected genetic issues are likely to influence embryo competence. Developments in both sample preparation and methods for DNA analysis are driving ever-increasing data yield from PGT platforms, permitting not only DNA quantitation, but also allowing qualitative evaluation of genotyping data in parallel. This opens the door to the possibility of overcoming some of the previous limitations of PGT, leading to a more comprehensive assessment of the genetic health and reproductive potential of embryos. How to use this increasing amount of information, and if it can tangibly improve test accuracy and clinical outcomes, remains open to debate. There is, for instance, no consensus on how to interrogate genotyping data for better distinction of clinically relevant aneuploidy as well as genome wide (ploidy) abnormalities and exogenous DNA contamination, which could impact the correct reporting of PGT results. There is also no consensus on the potential benefit of genotyping data to be used for the accurate distinction of meiotic recombination by linkage analysis, nor for fingerprinting of embryos to identify rare, but catastrophic, lab error events as a routine part of treatment. Finally, there is no clear path on how to utilise these improvements in embryo genotyping, to detect sub-chromosomal de novo genetic abnormalities that could impact embryo viability beyond the scope of current testing for chromosomal abnormalities alone. The aim of this presentation is therefore to focus on the current state of the ART and address the current and potential future uses of genotyping in PGT. Topics covered will include identification of biopsy sample contamination to determine the truth from the noise, through to how we can rescue embryos by utilising PGT as a molecular fertilisation check and how fingerprinting of embryo can be an invaluable tool in the clinic. The origin of aneuploidy will be explored and how genotyping is reshaping our understanding of aneuploidy landscape of the preimplantation embryo. From a more basic science perspective, the potential of genotyping to identify meiotic recombination will be discussed and how this fundamental element of human reproduction could be an important biomarker for reproductive competence. Lastly future perspectives on how the evolution of PGT technologies can bring us closer to the accurate detection of de novo genomic changes will be explored and how this is taking PGT-A beyond just aneuploidy detection. It is no secret that PGT for embryo selection continues to be a controversial area of reproductive medicine, and the field of PGT-A especially continues to show disquieting inconsistency in data analysis and reporting. This new era of genotyping brings with it information that can be used as a standardization tool helping to focus and facilitate improvements in the field of PGT for better and more consistent clinical reporting and outcomes.

P-387 The use of cell-free DNA analysis to identify fetal aneuploidies in early pregnancy loss

Abstract Study question Can cell-free (cf) DNA-based analysis of a maternal blood sample be used to identify presence of fetal aneuploidies in early pregnancy loss (EPL) cases? Summary answer CfDNA analysis was able to detect fetal aneuploidies in EPL cases with 73.5% sensitivity and 100% specificity. What is known already Miscarriages occur in about 10%–20% of pregnancies, and the majority occur in the first trimester. About 50% of EPL cases result from the presence of fetal aneuploidy. Knowing the etiology of a miscarriage can be helpful for future reproductive planning along with providing a psychological benefit for patients. Although products of conception (POC) samples can be collected and assessed for presence of fetal aneuploidies, this is not always possible. Recent studies have shown that a noninvasive approach using cfDNA analysis of a blood sample can identify fetal aneuploidies in patients that experience EPL. Study design, size, duration In this prospective study, samples were collected from 78 patients across the United States from June 2021–December 2022. Blood specimens were collected for cfDNA analysis and maternal cell contamination analysis, and POC samples were collected following surgical evacuation for microarray analysis. Performance of the cfDNA assay was determined by comparing results from the cfDNA analysis against the gold standard of microarray results. Participants/materials, setting, methods Patients were recruited from six reproductive endocrinology/infertility practices. Eligible participants were between 5–20 weeks of gestation with miscarriage of a singleton pregnancy diagnosed by ultrasound and presence of pregnancy tissue in utero. Limited clinical information was collected, including demographics and expected clinical gestational age (GA) at sample collection. Blood samples underwent cfDNA analysis using an adapted version of a noninvasive prenatal test, which included establishment and use of pregnancy loss-specific log likelihood ratio thresholds. Main results and the role of chance Seventy-eight patients were recruited, of which two were excluded due to blood sample collection issues. Eleven of the 76 patients that underwent cfDNA analysis were excluded from performance calculations for several reasons including maternal cell contamination of POC samples and detection of triploidy by microarray. The final 65 samples included 49 affected and 16 unaffected samples based on POC microarray results; this included 42 with one fetal aneuploidy, six with two fetal aneuploidies, and one with three fetal aneuploidies. Average fetal fraction of these 65 samples was 4.9% (range: 0.6%–13.9%) and average expected clinical GA at time of sample collection was 8.7 weeks (range: 5.9–12.1 weeks). Performance of the cfDNA assay was determined by comparing cfDNA analysis results with POC microarray results using either a full concordance approach (correct classification of all affected chromosomes in an affected sample) or a partial concordance approach (correct classification of at least one affected chromosome in an affected sample). Based on the full concordance approach, sensitivity of the cfDNA assay was 69.4% and specificity was 100%. For the partial concordance approach, sensitivity of the cfDNA assay increased to 73.5% whilst specificity remained at 100%. The cfDNA assay failure rate was 0%. Limitations, reasons for caution Study limitations include a small study cohort, the inability of the cfDNA assay to detect triploidy or partial deletions/duplications <7 Mb and possibly mosaicism, and that this cfDNA analysis approach can only be used for EPL cases that are identified before complete expulsion of the products of conception. Wider implications of the findings This study provides further evidence of the ability of cfDNA analysis to detect fetal aneuploidies in EPL cases. A clinically available cost-effective noninvasive approach to determine the etiology of a miscarriage could help inform medical management of patients for future reproductive planning and could provide psychological benefits to patients. Trial registration number NCT04935138

P-505 Clinical rescue rate of abnormally fertilized oocytes and the relationship with patient, embryo and laboratory features

Abstract Study question Which are the main patient, embryonic and laboratory variables associated with a diploid result in abnormally fertilized embryos? Summary answer Embryo diploid constitution is associated with maternal age, trophectoderm and inner cell mass quality as well as pronuclear (PN) number predicted by time-lapse incubator. What is known already In conventional in vitro fertilization cycles, morphological PN evaluation can identify proper fertilization and predict embryo ploidy constitution. Atypical PN patterns like 0PN, 1PN or more than 2PN are associated with ploidy abnormalities. However, we have previously shown that PN number is insufficient to predict embryo ploidy composition, and advanced single nucleotide polymorphism (SNP)-based methodologies for preimplantation genetic testing (PGT) detect a significant number of genetically diploid embryos from presumed abnormally fertilized oocytes. In this study, we characterized the diploid rescue rate associated with abnormal PN configurations, uncovering the link between ploidy results and relevant patient, embryonic and clinical/laboratory parameters. Study design, size, duration Retrospective observational study evaluating the association between diploid rescue rate of abnormally fertilized embryos and different patient, embryonic and laboratory features. Embryos were cultured in conventional or EmbryoScope™ time-lapse incubator (Vitrolife) until blastocyst stage and classified according to Gardner embryo grading system. Ploidy assessment was performed on 343 euploid trophectoderm (TE) biopsies collected between January 2021 and November 2023. Results were stratified according to patients age, embryo quality parameters and different laboratory procedures. Participants/materials, setting, methods Multi-center international study involving consenting patients using autologous gametes and undergoing PGT for aneuploidies (PGT-A) combined with ploidy analysis. Ploidy protocol was performed using a validated targeted NGS approach composed of a custom panel of 357 SNPs and a proprietary pipeline of analysis. Reliable ploidy classification was obtained using a combined algorithm strategy based on SNPs allele frequencies. Categorical variables were expressed in percentages. Nominal variables were analysed using the Cochran-Armitage test to detect trends. Main results and the role of chance Among 343 euploid embryos, diploidy rates obtained for 0PN, 1PN, 2.1PN and 3PN groups were 86.8% (n = 118/136;95%CI=79.89-91.96) 43.7% (n = 59/135;95%CI=35.19-52.50), 65.0% (n = 13/20;95%CI=40.78-84.61) and 26.9% (n = 14/52;95%CI=15.57-41.02) respectively. Regarding patient parameters, advanced maternal age, but not paternal age, was significantly associated with lower diploid rescue rates, with a decreasing trend from 72.5% (n = 79/109;95%CI=63.10-80.60) below age 35 to 42.9% (n = 30/70;95%CI=31.09-55.25) above age 40 (p < 0.01). When considering embryo morphological evaluations, Cochran Armitage test revealed a significant link between diploidy rates and TE quality with a decreasing trend going from 72.1% (n = 80/111;95%CI=62.76-80.17) to 52.7% (n = 79/150;95%CI=44.36-60.87) and 45.8% (n = 22/48;95%CI=31.37-60.83) for embryos classified with TE grade as A, B, and C, respectively (p-value<0.01). Similarly, a decreasing trend was reported in relation to inner cell mass (ICM) quality, when moving from grade A (67,1%, n = 94/140;95%CI=58.23-75.33) to grade C (54.8%, n = 17/31;95%CI=36.03-72.68) (p = 0.03). No clear association was reported for embryo expansion degree. Finally, among laboratory variables (oocyte freezing procedure, fertilization method, incubator type), only time-lapse significantly impacted expected diploid results. Overall, if abnormal PN number is confirmed by time-lapse (n = 42 samples), the accuracy in predicting ploidy abnormalities increased from 29.2% (n = 82/281;95%CI=23.93-34.87), in conventional incubators, to 83.3% (n = 35/42;95%CI=68.64-93.03) (p < 0.01). Consequently, expected diploid rescue rate decreased from 65.5% (n = 184/281;95%CI=59.60-71.03) to 16.7% (n = 7/42;95%CI=6.97-31.36) (p < 0.01). Limitations, reasons for caution Parental DNA analysis should be included to rule-out the residual risk of uniparental disomy in diploid embryos. The multi-center nature of the study didn’t support a uniform PN annotation, especially for centers lacking time-lapse observation. Future studies should focus on the clinical follow-up after the transfer of rescued euploid-diploid embryos. Wider implications of the findings We believe we reported the first evidence of maternal age effect on ploidy results in the largest dataset of abnormally fertilized embryos. We revealed a link between ploidy constitution and blastocyst morphological quality, providing important information for patient counselling. Time-lapse incubators offer a more accurate identification of abnormally fertilized oocytes. Trial registration number n/a

Epidemiological exploration of fleas and molecular identification of flea-borne viruses in Egyptian small ruminants

The study aimed to investigate molecularly the presence of flea-borne viruses in infested small ruminants with fleas. It was carried out in Egypt’s Northern West Coast (NWC) and South Sinai Governorate (SSG). Three specific primers were used targeting genes, ORF103 (for Capripoxvirus and Lumpy skin disease virus), NS3 (for Bluetongue virus), and Rdrp (for Coronavirus), followed by gene sequencing and phylogenetic analyses. The results revealed that 78.94% of sheep and 65.63% of goats were infested in the NWC area, whereas 49.76% of sheep and 77.8% of goats were infested in the SSG region. Sheep were preferable hosts for flea infestations (58.9%) to goats (41.1%) in the two studied areas. Sex and age of the animals had no effects on the infestation rate (p > 0.05). The season and site of infestation on animals were significantly different between the two areas (p < 0.05). Ctenocephalides felis predominated in NWC and Ctenocephalides canis in SSG, and males of both flea species were more prevalent than females. Molecular analysis of flea DNA revealed the presence of Capripoxvirus in all tested samples, while other viral infections were absent. Gene sequencing identified three isolates as sheeppox viruses, and one as goatpox virus. The findings suggest that Capripoxvirus is adapted to fleas and may be transmitted to animals through infestation. This underscores the need for ongoing surveillance of other pathogens in different regions of Egypt.

APEAch: Automated Pipeline for End-to-End Analysis of Epigenomic and Transcriptomic Data

With the advent of next-generation sequencing (NGS), experimental techniques that capture the biological significance of DNA loci or RNA molecules have emerged as fundamental tools for studying the epigenome and transcriptional regulation on a genome-wide scale. The volume of the generated data and the underlying complexity regarding their analysis highlight the need for robust and easy-to-use computational analytic methods that can streamline the process and provide valuable biological insights. Our solution, aPEAch, is an automated pipeline that facilitates the end-to-end analysis of both DNA- and RNA-sequencing assays, including small RNA sequencing, from assessing the quality of the input sample files to answering meaningful biological questions by exploiting the rich information embedded in biological data. Our method is implemented in Python, based on a modular approach that enables users to choose the path and extent of the analysis and the representations of the results. The pipeline can process samples with single or multiple replicates in batches, allowing the ease of use and reproducibility of the analysis across all samples. aPEAch provides a variety of sample metrics such as quality control reports, fragment size distribution plots, and all intermediate output files, enabling the pipeline to be re-executed with different parameters or algorithms, along with the publication-ready visualization of the results. Furthermore, aPEAch seamlessly incorporates advanced unsupervised learning analyses by automating clustering optimization and visualization, thus providing invaluable insight into the underlying biological mechanisms.

Assessing bias in the causal role of HPV in oral cancer: Asystematic review and meta-analysis.

High-risk human papillomaviruses (HPV) are an established cause of oropharyngeal cancer. Their relationship with oral cancer remains unclear with detection ranging from 0% to 100%. HPV DNA detection or evidence of exposure alone is insufficient to conclude causality. This systematic review assesses the extent of bias in studies of HPV detection in cancers of the oral cavity. PubMed, Ovid MEDLINE, EMBASE, and PsycInfo databases were searched for observational studies reporting the effect of HPV in oral cavity specific cancers. All 15 included studies presented HPV DNA detection or serum HPV-antibodies, none included mRNA E6/E7 analysis. Cases with oral cancer had 5.36 times (95% CI 3.29-8.72) higher odds of having HPV detected compared to controls. The odds of HPV detection were higher in cell-based (OR 6.93; 95% CI 0.82-58.55) and tissue samples (OR 5.28; 95% CI 3.41-8.18) than blood-based samples (OR 3.36; 95% CI 1.53-7.40). When cancer site is clearly differentiated between oropharynx and oral cavity, 12 studies showed strong association between HPV and oral cancer, but the available estimates lack internal validity due to inconsistent measurements, high confounding, and lack of gold standard testing. There is not high-quality evidence to conclude a causal relationship of HPV with oral cancer.

Novel buffer for long-term preservation of DNA in biological material at room temperature1.

The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8years, human blood stored for 3years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.

A study on methods for preimplantation genetic testing (PGT) on in vivo- and in vitro-produced equine embryos, with emphasis on embryonic sex determination.

Two methods for preimplantation genetic testing (PGT) have been described for equine embryos: trophoblast cell biopsy (TCB) or blastocoele fluid aspiration (BFA). While TCB is widely applied for both in vivo- and in vitro-produced embryos, BFA has been mostly utilized for in vivo-produced embryos. Alternative methods for PGT, including analysis of cell-free DNA (CFD) in the medium where in vitro-produced embryos have been cultured, have been reported in humans but not for equine embryos. In Experiment 1, in vivo- (n = 10) and in vitro-produced (n = 13) equine embryos were subjected to BFA, cultured for 24 hours, then subjected to TCB, and cultured for additional 24 hours. No detrimental effect on embryonic diameter or re-expansion rates was observed for either embryo group (P > 0.05). In Experiment 2, the concordance (i.e., agreement on detecting the same embryonic sex using two techniques) among BFA, TCB, and the whole embryo (Whole) was studied by detecting the sex-determining region Y (SRY) or testis-specific y-encoded protein 1 (TSPY) (Y-chromosome), and androgen receptor (AR; X-chromosome) genes using PCR. Overall, a higher concordance for detecting embryonic sex was observed among techniques for in vivo-produced embryos (67 – 100%; n = 14 embryos) than for in vitro-produced embryos (31 – 92%; n = 13 embryos). The concordance between sample types increased when utilizing TSPY (77 – 100%) instead of SRY (31 – 100%) as target gene. In Experiment 3, CFD analysis was performed on in vitro-produced embryos to determine embryonic sex via PCR (SRY [Y-chromosome] and amelogenin – AMEL [X- and Y-chromosomes]). Overall, CFD was detected in all medium samples, and the concordance between CFD sample and the whole embryo was 60% when utilizing SRY and AMEL genes. In conclusion, equine embryos can be subjected to two biopsy procedures (24 h apart) without apparent detrimental effects on embryonic size. For in vivo-, but not for in vitro-produced equine embryos, BFA can be considered a potential alternative to TCB for PGT. Finally, CFD can be further explored as a non-invasive method for PGT in in vitro produced equine embryos.

Longitudinal Analyses of Circulating-Tumor DNA for Detection of EGFR Mutation-Positive Advanced Non-Small Cell Lung Cancer Progression During Treatment: Data From FLAURA and AURA3

IntroductionEpidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI)-sensitizing and -resistance mutations may be detected in plasma via circulating tumor DNA (ctDNA). ctDNA level changes reflect alterations in tumor burden and could be a dynamic indicator of treatment effect. This analysis aimed to determine whether longitudinal EGFR-mutation ctDNA testing could detect progressive disease (PD) before radiologic detection. MethodsThis was a retrospective, exploratory ctDNA analysis in two phase 3 trials (FLAURA, NCT02296125; AURA3, NCT02151981). Patients had treatment-naïve (FLAURA) or EGFR-TKI pre-treated (AURA3) advanced non-small cell lung cancer (NSCLC) with EGFR mutations and on-study PD (RECIST), with a baseline ctDNA result and EGFR-mutation ctDNA monitoring beyond Cycle 3 Day 1. Patients received osimertinib versus comparator EGFR-TKIs (FLAURA) or chemotherapy (AURA3). Outcomes included time from ctDNA PD to RECIST PD, and to first subsequent treatment (FST; FLAURA only).Results: ctDNA PD preceded/co-occurred with RECIST-defined PD in 93/146 (64%) patients in FLAURA and 82/146 (56%) in AURA3. Median time from ctDNA PD to RECIST-defined PD (months) was 3.4 and 2.6 in the osimertinib and comparator EGFR-TKI arms (FLAURA) and 2.8 and 1.5 in the osimertinib and chemotherapy arms (AURA3). In FLAURA, median time from ctDNA PD to FST (months) was 6.0 and 4.7 in the osimertinib (n = 51) and comparator EGFR-TKI arms (n = 70). ConclusionsAmong patients with EGFR mutation-positive advanced NSCLC receiving EGFR-TKI or chemotherapy with ctDNA data and RECIST-defined PD, ctDNA PD preceded/co-occurred with RECIST-defined PD in approximately 60% of cases. Longitudinal ctDNA monitoring may detect PD before radiologic PD.

Streptococcus suis subsp. hashimotonensis subsp. nov.: Lancefield group A antigen–positive organisms isolated from human clinical specimens and wild boar oral cavity samples

Three Streptococcus suis-like strains positive for Lancefield antigen group A were isolated from human boar bite wounds and the oral cavities of boars in Hashimoto City, Wakayama Prefecture, Japan, and their taxonomic positions were investigated. Application of the VITEK2 system identified all three isolates as S. suis with > 94 % probability. The isolates were assigned to S. suis based on the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis (Biotyper score of 2.382) but were differentiated according to the characteristic signal peaks (4709 m/z and 9420 m/z) that were not present for S. suis. Sequence analysis of the 16S rRNA and sodA genes determined that the isolates were similar to S. suis; however, these genes appeared on a phylogenetic sub-branch. Phylogenetic analysis of the whole chromosomal DNA showed that the isolate formed a cluster with S. suis but with clear divergence. The average nucleotide index using BLAST between the clinical isolate (PAGU 2482) and a closely related reference strain of S. suis was 94.75 %, which was not clearly conclusive; however, digital DNA-DNA hybridization showed a value of 61.2 %. Biochemical reactions, including those with acid phosphatase, α-chymotrypsin, and tagatose (acidification), distinguished our isolates from S. suis. Thus, based on phylogenetic, genomic, and phenotypic characteristics and MALDI-TOF-MS signal patterns, we propose that the isolate with Lancefield group A positive characteristics be designated as a novel subspecies, Streptococcus suis subsp. hashimotonensis subsp. nov, with the type strain PAGU 2482T (GTC 18290T = CCUG 77434T).

SNP Array for Small-Shrimp (Genus Acetes) Origin Determination Using Machine Learning.

Accurate origin determination of seafood is crucial for consumer trust and safety. This study was performed to develop a machine learning-based single-nucleotide polymorphism (SNP) analysis technique to determine the origin of Acetes species in salted small-shrimp products. Mitochondrial DNA (COI and 16S rRNA) analysis revealed genetic variations among species and origins. Eight candidate SNPs were identified, six of which were developed into markers for genotyping analysis. Using the developed markers, an SNP array was created and SNP data from salted small-shrimp samples were obtained. Machine learning analysis using a supervised learning algorithm achieved 100% accuracy in classifying the origin of Acetes based on SNP data. This method offers a reliable method for regulatory bodies to combat food fraud and ensure product integrity. The approach can be further improved by expanding the data set to encompass a wider range of species and origins. This study highlights the potential of SNP analysis and machine learning for ensuring seafood authenticity and promoting sustainable practices.

Human Papilloma Virus-Independent/p53abnormal Keratinizing Squamous Cell Carcinoma of the Uterine Cervix Associated With Uterine Prolapse.

Knowledge about the morphologic and molecular characteristics of cervical squamous cell carcinomas (CSCCs) associated with uterine prolapse is very limited. Detailed histopathological and immunohistochemical (p16, p53, and cytokeratin 17), as well as molecular evaluation for human papillomavirus (HPV)-DNA and p53-mutational analyses in 4 consecutive CSCCs associated with uterine prolapse with definition of a hitherto not well-described HPV-independent/p53abnormal precursor lesion (HPV-independent cervical intraepithelial neoplasia [CIN; differentiated CIN]) and molecular tumorigenetic pathway. Cases diagnosed within 7 years with a mean age of 75 (range: 69-83) years and a mean tumor size of 7.3cm (range: 5.2-9.4cm). All patients presented with locally advanced disease, and 1 woman died of the disease within 4, and another within 14 months of follow-up. All CSCCs and their adjacent precursor lesions were negative for p16, with aberrant p53-expression and diffuse and strong staining for cytokeratin 17. Both the CSCCs and their precursors were negative for HPV-DNA but harbored a TP53 mutation. The precursor lesions were characterized by epithelial thickening with superficial keratinization, and the presence of basal and parabasal keratinocytes with mitotic figures beyond the basal layer, thus showing features similar to those seen in differentiated types of vulvar intraepithelial lesions (vulvar intraepithelial neoplasia [VIN] syn. HPV-independent/p53abn VIN), suggesting the terminology of differentiated CIN or HPV-independent/p53abn CIN. An HPV-independent pathogenetic pathway with a p53-alteration was identified for these cases. CSCC associated with uterine prolapse represents HPV-independent tumors harboring a TP53 mutation. For the first time, a precursor lesion of HPV-independent CSCC of the uterine cervix is described with a differentiated VIN-like morphology, and a separate tumorigenic pathway defined.

Sensitive and rapid detection of three foodborne pathogens in meat by recombinase polymerase amplification with lateral flow dipstick (RPA-LFD)

Foodborne illnesses, caused by harmful microorganisms in food, are a significant global health issue. Current methods for identifying these pathogens are both labor-intensive and time-consuming. In this research, we devised a swift and precise detection technique using recombinase polymerase amplification combined with a lateral flow dipstick (RPA-LFD) for three foodborne pathogens found in meat. By employing a dedicated detection device, RPA-LFD allows for the rapid analysis of DNA from Escherichia coli O157 (E. coli O157), Salmonella, and Shigella—pathogens that are prohibited in food. The detection thresholds for E. coli O157, Salmonella, and Shigella are 0.168 fg/μl (1.04 CFU/ml), 0.72 fg/μl (27.49 CFU/ml), and 1.25 fg/μl (48.84 CFU/ml), respectively. This method provides a short detection window, operates at low temperatures, follows simple procedures, and exhibits high sensitivity. Our study establishes the RPA-LFD method for simultaneously identifying the nucleic acid of three foodborne pathogens, offering an efficient solution for quickly identifying multiple contaminants.

The advent of forensic DNA databases: it’s time to agree on some international governance principles!

National forensic DNA databases are a valuable investigative tool, that have the potential to increase the efficacy of criminal investigations. Their unfettered expansion in recent years raises unsettling ethical issues that require close attention. DNA database expansion threatens the rights to privacy, non-discrimination, and equality, and can undermine public trust in government. This perspective piece relies on data from an international mapping study of Forensic DNA Databases to document the expansion of these databases, highlight the ethical issues they raise, and propose key recommendations for more responsible use of this infrastructure.

The Efficiency of the Alu Insertion Sequence in Discrimination Among some Individuals

Background: The Alu element is a widely distributed short interspersed nuclear element (SINE) in the human genome and has important applications in forensic science. The current study focused on assessing the effectiveness of Alu insertion polymorphism in forensic DNA profiling to identifying samples of some individuals living in the Babylon Governorate. Materials and methods: DNA was extracted From frozen blood samples (60) individuals were collected from Babylon - Al-Hilla Governorate from 8/8/2022 until 8/9/2022. Results: purified then a PCR technique Alu insertions were A(2q21.1)(111-115bp) 0.75, Alu deletion (0.25), B(8q23.1) (0.375) (0.625) C(13q34) (0.5)(0.5), D(15q23) (0.775) (0.225), E(16q23.3) (0.692) (0.308) and F(19q13.12)(0.616)(0.384) respectively.The alleles with Alu insertions at (2q21.1) were the most prevalent, whereas the Alu insertions at (8q23.1) were the least common. The similarity coefficient among individuals varied from 0.4 to 1, based on the proportion of genetic relatedness between them. Conclusions: Alu elements have efficacy in families’ discrimination it can be used more than one site, set of Alu insertion sequences should be used to accurate results.

Comparison of CRISPR typing and conventional molecular methods for distinguishing Laribacter hongkongensis isolates from fish, frogs and humans

High-resolution and efficient typing for Laribacter hongkongensis (L. hongkongensis) is essential for epidemiological investigation of such emerging foodborne pathogens. Clustered regularly interspaced short palindromic repeats (CRISPR) typing is an innovative molecular method that shows great promise for L. hongkongensis typing. Here, we explored the CRISPR typing method by combining CRISPR1 and CRISPR2 loci to characterize a collection of 109 L. hongkongensis isolates from humans and animals and compared it to current molecular methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The results showed that all three methods have high discriminatory power (diversity index was 0.9902 for PFGE, 0.9663 for CRISPR and 0.9562 for MLST); strong congruence was observed between them (Rand index was 0.969 between CRISPR and PFGE, 0.953 between CRISPR and MLST, 0.958 between PFGE and MLST). CRISPR typing could well distinguish the isolates in the same STs or PFGE profiles, and the genetic information contained by the CRISPR array is useful for deep phylogenetic typing. We demonstrate that rapid CRISPR typing is a practical genetic fingerprinting tool with high resolution, comparable ease of use and lower cost, ability to track the source of various groups of L. hongkongensis strains and indication of genetic characteristics.

Enhancing public health safety: Development and application of a MoS2@CNT-Chit electrochemical DNA biosensor for rapid and accurate detection of S. Typhi

This study introduces an advanced electrochemical biosensor that utilizes MoS2@CNT as an electrode material combined with a specific DNA probe to detect Salmonella Typhi rapidly and accurately. The sensor offers a broad detection range from 1.0 × 10−6 to 1.0 × 10−18 molL−1 and boasts an exceptionally low limit of detection (LOD) of 1.0 × 10−20 molL−1 for the target bacterium. It demonstrates a detection range from 1.0 × 104 to 1.0 × 1011 CFUml−1 in real samples, with a corresponding LOD of 1.0 × 104 CFUml−1. Rigorous testing against base mismatches and various bacterial strains confirms its specificity, ensuring reliable performance. Validated in real samples, the biosensor can accurately identify Salmonella Typhi in water and milk, achieving recoveries ranging from 92.95 % to 99.58 %. The exceptional performance of the biosensor is attributed to the MoS2@CNT electrode material and the specific DNA recognition probe, which enhance electron transfer and reduce steric impedance. These improvements contribute to the sensor's enhanced sensitivity and specificity, making it a significant advancement in public health safety by providing a rapid and accurate tool for detecting Salmonella Typhi in food samples.

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence.

The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.