Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding extended spectrum ß-lactamases (ESBLs).

A study was conducted to investigate the impact of raw wastewater use for irrigation on dissemination of bacterial resistance in urban agriculture in African cities. The pollution of agricultural fields by selected antibiotic residues was assessed. The structure and functions of the soil microbial communities, presence of antibiotic resistance genes of human clinical importance and Enterobacteriaceae plasmid replicons were analysed using high throughput metagenomic sequencing. In irrigated fields, the richness of Bacteroidetes and Firmicutes phyla increased by 65% and 15.7%, respectively; functions allocated to microbial communities' adaptation and development increased by 3%. Abundance of antibiotic resistance genes of medical interest was 27% greater in irrigated fields. Extended spectrum ß-lactamase genes identified in irrigated fields included blaCARB-3, blaOXA-347, blaOXA-5 and blaRm3. The presence of ARGs encoding resistance to amphenicols, ß-lactams, and tetracyclines were associated with the higher concentrations of ciprofloxacin, enrofloxacin and sulfamethoxazole in irrigated fields. Ten Enterobacteriaceae plasmid amplicon groups involved in the wide distribution of ARGs were identified in the fields. IncQ2, ColE, IncFIC, IncQ1, and IncFII were found in both farming systems; IncW and IncP1 in irrigated fields; and IncY, IncFIB and IncFIA in non-irrigated fields. In conclusion, raw wastewater irrigated soils in African cities could represent a vector for the spread of antibiotic resistance, thus threatening human and animal health. Consumers of products from these farms and farmers could be at risk of acquiring infections due to drug-resistant bacteria.

High-throughput sequencing data and antibiotic resistance mechanisms of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities.

High-throughput sequencing data of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities are presented in this report. These data were collected to study the potential of wastewater use in urban agriculture to disseminate bacterial resistance in soil. Soil samples were collected in three cities in two African countries. Each city had two sectors (irrigated and non-irrigated). After collection, biomass samples were purified, DNA from soil was extracted, quantified and sequenced using multiplex Illumina high-throughput sequencing. The sequence count of the six metagenome datasets ranges from 3,258,523,350 bp to 4,120,454,250 bp; the mean sequence length post quality control average was 149 ± 3 bp. The mechanisms of resistance encoded by the identified antibiotic resistance genes (ARGs) in the metagenomic data were dominated by antibiotic inactivation enzymes (64.7% and 71.9%), followed by antibiotic target replacement (14.7% and 12.5%), antibiotic target protection (11.8% and 9.4%) and efflux pumps (6.3% and 8.8%) in bacterial DNA isolated from irrigated and non-irrigated fields, respectively. The datasets will be useful for the scientific community working in the area of bacterial resistance dissemination from the environment. They can be used for further understanding of bacterial drug-resistance gene prevalence and acquisition in wastewater irrigated soils. The data reported herein was used for the article, titled "Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding Extended spectrum ß-lactamase (ESBLs)" Bougnom et al. (2020) [1].

Biochar-mediated sorption of antibiotics in pig manure.

Using manure contaminated with antibiotics as fertilizer is a primary source of soil pollution with antibiotics and concomitantly with antibiotic resistance genes (ARG). Bioavailable antibiotics trigger further ARG amplification during manure storage. Consequently it is aimed to facilitate the immobilization of antibiotics in manure. To this end, five biochars derived from pine cone (BCP), rice husk, sewage sludge, digestate and Miscanthus were tested as additional sorbents in liquid pig manure for sulfamethazine, ciprofloxacin, oxytetracycline and florfenicol. Non-linear sorption was best-fit using the Freundlich isotherm (R2 > 0.82) and the pseudo-second-order model best described sorption kinetics (R2 > 0.94). Antibiotics' sorption onto manure increased in the order sulfamethazine < florfenicol < ciprofloxacin < oxytetracycline. Admixtures of BCP to manure changed the order to sulfamethazine < oxytetracycline < florfenicol = ciprofloxacin. Generally, with the addition of biochar, sorption coefficients of florfenicol increased most (by factors>2.7) followed by sulfamethazine and ciprofloxacin. Yet, oxytetracycline was mostly mobilized probably due to competitive adsorption. Effects depended on the proportion of biochar added and the type of biochar, whereby plant-derived biochar exhibited better immobilization of antibiotics. Depending on the type and portion of biochar, admixtures to manure can be used to lower the mobility and hence bioavailability of fenicols, fluoroquinolones and sulfonamides.

Effects of pig slurry on the sorption of sulfonamide antibiotics in soil.

Sorption of p-aminobenzoic acid (pABA) and five sulfonamide antibiotics to loess Chernozem topsoil amended with varied additions of pig slurry was investigated in batch trials. In unfertilized soil, partition coefficients (Kd) of sulfonamides ranged from 0.3 to 2.0. Strong sorption nonlinearity (1/n = 0.5 to 0.8) was best fitted by the Freundlich isotherm (R2 = 0.7 to 1.0) and was indicative for specific sorption mechanisms. Adsorption to pig slurry was much stronger, and nondesorbable portions were increased compared with soil. However, in a mixture of soil and slurry (50:1 w/w), sorption of the antibiotics was significantly decreased at a lower concentration range of pABA and the sulfonamides. This was attributed to competitive adsorption of dissolved organic matter (DOM) constituents from manure. An increase in pig slurry amendment resulted in increased total organic matter, DOM concentration, and ionic strength, but pH decreased. As a result, the nonadsorbed portions of pABA, sulfanilamide, and sulfadiazine (logD(ow) < -0.4) ranged from 47% to 82% of the applied concentration in the differently manured substrates. Dissolved fractions of the antibiotics reached a maximum at a soil-slurry ratio of 9:1 and decreased with further addition of manure. This decrease was related to the formation of less-effective DOM associates in solution. The adsorbed and desorbed portions of the less-polar substances--sulfadimidine, sulfadimethoxine, and sulfapyridine (logD(ow) > 0.1)--remained nearly constant in the presence of increased manure input. The pH changes caused by manure amendment strongly affected ionisation status of the latter compounds, thus resulting in increased adsorption, which compensated the mobilizing effect of DOM. It is suggested that the effect of manure be considered in test methods to determine the soil retention of pharmaceutical substances.

Sorption of sulfonamide pharmaceutical antibiotics on whole soils and particle-size fractions.

Residues of pharmaceutical antibiotics are found in the environment, whose fate and effects are governed by sorption. Thus, the extent and mechanisms of the soil sorption of p-aminobenzoic acid and five sulfonamide antibiotics (sulfanilamide, sulfadimidine, sulfadiazine, sulfadimethoxine, and sulfapyridine) were investigated using topsoils of fertilized and unfertilized Chernozem and their organic-mineral particle-size fractions. Freundlich adsorption coefficients (K(f)) ranged from 0.5 to 6.5. Adsorption increased with aromaticity and electronegativity of functional groups attached to the sulfonyl-phenylamine core. Adsorption to soil and particle-size fractions increased in the sequence: coarse silt < whole soil < medium silt < sand < clay < fine silt and was influenced by pH. Sorption nonlinearity (1/n