Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

• Distribution of ARGs in decentralized sewage facilities were investigated. • Bacitracin-ARGs were most predominant ARGs in rural wastewater. • ARGs were identified in bacterial and viral community. • ARGs of rpoB, drfE, gyrA and parC were both correlated with bacteria and phages. • More attention should be paid to the risk of spreading ARG by phages. The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG’s proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.     

Antibiotic resistance and virulence factors of Escherichia coli from eagles and goshawks

One of the major global problems in medicine is microbial resistance to antibiotics (antimicrobial resistance) and this has become an increasingly frequent research topic. This study focuses on antimicrobial resistance, phylogenetic and genetic characterization of Escherichia coli from wild birds: ten isolates from eagles (Aquila chrysaetos), nine from goshawks (Accipiter gentilis) and 24 from broilers in the Slovak Republic. Twenty-two strains with presence of int1 gene were selected and examined for the presence or absence of transposon gene (tn3), genes of antibiotic resistance and virulence factors. We detected sequence type (ST) in eagles ST 442 with genes iss, papC, iutA, cvaC, tsh, fyuA, iroN, kps, feoB, sitA, irp2, ireA for virulence factors and tetA, sul1, sul2, dfrA, aadA for antibiotic resistance; in goshawks ST 1011 with iss, papC, fyuA, iroN, feoB, sitA and qnrS1, tetA, sul1, sul2, dfrA, aadA, respectively. These ST types have been found in humans too and should be evaluated further for possible zoonotic potential and transfer of resistance genes from the environment.     

Mechanisms of allicin exposure for the sludge fermentation enhancement: Focusing on the fermentation processes and microbial metabolic traits

As a frequently used product with antimicrobial activity, consumed allicin might be discharged and concentrated in waste-activated sludge (WAS). However, the influence of allicin (as an exogenous pollutant) on WAS fermentation has not been clearly revealed. This study aimed to disclose the impacts of allicin on volatile fatty acid (VFA) generation during WAS fermentation. The results showed that the appropriate presence of allicin (10 mg/g TSS) significantly enhanced the VFA yield (1894 versus 575 mg COD/L in the control) with increased acetate proportion (24.3%). Further exploration found that allicin promoted WAS solubilization, hydrolysis and acidification simultaneously. Metagenomic analysis revealed that the key genes involved in extracellular hydrolysis metabolism (i.e., CAZymes), membrane transport (i.e., gtsA and ytfT), substrate metabolism (i.e., yhdR and pfkC) and fatty acid synthesis (i.e., accA and accD) were all highly expressed. Allicin also induced the bacteria to produce more signalling molecules and regulate cellular functions, thereby enhancing the microbial adaptive and regulatory capacity to the unfavourable environment. Moreover, the variations in fermentative microbes and their contributions to the upregulation of functional genes (i.e., ytfR, gltL, INV, iolD and pflD) for VFA generation were disclosed. Overall, the simultaneous stimulation of functional microbial abundances and metabolic activities contributed to VFA production in allicin-conditioned reactors.     

铜对蚯蚓转化牛粪过程抗生素抗性基因的影响

以赤子爱胜蚓（Eisenia fetida）为试验蚓种,设定不同Cu浓度梯度,研究蚯蚓转化牛粪过程中Cu对ARGs消长的影响.结果表明,不同Cu浓度处理下,ARGs累积总丰度呈现出CF （未添加Cu）-1降低至4.33×10^-1copies/16S copies.低、中浓度Cu的添加显著提高了样品中ARGs的总丰度水平（P<0.05）.通过研究不同类型ARGs在不同时间阶段的变化,发现低、高浓度Cu处理组（T1、T3）在蚯蚓转化过程中提高了tet-ARGs、erm-ARGs和str-ARGs的丰度,而中浓度Cu处理组（T2）中tet-ARGs和str-ARGs丰度降低.冗余分析（RDA）得出pH值显著影响蚯蚓转化过程中ARGs相对丰度的变化（P<0.05）,且TOC、TN和Cu对ARGs的消长也发挥着重要作用.蚯蚓转化可加速牛粪中ARGs丰度的削减,一定程度上能够减少其环境风险,但牛粪中Cu的残留可导致蚯蚓转化过程中部分ARGs的富集,因此亟需进一步优化蚯蚓转化处理工艺.     

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...     

Genotypic characterization of quinolone resistant-Escherichia coli isolates from retail food in Morocco

This study was conducted to assess the retail food as a possible vehicle for antimicrobial resistant, particularly quinolones resistant and pathogenic Escherichia coli. We determined the prevalence and characteristics of nalidixic acid (Nal) resistant E. coli isolates from diverse retail food samples. In all, 70 (28%) of 250 E. coli isolates studied were Nal-resistant E. coli and 91% of these were multi-drug resistant. Plasmid mediated quinolone resistance genes were identified in 32 isolates, including aac(6′)-Ib-cr (n = 16), qnrS1 (n = 11) and qnrB19 (n = 7). Mutations in gyr A and par C genes were detected among 80% of the isolates, and the isolates showed substitution Ser83-Leu and Asp87-Asn in gyrA and Ser80-Ile in parC. In addition, three different gene cassettes were identified (aadA1, aadA7, aac(3)-Id) in 18%. Virulence-associated genes stx1, eae, sfa, hlyA and stx2 were found in six (8%), three (4%), two (3%), three (4%) and three (4%) isolates, respectively. E. coli isolates of phylogenetic group A were dominant (64%, 45/70). Pulsed field gel electrophoresis revealed none epidemiological relationship between these isolates. The results of this work report the higher frequency of Nal-resistant E. coli isolates from Moroccan retail food samples including MDR and pathogenic isolates.     

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.     

高原生境下A2O工艺对污水处理的微生物机制

基于Illumina MiSeq高通量测序技术,以高原生境下A²O工艺的活性污泥为研究对象,探讨不同温度下微生物群落结构、丰度及相关性.结合污染物分解、吸附及转化等代谢过程中的主要功能蛋白、功能基因、酶的种类及丰度在碳、氮、磷等污染物代谢途径中的作用,从生物化学和分子水平的角度分析了高原地区A²O工艺对污水处理的微生物学机制.结果表明：优势细菌门为变形菌门、拟杆菌门、放线菌门、厚壁菌门及绿弯菌门,优势细菌属为norank_f__AKYH767、腐败螺旋菌、Ottowia、伯克氏菌、IMCC26207、Novosphingobium.污染物去除和微生物群落发挥作用的效果在15℃为最优,微生物群落的COG、代谢途径、基因和酶活性最适宜的温度为20℃.主要功能蛋白为一般功能预测、氨基酸运输与代谢和基因转录;主要代谢途径为：ABC转运蛋白,细菌双组分调节系统,嘌呤、核糖体及嘧啶等代谢,主要功能基因的产物（酶）为：烯酰辅酶A水合酶、乙酰辅酶A C-乙酰转移酶、醛脱氢酶（NAD⁺）、硫代硫酸盐及外多磷酸酶.     

纳污河流抗性基因和微生物群落相关性

通过Miseq高通量测序分析和荧光定量PCR技术,研究某纳污河流中四环素类与磺胺类抗性基因（ARGs）的分布特征、传播情况及微生物群落结构相关性.结果表明：在河流地表水与沉积物中均检测到四环素类抗性基因tetA和tetB与磺胺类抗性基因sul1和sul2,四环素类抗性基因和磺胺类抗性基因的绝对丰度分别为5.09×10³~1.26×10⁷,3.94×10⁵~1.32×10⁹copics/L,磺胺sul1抗生素抗性基因丰度显著高于其它基因;河流主要优势菌门为Proteobacteria,Bacteroidetes,Firmicutes,Actinobacteria和Cyanobacteria,其平均总相对丰度占总比例的95.62%,且总体差异较小.抗性基因与微生物群落冗余分析显示,Methylotenera菌属是影响tetA抗性基因分布丰度的主要因素,Dechloromonas和Clostridium sensu stricto 1菌属是影响tetB抗性基因分布丰度的主要因素,Dechloromonas、Clostridium sensu stricto 1和Methylotenera菌属是影响sul1、sul2抗性基因分布丰度的主要因素.     

鸡粪和猪粪生物发酵过程中抗生素抗性基因的动态变化

畜禽粪便是储存和传播抗生素抗性基因(ARGs)的主要载体.为明确鸡粪和猪粪堆肥过程中ARGs和MGEs相对丰度的变化及影响其消减的关键环境因子,探索减少畜禽粪便堆肥中ARGs含量并降低其污染风险的有效方法,采用实时荧光定量PCR技术和16S rRNA高通量测序技术,测定了鸡粪和猪粪好氧堆肥75 d的过程中,不同阶段10种ARGs和7种可移动遗传元件(MGEs)的丰度变化和细菌群落变化,分析了ARGs和MGEs与细菌群落的相关性和堆体理化性质(温度、含水率、 pH和DOC)变化对ARGs和MGEs丰度的影响.结果表明,猪粪(PM)中ARGs和MGEs丰度显著高于鸡粪(CM).堆肥结束后,两种堆肥中9种ARGs和5种MGEs的相对丰度均显著降低,其中CM中3种ARGs(tetM、tetT和aacA)和4种MGEs(ISEcp1、IS1216、IS613和tnp614)的去除率达到99%; PM中9种ARGs[tetB(P)、tetL、tetM、tetO、tetT、aacA、aadD、aphA3和sat4]及4种MGEs(ISEcp1、IS26、IS1216和tnp614)去除率均达到99%...