Nationwide surveillance for pathogenic microorganisms in groundwater near carcass burials constructed in South Korea in 2010

Burying poultry carcasses on farms as a disposal option in crisis situations: learnings and perspectives from a field study during an avian influenza epizootic in France

Appropriate disposal of dead farming animals is required to guarantee effective disease control while protecting the environment. In crisis situations, alternatives to rendering can be used, including on-farm burial. The objectives of this study were to: (i) describe the burial and monitoring protocols used on poultry farms in France in response to major avian influenza outbreaks; (ii) assess the effectiveness of the burial protocol, in terms of both technical and biosecurity aspects, and microbiological, physical and chemical changes of the buried materials and the environment over time; (iii) provide recommendations for future burial and follow-up protocols. Five on-farm burial sites were monitored between March 2022 and March 2023, with at least four visits per farm. In addition to visual observations, soil, leachate, air and drilling water samples were collected, as well as boot swabs on/near the pit or on carcasses. For all five farms, microbiological analyses were performed to detect avian influenza virus (AIV), Clostridium botulinum and Salmonella spp. At one site, sampled drilling water was analysed to describe its physical and chemical properties. Visual anomalies were found at the sites over time, such as subsidence of the pits, presence of traces of wild and domestic animals, and rising to the surface of pieces of carcasses and feathers. AIV RNA was detected at all burial sites and in 4 % (8/201) of the collected samples. Viral genome was found up to nine months after burial on one farm. Clostridium botulinum was detected in 16 % (19/117) of the samples, whereas all samples tested negative for Salmonella spp. (0/109) at all sites and at all sampling points. All drilling water samples were compliant with drinking water standards. Our assessments demonstrated how the burial pits changed over time and the need to monitor them regularly so that corrective measures can be taken, if needed. In conclusion, our study can be used as a baseline for preparing better burial and follow-up protocols for future crisis situations. We recommend to standardise trench size and depth, to add mounding soil to the top of the pit and to set up a fence around. Proper pre-planning in peacetime will make it easier to meet the challenges associated with the management of repeated, high-frequency crises or crises of a new nature.

Occurrence of human pathogenic viruses in drinking water and in its sources: A review

Since many waterborne diseases are caused by human pathogenic viruses, virus monitoring of drinking water (DW) and DW sources is crucial for public health. Therefore, the aim of this review was to describe the occurrence of human pathogenic viruses in DW and DW sources; the occurrence of two viruses proposed as novel indicators of human faecal contamination (Pepper mild mottle virus and Tobacco mosaic virus) was also reported. This research was focused on articles that assessed viral occurrence using molecular methods in the surface water used for DW production (SW-D), groundwater used for DW production (GW-D), DW and bottled-DW (BW). A total of 1544 studies published in the last 10 years were analysed, and 79 were ultimately included. In considering the detection methods, filtration is the most common concentration technique, while quantitative polymerase chain reaction is the most common quantification technique. Regarding virus occurrence in SW-D, GW-D, and DW, high percentages of positive samples were reported for adenovirus, polyomavirus and Pepper mild mottle virus. Viral genomes were frequently detected in SW-D and rarely in GW-D, suggesting that GW-D may be a safe DW source. Viral genomes were also detected in DW, posing a possible threat to human health. The lowest percentages of positive samples were found in Europe, while the highest were found in Asia and South America. Only three articles assessed viral occurrence in BW. This review highlights the lack of method standardization and the need for legislation updates.

A supervised machine learning approach to discriminate the effect of carcass leachate on shallow groundwater quality around on-farm livestock mortality burial sites

The evaluation of leachate leakage at livestock mortality burial sites is challenging, particularly when groundwater is previously contaminated by agro-livestock farming. Supervised machine learning was applied to discriminate the impacts of carcass leachate from pervasive groundwater contamination in the following order: data labeling, feature selection, synthetic data generation, and classification. Physicochemical data of 359 water samples were collected from burial pits (LC), monitoring wells near pits (MW), pre-existing shallow household wells (HW), and background wells with pervasive contamination (BG). A linear classification model was built using two representative groups (LC and BG) affected by different pollution sources as labeled data. A classifier was then applied to assess the impact of leachate leakage in MW and HW. As a result, leachate impacts were observed in 40% of MW samples, which indicates improper construction and management of some burial pits. Leachate impacts were also detected in six HW samples, up to 120 m downgradient, within one year. The quantitative decision-making tool to diagnose groundwater contamination with leachate leakage can contribute to ensuring timely responses to leakage. The proposed machine learning approach can also be used to improve the environmental impact assessment of water pollution by improper disposal of organic waste.

Animal carcass burial management: implications for sustainable biochar use

This review focuses on existing technologies for carcass and corpse disposal and potential alternative treatment strategies. Furthermore, key issues related to these treatments (e.g., carcass and corpse disposal events, available methods, performances, and limitations) are addressed in conjunction with associated environmental impacts. Simultaneously, various treatment technologies have been evaluated to provide insights into the adsorptive removal of specific pollutants derived from carcass disposal and management. In this regard, it has been proposed that a low-cost pollutant sorbent may be utilized, namely, biochar. Biochar has demonstrated the ability to remove (in)organic pollutants and excess nutrients from soils and waters; thus, we identify possible biochar uses for soil and water remediation at carcass and corpse disposal sites. To date, however, little emphasis has been placed on potential biochar use to manage such disposal sites. We highlight the need for strategic efforts to accurately assess biochar effectiveness when applied towards the remediation of complex pollutants produced and circulated within carcass and corpse burial systems.

Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review

Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a "safe" drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.

Challenges and opportunities for using national animal datasets to support foot-and-mouth disease control

National level databases of animal numbers, locations and movements provide the essential foundations for disease preparedness, outbreak investigations and control activities. These activities are particularly important for managing and mitigating the risks of high-impact transboundary animal disease outbreaks such as foot-and-mouth disease (FMD), which can significantly affect international trade access and domestic food security. In countries where livestock production systems are heavily subsidized by the government, producers are often required to provide detailed animal movement and demographic data as a condition of business. In the remaining countries, it can be difficult to maintain these types of databases and impossible to estimate the extent of missing or inaccurate information due to the absence of gold standard datasets for comparison. Consequently, competent authorities are often required to make decisions about disease preparedness and control based on available data, which may result in suboptimal outcomes for their livestock industries. It is important to understand the limitations of poor data quality as well as the range of methods that have been developed to compensate in both disease-free and endemic situations. Using FMD as a case example, this review first discusses the different activities that competent authorities use farm-level animal population data for to support (1) preparedness activities in disease-free countries, (2) response activities during an acute outbreak in a disease-free country, and (3) eradication and control activities in an endemic country. We then discuss (4) data requirements needed to support epidemiological investigations, surveillance, and disease spread modelling both in disease-free and endemic countries.

Nationwide groundwater monitoring around infectious-disease-caused livestock mortality burials in Korea: Superimposed influence of animal leachate on pre-existing anthropogenic pollution

A foot-and-mouth disease (FMD) outbreak during 2010 affected the entire country of South Korea and approximately 3.4 million swine and bovine mortalities were disposed of at approximately 4800 on-farm burial sites for a few months following the first outbreak. Furthermore, outbreaks of avian influenza (AI) have struck Korea consistently since 2014. Public concern regarding the deterioration of the surrounding environment has been raised aiming at the enormous infected animal carcass burials. On behalf of the Ministry of Environment (ME) of the Korean government, we conducted groundwater monitoring at approximately 3000 wells around the burial sites for 7 years from 2011 to 2017. The baseline groundwater already had enriched levels of nitrogen and chloride compounds masking the influence of leachate with the pre-existing anthropogenic contamination. Based on the trend analysis, most monitoring wells had no significant trends in NO₃-N and Cl implying that an abrupt degradation in water quality was not expected across the country. Increasing proportions of total coliform detection in the groundwater of the majority of provinces will cause potential damage to human health around the carcass burial sites. Wells showing frequent upward and downward trends near the carcass burial pits were targeted for principal component analysis (PCA) and the results showed that NH₄-N, TOC, Cl, and K could be indicators distinguishing the sole impacts of animal leachate on the groundwater. Analyses of the nationwide monitoring data indicated possibly delayed and prolonged impacts of the widespread burials of livestock mortalities on the groundwater environment. The finding provides realistic insight regarding how to manage the mass burial of livestock mortalities to protect groundwater resources.

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure

We investigated the impacts of leachates from a swine carcass burial site and a cow manure heap on the geochemical and microbiological properties of agricultural water samples, including leachate, groundwater from monitoring wells and background wells, and stream water. The leachate from the livestock burial site showed extremely high electrical conductivity, turbidity, and major ion concentrations, but low redox potential and dissolved oxygen levels. The groundwater in the monitoring wells adjacent to both sites showed severe contamination from the leachate, as indicated by the increases in EC, turbidity, Cl^-, and SO₄^2-. Bacteria from the phylum Firmicutes and Bacteriodetes and Archaea from the phylum Euryarchaeota were the major phyla in both the leachates and manure heap. However, the class- or genus-level components of these phyla differed markedly between the leachate and manure heap samples. The relative abundance of Firmicutes decreased from 35% to 0.3~13.9% in the monitoring wells and background wells at both sites. The Firmicutes in these wells was unlikely to have originated from the transportation of leachate to the surrounding environment because Firmicutes genera differed drastically between the leachate and monitoring wells. Meanwhile, sulfate-reducing bacteria (SRB) from the livestock carcass burial site were detected in the monitoring wells close to the leachate. This was likely because the release of carcass decomposition products, such as organic acids, to adjacent areas improved the suitability of the local environments for SRB, which were not abundant in the leachate. This study highlights the need to better understand microbial community dynamics along groundwater flow paths to evaluate bacterial transport in subsurface environments and provides new insights into the effective management of groundwater quality at both farm and regional scales.

Effects of solids retention time on the fate of tetracycline resistance in SBRs for the treatment of carcass leachate

In the event of a foot and mouth disease outbreak, further spread of the virus is generally prevented by culling of infected animals in burial pits. This practice may eventually lead to groundwater contamination through leaching of wastewater from the animal carcasses. Wastewater from carcass leachate often contains antibiotic resistant bacteria and genes as well as traces of pharmaceuticals, and a high nutrient content. The role of operational parameters used in activated sludge treatment of this wastewater in the spread of antibiotic resistance has not been fully understood. This study investigated the fate of tetracycline-resistant bacteria and genes in sequencing batch reactors with synthetic carcass leachate at different solid retention times. Escherichia coli DH5α was used as the representative tetracycline-resistant bacteria with multiple antibiotic-resistant genes encoded in plasmid pB10. Solids retention time contributed to an increase in antibiotic resistance in SBRC (SRT = 25 days) with TRB values up to 1.25 × 10(7) CFU/mL which is one log higher than the influent. Microbial community analysis of the DNA samples from effluent of SBRC showed four major phyla: Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria under which are ecologically-important microbial species. It was shown that antibiotic resistance genes cannot be eliminated during treatment of synthetic carcass leachate in a lab-scale sequencing batch reactor.

Distribution of Human Norovirus in the Coastal Waters of South Korea

The presence of human norovirus in the aquatic environment can cause outbreaks related to recreational activities and the consumption of norovirus-contaminated clams. In this study, we investigated the prevalence of norovirus genogroups I (GI) and II (GII) in the coastal aquatic environment in South Korea (March 2014 to February 2015). A total of 504 water samples were collected periodically from four coastal areas (total sites = 63), of which 44 sites were in estuaries (clam fisheries) and 19 were in inflow streams. RT-PCR analysis targeting ORF2 region C revealed that 20.6% of the water samples were contaminated by GI (13.3%) or GII (16.6%). The prevalence of human norovirus was higher in winter/spring than in summer/fall, and higher in inflow streams (50.0%) than in estuaries (7.9%). A total of 229 human norovirus sequences were identified from the water samples, and phylogenetic analysis showed that the sequences clustered into eight GI genotypes (GI.1, 2, 3, 4, 5, 6, 7, and 9) and nine GII genotypes (GII.2, 3, 4, 5, 6, 11, 13, 17, and 21). This study highlighted three issues: 1) a strong correlation between norovirus contamination via inflow streams and coastal areas used in clam fisheries; 2) increased prevalence of certain non-GII.4 genotypes, exceeding that of the GII.4 pandemic variants; 3) seasonal shifts in the dominant genotypes of both GI and GII.

Molecular epidemiology of norovirus in South Korea

Norovirus is a major cause of viral gastroenteritis and a common cause of foodborne and waterborne outbreaks. Norovirus outbreaks are responsible for economic losses, most notably to the public health and food industry field. Norovirus has characteristics such as low infectious dose, prolonged shedding period, strong stability, great diversity, and frequent genome mutations. Besides these characteristics, they are known for rapid and extensive spread in closed settings such as hospitals, hotels, and schools. Norovirus is well known as a major agent of food-poisoning in diverse settings in South Korea. For these reasons, nationwide surveillance for norovirus is active in both clinical and environmental settings in South Korea. Recent studies have reported the emergence of variants and novel recombinants of norovirus. In this review, we summarized studies on the molecular epidemiology and nationwide surveillance of norovirus in South Korea. This review will provide information for vaccine development and prediction of new emerging variants of norovirus in South Korea.

Development of enhanced primer sets for detection of norovirus

Norovirus (NV) is a major viral pathogen that causes nonbacterial acute gastroenteritis and outbreaks of food-borne disease. The genotype of NV most frequently responsible for NV outbreaks is GII.4, which accounts for 60–80% of cases. Moreover, original and new NV variant types have been continuously emerging, and their emergence is related to the recent global increase in NV infection. In this study, we developed advanced primer sets (NKI-F/R/F2, NKII-F/R/R2) for the detection of NV, including the variant types. The new primer sets were compared with conventional primer sets (GI-F1/R1/F2, SRI-1/2/3, GII-F1/R1/F2, and SRII-1/2/3) to evaluate their efficiency when using clinical and environmental samples. Using reverse transcription polymerase chain reaction (RT-PCR) and seminested PCR, NV GI and GII were detected in 91.7% (NKI-F/R/F2), 89.3% (NKII-F/R/R2), 54.2% (GI-F1/R1/F2), 52.5% (GII-F1/R1/F2), 25.0% (SRI-1/2/3), and 32.2% (SRII-1/2/3) of clinical and environmental specimens. Therefore, our primer sets perform better than conventional primer sets in the detection of emerged types of NV and could be used in the future for epidemiological diagnosis of infection with the virus.