Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce

Do animal husbandry operations contaminate groundwater sources with antimicrobial resistance: systematic review

Antimicrobial resistance (AMR) is a critical global health concern. Animal husbandry operations are AMR hotspots due to heavy antibiotic use and dissemination of animal waste into the environment. In this systematic review, we examined the impact of swine, poultry, and cattle operations on AMR in groundwater. We searched PubMed, Web of Science, CAB Direct, and the North Carolina State University Agricultural and Environmental Science databases in June 2022. The search returned 2487 studies. Of the 23 eligible studies, 17 were conducted in high-income countries (primarily the USA, also Canada, Saudi Arabia, Cyprus), and 6 were conducted in a single upper-middle-income country (China). Studies investigated facilities for swine (13), poultry (4), cattle (3), and multiple types of animals (3). The sampling distance ranged from onsite to > 20 km from facilities; the majority of studies (19) sampled onsite. Most studies collected samples from monitoring wells; only 5 studies investigated private drinking water wells. AMR in groundwater was associated with animal husbandry operations in 74% (17/23) of all studies, 65% (11/17) of studies in high-income countries, and 100% (6/6) of studies in China. Contamination was mostly found in onsite wells, especially downgradient of waste lagoons, but also in offsite private wells up to 2-3 km away. Few studies reported weather data, but AMR contamination appeared to increase with rainy conditions. Future studies should sample private wells at varying distances from animal husbandry operations under different weather conditions and include low- and middle-income countries where food animal production is intensifying.

Risk assessment of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa in environmental water sources: Development of surrogate models for antibiotic resistance genes

The presence of Enterococcus faecium (E. faecium), Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), and the aminoglycoside resistance genes, aac(6')-Ib and aac(6')-aph(2″), was investigated in environmental water sources obtained from informal settlements in the Western Cape (South Africa). Using ethidium monoazide bromide quantitative polymerase chain reaction (EMA-qPCR) analysis, E. faecium, K. pneumoniae, and P. aeruginosa were detected in 88.9 %, 100 %, and 93.3 % of the samples (n = 45), respectively, with a significantly higher mean concentration recorded for K. pneumoniae (7.83 × 104 cells/100 mL) over the sampling period. The aac(6')-Ib gene was detected in 95.6 % (43/45) of the environmental water samples [mean concentration of 7.07 × 106 gene copies (GC)/100 mL], while the aac(6')-aph(2″) gene was detected in 100 % (n = 45) of the samples [mean concentration of 6.68 × 105 GC/100 mL]. Quantitative microbial risk assessment (QMRA) subsequently indicated that the risks posed by K. pneumoniae and P. aeruginosa were linked to intentional drinking, washing/bathing, cleaning of the home, and swimming, in the samples collected from the various sampling sites. Surrogate risk assessment models were then designed and applied for Gram-positive [aac(6')-aph(2″) gene] and Gram-negative [aac(6')-Ib gene] pathogens that may exhibit aminoglycoside resistance. The results indicated that only the Gram-negative pathogens posed a risk (>10-4) in all the samples for cleaning of the home and intentional drinking, as well as for washing laundry by hand, garden hosing, garden work, washing/bathing, accidental consumption, and swimming at the stream and marsh sites. Thus, while environmental waters may pose a health risk of exposure to pathogenic bacteria, the results obtained indicate that screening for antibiotic resistant genes, associated with multiple genera/species, could serve as a surrogate model for estimating risks with the target group under investigation.

Cyanotoxins in groundwater; occurrence, potential sources, health impacts and knowledge gap for public health

Groundwater is a significant source of water across the world and constitutes about 30% of the earth's freshwater. This water source is likely to be contaminated by cyanobacteria that produce secondary metabolites called cyanotoxins. Studies on contamination of groundwater by cyanobacteria have been sketchy with limited information. There is a need for better evidence regarding groundwater contamination by cyanobacteria as their presence in surface water bodies could cause contamination of groundwater via infiltration and percolation during rainfall events or during groundwater-surface water interaction, bank infiltration or water quality exchange. Therefore, this review is aimed at exploring the occurrences and potential sources of cyanotoxins in groundwater. This was achieved by summarising the existing data on the occurrence of cyanobacteria in groundwater and their potential sources across the world. Groundwater cyanobacteria contamination can possibly pose threat to water quality because many of the cyanotoxins produced by cyanobacteria pose a severe threat to human health, animals and the environment. Concentrations of microcystins (MCs) in groundwater have been recorded in China (Chaohu), Saudi Arabia, and China (Huai River Basin), with concentrations of 1.446 μg/L, 1.8  μg/L and 1.07 μg/L, respectively. In humans, exposure to these cyanotoxins can cause symptoms such as vomiting, diarrhea, and skin irritation, to mention a few. This work highlights the importance of providing information or knowledge regarding public health implications of exposure to groundwater contaminated with cyanotoxins and the need to undertake risk management actions through national and international regulation. This review also points out current knowledge gaps, which could lead to future research.

Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples

BACKGROUND

Microbial community samples have been accumulating at a speed faster than ever, with hundreds of thousands of samples been sequenced each year. Mining such a huge amount of multisource heterogeneous data is becoming an increasingly difficult challenge, so efficient and accurate compare and search of samples is in urgent need: faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy.

FINDINGS

Here we proposed Meta-Prism 2.0, a microbial community sample analysis method that has pushed the time and memory efficiency to a new limit without compromising accuracy. Based on sparse data structure, time-saving instruction pipeline, and SIMD optimization, Meta-Prism 2.0 has enabled ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Meta-Prism 2.0 was put to test on several data sets, with the largest containing 1 million samples. Results show that Meta-Prism 2.0's 0.00001-s per sample pair compare speed and 8-GB memory needs for searching against 1 million samples have made it one of the most efficient sample analysis methods. Additionally, Meta-Prism 2.0 can achieve accuracy comparable with or better than other contemporary methods. Third, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking. Finally, we have provided a web server for fast search of microbial community samples online.

CONCLUSIONS

In summary, Meta-Prism 2.0 has changed the resource-intensive sample search scheme to an effective procedure, which could be conducted by researchers every day even on a laptop, for insightful sample search, similarity analysis, and knowledge discovery. Meta-Prism 2.0 can be accessed at https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0, and the web server can be accessed at https://hust-ningkang-lab.github.io/Meta-Prism-2.0/.

An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.

Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches

The taxonomic structure of microbial community sample is highly habitat-specific, making source tracking possible, allowing identification of the niches where samples originate. However, current methods face challenges when source tracking is scaled up. Here, we introduce a deep learning method based on the Ontology-aware Neural Network approach, ONN4MST, for large-scale source tracking. ONN4MST outperformed other methods with near-optimal accuracy when source tracking among 125,823 samples from 114 niches. ONN4MST also has a broad spectrum of applications. Overall, this study represents the first model-based method for source tracking among sub-million microbial community samples from hundreds of niches, with superior speed, accuracy, and interpretability. ONN4MST is available at https://github.com/HUST-NingKang-Lab/ONN4MST.

Administration of the Probiotic Escherichia coli Strain A0 34/86 Resulted in a Stable Colonization of the Human Intestine During the First Year of Life

Colinfant New Born (CNB) is an orally administered probiotic preparation containing the Escherichia coli strain A0 34/86, which is specially marketed for use in newborns and infants. Although the impact of different probiotics on the composition of the human gut microbiota has been previously described, the effects of E. coli probiotic consumption during infancy on the development of intestinal microbiota are not known. The effect of oral administration of CNB on the Enterobacteriaceae population was mapped using 16S rRNA gene sequencing in DNA samples isolated from the stools of one infant collected at 177 different time points during the first year of life. E. coli strains turnover was analyzed based on the detection of 26 genetic determinants, phylogroups, and pulsed-field gel electrophoresis (PFGE) analysis. Administration of CNB during the second and third month of life introduced the Escherichia genus to the infant's intestinal tract, and Escherichia became dominant among the Enterobacteriaceae family (p < 0.01). Genetic determinants, typical for probiotic E. coli A0 34/86 strain, were detected on the first day after application of CNB and persisted all year. In addition, nine transient E. coli strains were identified; these strains harbored different genetic determinants and showed different PFGE profiles. Transient strains were detected from 2 to 24 days in the stool samples. The first Escherichia colonizer originated from the application of the CNB probiotic preparation. Probiotic E. coli A0 34/86 successfully colonized the intestinal tract of an infant and became resident during the first year of life.

Mycotoxin-contaminated food and feed in Saudi Arabia: review of occurrence and toxicity

Introduction. Mycotoxins are reported to have a considerable impact on the health of consumers. There has been plentiful research into the effects of mycotoxins, fungi, and bacteria on the safety and quality of food and feed. This research paper reviews the literature on mycotoxins. Study objects and methods. The study focused on mycotoxins in food and feed produced in Saudi Arabia. We reviewed literature on the occurrence and health impacts of foodborne mycotoxins. We also studied the presence of mycotoxins in herbs, nuts, cereals, dried fruits and vegetables, infant formulas and baby foods, as well as dairy products. Finally, the paper offers a review of mycotoxin analysis methods. Results and discussion. The findings showed that mycotoxins attract a lot of scientific interest in Saudi Arabia. Certain types of mycotoxins (zearalenone, aflatoxins) and fungi (Aspergillus flavus, Penicillium chrysogenum, and Aspergillus niger) were common in the samples (isolates) of products tested in the Saudi regions. Furthermore, the researchers used different techniques of analysis such as the HPLC method, dilution plate method, thin layer chromatography, total plate count method, and seed-plate method to detect, identify, and isolate mycotoxins. Conclusion. Most importantly, the results showed that mycotoxins have serious health impacts on consumers and most of the contamination cases are caused by improper storage conditions and/or inappropriate handling and harvesting practices.

EMA-amplicon-based sequencing informs risk assessment analysis of water treatment systems

Illumina amplicon-based sequencing was coupled with ethidium monoazide bromide (EMA) pre-treatment to monitor the total viable bacterial community and subsequently identify and prioritise the target organisms for the health risk assessment of the untreated rainwater and rainwater treated using large-volume batch solar reactor prototypes installed in an informal settlement and rural farming community. Taxonomic assignments indicated that Legionella and Pseudomonas were the most frequently detected genera containing opportunistic bacterial pathogens in the untreated and treated rainwater at both sites. Additionally, Mycobacterium, Clostridium sensu stricto and Escherichia/Shigella displayed high (≥80%) detection frequencies in the untreated and/or treated rainwater samples at one or both sites. Numerous exposure scenarios (e.g. drinking, cleaning) were subsequently investigated and the health risk of using untreated and solar reactor treated rainwater in developing countries was quantified based on the presence of L. pneumophila, P. aeruginosa and E. coli. The solar reactor prototypes were able to reduce the health risk associated with E. coli and P. aeruginosa to below the 1 × 10^-4 annual benchmark limit for all the non-potable uses of rainwater within the target communities (exception of showering for E. coli). However, the risk associated with intentional drinking of untreated or treated rainwater exceeded the benchmark limit (E. coli and P. aeruginosa). Additionally, while the solar reactor treatment reduced the risk associated with garden hosing and showering based on the presence of L. pneumophila, the risk estimates for both activities still exceeded the annual benchmark limit. The large-volume batch solar reactor prototypes were thus able to reduce the risk posed by the target bacteria for non-potable activities rainwater is commonly used for in water scarce regions of sub-Saharan Africa. This study highlights the need to assess water treatment systems in field trials using QMRA.

Hospital wastewaters: A reservoir and source of clinically relevant bacteria and antibiotic resistant genes dissemination in urban river under tropical conditions

The occurrence and dissemination of antibiotic resistant genes (ARGs) that are associated with clinical pathogens and the evaluation of associated risks are still under-investigated in developing countries under tropical conditions. In this context, cultivable and molecular approaches were performed to assess the dissemination of bacteria and the antibiotic resistance genes in aquatic environment in Kinshasa, Democratic Republic of the Congo. Cultivable approach quantified β-lactam, carbapenem resistant, and total Escherichia coli and Enterobacteriaceae in river sediments and surface waters that receive raw hospital effluents. The molecular approach utilized Quantitative Polymerase Chain Reaction (qPCR) to quantify the total bacteria and the richness of relevant bacteria (Escherichia coli, Enterococcus, and Pseudomonas), and antibiotic resistance genes (ARGs: bla_OXA-48, bla_CTX-M, bla_IMP, bla_TEM) in sediment samples. Statistical analysis were employed to highlight the significance of hospital contribution and seasonal variation of bacteria and ARGs into aquatic ecosystems in suburban municipalities of Kinshasa, Democratic Republic of the Congo. The contribution of hospitals to antibiotic resistance proliferation is higher in the dry season than during the wet season (p < 0.05). Hospital similarly contributed Escherichia coli, Enterococcus, and Pseudomonas and ARGs significantly to the sediments in both seasons (p < 0.05). The organic matter content correlated positively with E. coli (r = 0.50, p < 0.05). The total bacterial load correlated with Enterococcus, and Pseudomonas (0.49 < r < 0.69, p < 0.05). Each ARG correlated with the total bacterial load or at least one relevant bacteria (0.41 < r < 0.81, p < 0.05). Our findings confirm that hospital wastewaters contributed significantly to antibiotic resistance profile and the significance of this contribution increased in the dry season. Moreover, our analysis highlights this risk from untreated hospital wastewaters in developing countries, which presents a great threat to public health.

Employing indicator-based geostatistics and quantitative microbial risk analysis to assess the health risks of groundwater use for household demands on the Pingtung Plain, Taiwan

Because of the limited surface water on the Pingtung Plain, Taiwan, the plain's residents frequently extract groundwater to meet their daily household water demands. The residents may experience gastrointestinal infections due to incidental ingestion of groundwater with fecal pollution. This study used indicator kriging (IK) and quantitative microbial risk analysis (QMRA) to assess the health risks of using groundwater for household cleaning and horticultural irrigation on the Pingtung Plain. First, IK was employed to determine the conditional cumulative distribution function (CCDF) of groundwater Escherichia coli (E. coli). Nonparametric Monte Carlo simulation based on established CCDF was then adopted to characterize the distributions and uncertainty of groundwater E. coli. Finally, QMRA was employed to determine health risks of groundwater use for household cleaning and horticultural irrigation, and the 95th percentiles of the risk distributions were calculated to obtain a representative risk. The study results indicated that the health risks of groundwater use ranged from 3.95 × 10^-5 to 2.49 × 10^-2 infections/user/year and exceeded the acceptable level, 1 × 10^-4 infections/user/year, in most of the aquifers. Accordingly, residents of this plain should not directly extract groundwater for use in daily life.

Assessment of Major and Trace Elements in Drinking Groundwater in Bisha Area, Saudi Arabia

Drinking groundwater represents 30% of the world’s fresh water and 0.9% of the whole world’s water. Therefore, routine analysis and monitoring of the groundwater is a paramount issue, specifically the measurement of elemental concentrations due to aquifer characterization. Consequently, the purpose of this study was to determine major and trace elements in groundwater. In total, 25 samples of groundwater were collected from wells in the Bisha area, Asir province, Saudi Arabia. All samples were analyzed for major and trace elements by using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). In total, 15 elements were measured including four major elements (Na, K, Mg, and Ca) and 11 trace elements (V, Cr, Mn, Co, Ni, Cu, Zn, As, Se, Cd, and Pb). Major elements (Na, Mg, and Ca) exceeded the guideline limits in some samples. In addition, only one trace element (Se) exceeded the World Health Organization (WHO) permissible limits in some samples. This could be due to rock characteristics in aquifers. Very hard water was shown in 92% of the samples. Moreover, a high percentage (32%) of the analyzed samples also exceeded the guideline levels for chloride. ANOVA analysis showed significant difference (p<0.05) between Bisha samples (North and South), Bisha samples (North), and the remaining samples, for V and pH, and Na, Cl−, EC, and TDS, respectively. No significant differences (p>0.05) were reported for Na, K, Mg, Ca, Cr, Mn, Co, Ni, Cu, Zn, As, Se, Cd, and Pb between all samples. In general, 25 significant (p>0.05) correlations were reported among the measured elements. For the positive correlations, similar distribution for the elements is anticipated. In conclusion, the groundwater in this study is not suitable for domestic use due to its hardness and only some are suitable for irrigation. More studies are needed to confirm our findings in the study area.

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Delineating the origins of the multidrug-resistant pathogens in ornamental fish farms by multilocus sequence typing and identification of a novel multidrug-resistant plasmid

To evaluate the overuse of antibiotics and to identify the origin of pathogens in the ornamental fish industry, we conducted a field investigation of three representative fish farms in Liaoning province, China. Drug-resistant pathogens in the fishponds and groundwater were isolated and subtyped by multilocus sequence typing (MLST). In total, 33 pathogenic strains, including Aeromonas veronii and five other pathogens, were isolated from diseased fish and from groundwater. MLST revealed that A. veronii obtained from diseased fish in three fish farms can be subtyped into four sequence types, which were also identified in the corresponding groundwater. All of the isolates obtained from diseased fish showed resistance to at least four antibiotics. Notably, Citrobacter freundii JY-17 exhibited resistance to the majority of the antibiotics and was a carrier of a megaplasmid with 15 drug resistance genes. PCR assays targeting β-lactam, kanamycin, macrolide, phenicol, sulfonamide, and trimethoprim resistance genes in the pathogens from the diseased fish and groundwater were also conducted. The results revealed strong correlations between antibiotic treatment and increased antimicrobial resistance in fish pathogens. The results suggested that groundwater is the origin of the pathogens in ornamental fish. Antibiotic treatment of ornamental fish promoted the emergence of resistant pathogens.

Composition of gut microbiota in infants in China and global comparison

Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders. However, systematic investigation of the acquisition and development of gut microbial communities during early infancy are relatively rare, particularly for infants from non-Western countries. In this study, we characterize the colonization and development of infant microbiota in healthy Chinese infants and compare the pattern with those from other countries. The fecal microbiota of 2-month-old infants was considerably more diverse than that of neonates, as indicated by higher relative abundances of Veillonella, Clostridium, Bacteroides, Lactobacillus, Collinsella and Prevotella, and reduction of Escherichia and Enterococcus. The fecal microbiota of vaginally delivered infants (both neonates and 2-month-old) had significant enrichment of Bacteroides, Parabacteroides and Megamonas, whereas cesarean delivered infants had enrichment of Prevotella, Streptococcus and Trabulsiella. By global comparison, we identify three different enterotypes, referred as “P-type”, “A-type ”and “F-type” which were highly abundant in Proteobacteria, Actinobacteria and Firmicutes, respectively. The three enterotypes’ compositons vary geographically. All Chinese infants in our study belong to the P-type. These findings may provide novel insights into our understanding of the establishment of infant fecal bacterial communities.