Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils

Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.     

Characterizing the antibiotic resistance genes in a river catchment: Influence of anthropogenic activities

Previous studies on environmental antibiotics resistance genes(ARGs) have focused on the pollution sources such as wastewater treatment plants, aquaculture and livestock farms,etc. Few of them had addressed this issue in a regional scale such as river catchment. Hence,the occurrence and abundances of 23 ARGs were investigated in surface water samples collected from 38 sites which located from the river source to estuary of the Beijiang River.Among them, 11 ARGs were frequently detected in this region and 5 ARGs(sul I, sul II, tet B,tet C, and tet W) were selected for their distribution pattern analysis. The abundances of the selected ARGs were higher in the upstream(8.70 × 10~6 copies/ng DNA) and downstream areas(3.17 × 10~6 copies/ng DNA) than those in the midstream areas(1.23 × 10~6 copies/ng DNA), which was positively correlated to the population density and number of pollution sources. Pollution sources of ARGs along the Beijiang River not only had a great impact on the abundances and diversity, but also on the distribution of specific ARGs in the water samples. Both sul I and sul II were likely originated from aquaculture farms and animal farms,tet W gene was possibly associated with the mining/metal melting industry and the electric waste disposal and tet C gene was commonly found in the area with multiple pollution sources.However, the abundance of tet B was not particularly related to anthropogenic impacts. These findings highlight the influence of pollution sources and density of population on the distribution and dissemination of ARGs at a regional scale.     

Occurrence and distribution of antibiotic resistance genes in the sediments of the East China Sea bays

The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980 s, resulting in severe pollution of its environments.Antibiotic resistance genes(ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay(HB),Xiangshan Bay(XB), and Taizhou Bay(TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron–integrase gene(intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB(based on both the absolute and relative abundances) and dfrA13 was higher in HB(based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and blaPSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and blaPSE-1. In addition, the joint effect of heavy metals and nutrients organic pollutants might be crucial for the fate of ARGs in the coastal sediments.     

Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment

Antibiotic resistance genes(ARGs), human pathogenic bacteria(HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis(contig Intestine_364647)and Enterococcus faecium(contig Intestine_80272) carrying efr A, efr B and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica(contig Sediment_825143) and Escherichia coli(contig Sediment_188430) carrying mex B and APH(3′)-IIa were found in sediments, and Laribacter hongkongensis(contig Water_478168 and Water_369477), Shigella sonnei(contig Water_880246),and Acinetobacter baumannii(contig Water_525520) carrying sul1, sul2, ere A, qac H, OXA-21, and mph D were found in pond water. Mobile genetic elements(MGEs) analysis indicated that horizontal gene transfer(HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.     

水产养殖尾水中抗生素抗性基因的去除及磺胺类耐药细菌研究

水产养殖环境中抗生素的大量使用促进了抗生素耐药细菌（antibiotic resistant bacteria,ARB）和抗生素抗性基因（antibiotic resistance genes,ARGs）的出现及传播.利用荧光定量PCR分析了浙江省某水产养殖尾水集中处理系统中8种ARGs的分布特征.结果表明,出水中ARGs的绝对丰度降低了0.91个数量级.磺胺类抗性基因（sul1、sul2）在所检测的抗性基因中占主导地位,且绝对丰度在出水中依然维持较高水平(4.94×10⁹、1.79×10⁹copies·L^-1).16S r RNA基因高通量测序结果显示变形菌门、蓝藻门、拟杆菌门、厚壁菌门和放线菌门是优势菌门,变形菌门和绿弯菌门与sul1、sul2和sul3呈显著相关.筛选出一株对磺胺类抗生素具有耐药性的弗氏柠檬酸杆菌,该菌株为条件致病菌,全基因组测序结果显示该菌株共携带了17个ARGs,其中sul1、sul2、tet A、bla_TEM-1等ARGs均位于1个Inc FIB质粒上,质粒图谱揭示了磺胺...     

Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments

Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM₁₀) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 10⁴, 5.6 × 10⁴ and 5.1 × 10² copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.     

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting

As a major reservoir of antibiotics,animal manure contributes a lot to the augmented environmental pressure of antibiotic resistance genes(ARGs).This might be the first study to explore the effects of different ventilation types on the control of ARGs and to identify the relationships between archaeal communities and ARGs during the composting of dairy manure.Several ARGs were quantified via Real-time qPCR and microbial communities including bacteria and archaea were analyzed by High-throughput ...     

Coastal mudflats as reservoirs of extracellular antibiotic resistance genes: Studies in Eastern China

Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems, little is known about the profiles of antibiotic resistance genes (ARGs) in this area. In this study, characteristics of typical ARGs, involving both intracellular (iARGs) and extracellular ARGs (eARGs) at different physical states, were explored in over 1000 km of coastal mudflats in Eastern China. Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles. The abundance of eARGs was significantly higher than that of iARGs (87.3% vs 12.7%), and their dominance was more significant than those in other habitats (52.7%-76.3%). ARG abundance, especially for eARGs, showed an increasing trend (p < 0.05) from southern (Nantong) to northern (Lianyungang) coastal mudflats. Higher salinity facilitated the transformation from iARGs to eARGs, and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats. This study addresses the neglected function of coastal mudflats as eARGs reservoirs.     

医院空调回风口滤网积尘中抗生素抗性基因污染的比较

为了解医院环境中抗生素抗性基因(ARGs)的污染情况与分布特征,于2018年11月至2021年4月期间分批次采集了武汉市两家医院部分病房空调回风口滤网积尘样本127份,对其进行β-内酰胺类ARGs (mecA、bla_TEM、bla_CTX-M、bla_SHV)和碳青霉烯类ARGs (bla_KPC、bla_NDM-1、bla_IMP、bla_VIM、bla_OXA-51)及一类整合酶基因intI 1的定性与定量检测与评价.结果表明,医院不同科室及ICU空调滤网积尘中可检出以上9种β-内酰胺类,碳青霉烯类ARGs及intI 1,平均检出率分别为55.12%、37.64%和81.89%.ICU的β-内酰胺类与碳青霉烯ARGs的平均检出率显著高于外科与内科(P<0.05);4种β-内酰胺类ARGs中的bla_TEM、mecA检出率及其相对丰度在内科、外科最高(P<0.05);ICU的bla_SHV检出率及其相对丰度高于内科、外科(P<0.05).5种碳青霉烯类ARGs中的bla_NDM-1检出率及其相对丰度在内科、外科显著高于bla_KPC、bla_IMP(P<0.05).intI 1与9种ARGs的相对丰度均呈显著正相关(P<0.05).研究结果表明,两家医院不同科室病房空调滤网积尘中存在β-内酰胺类和碳青霉烯类ARGs以及一类整合酶基因intI 1的污染,内科、外科、ICU均以bla_TEM、mecA、bla_NDM-1为主,由此可认为医院不同科室空气及相关环境中可能存在与此等ARGs相关的耐甲氧西林金黄色葡萄球菌、产ESBLs肠杆菌科细菌、耐碳青霉烯大肠埃希菌与鲍曼不动杆菌等耐药菌的现时与既往污染,并且存在ARGs水平转移的风险;ICU空调滤网积尘中β-内酰胺类与碳青霉烯ARGs的污染较内科、外科严重,其中bla_SHV污染高于内科、外科,由此表明,ICU是ARGs及相关耐药菌污染的高风险科室.     

Impacts of cadmium addition on the alteration of microbial community and transport of antibiotic resistance genes in oxytetracycline contaminated soil

The large-scale development in livestock feed industry has increased the chances of antibiotics and heavy metals contamination in the soil. The fate of antibiotic resistance genes (ARGs) and microbial community in heavy metals and antibiotic contaminated soil is still unclear. In this study, we investigated the effect of cadmium (Cd) addition on the transport of ARGs, microbial community and human pathogenic bacteria in oxytetracycline (OTC) contaminated soil. Results showed that the addition of OTC significantly increased the abundance of ARGs and intI1 in the soil and lettuce tissues. The addition of Cd to OTC treated soil further increased the abundance and translocation of ARGs and intI1. Moreover, Cd promoted the transfer of potential human pathogenic bacteria (HPB) into lettuce tissues. Compared with O10 treatment, the addition of Cd decreased the concentration of OTC in soil and lettuce tissue, but slightly increased the fresh weight of lettuce tissues. Redundancy analysis indicated that bacterial community succession is a major factor in ARGs variation. Network analysis indicated that the main host bacteria of ARGs were mainly derived from Proteobacteria. Correlation analysis showed that intI1 was significantly correlated with tetG, tetC, sul1, sul2, ermX, and ermQ. Meanwhile, potential HPB (Clostridium, and Burkholderia) was significantly correlated with intI1 and eight ARGs (tetG, tetC, tetW, tetX, sul1, sul2, ermX, and ermQ.). The findings of this study suggest that the addition of heavy metals to agricultural fields must be considered in order to reduce the transfer of ARGs in the soil and crops.     

Temporal variation and sharing of antibiotic resistance genes between water and wild fish gut in a peri-urban river

Antibiotic resistance genes (ARGs) as emergence contaminations have spread widely in the water environment. Wild fish may be recipients and communicators of ARGs in the water environment, however, the distribution and transmission of ARGs in the wild fish and relevant water environment were rarely reported. Here, we have profiled ARGs and bacterial communities in wild freshwater fish and relevant water in a peri-urban river using high-throughput qPCR and 16S rRNA gene sequence. A total of 80 and 220 unique ARG subtypes were identified in fish and water samples. Fish and water both showed significant ARG seasonal variations (P < 0.05). The highest absolute abundance of ARGs in fish and water occurred in summer (1.32 × 10⁹ copies per g, on average) and autumn (9.04 × 10⁶ copies per mL), respectively. In addition, the bipartite network analysis showed that 9 ARGs and 1 mobile genetic element continuously shared in fish and water. Furthermore, bacteria shared in fish and water were found to significantly correlate with shard ARGs. The findings demonstrate that bacteria and ARGs in fish and water could interconnect and ARGs might transfer between fish and water using bacteria as a spreading medium.     

养殖鱼塘底泥微生物抗生素耐药基因分布分析

针对水产养殖中抗生素滥用引起微生物耐药基因污染的现象,本实验以杭州市某水产养殖区底泥样品为研究对象,测定了底泥样品中抗生素含量,并从其中分离出74株可培养细菌.采用PCR方法对分离菌株中磺胺类、四环素类、喹诺酮类、氯霉素类抗性基因(antibiotic resistance genes,ARGs)和整合子基因进行了检测.结果表明,除tet A(四环素类)耐药基因未被检出外,其余3种耐药基因及整合子基因均被检出,其中qnr S(喹诺酮类)耐药基因的检出率最高,为50.00%.另外,利用16S r DNA序列分析技术将分离菌株鉴定为12个属、19个种,包括环境中多种常见土著细菌及部分致病菌,其中气单胞菌(Aeromonas spp.)数量最多(29株),占分离菌株的39.19%.掌握水产养殖区中ARGs的污染现状,对控制其传播、保障食品安全和保护微生态环境具有重要指导意义.     

土壤中抗生素抗性基因的分布及迁移转化

为明晰土壤中抗生素抗性基因的存在及传播状况,并为开展抗生素抗性基因土壤污染的风险评价工作提供科学的理论依据.本文根据抗生素抗性基因存在和转移的理论基础,结合国内外研究进展,详细阐述了土壤中抗生素抗性基因的来源、分布传播及其影响因素,发现已有研究对外源抗生素抗性基因在土壤中的丰度和种类变化的研究较为深入,而对其在土壤中的空间分布特征、传播扩散及行为机理等研究工作尚处于起步阶段.因此提出未来土壤抗生素抗性基因的研究重点应为掌握抗生素抗性基因的空间分布、溯源、迁移转化规律及其关键制约因子,并建立相应的数量关系.     

基于病毒宏基因组学鉴定水环境中噬菌体携带的新型耐药基因及其耐药特点分析

水环境作为耐药基因的存储库,为耐药基因的水平转移和新型耐药基因的产生提供重要场所.但到目前为止,对水环境中病毒携带耐药基因的特征及其功能还知之甚少.因此以南四湖和东平湖为研究对象,利用病毒宏基因组学结合体外实验的方法探讨水环境中病毒携带新型耐药基因的情况及其耐药特点.通过分析病毒基因组的片段（reads）和重叠群（contigs）,鉴定出多种耐药基因,包括AAC（6’）、Qnr A、Van Y、Vat和β-内酰胺酶基因.值得关注的是,通过核心序列比对和进化分析,挖掘出两种噬菌体携带的新型β-内酰胺酶基因bla_NSDPV-1和bla_NSVM-1.最小抑菌浓度试验表明,这两种编码新型β-内酰胺酶的耐药基因对临床常用头孢类和碳青霉烯类抗生素具有一定的耐药性.综上所述,水环境中噬菌体很可能在新型耐药基因的产生和耐药基因散播中起着重要的作用.另外,病毒宏基因组学结合体外实验是发现噬菌体携带新型耐药基因的重要方法.     

Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system

This study aimed to reveal how amoxicillin(AMX) affected the microbial community and the spread mechanism of antibiotic resistance genes(ARGs) in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed(EGSB) reactor was designed and run for 241 days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA_(-1), OXA_(-2), OXA_(-10), TEM_(-1), CTX-M_(-1), class I integrons(intI1) and 16 SrRNA genes were also examined in sludge samples. The results showed that the genera Ignavibacterium, Phocoenobacter,Spirochaeta, Aminobacterium and Cloacibacillus contributed to the degradation of different organic compounds(such as various sugars and amines). And the relative quantification of eachβ-lactam resistance gene in the study was changed with the increasing of AMX concentration.Furthermore the vertical gene transfer was the main driver for the spread of ARGs rather than horizontal transfer pathways in the system.     

大型溞对水环境中抗生素抗性菌与抗性基因的摄食与去除

原后生动物是污水生物处理系统中的常见生物,了解它们是否能够摄食与去除抗生素抗性菌(ARB)和抗生素抗性基因(ARGs),对于建立藉捕食作用的ARB和ARGs去除技术具有重要意义.本研究以大型溞作为代表生物,探究了其对ARB和ARGs的摄食、去除效果与机制.使用荧光抗性菌直接观察其摄食过程,证实大型溞对ARB的摄食与富集...     

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis

Wastewater treatment plants(WWTPs) are deemed reservoirs of antibiotic resistance genes(ARGs). Bacterial phylogeny can shape the resistome in activated sludge. However, the co-occurrence and interaction of ARGs abundance and bacterial communities in different WWTPs located at continental scales are still not comprehensively understood. Here, we applied quantitative PCR and Miseq sequence approaches to unveil the changing profiles of ARGs(sul1, sul2, tet W, tet Q, tet X), int I1 gene, and bacterial communities in 18 geographically distributed WWTPs. The results showed that the average relative abundance of sul1 and sul2 genes were 2.08 × 10~(-1) and 1.32 × 10~(-1) copies/16 S rRNA copies, respectively. The abundance of tet W gene was positively correlated with the Shannon diversity index(H′), while both studied sul genes had significant positive relationship with the int I1 gene. The highest average relative abundances of sul1, sul2, tet X, and int I1 genes were found in south region and oxidation ditch system. Network analysis found that 16 bacterial genera co-occurred with tet W gene. Co-occurrence patterns were revealed distinct community interactions between aerobic/anoxic/aerobic and oxidation ditch systems. The redundancy analysis model plot of the bacterial community composition clearly demonstrated that the sludge samples were significant differences among those from the different geographical areas,and the shifts in bacterial community composition were correlated with ARGs. Together,these findings from the present study will highlight the potential risks of ARGs and bacterial populations carrying these ARGs, and enable the development of suitable technique to control the dissemination of ARGs from WWTPs into aquatic environments.     

噬菌体编码的抗生素抗性基因研究进展

噬菌体作为地球上丰度最高的生物体,对于全球生态系统的微生物群落组成与动态,生物地球化学循环和细菌进化等都具有重要作用,但噬菌体对抗生素抗性的贡献还所知甚少.通过宏基因组测序和定量PCR等技术,发现了海洋,河流,土壤,动物肠道等环境的噬菌体基因组中存在多种耐药基因(antibiotic resistance genes,ARGs).因此,噬菌体及其介导的转导作用可能对ARGs的富集扩散发挥着重要作用.本文综述了不同环境介质的噬菌体基因组中ARGs的分布特征以及噬菌体介导的ARGs水平转移的研究进展,同时展望了为阐明噬菌体对抗生素抗性贡献需要解决的科学问题.本文将为了解噬菌体在ARGs传播扩散中的作用以及扩展对可移动抗性组的认知奠定基础.     

河套灌区沉积物中抗生素抗性基因的分布研究

抗生素抗性基因(Antibiotic resistance genes, ARGs)作为一种新型污染物已经成为国内外研究的热点.为了探究河套灌区不同排水渠(3N、3S、5N、5S和7N)沉积物中ARGs的分布情况,采用定量PCR测定了沉积物中ARGs、整合酶基因(intⅠ1和intⅡ2)和转座酶基因(tnpA)的丰度.结果表明,36种ARGs中检测到31种,在各样地中均能检测到intⅠ1和tnpA基因,而intⅡ2基因未检测到.在各样地中,tetA、tetS、sulⅠ和aadA1基因丰度较高;在5N样地ereA基因丰度最高,为1.65×10~9 copies·g~(-1);15种ARGs在7N样地与其它样地之间有显著差异,其中,aadA1基因在7N样地丰度最高,为1.37×10~9 copies·g~(-1).氮含量与sulIII、ereB、bla_(ampC)基因丰度显著正相关,而pH与tetX、tetO和tetM基因丰度呈负相关关系.综上所述,抗生素抗性基因广泛存在于河套灌区的沉积物中.     

城市污水处理厂抗生素抗性基因研究进展

抗生素抗性基因（ARGs）是一类对自然环境及人体健康造成极大威胁的新型污染物,城市污水处理厂是ARGs的重要源和汇,具有重大潜在生态风险。系统梳理了污水处理过程中不同类型ARGs的组成变化特征和转移机制,提出β-内酰胺类、大环内酯类、四环素类、磺胺类、氨基糖苷类等类型ARGs广泛存在于全球污水处理厂中,但不同类型ARGs的丰度随污水处理过程的变化特征各异,且不同处理单元中的高丰度ARGs存在差异,水平转移是ARGs的主要转移机制。总结了环境条件、进水水质、操作参数等常见因素对ARGs丰度和分布的影响。在此基础上提出,识别具有指示作用的ARGs及其关键影响因素,定量分析各类因素对ARGs丰度、种类及水平转移机制的影响,以及建立ARGs风险评价标准体系是城市污水处理厂监测与控制ARGs潜在生态风险的未来发展方向。