Enzyme characteristics of beta-D-galactosidase- and beta-D-glucuronidase-positive bacteria and their interference in rapid methods for detection of waterborne coliforms and Escherichia coli

Microfluidic paper analytic device (μPAD) technology for food safety applications

Foodborne pathogens, food adulterants, allergens, and toxic chemicals in food can cause major health hazards to humans and animals. Stringent quality control measures at all stages of food processing are required to ensure food safety. There is, therefore, a global need for affordable, reliable, and rapid tests that can be conducted at different process steps and processing sites, spanning the range from the sourcing of food to the end-product acquired by the consumer. Current laboratory-based food quality control tests are well established, but many are not suitable for rapid on-site investigations and are costly. Microfluidic paper analytical devices (μPADs) are a fast-growing field in medical diagnostics that can fill these gaps. In this review, we describe the latest developments in the applications of microfluidic paper analytic device (μPAD) technology in the food safety sector. State-of-the-art μPAD designs and fabrication methods, microfluidic assay principles, and various types of μPAD devices with food-specific applications are discussed. We have identified the prominent research and development trends and future directions for maximizing the value of microfluidic technology in the food sector and have highlighted key areas for improvement. We conclude that the μPAD technology is promising in food safety applications by using novel materials and improved methods to enhance the sensitivity and specificity of the assays, with low cost.

Distribution of Fluoroquinolone-Resistant Escherichia coli in Parent Flocks Treated with Fluoroquinolones on Chick Stage and their Broiler Offspring

This study investigated the distribution of ofloxacin-resistant Escherichia coli (OFXR-EC) in broiler parent flocks (PS) treated with ofloxacin for 5 days from the time the chicks arrived at the poultry house, and their broiler offspring. OFXR-EC was detected in 22.95% of neonatal parent stock chicks (PSN) arriving at the poultry house. The detection rate of OFXR-EC in PS rearing was 72.49%, which was significantly higher than that detected in PSN. In addition, the detection rate of OFXR-EC was significantly lower in neonatal chicks of their offspring broilers (CSN) at 7.06% than that of PS, but was 24.62% in offspring broiler flocks (CS) at approximately 6 weeks of age. The OFXR-EC detection rate was significantly higher in CS than that in CSN, even though no therapeutic antimicrobials, including ofloxacin, were used from CSN to CS. In addition, the proportions of OFXR-ECs in E. coli isolated from samples in which OFXR-ECs were detected were 63.85% for PSN, 10.52% for PS, 62.00% for CSN, and 8.25% for CS. There was little difference in the composition ratio of OFXR-EC between PSN and CSN, or between PS and CS.

Gut Microbiota Plays Essential Roles in Soyasaponin's Preventive Bioactivities against Steatohepatitis in the Methionine and Choline Deficient (MCD) Diet-Induced Non-Alcoholic Steatohepatitis (NASH) Mice

SCOPE

Gut microbiota (GM) is involved in nonalcoholic steatohepatitis (NASH) development. Phytochemicals soyasaponins can prevent NASH possibly by modulating GM. This study aims to investigate the preventive bioactivities of soyasaponin monomers (SS-A1 and SS-Bb) against NASH and explores the mechanisms by targeting GM.

METHODS AND RESULTS

Male C57BL/6 mice are fed with methionine and choline deficient (MCD) diet containing SS-A1 , SS-Bb, or not for 16 weeks. Antibiotics-treated pseudo germ-free (PGF) mice are fed with MCD diet containing SS-A1 , SS-Bb, or not for 8 weeks. GM is determined by 16S rRNA amplicon sequencing. Bile acids (BAs) are measured by UPLC-MS/MS. In NASH mice, SS-A1 and SS-Bb alleviate steatohepatitis and fibrosis, reduce ALT, AST, and LPS in serum, decrease TNF-α, IL-6, α-SMA, triglycerides, and cholesterol in liver. SS-A1 and SS-Bb decrease Firmicutes, Erysipelotrichaceae, unidentified-Clostridiales, Eggerthellaceae, Atopobiaceae, Aerococcus, Jeotgalicoccus, Gemella, Rikenella, increase Proteobacteria, Verrucomicrobia, Akkermansiaceae, Romboutsia, and Roseburia. SS-A1 and SS-Bb alter BAs composition in liver, serum, and feces, activate farnesoid X receptor (FXR) in liver and ileum, increase occludin and ZO-1 in intestine. However, GM clearance abrogates the preventive bioactivities of SS-A1 and SS-Bb against NASH.

CONCLUSION

GM plays essential roles in soyasaponin's preventive bioactivities against steatohepatitis in MCD diet-induced NASH mice.

Evaluation of a Tetracycline-Resistant E. coli Enumeration Method for Correctly Classifying E. coli in Environmental Waters in Kentucky, USA

The global concern over antimicrobial resistance (AMR) and its impact on human health is evident, with approximately 4.95 million annual deaths attributed to antibiotic resistance. Regions with inadequate water, sanitation, and hygiene face challenges in responding to AMR threats. Enteric bacteria, particularly E. coli, are common agents linked to AMR-related deaths (23% of cases). Culture-based methods for detecting tetracycline-resistant E. coli may be of practical value for AMR monitoring in limited resource environments. This study evaluated the ColiGlow™ method with tetracycline for classifying tetracycline-resistant E. coli. A total of 61 surface water samples from Kentucky, USA (2020-2022), provided 61 presumed E. coli isolates, of which 28 isolates were obtained from tetracycline-treated media. Species identification and tetracycline resistance evaluation were performed. It was found that 82% of isolates were E. coli, and 18% were other species; 97% were identified as E. coli when using the API20E identification system. The MicroScan system yielded Enterobacter cloacae false positives in 20% of isolates. Adding tetracycline to ColiGlow increased the odds of isolating tetracycline-resistant E. coli 18-fold. Tetracycline-treated samples yielded 100% tetracycline-resistant E. coli when the total E. coli densities were within the enumeration range of the method. ColiGlow with tetracycline shows promise for monitoring tetracycline-resistant E. coli in natural waters and potentially aiding AMR surveillance in resource-limited settings among other environments.

Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States

BACKGROUND

Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.

OBJECTIVES

The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).

METHODS

Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.

RESULTS

Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.

CONCLUSIONS

Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.

Target Enzyme-Triggered Click Chemistry and Hybridization Chain Reaction for Fluorescence Nonculture Homogeneous Analysis of E. coli in Bloodstream Infections

Escherichia coli is the major pathogen that causes bloodstream infections (BSI). It is critical to develop nonculture identification methods which can meet the urgent need of clinical diagnosis and treatment. In this study, we reported a homogeneous fluorescence E. coli analysis system using β-galactosidase (β-Gal) as the biomarker and double-stranded DNA-templated copper nanoparticles (dsDNA-Cu NPs) as the signal output. The product of the enzymatic hydrolysis reaction, p-aminophenol (PAP), could reduce Cu²⁺ to Cu⁺, triggering the alkyne-azido cycloaddition reaction (CuAAC). Subsequently, the hybrid chain reaction (HCR) was initiated, producing the dsDNA template used to generate Cu NPs in situ. The system achieved a wide linear range for β-Gal and E. coli 1-10⁴ mU/L and 10^-2-10 colony-forming unit (CFU)/mL, and a detection limit of 0.3 mU/L and 0.003 CFU/mL, respectively. 65 samples (45 blood and 20 urine) were collected to evaluate the clinical practicality. The results demonstrated remarkable area under the curve (AUC) values of 0.95 and 0.916 from uncultured urine and blood, respectively. It had 100% specificity and 83.3% sensitivity. The whole duration of the strategy was 3.5 h, which significantly reduced the turnaround time (TAT) and facilitated early BSI diagnosis to improve patients' prognosis. Our work had the potential to be an alternative to culture-based methods in clinics.

Radix Paeoniae Alba attenuates Radix Bupleuri-induced hepatotoxicity by modulating gut microbiota to alleviate the inhibition of saikosaponins on glutathione synthetase

Radix Bupleuri (RB) is commonly used to treat depression, but it can also lead to hepatotoxicity after long-term use. In many anti-depression prescriptions, RB is often used in combination with Radix Paeoniae Alba (RPA) as an herb pair. However, whether RPA can alleviate RB-induced hepatotoxicity remain unclear. In this work, the results confirmed that RB had a dose-dependent antidepressant effect, but the optimal antidepressant dose caused hepatotoxicity. Notably, RPA effectively reversed RB-induced hepatotoxicity. Afterward, the mechanism of RB-induced hepatotoxicity was confirmed. The results showed that saikosaponin A and saikosaponin D could inhibit GSH synthase (GSS) activity in the liver, and further cause liver injury through oxidative stress and nuclear factor kappa B (NF-κB)/NOD-like receptor thermal protein domain associated protein 3 (NLRP3) pathway. Furthermore, the mechanisms by which RPA attenuates RB-induced hepatotoxicity were investigated. The results demonstrated that RPA increased the abundance of intestinal bacteria with glycosidase activity, thereby promoting the conversion of saikosaponins to saikogenins in vivo. Different from saikosaponin A and saikosaponin D, which are directly combined with GSS as an inhibitor, their deglycosylation conversion products saikogenin F and saikogenin G exhibited no GSS binding activity. Based on this, RPA can alleviate the inhibitory effect of saikosaponins on GSS activity to reshape the liver redox balance and further reverse the RB-induced liver inflammatory response by the NF-κB/NLRP3 pathway. In conclusion, the present study suggests that promoting the conversion of saikosaponins by modulating gut microbiota to attenuate the inhibition of GSS is the potential mechanism by which RPA prevents RB-induced hepatotoxicity.

Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance

Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.

Metabolically-targeted dCas9 expression in bacteria

The ability to restrict gene expression to a relevant bacterial species in a complex microbiome is an unsolved problem. In the context of the human microbiome, one desirable target metabolic activity are glucuronide-utilization enzymes (GUS) that are implicated in the toxic re-activation of glucuronidated compounds in the human gastrointestinal (GI) tract, including the chemotherapeutic drug irinotecan. Here, we take advantage of the variable distribution of GUS enzymes in bacteria as a means to distinguish between bacteria with GUS activity, and re-purpose the glucuronide-responsive GusR transcription factor as a biosensor to regulate dCas9 expression in response to glucuronide inducers. We fused the Escherichia coli gusA regulatory region to the dCas9 gene to create pGreg-dCas9, and showed that dCas9 expression is induced by glucuronides, but not other carbon sources. When conjugated from E. coli to Gammaproteobacteria derived from human stool, dCas9 expression from pGreg-dCas9 was restricted to GUS-positive bacteria. dCas9-sgRNAs targeted to gusA specifically down-regulated gus operon transcription in Gammaproteobacteria, with a resulting ∼100-fold decrease in GusA activity. Our data outline a general strategy to re-purpose bacterial transcription factors responsive to exogenous metabolites for precise ligand-dependent expression of genetic tools such as dCas9 in diverse bacterial species.

Decreased Tissue Omega-6/Omega-3 Fatty Acid Ratio Prevents Chemotherapy-Induced Gastrointestinal Toxicity Associated with Alterations of Gut Microbiome

Gastrointestinal toxicity (GIT) is a debilitating side effect of Irinotecan (CPT-11) and limits its clinical utility. Gut dysbiosis has been shown to mediate this side effect of CPT-11 by increasing gut bacterial β-glucuronidase (GUSB) activity and impairing the intestinal mucosal barrier (IMB). We have recently shown the opposing effects of omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFA) on the gut microbiome. We hypothesized that elevated levels of tissue n-3 PUFA with a decreased n-6/n-3 PUFA ratio would reduce CPT-11-induced GIT and associated changes in the gut microbiome. Using a unique transgenic mouse (FAT-1) model combined with dietary supplementation experiments, we demonstrate that an elevated tissue n-3 PUFA status with a decreased n-6/n-3 PUFA ratio significantly reduces CPT-11-induced weight loss, bloody diarrhea, gut pathological changes, and mortality. Gut microbiome analysis by 16S rRNA gene sequencing and QIIME2 revealed that improvements in GIT were associated with the reduction in the CPT-11-induced increase in both GUSB-producing bacteria (e.g., Enterobacteriaceae) and GUSB enzyme activity, decrease in IMB-maintaining bacteria (e.g., Bifidobacterium), IMB dysfunction and systemic endotoxemia. These results uncover a host-microbiome interaction approach to the management of drug-induced gut toxicity. The prevention of CPT-11-induced gut microbiome changes by decreasing the tissue n-6/n-3 PUFA ratio could be a novel strategy to prevent chemotherapy-induced GIT.

A Model System for Sensitive Detection of Viable E. coli Bacteria Combining Direct Viability PCR and a Novel Microarray-Based Detection Approach

We established an innovative approach that included direct, viability, and nested PCR for rapid and reliable identification of the fecal indicator organism Escherichia coli (E. coli). Direct PCR enabled successful amplification of the target uidA gene, omitting a prior DNA isolation or purification step. Furthermore, we applied viability PCR (v-PCR) to ensure the detection of only relevant viable bacterial cells. The principle involves the binding of propidium monoazide (PMA), a selective nucleic acid intercalating dye, to accessible DNA of heat killed bacteria cells and, consequently, allows viable and heat killed E. coli cells to be discriminated. To ensure high sensitivity, direct v-PCR was followed by a nested PCR step. The resulting amplicons were analyzed by a rapid 30 min microarray-based DNA hybridization assay for species-specific DNA detection of E. coli. A positive signal was indicated by enzymatically generated silver nanoparticle deposits, which served as robust endpoint signals allowing an immediate visual readout. The presented novel protocol allows the detection of 1 × 101 viable E. coli cells per PCR run.

Recent Advancements in the Technologies Detecting Food Spoiling Agents

To match the current life-style, there is a huge demand and market for the processed food whose manufacturing requires multiple steps. The mounting demand increases the pressure on the producers and the regulatory bodies to provide sensitive, facile, and cost-effective methods to safeguard consumers' health. In the multistep process of food processing, there are several chances that the food-spoiling microbes or contaminants could enter the supply chain. In this contest, there is a dire necessity to comprehend, implement, and monitor the levels of contaminants by utilizing various available methods, such as single-cell droplet microfluidic system, DNA biosensor, nanobiosensor, smartphone-based biosensor, aptasensor, and DNA microarray-based methods. The current review focuses on the advancements in these methods for the detection of food-borne contaminants and pathogens.

In vitro anthelmintic activity of an aqueous extract of Glycyrrhiza glabra and of glycyrrhetinic acid against gastrointestinal nematodes of small ruminants

This study evaluated the in vitro anthelmintic activity of a liquorice (Glycyrrhiza glabra) root aqueous extract and of glycyrrhetinic acid at 30, 10, 5, 1, and 0.5 mg/mL against sheep gastrointestinal nematodes (GINs), using the egg hatch test (EHT), the larval development test (LDT), and the larval migration inhibition test (LMIT). The compounds were applied on a mixture of GIN eggs and larvae, mainly Trichostrongylus spp. and Teladorsagia/Ostertagia spp. Cytotoxicity assays were also performed. In the EHT, both candidates showed significant concentration-dependent efficacy and were significantly more effective (p < 0.001) at the highest concentrations (30 and 10 mg/mL) than the lowest ones. In the LDT, only G. glabra showed a concentration-dependent effect (R2 = 0.924), but glycyrrhetinic acid (R2 = 0.910) had significantly higher efficacy than G. glabra root extract. Moreover, the efficacy of glycyrrhetinic acid at 30, 10, and 5 mg/mL was significantly higher (p < 0.001) than at lower concentrations. In the LMIT, G. glabra showed concentration-dependent efficacy (R2 = 0.971), while considerably reduced efficacy was observed for glycyrrhetinic acid (R2 = 0.855) at the lowest concentrations. These data suggest that the two compounds may have different mechanisms of action. In the LMIT, the 50% lethal concentration (LC50) of glycyrrhetinic acid (~5.12 mg/mL) was > 2.0-fold lower when compared to G. glabra (12.25 mg/mL). Analysis and previous findings indicated low toxicity for both compounds. The results obtained encourage in vivo studies aimed at evaluating the potential use of the tested compounds as natural de-wormers in ruminants.

MILK Symposium review: Microbiological quality and safety of milk from farm to milk collection centers in Rwanda

The aim of this study was to generate knowledge on the most important milk quality and safety attributes, including somatic cell count (SCC), total bacterial count (TBC), Escherichia coli, Salmonella, and Brucella spp. antibodies and antibiotic residues in milk in the chain from farm to milk collection center (MCC) in Rwanda. In addition, we investigated farm and management factors associated with high TBC, SCC, and Salmonella counts. Raw milk was sampled at the farm and MCC levels. Milk samples were taken from dairy farms linked to 2 selected MCC in each of the 4 provinces in Rwanda. In total, 406 bulk milk samples from 406 farms and 32 bulk milk samples from 8 MCC were collected and analyzed. Farm milk average SCC varied between 180 × 10³ and 920 × 10³ cells/mL, whereas average SCC in milk samples at MCC varied between 170 × 10³ and 1,700 × 10³ cells/mL. The mean milk TBC of different farms per MCC varied between 1.1 × 10⁶ and 1.6 × 10⁷ cfu/mL, whereas in milk samples from different MCC, the mean TBC ranged between 5.3 × 10⁵ and 2.4 × 10⁸ cfu/mL. The high TBC in milk from MCC suggests proliferation or recontamination of milk by bacteria during transportation. Escherichia coli was detected in 35 of 385 farm milk samples and ranged between 5 cfu/mL and 1.1 × 10⁴ cfu/mL, whereas in milk samples from the MCC, it was detected in 20 out 32 samples varying between 5 cfu/mL and 2.9 × 10³ cfu/mL. Overall farm prevalence of Salmonella in milk samples was 14%, but no milk samples from MCC were positive for Salmonella. Five out of 22 bulk milk samples from different MCC were positive for Brucella spp. antibodies, but no Brucella antibodies were detected in milk samples from farms. The prevalence of antibiotic residues as detected by the Delvotest SP NT (DSM, Delft, the Netherlands) was low: 1.3% in farm milk samples and undetected in MCC milk samples. Lack of a separate milking area was associated with high TBC, whereas offering of supplemental feeds, keeping data of past diseases, and an unhygienic milking area were associated with high SCC. Lack of teat washing before milking was the only factor associated with Salmonella contamination of milk at the farm level. This study indicated high TBC and SCC of milk samples at the farm and MCC levels, which indicates both microbial contamination of milk and poor udder health in dairy cows. Presence of E. coli, Salmonella, and Brucella antibodies in milk was common, but finding antibiotic residues in milk was uncommon.

Point-of-Need Diagnostics for Foodborne Pathogen Screening

Foodborne illness is a major public health issue that results in millions of global infections annually. The burden of such illness sits mostly with developing countries, as access to advanced laboratory equipment and skilled lab technicians, as well as consistent power sources, is limited and expensive. Current gold standards in foodborne pathogen screening involve labor-intensive sample enrichment steps, pathogen isolation and purification, and costly readout machinery. Overall, time to detection can take multiple days, excluding the time it takes to ship samples to off-site laboratories. Efforts have been made to simplify the workflow of such tests by integrating multiple steps of foodborne pathogen screening procedures into a singular device, as well as implementing more point-of-need readout methods. In this review, we explore recent advancements in developing point-of-need devices for foodborne pathogen screening. We discuss the detection of surface markers, nucleic acids, and metabolic products using both paper-based and microfluidic devices, focusing primarily on developments that have been made between 2015 and mid-2020.

Recent progress and challenges on the bioassay of pathogenic bacteria

The present review (containing 242 references) illustrates the importance and application of optical and electrochemical methods as well as their performance improvement using various methods for the detection of pathogenic bacteria. The application of advanced nanomaterials including hyper branched nanopolymers, carbon-based materials and silver, gold and so on. nanoparticles for biosensing of pathogenic bacteria was also investigated. In addition, a summary of the applications of nanoparticle-based electrochemical biosensors for the identification of pathogenic bacteria has been provided and their advantages, detriments and future development capabilities was argued. Therefore, the main focus in the present review is to investigate the role of nanomaterials in the development of biosensors for the detection of pathogenic bacteria. In addition, type of nanoparticles, analytes, methods of detection and injection, sensitivity, matrix and method of tagging are also argued in detail. As a result, we have collected electrochemical and optical biosensors designed to detect pathogenic bacteria, and argued outstanding features, research opportunities, potential and prospects for their development, according to recently published research articles.

Near real-time notification of water quality impairments in recreational freshwaters using rapid online detection of β-D-glucuronidase activity as a surrogate for Escherichia coli monitoring

Waterborne disease outbreaks associated with recreational waters continue to be reported around the world despite existing microbiological water quality monitoring frameworks. Most regulations resort to the use of culture-based enumeration of faecal indicator bacteria such as Escherichia coli to protect bathers from gastrointestinal illness risks. However, the long sample-to-result time of standard culture-based assays (minimum 18-24 h) and infrequent regulatory sampling (weekly or less) do not enable detection of episodic water quality impairments and associated public health risks. The objective of this study was to assess the suitability of an autonomous online technology measuring β-D-glucuronidase (GLUC) activity for near real-time monitoring of microbiological water quality in recreational waters and for the resulting beach management decisions. GLUC activity and E. coli concentrations were monitored at three freshwater sites in Quebec, Canada (sites Qc1-3) and one site in New Zealand (site NZ) between 2016 and 2018. We found site-dependent linear relationships between GLUC activity and E. coli concentrations and using confusion matrices, we developed site-specific GLUC activity beach action values (BAVs) matching the regulatory E. coli BAVs. Using the regulatory E. coli BAV as the gold standard, rates of false alarms (unnecessary beach advisories using GLUC activity BAV) and failures to act (failure to trigger advisories using GLUC activity) ranged between 0 and 32% and between 3 and 10%, respectively, which is comparable to the rates reported in other studies using qPCR-defined BAVs. However, a major benefit of the autonomous enzymatic technology is the real-time reporting of threshold exceedances, while temporal trends in GLUC activity can assist in understanding the underlying dynamics of faecal pollution and potential health risks. Our study is the first to describe the applicability of online near real-time monitoring of microbiological water quality as a tool for improved beach management and public health protection.

Fieldwork-based determination of design priorities for point-of-use drinking water quality sensors for use in resource-limited environments

Improved capabilities in microfluidics, electrochemistry, and portable assays have resulted in the development of a wide range of point-of-use sensors intended for environmental, medical, and agricultural applications in resource-limited environments of developing countries. However, these devices are frequently developed without direct interaction with their often-remote intended user base, creating the potential for a disconnect between users' actual needs and those perceived by sensor developers. As different analytical techniques have inherent strengths and limitations, effective measurement solution development requires determination of desired sensor attributes early in the development process. In this work, we present our findings on design priorities for point-of-use microbial water sensors based on fieldwork in rural India, as well as a guide to fieldwork methodologies for determining desired sensor attributes. We utilized group design workshops for initial identification of design priorities, and then conducted choice-based conjoint analysis interviews for quantification of user preferences among these priorities. We found the highest user preference for integrated reporting of contaminant concentration and recommended actions, as well as significant preferences for mostly reusable sensor architectures, same-day results, and combined ingredients. These findings serve as a framework for future microbial sensor development and a guide for fieldwork-based understanding of user needs.

A sensitive electrochemical strategy via multiple amplification reactions for the detection of E. coli O157: H7

The sensitive and efficient strategy remains a central challenge for early diagnosis of pathogenic bacteria. Herein, an ultrasensitive electrochemical biosensor was proposed based on the multiple amplification strategy via the 3D DNA walker, rolling circle amplification (RCA) and hybridization chain reaction (HCR) for the accurate detection of Escherichiacoli O157:H7 (E. coli O157:H7). Firstly, the target sequence extracted from E. coli O157:H7 was transformed and amplified by the DNA walker firstly. Subsequently, a large number of transformed nucleic acid sequences were amplified by the RCA reaction. And then, the progress of HCR was triggered by every fragment in RCA products to form a long double-stranded DNA sequence to immobilize electrochemical indicators, generating a significantly enhanced electrochemical signal. As expected, a high sensitivity with a detection limit of 7 CFU/mL was achieved based on the proposed multiple amplification strategy, which is superior to most current methods for E. coli O157: H7 assay. The multiple amplification strategy could be readily expanded for the detection of various pathogenic bacteria, providing a new approach for early diagnosis of pathogenic microorganisms or other diseases.

Label-free and enzyme-free sensitive fluorescent method for detection of viable Escherichia coli O157:H7

We have developed a label-free, enzyme-free, modification-free and DNA extraction-free fluorescent aptasensing (LEFA) method for detection of E. coli O157:H7 based on G-quadruplex formation using two ingeniously designed hairpin probes (GHP1 and GHP2). In the presence of E. coli O157:H7, it released the single stranded initiation sequence (IS) resulting in the toehold strand displacement between GHP1 and GHP2, which in turn led to the cyclic reuse of the production of DNA assemblies with numerous G-quadruplex structures and initiation sequences. Then these G-quadruplex structures can be recognized quickly by N-methyl mesoporphyrin IX (NMM) resulting in significantly enhanced fluorescence. The LEFA method was successfully implemented for detecting E. coli O157:H7 with a detection limit of 66 CFU/mL in pure culture, 10 CFU/mL and 1 CFU/mL after pre-incubation of the milk and tap water for 4 and 8 h, respectively. Moreover, the strategy could distinguish viable E. coli O157:H7 from dead E. coli O157:H7 and other species of pathogen cells. Furthermore, the whole process of the strategy is accomplished within 100 min. The results indicated that the approach may be used to effectively control potential microbial hazards in human health, food safety, and animal husbandry.

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well-defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm-associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high-discharge situations, surface-associated microbes and nutrients such as from soil habitats or human settlements-potentially containing fecal-associated pathogens as the most critical water-quality hazard-may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near-real-time online water quality monitoring, microbial source tracking (MST) and MST-guided quantitative microbial-risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems.

Ultrasound-assisted d-tartaric acid whole-cell bioconversion by recombinant Escherichia coli

d-Tartaric acid has wide range of application in the pharmaceutical industry and scarcely exists in nature. In this study, cis-epoxysuccinate hydrolase (CESH)-containing Escherichia coli was used to perform whole-cell bioconversion of cis-epoxysuccinate (CES) to D-tartaric acid and the catalytic efficiency was investigated by ultrasound treatment. The bioconversion rate of CES sodium reached 70.36% after 60 min treated after ultrasound, which is 3-fold higher than that in the control. The specific rate could be further improved by 2-fold after 5 repeated batches compared with the first one, however, the specific rate gradually decreased with the increase of repeat batches (>5 batches). The CESH from Bordetella sp. BK-52 was a typical Michaelis-Menten enzyme with V_max and K_m values of 28.17 mM/h/g WCW (wet of cell weight) and 30.18 mM, respectively. The process for the d-tartaric acid bioconversion, which consisted of 102.31 g/L CES sodium, 8.78 mg/mL whole cell and ultrasound power of 79.36 W, is further optimized using response surface methodology. The specific rate finally reached 194.79 ± 1.78 mM/h/g WCW under the optimal conditions. Furthermore, the permeability of inner and outer membrane was improved approximately 1.6 and 1.4-fold after ultrasound treatment, respectively, which may be a crucial factor for improvement of the bioconversion efficiency.

Detection and discrimination of five E. coli pathotypes using a combinatory SYBR® Green qPCR screening system

A detection and discrimination system for five Escherichia coli pathotypes, based on a combination of 13 SYBR® Green qPCR, has been developed, i.e., combinatory SYBR® Green qPCR screening system for pathogenic E. coli (CoSYPS Path E. coli). It allows the discrimination on isolates and the screening of potential presence in food of the following pathotypes of E. coli: shigatoxigenic (STEC) (including enterohemorrhagic (EHEC)), enteropathogenic (EPEC), enteroaggregative (EAggEC), enteroaggregative shigatoxigenic (EAggSTEC), and enteroinvasive (EIEC) E. coli. The SYBR® Green qPCR assays target the uidA, ipaH, eae, aggR, aaiC, stx1, and stx2 genes. uidA controls for E. coli presence and all the other genes are specific targets of E. coli pathotypes. For each gene, two primer pairs have been designed to guarantee a sufficient detection even in case of deletion or polymorphisms in the target gene. Moreover, all the qPCR have been designed to be run together in a single analytical PCR plate. This study includes the primer pairs' design, in silico and in situ selectivity, sensitivity, repeatability, and reproducibility evaluation of the 13 SYBR® Green qPCR assays. Each target displayed a selectivity of 100%. The limit of detection of the 13 assays is between 1 and 10 genomic copies. Their repeatability and reproducibility comply with the European requirements. As a preliminary feasibility study on food, the CoSYPS Path E. coli system was subsequently evaluated on four food matrices artificially contaminated with pathogenic E. coli. It allowed the detection of an initial contamination level as low as 2 to 7 cfu of STEC/25 g of food matrix after 24 h of enrichment.

Hydrogel Based Biosensors for In Vitro Diagnostics of Biochemicals, Proteins, and Genes

Hydrogel-based biosensors have drawn considerable attention due to their various advantages over conventional detection systems. Recent studies have shown that hydrogel biosensors can be excellent alternative systems to detect a wide range of biomolecules, including small biochemicals, pathogenic proteins, and disease specific genes. Due to the excellent physical properties of hydrogels such as the high water content and stimuli-responsive behavior of cross-linked network structures, this system can offer substantial improvement for the design of novel detection systems for various diagnostic applications. The other main advantage of hydrogels is the role of biomimetic three-dimensional (3D) matrix immobilizing enzymes and aptamers within the detection systems, which enhances their stability. This provides ideal reaction conditions for enzymes and aptamers to interact with substrates within the aqueous environment of the hydrogel. In this review, we have highlighted various novel detection approaches utilizing the outstanding properties of the hydrogel. This review summarizes the recent progress of hydrogel-based biosensors and discusses their future perspectives and clinical limitations to overcome.

Automating multi-step paper-based assays using integrated layering of reagents

We describe a versatile and simple method to perform sequential reactions on paper analytical devices by stacking dry pullulan films on paper, where each film contains one or more reagents or acts as a delay layer. Exposing the films to an aqueous solution of the analyte leads to sequential dissolution of the films in a temporally controlled manner followed by diffusive mixing of the reagents, so that sequential reactions can be performed. The films can be easily arranged for lateral flow assays or for spot tests (reactions take place sequentially in the z-direction). We have tested the general feasibility of the approach using three different model systems to demonstrate different capabilities: 1) pH ramping from low to high and high to low to demonstrate timing control; 2) rapid ready-to-use two-step Simon's assays on paper for detection of drugs of abuse utilizing a 2-layer stack containing two different reagents to demonstrate the ability to perform assays in the z-direction; and 3) sequential cell lysing and colorimetric detection of an intracellular bacterial enzyme, to demonstrate the ability of the method to perform sample preparation and analysis in the form of a spot assay. Overall, these studies demonstrate the potential of stacked pullulan films as useful components to enable multi-step assays on simple paper-based devices.

Evaluation of β-d-glucuronidase and particle-size distribution for microbiological water quality monitoring in Northern Vietnam

In many karst regions in developing countries, the populations often suffer from poor microbial water quality and are frequently exposed to bacterial pathogens. The high variability of water quality requires rapid assays, but the conventional cultivation-based analysis of fecal indicator bacteria, such as Escherichia coli (E. coli), is very time-consuming. In this respect, the measurement of the enzymatic activity of E. coli could prove to be a valuable tool for water quality monitoring. A mobile automated prototype device was used for the investigation of β-d-glucuronidase (GLUC) activity at a remote karst spring, connected to a sinking surface stream, in Northern Vietnam. To assess the relationship between GLUC activity, discharge dynamics and contamination patterns, multiple hydrological, hydrochemical, physicochemical and microbiological parameters, including discharge, turbidity, particle-size distributions, and E. coli, were measured with high temporal resolution during ten days of on-site monitoring. A complex contamination pattern due to anthropogenic and agricultural activities led to high E. coli concentrations (270 to >24,200 MPN/100ml) and a GLUC activity between 3.1 and 102.2 mMFU/100ml. A strong daily fluctuation pattern of GLUC activity and particle concentrations within small size classes (<10μm) could be observed, as demonstrated by autocorrelations. A Spearman's rank correlation analysis resulted in correlation coefficients of rs=0.56 for E. coli and GLUC activity and rs=0.54 for GLUC activity and the concentration of 2-3μm particles. On an event scale, correlations were found to be higher (rs=0.69 and 0.87, respectively). GLUC activity and E. coli displayed a general contamination pattern, but with significant differences in detail, which may be explained by interferences of e. g. viable but non-culturable cells. Although further evaluations are recommended, GLUC activity is a promising, complementary parameter for on-site and near real-time water quality monitoring.

The species accuracy of the Most Probable Number (MPN) European Union reference method for enumeration of Escherichia coli in marine bivalves

Continuous European Union programmes with specified methods for enumeration of Escherichia coli in bivalves for human consumption are currently running. The objective of this research was to examine the species accuracy of the five times three tube Most Probable Number (MPN) EU reference method used for detection of E. coli in marine bivalves. Among 549 samples of bivalves harvested from Norwegian localities during 2014 and 2015, a total number of 200 bacterial isolates were prepared from randomly selected culture-positive bivalves. These presumptive E. coli isolates were characterized biochemically by the Analytical Profile Index (API) 20E, as well as by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). The majority of isolates (90%) were identified as E. coli, by both API 20E and MALDI-TOF MS. Ten isolates (5%) were identified as Klebsiella pneumoniae, while one isolate was identified as K. oxytoca by both methods, whereas three isolates were identified as Acinetobacter baumannii, Citrobacter braakii, and Enterobacter cloacae, respectively. The identification of the remaining six isolates were not in compliance between the two methods.

A hydrogel based rapid test method for detection of Escherichia coli (E. coli) in contaminated water samples

We have formulated a new chemical composition for rapid detection ofEscherichia coli(E. coli) with currently available enzymatic substrates.

Fluorescence assay for evaluating microbicidal activity of hand antiseptics

We developed a fluorescent β-d-glucuronidase activity (BGA)-based assay for detecting and quantifying Escherichia coli in samples to assess the biocide efficacy of hand antiseptics. The fluorescence level is proportional to the number of viable E. coli organisms present. We compared our assay results to those of the E. coli plate count method specified by the European standard for testing hygienic hand rub disinfectant products (EN1500). The plate count method requires excessive handling and materials and is not valid if the number of organisms per plate is too low or high for counting in many of the samples. We optimized the fluorescent assay based on the cleavage of 4-methylumbelliferyl-β-d-glucuronide by adding 4-nitrophenyl-β-d-glucuronide, a nonfluorogenic BGA substrate, to induce glucuronidase activity and reduce assay time. Furthermore, our method can be automated and eliminates the need for multiple dilutions. Fluorescence was temporally monitored, and the time required to reach a specific value of fluorescence was correlated with the initial number of viable E. coli organisms on the samples. There was a positive correlation (P < 0.05) with a high correlation coefficient (R(2) = 0.82) between the E. coli counts by plate count and fluorescence methods. Reported effects in fluorescent BGA were compared to the EN1500 plate count method with five hand disinfectants. We found our method more advantageous, because it was as sensitive as the EN1500 method, requires less time to complete, and is less expensive and less laborious than conventional plating techniques.

Phenotypic and Phylogenetic Identification of Coliform Bacteria Obtained Using 12 Coliform Methods Approved by the U.S. Environmental Protection Agency

The current definition of coliform bacteria is method dependent, and when different culture-based methods are used, discrepancies in results can occur and affect the accuracy of identification of true coliforms. This study used an alternative approach to the identification of true coliforms by combining the phenotypic traits of the coliform isolates and the phylogenetic affiliation of 16S rRNA gene sequences with the use of lacZ and uidA genes. A collection of 1,404 isolates detected by 12 U.S. Environmental Protection Agency-approved coliform-testing methods were characterized based on their phylogenetic affiliations and responses to their original isolation media and lauryl tryptose broth, m-Endo, and MI agar media. Isolates were phylogenetically classified into 32 true-coliform, or targeted Enterobacteriaceae (TE), groups and 14 noncoliform, or nontargeted Enterobacteriaceae (NTE), groups. It was shown statistically that detecting true-positive (TP) events is more challenging than detecting true-negative (TN) events. Furthermore, most false-negative (FN) events were associated with four TE groups (i.e., Serratia group I and the Providencia, Proteus, and Morganella groups) and most false-positive (FP) events with two NTE groups, the Aeromonas and Plesiomonas groups. In Escherichia coli testing, 18 out of 145 E. coli isolates identified by enzymatic methods were validated as FN. The reasons behind the FP and FN reactions could be explained through analysis of the lacZ and uidA genes. Overall, combining the analyses of the 16S rRNA, lacZ, and uidA genes with the growth responses of TE and NTE on culture-based media is an effective way to evaluate the performance of coliform detection methods.

Improved detection of Escherichia coli and coliform bacteria by multiplex PCR

BACKGROUND

The presence of coliform bacteria is routinely assessed to establish the microbiological safety of water supplies and raw or processed foods. Coliforms are a group of lactose-fermenting Enterobacteriaceae, which most likely acquired the lacZ gene by horizontal transfer and therefore constitute a polyphyletic group. Among this group of bacteria is Escherichia coli, the pathogen that is most frequently associated with foodborne disease outbreaks and is often identified by β-glucuronidase enzymatic activity or by the redundant detection of uidA by PCR. Because a significant fraction of essential E. coli genes are preserved throughout the bacterial kingdom, alternative oligonucleotide primers for specific E. coli detection are not easily identified.

RESULTS

In this manuscript, two strategies were used to design oligonucleotide primers with differing levels of specificity for the simultaneous detection of total coliforms and E. coli by multiplex PCR. A consensus sequence of lacZ and the orphan gene yaiO were chosen as targets for amplification, yielding 234 bp and 115 bp PCR products, respectively.

CONCLUSIONS

The assay designed in this work demonstrated superior detection ability when tested with lab collection and dairy isolated lactose-fermenting strains. While lacZ amplicons were found in a wide range of coliforms, yaiO amplification was highly specific for E. coli. Additionally, yaiO detection is non-redundant with enzymatic methods.

Dark Agouti rat model of chemotherapy-induced mucositis: establishment and current state of the art

Mucositis is a major oncological problem. The entire gastrointestinal and genitourinary tract and also other mucosal surfaces can be affected in recipients of radiotherapy, and/or chemotherapy. Major progress has been made in recent years in understanding the mechanisms of oral and small intestinal mucositis, which appears to be more prominent than colonic damage. This progress is largely due to the development of representative laboratory animal models of mucositis. This review focuses on the development and establishment of the Dark Agouti rat mammary adenocarcinoma model by the Mucositis Research Group of the University of Adelaide over the past 20 years to characterize the mechanisms underlying methotrexate-, 5-fluorouracil-, and irinotecan-induced mucositis. It also aims to summarize the results from studies using different animal model systems to identify new molecular and cellular markers of mucositis.

On the track for an efficient detection of Escherichia coli in water: A review on PCR-based methods

Ensuring water safety is an ongoing challenge to public health providers. Assessing the presence of fecal contamination indicators in water is essential to protect public health from diseases caused by waterborne pathogens. For this purpose, the bacteria Escherichia coli has been used as the most reliable indicator of fecal contamination in water. The methods currently in use for monitoring the microbiological safety of water are based on culturing the microorganisms. However, these methods are not the desirable solution to prevent outbreaks as they provide the results with a considerable delay, lacking on specificity and sensitivity. Moreover, viable but non-culturable microorganisms, which may be present as a result of environmental stress or water treatment processes, are not detected by culture-based methods and, thus, may result in false-negative assessments of E. coli in water samples. These limitations may place public health at significant risk, leading to substantial monetary losses in health care and, additionally, in costs related with a reduced productivity in the area affected by the outbreak, and in costs supported by the water quality control departments involved. Molecular methods, particularly polymerase chain reaction-based methods, have been studied as an alternative technology to overcome the current limitations, as they offer the possibility to reduce the assay time, to improve the detection sensitivity and specificity, and to identify multiple targets and pathogens, including new or emerging strains. The variety of techniques and applications available for PCR-based methods has increased considerably and the costs involved have been substantially reduced, which together have contributed to the potential standardization of these techniques. However, they still require further refinement in order to be standardized and applied to the variety of environmental waters and their specific characteristics. The PCR-based methods under development for monitoring the presence of E. coli in water are here discussed. Special emphasis is given to methodologies that avoid pre-enrichment during the water sample preparation process so that the assay time is reduced and the required legislated sensitivity is achieved. The advantages and limitations of these methods are also reviewed, contributing to a more comprehensive overview toward a more conscious research in identifying E. coli in water.

Draft Genome Sequence of Raoultella planticola, Isolated from River Water

We isolated Raoultella planticola from a river water sample, which was phenotypically indistinguishable from Escherichia coli on MI agar. The genome sequence of R. planticola was determined to gain information about its metabolic functions contributing to its false positive appearance of E. coli on MI agar. We report the first whole genome sequence of Raoultella planticola.

Synthesis and application of resorufin β-D-glucuronide, a low-cost chromogenic substrate for detecting Escherichia coli in drinking water

The development of low-cost tests for Escherichia coli is hampered by the expense and limited choice of enzyme substrates. Most chromogenic substrates are required in costly amounts, while fluorogenic substrates require an additional apparatus (e.g., an ultraviolet lamp) to be detected. Herein, we propose an alternative chromogenic substrate, resorufin β-d-glucuronide (REG), which is exceptionally sensitive and may be employed in very small amounts. We show that REG can be produced similarly to other simple glucuronides and should therefore be no more expensive. The compound is used by both healthy and injured E. coli, resulting in a pronounced color change from orange to a bright pink. Because the released dye (resorufin) has a high extinction coefficient, substantially lower amounts are needed than for commercially available substrates. The potential of this substrate is demonstrated by a presence/absence test requiring just 0.1 mg of REG/100 mL of water sample, one hundredth of the quantity needed for common chromogenic substrates, with an estimated bulk cost of ≤0.1 U.S. cents/test. REG shows promise as a chromogenic substrate for E. coli detection and should be considered in the development of new water tests, especially for low-income settings.