Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples

Emerging Bioanalytical Devices and Platforms for Rapid Detection of Pathogens in Environmental Samples

The development of robust bioanalytical devices and biosensors for infectious pathogens is progressing well with the advent of new materials, concepts, and technology. The progress is also stepping towards developing high throughput screening technologies that can quickly identify, differentiate, and determine the concentration of harmful pathogens, facilitating the decision-making process for their elimination and therapeutic interventions in large-scale operations. Recently, much effort has been focused on upgrading these analytical devices to an intelligent technological platform by integrating them with modern communication systems, such as the internet of things (IoT) and machine learning (ML), to expand their application horizon. This review outlines the recent development and applications of bioanalytical devices and biosensors to detect pathogenic microbes in environmental samples. First, the nature of the recent outbreaks of pathogenic microbes such as foodborne, waterborne, and airborne pathogens and microbial toxins are discussed to understand the severity of the problems. Next, the discussion focuses on the detection systems chronologically, starting with the conventional methods, advanced techniques, and emerging technologies, such as biosensors and other portable devices and detection platforms for pathogens. Finally, the progress on multiplex assays, wearable devices, and integration of smartphone technologies to facilitate pathogen detection systems for wider applications are highlighted.

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.

Comparison of the culture method with multiplex PCR for the confirmation of Legionella spp. and Legionella pneumophila

AIMS

The detection and enumeration of Legionella spp. in water samples are typically performed via a cultural technique standardized in ISO 11731. This method is time-consuming (up to 15 days), and the specificity of the confirmation step is questionable. This study proposes the use of multiplex polymerase chain reaction (PCR) to confirm presumptive Legionella colonies directly from the culture plate; this shortens the response time by 2-5 days while still reporting results in colony forming units (CFU).

METHODS AND RESULTS

Two laboratories analysed a total of 290 colonies to compare the confirmation step of Legionella spp. and Legionella pneumophila in accordance with ISO 11731 by culture growth and agglutination vs multiplex PCR. Discordant results were resolved by the swiss national reference laboratory. The data were evaluated following ISO 16140 and showed that the PCR-technique had higher specificity.

CONCLUSIONS

The confirmation of Legionella spp., L. pneumophila and L. pneumophila serogroup 1 by multiplex PCR allows detection of positive colonies more rapidly and with higher specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study highlights a possibility to shorten the response time significantly during the enumeration of Legionella spp. and achieving a higher specificity while adhering to the legally recognized reporting in CFU.

Escherichia coli Capacity to Repopulate Microcosms Under Osmotic/U.V. Synergic Stress in Tropical Waters

In both Brazilian and European regulations, the impact assessment of sewage discharges into coastal waters is based on microbiological analyses of fecal indicators such as Escherichia coli, frequently used in prevision hydrodynamic models. However, the decay rates of E. coli vary depending on environmental conditions, and analysis may lead to inaccurate conclusions. This study aimed to analyze the decay of culturable and viable (but not culturable) E. coli in outdoor conditions, by creating microcosms inoculated with pre-treated sewage. The microcosms were filled with 9.88 L of filtered water (0.22 μm membrane), 3.5% salt, 0.1-0.2% BHI, and 1% bacterial suspension obtained by reverse filtration. PMA-qPCR of E. coli uidA gene and Colilert measurements were applied to evaluate population counts after 2 h, 4 h, and 26 h. After nine hours of exposure to solar radiation, the viable cells decreased to 2.76% (interpolated value) of the initial population, and the cultivable fraction of the viable population accounted for 0.50%. In the dark period, the bacteria grew again, and viable cells reached 8.54%, while cultivable cells grew to 48.14% of initial population. This behavior is possibly due to the use of nutrients recycled from dead cells. Likewise, populations of E. coli in sewage outfalls remain viable in the sediments, where resuspension can renew blooming.

Recombinase polymerase amplification for fast, selective, DNA-based detection of faecal indicator Escherichia coli

The bacterium Escherichia coli is commonly associated with the presence of faecal contamination in environmental samples, and is therefore subject to statutory surveillance. This is normally done using a culture-based methodology, which can be slow and laborious. Nucleic acid amplification for the detection of E. coli DNA sequences is a significantly more rapid approach, suited for applications in the field such as a point of sample analysis, and to provide an early warning of contamination. An existing, high integrity qPCR method to detect the E. coli ybbW gene, which requires almost an hour to detect low quantities of the target, was compared with a novel, isothermal RPA method, targeting the same sequence but achieving the result within a few minutes. The RPA technique demonstrated equivalent inclusivity and selectivity, and was able to detect DNA extracted from 100% of 99 E. coli strains, and exclude 100% of 30 non-target bacterial species. The limit of detection of the RPA assay was at least 100 target sequence copies. The high speed and simple, isothermal amplification chemistry may indicate that RPA is a more suitable methodology for on-site E. coli monitoring than an existing qPCR technique.

Sample Preparation for qPCR Detection of Listeria from Food

Quantitative PCR, if performed properly, is a highly sensitive and robust tool. Nevertheless, its application to the particular case of pathogen detection from foodstuffs necessitates special requirements for reliable results. Firstly, a robust analytical chain, involving sample preparation and DNA isolation with purification, is necessary to ensure optimal performance. Secondly, for reliable quantification of Listeria monocytogenes from food, reproducible controls for all steps of the analytical chain are needed, which can give quantitative information about the performance of each individual step of the detection chain. Ideally, each individual sample should include a so-called internal sample process control (ISPC) which passes through all steps of the analytical chain and is phenotypically similar to the target organism (in this case L. monocytogenes).This chapter describes the modular and rapid (3 h) sample preparation method "matrix lysis" for the quantification of L. monocytogenes from food and gives detailed information regarding the application of an ISPC based on the example of the L. monocytogenes Δ-prfA/+IAC strain.

Phenotypic and genotypic characterization of biofilm forming, antimicrobial resistant, pathogenic Escherichia coli isolated from Indian dairy and meat products

Escherichia coli are commensal gastrointestinal microflora of humans, but few strains may cause food-borne diseases. Present study aimed to identify antimicrobial resistant (AMR), biofilm-forming E. coli from Indian dairy and meat products. A total of 32 E. coli isolates were identified and evaluated for biofilm-formation. EMC17, an E. coli isolate was established as a powerful biofilm-former that attained maximum biofilm-formation within 96 h on glass and stainless-steel surfaces. Presence and expression of virulence-associated genes (adhesins, invasins and polysaccharides) and ability to adhere and invade human liver carcinoma HepG2 cell lines implicates EMC17 to be pathotype belonging to Extra-intestinal Pathogenic E. coli (ExPEC). Antibiotic profiling of EMC17 identified it as multi-drug resistant (MDR) strain, possessing extended spectrum β-lactamases (ESBL's) and biofilm phenotype. Early production of quorum sensing molecules (AHLs) alongside EPS production facilitated early onset of biofilm formation by EMC17. Furthermore, the biofilm-forming genes of EMC17 were significantly upregulated 3-27 folds in the biofilm-state. This study showed prevalence of MDR, biofilm-forming, pathogenic E. coli in Indian dairy and meat products that potentially serve as reservoirs for transmission of antimicrobial-resistant (AMR) genes of bacteria from food to humans and pose serious food safety threat.

Separation of Escherichia coli from natural samples for identification of sources and microcosm inoculation

Obtaining uncultured Escherichia coli from natural waters is an important step in the study of microbes in the environment, which are critical for bacterial decay and microbial source tracking. The quality of the samples used can influence the assays, because high contaminant concentrations, differing cell ages, and physiologic states can impair results. The proposed separation is based on a three-step filtration method applied to replicates of seven samples from a sewage plant affluent, collected in different periods. Aliquots of the leachate were inoculated into microcosms, aiming to observe the cultivability of the cells. The assay resulted in colimetry values ranging between 10⁴ and 10⁵ cells. In the leachate, averages of 1.05% of total coliforms and 1.10% of Escherichia coli were recovered from original samples. Although enduring unfavorable temperatures, salinities, and nutritional conditions, the inoculated microcosm populations grew approximately 310 times after 24 h. The final leachate contained cultivable cells in appropriate physiological states and quantities for inoculum in microcosm sets. The bacteria obtained from the leachate were also appropriate for surveys of microbial source tracking, because, in the developed procedure, organisms were separated from contaminants, while cell concentrations were sufficient for inocula.

Isolation ssDNA aptamers specific for both live and viable but nonculturable stateVibrio vulnificususing whole bacteria-SEILEX technology

Vibrio vulnificus is a ubiquitous marine bacterium that may cause rapid and deadly infection, threatening lives of people living around natural bodies of water, especially in coastal regions. However, traditional culture-based methods are time-consuming and unable to detect Viable But Non-Culturable (VBNC) V. vulnificus cells. In this work, we isolated a batch of detection aptamers specifically binding to V. vulnificus in all culture status. With traditional whole bacteria-SELEX (Systematic Evolution of Ligands by EXponential enrichment), flow cytometer analysis and imaging, we identify 18 candidates and validated two of them (V8 and V13) as applicable aptamers. Their truncated sequences also showed comparable performance. The dissociation constant (KD) value of V8 is shown to be as low as 11.22 ± 1.32 nM. Optimal aptamers V8 and V13 are also validated to be effective to detect different Vibrio vulnificus strains under different binding environments using flow cytometry. As for detection parameters, the LOD of the V8 from cytometry is 29.96 CFU mL⁻¹, and the linear range is 10²–5 × 10⁵ CFU mL⁻¹. This is the first case demonstrating that aptamers can detect the existence of VBNC bacteria as well as live bacteria.

With whole-bacteria SELEX, we got aptamers that can bind to V. vulnificus in VBNC Status for the first time.

Optimization of Bacterial Concentration by Filtration for Rapid Detection of Foodborne Escherichia coli O157:H7 Using Real-Time PCR Without Microbial Culture Enrichment

Escherichia coli O157:H7 is an important foodborne pathogen and has been implicated in numerous food poisoning outbreaks worldwide. Although several microbiological and molecular methods have been developed to detect E. coli O157:H7, the difficulty to rapidly detect low levels of the foodborne bacteria persists. Here, the optimization of a filtration technique to concentrate and rapidly detect E. coli O157:H7 was conducted. Using homogenates prepared from freshly cut lettuce and cabbage samples, the E. coli O157:H7 concentration efficiencies of seven membrane filters were compared. Mixed cellulose ester (MCE) and polyvinylidene difluoride (PVDF) filters demonstrated the highest bacterial recoveries. In addition, the optimal E. coli O157:H7 detachment method from MCE filters after filtration was investigated. Tapping for 80 s was demonstrated to be the most effective method for detaching bacteria from the filters. Further, the possibility of the rapid detection of low levels of E. coli O157:H7 in lettuce and cabbage was evaluated using real-time polymerase chain reaction after bacterial concentration using MCE and PVDF filters. The use of MCE filters enabled the detection of 10° CFU/g (5 CFU/g) of E. coli O157:H7 within 2 hr without microbial enrichment culture. Therefore, concentration by filtration can be used for the rapid detection of low levels of foodborne pathogens. PRACTICAL APPLICATION: The modified method, which has been verified in this study, has been optimized to reduce the analysis time and to detect very low concentrations of E. coli O157:H7 within 2 hr. All these detection systems have a direct economic impact on the food analysis of producers, health authorities, or third-party laboratories.

A novel method for rapid and sensitive detection of viable Escherichia coli cells using UV-induced PMA-coupled quantitative PCR

We report a specific and sensitive method to improve the coupling of propidium monoazide (PMA) with DNA derived from killed cells of Escherichia coli using UV light of 365 nm. UV light of three different intensities mainly 2.4 × 10³, 4.8 × 10³, and 7.2 × 10³ μJ/cm² was applied to E. coli cells each for 1, 3, and 5 min. PMA was found to be successfully cross-linked with the DNA from killed cells of E. coli at 4.8 × 10³ μJ/cm² in 3 min leading to the complete inhibition of PCR amplification of DNA derived from PMA-treated heat-killed cells. In spiked phosphate-buffered saline and potable water samples, the difference of the Cq values between PMA-treated viable cells and PMA-untreated viable cells ranged from -0.17 to 0.2, demonstrating that UV-induced PMA activation had a negligible effect on viable cells. In contrast, the difference of the Cq values between PMA-treated heat-killed cells and PMA-untreated heat-killed cells ranged from 8.9 to 9.99, indicating the ability of PMA to inhibit PCR amplification of DNA derived from killed cells to an equivalent as low as 10⁰ CFU. In conclusion, this UV-coupled PMA-qPCR assay provided a rapid and sensitive methodology to selectively detect viable E. coli cells in spiked water samples within 4 h.

The etiology of acute meningitis and encephalitis syndromes in a sentinel pediatric hospital, Shenzhen, China

Background

Acute meningitis and encephalitis syndromes (AMES) is a severe neurological infection which causes high case fatality and severe sequelae in children. To determine the etiology of childhood AMES in Shenzhen, a hospital-based study was undertaken.

Methods

A total of 240 cerebrospinal fluid (CSF) samples from 171 children meeting the case definition were included and screened for 12 common causative organisms. The clinical data and conventional testing results were collected and analyzed. Whole genome sequencing was performed on a Neisseria meningitidis isolate.

Results

A pathogen was found in 85 (49.7%) cases; Group B Streptococcus (GBS) was detected in 17 cases, Escherichia coli in 15, Streptococcus pneumoniae in 14, enterovirus (EV) in 13, herpes simplex virus (HSV) in 3, N. meningitidis in 1, Haemophilus influenzae in 1, and others in 23. Notably, HSV was found after 43 days of treatment. Twelve GBS and 6 E. coli meningitis were found in neonates aged less than 1 month; 13 pneumococcal meningitis in children aged > 3 months; and 12 EV infections in children aged > 1 year old. The multilocus sequence typing of serogroup B N. meningitidis isolate was ST-3200/CC4821. High resistance rate to tetracycline (75%), penicillin (75%), and trimethoprim/sulfamethoxazole (75%) was found in 4 of S. pneumoniae isolates; clindamycin (100%) and tetracycline (100%) in 9 of GBS; and ampicillin (75%) and trimethoprim/sulfamethoxazole (67%) in 12 of E. coli.

Conclusions

The prevalence of N. meningitidis and JEV was very low and the cases of childhood AMES were mainly caused by other pathogens. GBS and E. coli were the main causative organisms in neonates, while S. pneumoniae and EV were mainly found in older children. HSV could be persistently found in the CSF samples despite of the treatment. A better prevention strategy for GBS, the introduction of pneumococcal vaccine, and incorporation of PCR methods were recommended.

Development of a filtration-based LAMP-LFA method as sensitive and rapid detection of E. coli O157:H7

Rapid detection of low number of pathogenic bacteria in food is difficult. This study tested the filter-based loop-mediated isothermal amplification-lateral flow immunoassay (LAMP-LFA) method for rapid detection of pathogens in real food. Escherichia coli O157:H7 was inoculated on 25 g of beef and the homogenized sample was filtered with 0.45 μm cellulose nitrate filter, and concentrated E. coli was recovered and DNA was extracted and analyzed by LAMP. LFA reaction was performed by hybridization of digoxygenin-labeled LAMP amplicon and biotinylated probe. The sensitivity of the filtered sample was 100 times more sensitive than that of the unfiltered sample. The total reaction time used for detection from sample preparation to confirmation of E. coli was within 3 h. These results suggest that the LAMP-LFA method can be used in real food systems as point-of-care testing for E. coli O157:H7 in beef.

Real-time detection of faecally contaminated drinking water with tryptophan-like fluorescence: defining threshold values

We assess the use of fluorescent dissolved organic matter at excitation-emission wavelengths of 280nm and 360nm, termed tryptophan-like fluorescence (TLF), as an indicator of faecally contaminated drinking water. A significant logistic regression model was developed using TLF as a predictor of thermotolerant coliforms (TTCs) using data from groundwater- and surface water-derived drinking water sources in India, Malawi, South Africa and Zambia. A TLF threshold of 1.3ppb dissolved tryptophan was selected to classify TTC contamination. Validation of the TLF threshold indicated a false-negative error rate of 15% and a false-positive error rate of 18%. The threshold was unsuccessful at classifying contaminated sources containing <10 TTC cfu per 100mL, which we consider the current limit of detection. If only sources above this limit were classified, the false-negative error rate was very low at 4%. TLF intensity was very strongly correlated with TTC concentration (ρ_s=0.80). A higher threshold of 6.9ppb dissolved tryptophan is proposed to indicate heavily contaminated sources (≥100 TTC cfu per 100mL). Current commercially available fluorimeters are easy-to-use, suitable for use online and in remote environments, require neither reagents nor consumables, and crucially provide an instantaneous reading. TLF measurements are not appreciably impaired by common intereferents, such as pH, turbidity and temperature, within typical natural ranges. The technology is a viable option for the real-time screening of faecally contaminated drinking water globally.

Three-Dimensional Reservoir-Based Dielectrophoresis (rDEP) for Enhanced Particle Enrichment

Selective enrichment of target species is crucial for a wide variety of engineering systems for improved performance of subsequent processes. Dielectrophoresis (DEP) is a powerful electrokinetic method that can be used to focus, trap, concentrate, and separate a variety of species in a label-free manner. The commonly employed methods for DEP suffer from limitations such as electrode fouling and high susceptibility to Joule heating effects. Recently, our group has demonstrated DEP-based manipulations of particles and cells using a novel method of reservoir-based dielectrophoresis (rDEP) which exploits the naturally produced electric field gradients at the reservoir-microchannel junction. Although this method reasonably addresses the limitations mentioned above while maintaining a high simplicity of fabrication, all of our demonstrations so far have used a two-dimensional rDEP, which limits the performance of the devices. This work aims to improve their performance further by making the DEP three-dimensional. Through detailed experimental and numerical analysis, we demonstrate a six-fold increase in the enrichment performance of latex beads and a significant reduction in the power consumption for the new devices, which would allow a more reliable integration of the same into micro-total analysis systems.

A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters

The presence of Escherichia coli in environmental waters is considered as evidence of faecal contamination and is therefore commonly used as an indicator in both water quality and food safety analysis. The long period of time between sample collection and obtaining results from existing culture based methods means that contamination events may already impact public health by the time they are detected. The adoption of molecular based methods for E. coli could significantly reduce the time to detection. A new quantitative real-time PCR (qPCR) assay was developed to detect the ybbW gene sequence, which was found to be 100% exclusive and inclusive (specific and sensitive) for E. coli and directly compared for its ability to quantify E. coli in environmental waters against colony counts, quantitative real-time NASBA (qNASBA) targeting clpB and qPCR targeting uidA. Of the 87 E. coli strains tested, 100% were found to be ybbW positive, 94.2% were culture positive, 100% were clpB positive and 98.9% were uidA positive. The qPCR assays had a linear range of quantification over several orders of magnitude, and had high amplification efficiencies when using single isolates as a template. This compared favourably with qNASBA which showed poor linearity and amplification efficiency. When the assays were applied to environmental water samples, qNASBA was unable to reliably quantify E. coli while both qPCR assays were capable of predicting E. coli concentrations in environmental waters. This study highlights the inability of qNASBA targeting mRNA to quantify E. coli in environmental waters, and presents the first E. coli qPCR assay with 100% target exclusivity. The application of a highly exclusive and inclusive qPCR assay has the potential to allow water quality managers to reliably and rapidly detect and quantify E. coli and therefore take appropriate measures to reduce the risk to public health posed by faecal contamination.

CRENAME, A Molecular Microbiology Method Enabling Multiparametric Assessment of Potable/Drinking Water

The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water.

Multiplex Polymerase Chain Reaction for Identification of Shigellae and Four Shigella Species Using Novel Genetic Markers Screened by Comparative Genomics

In the detection of Shigella species using molecular biological methods, previously known genetic markers for Shigella species were not sufficient to discriminate between Shigella species and diarrheagenic Escherichia coli. The purposes of this study were to screen for genetic markers of the Shigella genus and four Shigella species through comparative genomics and develop a multiplex polymerase chain reaction (PCR) for the detection of shigellae and Shigella species. A total of seven genomic DNA sequences from Shigella species were subjected to comparative genomics for the screening of genetic markers of shigellae and each Shigella species. The primer sets were designed from the screened genetic markers and evaluated using PCR with genomic DNAs from Shigella and other bacterial strains in Enterobacteriaceae. A novel Shigella quintuplex PCR, designed for the detection of Shigella genus, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, was developed from the evaluated primer sets, and its performance was demonstrated with specifically amplified results from each Shigella species. This Shigella multiplex PCR is the first to be reported with novel genetic markers developed through comparative genomics and may be a useful tool for the accurate detection of the Shigella genus and species from closely related bacteria in clinical microbiology and food safety.

Survival, Biofilm Formation, and Growth Potential of Environmental and Enteric Escherichia coli Strains in Drinking Water Microcosms

Escherichia coli is the most commonly used indicator for fecal contamination in drinking water distribution systems (WDS). The assumption is that E. coli bacteria are of enteric origin and cannot persist for long outside their host and therefore act as indicators of recent contamination events. This study investigates the fate of E. coli in drinking water, specifically addressing survival, biofilm formation under shear stress, and regrowth in a series of laboratory-controlled experiments. We show the extended persistence of three E. coli strains (two enteric isolates and one soil isolate) in sterile and nonsterile drinking water microcosms at 8 and 17°C, with T90 (time taken for a reduction in cell number of 1 log10 unit) values ranging from 17.4 ± 1.8 to 149 ± 67.7 days, using standard plate counts and a series of (reverse transcription-)quantitative PCR [(RT-)Q-PCR] assays targeting 16S rRNA, tuf, uidA, and rodA genes and transcripts. Furthermore, each strain was capable of attaching to a surface and replicating to form biofilm in the presence of nutrients under a range of shear stress values (0.6, 2.0, and 4.4 dynes [dyn] cm(-2); BioFlux system; Fluxion); however, cell numbers did not increase when drinking water flowed over the biofilm (P > 0.05 by t test). Finally, E. coli regrowth within drinking water microcosms containing polyethylene PE-100 pipe wall material was not observed in the biofilm or water phase using a combination of culturing and Q-PCR methods for E. coli The results of this work highlight that when E. coli enters drinking water it has the potential to survive and attach to surfaces but that regrowth within drinking water or biofilm is unlikely.

IMPORTANCE

The provision of clean, safe drinking water is fundamental to society. WDS deliver water to consumers via a vast network of pipes. E. coli is used as an indicator organism for recent contamination events based on the premise that it cannot survive for long outside its host. A key public health concern therefore arises around the fate of E. coli on entering a WDS; its survival, ability to form a biofilm, and potential for regrowth. In particular, if E. coli bacteria have the ability to incorporate and regrow within the pipe wall biofilm of a WDS, they could reinoculate the water at a later stage. This study sheds light on the fate of environmental and enteric strains of E. coli in drinking water showing extended survival, the potential for biofilm formation under shear stress, and importantly, that regrowth in the presence of an indigenous microbial community is unlikely.

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

BACKGROUND

Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.

RESULTS

We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.

CONCLUSION

This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.

Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview

Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.

High-throughput malaria parasite separation using a viscoelastic fluid for ultrasensitive PCR detection

A novel microfluidic device for high-throughput particle separation using a viscoelastic fluid, which enables the rapid detection of extremely rare malaria parasites by using PCR analysis, is proposed. Our device consists of two segments: the 1st stage for sheathless pre-alignment and the 2nd stage for separation based on size-dependent viscoelasticity-induced lateral migration. The use of a high-aspect ratio channel and a viscoelastic polymer solution with low viscosity enables high-throughput processing. The device performance was first optimized using synthetic particles. A mixture of 2 and 10 μm particles was focused at the center plane in the 1st stage. The smaller particles, serving as surrogates for malaria parasites, were subsequently separated in the 2nd stage with a recovery rate of ∼96% at 400 μl min(-1). Finally, separation of the malaria parasites from the white blood cells was performed. At 400 μl min(-1), almost all white blood cells were removed and the malaria parasites were separated with a ∼94% recovery rate and ∼99% purity. Although the initial concentration of the malaria parasites was too low to be detected by PCR analysis, WBC depletion and buffer removal increased the parasite concentration sufficiently such that PCR detection was possible.

Evaluating exposure of pedestrians to airborne contaminants associated with non-potable water use for pavement cleaning

Climate change and increasing demography press local authorities to look after affordable water resources and replacement of drinking water for city necessities like street and pavement cleaning by more available raw water. Though, the substitution of drinking by non-drinking resources demands the evaluation of sanitary hazards. This article aims therefore to evaluate the contribution of cleaning water to the overall exposure of city dwellers in case of wet pavement cleaning using crossed physical, chemical and biological approaches. The result of tracer experiments with fluorescein show that liquid water content of the cleaning aerosol produced is about 0.24 g m(-3), rending possible a fast estimation of exposure levels. In situ analysis of the aerosol particles indicates a significant increase in particle number concentration and particle diameter, though without change in particle composition. The conventional bacterial analysis using total coliforms as tracer suggests that an important part of the contamination is issued from the pavement. The qPCR results show a more than 20-fold increase of background genome concentration for Escherichia coli and 10-fold increase for Enterococcus but a negligible contribution of the cleaning water. The fluorescence analysis of the cleaning aerosol confirms the above findings identifying pavement surface as the major contributor to aerosol organic load. The physical, chemical and microbiological approaches used make it possible to describe accurately the cleaning bioaerosol and to identify the existence of significantly higher levels of all parameters studied during the wet pavement cleaning. Though, the low level of contamination and the very short time of passage of pedestrian in the zone do not suggest a significant risk for the city dwellers. As the cleaning workers remain much longer in the impacted area, more attention should be paid to their chronic exposure.

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.

Efficacy of coral-hydroxyapatite and biphasic calcium phosphate for early bacterial detection

Nano- or microhydroxyapatites with microbiological properties are being used to detect pathogens in clinical samples and industrial environments. In this study, the calcium phosphates coral-hydroxyapatite and biphasic calcium phosphate were characterized physicochemically using x-ray diffraction, thermogravimetric, and differential thermal analysis. The morphology, texture, and chemical composition of the ceramics were also investigated using scanning electron microscopy with energy dispersive spectroscopy. The biocompatibility of the ceramics was evaluated using Escherichia coli and Enterococcus faecalis. Microorganisms were detected by incorporating the enzyme markers 4-metilumbelliferil-β-d-glucoside and 4-metilumbelliferil-β-d-glucuronide in the ceramic powders and evaluating fluorescence. The characterization of the ceramics revealed typical characteristics, such as crystallinity, thermal stability, and chemical composition, consistent with other calcium phosphates. The calcium phosphates coral-hydroxyapatite and biphasic calcium phosphate ceramics differed from one another in morphology, structural topography, particle size distribution, and the capacity to absorb water. These properties can influence the rates of microbiological responses and bacterial detection. Although both materials are suitable for use as structural supports in microbial diagnostic systems, BCP was more efficient and detected E. coli and E. faecalis more rapidly than CHA.

On-line monitoring of Escherichia coli in raw water at Oset drinking water treatment plant, Oslo (Norway)

The fully automated Colifast ALARM^TM has been used for two years for daily monitoring of the presence/absence of Escherichia coli in 100 mL raw water at Oset drinking water treatment plant in Oslo, Norway. The raw water is extracted from 35 m depth from the Lake Maridalsvannet. E. coli was detected in 18% of the daily samples. In general, most samples positive for E. coli were observed during the autumn turnover periods, but even in some samples taken during warm and dry days in July, with stable temperature stratification in the lake, E. coli was detected. The daily samples gave useful additional information compared with the weekly routine samples about the hygienic raw water quality and the hygienic barrier efficiency of the lake under different weather conditions and seasons. The winter 2013/2014 was much warmer than the winter 2012/2013. The monitoring supported the hypothesis that warmer winters with shorter periods with ice cover on lakes, which may be a consequence of climate changes, may reduce the hygienic barrier efficiency in deep lakes used as drinking water sources.

Abilities of the mCP Agar method and CRENAME alpha toxin-specific real-time PCR assay to detect Clostridium perfringens spores in drinking water

We first determined the analytical specificity and ubiquity (i.e., the ability to detect all or most strains) of a Clostridium perfringens-specific real-time PCR (rtPCR) assay based on the cpa gene (cpa rtPCR) by using a bacterial strain panel composed of C. perfringens and non-C. perfringens Clostridium strains. All non-C. perfringens Clostridium strains tested negative, whereas all C. perfringens strains tested positive with the cpa rtPCR, for an analytical specificity and ubiquity of 100%. The cpa rtPCR assay was then used to confirm the identity of 116 putative C. perfringens isolates recovered after filtration of water samples and culture on mCP agar. Colonies presenting discordant results between the phenotype on mCP agar and cpa rtPCR were identified by sequencing the 16S rRNA and cpa genes. Four mCP(-)/rtPCR(+) colonies were identified as C. perfringens, whereas 3 mCP(+)/rtPCR(-) colonies were identified as non-C. perfringens. The cpa rtPCR was negative with all 51 non-C. perfringens strains and positive with 64 of 65 C. perfringens strains. Finally, we compared mCP agar and a CRENAME (concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment) procedure plus cpa rtPCR (CRENAME + cpa rtPCR) for their abilities to detect C. perfringens spores in drinking water. CRENAME + cpa rtPCR detected as few as one C. perfringens CFU per 100 ml of drinking water sample in less than 5 h, whereas mCP agar took at least 25 h to deliver results. CRENAME + cpa rtPCR also allows the simultaneous and sensitive detection of Escherichia coli and C. perfringens from the same potable water sample. In itself, it could be used to assess the public health risk posed by drinking water potentially contaminated with pathogens more resistant to disinfection.

Comparative analysis of classical and molecular microbiology methods for the detection of Escherichia coli and Enterococcus spp. in well water

The microbiological quality of 165 1 litre well water samples collected in the Québec City region was assessed by culture-based methods (mFC agar, Chromocult coliform agar, Colilert(®), MI agar, Chromocult enterococci, Enterolert™, and mEI agar) and by a molecular microbiology strategy, dubbed CRENAME-rtPCR, developed for the detection of Escherichia coli, Enterococcus spp., Enterococcus faecalis/faecium, and Bacillus atrophaeus subsp. globigii. In these drinking water samples, approved culture-based methods detected E. coli at rates varying from 1.8 to 3.6% and Enterococcus spp. at rates varying from 3.0 to 11.5%, while the molecular microbiology approach for E. coli was found to be as efficient, detecting contamination in 3.0% of samples. In contrast, CRENAME-rtPCR detected Enterococcus spp. in 27.9% of samples while the E. faecalis/faecium molecular assay did not uncover a single contaminated sample, thereby revealing a discrepancy in the coverage of waterborne enterococcal species detected by classical and molecular microbiology methods. The validation of the CRENAME-E. coli rtPCR test as a new tool to assess the quality of drinking water will require larger scale studies elaborated to demonstrate its equivalence to approved methods.

Rapid detection and respirometric profiling of aerobic bacteria on panels of selective media

AIMS

To evaluate high-throughput optical oxygen microrespirometry for selective detection and predictive identification of aerobic bacteria.

METHODS AND RESULTS

Using GreenLight probe, standard 384-well plates and time-resolved fluorescence reader, a representative panel of 16 partially selective media and 9 aerobic bacteria (Escherichia coli, Bacillus cereus, Staphylococcus aureus, Campylobacter jejuni, Yersinia enterocolitica, Pseudomonas aeruginosa, Streptococcus pyogenes, Salmonella typhimurium and Listeria innocua) were analysed. For each medium, bacterial strain and dilution, growth profiles were recorded, from which calibrations, doubling/generation times and growth patterns in different media were determined. Analytical performance, selectivity and general usability of the method were assessed, and mixed bacterial cultures were analysed.

CONCLUSION

The microrespirometry platform facilitates simple, real-time detection and predictive identification of aerobic bacteria by looking at the patterns of their growth and respiration in several media and determining their growth and doubling times.

SIGNIFICANCE AND IMPACT OF THE STUDY

The new screening method can be used for routine microbiological analysis and testing of aerobic bacterial cultures as well as complex food, environmental and clinical samples.