It is so far unclear how the COVID-19 winter waves started and what should be done to prevent possible future waves. In this study, we deciphered the dynamic course of a winter wave in 2021 in Saxony, a state in Eastern Germany neighbouring the Czech Republic and Poland. The study was carried out through the integration of multiple virus genomic epidemiology approaches to track transmission chains, identify emerging variants and investigate dynamic changes in transmission clusters. For identified local variants of interest, functional evaluations were performed. Multiple long-lasting community transmission clusters have been identified acting as driving force for the winter wave 2021. Analysis of the dynamic courses of two representative clusters indicated a similar transmission pattern. However, the transmission cluster caused by a locally occurring new Delta variant AY.36.1 showed a distinct transmission pattern, and functional analyses revealed a replication advantage of it. This study indicated that long-lasting community transmission clusters starting since early autumn caused by imported or locally occurring variants all contributed to the development of the 2021 winter wave. The information we achieved might help future pandemic prevention.

Today’s water-treatment plants combine practices designed to cope individually with various types of purification challenges. In some cases, the solution to one has detrimental effects on others, e.g. disinfection by chlorination forming hazardous organic contaminants. Water-treatment plants have large ecological footprints and operational costs, making the availability of high-quality water in developing areas almost impossible, due to lack of resources and infrastructure. Indeed, >2 billion people are exposed to diseases caused by contaminated water. Clearly, bringing safe, clean drinking water to people’s homes is essential to a good quality of life. Clay minerals may offer technologies and innovative practices which would help to develop a reliable, low-maintenance device with a small environmental footprint that processes stream, lake, or pond water into high-quality potable water. The basis for such technologies has already been established and improved approaches are being introduced on an ongoing basis by clay scientists: nanocomposite pre-treatment and disinfection, photodegradation of organic pollutants using clay-based catalysts, polishing of inorganic contaminants, and removal of biological pathogens by adsorption or deactivation onto specifically designed clay-based filters, etc. This short review presents a vision for combining those technologies in a tandem system for the delivery of high-quality water that is low-maintenance, affordable, and environmentally sustainable for the benefit of mankind.

Geophagy is the intentional consumption of earth. Although widely documented among vulnerable populations, including children and pregnant women, the causes and consequences of geophagy remain poorly understood. Relevant literature was, therefore, reviewed to describe geophagy across species, geographies, life stages, and disease states. After a brief consideration of hypothesized etiologies, the potential harmful and beneficial consequences of geophagy are described, considering current evidence for each. Data available to date suggest that the greatest potential risks of geophagy include toxicity or heavy metal poisoning, and diseases resulting from consumed clays binding nutrients and beneficial pharmaceuticals in the gut. Evidence also suggests that geophagy may be beneficial by protecting against harmful pathogens and toxins through two distinct physiological pathways. Future research should explore causal relationships between geophagy and iron deficiency, as well as investigate the biological and psychosocial conditions that govern geophagy.

During the COVID-19 pandemic the international community repeatedly called for the equitable distribution of vaccines and other medical countermeasures. However, there was a substantial gap between this rhetoric and State action. High-income countries secured significantly more doses than they required, leaving many low-income countries unable to vaccinate their populations. Current negotiations for the new Pandemic Treaty under the World Health Organization (WHO) attempt to narrow the gap between rhetoric and behaviour by building the concept of equity into the Treaty's substantive content. However, equity is difficult to define, much less to operationalize. Presently, WHO Member States appear to have chosen ‘access and benefit-sharing’ (ABS) as the predominant mechanism for operationalizing equity in the Treaty. This article examines ABS as a mechanism, its use in public health, and argues that ABS is fundamentally flawed, unable to achieve equity. It proposes other options for an equitable international response to future pandemic threats.

Tropical coastal ecosystems are in decline worldwide due to an increasing suite of human activities, which threaten the biodiversity and human wellbeing that these ecosystems support. One of the major drivers of decline is poor water quality from land-based activities. This review summarises the evidence of impacts to coastal ecosystems, particularly coral reefs, from sediments, nutrients, chemicals and pathogens entering coastal zones through surface and groundwater. We also assess how these pollutants affect the health of coastal human populations through: (1) enhanced transmission of infectious diseases; (2) reduced food availability and nutritional deficit from decline of fisheries associated with degraded habitat; and (3) food poisoning from consumption of contaminated seafood. We use this information to identify opportunities for holistic approaches to integrated watershed management (IWM) that target overlapping drivers of ill-health in downstream coastal ecosystems and people. We demonstrate that appropriate management requires taking a multi-sector, systems approach that accounts for socio-ecological feedbacks, with collaboration required across environmental, agricultural, public health, and water, sanitation and hygiene sectors, as well as across the land–sea interface. Finally, we provide recommendations of key actions for IWM that can help achieve multiple sustainable development goals for both nature and people on coasts.

This study aims to evaluate the impact of non-pharmaceutical interventions (NPIs) on the prevalence of respiratory pathogens among hospitalised children with acute respiratory infections (ARIs) in Suzhou. Children with ARIs admitted to the Children’s Hospital of Soochow University between 1 September 2021 and 31 December 2022 and subjected to 13 respiratory pathogen multiplex PCR assays were included in the study. We retrospectively collected demographic details, results of respiratory pathogen panel tests, and discharge diagnostic information of the participants, and described the age and seasonal distribution of respiratory pathogens and risk factors for developing pneumonia. A total of 10,396 children <16 years of age, including 5,905 males and 4,491 females, were part of the study. The positive rates of the 11 respiratory pathogen assays were 23.3% (human rhinovirus (HRV)), 15.9% (human respiratory syncytial virus (HRSV)), 10.5% (human metapneumovirus (HMPV)), 10.3% (human parainfluenza virus (HPIV)), 8.6% (mycoplasma pneumoniae (MP)), 5.8% (Boca), 3.5% (influenza A (InfA)), 2.9% (influenza B (InfB)), 2.7% (human coronavirus (HCOV)), 2.0% (adenovirus (ADV)), and 0.5% (Ch), respectively. Bocavirus and HPIV detection peaked during the period from September to November (autumn), and MP and HMPV peaked in the months of November and December. The peak of InfA detection was found to be in summer (July and August), whereas the InfB peak was observed to be in winter (December, January, and February). HRSV and HRV predominated in the <3 years age group. HRV and HMPV were common in the 3–6 years group, whereas MP was predominant in the ≥6 years group. MP (odds ratio (OR): 70.068, 95%CI: 32.665–150.298, P < 0.01), HMPV (OR: 6.493, 95%CI: 4.802–8.780, P < 0.01), Boca (OR: 3.300, 95%CI: 2.186–4.980, P < 0.01), and HRSV (OR: 2.649, 95%CI: 2.089–3.358, P < 0.01) infections were more likely to develop into pneumonia than the other pathogens. With the use of NPIs, HRV was the most common pathogen in children with ARIs, and MP was more likely to progress to pneumonia than other pathogens.

We evaluated the presence of bacterial pathogens in the milk of goats and their relationship with somatic cell count (SCC) and milk composition. The study was performed on a dairy farm in northern Slovakia. Half udder milk samples were collected from goats in June and July. The samples were divided on the basis of SCC into 4 bands (SCC1 lowest to SCC4 highest). Bacterial pathogens were only detected in 13% of samples. SCC3 and SCC4 had 15 and 25% positive samples respectively compared with SCC1 (2%) and SCC2 (14%). Coagulase-negative staphylococci (CNS) were the most common isolates (73%), of which Staphylococcus caprae was the most frequently isolated (65%). In samples with ≥ 1000 × 103 cells ml− 1 (SCC3, SCC4) there was higher somatic cell score (SCS) in the presence of a pathogen (7.48 ± 0.11) than without a pathogen (7.16 ± 0.05, P < 0.01). Statistically significant but weak negative correlations were observed between SCS and lactose, dry matter and non-fat dry matter. In conclusion, a higher percentage of bacteriologically positive milk samples was observed in both SCC3 and SCC4 groups but this does not explain the aetiology of high SCC in the milk of goats that are apparently free of bacteria. As a diagnostic tool, SCC is probably less useful in goats than in cows.

One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.

The tapeworms of fishes (Chondrichthyes and Actinopterygii) account one-third (1670 from around 5000) of the total tapeworm (Platyhelminthes: Cestoda) species diversity. In total 1186 species from 9 orders occur as adults in elasmobranchs (sharks, rays and chimaeras), and 484 species from 8 orders mature in ray-finned fishes (referred to here as teleosts). Teleost tapeworms are dominated by freshwater species (78%), but only 3% of elasmobranch tapeworms are known from freshwater rays of South America and Asia (Borneo). In the last 2 decades, vast progress has been made in understanding species diversity, host associations and interrelationships among fish tapeworms. In total, 172 new species have been described since 2017 (149 from elasmobranchs and 23 from teleosts; invalidly described taxa are not included, especially those from the Oriental region). Molecular data, however, largely limited to a few molecular markers (mainly 28S rDNA, but also 18S and cox1), are available for about 40% of fish tapeworm species. They allowed us to significantly improve our understanding of their interrelationships, including proposals of a new, more natural classification at the higher-taxonomy level (orders and families) as well as at the lower-taxonomy level (genera). In this review, we summarize the main advances and provide perspectives for future research.

Urban rodents are associated with parasites and pathogens, which present health risks for humans, but information on factors related to parasite and pathogen infection in rodents in cities of Latin America is scarce. This study analyzes the hosts, host community structure and environmental characteristics of parasite and pathogen fauna present in the three species of urban rodents in an urban area of South America. Rodents were captured seasonally in seven different neighborhoods. Digestive tracts were dissected under stereoscopic microscopy and feces were processed using a sedimentation technique. Protozoa and bacteria were detected through polymerase chain reaction and indirect immunofluorescence techniques. In Rattus norvegicus, Rattus rattus and Mus musculus, ten helminths, three protozoa and two bacteria were found. Six were zoonotic: Toxoplasma gondii; Hymenolepis diminuta; Rodentolepis nana; Strobilocercus fasciolaris; Leptospira borgpetersenii; and Leptospira interrogans. The parasite and pathogen infections were influenced by the host species, the host community structure, the season, and the presence of streams in the neighborhood. Urban rodents may be the infection source of many zoonotic diseases and it is important to generate public policies for this problem. This study is one example of the situation of many cities of Latin America, where peripheral neighborhoods are growing dramatically.

In 2015, plants of Sumatran fleabane [Conyza sumatrensis (Retz.) E. Walker] were identified in a crop field with an unusual rapid necrosis herbicide symptom after application of 2,4-D. An initial study identified that the symptoms began about 2 h after herbicide application, the resistance factor was high (resistance factor = 19), and the resistance decreased at low light. The mechanism of resistance is not yet known, but the symptomatology suggests it may be related to reduced translocation, ATP-binding cassette (ABC) class B transporters, changes on auxin perception genes, or induction of genes involved in response to pathogens and abiotic stresses. The objective of this study was to use inhibitors of enzymes involved in detoxification and carriers to investigate the mechanisms involved in the resistance to 2,4-D caused by rapid necrosis. Neither the inhibitors of ABC and auxin transporters, triiodobenzoic acid (TIBA), 1-N-naphythylphthalamic acid (NPA), verapamil, and orthovanadate, nor the inhibitors of detoxifying enzymes, such as malathion, 4-chloro-7-nitrobenzofurazan (NBD-Cl), and imidazole, reduced the frequency of the rapid necrosis phenotype. However, orthovanadate and sodium azide (possibly related to auxin transport) were able to partially reduce oxidative stress in leaf disks. The expression of ABCM10 (an ABCD transporter gene), TIR1_1 (an auxin receptor gene), and CAT4 (an amino acid transporter gene) was quickly reduced after 2,4-D application in the resistant accession. Contrary to our hypothesis, LESION SIMULATING DISEASE RESISTANCE 1_3 (LSD1_3) expression increased in response to 2,4-D. LSD1_3 is important for the response to pathogen and abiotic stresses. The rapid necrosis mechanism is not related to 2,4-D detoxification but might be related to changes in the TIR receptor or auxin transport. Mutations in other transporters or in proteins involved in abiotic and pathogen stresses cannot be ruled out.

The aim of the present study was to investigate the effects of milk composition changes on the in vitro growth of bovine mastitis pathogens. Nutritional requirements of three major bovine mastitis pathogens Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Streptococcus uberis (S. uberis) were investigated in vitro. We used ultra-high temperature (UHT) treated milk with different contents of fat, protein, and carbohydrates to test the influence of the availability of various milk constituents on pathogen growth characteristics. Additionally, the bacterial growth was investigated under experimentally modified nutrient availability by dilution and subsequent supplementation with individual nutrients (carbohydrates, different nitrogen sources, minerals, and different types of B vitamins) either to milk or to a conventional medium (thioglycolate broth, TB). Varying contents of fat, protein or lactose did not affect bacterial growth with the exception of growth of S. uberis being promoted in protein-enriched milk. The addition of nutrients to diluted whole milk and TB partly revealed different effects, indicating that there are media-specific growth limiting factors after dilution. Supplementation of minerals to diluted milk did not affect growth rates of all studied bacteria. Bacterial growth in diluted whole milk was decreased by the addition of high concentrations of amino acids in S. aureus, and by urea and additional B vitamins in E. coli and S. aureus. The growth rate of S. uberis was increased by the addition of B vitamins to diluted whole milk. The present results demonstrate that growth-limiting nutrients differ among pathogen types. Because reduced bacterial growth was only shown in diluted milk or TB, it is unlikely that alterations in nutrient availability occurring as a consequence of physiological changes of milk composition in the cow's udder would directly affect the susceptibility or course of bovine mastitis.

Bacteriophages are the most abundant form of life on earth and are present everywhere. The total number of bacteriophages has been estimated to be 1032 virions. The main division of bacteriophages is based on the type of nucleic acid (DNA or RNA) and on the structure of the capsid. Due to the significant increase in the number of multi-drug-resistant bacteria, bacteriophages could be a useful tool as an alternative to antibiotics in experimental therapies to prevent and to control bacterial infections in people and animals. The aim of this review was to discuss the history of phage therapy as a replacement for antibiotics, in response to EU regulations prohibiting the use of antibiotics in livestock, and to present current examples and results of experimental phage treatments in comparison to antibiotics. The use of bacteriophages to control human infections has had a high success rate, especially in mixed infections caused mainly by Staphylococcus, Pseudomonas, Enterobacter, and Enterococcus. Bacteriophages have also proven to be an effective tool in experimental treatments for combating diseases in livestock.