Traditional Culture-based Methods Research Articles

Enhancing pneumococcal bacteraemia diagnosis: A comparative assessment of culture-independent assays (MALDI–TOF–MS Sepsityper® module and a lateral flow inmunochromatography test)

IntroductionPneumococcal bacteraemia is a major contributor to global morbidity and mortality. Traditional culture-based methods lack sensitivity and are time-consuming. This study aimed to assess the effectiveness of two culture-independent assays, the MALDI–TOF–MS Sepsityper® module and the lateral flow inmunochromatography test (LFICT) with the Standard F® Streptococcus pneumoniae, directly from positive blood culture (BC) bottles. MethodsA prospective study was conducted from December 2021 to July 2022. For all BC positives for S. pneumoniae a double centrifugation protocol was implemented. The resulting pellet was subsequently processed using both techniques. ResultsThe LFICT showed exceptional performance with 100% sensitivity and specificity, outperforming the MALDI–TOF–MS Sepsityper® module, which achieved 85.2% sensitivity and 100% specificity. Nevertheless, the combination of these assays offers a robust and comprehensive approach to diagnosis. ConclusionsThe simultaneous use of both techniques offers a promising alternative that can be integrated into routine practices directly from BC samples.

Development of PCR-based assays for the detection of the evident and latent infection with Stilbocrea banihashemiana, the causal agent of fruit tree cankers

The fig Bionectria canker, caused by Stilbocrea banihashemiana, is rapidly spreading in fruit trees, posing a significant threat to the horticultural industry. Early and specific detection of this pathogen is crucial for effective management. We developed a PCR-based assay using species-specific primers designed by exploiting sequence differences in the translation elongation factor 1-alpha (tef1) gene for early, rapid, and reliable diagnostics of this pathogen. The primers successfully amplified the target pathogen and did not react with other non-target fig canker-causing agents in direct and nested PCR. The designated primer pair, TEF-Sb3, with a 577 bp amplicon, demonstrated its efficacy by successfully detecting the pathogen with the lowest detectable concentration of 1 × 10−15 and 1 × 10−17 g.L−1 in direct and nested PCR, respectively. Furthermore, the selected primer pair had high performance in detecting the target pathogen in naturally infected samples with evident canker symptoms in nested PCR. Moreover, our molecular tool has effectively identified latent infection of S. banihashemiana in asymptomatic samples from fig and walnut trees from three different regions of Fars Province. This is a notable advancement, as traditional culture-based methods have failed to detect these infections. Our results suggested that the designed species-specific PCR assays were sufficiently sensitive, specific, and reliable for identifying S. banihashemiana from pure cultures and detecting the pathogen in symptomatic and asymptomatic trees. This assay can be a rapid and cost-effective tool for monitoring and managing Bionectria canker caused by S. banihashemiana in natural and potential host trees.

Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel.

Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.

Breaking the Mold: Towards Rapid and Cost-Effective Microbial Contamination Detection in Paints and Cosmetics Using ATP-Bioluminescence

Traditional culture-based methods, though a “gold standard” for bacterial detection in various industrial sectors, do often not fulfill today’s high requirements regarding rapidity, on-site applicability, and cost-efficiency both during operation and evaluation. Here, the feasibility of using an adenosine triphosphate (ATP)-based assay for determining microbial contaminations in paints and cosmetics was investigated and compared with standard plate count techniques and dipslides. Therefore, we initially determined the level of sensitivity and assessed the accuracy and concordance among the different methods via spiking tests using a mix of frequently abundant bacterial species to simulate microbial contamination. Bioluminescence intensity was linearly proportional to log colony counts over five orders of magnitude (R2 = 0.99), indicating a high level of sensitivity. Overall, the accuracy varied depending on the test specimen, most probably due to matrix-related quenching effects. Although the degree of conformity was consistently higher at target concentrations ≥ 105 CFU·mL−1, microbial contaminations were detectable down to 103 CFU·mL−1, thus meeting the high requirements of various industries. ATP-based results tended to be within an order of magnitude lower than the reference. However, bearing that in mind, the developed assay serves as a rapid, real-time alternative for routine quality control and hygiene monitoring.

A New Peptide Nucleic Acid Fluorescence In Situ Hybridization Probe for the Specific Detection of Salmonella Species in Food Matrices.

Salmonella spp. is among the most central etiological agents in foodborne bacterial disorders. To identify Salmonella spp., numerous new molecular techniques have been developed conversely to the traditional culture-based methods. In this work, a new peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method was developed for the specific detection of Salmonella species, allowing a faster analysis compared with the traditional methods (ISO 6579-1: 2017). The method was optimized based on a novel PNA probe (SalPNA1692) combined with a blocker probe to detect Salmonella in food samples through an assessment of diverse-rich and selective enrichment broths. Our findings indicated that the best outcome was obtained using a 24-h pre-enrichment step in buffered peptone water, followed by RambaQuick broth selective enrichment for 16 h. For the enrichment step performance validation, fresh ground beef was artificially contaminated with two ranges of concentration of inoculum: a low level (0.2-2 colony-forming units [CFUs]/25 g) and a high level (2-10 CFUs/25 g). The new PNA-FISH method presented a specificity of 100% and a detection limit of 0.5 CFU/25 g of food sample, which confirms the great potential of applying PNA probes in food analysis.

Optical fiber immunosensors based on surface plasmon resonance for the detection of Escherichia coli.

Every year, millions of people suffer some form of illness associated with the consumption of contaminated food. Escherichia coli (E. coli), found in the intestines of humans and other animals, is commonly associated with various diseases, due to the existence of pathogenic strains. Strict monitoring of food products for human consumption is essential to ensure public health, but traditional cell culture-based methods are associated with long waiting times and high costs. New approaches must be developed to achieve cheap, fast, and on-site monitoring. Thus, in this work, we developed optical fiber sensors based on surface plasmon resonance. Gold and cysteamine-coated fibers were functionalized with anti-E. coli antibody and tested using E. coli suspensions with concentrations ranging from 1 cell/mL to 105 cells/mL. An average logarithmic sensitivity of 0.21 ± 0.01 nm/log(cells/mL) was obtained for three independent assays. An additional assay revealed that including molybdenum disulfide resulted in an increase of approximately 50% in sensitivity. Specificity and selectivity were also evaluated, and the sensors were used to analyze contaminated water samples, which verified their promising applicability in the aquaculture field.

Microbiota in adult perianal abscess revealed by metagenomic next-generation sequencing.

The microbiota of perianal abscesses is scarcely investigated. Identifying causative bacteria is essential to develop antibiotic therapy. However, culture-based methods and molecular diagnostics through 16S PCR technology are often hampered by the polymicrobial nature of perianal abscesses. We sought to characterize the microbiota composition of perianal abscesses via metagenomic next-generation sequencing (mNGS). Fourteen patients suffering from perianal abscesses between March 2023 and August 2023 underwent retrospective assessment. Information from medical records was used, including clinical information, laboratory data, and culture and mNGS results. Forty bacterial taxa were identified from perianal abscesses through mNGS, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) representing the most prevalent species. mNGS identified an increased number of bacterial taxa, with an average of 6.1 compared to a traditional culture-based method which only detected an average of 1.1 in culture-positive perianal abscess patients, predominantly E. coli (75.0%), revealing the polymicrobial nature of perianal abscesses. Our study demonstrates that a more diverse bacterial profile is detected by mNGS in perianal abscesses, and that Bilophila wadsworthia is the most prevalent microorganism, potentially serving as a potential biomarker for perianal abscess.IMPORTANCEAccurately, identifying the bacteria causing perianal abscesses is crucial for effective antibiotic therapy. However, traditional culture-based methods and 16S PCR technology often struggle with the polymicrobial nature of these abscesses. This study employed metagenomic next-generation sequencing (mNGS) to comprehensively analyze the microbiota composition. Results revealed 40 bacterial taxa, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) being the most prevalent species. Compared to the culture-based approach, mNGS detected a significantly higher number of bacterial taxa (average 6.1 vs 1.1), highlighting the complex nature of perianal abscesses. Notably, Bilophila wadsworthia emerged as a potential biomarker for these abscesses. This research emphasizes the importance of mNGS in understanding perianal abscesses and suggests its potential for improving diagnostic accuracy and guiding targeted antibiotic therapy in the future.

Microbial water quality investigation through flow cytometry fingerprinting: from source to tap

Abstract Ensuring the quality of treated drinking water is crucial for preventing potential health impacts, regulatory fines, and reputation damage. Traditional culture-based microbiological methods often fail to capture the heterogeneity of the bacterial communities in drinking water. This study employed daily interstage monitoring and flow cytometry (FCM) analysis over a period of one year to investigate the dynamics of water treatment processes and service reservoirs. The objective of this study was to test the utility of FCM fingerprints for aiding in microbial event detection. We found that the chlorine concentration contact time was pivotal for microbial log reduction across the treatment works. FCM fingerprints exhibited significant deviations during operational events, such as process interruptions, but did not correlate with the presence of bacterial indicator organisms in the distributed and tap water. Furthermore, the diversity of bacterial fingerprints, quantified by the Bray–Curtis dissimilarity index, served as an indicator for identifying potentially poor microbial water quality. In chlorinated waters with low cell counts, the background signal shows potential as a metric to differentiate between different water sources, thereby offering the possibility to characterize breakthrough events in these circumstances that challenge most other microbial analytical methods. Interestingly, groundwater from simpler treatment works showed a higher occurrence of bacterial indicators, whereas surface water works had a lower incidence. These findings underpin the importance of appropriate disinfection even for “low-risk” source waters and the added value that the statistical interpretation of FCM data can offer objective decision making.

Isolation and Identification of Microorganisms and Antibiotic Resistance Microorganisms from Beehives Located in Palm, Corn and Longan Plantations, Thailand.

This study aims to determine the prevalence of microorganisms and antibiotic-resistant microorganisms in beehives located on different plantations in Thailand. Seventeen swabs immersed in transport media were utilized for samples from different zones within beehives. Traditional microbial culture-based methods, biochemical tests, MALDI-TOF MS (VITEK® MS, bioMerieux, Marcy-l'Étoile, France), and antibiotic drug susceptibility (disk-diffusion) tests were used to detect microorganism and antimicrobial resistance bacteria. The results from 16 beehive swabs found Gram-positive bacteria at 59.5%, Gram-negative bacteria at 35.1%, and fungi (yeast) at 5.4%. These organisms are classified as 11, 11, and 2 types of Gram-positive bacteria, Gram-negative bacteria, and fungi (yeast), respectively. Furthermore, no organism showed resistance to vancomycin or cefoxitin for antibiotic drug susceptibility testing. In contrast, all Acinetobacter spp. were susceptible to ciprofloxacin, levofloxacin, ceftazidime, cefotaxime, imipenem, and meropenem, except for Acinetobacter schindleri, which was resistant to ceftazidime and cefotaxime. For other organisms, due to the limitations of tests to identify some environmental microbial species, the antimicrobial susceptibility test results cannot be interpreted as resistant or susceptible to the drug for these organisms. The study's findings will support prevention, healthcare services, and public health systems.

Real-Time and Rapid Detection of Phytopythium vexans Using Loop-Mediated Isothermal Amplification Assay.

Phytopythium vexans (de Bary) Abad, de Cock, Bala, Robideau, A. M. Lodhi & Levesque is an important waterborne and soil-inhabiting oomycete pathogen causing root and crown rot of various plants including certain woody ornamentals, fruit, and forest trees. Early and accurate detection of Phytopythium in the nursery production system is critical, as this pathogen is quickly transported to neighboring healthy plants through the irrigation system. Conventional methods for the detection of this pathogen are tedious, frequently inconclusive, and costly. Hence, a specific, sensitive, and rapid molecular diagnostic method is required to overcome the limitations of traditional identification. In the current study, loop-mediated isothermal amplification (LAMP) for DNA amplification was developed for the identification of P. vexans. It was evaluated using real-time and colorimetric assays. Several sets of LAMP primers were designed and screened, but PVLSU2 was found to be specific to P. vexans as it did not amplify other closely related oomycetes, fungi, and bacteria. Moreover, the developed assays were sensitive enough to amplify DNA up to 102 fg per reaction. The real-time LAMP assay was more sensitive than traditional PCR and culture-based methods to detect infected plant samples. In addition, both LAMP assays detected as few as 100 zoospores suspended in 100 ml water. These LAMP assays are anticipated to save time in P. vexans detection by disease diagnostic laboratories and research institutions and enable early preparedness in the event of disease outbreaks.

Risk-based detection as a cost-effective strategy to reduce foodborne illness due to salmonella

BackgroundSalmonella, a widespread pathogen, poses a significant threat to global food safety, leading to foodborne diseases and substantial economic losses. The timely and accurate detection of foodborne pathogens is pivotal for averting food contamination and outbreaks across the food production chain. This study assesses the cost-effectiveness of traditional culture-based methods versus risk-based approaches, incorporating polymerase chain reaction (PCR) for Salmonella detection. MethodsWe employed a stochastic scenario tree model to simulate scenarios based on the sampling inspection plan for raw aquatic products conducted by the Guangzhou Center for Disease Control and Prevention from 2018 to 2020. Various detection methods (culture or PCR) were applied to these aquatic products based on their categorized risk level. Sensitivity values were derived from published data, and incremental cost-effectiveness ratios were used to compare the different scenarios against the traditional culture method. ResultsA total of 360 samples were collected for analysis. The cost of culture-based detection alone amounted to 125,423.20 Chinese Yuan (CNY) and yielded nine instances of positive Salmonella detections. The risk-based detection strategy, which combined the more sensitive PCR method with high-risk sample characteristics, while employing the culture method for the remaining combinations, imposed a total cost of 128,775.83 CNY and yielded ten positive detections. This approach cost approximately 3391.74 CNY per additional positive sample detected compared to the culture method alone. Meanwhile, PCR-only detection imposed a total cost of 62,960.03 CNY. ConclusionsIn comparison to traditional culture-based methods, both the risk-based detection strategy and the PCR-only approach demonstrated superior capabilities with respect to detecting contaminated aquatic products. Implementing risk-based detection strategies can enhance cost-effectiveness, not only ensuring food safety but also reducing the incidence and economic burden of foodborne diseases.

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria.

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Methods for detection and enumeration of coliforms in drinking water: a review

Abstract Ensuring the microbiological safety of drinking water is of paramount importance to protect public health. Coliform bacteria, including Escherichia coli, serve as key indicators of water contamination and the potential presence of harmful pathogens. Accurate and reliable detection and enumeration of coliforms in drinking water are essential for monitoring water quality and implementing appropriate interventions. This review article provides an overview of various traditional culture-based methods and rapid molecular methods employed for the analysis of coliforms in drinking water, highlighting their strengths, limitations, and advancements. Culture-based methods such as multiple-tube fermentation (most probable number) and membrane filtration techniques have long been used as standard methods for coliform detection. The emerging molecular-based approaches, including polymerase chain reaction (PCR), quantitative PCR, and nucleic acid sequencing offer improved sensitivity, specificity, and turnaround time. This comprehensive review provides a valuable resource for researchers, water quality professionals, and policymakers engaged in the detection and enumeration of coliform bacteria in drinking water. It offers an up-to-date understanding of different methods, their advancements, and the potential integration of novel technologies. By critically evaluating these approaches, this review aims to contribute to the ongoing efforts toward ensuring safe drinking water for all.

A sensitive mass spectrometry-based method to identify common respiratory pathogens in children.

Public health threats posed by emerging respiratory infections are a significant concern, particularly in children and infants. Traditional culture-based detection methods are time-consuming and typically require 1-3 days. Herein, we developed and evaluated a 23-plex common respiratory pathogen mass spectrometry assay that enables the simultaneous detection of 18 common respiratory pathogens in children. This assay combines matrix-assisted laser desorption/ionization time of flight mass spectrometry with multiplex reverse transcription-PCR and targets 11 bacterial and 7 viral pathogens (including 10 subtypes), and two internal controls. The detection limit of the common respiratory pathogen mass spectrometry assay was as low as 1 copy/µL, with no cross-reactivity with other organisms. We assessed the clinical performance of the common respiratory pathogen mass spectrometry assay using respiratory samples from 450 children. The total 450 clinical specimens underwent analysis via matrix-assisted laser desorption/ionization time of flight mass spectrometry, and the outcomes were juxtaposed with those derived from real-time reverse-transcriptase PCR conducted concurrently. The concordance between these methods was 96.0%, and the multiple infection identification rate was 7.1%. This innovative approach enables the simultaneous analysis of numerous outcomes from a solitary examination across 192 specimens within a timeframe of approximately 7 hours, with a dramatically reduced sample use and cost. In summary, the common respiratory pathogen mass spectrometry assay is a sensitive, accurate, and cost-effective method for detecting common respiratory pathogens in children and has the potential to revolutionize the diagnosis of respiratory tract infections. IMPORTANCE This study aimed to present and evaluate a novel co-detection method that enables the simultaneous identification of 11 bacterial and 7 viral pathogens in about 7 hours using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Our approach utilizes a combination of multiplex reverse transcription-PCR and matrix-assisted laser desorption/ionization time of flight mass spectrometry, which overcomes the limitations of conventional assays, which include a long assessment time, technical difficulty, and high costs. As a screening method for common respiratory pathogens in children, common respiratory pathogen mass spectrometry assay has the potential to revolutionize the diagnosis of respiratory tract infections by providing an accurate etiological diagnosis. The common respiratory pathogen mass spectrometry assay is expected to be a critical tool for the diagnosis of respiratory infections in children, offering a more efficient, cost-effective, and accurate approach for the detection of common respiratory pathogens.

Role of Bacillus spp. Plant Growth Promoting Properties in Mitigating Biotic and Abiotic Stresses in Lowland Rice (Oryza sativa L.).

The ability of microorganisms to promote plant growth and mitigate abiotic and biotic stresses makes them an interesting tool for sustainable agriculture. Numerous studies aim to identify new, promising bacteria isolates. Traditional culture-based methods, which focus on selecting microorganisms with plant-growth-promoting traits, such as hormone production, nutrient solubilization, and antifungal properties, are widely used. This study aims to investigate the role of plant-growth-promoting properties in bacteria-mediated stress mitigation and the suitability of traditional culture-based methods as a screening tool for the identification of beneficial bacteria. To this end, we tested three endophytic Bacillus isolates, which have previously been shown to affect tolerance against iron toxicity in lowland rice, (a) for their effect on the resistance against brown spot disease, and (b) for plant-growth-promoting traits using common culture-based methods. Both B. pumilus isolates inhibited fungal growth in vitro and reduced brown spot disease in two of three rice cultivars in planta, although they tested negative for all plant-growth-promoting traits. While B. megaterium was negative for ACC deaminase activity and nutrient solubilization, it exhibited auxin production. Nevertheless, B. megaterium did not suppress brown spot disease in any of the three rice cultivars. This study shows that bacteria do not necessarily have to possess classical plant-growth-promoting properties in order to be beneficial to plants, and it emphasizes the limitation of common culture-based methods in effectively identifying beneficial bacteria. Moreover, our results highlight the significance of the interaction between bacteria and plant cultivars in determining the beneficial effects of Bacillus spp. on plants under biotic or abiotic stresses.

Microbial Detection and Quantification of Low-Biomass Water Samples Using an International Space Station Smart Sample Concentrator.

The pressing need to safeguard the health of astronauts aboard the International Space Station (ISS) necessitates constant and rigorous microbial monitoring. Recognizing the shortcomings of traditional culture-based methods, NASA is deliberating the incorporation of molecular-based techniques. The challenge, however, lies in developing and validating effective methods for concentrating samples to facilitate this transition. This study is dedicated to investigating the potential of an ISS Smart Sample Concentrator (iSSC) as an innovative concentration method. First, the iSSC system and its components were tested and optimized for microgravity, including various testing environments: a drop tower, parabolic flight, and the ISS itself. Upon confirming the system's compatibility with microgravity, we further evaluated its proficiency and reliability in concentrating large volumes (i.e., 1 L) of water samples inoculated with different microbes. The samples carried 102 to 105 colony-forming units (CFUs) of Sphingomonas paucimobilis, Ralstonia pickettii, or Cupriavidus basilensis per liter, aligning with NASA's acceptable limit of 5 × 104 CFU/L. The average retrieved volume post-concentration was ≈450 µL, yielding samples that were ≈2200 times more concentrated for subsequent quantitative PCR (qPCR) and CFU analysis. The average microbial percent recovery, as assessed with CFU counts, demonstrated consistency for C. basilensis and R. pickettii at around 50% and 45%, respectively. For S. paucimobilis, the efficiency oscillated between 40% and 80%. Interestingly, when we examined microbial recovery using qPCR, the results showed more variability across all tested species. The significance of these findings lies not merely in the successful validation of the iSSC but also in the system's proven consistency, as evidenced by its alignment with previous validation-phase results. In conclusion, conducted research underscored the potential of the iSSC in monitoring microbial contamination in potable water aboard the ISS, heralding a paradigm shift from culture-based to molecular-based monitoring methods.

Sensitive Molecular Detection for Salmonella Enterica Serovars Typhimurium

Introduction: Salmonella infections contribute significantly to gastroenteritis cases, with the National Salmonella Reference Laboratory reporting 500 isolates in 2022. However, traditional culture-based methods for detecting Salmonella in samples can take 4 to 7 days to confirm a positive result, which poses health risks due to delayed detection. Given these health risks, swift and accurate detection methods are essential to minimize both false-positive and false-negative outcomes. Salmonella, a gram-negative bacterium within the Enterobacteriaceae family, demonstrates remarkable hardiness, surviving for several weeks in dry environments and months in water. Although most serotypes of Salmonella cause relatively mild gastroenteritis, some, particularly those transmitted from animals to humans, can lead to severe, life-threatening conditions
 Methods: The qRT-PCR procedure involved the design of primers and probes targeting the same genes as the mPCR assay. These primer sets were reconfigured to generate smaller amplicons suitable for qRT-PCR systems
 Results: qRT-PCR process, TaqMan probes were meticulously designed for specific target genes: FAM dye was employed to detect STM2745, Cy5 dye was used for STM4492, and Rox dye was utilized to detect. A standard curve was constructed using Typhimurium LT2 genomic DNA. Each sample underwent duplicate analysis, and Rotor-Gene software was employed to assign threshold values for each channel.
 Conclusion: The effectiveness of our qPCR assay for the detection of Salmonella across a diverse array of matrices. Notably, our results unveiled distinct limits of detection for Salmonella in various samples. Specifically, a parallel vein, the deployment of a PCR assay, leveraging an immunomagnetic separation technique for DNA extraction, was studied by another group. While subsequent analysis of Salmonella detected via our assay may necessitate the full ISO SMT method for live culture isolation, this supplementary step can be seamlessly conducted alongside qRT-PCR.

Emerging paradigms in exploring the interactions among diet, probiotics, and cancer immunotherapeutic response

Emerging paradigms in exploring the interactions among diet, probiotics, and cancer immunotherapeutic response

Automatic recognition of food bacteria using Raman spectroscopy and chemometrics: A comparative study of multivariate models

Food safety is the foundation of trust for food stakeholders. Contamination, especially from biological sources, at food processing plants can threaten this foundation, resulting in negative impacts on consumer health and substantial economic losses. Therefore, a rapid, effective, and noninvasive method for detecting bacteria in the food industry is essential. In this study, Raman micro-spectroscopy with advanced statistical tools is proposed as a mean of detecting and differentiating between various types of bacteria. This approach circumvents the complexities of traditional culture-based detection methods. Specifically, fifty-two bacterial strains of 39 different genera were analyzed using Raman spectroscopy. As a result, about 2563 Raman spectra were generated and integrated into the database. This huge amount of spectral data was analyzed using several chemometric tools, including principal component analysis (PCA), factorial discriminant analysis (FDA) k-nearest neighbors’ algorithm (KNN), and convolutional neural network (CNN). Our multivariate data analysis showed that the developed method is rapid and capable of distinguishing several strains. While, FDA models showed mediocre performances, KNN models provided good bacterial classification for most of the analyzed strains (average correct classification 90–95%). In comparison, CNN achieved a higher classification accuracy, of 97%, compared with other models. Combining Raman spectroscopy with chemometric tools yields a robust bacterial assessment method that is simple, rapid, and efficient.

Monitoring Adenosine Triphosphate Concentrations in a Chloraminated Drinking Water Distribution System for Risk and Asset Management

Utilities rely on reliable and robust monitoring systems to inform decisions around asset operation and management in the drinking water distribution system (DWDS) to deliver high quality, biologically stable drinking water to consumers. However, traditional culture-based testing methods present challenges that make the timely detection of regrowth in the DWDS difficult. This study reports the results of an extensive adenosine triphosphate (ATP) monitoring campaign—a non-regulated parameter—in an urban, chloraminated drinking water system that analyzed over 5000 samples from two drinking water treatment plants (DWTPs), associated DWTP reservoirs, twelve outlying reservoirs and the DWDS between 2019–2022. ATP concentrations increased significantly between the two DWTP reservoirs and outlying reservoirs but decreased between the outlying reservoirs and DWDS samples. Relationships between ATP concentrations and other water quality variables varied depending on sampling location. Heterotrophic plate counts (HPC) were mainly non-detects (<1 CFU/mL) providing limited operational guidance compared to ATP. ATP concentrations exhibited temporal and spatial variation but did not exceed the proposed 10 pg/mL corrective action limit suggested by the manufacturer. ATP concentrations were also able to inform outlying reservoir management decisions. Monitoring ATP could serve as a useful indicator of biological stability in the DWDS for the utility of the future.