Machine Learning Guided Polyamide Membrane with Exceptional Solute-Solute Selectivity and Permeance.

Designing polymeric membranes with high solute-solute selectivity and permeance is important but technically challenging. Existing industrial interfacial polymerization (IP) process to fabricate polyamide-based polymeric membranes is largely empirical, which requires enormous trial-and-error experimentations to identify optimal fabrication conditions from a wide candidate space for separating a given solute pair. Herein, we developed a novel multitask machine learning (ML) model based on an artificial neural network (ANN) with skip connections and selectivity regularization to guide the design of polyamide membranes. We used limited sets of lab-collected data to obtain satisfactory model performance over four iterations by introducing human expert experience in the online learning process. Four membranes under fabrication conditions guided by the model exceeded the present upper bound for mono/divalent ion selectivity and permeance of the polymeric membranes. Moreover, we obtained new mechanistic insights into the membrane design through feature analysis of the model. Our work demonstrates a ML approach that represents a paradigm shift for high-performance polymeric membranes design.

Distribution and Characterization of Salmonella enterica Isolates from Irrigation Ponds in the Southeastern United States.

Irrigation water has been implicated as a likely source of produce contamination by Salmonella enterica. Therefore, the distribution of S. enterica was surveyed monthly in irrigation ponds (n = 10) located within a prime agricultural region in southern Georgia and northern Florida. All ponds and 28.2% of all samples (n = 635) were positive for Salmonella, with an overall geometric mean concentration (0.26 most probable number [MPN]/liter) that was relatively low compared to prior reports for rivers in this region. Salmonella peaks were seasonal; the levels correlated with increased temperature and rainfall (P < 0.05). The numbers and occurrence were significantly higher in water (0.32 MPN/liter and 37% of samples) than in sediment (0.22 MPN/liter and 17% of samples) but did not vary with depth. Representative isolates (n = 185) from different ponds, sample types, and seasons were examined for resistance to 15 different antibiotics; most strains were resistant to streptomycin (98.9%), while 20% were multidrug resistant (MDR) for 2 to 6 antibiotics. DiversiLab repetitive extragenic palindromic-element sequence-based PCR (rep-PCR) revealed genetic diversity and showed 43 genotypes among 191 isolates, as defined by >95% similarity. The genotypes did not partition by pond, season, or sample type. Genetic similarity to known serotypes indicated Hadar, Montevideo, and Newport as the most prevalent. All ponds achieved the current safety standards for generic Escherichia coli in agricultural water, and regression modeling showed that the E. coli level was a significant predictor for the probability of Salmonella occurrence. However, persistent populations of Salmonella were widely distributed in irrigation ponds, and the associated risks for produce contamination and subsequent human exposure are unknown, supporting continued surveillance of this pathogen in agricultural settings.

Removing 65 Years of Approximation in Rotating Ring Disk Electrode Theory with Physics-Informed Neural Networks.

The rotating Ring Disk Electrode (RRDE), since its introduction in 1959 by Frumkin and Nekrasov, has become indispensable with diverse applications in electrochemistry, catalysis, and material science. The collection efficiency (N) is an important parameter extracted from the ring and disk currents of the RRDE, providing valuable information about reaction mechanism, kinetics, and pathways. The theoretical prediction of N is a challenging task: requiring solution of the complete convective diffusion mass transport equation with complex velocity profiles. Previous efforts, including by Albery and Bruckenstein who developed the most widely used analytical equations, heavily relied on approximations by removing radial diffusion and using approximate velocity profiles. 65 years after the introduction of RRDE, we employ a physics-informed neural network to solve the complete convective diffusion mass transport equation, to reveal the formerly neglected edge effects and velocity corrections on N, and to provide a guideline where conventional approximation is applicable.

Occurrence and population density of Campylobacter jejuni in irrigation ponds on produce farms in the Suwannee River Watershed.

Campylobacter spp., especially Campylobacter jejuni, are common causal agents of gastroenteritis globally. Poultry, contaminated water, and fresh produce are considered to be the main sources for infection by this pathogen. In this study, occurrence and population density of C. jejuni from vegetable irrigation ponds in the Suwannee River watershed were investigated and the relationship to environmental factors was analyzed. Two water samples were collected from each of 10 ponds every month from January 2011 to February 2012. Campylobacter jejuni was detected by quantitative real-time PCR. Nine of the 10 ponds were positive for C. jejuni some of the time with an overall prevalence of 19.3%. The highest counts were obtained in spring 2011. Oxidation-reduction potential and total nitrogen concentration were positively correlated (P < 0.05) with mean population and occurrence of C. jejuni, while temperature and dissolved oxygen percent saturation (DO%) were negatively correlated with mean population (P < 0.05). Presence of this pathogen was related to bacterial community composition. No correlations were found between C. jejuni and fecal indicators. Increasing DO% of irrigation water and limiting nitrogen pollution in the ponds are suggested to reduce the contamination risk of C. jejuni in a major fruit and vegetable growing area.

Factors affecting the occurrence of Escherichia coli O157 contamination in irrigation ponds on produce farms in the Suwannee River Watershed.

Outbreaks of enteritis caused by Escherichia coli O157 associated with fresh produce have resulted in questions about the safety of irrigation water; however, associated risks have not been systematically evaluated. In this study, the occurrence and distribution of the human pathogen E. coli O157 from vegetable irrigation ponds within the Suwannee River Watershed in Georgia were investigated, and the relationship to environmental factors was analyzed. Surface and subsurface water samples were collected monthly from 10 vegetable irrigation ponds from March 2011 to February 2012. Escherichia coli O157 was isolated from enriched filtrates on CHROMagar and sorbitol MacConkey agar media and confirmed by an agglutination test. Presence of virulence genes stx1, stx2 , and eae was tested by polymerase chain reaction. In addition, 27 environmental variables of the sampled ponds were measured. Denaturing gradient gel electrophoresis was conducted for the analysis of bacterial communities in the water samples. Biserial correlation coefficients were calculated to evaluate the log10 colony-forming unit per millilitre correlations between the environmental factors and the occurrence of E. coli O157. Stepwise and canonical discriminant analyses were used to determine the factors that were associated with the presence and absence of E. coli O157 in water samples. All 10 ponds were positive for E. coli O157 some of the time, mainly in summer and fall of 2011. The temporal distribution of this bacterium differed among the 10 ponds. Temperature, rainfall, populations of fecal coliform, and culturable bacteria were positively correlated with the occurrence of E. coli O157 (P < 0.05), while the total nitrogen concentration, oxidation-reduction potential, and dissolved oxygen concentration were negatively correlated with the occurrence of this pathogen (P < 0.05). Temperature and rainfall were the most important factors contributing to the discrimination between samples with and without E. coli O157, followed by bacterial diversity and culturable bacteria population density. Bacterial numbers and diversity, including fecal coliforms and E. coli O157, increased after rainfall (and possibly runoff from pond margins) in periods with relatively high temperatures, suggesting that prevention of runoff may be important to minimize the risk of enteric pathogens in irrigation ponds.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia.

The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.

Development of a novel cross-streaking method for isolation, confirmation, and enumeration of Salmonella from irrigation ponds.

The 2013 Produce Safety Rules in Food Safety Modernization Act (FSMA) require regular testing for generic Escherichia coli in agricultural water intended for pre-harvest contact with the edible portion of fresh produce. However, the use of fecal contamination indicators frequently does not correctly reflect distribution of foodborne pathogens such as Salmonella enterica, and ensuring food safety may require direct detection and enumeration of pathogens in agricultural settings. Herein we report the evaluation of different cost-effective methods for quantification, isolation, and confirmation of Salmonella in irrigation pond water and sediment samples. A most probably number (MPN) dual enrichment culture method was used in combination with differential and selective agars, XLT4 and CHROMagar™ Salmonella plus (CSP). The necessity for PCR confirmation was evaluated, and methods were compared by cost and performance measures (i.e., sensitivity, specificity, positive predictive value, and negative predictive value). Statistical analyses showed that using XLT4 as the initial selective agar to isolate Salmonella colonies improved recovery compared to CSP agar; however, PCR confirmation was required to avoid false positive results on either agar. Therefore, a novel cross-streaking method utilizing CHROMagar™ agar for individual colony confirmation of Salmonella presence/absence on XLT4 was developed. This method classifies the colony as positive if typical Salmonella appearance is observed on both agars. Statistical analysis showed that this method was as effective as PCR for species confirmation of pure individual strains isolated from enrichment cultures (sensitivity=0.99, specificity=1.00, relative to PCR). This method offers a cost-effective alternative to PCR that would increase the capacity and sensitivity of Salmonella evaluation.

Multiple novel and prevalent astroviruses in pigs.

Knowledge of porcine astrovirus diversity and epidemiology remains limited. We used a broad range PCR approach to investigate the presence and diversity of astroviruses in healthy pigs of different ages on 20 farms and in 3 slaughterhouses situated in the province of Quebec, Canada between 2005 and 2007. Our study unexpectedly revealed remarkable levels of genetic diversity and high prevalence of astroviruses in pigs of this province. Astroviruses were detected on every farm investigated and in all age groups of pigs, from suckling piglets to adults. In addition, we found that nearly 80% of healthy finisher pigs harbour astroviruses in their intestine at slaughter. Phylogenetic evidence based on partial polymerase and complete capsid sequences, suggests that porcine astroviruses do not form a monophyletic group but are rather found on separate branches across the mamastrovirus tree. In addition to type species strains, we found highly divergent strains that form two additional lineages, one of which falls outside existing taxonomic groups. The presence of diverse astroviruses in a majority of healthy pigs likely represents a continuous source of infection to piglets and possibly to other animal species including humans. Porcine astrovirus strains appeared phylogenetically related not only to prototypical human astroviruses, as was already known, but also to novel human strains recently discovered suggesting multiple cross species transmission events between these hosts and other animal species. Overall, the findings reported in this study suggest an active role of pigs in the evolution and ecology of the Astroviridae.

Development and validation of a microarray for the confirmation and typing of norovirus RT-PCR products.

Noroviruses are implicated in many worldwide institutional, food and waterborne outbreaks each year. Genetic typing of isolates is valuable for monitoring outbreak spread as well as variation in circulating strains. Microarrays have the potential to provide rapid genotype information for norovirus samples. The NoroChip v3.0 provides an oligonucleotide hybridization platform to screen for over 600 potential interactions in each experiment. The NoroChip v3.0 was developed at Health Canada and validated in seven international partner laboratories. Each laboratory validated the NoroChip v3.0 using norovirus amplicons routinely characterized in their testing protocols. Fragments from the capsid region (region C) and a 2.4 kb amplicon spanning polymerase and capsid sequences (region AD) were validated in six of the partner laboratories and provided correct genogroup typing information (GI or GII) when hybridized to the NoroChip v3.0. Results indicate that the current limiting factor for implementing the NoroChip v3.0 as a strain typing tool is the difficulty obtaining a long, specific amplicon from all circulating norovirus strains. Data obtained with the longer region AD amplicon provided the best discrimination between norovirus strains.