Evaluation of a new medium for the enumeration of total coliforms and Escherichia coli in Japanese surface waters

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations

Screening assays are used to test if one or more microbes suppress a pathogen of interest. In the presence of more than one microbe, the screening method must be able to accurately distinguish viable pathogen cells from non-viable and non-target microbes in a sample. Current screening methods are time-consuming and require special reagents to detect viability in mixed microbial communities. Screening assays performed using soil or other complex matrices present additional challenges for screening. Here, we develop an experimental workflow based on the most probable number (MPN) assay for testing the ability of synthetic microbial communities to suppress a soil-borne pathogen. Our approach, fluorMPN, uses a fluorescently labeled pathogen and microplate format to enable high-throughput comparative screening. In parallel, we developed a command-line tool, MicroMPN, which significantly reduces the complexity of calculating MPN values from microplates. We compared the performance of the fluorMPN assay with spotting on agar and found that both methods produced strongly correlated counts of equal precision. The suppressive effect of synthetic communities on the pathogen was equally recoverable by both methods. The application of this workflow for discriminating which communities lead to pathogen reduction helps narrow down candidates for additional characterization. Together, the resources offered here are meant to facilitate and simplify the application of MPN-based assays for comparative screening projects.IMPORTANCEWe created a unified set of software and laboratory protocols for screening microbe libraries to assess the suppression of a pathogen in a mixed microbial community. Existing methods of fluorescent labeling were combined with the most probable number (MPN) assay in a microplate format to enumerate the reduction of a pathogenic soil microbe from complex soil matrices. This work provides a fluorescent expression vector available from Addgene, step-by-step laboratory protocols hosted by protocols.io, and MicroMPN, a command-line software for processing plate reader outputs. MicroMPN simplifies MPN estimation from 96- and 384-well microplates. The microplate screening assay is amenable to robotic automation with standard liquid handling robots, further reducing the hands-on processing time. This tool was designed to evaluate synthetic microbial communities for use as microbial inoculates or probiotics. The fluorMPN method is also useful for screening chemical and antimicrobial libraries for pathogen suppression in complex bacterial communities like soil.

Investigation of some physical, chemical, and bacteriological parameters of water quality in some dams in Albaha region, Saudi Arabia

This study was conducted to evaluate the quality of water in selected dams in Albaha region, Kingdom of Saudi Arabia. Water samples from eight dams were subjected to physical, chemical, and bacteriological assessment using standardized procedures of conductivity, total dissolved solids, ions, acidity & alkalinity, and EC blue 100® coliform detection. About three fourth (75%) of dams’ water samples exceeded the permissible levels of pH, total dissolved solids, turbidity, Mn and NO₃ set by Saudi standards. Average levels of total dissolved solids, Fe, Mn, SO₄, NO₃, and NO₂ were 3065.00, 0.10, 0.89, 68.25, 17.91 and 0.016 mg/L, respectively. However, the average pH of water samples was 7.95 ± 0.66 which still within the accepted range set by national and global standards. Moreover, total dissolved solids also exceeded regular standards of Food and Agriculture Organization for irrigation water quality. Coliform bacteria were detected in 37.5% of dams without any significant spatial differences between dams and sites as groups. Correlations were found between pH & NO₃, SO₄ & NO₃, coliform bacteria & turbidity, coliform bacteria & NO₂ levels. Increased concentrations of assessed parameters in dams may be attributed to agricultural activities as well as animal and human wastes deposited into dams via rainfalls and flash floods. Proper treatment of dams needs to be taken into account before consumption and irrigation.

Increased E. coli bio-adsorption resistance of microfiltration membranes, using a bio-inspired approach

Cells have inherent anti-fouling properties. The mechanisms underpinning these natural properties inform the design of an anti-biosorption coating for a polyethersulfone microfiltration membrane, which includes polydopamine and chitosan layers. This tri-layered membrane is created using quick and easy synthesis method. Its ability to resist bio-adsorption and membrane extracellular polymeric substances (EPS) formation is investigated using the bacterium E. coli (ATCC 11775, 1.5 × 10⁷ CFU/mL). In addition, the proliferative bio-adsorption process is explored on the microfiltration membrane surface, using natural water under static and shaken conditions, while monitoring the bio-adsorption kinetics and EPS dynamic changes. The characterization results show that the modification by polydopamine and chitosan change the membrane surface morphology and increase its hydrophilicity. After 10 min dipping in 5 g/L chitosan solution, the pure water flux of the modified membrane is 5469 ± 30 L/(m²·h) (0.2 bar) and the contact angle decreases to 36.7 ± 1.0°, compared with 9889 ± 23 L/(m²·h) (0.2 bar) and 60.3 ± 1.5° for the unmodified polyethersulfone membrane, respectively. In proliferative bio-adsorption tests, the modified membrane is shown to decrease bio-adsorption by 0.4-2.3 orders of magnitude. However, no antimicrobial function is observed, probably due to the alkaline environment and insufficient functional amino groups. A series of linear and non-linear kinetic models is applied to fit the proliferative bio-adsorption process. The pseudo-second-order model is found to describe the proliferative bio-adsorption process best. Neither total organic carbon (TOC) nor protein is detected on the modified membrane surface. In contrast, on the unmodified PES membrane the ratios of protein/TOC (%), TOC/abundance ((μg/cm²)/CFU (log)) and protein/abundance ((μg/cm²)/CFU(log)) are 10%-16%, 0.17-0.28 and 0.02-0.04, respectively. No significant difference (p > 0.05) is found between static and shaken conditions. All these results point to improved anti-biosorption properties for water treatment applications, encouraging further studies on this membrane.

Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water

There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert^® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert^® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for downstream applications which require cultivated isolates.

Evaluation of an Inexpensive Growth Medium for Direct Detection of Escherichia coli in Temperate and Sub-Tropical Waters

The cost and complexity of traditional methods for the detection of faecal indicator bacteria, including E. coli, hinder widespread monitoring of drinking water quality, especially in low-income countries and outside controlled laboratory settings. In these settings the problem is exacerbated by the lack of inexpensive media for the detection of E. coli in drinking water. We developed a new low-cost growth medium, aquatest (AT), and validated its use for the direct detection of E. coli in temperate and sub-tropical drinking waters using IDEXX Quanti-Tray^®. AT was compared with IDEXX Colilert-18^® and either EC-MUG or MLSB for detecting low levels of E. coli from water samples from temperate (n = 140; Bristol, UK) and subtropical regions (n = 50, Pretoria/Tshwane, South Africa). Confirmatory testing (n = 418 and 588, respectively) and the comparison of quantitative results were used to assess performance. Sensitivity of AT was higher than Colilert-18^® for water samples in the UK [98.0% vs. 86.9%; p<0.0001] and South Africa [99.5% vs. 93.2%; p = 0.0030]. There was no significant difference in specificity, which was high for both media (>95% in both settings). Quantitative results were comparable and within expected limits. AT is reliable and accurate for the detection of E. coli in temperate and subtropical drinking water. The composition of the new medium is reported herein and can be used freely.

Evaluation of a new most-probable-number (MPN) dilution plate method for the enumeration of Escherichia coli in water samples

The purpose of this study was to evaluate the most-probable-number dilution plate (MPN plate) method developed for the enumeration of Escherichia coil in water samples. Sterilized water was inoculated with E. coli ATCC 11775 to give between 2-1600 MPN/100 ml. The MPN was determined for both the MPN plate and 5-tube methods from the MPN table. The average of the natural logarithm (In) MPN with standard deviations in 95 samples was 4.26 +/- 1.48 by the 5-tube-method and 4.18 +/- 1.45 by the MPN plate method. The correlation coefficient was 0.96. These results were not significantly different according to the paired t-test (p > 0.05).