ARGs-OAP v3.0:Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization

Antibiotic resistance,which is encoded by antibiotic-resistance genes(ARGs),has proliferated to become a growing threat to public health around the world.With technical advances,especially in the popularization of metagenomic sequencing,scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed.To analyze thousands of ARGs in a highthroughput way,standardized and integrated pipelines are needed.The new version(v3.0)of the widely used ARGs online analysis pipeline(ARGs-OAP)has made significant improvements to both the reference database-the structured ARG(SARG)database-and the integrated analysis pipeline.SARG has been enhanced with sequence curation to improve annotation reliability,incorporate emerging resistance genotypes,and determine rigorous mechanism classification.The database has been further organized and visualized online in the format of a tree-like structure with a dictionary.It has also been divided into sub-databases for different application scenarios.In addition,the ARGs-OAP has been improved with adjusted quantification methods,simplified tool implementation,and multiple functions with userdefined reference databases.Moreover,the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles.The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia,governmental management,and consultation regarding risk assessment of the environmental prevalence of ARGs.

Trifunctional Cu-Mesh/Cu_(2)O@FeO Nanoarrays for Highly Efficient Degradation of Antibiotic, Inactivation of Antibiotic-Resistant Bacteria, and Damage of Antibiotics Resistance Genes

Trifunctional Cu-mesh/Cu_(2)O@FeO nanoarrays heterostructure is designed and fabricated by integrating CuCu_(2)O@FeO nanoarrays onto Cu-mesh(CM)via an in situ growth and phase transformation process.It is successfully applied to efficiently mitigate the antibiotic pollution,including degradation of antibiotics,inactivation of antibiotic-resistant bacteria(ARB),and damage of antibiotics resistance genes(ARGs).Under visible-light irradiation,CM/CuCu_(2)O@FeO nanoarrays exhibit a superior degradation efficiency on antibiotics(e.g.,up to 99%in 25 min for tetracycline hydrochloride,TC),due to the generated reactive oxygen species(ROS),especially the dominant·O^(2−).It can fully inactivate E.coli(HB101)with initial number of~108 CFU mL^(−1) in 10 min,which is mainly attributed to the synergistic effects of 1D nanostructure,dissolved metal ions,and generated ROS.Meanwhile,it is able to damage ARGs after 180 min of photodegradation,including tetA(vs TC)of 3.3 log 10,aphA(vs kanamycin sulfate,KAN)of 3.4 log 10,and tnpA(vs ampicillin,AMP)of 4.4 log 10,respectively.This work explores a green way for treating antibiotic pollution under visible light.

Behavior of Antibiotic-Resistant Fecal Coliforms in the Stream of a Sewage Treatment Plant in Tokyo

We are confronting a new threat in the prevalence of antibiotic-resistant bacteria followed by epidemic spread in aquatic environments in metropolitan areas because damage from river floods is increasing remarkably in Japan due to global extreme weather. The sewer penetration rate is about 100% in Tokyo and reclaimed water from sewage treatment plants accounts for over 50% of all water in both the down- and mid-stream areas of local rivers. The water quality of these rivers, which contain microflora, seems to be seriously affected by reclaimed water. In this study, we collected water samples on July 17, 2018 and examined the behavior of antibiotic-resistant fecal coliforms in the stream of a sewage treatment plant in Tokyo. Extended-spectrum β-lactamase (ESBL)-producing fecal coliforms with encoding genes were found;the CTX-M-1, CTX-M-9, TEM, and SHV groups were found to have survived in the final effluent to the river after sterilization with sodium hypochlorite.

Zoliflodacin: a hope to treat antibiotic-resistant Neisseria gonorrhoeae

Background:Neisseria gonorrhoeae is a gram-negative diplococcus that leads to sexually transmitted infection.N.gonorrhoeae is an obligate human pathogen that causes infection to the mucus-secreting epithelial cells both in males and females.In 2017 the center for disease control and the World Health Organization published the list of global priority pathogens-12 with denting therapeutic options,including antibiotic-resistant N.gonorrhoeae.Methods:we thoroughly characterized zoliflodacin antibiotic,its clinical trials and effect on human health by using different keywords like“zoliflodacin”,“COVID-19”,“clinical trials”from different data sources like Pub-Med,Google-Scholar,and Science-Direct.Results:Zoliflodacin shows a therapeutic approach against N.gonorrhoeae.It acts by inhibiting bacterial type 2 topoisomerase with the binding sites in bacterial gyrase.It shows promising results against N.gonorrhoeae.Zoliflodacin is effective in treating gonococcal urogenital and rectal infection.Conclusion:Currently,antibiotic is the only option to treat N.gonorrhoeae with no vaccine available to treat it.The new drug,zoliflodacin,specifically targets antibiotic-resistant gonorrhea and it has given a hope to researchers.This review elaborates the discovery of zoliflodacin,its mechanism of action,current clinical trials,and its effectiveness.

CRISPR-Cas9 mediated phage therapy as an alternative to antibiotics

Inappropriate use of antibiotics is globally creating public health hazards associated with antibiotic resistance.Bacteria often acquire antibiotic resistance by altering their genes through mutation or acquisition of plasmid-encoding resistance genes.To treat drug-resistant strains of bacteria,the recently developed CRISPR-Cas9 system might be an alternative molecular tool to conventional antibiotics.It disables antibiotic-resistance genes(plasmids)or deactivates bacterial virulence factors and sensitizes drug-resistant bacteria through site-specific cleavage of crucial domains of their genome.This molecular tool uses phages as vehicles for CRISPR-cas9 delivery into bacteria.Since phages are species-specific and natural predators of bacteria,they are capable of easily injecting their DNA to target bacteria.The CRISPR system is packaged into phagemid vectors,in such a way that the bacteria containing the antibiotic-resistance plasmid sequence or that containing specific DNA sequences were made to be targeted.Upon CRISPR delivery,Cas9 is programmed to recognize target sequences through the guide RNA thereby causing double-strand cleavage of targeted bacterial DNA or loss of drug resistance plasmid,which results in cell death.Remarkably,the safety and efficacy of this newly developed biotechnology tool and the biocontrol product need to be further refined for its usage in clinical translation.

Epidemiology of antibiotic resistance in Burkina Faso

Burkina Faso(West Africa) is a tropical country with a high incidence of infectious diseases.The uncontrolled use of antibiotics against bacterial pathogens has given rise to the emergence of antibiotic resistance in this country.The aims of this study were;i) to determine the prevalences of the most important pathogenic bacteria isolated in the town of Ouagadougou;ii) to identify the bacterial species which have acquired resistance as a result of antibiotic selection;iii) to compare antibiotic-resistances of Escherichia coli isolated from stool culture in the present study with results obtained in 2002 from strains collected in the same structure in Burkina Faso;iv) to determine the trend of antibiotic resistance in Burkina Faso in order to give local advice on the most appropriate empiric antibiotic therapy.Six thousand two hundred and sixty four samples of blood,stools, urine,sputum,pus and vaginal secretion were collected and analyzed in Saint Camille Medical Center(SCMC) laboratory from May 2001 to May 2006.Out of the 6264 samples tested no pathogen was identified in 1583(25.31%),whilst 4681(74.73%) were positive with the incidence of the microrganisms isolated being as follows;Escherichia coli 1291(27.6%),Staphylococcus aureus 922(19.7%),Salmonella spp 561(12. 0%),Streptococcus spp 499(10.7%),Klebsiella spp 359(7.7%),Shigella spp(6.3%),Acinetobacter spp 266(5.7%) and others 783(16.7%).Among the isolated pathogens,the highest resistance was found to amoxicillin:Proteus spp 95,6%,Escherichia coli 78,2%,Salmonella spp 62,2%,Shigella spp 73,4% and Klebsiella spp 89,9%,followed by resistance to ampicillin and cotrimoxazole.Comparing the prevalence of antibiotic resistance of Escherichia cob’from stool cultures isolated during 1999-2000 to that of 2001-2006, a significant reduction was found which could be due to the improved use of antibiotics in recent years.The reduced antibiotic-resistance observed in pathogens isolated in Burkina Faso during this study as compared to previous data,could be the result of setting up microbiological epidemiological monitoring centres,in tropical countries,to better control the emergence of bacterial antibiotic-resistance.

Inhibition mechanisms of secretome proteins from Paenibacillus polymyxa Kp10 and Lactococcus lactis Gh1 against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus

Objective:To determine the inhibition mechanisms of secretome protein extracted from Paenibacillus polymyxa Kp10(Kp10)and Lactococcus lactis Gh1(Gh1)against methicillin-resistant Staphylococcus aureus(MRSA)and vancomycin-resistant Enterococcus(VRE).Methods:The sensitivity and viability of MRSA and VRE treated with secretome proteins of Kp10 and Gh1 were determined using minimal inhibitory concentration,minimum bactericidal concentration,and time-to-kill assays.The morphological changes were observed using scanning electron microscopy and transmission electron microscopy.To elucidate the antimicrobial mechanism of secretome protein of Kp10 and Gh1 against MRSA and VRE,2D gel proteomic analysis using liquid chromatography-mass spectrometry was run by comparing upregulated and downregulated proteins,and the proton motive force study including the efflux of ATP,pH gradient,and the membrane potential study were conducted.Results:MRSA and VRE were sensitive to Kp10 and Gh1 secretome protein extracts and displayed apparent morphological and internal composition changes.Several proteins associated with cellular component functions were either downregulated or upregulated in treated MRSA and VRE by changing the membrane potential gradient.Conclusions:Kp10 and Gh1 secretome proteins reduce the growth of VRE and MRSA by damaging the cell membrane.Cell division,cell wall biosynthesis,and protein synthesis are involved in the inhibition mechanism.

Penicillin-Resistant <i>Aerococcus viridans</i>Bacteremia Associated with Bovine Severe Respiratory Syndrome

Aerococcus viridans, a less frequently isolated bacteria, is a gram-positive, catalase-negative coccus, found singly or in tetrads, with biochemical and growth characteristics of streptococci and enterococci. This microorganism, usually susceptible to penicillin, is often found in the environment and is infrequently associated with human/veterinary infections. We described a case of Holstein Friesian female calf, 150-day-old, affected by respiratory emergencies. Following the clinical signs, radiographic analysis and bacteriological/molecular examinations carried out on blood culture, a diagnosis of severe broncho-pulmonary disease associate with a multidrug-resistant A. viridans bacteremia was done. The present case highlights the invasive nature of a saprophytic bacterium showing a broad profile of antibiotic-resistance including β-lactams. Furthermore, this report confirms that the effectiveness of an antibiotic therapy is based primarily on a sure diagnosis including susceptibility testing.

It’s Possible to Predict a Decreased Bactericidal Effect of Biocides, through Antibiotic Resistance in ICU: Study Using a Large Sample of Bacteria and Multivariate Analysis

Objective: To determine whether there was any association between resistance to antibiotics and decreased susceptibility to antiseptics and disinfectants and their importance in clinical practice. Methods: We studied a large number of microorganisms isolated from ICU patients (high percentage of cases of antibiotic resistance). The antibiogram (Kirby-Bauer) was determined and, in parallel, the bactericidal effect was assessed by two methods, according to the product used: 1) Effect on rough material (endodontic files) in 10 min, using five disinfectants;2) Effect on a skin equivalent (sterile cotton cloth) in 30 sec, for two alcohol solutions. A predictive equation of the bactericidal effects versus microorganisms’ antibiogram was obtained by multivariate methods. Results:?Bactericidal efficacy was very similar for all the products with the exception of 1% povidone-iodine. Within each product there were no significant differences between the three groups of microorganisms: “Enterobacteria”, “Non Fermentative Gram Negative Bacteria” and “cocci”. Multivariate study only obtained one significant equation: 1% chlorhexidine resistance was directly correlated with aztreonam resistance (OR = 2.16), while resistance to imipenem and to phosphomycin acted as protection factors (OR < 1). Conclusion: There is no necessary to change the indications for antiseptics or disinfectants in ICUs, except if aztreonam resistance is high. In which caseis better to use greater concentration than 1% of Chlorhexidine.

In Vitro Bactericidal Activity of Jinghua Weikang Capsule(荆花胃康胶丸)and Its Individual Herb Chenopodium Ambrosioides L.against Antibiotic-Resistant Helicobacter Pylori

Objective： To investigate the bactericidal effects of Jinghua Weikang Capsule （荆花胃康胶丸） and its major component Chenopodium ambrosioides L. on antibiotic-resistant Helicobacter pylori. Methods： Four clinical antibiotic-resistant H. pylori strains were isolated and incubated in liquid medium containing Jinghua Weikang Capsule or Chenopodium ambrosioides L. By means of time-kill curve method, the average colony counts and bactericidal rate were calculated at time points of 0, 4, 8 and 24 h after the incubation and the time-kill curves were charted. Results： Both Jinghua Weikang Capsule and Chenopodium ambrosioides L. at a concentration of 0.64 g/L showed obvious bactericidal effect against antibiotic-resistant H. pylori after 4 h of incubation. Conclusion： Jinghua Weikang Capsule and Chenopodium ambrosioides L. are considered to be active against antibiotic-resistant H. pylori in vitro.

The exposure risks associated with pathogens and antibiotic resistance genes in bioaerosol from municipal landfill and surrounding area

Pathogenic microbes with antibiotic resistance can thrive on municipal solid waste as nutrients and be aerosolized and transported to vicinities during waste disposal processes.However,the characterization of pathogenic bioaerosols and assessment of their exposure risks are lacking.Herein,particle size,concentration,activity,antibiotic resistance,and pathogenicity of airborne microorganisms were assessed in different sectors of a typical landfill.Results showed that active sector in downwind direction has the highest bioaerosol level(1234 CFU/m3),while residential area has the highest activity(14.82 mg/L).Botanical deodorizer from mist cannon can effectively remove bioaerosol.Most bioaerosols can be inhaled into respiratory system till bronchi with sizes ranging from 2.1−3.3 and 3.3−4.7μm.Pathogenic bacteria(Bacilli,Bacillus,and Burkholderia-Paraburkholderia)and allergenic fungi(Aspergillus,Cladosporium,and Curvularia)prevailed in landfill.Although high abundance of microbial volatile organic compounds(mVOCs)producing bioaerosols were detected,these mVOCs contributed little to odor issues in landfill.Notably,surrounding areas have higher levels of antibiotic-resistance genes(ARGs)than inner landfill with tetC,acrB,acrF,mdtF,and bacA as dominant ones.Most ARGs were significantly correlated with bacterial community,while environmental parameters mainly influenced fungal prevalence.These findings can assist in reducing and preventing respiratory allergy or infection risks in occupational environments relating to waste management.

Antibiotic Resistance Genes in the Human-Impacted Environment:A One Health Perspective

Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated components.This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal.Recently, much work has been done describing antibiotic resistance genes in various environments;now quantitative, mechanistic,and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.

Use of antimicrobials in food animals and impact of transmission of antimicrobial resistance on humans

Antimicrobial resistance leads to failure of clinical antimicrobial therapy,and has raised urgent global public health concern.Humans can acquire antimicrobial resistance fromdrugs through the food chain or the environment(contaminated water,air,soil,or manure).While antimicrobials have been regular supplements in animal feed that maintain health and improve productivity of livestock,their over-use in feeding forage has led to a rise in antibacterial resistance.This review summarizes the current use of antimicrobials in livestock,the harmful effects of antimicrobial resistance,and the comprehensive combat measures.

Fungal defensins, an emerging source of anti-infective drugs

With the rapid increase of antibiotic-resistant pathogens and the decline of discovery and development of new antibiotics,there is an urgent need to exploit alternative anti-infective drugs.Fungal defensin-like peptides are emerging as a class of new source of anti-infective drugs due to their potent antibacterial activity,low toxicity,and high serum stability.Fungal genome sequencing projects combined with the development of recombinant expression techniques will accelerate the discovery of fungal defensinlike peptides.