Molecular analysis of blood groups is important in transfusion medicine, allowing the prediction of red blood cell (RBC) antigens. Many blood banks use single nucleotide variant (SNV) based methods ...for blood group analysis. While this is a well-established approach, it is limited to the polymorphisms included in genotyping panels. Thus, variants that alter antigenic expression may be ignored, resulting in incorrect prediction of phenotypes. The popularization of next-generation sequencing (NGS) has led to its application in transfusion medicine, including for RBC antigens determination. The present review/meta-analysis aimed to evaluate the applicability of the NGS for the prediction of RBC antigens. A systematic review was conducted following a comprehensive literature search in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. Studies were selected based on predefined criteria and evaluated using Strengthening the Reporting of Observational studies in Epidemiology guidelines. The characteristics and results of the studies were extracted and meta-analysis was performed to verify the agreement between results from standard molecular methods and NGS. Kell (rs8176058), Duffy (rs2814778, rs12078), or Kidd (rs1085396) alleles were selected as a model for comparisons. Additionally, results are presented for other blood group systems. Of the 864 eligible studies identified, 10 met the inclusion criteria and were selected for meta-analysis. The pooled concordance proportion for NGS compared to other methods ranged from 0.982 to 0.994. The sequencing depth coverage was identified as crucial parameters for the reliability of the results. Some studies reported difficulty in analyzing more complex systems, such as Rh and MNS, requiring the adoption of specific strategies. NGS is a technology capable of predicting blood group phenotypes and has many strengths such as the possibility of simultaneously analyzing hundred individuals and gene regions, and the ability to provide comprehensive genetic analysis, which is useful in the description of new alleles and a better understanding of the genetic basis of blood groups. The implementation of NGS in the routine of blood banks depends on several factors such as cost reduction, the availability of widely validated panels, the establishment of clear quality parameters and access to bioinformatics analysis tools that are easy to access and operate.
Background: Post-operative wound contamination with non-tuberculous mycobacterial (NTM) organisms is not rare, however, it poses difficulty in identification and isolation using routine standard ...laboratory tests. Objective: In past decades, numerous molecular techniques were introduced to solve this issue however, the results were heterogeneous. There is a need for identification of rapid, sensitive, and effective molecular methods for NTM detection. Methods: Published articles relevant to research questions were searched in the database (PubMed, Scopus, Web of Science). Additionally, studies were searched through snowballing. The articles were included as per eligibility for data extraction. The included articles were assessed on quality reporting and results were presented using the descriptive analysis.Results:27 studies articles (131 patients) out of 3439 searches were included. 12 and 15 were case series and case reports respectively. Cases were reported mostly from India, Brazil, South Korea, and the United States of America. 16srRNA gene sequencing and reverse hybridization techniques were the common techniques used. Most frequently isolated NTM reported in POWI was M. abscessus followed by M. chelonae. Overall quality of case reports and case series were high to moderate, however, in general evidence level from case report and case series is considered a slow. Conclusion: The 16sr RNA gene sequencing and reverse hybridization techniques were the most common, faster, sensitive and specific diagnostic method sutilized in hospitals to detect NTM. However, most of this evidence is presented from the case reports and case series, prospective randomized clinical trials with a quality methodology should be conducted to ascertain the real effect estimate.
ABSTRACTObjectives: Mycobacterium tuberculosis (MTB) remains one of the most significant causes of mortality and morbidity in developing countriesespecially India. India has the highest burden of TB, ...with an estimated incidence figure of 2.1 million cases out of the 9 million cases of TB globally.Diagnosis of TB relies on conventional microscopy and culture with drawbacks related to sensitivity, specificity, turn around time (TAT). The aim ofthis study was to evaluate the performance of Xpert MTB/rifampicin (RIF) assay (GX) for MTB detection in pulmonary and extrapulmonary clinicalsamples.Methods: A total of 209 clinical specimens (182: pulmonary and 27: extrapulmonary) were processed using auramine smear, culture by mycobacteriagrowth indicator tube and GenXpert.Results: The sensitivity of GenXpert was 62.63% for pulmonary and 55% for extrapulmonary samples. The sensitivity and specificity of GX were100% for the smear positive cases. The sensitivity, specificity, positive predictive value, and negative predictive value of the GX for smear negativecases were 67.8%, 97.5%, 90.4%, and 89.6%, respectively. RIF resistance was detected in 3.8% the samples.Conclusion: GenXpert, with short TAT, high sensitivity, specificity and less technical expertise required is a promising tool in TB diagnostics for thefuture.Keywords: GenXpert, Tuberculosis diagnosis, Molecular method, Rifampicin resistance.
A previous study confirmed the contamination of water sources with this parasite in Arak, Markazi Province, Iran. The current study investigated soil sources and determined the predominant genotype ...of Acanthamoeba in this region of Iran.
Forty-eight soil samples, collected from different regions of Arak, Markazi province, Iran, were evaluated in this study. The samples were processed and identified by culturing on a specific medium, performing PCR assay, and sequencing the PCR products. Finally, using the NCBI database, the genotypes were determined.
Of 48 soil samples, 33.3% and 31.25% were contaminated with Acanthamoeba according to the culture and molecular assays, respectively. The majority of these isolates belonged to the T4, T5 and T6 genotypes of Acanthamoeba.
The genotypes of most isolates from soil samples in Arak similar to other regions of Iran belong to T4 genotype of this parasite. New sequence accession numbers include MG066681 and MG298785-MG298794.
•Virus removal values by full-scale MF, UF, and RO processes were determined.•AiV, PMMoV, CGMMV, and crAssphage were used as process indicators.•MF and UF showed high virus removal compared with ...credited values.•PMMoV and CGMMV were the most abundant and were detected after the RO process.
Treatment of wastewater for potable reuse is increasingly becoming a suitable alternative water source to meet the growing urban water needs worldwide. Potable reuse requires reduction of enteric viruses to levels at which they do not pose a risk to human health. Advanced water treatment trains (e.g., microfiltration (MF), ultrafiltration (UF), reverse osmosis (RO), and ultraviolet light and advanced oxidation process (UV/AOP)) provide significant protection and reduce virus loads in highly treated final product waters. Even though viruses are a principal concern, the performance of virus removal by membrane processes is not easily determined. The objective of this study was to evaluate the applicability of Aichi virus (AiV), pepper mild mottle virus (PMMoV), cucumber green mottle mosaic virus (CGMMV), and cross-assembly phage (crAssphage) removal as possible process indicators for MF, UF, and RO. Virus log reduction values (LRVs) based on gene copies measured using molecular methods were determined for MF and UF. The median LRVs of all viruses obtained after MF and UF were 2.9 and 3.1, respectively. The LRVs of the proposed indicators were lower than those of human enteric viruses. The morphological and physicochemical difference among indicators was not found to affect LRVs. Therefore, all proposed indicator viruses were determined to be suitable candidates as process indicators for MF and UF. Regarding RO, most of the viruses measured in this study were undetectable in permeate. Only PMMoV and CGMMV were detected showing median LRVs of 2.8 and 2.5, respectively. PMMoV and CGMMV are recommended as good process indicators of physical virus removal for the overall water treatment process.
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Background
In superficial fungal infections, prompt diagnosis and treatment are essential to prevent the spread of infection and minimise the impact on patients' quality of life. Traditional ...diagnostic methods, such as KOH smear and fungal culture, have limitations in terms of sensitivity and turnaround time. Recently, the PCR‐reverse blot hybridization assay (PCR‐REBA) has been developed for the direct detection of dermatophyte DNA. However, there is a lack of information assessing the diagnostic accuracy of PCR‐REBA.
Objectives
This systematic review aimed to evaluate the diagnostic accuracy of PCR‐REBA in superficial fungal infections compared to conventional and molecular methods.
Methods
The comprehensive search containing Ovid MEDLINE and Embase databases was conducted on 7 August 2022. Two reviewers independently reviewed the included articles. Quality assessment was performed using the Newcastle‐Ottawa Scale tool.
Results
The included studies were conducted in Korea (five studies) and the Netherlands (two studies), all of which were conducted in a single institution. The quality assessment of these studies indicated low risk of bias. When compared to the potassium hydroxide (KOH) smear and fungus culture, the sensitivity of PCR‐REBA ranged from 85% to 100%, and the positive predictive values ranged from 58.9% to 100%. When compared to the RT‐PCR, the sensitivity of PCR‐REBA ranged from 93.3% to 100%, and the positive and negative predictive values were 91.6%–99.6% and 81.0%–89.1%, respectively.
Conclusions
The PCR‐REBA shows promise as a valuable diagnostic tool for dermatophytosis, offering practical and cost‐effective benefits.
Potato (Solanum tuberosum L.) is one of the major crops for human nutrition. Columbia root‐knot nematode, Meloidogyne chitwoodi Golden et al. (1980), can cause significant decrease in potato yields ...in the world. The aim of the study was to develop a novel molecular method for the rapid and accurate detection of M. chitwoodi on infested potato tubers. Total DNA from peel and tissues of potato were directly isolated from M. chitwoodi‐infested potato tubers without using any nematode extraction method. Meloidogyne chitwoodi was successfully detected and identified in total DNA isolated using species‐specific primers. Meloidogyne chitwoodi was also successfully identified in DNA isolated from only one necrotic spot in potato. Our results show that this molecular method is quite useful for fast and accurate identification of M. chitwoodi on potato. Based on these results, it seems that useful practical and applicable aspects for direct detection of M. chitwoodi from potato tubers without nematode extraction. The novel technique can be used in quarantine laboratories and potato seed producer companies. To the best of the authors' knowledge, this is the first report to identify M. chitwoodi using a novel molecular method from potato tubers without nematode extraction.
Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In ...the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0.
Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data.
We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.
Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods ...provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.
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