Enteropathogens in Under-Five Children with Diarrhea in Health Facilities of Debre Berhan Town, North Shoa, Ethiopia

BACKGROUND: Diarrheal disease is a major cause of mortality and morbidity for under-five children in Ethiopia. The purpose of this study was to investigate the behavioral and socioeconomic risk factors, etiology, and drug susceptibility of bacteria isolated from under-five children with acute diarrhea who were treated at Debre Berhan Referral Hospital or Health Center in Ethiopia.METHODS: A health facility based cross-sectional study design was used to investigate enteropathogens from 163 under-five children with acute diarrhea. After obtaining written consent from parents or guardians, data were collected using a standardized questionnaire. Freshly passed stool samples were collected for microbiological tests for bacteria and parasites. The chi-square test was used for assessing the relationships of variables.RESULTS: Enteropathogens were detected among 55.8% (91/163) participants. There was a 46%(75/163) bacterial culture positivity rate and a 9.8%(16/163) prevalence of parasites. The isolated enteropathogens were Escherchia coli, Klebsiella specie, Proteus species, Salmonella species, Shigella species, Enterobacter species, Giardia lamblia, Enteameba histolytica, Ascaris lumbricoides, Trichuris trichiura and Hymnoleps nana. Level of antimicrobial resistance of bacterial isolates ranged from 0 to 87.2%. Poor hand washing and poor cleaning of feeding utensils showed significant association with the presence of enteropathogens.CONCLUSION: Bacterial enteropathogens with drug resistance were observed in this study. Continuous health education and promotion about diarrheal disease for mothers/caretakers and regular surveillance of entropathogenes are recommended to reduce under-five mortality.

Wastewater monitoring of SARS-CoV-2 in on-grid, partially and fully off-grid Bedouin communities in Southern Israel

BackgroundWastewater based epidemiology (WBE) has become an important tool in SARS-CoV-2 surveillance and epidemiology. While WBE measurements generally correlate with observed case numbers in large municipal areas on sewer grids, there are few studies on its utility in communities that are off-grid (non-sewered).Methods and materialsTo explore the applicability of wastewater surveillance in our region, five Bedouin communities along the Hebron Stream in Southern Israel (Negev desert) were sampled. One point (El-Sayed) represents a community with partial connection to the sewer grid system and another point (Um Batin) represents a community with no access to the sewer grid system. The towns of Hura, Lakia, and Tel Al-Sabi/Tel Sheva were on-grid. A total of 87 samples were collected between August 2020 to January 2021 using both grab and composite sampling. RNA was extracted from the raw sewage and concentrated sewage. RT-qPCR was carried out with N1, N2, and N3 gene targets, and findings were compared to human case data from the Israeli Ministry of Health.ResultsSARS-CoV-2 was detected consistently over time in on-grid Bedouin towns (Lakia, Tel Sheva/Tel as-Sabi, and Hura) and inconsistently in smaller, off-grid communities (El-Sayed and Um Batin). The trend in maximum copy number/L appears to be driven by population size. When comparing case numbers normalized to population size, the amount of gene copies/L was inconsistently related to reported case numbers. SARS-CoV-2 was also detected from sewage-impacted environmental waters representing communities with no access to the wastewater grid. When grab sampling and composite sampling data were compared, results were generally comparable however composite sampling produced superior results.ConclusionsThe mismatch observed between detected virus and reported cases could indicate asymptomatic or “silent” community transmission, under-testing within these communities (due to factors like mistrust in government, stigma, misinformation) or a combination therein. While the exact reason for the mismatch between environmental SARS-CoV-2 signals and case numbers remains unresolved, these findings suggest that sewage surveillance, including grab sampling methodologies, can be a critical aspect of outbreak surveillance and control in areas with insufficient human testing and off-grid communities

Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates

Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor database (VFDB) and in silico PCR (for the genes BetB, BPE275, BSPB, manA, mviN, omp19, perA, PrpA, VceC, and ureI) were used for identifying virulence genes, and a total of 61 virulence genes were identified in short-read, long-read, and hybrid assemblies of all 18 isolates. The phylogenetic analysis using long-read assemblies revealed several inconsistencies in cluster assignment as compared to using hybrid and short-read assemblies. Overall, hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. For genomic epidemiology studies, stand-alone ONP sequencing may require further refinement in order to be useful in endemic settings

Trends in neonicotinoid pesticide residues in food and water in the United States, 1999–2015

Abstract Background Neonicotinoids are a class of systemic insecticides widely used on food crops globally. These pesticides may be found in “off-target” food items and persist in the environment. Despite the potential for extensive human exposure, there are limited studies regarding the prevalence of neonicotinoid residues in foods sold and consumed in the United States. Methods Residue data for seven neonicotinoid pesticides collected between 1999 and 2015 by the US Department of Agriculture’s Pesticide Data Program (PDP) were collated and summarized by year across various food commodities, including fruit, vegetable, meat, dairy, grain, honey, and baby food, as well as water to qualitatively describe and examine trends in contamination frequency and residue concentrations. Results The highest detection frequencies (DFs) for neonicotinoids by year on all commodities were generally below 20%. Average DFs over the entire study period, 1999–2015, for domestic and imported commodities were similar at 4.5%. For all the samples (both domestic and imported) imidacloprid was the neonicotinoid with the highest overall detection frequency at 12.0%. However, higher DFs were observed for specific food commodity-neonicotinoid combinations such as: cherries (45.9%), apples (29.5%), pears (24.1%) and strawberries (21.3%) for acetamiprid; and cauliflower (57.5%), celery (20.9%), cherries (26.3%), cilantro (30.6%), grapes (28.9%), collard greens (24.9%), kale (31.4%), lettuce (45.6%), potatoes (31.2%) and spinach (38.7%) for imidacloprid. Neonicotinoids were also detected in organic commodities, (DF < 6%). Individual commodities with at least 5% of samples testing positive for two or more neonicotinoids included apples, celery, and cherries. Generally, neonicotinoid residues on food commodities did not exceed US Environmental Protection Agency tolerance levels. Increases in detection trends for both finished and untreated water samples for imidacloprid were observed from 2004 to 2011. Conclusions Analysis of PDP data indicates that low levels of neonicotinoids are present in commonly-consumed fruits and vegetables sold in the US. Trends in detection frequencies suggest an increase in use of acetamiprid, clothianidin and thiamethoxam as replacements for imidacloprid. Given these findings, more extensive surveillance of the food and water supply is warranted, as well as biomonitoring studies and assessment of cumulative daily intake in high risk groups, including pregnant women and infants

Biochar and zero-valent iron sand filtration simultaneously removes contaminants of emerging concern and Escherichia coli from wastewater effluent

Abstract Advanced treated municipal wastewater is an important alternative water source for agricultural irrigation. However, the possible persistence of chemical and microbiological contaminants in these waters raise potential safety concerns with regard to reusing treated wastewater for food crop irrigation. Two low-cost and environmentally-friendly filter media, biochar (BC) and zero-valent iron (ZVI), have attracted great interest in terms of treating reused water. Here, we evaluated the efficacy of BC-, nanosilver-amended biochar- (Ag-BC) and ZVI-sand filters, in reducing contaminants of emerging concern (CECs), Escherichia coli (E. coli) and total bacterial diversity from wastewater effluent. Six experiments were conducted with control quartz sand and sand columns containing BC, Ag-BC, ZVI, BC with ZVI, or Ag-BC with ZVI. After filtration, Ag-BC, ZVI, BC with ZVI and Ag-BC with ZVI demonstrated more than 90% (> 1 log) removal of E. coli from wastewater samples, while BC, Ag-BC, BC with ZVI and Ag-BC with ZVI also demonstrated efficient removal of tested CECs. Lower bacterial diversity was also observed after filtration; however, differences were marginally significant. In addition, significantly (p < 0.05) higher bacterial diversity was observed in wastewater samples collected during warmer versus colder months. Leaching of silver ions occurred from Ag-BC columns; however, this was prevented through the addition of ZVI. In conclusion, our data suggest that the BC with ZVI and Ag-BC with ZVI sand filters, which demonstrated more than 99% removal of both CECs and E. coli without silver ion release, may be effective, low-cost options for decentralized treatment of reused wastewater. Graphical Abstrac

Longitudinal Assessment of the Dynamics of Escherichia coli, Total Coliforms, Enterococcus spp., and Aeromonas spp. in Alternative Irrigation Water Sources: a CONSERVE Study.

As climate change continues to stress freshwater resources, we have a pressing need to identify alternative (nontraditional) sources of microbially safe water for irrigation of fresh produce. This study is part of the center CONSERVE, which aims to facilitate the adoption of adequate agricultural water sources. A 26-month longitudinal study was conducted at 11 sites to assess the prevalence of bacteria indicating water quality, fecal contamination, and crop contamination risk (Escherichia coli, total coliforms [TC], Enterococcus, and Aeromonas). Sites included nontidal freshwater rivers/creeks (NF), a tidal brackish river (TB), irrigation ponds (PW), and reclaimed water sites (RW). Water samples were filtered for bacterial quantification. E. coli, TC, enterococci (∼86%, 98%, and 90% positive, respectively; n = 333), and Aeromonas (∼98% positive; n = 133) were widespread in water samples tested. Highest E. coli counts were in rivers, TC counts in TB, and enterococci in rivers and ponds (P &lt; 0.001 in all cases) compared to other water types. Aeromonas counts were consistent across sites. Seasonal dynamics were detected in NF and PW samples only. E. coli counts were higher in the vegetable crop-growing (May-October) than nongrowing (November-April) season in all water types (P &lt; 0.05). Only one RW and both PW sites met the U.S. Food Safety Modernization Act water standards. However, implementation of recommended mitigation measures of allowing time for microbial die-off between irrigation and harvest would bring all other sites into compliance within 2 days. This study provides comprehensive microbial data on alternative irrigation water and serves as an important resource for food safety planning and policy setting.IMPORTANCE Increasing demands for fresh fruit and vegetables, a variable climate affecting agricultural water availability, and microbial food safety goals are pressing the need to identify new, safe, alternative sources of irrigation water. Our study generated microbial data collected over a 2-year period from potential sources of irrigation (rivers, ponds, and reclaimed water sites). Pond water was found to comply with Food Safety Modernization Act (FSMA) microbial standards for irrigation of fruit and vegetables. Bacterial counts in reclaimed water, a resource that is not universally allowed on fresh produce in the United States, generally met microbial standards or needed minimal mitigation. We detected the most seasonality and the highest microbial loads in river water, which emerged as the water type that would require the most mitigation to be compliant with established FSMA standards. This data set represents one of the most comprehensive, longitudinal analyses of alternative irrigation water sources in the United States

Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation

Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future

Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study

Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p &lt; 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions