Effect of pH on the mitigation of extracellular/intracellular antibiotic resistance genes and antibiotic resistance pathogenic bacteria during anaerobic fermentation of swine manure.

Effects of various initial pH values (i.e., 3, 5, 7, 11) during anaerobic fermentation of swine manure on intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) and ARG-carrying potential microbial hosts were investigated. The abundance of almost all iARGs and eARGs decreased by 0.1-1.7 logs at pH 3 and pH 5. The abundance of only three iARGs and eARGs decreased by 0.1-0.9 logs at pH 7 and pH 11. Under acidic initial fermentation conditions (pH 3 and pH 5), the ARG removal effect was more pronounced. Acidic conditions (pH 3 and pH 5) significantly reduced the diversity and abundance of the microbial community, thereby eliminating many potential ARG hosts and antibiotic-resistant pathogenic bacteria (ARPB). Therefore, the study results contribute to the investigation of the effects of swine manure anaerobic fermentation on the removal and risk of contamination of ARGs and ARPB.

Driving factors of spatial-temporal difference in China's transportation sector carbon productivity: an empirical analysis based on Geodetector method.

Carbon productivity is the core index to measure the performance of carbon emission reduction. Exploring the driving factors of the spatial-temporal differences in China's transportation sector, carbon productivity (TSCP) is conducive to the low-carbon sustainable development of the transportation sector. Based on the calculation of TSCP in 30 provinces in China from 2000 to 2019, we use time series, spatial visualization, and Dagum Gini coefficient to reveal the characteristics of spatial-temporal evolution and regional differences of TSCP, and uses Geodetector to identify the driving factors that affecting the spatial-temporal differences of TSCP. The results are as follows: (1) from 2000 to 2019, China's TSCP shows a U-shaped change trend of "decline to rise," and shows a spatial pattern of "high in the eastern and central, low in the western". (2) There are obvious regional differences in China's TSCP. The differences within each region show the trend of "eastern > central > western," while the differences between regions show the trend of "central-western > eastern-western > eastern-central," and the differences between regions are the main reason for the overall differences. (3) The spatial-temporal differences in China's TSCP are affected by many factors, such as social economy and self-endowment. Overall, energy intensity, foreign trade, technological innovation level, energy structure, and industrial structure are the dominant factors. Additionally, the interaction between the driving factors enhances the impact on the spatial-temporal differences of TSCP. Finally, according to the analysis results, some policy suggestions are put forward to improve TSCP.

Supercarriers of antibiotic resistome in a world's large river.

BACKGROUND: Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as "terrestrial gut." RESULTS: By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by "natural" supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins. CONCLUSIONS: We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world's large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally. Video Abstract.

Deciphering changes in the abundance of intracellular and extracellular antibiotic resistance genes and mobile genetic elements under anaerobic fermentation: Driven by bacterial community.

Antibiotic resistance genes (ARGs) are considered to be a new environmental pollutant and the removal of ARGs from swine manure by anaerobic fermentation was a crucial topic. This research discusses effects of initial pH values (3, 5, 7, 11) on intracellular and extracellular ARGs (iARGs and eARGs) as well as mobile genetic elements (MGEs) during anaerobic fermentation of swine manure had been examined. The initial pH during fermentation was found to be acidic (pH 3 and 5) in results, which was conducive to the removal of six eARGs and seven iARGs. Similarly, intracellular and extracellular MGEs were effectively eliminated with an initial pH of 3 and 5. The abundance of MGEs and four ARGs were enriched with an initial pH of 7 and 11. Acidic conditions can greatly deduce the diversity as well as abundance of the microbial community, ensuing removal of MEGs and ARGs. These findings are critical for risk assessment and management of ARGs.

GRIM: A General, Real-Time Deep Learning Inference Framework for Mobile Devices Based on Fine-Grained Structured Weight Sparsity.

It is appealing but challenging to achieve real-time deep neural network (DNN) inference on mobile devices, because even the powerful modern mobile devices are considered as "resource-constrained" when executing large-scale DNNs. It necessitates the sparse model inference via weight pruning, i.e., DNN weight sparsity, and it is desirable to design a new DNN weight sparsity scheme that can facilitate real-time inference on mobile devices while preserving a high sparse model accuracy. This paper designs a novel mobile inference acceleration framework GRIM that is General to both convolutional neural networks (CNNs) and recurrent neural networks (RNNs) and that achieves Real-time execution and high accuracy, leveraging fine-grained structured sparse model Inference and compiler optimizations for Mobiles. We start by proposing a new fine-grained structured sparsity scheme through the Block-based Column-Row (BCR) pruning. Based on this new fine-grained structured sparsity, our GRIM framework consists of two parts: (a) the compiler optimization and code generation for real-time mobile inference; and (b) the BCR pruning optimizations for determining pruning hyperparameters and performing weight pruning. We compare GRIM with Alibaba MNN, TVM, TensorFlow-Lite, a sparse implementation based on CSR, PatDNN, and ESE (a representative FPGA inference acceleration framework for RNNs), and achieve up to 14.08× speedup.

New insight into fates of sulfonamide and tetracycline resistance genes and resistant bacteria during anaerobic digestion of manure at thermophilic and mesophilic temperatures.

This study investigated the variations in antibiotic (sulfonamide and tetracycline) resistance genes (ARGs) and resistant bacteria (ARB) during manure anaerobic digestion (AD) at 35 ℃ and 55 ℃, and discussed the mechanisms of variations in ARGs. The AD lasted for 60 days, five ARGs and intI1 each decreased in abundance after AD at the thermophilic temperature, while only half decreased at the mesophilic temperature. On days 10, 30, and 60, sulfonamide and tetracycline ARB were screened on selective media. During thermophilic AD, ARB numbers reduced by 4-log CFUs per gram dry manure, but only by approximately 1-log CFU at the mesophilic temperature. However, ARB composition analysis showed that at either temperature, no significant reduction in identified ARB species was observed. Furthermore, 72 ARB clones were randomly selected to detect the ARGs they harbored, and the results showed that each ARG was harbored by various hosts, and no definitive link existed between ARGs and bacterial species. In addition, by comparison with the identified host by culture method, the host prediction results based on the correlation analysis between ARGs and the bacterial community was proven to be unreliable. Overall, these findings indicated that relationships between ARB and ARGs were intricate.

Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG.

The emergence and spread of antibiotic resistance has pose a huge threat to both human health and environmental ecosystem. However, little is known regarding the pool of ARGs in extracellular DNA (eDNA). In this study ten ARGs (sul1, sul2, tetW, tetX, ermA, ermB, blaTEM, ampC, cat and cmr) and class I integron (intI1) in the sludge from hospital, pharmaceutical industry, wastewater treatment plant (WWTP), and swine manure, and sediment in urban lake in the form of both eDNA and intracellular DNA (iDNA) were evaluated by quantitative polymerase chain reaction (qPCR). The results showed that every gram of sludge dry weight contained from 7.31 × 103 to 1.16 × 1010 copies of extracellular ARGs (eARGs) and from 1.04 × 105 to 2.74 × 1012 copies of intracellular ARGs (iARGs). The sludge from hospital with the highest ratio of eARGs to total ARGs (11.02-89.63%), followed by the sediment from urban lake, implying that most of the ARGs in these regions were contributed by eARGs. The relative abundance of eARGs were higher than iARGs in sludge from WWTP and pharmaceutical industry, moreover, 1/3 and 5/9 detected eARGs were higher than the ARGs in the iDNA extracted from sludge of hospital and sediment from urban lake, respectively. Furthermore, the transforming ability of eARGs suggesting that adsorbed eARG is more preferentially coupled to the competent cells than free eARG. These findings highlight the need to focus attention on the contribution of eARGs to the dissemination of antibiotic resistance into environment, and also future needs in mitigating the spread of eARGs in the environment.

Occurrence of antibiotic resistance genes and bacterial pathogens in water and sediment in urban recreational water.

The emergence and prevalence of antibiotic resistance genes (ARGs) and pathogens in the environment are serious global health concern. However, information about the occurrence of ARGs and pathogens in recreational water is still limited. Accordingly, we investigated the occurrence of six ARGs and human pathogens in three recreational lakes, and the correlations between ARGs and one mobile genetic element (intI1) were analyzed. The quantitative PCR results showed that the concentration of ARGs ranged from 4.58 × 100 to 5.0 × 105 copies/mL in water and from 5.78 × 103 to 5.89 × 108 copies/g dry weight (dw) in sediment. Sul1 exhibited the highest level among the five quantifiable ARGs. The concentrations of sul1, bla-TEM, and tetX exhibited significant positive correlations with intI1 (p < 0.05), indicating that intI1 may be involved in their proliferation. The detection frequencies of ARGs ranged from 75%-100%, indicating the prevalence of these risks in this region. The concentration of Escherichia coli, Aeromonas spp., Mycobacterium avium, Pseudomonas aeruginosa, and Salmonella enterica ranged from 103 to 105 copies/100 mL in water and 104-106 copies/g dw in sediment. In total, 25% of the samples harbored all pathogen genes, indicating the prevalence of these pathogens in recreational lakes. Furthermore, the next-generation sequencing results showed that 68 genera of pathogens were present, among which Aeromonas, Mycobacterium, and Pseudomonas were the dominant ones in this region, posing a considerable potential health risk to public health. Overall, the widespread distribution of ARGs and pathogens underscores the need to better monitor and mitigate their propagation in recreational lakes and the associated risks to human health.

Diversity of potential antibiotic-resistant bacterial pathogens and the effect of suspended particles on the spread of antibiotic resistance in urban recreational water.

Evidence of the increasing incidence of antibiotic resistance in watersheds has attracted worldwide attention. Limited in formation is available on the occurrences of health-related antibiotic-resistant bacterial pathogens (ARBPs) in recreational waters. The effects of certain environmental factors (e.g., suspended particles) on the spread of resistance also has not been characterized to date. In this study, a combination of culture and molecular methods was employed to comprehensively investigate the patterns of microbial resistance to representative antibiotics in samples from three recreational lakes in Beijing. The antibiotic resistance index (ARI) based on the gradient concentration assay revealed that samples showed high resistance to penicillin-G, moderate resistance to ampicillin, vancomycin and erythromycin and low resistance to ceftriaxone, gentamycin, tetracycline and chloramphenicol. Antibiotic-resistant bacteria (ARB) were cultured and collected, and the diversity of potential ARBP species was further explored using next-generation sequencing (NGS). The results showed that most of the identified ARBPs were environmental opportunistic pathogens with emerging clinical concerns, e.g., the multidrug-resistant Acinetobacter junii. Furthermore, particle-attached (PA) fractions presented higher ARI values than free-floating (FL) fractions did, indicating that the PA fractions were more resistant to selected antibiotics. And the NGS results revealed that the PA fractions showed higher similarity in the screened ARB community compositions in comparison with the FL fractions, primarily due to a protective effect provided by the particles. Accordingly, ARBPs could persist for a longer time in protective particle matrices. However, quantification of antibiotic-resistant genes (ARGs) by qPCR showed no significant abundance differences between the two fractions. Overall, these findings suggest a potential health risk from the prevalence of ARBPs in recreational waters and provides a better understanding of the contribution of particles in the spread of antibiotic resistance in aquatic systems, with implications for the control of excessive suspended particles by water management.

Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management.

The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5µm) and particle-attached (PA, >5µm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp. (aerA), Mycobacterium avium (16S) and Pseudomonas aeruginosa (oaa). The NGS results showed stable pathogen genera composition distinctions between the PA and FL fractions. Some genera, such as Aeromonas and Mycobacterium, exhibited higher abundances in the PA fractions. qPCR revealed that most of the gene concentrations were higher within particles than were FL fractions. Some gene levels showed correlations with the particle concentrations and lake nutrient levels. Further quantitative microbial risk assessment (QMRA) of selected strains (S. enterica and M. avium) indicated a higher health risk during secondary contact activities in lakes with more nutrients and particles. We concluded that suspended particles (mainly composed of algae) in urban recreational water might influence the pathogen distribution and could serve as reservoirs for pathogen contamination, with important management implications.

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR.

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 104-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR.

Oleiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield.

A yellow-pigmented strain, designated strain 3.5X(T), was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Xanthomonadaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The closest relative of strain 3.5X(T) was Fulvimonas soli DSM 14263(T) (94% similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C17 : 0, iso-C15 : 0, iso-C17 : 1ω9c and/or C16 : 010-methyl and iso-C11 : 0 as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely Oleiagrimonas soli gen. nov., sp. nov. The type strain is 3.5X(T) ( =NBRC 110685(T) =KCTC 42351(T) =CPCC 100614(T)).

Phaeocystidibacter luteus gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from the marine alga Phaeocystis globosa, and emended description of Owenweeksia hongkongensis.

A taxonomic study was carried out on strain PG2S01(T), isolated from a culture of Phaeocystis globosa, a haemolytic, toxin-producing, harmful marine alga. Cells of strain PG2S01(T) were Gram-negative, strictly aerobic, non-motile, non-fermentative, orange-pigmented, moderately halophilic rods. Growth was observed in the presence of 0.25-7.5 % NaCl and at 10-40 °C. The dominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and several unidentified aminolipids, phospholipids and other lipids. The G+C content of the chromosomal DNA was 44.6 mol%. 16S rRNA gene sequence comparison showed that strain PG2S01(T) was most closely related to Owenweeksia hongkongensis UST20020801(T) (88.9 % 16S rRNA gene sequence similarity); levels of similarity between strain PG2S01(T) and the type strains of recognized representatives of genera in the family Cryomorphaceae were <88 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PG2S01(T) formed a distinct evolutionary lineage within the family Cryomorphaceae. Strain PG2S01(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic data and phylogenetic inference, strain PG2S01(T) represents a novel species in a new genus in the family Cryomorphaceae, for which the name Phaeocystidibacter luteus gen. nov., sp. nov. is proposed. The type strain of the type species is PG2S01(T) ( = CCTCC AB 209288(T)  = LMG 25704(T)  = MCCC 1F01079(T)). An emended description of O. hongkongensis Lau et al. 2005 is also proposed.

Sinobacterium caligoides gen. nov., sp. nov., a new member of the family Oceanospirillaceae isolated from the South China Sea, and emended description of Amphritea japonica.

A taxonomic study was carried out on strain SCSWE24(T), isolated from a seawater sample collected from the South China Sea. Cells of strain SCSWE24(T) were Gram-negative, rod-shaped, non-motile, moderately halophilic and capable of reducing nitrate to nitrite. Growth was observed at salinities from 1.5 to 4.5% and at 4-37 °C; it was unable to degrade gelatin. The dominant fatty acids (>15%) were summed feature 3 (C16:1ω7c and/or C16:1ω6c; 50.4%) and C16:0 (21.1%). The G+C content of the chromosomal DNA was 58.8 mol%. 16S rRNA gene sequence comparisons showed that strain SCSWE24(T) was most closely related to an uncultured bacterium clone Tun3b.F5 (98%; GenBank accession no. FJ169216), and showed 92% similarity to an endosymbiont bacterium from the bone-eating worm Osedax mucofloris (clone Omu 9 c4791; FN773233). Levels of similarity between strain SCSWE24(T) and type strains of recognized species in the family Oceanospirillaceae were less than 93%; the highest similarity was 92%, to both Amphritea japonica JAMM 1866(T) and 'Oceanicoccus sagamiensis' PZ-5. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SCSWE24(T) formed a distinct evolutionary lineage within the family Oceanospirillaceae. Strain SCSWE24(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain SCSWE24(T) represents a novel species of a new genus, for which the name Sinobacterium caligoides gen. nov., sp. nov. is proposed. The type strain of Sinobacterium caligoides is SCSWE24(T) (=CCTCC AB 209289(T) =LMG 25705(T) =MCCC 1F01088(T)). An emended description of Amphritea japonica is also provided.