Antibiotic resistance genes in China: occurrence, risk, and correlation among different parameters

Antibiotic-Resistant Bacteria in Hydroponic Lettuce in Retail: A Comparative Survey

Hydroponic produce is gaining popularity due to its suitability for urban agriculture. The general public also considers that hydroponic produce is free from microbiological contamination. In this study, we compared the frequency and abundance of tetracycline-resistant and sulphadiazine-resistant bacteria and the minimal inhibitory concentration (MIC) of these isolates in conventional, organic, and hydroponic lettuce sold in retail. We also determined the frequency of samples carrying tetB, tetX, sul1, sul2, and int1 genes by PCR and further quantified the copy number of tetX, sul1, and int1 genes in samples positive for these genes using qPCR. As expected, the number of resistant bacteria and the MICs of these isolates were lowest in hydroponic lettuce and highest in organic lettuce. All tested resistant genes, except int1, were detected in samples of all three production methods, but no significant difference was observed between the three groups in the frequency of samples carrying the resistance genes examined or in their copy number. To the best of our knowledge, it is the first study directly reporting the existence of antibiotic-resistant bacteria and resistance genes in hydroponic vegetables sold in retail. The result highlights that the risk of antibiotic-resistant bacteria contamination in hydroponic produce should be further investigated.

Wastewater discharge drives ARGs spread in the coastal area: A case study in Hangzhou Bay, China

The distribution of 14 ARGs, intI1, and 16S rDNA were analysed in 4 wastewater treatment plants (WWTPs), 2 effluent receiving areas (ERAs), and Hangzhou Bay (HZB). The results showed that each integrated WWTP (IWWTP) received higher abundance of ARGs than pharmaceutical WWTPs (PWWTPs), and IWWTPs removed ARGs more efficiently than PWWTPs. The WWTP effluents greatly contributed to the ARGs pollution in the water environments of the ERAs and HZB, and the total abundance of the ARGs displayed a distance decay pattern. In coastal sediments, more ARGs were accumulated in remote sites. The correlation analysis showed that the occurrence of ARGs was more related to 16S rDNA and intI1 in the WWTPs. Three macrolides resistance genes (ermB, mphA, and vatB) had strong correlations with 16S rDNA and intI1 in all the sample groups. Our study clearly reveals the link between land WWTPs discharge and emerging pollution of ARGs in coastal environments.

Identification and quantification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes for aquatic microbiological risk assessment

Aquatic ecosystems have been increasingly threatened by anthropogenic activities, e.g., wastewater discharge and farm operation. Several methods are adopted to evaluate the effects of anthropogenic activities on biological risk in the environment, such as qPCR and amplicon next-generation sequencing. However, these methods fall short of providing genomic information of target species, which is vital for risk assessment from genomic aspect. Here, we developed a novel approach integrating metagenomic analysis and flow cytometry to identify and quantify potential pathogenic antibiotic resistant bacteria (PARB; carrying both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs)) in the environment, which are of particular concern due to their infection ability and antibiotic resistance. Based on the abundance/density of PARB, we evaluated microbiological risk in a river impacted by both municipal drainage and agriculture runoff. We collected samples upstream (mountainous area) as the control. Results showed that 81.8% of dominant PARB (33) recovered using our approach were related to known pathogenic taxa. In addition, intragenomic ARGs-VFGs coexistence patterns in the dominant Pseudomonas genomes (20 out of 71 PARB) showed high similarity with the most closely related Pseudomonas genomes from the NCBI RefSeq database. These results reflect acceptable reliability of the approach for (potential) pathogen identification in environmental samples. According to the PARB density, microbiological risk in samples from the agricultural area was significantly higher than in samples from the urban area. We speculated that this was due to the higher antibiotic usage in agriculture as well as intragenomic ARGs-VFGs co-evolution under antibiotic selective pressure. This study provides an alternative approach for the identification and quantification of PARB in aquatic environments, which can be applied for microbiological risk assessment.

Occurrence of antibiotics and their associations with antibiotic resistance genes and bacterial communities in Guangdong coastal areas

The concentration of 8 antibiotics and 21 antibiotic resistance genes were investigated in the coastal areas of Guangdong, China. Total concentrations of antibiotics ranged from 0.43 ng/L to 1040.31 ng/L. The concentrations of tetracyclines were much higher than that of sulfonamides in most sampling sites. The abundance of target antibiotic resistance genes ranged from 1.82 × 10⁵ to 5.9 × 10⁹ copies/mL and tetM accounted for the highest percentages of detected antibiotic resistance genes in most sampling sites. Furthermore, the dominant phyla in water samples were Proteobacteria, Bacteroidetes and Actinobacteria. The relationship between antibiotics, antibiotic resistance genes, and bacterial communities was also investigated. As a result, the abundance of sul1 was positively correlated with the concentration of sulfadiazine, sulfamethoxazole and sulfonamide p-methyl oxypyrimidine. Besides, sulfonamide p-methyl oxypyrimidine, sulfadiazine and p-aminobenzenesulfonamide were significantly correlated with the bacterial communities. These findings suggested that the residues of antibiotics in coastal areas of Guangdong affect the distribution of antibiotic resistance genes and alter the microbial communities.

Rapid removal of tetracycline by Myriophyllum aquaticum: Evaluation of the role and mechanisms of adsorption

As a floating plant, Myriophyllum aquaticum provides a large surface area under water, and thus has high potential for the removal of pollutants through adsorption. The aim of this study was to evaluate the potential adsorption of tetracycline (TC) by M. aquaticum, and examine the underlying mechanisms. M. aquaticum exhibited a high potential for TC removal from water. Adsorption was the main mechanism for rapid TC removal by live M. aquaticum plants, due to its large contact area and ion exchange, accounting for about 99% and 54% of the total amount of TC removed within 2 h and 5 d, respectively. Further, the roots of M. aquaticum exhibited a higher adsorption capacity than the stems or leaves, as the roots had the largest specific surface area. Fourier transform infrared spectroscopy analysis and identification of functional groups showed that -OH, -COOH, and -NH₂ groups are involved in the adsorption process. The use of M. aquaticum may be a promising approach for TC removal from aquatic environments, especially in terms of shortening reaction times.

Occurrence and distribution of antibiotics and antibiotic resistant genes in water and sediments of urban rivers with black-odor water in Guangzhou, South China

Urban rivers in some countries have been heavily polluted and the water became black and odor. Nevertheless, only few studies reported the occurrence of antibiotics and their corresponding antibiotic resistant genes (ARGs) in urban rivers with black-odor water with and without remediation. In this study, nine antibiotics (belonging to sulfonamides, tetracyclines, quinolones, and macrolides) and their corresponding ARGs in water and sediments of six urban rivers in Guangzhou, South China were analyzed to investigate their spatial distribution and the influence of water remediation. The concentrations of individual antibiotics varied from ND (not detectable) to 2702 ng/L and ND to 449 μg/kg in surface water and sediments, respectively. Norfloxacin displayed the highest average concentrations, followed by ciprofloxacin. The relative abundance of quinolone-resistance gene qnrA (~10³ ARGs/16S rRNA) was the highest, followed by tetracyclines-resistance genes tetC (~10^-2 ARGs/16S rRNA). The antibiotics and ARGs in sediments from various rivers exhibited distinct spatial distribution with large variation from upstream to downstream. Generally, levels of antibiotics and tetracyclines-resistance genes (tetA, tetC and tetM) in urban rivers with black-odor water (affected by industrial and domestic sewage) were higher than those in remediated urban rivers. Significant positive correlations were observed only between the relative abundances of tetA (or tetC) with the concentrations of some antibiotics (e.g., ciprofloxacin and norfloxacin). TetA was also significantly positively correlated with the concentrations of Ni, Cr, and As in sediments. This study found that urban rivers remediated with dredging might lower antibiotic levels in sediment, but high relative abundance of certain ARGs (e.g., tetB, qnrA) may still exist.

Occurrence and distribution of antibiotics and resistance genes in greenhouse and open-field agricultural soils in China

This study conducted a national scale survey to assess the levels and distributions of 13 commonly used antibiotics and nine antibiotic resistance genes (ARGs) in the greenhouse and open-field agricultural soils in China. The concentrations of antibiotics in the greenhouse and open-field soils were 428 ng/g (n = 51) and 193 ng/g (n = 51), respectively. The abundances of ARGs ranged from 1.15 × 10^-7 to 9.78 × 10^-2 copies/16S rRNA copies and from <LOD to 4.92 × 10^-2 copies/16S rRNA copies in the greenhouse and open-field soils, respectively. The levels of antibiotics in the greenhouse were significantly higher than those in the open-field soils (p < 0.05). The concentrations of antibiotics in eastern and northern China were higher than those in the other regions of China. The abundances of ARGs were relatively higher in Guangdong, Shandong, Beijing, and Liaoning provinces. The sulII, tetA, tetG, tetO, and tetX in the greenhouse soils and sulII, tetG, and tetX in the open-field soils were significantly correlated with the levels of total antibiotics. The intI1 played a key role in the transfer of three classes of ARGs, especially in the greenhouse soils. These may indicate that the ARGs in the greenhouse could be easily affected by antibiotics and intI1 genes compared with those in the open-field soils. This study provides useful information to evaluate pollution of ARGs and contamination management in greenhouse agriculture in China.

Effect of cation type in mixed Ca-Na systems on transport of sulfonamide antibiotics in saturated limestone porous media

Retention and transport of sulfonamides (SAs) in subsurface can strongly affect groundwater quality. In this work, a range of laboratory batch sorption and column transport experiments were conducted to determine the effect of cation type in mixed Ca-Na systems on the retention and transport of two typical SAs, sulfadimethoxine (SDM) and sulfacetamide (SCA), in saturated limestone porous media. Column experimental data showed divalent cation Ca²⁺ played a more important role than monovalent cation Na⁺ in decreasing the transport of only SDM in co-cation systems in the saturated limestone media. Further, in the single-cation (i.e., including either Ca²⁺ or Na⁺) system, increasing ionic strength (IS) of either NaCl or CaCl₂ had little effect on SCA transport; however, increasing of IS of CaCl₂ promoted the retention of SDM in the saturated limestone porous media. This is mainly due to the cation bridging effect of Ca²⁺ on SDM and limestone. Overall, SDM showed much higher retention in the limestone columns than SCA, which can be attributed to the two SAs' different physicochemical properties. Moreover, limestone showed stronger ability to retain the two SAs than quartz sand. Findings in this study suggest that cation type and the concentration of certain electrolyte (e.g., CaCl₂) as well as medium type play an important role in controlling the environmental fate and transport of antibiotics.

Biochar combined with polyvalent phage therapy to mitigate antibiotic resistance pathogenic bacteria vertical transfer risk in an undisturbed soil column system

The vertical migration of antibiotic resistance pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in the surface soil-vadose soil system has become a new threat to ecological safety and public health; there is an imperative need to develop an efficient technique for targeted control and inactivation of ARPB in these systems. In this work, undisturbed soil columns (0 ∼ -5 m) were constructed to investigate the impact of biochar amendment or/and polyvalent bacteriophage (ΦYSZ-KK) therapy on the vertical control and inactivation of tetracycline-resistant Escherichia coli K-12 and chloramphenicol-resistant Klebsiella pneumonia K-6. The simultaneous application of polyvalent phage and biochar impeded the vertical migration of ARPB from the top soil to lower soil layers and stimulated the ARPB dissipation in the soil column. After 60-day incubation, levels of ARPB and ARGs decreased significantly in the soil column by magnitudes of 2-6. Additionally, high throughput sequencing indicated that the simultaneous application of biochar and phage clearly maintained the structure and diversity of the soil microbial communities (p <  0.05). This work therefore demonstrates that the application of a biochar/phage combination is an environmentally friendly, efficacious measure for the control and inactivation of ARPB/ARGs in vertical soil column systems.