Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of AMR, and human activities can strongly influence their resistome.The main goal of this work was to study the resistome of wild boar faecal microbiome, one of the most important game species in Europe using metagenomic and culturing approaches. The most abundant genes identified by the high-throughput qPCR array encode mobile genetic elements, including integrons, which can promote the dissemination of AMR determinants. A diverse set of genes (n = 62) conferring resistance to several classes of antibiotics (ARGs), some of them included in the WHO list of critically important antimicrobials were also detected. The most abundant ARGs confer resistance to tetracyclines and aminoglycosides. The phenotypic resistance of E. coli and Enterococcus spp. were also investigated, and together supported the metagenomic results.As the wild boar is an omnivorous animal, it can be a disseminator of AMR bacteria and ARGs to livestock, humans, and the environment. This study supports that wild boar can be a key sentinel species in ecosystems surveillance and should be included in National Action Plans to fight AMR, adopting a One Health approach.

The use of the phenicol antibiotic florfenicol in livestock can select for the optrA gene, which also confers resistance to the critically important oxazolidinone antibiotic linezolid. However, the occurrence and dissemination of florfenicol and linezolid cross-resistance genes in anaerobic treatment systems for livestock waste are unknown. Herein, the phenotypes and genotypes (optrA, fexA, fexB, and cfr) of florfenicol and linezolid cross-resistance were investigated in 339 enterococci strains isolated from lab- and full-scale mesophilic anaerobic digestion systems treating swine waste. It was found that optrA, fexA, and fexB were frequently detected in isolated enterococci in both systems by PCR screening, whereas cfr was not detected. The most abundant gene was optrA, which was detected in 73.5% (n = 50) and 38.9% (n = 23) of enterococci isolates in the full-scale influent and effluent, respectively. Most strains carried more than two resistance genes, and the average percentage of co-occurrence of optrA/fexA was 16.6%. Based on minimum inhibitory concentrations of the enterococci strain phenotypes, 85.7%, 77.5%, and 77.5% of strains in influent were resistant to chloramphenicol, florfenicol, and linezolid, respectively, while 56.3%, 65.2%, and 13% in the effluent isolates were found, respectively, which was consistent with the genotype results. The phenotypes and genotypes of florfenicol and linezolid resistance were relative stable in the enterococci isolated from the influent and effluent in lab-scale anaerobic digestion system. The findings signify the enterococci isolates harboring the optrA gene remained in effluents of both full- and lab-scale swine waste anaerobic digestion system; hence, effective management strategies should be implemented to prevent the discharge of antibiotic resistance from the livestock waste treatment systems.

The development of antibiotic resistance and dissemination of its determinants is an emerging public health problem as it compromises treatment options of infections that were, until recently, treatable. Investigation of outbreaks of vancomycin resistant enterococci (VRE) suggests that the environment serves as a significant reservoir for antibiotic resistance genes (ARGs). However, there is a paucity of data regarding the presence of ARGs in the water sources in South Africa. In this study, water samples collected from wastewater treatment plants (WWTPs), surface water and hospital sewage were screened for enterococci harbouring genes conferring resistance to four classes of antibiotics. Enterococci isolates harbouring ARGs were detected in raw influent and treated wastewater discharge from WWTPs and hospital sewage water. Plasmid and transposon encoded ermB (macrolide), tetM and tetL (tetracycline) as well as aph(3’)-IIIa (aminoglycosides) genes were frequently detected among the isolates, especially in E. faecalis. The presence of enterococci harbouring ARGs in the treated wastewater suggest that ARGs are discharged into the environment where their proliferation could be perpetuated. Among the enterococci clonal complexes (CCs) recovered from wastewater were E. faecium CC17 (ST18), which is frequently associated with hospital outbreaks and a novel E. faecalis sequence type (ST), ST780.

Depending on their concentrations, sizes, and types, particulate matters of biological origins (bioPM) significantly affect human health. However, for different air environments, they are not well characterized and can vary considerably. As an example, we investigated the bioPM differences at an urban (Beijing) site and a rural (Wangdu) site in the North China Plain (NCP) using an online monitoring instrument, an ultraviolet aerodynamic particle sizer (UV-APS), the limulus amebocyte lysate (LAL) assay, and a high-throughput sequencing method. Generally, lower concentrations of viable bioPM (hourly mean: 1.3 × 10³ ± 1.6 × 10³ m⁻³) and endotoxin (0.66 ± 0.16 EU/m³) in Beijing were observed compared to viable bioPM (0.79 × 10⁵ ± 1.4 × 10⁵ m⁻³) and endotoxin (15.1 ± 23.96 EU/m³) at the Wangdu site. The percentage of viable bioPM number concentration in the total PM was 3.1% in Beijing and 6.4% in Wangdu. Approximately 80% of viable bioPM was found to be in the range from 1 to 2.5 μm. Nevertheless, the size distribution patterns for viable bioPM at the Beijing and Wangdu sites differed and were affected by PM pollution, leading to distinct lung deposition profiles. Moreover, the distinct diurnal variations in viable bioPM on clean days were dimmed by the PM pollution at both sites. Distinct bacterial community structures were found in the air from the Beijing and Wangdu sites. The bacterial community in urban Beijing was dominated by genus Lactococcus (49.5%) and Pseudomonas (15.1%), while the rural Wangdu site was dominated by Enterococcus (65%) and Paenibacillus (10%). Human-derived genera, including Myroides, Streptococcus, Propionibacterium, Dietzia, Helcococcus, and Facklamia, were higher in Beijing, suggesting bacterial emission from humans in the urban air environment. Our results show that different air harbors different biological species, and people residing in different environments thus could have very different biological particle exposure.

Waste water of the Kettara village, as well as the abandoned tailings, constitute a potential environmental issue with direct consequences on air, soil, water resources qualities and, on human health. In this paper, experimental investigations examine the environmental impact which is induced by the wastewater, mine tailings and the lithological factors of rocks. This multidisciplinary research allows to i) understand the transfer of the Metallic Trace Elements (selenium, arsenic, nickel and zinc) and sulfate ions in the fractured shales media, ii) to assess the water potability by using the microbiological analysis. The microbiological results reveal the domestic impact by the presence of several kinds of bacteria in the groundwater resources: E. coli, Fecal coliforms, Total coliforms, Enterococci, Mesophilic Aerobic Flora, Sulphite-reducing bacteria and Salmonella.Selenium, arsenic and the bacteriological contamination of the groundwater could be explained by five kinds of factors: i) the geological formations and the nature of the hydrogeological system (unconfined layer), ii) the groundwater flow, the hydraulic relation between the hydrogeological wells and, the fractures network in the shale aquifer. The piezometric map allows to highlight the groundwater flow from the North-East to North-West and to the South-West, the drainage axis towards the P21 well and the presence of the dividing axis in the contaminated zone by the arsenic, iii) the absence of the unhealthy habitats with permeable traditional septic tanks in the village; iv) the transfer of the spreading animal excrements from the soil to groundwater and, v) the migration of the wastewater towards downstream of the groundwater flow. The presence of the reed beds could explain the reduction of bacteria in the hydrogeological wells of the study area.

This paper is a part of a multi-disciplinary research “Application of Decentralized On-Site Water Treatment System in Egypt for Use in Agriculture and Producing Safe Fish and Animal Proteins”.The project aimed to investigate the environmental impact of implementing sewage water before and after treatment using the effluent of the on-site decentralized Japanese' Johkasou system, in agriculture and producing fish protein. The aim is to establish such system in Egypt to strengthen the sanitary conditions of water resources. In the present study, the impact of the sewage pollution in some fish farms at El-Fayyum, Port Said and El-Dakahlia governorates in Egypt was carried out. Water and fish (Oreochromis niloticus and Mugil cephalus) samples were collected from private fish farms of such localities. Bacteriological and chemical examination of water samples revealed the existence of coliforms and many other bacterial species of significant human health hazards. The chemical parameters of water showed a marked deviation from normal levels while examination of fish flesh specimens indicated contamination with Streptococcus Sp., Staphylococcus Sp., and Salmonella in all examined localities. Other bacterial isolates of human health importance (Morganella morganii, Pseudomonas cepacia and Enterococcos durans) were identified. The parasitological examination revealed the presence of encysted metacercariae (EMC); Diplostomatidae, Prohemistomatidae and Heterphyidae. Moreover, two protozoan parasites (Mxyoboulus tilapiae and Ichthyophthirius multifilis) were also recorded. The histopathological examination revealed mild tissue reaction in case of bacterial infection and severe pathological lesions in different organs in case of EMC infection. Lamellar hyperplasia and mononuclear cell infiltration in branchial tissue was common findings. In skeletal muscles, atrophy of muscle fibres, myolysis and myophagia were detected.

Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 10⁷–6.88 × 10⁸ copies per g sediment (1.27 × 10⁻²–3.39 × 10⁻² copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.

Recently it was demonstrated that mealworm (Tenebrio molitor) larvae consume and biodegrade polystyrene. Thus, in this study a breeding investigation with various types of polystyrene was performed to follow the changes in the gut microbiome diversity. Polystyrene used for packaging purposes (PSp) and expanded polystyrene (EPS) were perceived as more favorable and attacked more frequently by mealworms compared to raw polystyrene (PS) and material commercially available for parcels (PSp). Although our studies showed that larvae could bite and chew selected materials, they are not able to degrade and use them for consumption purposes. In a next-generation sequencing experiment, among all samples, seven classes, Gammaproteobacteria, Bacilli, Clostridia, Acidobacteria, Actinobacteria, Alphaproteobacteria and Flavobacteria, were indicated as the most abundant, whereas the predominant genera were Enterobacter, Lactococcus and Enterococcus. Additionally, we isolated three bacteria strains able to use diverse types of bioplastic as a sole carbon source. The strains with biodegradable activity against bioplastic were identified as species of the genera Klebsiella, Pseudomonas and Serratia. The presence of a bacterial strain able to degrade bioplastic may suggest a potential niche for further investigations.

Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.

Sewage input and the relationship between chemical markers (linear alkylbenzenes and coprostanol) and fecal indicator bacteria (FIB, Escherichia coli and enterococci), were evaluated in order to establish thresholds values for chemical markers in suspended particulate matter (SPM) as indicators of sewage contamination in two subtropical estuaries in South Atlantic Brazil. Both chemical markers presented no linear relationship with FIB due to high spatial microbiological variability, however, microbiological water quality was related to coprostanol values when analyzed by logistic regression, indicating that linear models may not be the best representation of the relationship between both classes of indicators. Logistic regression was performed with all data and separately for two sampling seasons, using 800 and 100 MPN 100 mL⁻¹ of E. coli and enterococci, respectively, as the microbiological limits of sewage contamination. Threshold values of coprostanol varied depending on the FIB and season, ranging between 1.00 and 2.23 μg g⁻¹ SPM. The range of threshold values of coprostanol for SPM are relatively higher and more variable than those suggested in literature for sediments (0.10–0.50 μg g⁻¹), probably due to higher concentration of coprostanol in SPM than in sediment. Temperature may affect the relationship between microbiological indicators and coprostanol, since the threshold value of coprostanol found here was similar to tropical areas, but lower than those found during winter in temperate areas, reinforcing the idea that threshold values should be calibrated for different climatic conditions.