Benin’s waterways are affected by several forms of pollution that are linked in particular to anthropic activities. This study aims to detect the presence of antibiotic residues, the frequency of antibiotic resistant bacteria and the levels of heavy metals in Benin’s waterways. 160 surface water samples from streams in Benin were collected. They were filtered by the membrane filtration method, then incubated on different media. The isolated bacterial species were identified by API 20E gallery and specific biochemical tests. After detection of the resistance profile of the latter, the antibiotic residues were quantified in the samples by the ELISA technique on plate and the physicochemical analyses were performed by Multi 3630 IDS SET KS2 multimeter. Finally, heavy metal levels were detected by the MERCK test kit method specific to each metal. The bacterial species mostly identified were Klebsiella pneumoniae (56.59%), Klebsiella spp. (18.68%), Enterobacter spp. (12.63%). The most abundant resistance of bacterial strains was to amoxicillin + clavulanic acid (92%), followed by metronidazole (86%). Metronidazole was the antibiotic with the highest residue concentration in the samples (6.578 to 6.829 µg/L), followed by ciprofloxacin (2.142 to 9.299 µg/L). Benin streams contain heavy metals such as mercury (0.454±0.129 µg/L), lead (0.040±0.50 mg/L), zinc (6.120±16.017 mg/L), nickel (0.155±0.233 mg/L) and cadmium (0.154±0.132 mg/L). The analysis of the physico-chemical parameters showed that, apart from electrical conductivity, all parameters comply with Beninese and World Health Organization standards. Actions must be taken to clean up these rivers to preserve the integrity of aquatic ecosystems in Benin.

Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%–22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0ᵗʰ and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0ᵗʰ day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

Lincomycin mycelial residues (LMRs) are one kind of byproduct of the pharmaceutical industry. Hydrothermal treatment has been used to dispose of them and land application is an attractive way to reuse the treated LMRs. However, the safe dose for soil amendment remains unclear. In this study, a lab-scale incubation experiment was conducted to investigate the influence of the amendment dosage on lincomycin resistance genes and soil bacterial communities via quantitative PCR and 16S rRNA sequencing. The results showed that introduced lincomycin degraded quickly in soil and became undetectable after 50 days. Degradation rate of the high amendment amount (100 mg kg−1) was almost 4 times faster than that of low amendment amount (10 mg kg−1). Moreover, the introduced LMRs induced the increase of lincomycin resistance genes after incubation for 8 days, and two genes (lmrA and lnuB) showed a dosage-related increase. For example, the abundance of gene lmrA was 17.78, 74.13 and 128.82 copies g−1 soil for lincomycin concentration of 10, 50 and 100 mg kg−1, respectively. However, the abundance of lincomycin resistance genes recovered to the control level as the incubation period extended to 50 days, indicating a low persistence in soil. In addition, LMRs application markedly shifted the bacterial composition and significant difference was found between control soil, 10 mg kg−1 and 50 mg kg−1 lincomycin amended soil. Actually, several genera bacteria were significantly related to the elevation of lincomycin resistance genes. These results provided a comprehensive understanding of the effects of lincomycin dosage on the fate of resistance genes and microbial communities in LMRs applied soil.

Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances (RMS) in bacteria. The occurrence of ARGs in Italian swine farming – which has specific characteristics – was investigated in order to explore RMS dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.

The impact of commonly-used livestock antibiotics on soil nitrogen transformations under varying redox conditions is largely unknown. Soil column incubations were conducted using three livestock antibiotics (monensin, lincomycin and sulfamethazine) to better understand the fate of the antibiotics, their effect on nitrogen transformation, and their impact on soil microbial communities under aerobic, anoxic, and denitrifying conditions. While monensin was not recovered in the effluent, lincomycin and sulfamethazine concentrations decreased slightly during transport through the columns. Sorption, and to a limited extent degradation, are likely to be the primary processes leading to antibiotic attenuation during leaching. Antibiotics also affected microbial respiration and clearly impacted nitrogen transformation. The occurrence of the three antibiotics as a mixture, as well as the occurrence of lincomycin alone affected, by inhibiting any nitrite reduction, the denitrification process. Discontinuing antibiotics additions restored microbial denitrification. Metagenomic analysis indicated that Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were the predominant phyla observed throughout the study. Results suggested that episodic occurrence of antibiotics led to a temporal change in microbial community composition in the upper portion of the columns while only transient changes occurred in the lower portion. Thus, the occurrence of high concentrations of veterinary antibiotic residues could impact nitrogen cycling in soils receiving wastewater runoff or manure applications with potential longer-term microbial community changes possible at higher antibiotic concentrations.

Tetracyclines and sulfonamides are the two classes of antibiotics commonly used in the medical, industrial and agricultural activities. Their extensive usage has caused the proliferation and propagation of resistant bacteria (ARB) and resistance genes (ARGs) in the environment. In this study, the occurrence and distribution of tetracyclines (TC, OTC and CTC) and sulfonamides (SMX, SCX and TMP), their associated ARB and ARGs were quantified in water and sediments collected from the mainstream of Liaohe River, northeast China. The average concentration of tetracyclines was higher in May, while the concentration of sulfonamides was slightly higher in October. The highest concentrations of the total tetracyclines and sulfonamides in sediments were 2.7×103 ng/g and 2.1×102 ng/g respectively detected in May. All detected ARGs were found generally with high abundance. The tetA, tetB and tetE genes were dominant (4.4×10−2 to 9.8×10−1 copies of tet genes/copies of 16S rRNA genes) in total communities, and the average abundance of sul genes was expressed above 10−1 in the water samples in May and October. Redundance analysis (RDA) and principle component analysis (PCA) indicated that the antibiotic residue was the most important contributor to the level of tetracycline and sulfonamide resistance genes, and some hydrogeological conditions (e.g. flow rate, intersection settlement) influenced the distribution of resistance genes. Results from this study could help understand the proliferation and propagation of antibiotic resistance on a river catchment scale and mitigate the potential risks to public health.

Discharge of antimicrobial residues and resistant bacteria in hospital effluents is supposed to have strong impacts on the spread of antibiotic resistant bacteria in the environment. This study aimed to characterize the effluents of the Gabriel Montpied teaching hospital, Clermont-Ferrand, France, by simultaneously measuring the concentration of ciprofloxacin and of biological indicators resistant to this molecule in biofilms formed in the hospital effluent and by comparing these data to ciprofloxacin consumption and resistant bacterial isolates of the hospital. Determination of the measured environmental concentration of ciprofloxacin by spot sampling and polar organic chemical integrative (POCIS) sampling over 2 weeks, and comparison with predicted environmental concentrations produced a hazard quotient >1, indicating a potential ecotoxicological risk. A negative impact was also observed with whole hospital effluent samples using the Tetrahymena pyriformis biological model.During the same period, biofilms were formed within the hospital effluent, and analysis of ciprofloxacin-resistant isolates indicated that Gamma-Proteobacteria were numerous, predominantly Aeromonadaceae (69.56%) and Enterobacteriaceae (22.61%). Among the 115 isolates collected, plasmid-mediated fluoroquinolone-resistant genes were detected, with mostly aac(6′)-lb-cr and qnrS. In addition, 60% of the isolates were resistant to up to six antibiotics, including molecules mostly used in the hospital (aminosides and third-generation cephalosporins).In parallel, 1247 bacteria isolated from hospitalized patients and resistant to at least one of the fluoroquinolones were collected. Only 5 of the 14 species identified in the effluent biofilm were also found in the clinical isolates, but PFGE typing of the Gram-negative isolates found in both compartments showed there was no clonality among the strains.Altogether, these data confirm the role of hospital loads as sources of pollution for wastewater and question the role of environmental biofilms communities as efficient shelters for hospital-released resistance genes.

Due to the abusive usage of antibiotics in animal husbandry, a large amount of residual antibiotics has been released into the environment, therein posing great threat against both environment security and public health. Therefore, it is of great significance to investigate the toxicity of antibiotics on the widely-applied bioindicator-earthworm. In this work, the physiological parameters and the intestinal bacteria community of Metaphire guillelmi were monitored simultaneously to evaluate their sensitivity to the tetracycline (TC) exposure. As expected, the antioxidant enzyme activity and coelomocyte apoptosis acted fairly well as biomarkers for the TC toxicity. In contrast, the intestinal bacteria of Metaphire guillelmi responded varyingly to different TC doses. When TC concentration increased from 0 to 35.7 μg cm⁻², the percentage of the Proteobacteria phylum declined significantly from 85.5% to 34.4%, while the proportions of the Firmicutes, Planctomycetes and Atinomycete phyla clearly increased (p < 0.05). Meanwhile, the levels of TC resistance genes tetA, tetC, and tetW increased with the increasing TC concentration, in contrast to the declined abundance in denitrifying genes nirS and nosZ (p < 0.05). By analyzing the correlation between the antioxidant enzyme activity and the dominant intestinal bacteria in the worm gut, it is interesting to found that the four dominant bacteria genera Mesorhizobium, Aliihoeflea, Romboutsia, and Nitrospira are the promising bioindicator of TC stress due to their sensitive response. This work shed novel light on evaluating the ecotoxicological risks posed by residual TC in environment by using a combination of physiological parameters and intestinal bacterial activity in earthworms.

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.