Defence strategies and antibiotic resistance gene abundance in enterococci under stress by exposure to low doses of peracetic acid

partially_open12noPeracetic acid (PAA) is an organic compound used efficiently as disinfectant in wastewater treatments. Yet, at low doses it may cause selection; thus, the effect of low doses of PAA on Enterococcus faecium as a proxy of human-related microbial waste was evaluated. Bacteria were treated with increasing doses of PAA (from 0 to 25 mg L1 min) and incubated in regrowth experiments under non-growing, limiting conditions and under growing, favorable conditions. The changes in bacterial abundance, in bacterial phenotype (number and composition of small cell clusters), and in the abundance of an antibiotic resistance gene (ARG) was evaluated. The experiment demonstrated that the selected doses of PAA efficiently removed enterococci, and induced a long-lasting effect after PAA inactivation. The relative abundance of small clusters increased during the experiment when compared with that of the inoculum. Moreover, under growing favorable conditions the relative abundance of small clusters decreased and the number of cells per cluster increased with increasing PAA doses. A strong stability of the measured ARG was found, not showing any effect during the whole experiment. The results demonstrated the feasibility of low doses of PAA to inactivate bacteria. However, the stress induced by PAA disinfection promoted a bacterial adaptation, even if potentially without affecting the abundance of the ARG.openTurolla, Andrea; Sabatino, Raffaella; Fontaneto, Diego; Eckert, Ester M.; Colinas, Noemi; Corno, Gianluca; Citterio, Barbara; Biavasco, Francesca; Antonelli, Manuela; Mauro, Alessandro; Mangiaterra, Gianmarco; Di Cesare, AndreaTurolla, Andrea; Sabatino, Raffaella; Fontaneto, Diego; Eckert, Ester M.; Colinas, Noemi; Corno, Gianluca; Citterio, Barbara; Biavasco, Francesca; Antonelli, Manuela; Mauro, Alessandro; Mangiaterra, Gianmarco; Di Cesare, Andre

Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere

One effective approach to treating large amounts of wastewater produced during livestock production is to use it to irrigate crops. However, antibiotic compounds and antibiotic resistance genes (ARGs) associated with livestock wastewater may enter the soil and plants. ARGs are spread readily among microbial populations by mobile genetic elements, and may pose threats to human health. Compared with conventional furrow irrigation (CFI), alternate-furrow irrigation (AFI) can reduce water use and still achieve high yields. These different irrigation methods may influence the fate of ARGs in soil however, few reports have studied the combined effects of AFI and irrigation with livestock wastewater upon the distribution of ARGs in soil. Here, swine wastewater was used to irrigate cultivated peppers, and compared to relatively ARG-free groundwater. AFI was compared to CFI (100%) at three AFI irrigation rates (80%, 65% and 50% of CFI). The results showed that wastewater irrigation resulted in greater accumulation of antibiotic compounds and ARGs in soil than groundwater. The effect of wastewater was much more pronounced in the rhizosphere than non-rhizosphere soil. Compared with CFI, AFI using wastewater reduced the relative abundance of ARGs in the pepper rhizosphere, but the concentration of antibiotic compounds was largely unaffected; though antibiotic compound concentrations in roots were significantly lower, the abundance of ARGs in roots at 50% and 65% rates and in fruits at 50% rate were significantly increased when using wastewater. The soil bacterial communities did not change significantly between the different irrigation rates. Different behaviours were observed between ARGs and antibiotic compounds at different irrigation rates. Antibiotic compound availability plays an important role in the diffusion of ARGs. In conclusion, AFI of livestock wastewater can reduce the relative abundance of ARGs in rhizosphere soil, but low irrigation amount should be employed carefully for the safe agricultural production

Final Report for the CORE Organic II funded project "Restrictive use of antibiotics in organic animal farming – a potential for safer, high quality products with less antibiotic resistant bacteria - SafeOrganic"

• The level of antimicrobial resistance in bacteria from organic vs. conventional pigs has been compared for approximate 25 herds of each production system in DK, FR, IT and SE, by sampling faeces at farm or colon content at slaughterhouse from two pigs per herd. • An E. coli isolate was obtained from each sample and subjected to analysis of MIC (minimum inhibitory concentration) values for comparison of the resistance towards 10 antibiotics between production systems. Resistance to ampicillin, streptomycin, sulphonamides, tetracycline and trimethoprim was most common – ranging from 14% to 75% of E. coli isolates from conventional pigs and from 1% to 46% of isolates from organic pigs. The resistance towards these five antibiotics varied markedly between the four countries, but the resistance was always significantly lower in organic pigs than in conventional pigs, except for tetracycline in Sweden, where both production systems had a low occurrence. • However, DNA based real-time PCR quantification of cat, strA, sul2, sul1, tetA and tetB genes encoding resistances to chloramphenicol, streptomycin, sulphonamides and tetracycline, respectively, was unable to show a difference in the occurrence of resistance genes in the microbiota of organic vs. conventional pigs from the same country. • The quantitative level of antimicrobial resistance carried by the individual animal in faeces /intestinal content and on the carcass was assessed by determining the number of E. coli resistant to tetracycline (TET), out of total E. coli (i.e. proportion of TET E. coli). Tetracycline is one of the most commonly used antimicrobials in swine production. Except from Sweden, TET resistant E. coli was found in close to all pigs of both organic and conventional origin in DK, FR and IT. This was unexpected considering the restrictions on antimicrobial usage in organic pig production. Still, the proportion of E. coli carrying TET resistance in the colon was significant lower in the organic pigs, except in Sweden where both production systems had a low occurrence • Organic pigs are often slaughtered together with conventional pigs implying a risk of contaminating organic pork with resistant bacteria. Therefore, the bacteria present in pigs’ own intestinal content was compared with those present on their carcass at end of slaughter to elucidate potential cross-contamination. In France and Denmark, the prevalence of TET resistant E. coli was generally lower on the carcasses than in the colon. However, the observed difference in the proportion of TET resistant E. coli in the colon of organic vs. conventional pigs was no longer apparent on carcasses. This may indicate that organic pigs are prone to lose their inherent lower level of resistance during the slaughter process. France is already slaughtering organic pigs before conventional, which points to the importance of hygienic measures in general. • Different methods were applied in the search for potential markers for (imprudent) antibiotic use in organic animal production. The genetic diversity of bacteria was suggested to be a possible marker as the diversity was hypothesised to be higher in organic pigs due to less selection pressure from antimicrobials. This could however, not be supported as DNA genotyping by PFGE (pulse-field gel electrophoresis) in France revealed a very high genetic diversity of E. coli strains in both production systems and it was not possible to associate specific PFGE profiles to either organic or conventional origin. Also an examination of pigs’ entire intestinal microbiota by pyrosequencing was unable to resolve a difference between organic and conventional pigs. Alternatively, differences in antibiotic resistance profiles were investigated by PCA (Principal Component Analysis) for the potential as marker. PCA of MIC data for E. coli (IT and SE) was shown to be able to point out organic herds with unusual (conventional-like) resistance profiles. The PCA analysis is seen as a promising tool to enable a more targeted control of antimicrobial consumption in organic pig production. • Sampling at slaughterhouses is easier and more cost-effective than sampling of live animals at each farm, but foreign bacteria ingested from the surrounding environment (truck, lairage) may bias results obtained at slaughter. Therefore, we investigated for an intestinal sampling site where the level of antibiotic resistance can be considered to resemble the herd status. This was done by assessing the time for ingested particles to reach different intestinal sampling points. The particles were found to reach the mid-colon in 2 of 6 pigs within 4 h. However, the proportion of TET resistant E. coli in each pig seemed stable in both caecum and mid-colon independent on sampling time (up to 8 h). This supported that that our sampling procedure at slaughterhouse fitted the purpose of our project

An electronic irrigation system using IoT and neural networks

One of the approaches that fall under the alternative application of water on earth or soil is electronic irrigation. It is aware of the need to irrigate crops, restore the vegetation of difficult soil in arid areas, and because of dry spells, as our state has experienced in recent years. Other issues, such as increasing plant growth while lowering the value of agriculture, necessitate installing an irrigation system that cuts back effort, reduces farm and field employees, and minimizes monetary matters within the construction of agricultural comes is crucial. Soil wetness measure is incredibly tough; thus the economic maintaining of its target levels. The answer to this drawback is an automatic irrigation system. This analysis proposed an electronic irrigation system that reduces users' effort to plant care. The system kernel is the self-learning Kohonen Neural Network, which depends on the reading of the detector of soil wetness, plant type, and forecast data. The soil wetness detector indicates the soil wetness level. Also, the system is mechanically started once the wetness level is not up to the extent necessary for the plant's growth. When the system reaches the soil wetness level, it is mechanically stopped for a defined period of morning and evening. As a soil wetness level differs from one plant kind to a different, 3 plant varieties area unit used during this analysis. Beginning the system littered with the weather data, is saving time and effort for the employees

What we can learn from Covid19 pandemic: A zoom lens from Islamic viewpoint based on Hadith

This paper examines the responses of the Movement Control Order and acceptance of the COVID-19 among the Muslims. We selected participants (Muslim) through random sampling from Universiti Utara Malaysia international students. We interviewed them and asked four questions related to the responses and reactions on issues during COVID-19. We analysed the responses and its relation with compilation relevant Hadiths through inductive reasoning approach. Hence, we found that most of our respondents are have positive attitude towards the MCO and COVID-19 which all of the actions are closely supported by the Hadith

Effect of composting on reducing the abundance of tetracycline-resistant genes in cow manure

© SGEM2018. All rights reserved. Wastes from livestock farms contain significant amounts of antibacterial drugs and antibiotic–resistant genes. Due to weak adsorption in the animal's body, antibiotics are released into the environment in an unchanged form or as metabolites in the composition of manure. In addition to the antibacterial agents, the manure of treated animals contains antibiotic–resistant bacteria. The use of manure in untreated form as a soil fertilizer can lead to the spread of antibiotic resistance among soil microorganisms. Composting is an effective way to reduce the content of antibiotic–resistant genes in manure. In this paper, the effect of the composting of cow manure contaminated with different concentrations of oxytetracycline on the temporal change in the number of two tetracycline–resistant genes tet(M) and tet(X) was evaluated. The initial concentrations of oxytetracycline in the cow manure were 50 mg kg–1, 150 mg kg–1 and 300 mg kg–1. Composts mixtures were incubated for 4 months. The number of copies of tet(M) and tet(X) genes was evaluated by the real–time PCR method using specific primers. It was found that the introduction of oxytetracycline in manure leads to an increase in the level of resistant genes tet(M) and tet(X). The higher the dose of antibiotic, the more genes were found. With the passage of time of the composting process, the content of resistant genes decreases. On the 75th day, resistant genes were not found in all samples of compost mixtures

Antibiotic resistance in the wild: an eco-evolutionary perspective

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.Peer reviewe

Microbiota in monocultured Litopenaeus vannamei vs. polyculture with Trachinotus ovatus

The structures of the microbial community in the intestine, aquaculture water, and sediment of Litopenaeus vannamei, both in monoculture and mixed culture with Trachinotus ovatus, were analyzed by sequencing 16S rRNA amplicons. 1,120,500 valid reads were obtained from 21 samples, and 3,767 operational taxonomic units (OTUs) were classified. In the two culture modes, the abundance and diversity of bacterial in the sediment were significantly higher than in the L. vannamei intestine under the monoculture mode, in the water and intestines of L. vannamei and T. ovatus under the mix-culture mode (P 0.05). The dominant phyla in the sediment under two culture modes were Proteobacteria, Bacteroidetes, and Chloroflexi. The microbial community structure in the water and L. vannamei intestine were similar in both culture modes. The dominant phyla included Cyanobacteria, Proteobacteria, and Actinobacteria, with their abundances ranging from 80.88% to 97.10%. Proteobacteria was the dominant phylum in each group of samples, and the dominant genus in both culture modes was GpIIa. There was little difference in microbial community structures under the two culture modes; while the culture mode did not affect the core phyla/genera, there were differences in relative abundance. The experimental results provide a reference for the exploration of efficient and specific probiotic screening and microbial formulation techniques

Characterization of blaNDM-5-and blaCTX-M-199-producing ST167 Escherichia coli Isolated from shared bikes

Shared bikes as a public transport provide convenience for short-distance travel. Whilst they also act as a potential vector for antimicrobial resistant (AR) bacteria and antimicrobial resistance genes (ARGs). However, the understanding of the whole genome sequence of AR strains and ARGs-carrying plasmids collected from shared bikes is still lacking. Here, we used the HiSeq platform to sequence and analyze 24 Escherichia coli isolated from shared bikes around Metro Stations in Beijing. The isolates from shared bikes showed 14 STs and various genotypes. Two blaNDM-5 and blaCTX-M-199-producing ST167 E. coli have 16 resistance genes, four plasmid types and show >95% of similarities in core genomes compared with the ST167 E. coli strains from different origins. The blaNDM-5- or blaCTX-M-199-carrying plasmids sequencing by Nanopore were compared to plasmids with blaNDM-5- or blaCTX-M-199 originated from humans and animals. These two ST167 E. coli show high similarities in core genomes and the plasmid profiles with strains from hospital inpatients and farm animals. Our study indicated that ST167 E. coli is retained in diverse environments and carried with various plasmids. The analysis of strains such as ST167 can provide useful information for preventing or controlling the spread of AR bacteria between animals, humans and environments

Campylobacter coli in Organic and Conventional Pig Production in France and Sweden: Prevalence and Antimicrobial Resistance.

The purpose of the study was to evaluate and compare the prevalence and antimicrobial resistance of Campylobacter coli in conventional and organic pigs from France and Sweden. Fecal or colon samples were collected at farms or at slaughterhouses and cultured for Campylobacter. The minimum inhibitory concentrations of ciprofloxacin, nalidixic acid, streptomycin, tetracycline, erythromycin, and gentamicin were determined by microdilution for a total of 263 French strains from 114 pigs from 50 different farms and 82 Swedish strains from 144 pigs from 54 different farms. Erythromycin resistant isolates were examined for presence of the emerging rRNA methylase erm(B) gene. The study showed that within the colon samples obtained in each country there was no significant difference in prevalence of Campylobacter between pigs in organic and conventional productions [France: conventional: 43/58 (74%); organic: 43/56 (77%) and Sweden: conventional: 24/36 (67%); organic: 20/36 (56%)]. In France, but not in Sweden, significant differences of percentages of resistant isolates were associated with production type (tetracycline, erythromycin) and the number of resistances was significantly higher for isolates from conventional pigs. In Sweden, the number of resistances of fecal isolates was significantly higher compared to colon isolates. The erm(B) gene was not detected in the 87 erythromycin resistant strains tested