Silencing of CPNE1-TRAF2 Axis Restrains the Development of Pancreatic Cancer.

BACKGROUND: Copine 1 (CPNE1) acts as a promoter in the progression of many kinds of cancers with the exception of pancreatic cancer (PC). This research is designed to probe the function of the CPNE1-tumor necrosis factor receptor-associated factor 2 (TRAF2) axis in PC. METHODS: In vivo and in vitro models of PC were constructed, and a series of biological function tests, including MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide], colony formation, flow cytometry, and immunohistochemistry, were performed. RESULTS: The level of CPNE1 elevated dramatically in PC cells. Downregulation of CPNE1in PC cells resulted in the inhibition of colony formation and proliferation. In addition, the silencing of CPNE1 induced the G1/S arrest and apoptosis in PC cells. Additionally, TRAF2 positively interacted with CPNE1 in PANC cells. CPNE1 silencing also inhibited the growth of tumors in in vivo mouse models. Functional experiments revealed that the anti-tumor effect of CPNE1 silencing was counteracted by TRAF2 overexpression, and the tumor-promoting effect of TRAF2 overexpression was reversed by CPNE1 silencing. CONCLUSIONS: In summary, our findings indicate that the silencing of the CPNE1-TRAF2 axis restrains PC development.

A Flexible Wearable Supernumerary Robotic Limb for Chronic Stroke Patients.

In this study, we present a flexible wearable supernumerary robotic limb that helps chronic stroke patients with finger rehabilitation and grasping movements. The design of this innovative limb draws inspiration from bending pneumatic muscles and the unique characteristics of an elephant's trunk tip. It places a strong emphasis on crucial factors such as lightweight construction, safety, compliance, waterproofing, and achieving a high output-to-weight/pressure ratio. The proposed structure enables the robotic limb to perform both envelope and fingertip grasping. Human-robot interaction is facilitated through a flexible bending sensor, detecting the wearer's finger movements and connecting them to motion control via a threshold segmentation method. Additionally, the system is portable for versatile daily use. To validate the effectiveness of this innovation, real-world experiments involving six chronic stroke patients and three healthy volunteers were conducted. The feedback received through questionnaires indicates that the designed mechanism holds immense promise in assisting chronic stroke patients with their daily grasping activities, potentially improving their quality of life and rehabilitation outcomes.

Sixty Years of Frequency-Domain Monaural Speech Enhancement: From Traditional to Deep Learning Methods.

Frequency-domain monaural speech enhancement has been extensively studied for over 60 years, and a great number of methods have been proposed and applied to many devices. In the last decade, monaural speech enhancement has made tremendous progress with the advent and development of deep learning, and performance using such methods has been greatly improved relative to traditional methods. This survey paper first provides a comprehensive overview of traditional and deep-learning methods for monaural speech enhancement in the frequency domain. The fundamental assumptions of each approach are then summarized and analyzed to clarify their limitations and advantages. A comprehensive evaluation of some typical methods was conducted using the WSJ + Deep Noise Suppression (DNS) challenge and Voice Bank + DEMAND datasets to give an intuitive and unified comparison. The benefits of monaural speech enhancement methods using objective metrics relevant for normal-hearing and hearing-impaired listeners were evaluated. The objective test results showed that compression of the input features was important for simulated normal-hearing listeners but not for simulated hearing-impaired listeners. Potential future research and development topics in monaural speech enhancement are suggested.

CompNet: Complementary network for single-channel speech enhancement.

Recent multi-domain processing methods have demonstrated promising performance for monaural speech enhancement tasks. However, few of them explain why they behave better over single-domain approaches. As an attempt to fill this gap, this paper presents a complementary single-channel speech enhancement network (CompNet) that demonstrates promising denoising capabilities and provides a unique perspective to understand the improvements introduced by multi-domain processing. Specifically, the noisy speech is initially enhanced through a time-domain network. However, despite the waveform can be feasibly recovered, the distribution of the time-frequency bins may still be partly different from the target spectrum when we reconsider the problem in the frequency domain. To solve this problem, we design a dedicated dual-path network as a post-processing module to independently filter the magnitude and refine the phase. This further drives the estimated spectrum to closely approximate the target spectrum in the time-frequency domain. We conduct extensive experiments with the WSJ0-SI84 and VoiceBank + Demand datasets. Objective test results show that the performance of the proposed system is highly competitive with existing systems.

Efficacy and safety of Xiao-ai-ping injection add-on therapy to chemotherapy in patients with non-small cell lung cancer: A systematic review and meta-analysis.

BACKGROUND: Xiao-ai-ping injection (XAPI) combined with chemotherapy has potential efficacy and less side effects in the treatment of non-small cell lung cancer (NSCLC). At present, there are many clinical studies on XAPI combined with chemotherapy in the treatment of NSCLC, but the results are different. The purpose of this study was to evaluate the efficacy and safety of XAPI combined with chemotherapy in the treatment of NSCLC by meta-analysis system. METHODS: The databases to be searched include PubMed, Cochrane Library, Web of Science, Chinese National Knowledge Infrastructure, Chinese Biomedical Literature Database, Wanfang database, Chinese Scientific Journal Database, and so on. In addition, relevant journals and magazines will manually search in various fields as supplements. The search date is set from the establishment of the database until July 8, 2023. The 2 researchers will use Endnote X9 software for literature screening and data extraction and independently evaluate the quality. We then assessed the quality and risk of inclusion in the study and observed outcome indicators. RESULTS: A total of 28 trials were included in this study, 1947 patients with NSCLC (974 receiving XAPI combined chemotherapy and 973 receiving chemotherapy alone). The results of meta-analysis showed that: Objective tumor response rate of NSCLC (P < .00001). Improvement in Karnofsky performance score of NSCLC (P < .00001). Quality of life score of NSCLC (P < .00001). The result of CD3 + (P < .00001). The result of CD4 + (P < .00001). The result of CD8 + (P < .00001). The result of CD4+/CD8 + (P = .0001). Leukopenia (P < .00001). Thrombocytopenia (P < .00001). Hemoglobin decrease (P < .00001). Liver function (P = .04). Nausea and vomiting (P < .00001). CONCLUSION: Our meta-analyses demonstrated that XAPI adjunct with chemotherapy can improve the patient quality of life, reduce adverse reactions, and enhanced immune function, the treatment is effective and high safety. Which suggests that it might be used for NSCLC. However, a large sample of randomized controlled trials are needed to further study the long-term efficacy of XAPI.

Comparing the efficacy and safety of different thread-drawing surgery method for treating high complex anal fistula: a systematic review and network meta-analysis.

PURPOSE: To evaluate the effect of different surgical methods in the treatment of high complex anal fistula by systematic review and network meta-analysis. METHODS: Randomized controlled trials that met the inclusion criteria in PubMed, Cochrane Library, Embase, Web of Science, CBM, CNKI, WANFANG DATA, VIP were searched from the date of database construction to May 23, 2023. RESULTS: Among the 48 randomized controlled trials (RCTs), 4205 patients were included in the network meta-analysis. Incision thread-drawing counter-drainage procedure (ITCP) in improving the effective rate, the cure rate; reduce the recurrence rate, reduce the anal canal damage has a huge advantage. Directional line-hanging method (DLM) is optimal for safety and postoperative pain relief. Directional line-hanging method (ITSS) protect the optimal anal function after surgery. Sphincter preserving thread-hanging method (SPTM) has a significant advantage in accelerating wound healing time. Main tube incision combined with thread-hanging branch tube drainage (MIBD) is second only to incision thread-drawing counter-drainage procedure (ITCP) in improving effective rate, cure rate, reducing recurrence rate and reduce complication rate. CONCLUSION: In general, different thread-drawing surgery methods have good clinical effect for the treatment of high complex anal fistula. In general, these methods provide evidence-based medical evidence for early treatment in terms of improving clinical efficacy, relieving anal pain and reducing wound healing time. However, there are differences in the number of included literature studies, and further verification by large-sample, high-quality, multicenter RCTS is still needed in the next stage.

Calcineurin inhibitors or cyclophosphamide in the treatment of membranous nephropathy superimposed with FSGS lesions: a retrospective study from China.

BACKGROUND: Cyclophosphamide (CTX) and calcineurin inhibitors (CNIs) based regimens are recommended as immunosuppressive therapies for patients with idiopathic membranous nephropathy (IMN). Focal and segmental glomerular sclerosis (FSGS) lesions, which are common in membranous nephropathy (MN), are poor predictors of outcome. This study compared the differences of prognosis between two regimens in patients with IMN combined with FSGS lesions. METHODS: This retrospective study enrolled 108 patients with biopsy-proven IMN, accompanied with FSGS lesions, nephrotic syndrome and an estimated glomerular filtration rate (eGFR)≥60 mL/min/1.73 m2 who were treated with CTX or CNIs. We used propensity score matching (PSM) for balancing the confounding variables. RESULTS: During follow-up, 10 patients (10/55 [18.2%]; nine males) in the CNIs group showed a 50% decline in eGFR; eight had a not otherwise specified variant. Patients initially treated with CNIs had a significantly higher risk of progression to the primary outcome and a lower probability of complete or total remission. The relapse rate was higher in patients who initially received CNIs- than in those who received CTX-based treatment. Before PSM, age and 24-h urine protein level differed significantly between the groups. The PSM model included data from 72 patients. Worse outcomes were also noted among patients who initially received CNIs than those who received CTX-based treatments after matching. CONCLUSIONS: Patients with MN combined with FSGS lesions have a higher risk of renal functional decline and a higher rate of relapse after CNIs than after CTX therapy.

Efficacy of "Dihuang pill prescriptions" combined with conventional treatment for diabetic kidney disease: A network meta-analysis and systematic review.

BACKGROUND: With the increasing incidence of diabetic nephropathy, there is currently no means to completely cure the disease. However, a large number of clinical data proved that traditional Chinese medicine combined with modern medical conventional treatment of diabetic kidney disease has achieved better efficacy than simple Western medicine conventional treatment. METHODS: Based on the mesh meta-analysis method, the objective evaluation of clinical efficacy of conventional treatment of diabetic kidney disease and comparison provided more evidence-based basis for the treatment of diabetic kidney disease and further select effective intervention measures to delay the process of diabetic kidney disease. RESULTS: 41 randomized controlled trials were included, involving 4 kinds of "Dihuang pill prescriptions," with a total sample size of 3562 cases, including 1793 patients in the experimental group and 1769 patients in the control group. Network meta-analysis suggested that the best SUCRA-ranked 2 interventions were Jingui Shenqi pills/decoction + Western medicine routine" and Jisheng Shenqi pills/decoction + Western medicine routine in terms of reducing 24-hour urinary protein. In terms of reducing urinary albumin excretion rate, the top 2 SUCRA-ranked interventions were Zhibai Dihuang pills/decoction + Western medicine routine and Liuwei Dihuang Pills/decoction + Western medicine routine. In terms of reducing serum creatinine, the top 2 SUCRA ranked interventions were Jisheng Shenqi pills/decoction + Western medicine routine, Zhibai Dihuang Pills/decoction + Western medicine routine. In terms of lowering fasting blood glucose, the top 2 SUCRA-ranked interventions were Zhibai Dihuang pills/ decoction + Western medicine routine and Jisheng Shenqi pills/decoction + Western medicine routine. The results showed that the treatment plan of conventional Western medicine combined with Chinese patent medicine could reduce serum creatinine, 24-hour urinary protein, fasting blood glucose urine protein excretion rate and improve the total clinical effective rate. CONCLUSION: The combination of medicine was obviously better than conventional Western medicine alone.

The efficacy of Chinese herbal ointment in treating perianal eczema: A systematic review and meta-analysis.

BACKGROUND: Traditional Chinese herbal ointment has significant curative effect and few side effects in the treatment of perianal eczema (PE). Currently, there is no systematic evaluation on the treatment of PE with traditional Chinese medicine ointment. The current aim is to systematically evaluate the efficacy of traditional Chinese medicine ointment in the treatment of PE through meta-analysis. METHODS: Randomized controlled trials on the treatment of PE with Chinese herbal plaster were included in the meta-analysis, which was searched in Chinese and English databases up to March 1, 2023. The search will be conducted in accordance with the object of PICOS framework. Two research will independently use EndnoteX9 to extract the data and evaluate the quality assessment of included trails. Meta-analysis was performed using Revman5.4.1 provided by Cochrane Collaboration; when the outcome indicator is a dichotomous variable, relative risk (RR) was used as the effect size; when the outcome indicator is a continuous variable, weighted mean difference (MD) was used as the effect size, each effect size should be expressed as 95% confidence interval (CI). RESULTS: The results of meta-analysis showed that: The total effective rate of PE (RR: 1.22, 95% CI: 1.15, 1.30, P < .01; I2 = 32%, Q = 0.17). The cure rate of PE (RR: 3.37, 95% CI: 2.30, 4.94, P < .01; I2 = 21% Q = 0.26). The recurrence rate of PE (RR: 0.25, 95% CI: 0.13, 0.48, P < .01; I2 = 31%Q = 0.23). Itchy points (MD: 0.04, 95% CI: -0.19, 0.27; I2 = 26%) Skin damage area (MD: -0.37, 95% CI: -0.56, -0.19; I2 = 26%). Skin damage form (MD: -0.59, 95% CI: -0.81. -0.36; I2 = 0%). CONCLUSION: A total of 11 articles were included in this study for meta-analysis, and the results showed that Chinese medicine ointment is more helpful in improving the skin lesion area and skin damage form, significantly improve the response rate and cure rate, reduce the recurrence rate. Chinese herbal ointment has guiding significance for clinical practice which deserve to use ointments by further experimental and clinical investigation.

Modeling individual head-related transfer functions from sparse measurements using a convolutional neural network.

Individual head-related transfer functions (HRTFs) are usually measured with high spatial resolution or modeled with anthropometric parameters. This study proposed an HRTF individualization method using only spatially sparse measurements using a convolutional neural network (CNN). The HRTFs were represented by two-dimensional images, in which the horizontal and vertical ordinates indicated direction and frequency, respectively. The CNN was trained by using the HRTF images measured at specific sparse directions as input and using the corresponding images with a high spatial resolution as output in a prior HRTF database. The HRTFs of a new subject can be recovered by the trained CNN with the sparsely measured HRTFs. Objective experiments showed that, when using 23 directions to recover individual HRTFs at 1250 directions, the spectral distortion (SD) is around 4.4 dB; when using 105 directions, the SD reduced to around 3.8 dB. Subjective experiments showed that the individualized HRTFs recovered from 105 directions had smaller discrimination proportion than the baseline method and were perceptually undistinguishable in many directions. This method combines the spectral and spatial characteristics of HRTF for individualization, which has potential for improving virtual reality experience.

Low-latency monaural speech enhancement with deep filter-bank equalizer.

It is highly desirable that speech enhancement algorithms can achieve good performance while keeping low latency for many applications, such as digital hearing aids, mobile phones, acoustically transparent hearing devices, and public address systems. To improve the performance of traditional low-latency speech enhancement algorithms, a deep filter-bank equalizer (FBE) framework was proposed that integrated a deep learning-based subband noise reduction network with a deep learning-based shortened digital filter mapping network. In the first network, a deep learning model was trained with a controllable small frame shift to satisfy the low-latency demand, i.e., no greater than 4 ms, so as to obtain (complex) subband gains that could be regarded as an adaptive digital filter in each frame. In the second network, to reduce the latency, this adaptive digital filter was implicitly shortened by a deep learning-based framework and was then applied to noisy speech to reconstruct the enhanced speech without the overlap-add method. Experimental results on the WSJ0-SI84 corpus indicated that the proposed DeepFBE with only 4-ms latency achieved much better performance than traditional low-latency speech enhancement algorithms across several objective metrics. Listening test results further confirmed that our approach achieved higher speech quality than other methods.

Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes.

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.

Comparison of efficacy and safety of traditional Chinese patent medicines for diabetic nephropathy: A protocol for Bayesian network meta-analysis.

BACKGROUND: Diabetic nephropathy (DN) is one of the most serious complications of diabetes. It has become a global public health problem among humans. DN is the leading cause of end-stage renal disease. At present, there is no specific medicine or modern medicinal therapy. In recent years, studies have shown that traditional Chinese patent medicines have been effective in treating DN, with few side effects. There is no systematic review on the treatment of DN with Chinese patent medicines. The current systematic review aims to evaluate the efficacy and safety of Chinese patent medicines for the treatment of DN. METHODS: We will develop a search strategy to search major Chinese and English databases from inception to February 25, 2022 for randomized controlled trials examining the use of traditional Chinese patent medicine for the treatment of DN. The search will be conducted in accordance with the participants, interventions, comparisons, outcomes (PICOS) framework. Two researchers will use EndnoteX9 software to extract data and independently evaluate the quality of the included trials. Finally, the Bayesian network meta-analysis will be carried out by using software such as ReviewManager, Stata16.0, and WinBUGS1.4.3. RESULTS: The primary outcomes will be urine albumin excretion rate, urea nitrogen, serum creatinine, total effective rate, and adverse events, and the secondary outcomes will be body mass index, fasting blood glucose, and 2-hPG during 75-g OGTT. These outcomes will be examined to provide a reliable basis for the treatment of DN with different traditional Chinese patent medicines. CONCLUSION: This review will compare the efficacy and safety of different traditional Chinese patent medicines for treating DN. The results of the study will provide a basis for the selection of adjuvant treatment options for DN.

Deep learning-based stereophonic acoustic echo suppression without decorrelation.

Traditional stereophonic acoustic echo cancellation algorithms need to estimate acoustic echo paths from stereo loudspeakers to a microphone, which often suffers from the nonuniqueness problem caused by a high correlation between the two far-end signals of these stereo loudspeakers. Many decorrelation methods have already been proposed to mitigate this problem. However, these methods may reduce the audio quality and/or stereophonic spatial perception. This paper proposes to use a convolutional recurrent network (CRN) to suppress the stereophonic echo components by estimating a nonlinear gain, which is then multiplied by the complex spectrum of the microphone signal to obtain the estimated near-end speech without a decorrelation procedure. The CRN includes an encoder-decoder module and two-layer gated recurrent network module, which can take advantage of the feature extraction capability of the convolutional neural networks and temporal modeling capability of recurrent neural networks simultaneously. The magnitude spectra of the two far-end signals are used as input features directly without any decorrelation preprocessing and, thus, both the audio quality and stereophonic spatial perception can be maintained. The experimental results in both the simulated and real acoustic environments show that the proposed algorithm outperforms traditional algorithms such as the normalized least-mean square and Wiener algorithms, especially in situations of low signal-to-echo ratio and high reverberation time RT60.

On the importance of power compression and phase estimation in monaural speech dereverberation.

Previous studies have shown the importance of introducing power compression on both feature and target when only the magnitude is considered in the dereverberation task. When both real and imaginary components are estimated without power compression, it has been shown that it is important to take magnitude constraint into account. In this paper, both power compression and phase estimation are considered to show their equal importance in the dereverberation task, where we propose to reconstruct the compressed real and imaginary components (cRI) for training. Both objective and subjective results reveal that better dereverberation can be achieved when using cRI.

Characteristics of the antibiotic resistance genes in the soil of medical waste disposal sites.

The inappropriate disposal of medical waste allows bacteria to acquire antibiotic resistance, which results in a threat to public health. Antibiotic resistance gene (ARG) profiles were determined for 45 different soil samples containing medical waste and 15 nearby soil samples as controls. Besides physical and chemical analyses (i.e., dry matter content, pH value, and metal content), the genomes of microorganisms from the soil samples were extracted for high-throughput sequencing. ARG abundances of these samples were obtained by searching the metagenomic sequences against the antibiotic resistance gene database and the copies of ARGs per copy of the 16S rRNA gene at different levels were assessed. The results showed medical waste accumulation significantly enriched the contents of Cu, Cr, Pb, and As in the tested soil samples. Compared to the controls, the samples collected from areas containing medical waste were significantly enriched (p < 0.05, t-test) with ARGs annotated as sulfonamide and multidrug resistance genes, and in particular, the subtypes sul1 and sul2 (sulfonamide resistance genes), and multidrug_transporter (multidrug resistance gene). Moreover, the ARGs of the samples from the polluted areas were more diverse than those of the control samples (p < 0.05, t-test). The comparatively higher abundance and diversity of ARGs in contaminated soil pose a potential risk to human health.

Puerarin prevents high-fat diet-induced obesity by enriching Akkermansia muciniphila in the gut microbiota of mice.

Growing evidence indicates that the gut microbiota plays a significant role in the pathophysiological processes of obesity and its related metabolic symptoms in the host. Puerarin, an active ingredient in the root of Pueraria lobate has been suggested to have a potent anti-obesity effect. Herein, we tested whether this effect of puerarin is associated with changes in the gut microbiota. In addition to reducing body weight, inflammation, and insulin resistance, puerarin administration significantly altered the composition of the gut microbiota. Notably, puerarin treatment greatly increased the abundance of Akkermansia muciniphila, a mucin-degrading bacterium known to be beneficial for host metabolism and significantly downregulated in high-fat diet-fed mice. Further experiments revealed that puerarin increased intestinal expression levels of Muc2 and Reg3g and protected intestinal barrier function (normal permeability) by increasing the expression of ZO-1 and occludin in vivo and in vitro. These data suggest that puerarin's enriching effect on A. muciniphila is mediated, at least in part, by a host cellular response to protect the host from diet-induced metabolic disorders and other diseases.

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.

BACKGROUND: Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS: In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification. CONCLUSION: Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.

BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.

Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater.

With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.