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•Conventional methods and sensors for microbial detection are summarized.•Typical sensing mechanisms for rapid detection are discussed.•Rapid sensors for monitoring food, water and ...environment were critically reviewed.•Insights for the future development on rapid sensors are provided.
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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•eDNA metabarcoding effectively reflects diatoms at genus but not species level.•eDNA metabarcoding provides better illustration of beta diversity.•rbcL identification is preferable ...to 18S rDNA identification in diatom evaluation.
Benthic diatoms have been widely utilized for assessing the ecological status of rivers, due to their ability to reflect the environmental changes from natural and anthropogenic disturbance. However, the recognized limitations of traditional morphological method for diatom identification hinder its widespread application in local department monitoring and assessment efforts. Recently, eDNA metabarcoding methods have emerged as a promising alternative for efficient diatom identification. To reveal the feasibility of eDNA metabarcoding methods in diatom-based evaluation, this study comprehensively compared them with the traditional morphological method. The results revealed that eDNA metabarcoding effectively reflected diatom composition at genus but not species level. It recognized 80.4 % of genera identified morphologically through rbcL identification and 66.7 % through 18S rDNA identification. Despite species-level discrepancies in taxonomic composition, eDNA metabarcoding accurately indicated alpha diversity of diatoms, while also provided better illustration of beta diversity. Additionally, comparisons were performed in taxonomy-based and trait-based indices. It was suggested that no significance was observed between identification methods in any index. Linear regression analyses further supported rbcL identification as a preferred option over 18S rDNA identification due to its stronger congruency with morphological method. In all, this study presented two key suggestions: 1) rbcL identification is preferable to 18S rDNA identification in diatom taxonomy, and 2) eDNA metabarcoding is proposed to be a promising technique to assess river ecological status.
•Indole-3-carbaldehyde (I3A) is a biomolecule inducing defense responses in plants.•The first comprehensive quantitative data collection of I3A in food was reported.•I3A reacts with the hydrazine ...group of carbidopa giving a yellow colored aldazine.•A simple, safe, and low-cost assay was assessed in ethanolic extract of cabbage.•LC-MS confirmed the formation of yellow aldazine in ethanolic extract of cabbage.
A colorimetric assay was developed for detection of indole-3-carbaldehyde (I3A), a bioactive compound particularly abundant in vegetables of the Brassicaceae family, inducing plant defense responses and ensuring the human intestinal barrier integrity. The assay is based on the selective condensation reaction between the hydrazine group of carbidopa, used as a derivatizing agent, and the aldehyde group of I3A, generating a colored aldazine with a characteristic absorbance around 415 nm. As proof of concept, among the several natural sources here reported in a quantitative data collection, the colorimetric assay was assessed in white heart cabbage ethanolic extract. I3A content was determined by LC-MS analysis, which confirmed the colored aldazine formation in matrix. The LOD (10.4 ± 0.3 μM) obtained by the calibration curve from the visible absorbance (m = 565 ± 16 M−1, avRSD % 6.5, R2 = 0.9960) indicates that this simple, safe, and low-cost method could be beneficial also for current methodologies for identification and quantification of I3A in foods.
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Background and Objective: Meningitis is a medical emergency requiring immediate diagnosis and treatment. Bacterial and viral causative agents play a role in meningitis appearance to various degrees. ...Thus, effective vaccines and antimicrobial and supportive treatments need to be developed and monitoring should be performed in different regions for controlling this disease. Most previous studies have focused on a small number of bacterial agents, and the viral profile of this disease is not precisely monitored in Iran, especially in overpopulated regions. Moreover, limited new applied methods with high precision and sensitivity for the detection of meningitis agents indicate the necessity of determining meningitis agents by rapid molecular methods, which was the aim of the current study. Materials and Methods: Overall, 148 samples obtained from suspected meningitis patients from different age groups admitted to Tehran and Karaj hospitals were evaluated by new methods involving specific primers for 16s rRNA, PCR, and Real-time PCR tests. Results: It was found that viral infection, especially infection with human enterovirus, remains the main cause of meningitis in Iran, and Neisseria meningitides is the most common bacterial isolate detected in meningitis cases. Conclusion: Despite the decreasing trend in meningitis incidence, according to World Health Organization recommendation, implementing an enhanced surveillance system to provide high-quality data on the epidemiological profile of meningitis per each region is necessary.
Harmful algal blooms (HABs) represent a growing threat to aquatic ecosystems and humans. Effective HAB management and mitigation efforts strongly rely on the availability of timely and in-situ tools ...for the detection of microalgae. In this sense, nucleic acid-based (molecular) methods are being considered for the unequivocal identification of microalgae as an attractive alternative to the currently used time-consuming and laboratory-based light microscopy techniques. This review provides an overview of the progress made on new molecular biotechnological tools for microalgal detection, particularly focusing on those that combine a nucleic acid (DNA or RNA) amplification step with detection. Different types of amplification processes (thermal and isothermal) and detection formats (e.g. microarrays, biosensors, lateral flows) are presented, and a comprehensive overview of their advantages and limitations is provided Although isothermal techniques are an attractive alternative to thermal amplification to reach in-situ analysis, further development is still required. Finally, current challenges, critical steps and future directions of the whole analysis process (from sample procurement to in-situ implementation) are described.
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•A description of PCR and isothermal techniques to amplify microalgal DNA/RNA is provided.•Isothermal techniques are being used but major development is still required.•The critical steps to achieve true implementation of the molecular tools are considered.•Application of these new sensing tools is possible for an unlimited number of microalgal species.
The current study was conducted to statistically compare the SYBR® Green quantitative polymerase chain reaction (qPCR) assay and the conventional plate counting (PC) method to construct growth curves ...of a cocktail of Weissella viridescens in pure culture under different isothermal storage conditions (4, 8, 14, and 30 °C) and in mixed culture with Leuconostoc mesenteroides at 8 °C. The efficiency and specificity of the qPCR standard curves were confirmed, and both methods were adequate to quantify the growth kinetics of W. viridescens at all isothermal temperatures, demonstrating a good correlation and agreement. The efficiencies of the standard curves varied between 98% and 102%. The SYBR® Green qPCR assay was also able to differentiate the growth curves of W. viridescens and L. mesenteroides in the mixed culture at 8 °C. Additionally, the SYBR® Green qPCR method was considered a faster and more sensitive alternative to construct growth curves under different isothermal conditions and differentiate morphologically similar lactic acid bacteria. Overall, the results suggest that the SYBR® Green qPCR method is a reliable and efficient tool to study microbial growth kinetics in pure and mixed cultures.
•The recN primer pair demonstrated selective detection of W. viridescens.•Standard curves of W. viridescens cocktail had adequate efficiency values.•LoD values were suitable for W. viridescens quantification at 4, 8, 14, and 30 °C.•SYBR® Green qPCR and PC methods showed good correlation and agreement.•SYBR® Green qPCR method distinguished the growth curves of LAB in mixed culture.
The demand for fresh produce is rising daily as it's an excellent way to maintain a healthy lifestyle. The current work fixed the target employing culture-based and molecular techniques for isolating ...and identifying the pathogenic Vibrio parahaemolyticus from fresh produce. The colonial appearance on TCBS agar and CHROMagar culture plates revealed the prevalence of Vibrio spp. and V. parahaemolyticus in all examined samples, which were 45/112 (40.2%) and 40/112 (35.7%), with the highest load of up to 2.0x105cfu/g and 6.4x103cfu/g, respectively. Sixty isolates in all were chosen for further molecular characterization. Multiplex PCR results exhibited that all tested isolates were positive for tlh gene and six for tdh gene but none of isolate for trh gene. According to obtained data on antimicrobial susceptibility, the major portion of tested strains was found to be resistant to ampicillin (90%), tetracycline (80%), and streptomycin (70%). The range of the multiple antibiotic index was 0-0.33. This study finding revealed that the existence of potential pathogenic V. parahaemolyticus in tested fresh produce samples constitutes a risk to public health and consumer safety thus urging continued surveillance.
Five sibling species of the Lindesayi Complex of the genus Anopheles have been discovered in Bhutan: An. druki Somboon, Namgay & Harbach, An. himalayensis Somboon, Namgay & Harbach, An. lindesayi ...Giles, An. lindesayi species B, and An. thimphuensis Somboon, Namgay & Harbach. The species are morphologically similar in the adult and/or immature stages. This study aimed to develop a multiplex PCR assay to identify the 5 species. Allele-specific primers were designed for specific nucleotide segments of ITS2 sequences previously reported for each species. The assay provided products of 183 bp for An. druki, 338 bp for An. himalayensis, 126 bp for An. lindesayi, 290 bp for An. lindesayi species B, and 370 bp for An. thimphuensis.The use of the assay produced consistent results.The assay is relatively inexpensive, enables the rapid identification of a large number of specimens, and will foster further studies of the Lindesayi Complex.
Background & Objective: Microsatellite instability is common in familial colorectal cancers. It can be tested by the molecular and immunohistochemical methods. There are very few studies which ...address comparing the clinicopathological characteristics of microsatellite stable (MSS) and microsatellite unstable (MSI) colorectal cancers from Iran. n this study, we aimed to evaluate the clinicopathological and immunohistochemical findings of MSS and MSI colorectal cancers in our Center as the largest Center of gastrointestinal surgery and oncology in the South of Iran. We also compared the immunohistochemical method vs. molecular study using DNA sequencing.Methods: For 5 years (2015-2019), 34 patients who underwent operation in the affiliated Hospitals of Shiraz University of Medical Sciences were clinically suspected to microsatellite instability (MSI). The molecular diagnostic tests with DNA sequencing were performed. Clinicopathological and immunohistochemical findings of MSI colorectal cancers were compared with those who were stable. Results: In the South of Iran, MSI colorectal cancers were more common in males. These tumors were more common in the right side with more tendencies to produce mucin with lymphocytic infiltration. Conclusion: It was concluded that immunohistochemistry is a specific method for the diagnosis of MSI colorectal cancers, but false negative rate is high, and sensitivity is low. Therefore, we recommend performing molecular studies by DNA sequencing in colon cancer with clinical suspicion to MSI and negative immunohistochemistry
Background and purpose: Ureaplasma urealyticum is one of the most common causes of Non-Gonococcal Urethritis (NGU). Asymptomatic clinical infection caused by this bacterium can cause malnutrition of ...the sexual attachment glands and its presence in semen contributes to lower fertility. The aim of this study was to identify Ureaplasma urealyticum in semen of infertile men using PCR method as an accurate diagnostic method. Materials and methods: The PCR test was optimized by standard strain to detect Ureaplasma urealyticum and then was studied in terms of specificity and limit of detection (LOD). Semen samples were collected from 100 infertile men and each sample was divided into two parts: the first part was tested by semen analysis and the second part was tested by PCR method. DNA was extracted using phenol-chloroform method and the PCR test was done for detection of Ureaplasma urealyticum. Results: Among the semen samples, 16 cases (16%) were found to be positive for Ureaplasma urealyticum. According to the spermogram test, the leukocyte level was also more than normal level in these samples (0-1 Mil/ml). Conclusion: Screening of infertile couples for Ureaplasma urealyticum infection in those without clinical symptoms, thereby performing timely antibiotic therapy play key roles in treatment of infertility. Hence, PCR method is introduced as a valuable and reliable technique to identify Ureaplasma urealyticum.
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