Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region

Resistance and Biodegradation of Triclosan and Propylparaben by Isolated Bacteria from Greywater

We investigated the relationship between antibiotic-resistance genes and the antimicrobial agents, triclosan (TCS) and propylparaben (PPB). The greywater microbiome was repeatedly exposed to triclosan and propylparaben and the effect was analyzed using a combination of PCR, Etest, Biolog, 16S rRNA sequencing, and liquid chromatography. The taxonomic identification points to very similar or even identical isolates, however, the phenotypic analysis suggests that their metabolic potential is different, likely due to genomic variation or differences in the expression of the substrate utilization pathways. For both triclosan and propylparaben, the antibiotic resistance levels among isolates remain consistent regardless of the exposure duration. This suggests that antibiotic-resistance genes are acquired rapidly and that their presence is not directly proportional to the level of micropollutant exposure. In a biodegradation test, TCS was reduced by 50% after 7 h, while PPB decreased only after 75 h. For TCS, the minimal inhibition concentration (MIC) ranged from 64 to above 256 mg/mL. Conversely, for PPB the MIC for the tested strains ranged between 512 and 800 mg/mL. This study highlights the complex interaction between household xenobiotics, greywater microorganisms, and the emergence of antibiotic resistance.

The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates

The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.

Virulence Factors and Susceptibility to Ciprofloxacin, Vancomycin, Triclosan, and Chlorhexidine among Enterococci from Clinical Specimens, Food, and Wastewater

Enterococcus faecalis and E. faecium are opportunistic pathogens commonly found in the microbiota of humans and other animals as well as in the environment. This article presents the results of antimicrobial susceptibility testing using phenotypic methods (broth microdilution and standardized disk diffusion) on selected clinical, food, and wastewater isolates of E. faecalis and E. faecium. The isolates were divided into subgroups based on their sensitivity to the following antibiotics: vancomycin (VAN) and ciprofloxacin (CIP), and biocides triclosan (TCL) and chlorhexidine (CHX). The study also investigated in vitro virulence factors, including biofilm formation ability, cell surface hydrophobicity (CSH) and β-hemolysis, to explore aspects of pathogenesis. In our study, regardless of the isolation source, VAN-resistant (VAN-R) and CIP-resistant (CIP-R) E. faecalis and E. faecium were detected. The highest proportion of CIP-R strains was found among clinical isolates of E. faecalis and E. faecium, with clinical E. faecium also showing the highest proportion of VAN-R strains. But the highest proportion of VAN-R E. faecalis strains was found in wastewater samples. The highest TCL MIC90 values for E. faecalis were found in wastewater isolates, while for E. faecium, the highest TCL MIC90 values were observed in food isolates. The highest CHX MIC90 values for both E. faecalis and E. faecium were identified in clinical specimens. The results obtained for E. faecalis did not indicate differences in TCL MIC and CHX MIC values with respect to sensitivity to VAN and CIP. Higher CHX MIC50 and CHX MIC90 values were obtained for CIP-R and VAN-R E. faecium. Among the tested isolates, 97.75% of the E. faecalis isolates produced biofilm, while 72.22% of the E. faecium isolates did so as well. In biofilm-forming strength categories III and IV, statistically significantly higher proportions of CIP-susceptible (CIP-S) and VAN-susceptible (VAN-S) E. faecalis were determined. In category III, there is no statistically significant difference in E. faecium CIP sensitivity. In category IV, we had a significantly higher proportion of CIP-R strains. On the other hand, the association between the moderate or strong category of biofilm formation and E. faecium VAN susceptibility was not significant. E. faecalis isolated from wastewater had a CSH index (HI) ≥ 50%, categorizing them as "moderate", while all the other strains were categorized as "low" based on the CSH index. Among the E. faecalis isolates, cell surface hydrophobicity indices differed significantly across isolation sources. In contrast, E. faecium isolates showed similar hydrophobicity indices across isolation sources, with no significant difference found. Moreover, no correlation was found between the enterococcal cell surface hydrophobicity and biofilm formation in vitro. After anaerobic incubation, β-hemolytic activity was confirmed in 19.10% of the E. faecalis and 3.33% of the E. faecium strains.

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.

Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA

Antimicrobial resistance (AMR) is an increasingly important global challenge for healthcare systems as well as agricultural food production systems. Our ability to prepare for, and respond to, emerging AMR threats is dependent on our knowledge of genes able to confer AMR that are circulating within various environmental, animal, and human microbiomes. Targeted, sequence-specific, detection of AMR genes and functional resistance assays, described here, carried out on metagenomic DNA gives us unique insights into the presence of AMR genes and how these are associated with mobile genetic elements that may be responsible for their dissemination and can also provide important information about the mechanisms of resistance underpinning the phenotype.

Effectiveness of front line and emerging fungal disease prevention and control interventions and opportunities to address appropriate eco-sustainable solutions

Fungal pathogens contribute to significant disease burden globally; however, the fact that fungi are eukaryotes has greatly complicated their role in fungal-mediated infections and alleviation. Antifungal drugs are often toxic to host cells and there is increasing evidence of adaptive resistance in animals and humans. Existing fungal diagnostic and treatment regimens have limitations that has contributed to the alarming high mortality rates and prolonged morbidity seen in immunocompromised cohorts caused by opportunistic invasive infections as evidenced during HIV and COVID-19 pandemics. There is a need to develop real-time monitoring and diagnostic methods for fungal pathogens and to create a greater awareness as to the contribution of fungal pathogens in disease causation. Greater information is required on the appropriate selection and dose of antifungal drugs including factors governing resistance where there is commensurate need to discover more appropriate and effective solutions. Popular azole fungal drugs are widely detected in surface water and sediment due to incomplete removal in wastewater treatment plants where they are resistant to microbial degradation and may cause toxic effects on aquatic organisms such as algae and fish. UV has limited effectiveness in destruction of anti-fungal drugs where there is increased interest in the combination approaches such as novel use of pulsed-plasma gas-discharge technologies for environmental waste management. There is growing interest in developing alternative and complementary green eco-biocides and disinfection innovation. Fungi present challenges for cleaning, disinfection and sterilization of reusable medical devices such as endoscopes where they (example, Aspergillus and Candida species) can be protected when harboured in build-up biofilm from lethal processing. Information on the efficacy of established disinfection and sterilization technologies to address fungal pathogens including bottleneck areas that present high risk to patients is lacking. There is a need to address risk mitigation and modelling to inform efficacy of appropriate intervention technologies that must consider all contributing factors where there is potential to adopt digital technologies to enable real-time analysis of big data, such as use of artificial intelligence and machine learning. International consensus on standardised protocols for developing and reporting on appropriate alternative eco-solutions must be reached, particularly in order to address fungi with increasing drug resistance where research and innovation can be enabled using a One Health approach.

Do Triclosan Sutures Modify the Microbial Diversity of Surgical Site Infections? A Systematic Review and Meta-Analysis

Randomised controlled clinical trials (RCTs) report a lower incidence rate of surgical site infections (SSIs) with triclosan sutures (TSs) compared with non-triclosan sutures (NTSs). Do triclosan sutures modify the microbial diversity of culture-confirmed SSIs (ccSSIs)? If so, this would support the association between TS antimicrobial activity and the SSI incidence rate. This prospective systematic literature review (PROSPERO CRD42019125099) was conducted according to PRISMA. RCTs that compared the incidence of SSIs with TSs and NTSs and reported microbial counts from SSI cultures per suture group were eligible. The microbial species were grouped by genus, and the association between genera and sutures was tested. The pooled relative risk (RR) of ccSSIs was also calculated. Twelve RCTs were eligible. No publication bias was identified. The microorganism count was 180 in 124 SSIs with TSs versus 246 in 199 SSIs with NTSs. No significant difference in microbial diversity was found, but statistical power was low for test results to support or challenge the association between the antimicrobial activity of TSs and the reduced rate of SSIs. The RR of the ccSSIs was significant and consistent with comprehensive meta-analyses. The certainty of the pooled RR was moderate.

Reduced Susceptibility and Increased Resistance of Bacteria against Disinfectants: A Systematic Review

Disinfectants are used to reduce the concentration of pathogenic microorganisms to a safe level and help to prevent the transmission of infectious diseases. However, bacteria have a tremendous ability to respond to chemical stress caused by biocides, where overuse and improper use of disinfectants can be reflected in a reduced susceptibility of microorganisms. This review aims to describe whether mutations and thus decreased susceptibility to disinfectants occur in bacteria during disinfectant exposure. A systematic literature review following PRISMA guidelines was conducted with the databases PubMed, Science Direct and Web of Science. For the final analysis, 28 sources that remained of interest were included. Articles describing reduced susceptibility or the resistance of bacteria against seven different disinfectants were identified. The important deviation of the minimum inhibitory concentration was observed in multiple studies for disinfectants based on triclosan and chlorhexidine. A reduced susceptibility to disinfectants and potentially related problems with antibiotic resistance in clinically important bacterial strains are increasing. Since the use of disinfectants in the community is rising, it is clear that reasonable use of available and effective disinfectants is needed. It is necessary to develop and adopt strategies to control disinfectant resistance.

Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries

Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Are silver nanoparticles better than triclosan as a daily antimicrobial? Answers from the perspectives of gut microbiome disruption and pathogenicity

As an alternative to triclosan (TCS), the widespread use of silver nanoparticles (AgNPs) in daily products shows genuine potential. However, information regarding whether AgNPs are substantially better than TCS in their potential disruption of the gut microbiome and health effects is lacking. Using a simulator of the human intestinal microbial ecosystem (SHIME), we systemically compared the effects of TCS and AgNPs (at 1 μg/L and 30 μg/L) on the human gut microbiome in terms of changes in gut homeostasis, microbial community structure, antibiotic resistance profiles and abundances of opportunistic pathogens. Generally, TCS exerted more severe effects than AgNPs on gut disturbances (i.e., decreased production of short-chain fatty acids, increased contents of ammonium and total bile acids, and increased β-glucosidase activities) in a dose-dependent manner, whereas no clear dose effect was observed for the AgNP treatment because of potential nanoparticle transformation. The more serious effect of TCS than AgNPs on the microbiota composition was indicated by the dynamic increase in the Firmicutes/Bacteroidetes ratio determined using 16S rDNA sequencing. Metagenomic analyses revealed a more pronounced effect of TCS than AgNPs on the selection and dissemination of multiple resistance genes to antibiotics, TCS, and even Ag via the enrichment of genes encoding efflux pumps and mobile genetic elements. Consequently, the overgrowth of opportunistic pathogens was observed upon TCS exposure due to an imbalanced microbiome, in contrast to a slight increase in the abundance of some beneficial bacteria (i.e., Bifidobacterium) induced by the AgNP treatment. In conclusion, from the perspective of effects on gut health, AgNPs may prevail over TCS to some extent. However, the stress and potential selection of Ag resistance indicates the need for targeted surveillance of AgNP commercialization for daily use.

Environmental fate of Bacteroidetes, with particular emphasis on Bacteroides fragilis group bacteria and their specific antibiotic resistance genes, in activated sludge wastewater treatment plants

The aim of this study was to determine the effect of the activated sludge process on the abundance of anaerobic bacteria of the phylum Bacteroidetes, with special emphasis on Bacteroides fragilis group (BFG) bacteria, in twelve full-scale wastewater treatment plants. The composition of bacterial phyla and classes in wastewater samples were analyzed by next-generation sequencing. The presence of specific to BFG bacteria genes and the abundance of ARGs and genes encoding class 1 integrase in wastewater samples were determined by qPCR. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were dominant bacterial phyla in wastewater samples. Next-generation sequencing revealed similar proportions of Bacteroidia (<1.0-8.2 % of all bacteria) in wastewater influents and effluents, which suggest that these microorganisms are not completely eliminated in the activated sludge process. The average copy numbers of specific to BFG bacteria gene, were 10⁶, and 10⁴ copies in 1 mL of wastewater influents and effluents, respectively. The results revealed a correlation between the abundance of BFG bacteria and BFG-specific genes encoding resistance to antibiotics. The observed changes in the prevalence of BFG-specific genes and ARGs in untreated and treated wastewater indicate that the activated sludge process decreases the number of gene copies in the effluent evacuated to the environment.

Synergistic and antagonistic interactions of triclosan with various antibiotics in bacteria

Triclosan (TCS), a well-studied antimicrobial compound and an environmental pollutant, is present in many household products. A systematic survey of TCS-antibiotic-bacteria interactions is lacking. We wish to understand the origin of such interactions by testing 16 phylogenetically well-characterized bacteria for their sensitivities to 6 different classes of antibiotics with or without the presence of TCS. Our results show that TCS interacts synergistically with some antibiotics against some Bacilli species. TCS could also interact antagonistically with other antibiotics against certain bacteria, including pathogens such as Pseudomonas aeruginosa and Stenotrophomonas maltophilia. Antagonism between drugs often coincided with the concomitant enhanced removal of Ethidium bromide (EtBr) from the cells. Enterococcus faecalis shows a unique response to TCS. High levels of TCS inhibits E. faecalis. Cells survive at lower TCS concentrations, and these cells can remove EtBr more readily than unexposed cells. At even lower TCS concentration, cell-growth is inhibited again, causing the culture to exhibit a unique extra inhibition zone around the TCS-disk. The TCS-antibiotic-bacteria interaction profiles of some bacteria do not follow their bacterial phylogenetic relations. This suggests that such interactions may be related to horizontal gene transfer among different bacteria.

Associations between sensitivity to antibiotics, disinfectants and heavy metals in natural, clinical and laboratory isolates of Escherichia coli

Bacteria in nature often encounter non-antibiotic antibacterials (NAAs), such as disinfectants and heavy metals, and they can evolve resistance via mechanisms that are also involved in antibiotic resistance. Understanding whether susceptibility to different types of antibacterials is non-randomly associated across natural and clinical bacteria is therefore important for predicting the spread of resistance, yet there is no consensus about the extent of such associations or underlying mechanisms. We tested for associations between susceptibility phenotypes of 93 natural and clinical Escherichia coli isolates to various NAAs and antibiotics. Across all compound combinations, we detected a small number of non-random associations, including a trio of positive associations among chloramphenicol, triclosan and benzalkonium chloride. We investigated genetic mechanisms that can explain such associations using genomic information, genetic knockouts and experimental evolution. This revealed some mutations that are selected for by experimental exposure to one compound and confer cross-resistance to other compounds. Surprisingly, these interactions were asymmetric: selection for chloramphenicol resistance conferred cross-resistance to triclosan and benzalkonium chloride, but selection for triclosan resistance did not confer cross-resistance to other compounds. These results identify genetic changes involved in variable cross-resistance across antibiotics and NAAs, potentially contributing to associations in natural and clinical bacteria.

Investigation of mechanisms of toxicity and exclusion by transporters of the preservatives triclosan and propylparaben using batteries of Schizosaccharomyces pombe strains

Triclosan (TCS) and propylparaben (PPB) are antimicrobials widely used. They present many similarities in their applications and also in their human and environmental health risks. In order to investigate the mechanisms of toxic action and the efflux pumps involved in their detoxication, we used a strategy with batteries of Schizosaccharomyces pombe yeast strains, either defective in cell signalling, in detoxification pumps, or in cell surveillance mechanisms. Yeast were exposed up to 20 h in solid medium or in liquid medium in 96-well plates. The mechanisms of action investigated were spindle defects (mph1), stress (pmk1), DNA interference (rad3) or diverse effects (MDR-sup). The efflux pumps investigated were Bfr1, Pmd1, Mfs1 and Caf5 or the Pap1 transcription factor. Here we show that TCS was 75 times more toxic than PPB in the wild type fission yeast. More oxidative stress and less protection by exclusion pumps were observed for TCS than for PPB. The cytotoxicity produced by TCS decreased from bfr1>mfs1>pmd1 > pap1 and caf5A deficient strains. In contrast, cytotoxic concentrations of PPB caused only a mild stress. The protection provided for PPB by the transporters was more marked than for TCS, decreasing from Pmd1, Caf5, Mfs1 and Bfr1. Furthermore, microtubule and DNA interferences were revealed for PPB, according to the cytotoxicity of mph1 and rad3 defective cells, respectively. As both compounds present complex adverse effects at concentrations close to exposure, and their combination clearly causes a strong potentiation, more exhaustive controls and regulations in their use should be considered.