Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing

The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.

Advances in nitrogen removal and recovery technologies from reject water: Economic and environmental perspectives

This review critically assesses nitrogen removal technologies applied in the reject water treatment, across different stages of technological development, with a focus on their economic and environmental impacts. The prevalent use of biological processes raises concerns due to potential environmental impacts caused by N2O emissions. However, partial nitritation-anaerobic ammonium oxidation demonstrated economic benefits and the potential for positive environmental outcomes when properly operated and controlled. Furthermore, reject water, in many cases, provides sufficient nitrogen concentrations for nitrogen recovery processes, such as ammonia stripping, substituting production of industrial fertilizers and contributing to a circular economy. Nonetheless, their financial competitiveness is subject to various conditions, including the nitrogen concentration or reject water flow. As the environmental benefits of bioprocesses and economic benefits of nitrogen recovery processes may vary, it is crucial to further optimize both and investigate novel promising technologies such as electrochemical systems, denitrifying anaerobic methane oxidation or direct ammonia oxidation.

Monitoring of monkeypox viral DNA in Prague wastewater

Monkeypox virus (Mpxv) is a dsDNA virus that has become a global concern for human health in 2022. As both infected people and non-human hosts can shed the virus from their skin, faeces, urine and other body fluids, and the resulting sewage contains viral load representative of the whole population, it is highly promising to detect the spread of monkeypox virus in municipal wastewater. We established a methodology for sewage-based monitoring of Mpxv in Prague and analysed samples (n = 24) already early August-October of 2022 in a municipality with 1.4 million inhabitants that only reported 29 cumulative cases in this period. We isolated Mpxv DNA with the Wizard Enviro Total Nucleic Acid Kit, and thereafter detected Mpxv DNA using the EliGene® Monkeypox RT-PCR Kit. Prague wastewater was positive for Mpxv (in total 9 positive samples in periods with 1-9 new cases per week, coinciding with a weekly incidence of 0.07-0.64 per 100,000 inhabitants. The method for confirmation of wastewater positivity via semi-nested PCR and Sanger sequencing was successfully confirmed on positive controls including Mpxv particles and Mpxv-positive wastewater from the Netherlands. However, for Prague wastewater samples, amplification of Mpxv DNA via semi-semi-nested PCR was unsuccessful. This was probably due to extremely low case count, leading to the amplification of non-target bacterial DNA. Compared to other studies with much higher Mpxv prevalence, we show the outstanding sensitivity of our approach for monitoring the spread of monkeypox using wastewater.

Synergistic removal of pharmaceuticals and antibiotic resistance from ultrafiltered WWTP effluent: Free-floating ARGs exceptionally susceptible to degradation

To protect the environment and human health, antibiotic resistance genes (ARGs) and persistent pharmaceuticals need to be removed from WWTP effluent prior to its reuse. However, an efficient process for removing free-floating extracellular DNA (exDNA) in combination with a wide range of pharmaceuticals is yet to be reported for real process conditions. As a possible solution, we treated real ultrafiltered WWTP effluent with UV/H₂O₂ and combined GAC and zeolite sorption. In terms of exDNA, sequencing and high-throughput quantitative PCR (HT-qPCR) showed that exDNA is a potent carrier of numerous ARGs in ultrafiltered WWTP effluent (123 ARGs), including multi-drug efflux pump mexF that became the dominant exARG in GAC effluent over time. Due to the exposure to degradation agents, exDNA was reduced more efficiently than intracellular DNA, and overall levels of ARGs were substantially lowered. Moreover, GAC sorption was particularly effective in the removal of almost all the 85 detected pharmaceutical residues, with fresh GAC demonstrating an efficiency of up to 100%. However, zeolite (Si/Al 0.8) addition was needed to enhance the removal of persistent pollutants such as gabapentin and diclofenac to 57% and up to 100%, respectively. Our combined approach eminently decreases the hazardous effects of pharmaceuticals and antibiotic resistance in the ultrafiltered WWTP effluent, producing effluent suitable for multiple reuse options according to the latest legislation. In addition, we provided similarly promising but less extensive data for surface water and treated greywater.

Effect of temperature on the compositions of ladderane lipids in globally surveyed anammox populations

The adaptation of bacteria involved in anaerobic ammonium oxidation (anammox) to low temperatures will enable more efficient removal of nitrogen from sewage across seasons. At lower temperatures, bacteria typically tune the synthesis of their membrane lipids to promote membrane fluidity. However, such adaptation of anammox bacteria lipids, including unique ladderane phospholipids and especially shorter ladderanes with absent phosphatidyl headgroup, is yet to be described in detail. We investigated the membrane lipids composition (UPLC-HRMS/MS) and dominant anammox populations (16S rRNA gene amplicon sequencing, Fluorescence in situ hybridization) in 14 anammox enrichments cultivated at 10-37 °C. "Candidatus Brocadia" appeared to be the dominant organism in all but two laboratory enrichments of "Ca. Scalindua" and "Ca. Kuenenia". At lower temperatures, the membranes of all anammox populations were composed of shorter [5]-ladderane ester (reduced chain length demonstrated by decreased fraction of C20/(C18 + C20)). This confirmed the previous preliminary evidence on the prominent role of this ladderane fatty acid in low-temperature adaptation. "Ca. Scalindua" and "Ca. Kuenenia" had distinct profile of ladderane lipids compared to "Ca. Brocadia" biomasses with potential implications for adaptability to low temperatures. "Ca. Brocadia" membranes contained a much lower amount of C18 [5]-ladderane esters than reported in the literature for "Ca. Scalindua" at similar temperature and measured here, suggesting that this could be one of the reasons for the dominance of "Ca. Scalindua" in cold marine environments. Furthermore, we propose additional and yet unreported mechanisms for low-temperature adaptation of anammox bacteria, one of which involves ladderanes with absent phosphatidyl headgroup. In sum, we deepen the understanding of cold anammox physiology by providing for the first time a consistent comparison of anammox-based communities across multiple environments.

On anammox activity at low temperature: effect of ladderane composition and process conditions

The application of partial nitritation-anammox (PN/A) under mainstream conditions can enable substantial cost savings at wastewater treatment plants (WWTPs), but how process conditions and cell physiology affect anammox performance at psychrophilic temperatures below 15 °C remains poorly understood. We tested 14 anammox communities, including 8 from globally-installed PN/A processes, for (i) specific activity at 10-30 °C, (ii) composition of membrane lipids, and (iii) microbial community structure. We observed that membrane composition and cultivation temperature were closely related to the activity of anammox biomasses. The size of ladderane lipids and the content of bacteriohopanoids were key physiological components related to anammox performance at low temperatures. We also indicate that the adaptation of mesophilic cultures to psychrophilic regime necessitates months, but in some cases can take up to 5 years. Interestingly, biomass enriched in the marine genus "Candidatus Scalindua" displayed outstanding potential for nitrogen removal from cold streams. Collectively, our comprehensive study provides essential knowledge of cold adaptation mechanism, will enable more accurate modelling and suggests highly promising target anammox genera for inoculation and set-up of anammox reactors, in particular for mainstream WWTPs.

Physiology of anammox adaptation to low temperatures and promising biomarkers: A review

The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.

How biomass growth mode affects ammonium oxidation start-up and NOB inhibition in the partial nitritation of cold and diluted reject water

The inhibition of undesirable nitrite oxidizing bacteria (NOB) and desirable ammonium oxidizing bacteria (AOB) by free ammonia (FA) and free nitrous acid (FNA) in partial nitritation (PN) is crucially affected by the biomass growth mode (suspended sludge, biofilm, encapsulation). But, the limitations of these modes towards less concentrated reject waters (≤600 mg-N L^-1) are unclear. Therefore, this work compares the start-up and stability of three PN sequencing batch reactors (SBRs) with biomass grown in one of the three modes: suspended sludge, biofilm and biomass encapsulated in polyvinyl alcohol (PVA) pellets. The SBRs were operated at 15°C with influent total ammonium nitrogen (TAN) concentrations of 75-600 mg-TAN L^-1. PN start-up was twice as fast in the biofilm and encapsulated biomass SBRs than in the suspended sludge SBR. After start-up, PN in the biofilm and suspended sludge SBRs was stable at 150-600 mg-TAN L^-1. But, at 75 mg-TAN L^-1, full nitrification gradually developed. In the encapsulated biomass SBR, full nitrification occurred even at 600 mg-TAN L^-1, showing that NOB in this set-up can adapt even to 4.3 mg-FA L^-1 and 0.27 mg-FNA L^-1. Thus, PN in the biofilm was best for the treatment of an influent containing 150-600 mg-TAN L^-1.

Good servant, bad master: sulfide influence on partial nitritation of sewage

When applying partial nitritation (PN) to anaerobically pre-treated sewage, ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) will be exposed to dissolved sulfide and methane. Both sulfide and methane may inhibit nitrification. To gain knowledge necessary for sustaining PN under these conditions, we exposed an AOB enrichment and a mixed nitrifying culture to dissolved sulfide and methane. In the mixed nitrifying culture, sulfide selectively inhibited NOB activity (K_I,AOB1 = 150 mg-S L^-1, K_I,NOB = 10 mg-S L^-1) which shows that sulfide may help establish PN. The AOB enrichment showed similar K_I,AOB2 (130 mg-S L^-1), but nitritation activity lagged longer than the time necessary to remove sulfide from the liquid. This demonstrates that feeding of sulfide into established PN should be avoided. Methane inhibition of AOB enrichment was assessed in batch assays with 10 mg-CH₄ L^-1. As compared to control without methane, AOB enrichment activity was identical. Up to 51% of methane was converted to methanol, thus reducing the greenhouse gas emissions.

Quantitative analysis of global veterinary human resources

This analysis of global veterinary personnel was based on the available quantitative data reported by individual countries to international organisations. The analysis begins with a time series of globally reported numbers of veterinarians, starting in the year 1959 (140,391). In 2000 this number reached 691,379. Of this total, 27.77% of veterinarians were working as government officials, 15.38% were working in laboratories, universities and training institutions and 46.33% were working as private practitioners. The ratio of veterinarians to technicians was 1:0.63. The global average of resources serviced by each veterinarian was as follows: 8,760 inhabitants; 189 km2 of land area and 20 km2 of arable land; 1,925 cattle, 242 buffaloes, 87 horses, 1,309 pigs, 1,533 sheep and 20,714 chickens; in abattoirs: 401 slaughtered cattle, 699 slaughtered sheep and 1,674 slaughtered pigs; the production of 336 tonnes (t) of meat, 708 t cow milk and 74 t hen eggs; in international trade: 12 cattle, 23 sheep, 22 pigs, 1 horse, 1,086 chickens, 33 t meat and meat products; 2,289 units of livestock (50 minutes of annual veterinary working time for each unit). These averages were also analysed according to employment categories. The author also discusses factors influencing veterinary personnel analyses and planning.

History of the screwworm (Cochliomyia hominivorax) eradication in the Eastern Hemisphere

The screwworm caused by Cochliomyia Hominivorax, attacking warm-blooded animals and man, was discovered for the first time in the history outside of American continent, in the Eastern Hemisphere. After confirming the occurrence of this horrible myiasis in North Africa in 1989, Tripoli sheep import quarantine was traced as primary outbreak locality. The myiasis spread rapidly invading vast territory during several months. The invaded territory of 25000 km2 with more than 2.7 million domestic animals was identified between Mediterranean Sea and Sahara desert threatening territories in Africa and Mediterranean basin. From July 1989 up to eradication in April 1991 were discovered 14,111 cases. Classical control methods were not able to block screwworm spreading and eradicate it. Decision was made to use as the main method the sterile insect technique. Irradiated sterile flies were airlifted from Mexico factory. There were dispersed aerially about 1260 million flies covering invaded territories and 15000 km2 of protective barrier zones. Successful program cost almost 100 million US$. After the eradication Africa as well as Eastern Hemisphere could be declared to be again free of this myiasis. It was the most effective and successful international animal health program in the history of the United Nations Organization.

A method of accelerated eradication of bovine brucellosis in the Czech Republic

A method of accelerated eradication of bovine brucellosis was developed and applied in the Czech Republic, where livestock was reared primarily in large-scale units. Before this method was adopted, annual economic losses were about US dollars 20 million and thousands of people were estimated to suffer from brucellosis (e.g. 32.4% of tested veterinarians were positive). Initial mass serological testing confirmed 654 outbreaks with 99,787 intrafocal bovines distributed in half of the regions of the Republic. Disease incidence was 213 with a prevalence of 676 per 100,000 bovines. Systematic investigations detected all affected herds, including 91 new outbreaks. A depopulation policy was applied on farms and ranches with brucellosis-infected cattle, with the aim of totally eradicating the disease by a fixed deadline. Breeding on diseased ranches was temporarily discontinued and affected herds were replaced by healthy cattle from brucellosis-free regions. Since then, the incidence of the disease in cattle and humans has been maintained at level zero. Eradication without recurrence was achieved within five years, without reducing the cattle population, the rate of cattle production, or the income of farmers. Ten years after the eradication of the disease, the cumulative benefit/eradication cost ratio reached 7:1. Post-eradication surveillance has confirmed a brucellosis-free status. The eradication of bovine brucellosis has resulted in an increase in cattle production and trade. By 2000, eradication had averted losses of approximately US dollars 700 million and saved more than two thousand people from becoming affected with this zoonosis.

[History of the eradication of bovine brucellosis in the Czech Republic]

In the Czech republic, the program of recovery of the livestock from brucellosis caused by the micro-organisms Brucella abortus was successfully completed in 1964. The campaign started in 1959 by the exploration of the complete cattle population by agglutination tests. Incidence of the disease was 211 positive cases for each 100 thousands, prevalence was 0.676% (20,481 animal in 654 foci of 34 districts). The prevalence was significantly higher in large cattle units. Tens of new cases of the human brucellosis infections were reported. The process of sanitation was first based on the elimination of infected animals. In the later phase the more radical method was employed--the whole herds with infected individuals were eliminated and replaced. During the recovery program more than 41 thousands of infected animals were eliminated. It required solving many complex methodological, legislative, organisational, economical and social problems. Serological test applied to more the half of the livestock population together with epizootiological, epidemiological and laboratory investigation helped to detect all foci. Eradication brought about substantial improvement of the productive and reproductive features of the cattle and eliminated the risks of infection with this zoonosis to the human population.

[History of the elimination of bovine tuberculosis in the Czech Republic]

In 1968 in the Czech republic the programme of elimination of tuberculosis in cattle caused by germs of Mycobacterium bovis was successfully completed. The project proper was started in 1959 by examination of the whole population of cattle with tuberculin tests. The situation which was revealed was disastrous: the prevalence in cattle was on average 21.03% whereby it reached 32.26% in milking cows, i.e. every third cow had TB, as was also confirmed in slaughterhouses. Hundreds of cases in humans caused by M. bovis were notified. The annual economic losses were more than a billion crowns. The health campaign was based on the method "test and slaughter" and on the replacement of heavily infected herds by TB free ones. It was necessary to replace 1,360,000 heads of TB cattle. This called for the solution of many complicated methodical, legislative, organizational, economic and social problems. Mandatory pasteurization of milk was introduced. Tuberculin tests of the whole cattle population (on average twice a year) supplemented by epizootological, laboratory and postmortem examinations led to the detection of all foci. The final results are up to the present time reflected in the substantially better production capacity of the cattle, TB free milk and a marked decline of M. bovis in humans.

Computerised methods for animal health risk assessment using the EPIZOO 2.6 program

A computerised set of methods for the risk assessment of infectious diseases has been developed as part of a software package which deals with animal population health and disease analyses and programming (EPIZOO, version 2.6). This set includes methods for calculating the following: general indicators of risk of animal disease. Risk probability assessment of propagation of disease. Risk probability assessment of the introduction of disease through the importation of animals and their products, based on predefined criteria and on non-predefined criteria. Risk comparison of the introduction of one disease agent from several territories. Risk comparison of the introduction of several disease agents from one territory. Risk of disease propagation related to the movement and concentration of the animal population. Risk of disease propagation related to the transfer of animal products. Risk of the probability of negative test results in infected animals. Risk of the probability that at least one imported animal or animal product unit is infected.

EPIZOO: software for veterinary epidemiology training and problem-solving

Described is a computer software package, EPIZOO, which has been developed specifically for undergraduate and postgraduate education, self-training, problem-solving, and simulation studies in veterinary epidemiology. The program is based on action-oriented animal population health/disease analyses and programming. EPIZOO runs on IBM-compatible personal computers and can be used for any animal population diseases, including those transmissible to man. The software comprises an integral system of selected indicators contained in twelve modules, with about 200 widely applicable methods used in epizootiology. It is user-friendly and includes general methods related to the following: animal population characteristics of health/disease importance; analysis of animal population health and disease situations, structures, dynamics, diagnoses, and consequences; preparation, cost, and evaluation of animal population health programmes; and selected statistical techniques.

EPIZOO: a computer software package of methods for animal population health analysis and programming

An animal population health and disease software package entitled 'EPIZOO' has been developed. This computer program comprises an integral and complex system of selected indicators contained in ten modules and over one hundred sub-programs, with approximately two hundred methods for use in problem solving, training and simulation. This fully user-friendly software is applicable to any animal disease, and makes analysis and programming easier and quicker. The software includes general methods for use in a number of fields: animal population health and disease situation (structure, dynamics, diagnosis, analysis and consequences) animal population characteristics of epizootiological importance animal health programme preparation, cost calculation and evaluation selected sampling other statistical procedures. EPIZOO is a relatively simple tool for field and management veterinarians, as well as veterinary students.

Veterinary public health in world-wide animal health and production

The first section of this paper presents a concise analysis of the current world situation in animal health, zoonoses, food production and hygiene and Veterinary Services. The second section discusses future perspectives for healthy animal production in relation to veterinary public health problems. The coming decades will be crucial for the future of Veterinary Services. The protection of human health and the improvement of food production through animal health will continue to be the priorities of these services. Scientific and technological developments and the many associated changes in human living conditions and needs, as well as in animal production, call for a general revision of veterinary philosophy, strategy and programmes. In this context, it is recommended that efforts be made to significantly strengthen activities aimed at protecting human health against diseases of animal origin.