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The Science of the Total Environment May 2023Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid... (Review)
Review
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
Topics: Animals; DNA, Environmental; Biological Monitoring; DNA Barcoding, Taxonomic; Environmental Monitoring; Biodiversity; Fishes
PubMed: 36801404
DOI: 10.1016/j.scitotenv.2023.162322 -
Frontiers in Oral Health 2023Noma is a rapidly progressing periodontal disease with up to 90% mortality in developing countries. Poor, immunocompromised and severely malnourished children (2 to 6... (Review)
Review
Noma is a rapidly progressing periodontal disease with up to 90% mortality in developing countries. Poor, immunocompromised and severely malnourished children (2 to 6 years old) are mostly affected by Noma. Prevention and effective management of Noma is hindered by the lack of sufficient cohesive studies on the microbial etiology of the disease. Research efforts have not provided a comprehensive unified story of the disease. Bridging the gap between existing studies gives an insight on the disease pathogenesis. This current systematic review of etiological studies focuses on the key players of dysbiosis in Noma disease. This review was performed in accordance with the Preferred Reporting Items for Systemic review and Meta-Analyses (PRISMA) statement. Web of Science, MEDLINE PubMed, Cochrane Library, Scopus, and Science Direct were searched electronically for clinical trials which applied culture dependent or molecular techniques to identify oral microbiota from Noma patients. Trials which involved periodontal diseases except Noma were excluded. After screening 275 articles, 153 full-texts articles were assessed for eligibility of which eight full text articles were selected for data extraction and analysis. The results show that 308 samples from 169 Noma participants (6 months to 15 years old) have been used in clinical trials. There was some variance in the microbiome identified due to the use of 3 different types of samples (crevicular fluid, subgingival plaque, and swabbed pus) and the ambiguity of the stage or advancement of Noma in the studies. Other limitations of the studies included in this review were: the absence of age-matched controls in some studies; the constraints of colony morphology as a tool in distinguishing between virulent fusobacterium genus at the species level; the difficulty in culturing spirochaetes in the laboratory; the choice of primers in DNA amplification; and the selection of probe sets in gene sequencing. This systematic review highlights spirochaetes and P. intermedia as putative trigger organisms in Noma dysbiosis, shows that F. nucleatum promotes biofilms formation in late stages of the disease and suggests that future studies should be longitudinal, with high throughput genome sequencing techniques used with gingival plaque samples from early stages of Noma.
PubMed: 36937503
DOI: 10.3389/froh.2023.1095858 -
Epidemiology and Infection Nov 2015This systematic review-meta-analysis appraises and summarizes all the available research (128 papers) on the zoonotic potential of Mycobacterium avium ssp.... (Meta-Analysis)
Meta-Analysis Review
This systematic review-meta-analysis appraises and summarizes all the available research (128 papers) on the zoonotic potential of Mycobacterium avium ssp. paratuberculosis. The latter has been debated for a century due to pathogenic and clinical similarities between Johne's disease in ruminants and Crohn's disease (108 studies) in humans and recently for involvement in other human diseases; human immunodeficiency virus (HIV) infection (2), sarcoidosis (3), diabetes mellitus type 1 (T1DM) (7) and type 2 (3), multiple sclerosis (5) and Hashimoto's thyroiditis (2). Meta-analytical results indicated a significant positive association, consistently across different laboratory methods for Crohn's disease [odds ratio (OR) range 4·26-8·44], T1DM (OR range 2·91-9·95) and multiple sclerosis (OR range 6·5-7·99). The latter two and the thyroiditis hypothesis require further investigation to confirm the association. Meta-regression of Crohn's disease studies using DNA detection methods indicated that choice of primers and sampling frame (e.g. general population vs. hospital-based sample) explained a significant proportion of heterogeneity. Other epidemiological studies demonstrated a lack of association between high-risk occupations and development of Crohn's disease. Due to knowledge gaps in understanding the role of M. paratuberculosis in the development or progression of human disease, the evidence at present is not strong enough to inform the potential public health impact of M. paratuberculosis exposure.
Topics: Animals; Crohn Disease; Humans; Molecular Epidemiology; Mycobacterium avium subsp. paratuberculosis; Paratuberculosis; Zoonoses
PubMed: 25989710
DOI: 10.1017/S095026881500076X -
Tropical Medicine and Infectious Disease Feb 2024spp. are among the few enteric parasites with a prevalence that can reach up to approximately 80% in communities of developing countries. This systematic review updates... (Review)
Review
spp. are among the few enteric parasites with a prevalence that can reach up to approximately 80% in communities of developing countries. This systematic review updates and summarizes available literature on the molecular prevalence and subtype distribution of spp. in Latin American people. This work follows the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. The literature revised covers from 1 January 2015 to 6 October 2023 in seven different scientific databases, and the material was selected through inclusion and exclusion criteria. According to data found in the 36 selected articles, the prevalence of spp. in Latin America ranged between 5.8% (Bolivian rural communities) and 94.0% (Colombian general public). Generally, genomic DNA was extracted from approximately 200 mg fecal sediments using commercial kits, such as the QIAamp Stool Mini Kit (QIAGEN, Hilden, Germany) or the Norgen Stool DNA Isolation Kit (Norgen Biotek Corporation, Thorold, ON, Canada). Subtype-specific primers (such as the couple of primers BhRDr-RD5) developed from unique sequences of the SSU rRNA gene were applied to subtyping. Ten specific subtypes (STs) were found as well as various mixed infections, and the most circulating STs were in the order ST3, ST1, ST2, and ST4. The most recent data about spp. molecular epidemiology and the STs in communities of Latin America are limited to studies from specific countries. Novel scientific data from the other countries are required to obtain a complete picture and truly understand the distribution and prevalence of spp. and the STs.
PubMed: 38393127
DOI: 10.3390/tropicalmed9020038 -
BMC Pediatrics Feb 2019The early recognition of meningococcal disease in children is vital. During the prodrome however, meningococcal infection presents similarly to many self-limiting viral...
BACKGROUND
The early recognition of meningococcal disease in children is vital. During the prodrome however, meningococcal infection presents similarly to many self-limiting viral infections. This mandates a cautious approach with many children receiving unnecessary broad-spectrum parenteral antibiotics. Advances in nucleic acid amplification techniques mean that it is now possible to test for Neisseria meningitidis DNA using Loop-mediated-isothermal AMPlification (LAMP). This technique is quicker than traditional PCR techniques and can be performed using simple equipment.
METHODS
Prior to performing this systematic review, a protocol was developed adhering to PRISMA P standards and underwent full external peer review. This systematic review was registered with PROSPERO (CRD42017078026). The index test assessed was LAMP for Neisseria meningitidis and the reference standard was culture or qPCR of a sterile site detecting Neisseria meningitidis.
RESULTS
We identified 95 records in total: 94 records from the electronic databases and 1 additional study from the grey literature. After removal of duplicates, 36 studies were screened, and 31 studies excluded based on the title/abstract. Five full text studies underwent full text review and three studies, including 2243 tests on 1989 patients aged between 7 days and 18 years were included in the final systematic review. In all studies the LAMP assay and qPCR primers were directed against the ctrA region of the Neisseria meningitidis bacteria. The diagnostic accuracy of LAMP testing for invasive meningococcal disease was reported as high (sensitivity 0.84-1.0 and specificity 0.94-1.0) in all studies irrespective of the sample tested (CSF, Blood, Swab).
CONCLUSIONS
We included three studies with 2243 tests on 1989 patients using CSF, blood samples or naso/oropharyngeal swabs. The studies were all of a high quality and deemed at low risk of bias. Results show that LAMP testing on blood and CSF was highly accurate when compared to qPCR/culture. LAMP testing for Neisseria meningitidis is fast and highly accurate and therefore has the potential to be used to rapidly rule in/out meningococcal disease in children. Given the life-threatening nature of meningococcal infection further research is required to demonstrate the safety and efficacy of using LAMP testing for Neisseria meningitidis as a rule in/out test.
TRIAL REGISTRATION
This systematic review was registered prospectively with PROSPERO on the 29/11/2017 (CRD42017078026).
Topics: Humans; Meningococcal Infections; Neisseria meningitidis; Nucleic Acid Amplification Techniques; Reproducibility of Results
PubMed: 30732581
DOI: 10.1186/s12887-019-1403-0 -
Clinical Epigenetics May 2021Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a...
BACKGROUND
Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a head-to-head comparison of previously published DNA methylation markers and propose a potential prognostic model for clear cell RCC (ccRCC).
PATIENTS AND METHODS
Promoter methylation of PCDH8, BNC1, SCUBE3, GREM1, LAD1, NEFH, RASSF1A, GATA5, SFRP1, CDO1, and NEURL was determined by nested methylation-specific PCR. To identify clinically relevant methylated regions, The Cancer Genome Atlas (TCGA) was used to guide primer design. Formalin-fixed paraffin-embedded (FFPE) tissue samples from 336 non-metastatic ccRCC patients from the prospective Netherlands Cohort Study (NLCS) were used to develop a Cox proportional hazards model using stepwise backward elimination and bootstrapping to correct for optimism. For validation purposes, FFPE ccRCC tissue of 64 patients from the University Hospitals Leuven and a series of 232 cases from The Cancer Genome Atlas (TCGA) were used.
RESULTS
Methylation of GREM1, GATA5, LAD1, NEFH, NEURL, and SFRP1 was associated with poor ccRCC-specific survival, independent of age, sex, tumor size, TNM stage or tumor grade. Moreover, the association between GREM1, NEFH, and NEURL methylation and outcome was shown to be dependent on the genomic region. A prognostic biomarker model containing GREM1, GATA5, LAD1, NEFH and NEURL methylation in combination with clinicopathological characteristics, performed better compared to the model with clinicopathological characteristics only (clinical model), in both the NLCS and the validation population with a c-statistic of 0.71 versus 0.65 and a c-statistic of 0.95 versus 0.86 consecutively. However, the biomarker model had limited added prognostic value in the TCGA series with a c-statistic of 0.76 versus 0.75 for the clinical model.
CONCLUSION
In this study we performed a head-to-head comparison of potential prognostic methylation markers for ccRCC using a novel approach to guide primers design which utilizes the optimal location for measuring DNA methylation. Using this approach, we identified five methylation markers that potentially show prognostic value in addition to currently known clinicopathological factors.
Topics: Biomarkers, Tumor; Carcinoma, Renal Cell; DNA Methylation; Epigenomics; Humans; Kidney Neoplasms; Prognosis; Risk Assessment
PubMed: 33947447
DOI: 10.1186/s13148-021-01084-8