Environmental and clinical antibiotic resistomes, same only different

Environmental resistome-guided development of resistance-tolerant antibiotics

Failure to anticipate new forms of antibiotic resistance has led to resistance developing rapidly to virtually all antibiotics that have entered clinical use. Many of the most problematic types of resistance originated in the environment, where ancient arms races between antibiotic-producing microbes and their competitors have created vast arsenals of antibiotics and resistance. Seizing on the knowledge that resistance in nature is frequently a harbinger of future clinical resistance, we propose introducing an additional step into the antibiotic development process that exploits the susceptibility of development candidates to environmental resistance as a metric for prioritizing lead compounds and as a roadmap for their structural optimization. Using the antibiotic albicidin as a model, we show how the environmental resistome can guide the development of more resistance-tolerant leads. We used metagenomic surveys to identify resistance vulnerabilities for albicidin and guide the synthesis of analogs that evade the resistance threats. We found that natural albicidin analogs (congeners) were especially enriched in structural features that escape resistance, which inspired our syntheses and provided compelling evidence for the evolution of families of antibiotics in response to resistance in nature. The coupling of metagenomics-based resistance surveillance with structural optimizations of new antibiotics is a broadly applicable approach that is easily integrated into antibiotic development programs to generate compounds that are more resilient in the face of resistance.

Recent developments in Aspergillus fumigatus research: diversity, drugs, and disease

SUMMARYAdvances in modern medical therapies for many previously intractable human diseases have improved patient outcomes. However, successful disease treatment outcomes are often prevented due to invasive fungal infections caused by the environmental mold Aspergillus fumigatus. As contemporary antifungal therapies have not experienced the same robust advances as other medical therapies, defining mechanisms of A. fumigatus disease initiation and progression remains a critical research priority. To this end, the World Health Organization recently identified A. fumigatus as a research priority human fungal pathogen and the Centers for Disease Control has highlighted the emergence of triazole-resistant A. fumigatus isolates. The expansion in the diversity of host populations susceptible to aspergillosis and the complex and dynamic A. fumigatus genotypic and phenotypic diversity call for a reinvigorated assessment of aspergillosis pathobiological and drug-susceptibility mechanisms. Here, we summarize recent advancements in the field and discuss challenges in our understanding of A. fumigatus heterogeneity and its pathogenesis in diverse host populations.

Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions

Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.

Heavy metals promote the formation of multidrug-tolerant Staphylococcus aureus and Escherichia coli persisters

Bacterial persisters are dormant phenotypic variants that are tolerant to antibiotics, contributing to treatment failure and the emergence of antimicrobial resistance. Although the formation of persisters has been extensively studied in regards to bacterial infections and treatment, such as antibiotic exposure or intracellular survival within macrophages, the role of environmental stressors in persister formation remains largely unexplored. In this study, we investigate the role of environmental heavy metals, specifically arsenic (As), cadmium (Cd), and mercury (Hg), in promoting persister cell formation in Staphylococcus aureus and Escherichia coli. Log-phase cultures were exposed to heavy metals (5 mM As, 1.25 mM Cd, 4 µM Hg for S. aureus; 12.5 mM As, 2 mM Cd, and 15 µM Hg for E. coli) for 0.5 h to induce persister cells. We observed that exposure to these metals induced persister cell formation, confirmed by intracellular ATP levels through microscopy and luciferase assays, as well as by reactive oxygen species (ROS) levels using carboxy-H2DCFDA. Short-term heavy metal exposure strongly depleted intracellular ATP while generating ROS. Moreover, we observed enhanced expression of genes involved in the SOS response, including recA, umuC, dinB, rexA, rexB, sulA, rpoS, and soxR, as measured by qPCR. This response was likely induced by elevated ROS levels following heavy metal exposure. Furthermore, we demonstrate that heavy metal-induced bacterial persisters exhibited a substantially increased emergence of antibiotic resistance, as shown by ciprofloxacin resistance developing in the presence of heavy metals. Therefore, our results clearly demonstrate that heavy metals can induce persister cells by depleting cellular ATP and generating ROS, and these bacterial responses to heavy metals substantially contribute to antibiotic resistance. These findings highlight the intricate relationship between environmental heavy metals, bacterial persister formation, and antibiotic resistance, emphasizing the need for a "One Health" strategy to address the growing antibiotic resistance crisis.

Dynamics of drug delivery determines course of evolution of antibiotic responses in bacteria

To adjust to sudden shifts in conditions, microbes possess regulated genetic mechanisms that sense environmental challenges and induce the appropriate responses. The initial evolution of microbes in new environments is thought to be driven by regulatory mutations, but it is not clear how this evolution is affected by how quickly conditions change (i.e. dynamics). Here, we perform experimental evolution on continuous cultures of tetracycline resistant E. coli in different dynamical regimens of drug administration. We find that cultures evolved under gradually increasing drug concentrations acquire fine-tuning mutations adapting an alternative efflux pump to tetracycline. However, cultures that are instead periodically exposed to large drug doses evolve transposon insertions resulting in loss of regulation of the main mechanism of tetracycline resistance. A mathematical model shows that sudden drug exposures overwhelm regulated responses, which cannot induce resistance fast enough. These results help explain the frequent loss of regulation of resistance in clinical pathogens.

Whole Genome Analysis and Assessment of the Metabolic Potential of Streptomyces carpaticus SCPM-O-B-9993, a Promising Phytostimulant and Antiviral Agent

This work aimed to study the genome organization and the metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, a promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with very high salinity. The strain genome contains a linear chromosome 5,968,715 bp long and has no plasmids. The genome contains 5331 coding sequences among which 2139 (40.1%) are functionally annotated. Biosynthetic gene clusters (BGCs) of secondary metabolites exhibiting antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, and ansamycin) were identified in the genome. The most efficient period of SCPM-O-B-9993 strain cultivation was 72 h: during this period, the culture went from the exponential to the stationary growth phase as well as exhibited excellent phytostimulatory properties and antiviral activity against the cucumber mosaic virus in tomatoes under laboratory conditions. The Streptomyces carpaticus SCPM-OB-9993 strain is a biotechnologically promising producer of secondary metabolites exhibiting antiviral and phytostimulatory properties.

Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities

Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.

Interplay Between Antimicrobial Resistance and Global Environmental Change

Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.

Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range

Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.

Searching for links between environmental and clinical mecA+Staphylococcus aureus: A comparative genomics study

Staphylococcus aureus integrate the list of highly virulent and antibiotic resistant pathogens, mainly due to the mecA gene, associated with methicillin resistance. Given the ubiquity of this species, the aim of this study was to investigate whether closely related mecA+S. aureus found in the environment can be also thrive as clinical isolates and if the respective accessory genome may suggest bacterial adaptation. The genomes of environmental (water, animal facilities, food products, n = 111) isolates were compared with closely related genomes of clinical origin (human patients, n = 103). These genomes, available in the public database NCBI, were analysed for phylogeny, accessory genome, and presence of selected clinically relevant genes (n = 104). The genomes of environmental isolates belonged to 18 multi-locus sequence types (MLSTs), 11 of which also included clinical genomes, a result confirmed based on core-genome analysis. Genes significantly (p ≤ 0.05) more frequent among environmental genomes were related with resistance to β-lactams (blaI, blaPCI), aminoglycosides (ant(6)-Ia), macrolides (mph(C), erm(B)), enterotoxins (seg, sei, sem, sen, seo, seu) and serine protease functions (splB), among others. Genes significantly more frequent among clinical genomes were associated with resistance to macrolides (erm(C)), phenicols (fexA), fosfomycin (murA), the leucocidin virulence gene (lukS-PV), and serine protease functions (splA, splE). It is suggested that mecA+S. aureus can be exchanged between clinical and environmental settings, with accessory traits (particularly antibiotic resistance, virulence and stress response) possibly being associated with the habitat. The interplay between phylogeny and accessory genome is an interesting contribution to better understanding the ecology and evolution of mecA+S. aureus.

Carbapenemase-Producing Bacteria Isolated from ICU Patients of a Peruvian Government Hospital during the COVID-19 Pandemic: A Descriptive Analysis

Background and Objectives: In Peru, the presence of antimicrobial-resistant bacteria is a constant concern in hospitals and has likely increased in frequency during the pandemic. The objective of the study was to analyze the frequency of carbapenemase-producing bacteria resistant to two carbapenems (Imipenem and Meropenem), which were isolated from Peruvian patients in the intensive care unit of the Victor Lazarte Echegaray Hospital in Trujillo (Peru) during the COVID-19 pandemic. Materials and Methods: The biological samples of the patients hospitalized in the ICU were processed in the Microbiology Diagnostic Laboratory of the Víctor Lazarte Echegaray Hospital between May 2021 and March 2022. Antimicrobial sensitivity was determined with the automated system AutoScan-4, and for the identification of the type of carbapenemase, the RESISIT-3 O.K.N K-SET cassettes were used. Results: The results show that 76 cultures (76/129) had resistance to the two carbapenems (imipenem or meropenem), where the most frequent were Klebsiella pneuomoniae (31.6%), Pseudomonas aeruginosa (26.3%), and Acinetobacter baumannii (14.5%). Pseudomonas aeruginosa cultures showed at least three carbapenemase types (KPC, NDM, and OXA-48), while A. baumannii, Escherichia coli, and Burkholderia cepacia complex presented at least two carbapenemases (NDM and OXA-48). The carbapenemase NDM was detected in Enterobacter cloacae, Morganella morganii, and Proteus mirabilis, while KPC was present in all Klebsiella pneumoniae and Klebsiella oxytoca cultures. Conclusions: The samples from patients hospitalized in the Victor Lazarte Echegaray Hospital ICU showed a high prevalence of imipenem- and meropenem-resistant bacteria. These findings are relevant and concerning from the perspective of antibiotic-resistant bacteria monitoring, control, and disinfection. Thus, an appropriate antibiotic policy must be implemented.

Unrecognized risk of perfluorooctane sulfonate in promoting conjugative transfers of bacterial antibiotic resistance genes

Antibiotic resistance is a major global health crisis facing humanity, with horizontal gene transfer (HGT) as a principal dissemination mechanism in the natural and clinical environments. Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse effects on humans. However, it is unknown whether PFASs affect the HGT of bacterial antibiotic resistance. Using a genetically engineered Escherichia coli MG1655 as the donor of plasmid-encoded antibiotic resistance genes (ARGs), E. coli J53 and soil bacterial community as two different recipients, this study demonstrated that the conjugation frequency of ARGs between two E. coli strains was (1.45 ± 0.17) × 10-5 and perfluorooctane sulfonate (PFOS) at environmentally relevant concentrations (2-50 μg L-1) increased conjugation transfer between E. coli strains by up to 3.25-fold. Increases in reactive oxygen species production, cell membrane permeability, biofilm formation capacity, and cell contact in two E. coli strains were proposed as major promotion mechanisms from PFOS exposure. Weighted gene co-expression network analysis of transcriptome data identified a series of candidate genes whose expression changes could contribute to the increase in conjugation transfer induced by PFOS. Furthermore, PFOS also generally increased the ARG transfer into the studied soil bacterial community, although the uptake ability of different community members of the plasmid either increased or decreased upon PFOS exposure depending on specific bacterial taxa. Overall, this study reveals an unrecognized risk of PFOS in accelerating the dissemination of antibiotic resistance. IMPORTANCE Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse health effects. Although the influence of environmental pollutants on the spread of antibiotic resistance, one of the biggest threats to global health, has attracted increasing attention in recent years, it is unknown whether environmental residues of PFASs affect the dissemination of bacterial antibiotic resistance. Considering PFASs, often called "forever" compounds, have significantly higher environmental persistence than most emerging organic contaminants, exploring the effect of PFASs on the spread of antibiotic resistance is more environmentally relevant and has essential ecological and health significance. By systematically examining the influence of perfluorooctane sulfonate on the antibiotic resistance gene conjugative transfer, not only at the single-strain level but also at the community level, this study has uncovered an unrecognized risk of PFASs in promoting conjugative transfers of bacterial antibiotic resistance genes, which could be incorporated into the risk assessment framework of PFASs.

Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases

While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10-3 transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.

High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China

Emergence and dissemination of resistance to last-resort antibiotics such as carbapenem and colistin is a growing, global health concern. Wastewater treatment plants (WWTPs) link human activities and the environment, can act as reservoirs and sources for emerging antibiotic resistance, and likely play a large role in antibiotic resistance transmission. The aim of this study was to investigate occurrence and characteristics of colistin- and carbapenem-resistant Escherichia coli (CCREC) in wastewater and sludge samples collected over a one-year period from different functional areas of an urban WWTP in Jinan city, Shandong, China. A total of 8 CCREC were isolated from 168 samples with selective agar and PCR, corresponding to high prevalence of 4.8%, co-harboring carbapenem resistance genes (bla_NDM) and colistin resistance gene (mcr-1) and subsequently whole-genome sequenced. Additionally, all isolates were multidrug-resistant by antimicrobial susceptibility testing and carried a variety of antibiotic resistance genes. Two isolates carrying virulence genes associated with avian pathogenic E. coli were identified, one belonging to the high-risk clone O101:H9-ST167. Southern blotting was used to characterize CCREC isolates and plasmids carrying bla_NDM-genes or mcr-1 could be transferred to a recipient strain E. coli J53 by in vitro conjugation assays. Resistance to other antibiotic classes were sporadically co-transferred to the transconjugant. Transposition of and mcr-1-carrying element from a transferable IncHI2-plasmid was observed among two CCREC clones isolated within 4 days of each other. The occurrence of multidrug-resistant CCREC capable of transferring their antibiotic resistance genotypes via conjugative plasmids is alarming. WWTPs bring bacteria from different sources together, providing opportunities for horizontal exchange of DNA among compatible hosts. Further dissemination of the colistin-, carbapenem-, or both colistin- and carbapenem resistant E. coli could lead to a serious threat to public health.

Antimicrobial resistomes in food chain microbiomes

The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.

β-Lactams from the Ocean

The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains

Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.

Application of Nucleotide-Based Kinetic Modeling Approaches to Predict Antibiotic Resistance Gene Degradation during UV- and Chlorine-Based Wastewater Disinfection Processes: From Bench- to Full-Scale

This study investigated antibiotic resistance gene (ARG) degradation kinetics in wastewaters during bench- and full-scale treatment with UV light and chlorine─with the latter maintained as free available chlorine (FAC) in low-ammonia wastewater and converted into monochloramine (NH₂Cl) in high-ammonia wastewater. Twenty-three 142-1509 bp segments (i.e., amplicons) of seven ARGs (blt, mecA, vanA, tet(A), ampC, bla_NDM, bla_KPC) and the 16S rRNA gene from antibiotic resistant bacteria (ARB) strains Bacillus subtilis, Staphylococcus aureus, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were monitored as disinfection targets by qPCR. Rate constants for ARG and 16S rRNA gene amplicon degradation by UV, FAC, and NH₂Cl were measured in phosphate buffer and used to expand and validate several recently developed approaches to predict DNA segment degradation rate constants based solely on their nucleotide contents, which were then applied to model ARG degradation during bench-scale treatment in buffer and wastewater matrixes. Kinetics of extracellular and intracellular ARG degradation by UV and FAC were well predicted up to ∼1-2-log₁₀ elimination, although with decreasing accuracy at higher levels for intracellular genes, while NH₂Cl yielded minimal degradation under all conditions (agreeing with predictions). ARB inactivation kinetics varied substantially across strains, with intracellular gene degradation lagging cell inactivation in each case. ARG degradation levels observed during full-scale disinfection at two wastewater treatment facilities were consistent with bench-scale measurements and predictions, where UV provided ∼1-log₁₀ ARG degradation, and chlorination of high-ammonia wastewater (dominated by NH₂Cl) yielded minimal ARG degradation.

Unravelling the Diversity and Abundance of the Red Fox (Vulpes vulpes) Faecal Resistome and the Phenotypic Antibiotic Susceptibility of Indicator Bacteria

Simple Summary

Antimicrobial resistance was considered one of the major concerns of the twenty-first century by the World Health Organization in 2014. A holistic approach known as “One Health” recognizes the connections and interdependence between the health of people, domestic and wild animals, plants, and the ecosystem. The red fox is the most widespread wild canid in Europe that adapts easily and is distributed in natural environments and urban and peri-urban areas due to its increasing abundance. Foxes are reservoirs and disseminators of antibiotic resistance and zoonotic agents. They interact with watercourses, soils and livestock, and although they have no gastronomic interest, they are a game species, highlighting the potential risk of contamination between them and the hunters. Our main goal was to characterize antibiotic resistance in red foxes. Several clinically relevant antibiotic resistance genes were identified, as well as multidrug-resistant bacteria.

Abstract

The WHO considers that antimicrobial resistance (AMR) is among the ten greatest global public health risks of the 21st century. The expansion of human populations and anthropogenically related activities, accompanied by the fragmentation of natural habitats, has resulted in increased human–wildlife interaction. Natural ecosystems are therefore subjected to anthropogenic inputs, which affect the resistome of wild animals. Thus, urgent multisectoral action is needed to achieve the Sustainable Development Goals following the One Health approach. The present work falls within the scope of this approach and aims to characterize the AMR of the faecal microbiome of the red fox (Vulpes vulpes), an opportunistic and generalist synanthropic species whose abundance has been increasing in urban and peri-urban areas. A high number of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were screened and quantified using a high-throughput qPCR approach, and the antimicrobial susceptibility of cultivable E. coli and Enterococcus spp. were assessed interpreted with both ECOFFs and clinical breakpoints. The most abundant ARGs detected confer resistance to trimethoprim and tetracyclines, although the first were absent in one of the locations studied. Several ARGs considered to be threats to human health were identified in high relative abundances (bla_TEM, ermB, aadA, tetM, tetW, tetL, drfA1 and drfA17), especially in the geographical area with greater anthropogenic influence. Although at a low percentage, resistant and multidrug-resistant (MDR) E. coli and Enterococcus spp. were isolated, including one MDR E. coli showing resistance to 12 antimicrobials from 6 different classes.

Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective

Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern medicine. Effective prevention strategies are urgently required to slow the emergence and further dissemination of AMR. Given the availability of data sets encompassing hundreds or thousands of pathogen genomes, machine learning (ML) is increasingly being used to predict resistance to different antibiotics in pathogens based on gene content and genome composition. A key objective of this work is to advocate for the incorporation of ML into front-line settings but also highlight the further refinements that are necessary to safely and confidently incorporate these methods. The question of what to predict is not trivial given the existence of different quantitative and qualitative laboratory measures of AMR. ML models typically treat genes as independent predictors, with no consideration of structural and functional linkages; they also may not be accurate when new mutational variants of known AMR genes emerge. Finally, to have the technology trusted by end users in public health settings, ML models need to be transparent and explainable to ensure that the basis for prediction is clear. We strongly advocate that the next set of AMR-ML studies should focus on the refinement of these limitations to be able to bridge the gap to diagnostic implementation.

Arctic Psychrotolerant Pseudomonas sp. B14-6 Exhibits Temperature-Dependent Susceptibility to Aminoglycosides

Bacteria can evade antibiotics by acquiring resistance genes, as well as switching to a non-growing dormant state without accompanying genetic modification. Bacteria in this quiescent state are called persisters, and this non-inheritable ability to withstand multiple antibiotics is referred to as antibiotic tolerance. Although all bacteria are considered to be able to form antibiotic-tolerant persisters, the antibiotic tolerance of extremophilic bacteria is poorly understood. Previously, we identified the psychrotolerant bacterium Pseudomonas sp. B14-6 from the glacier foreland of Midtre Lovénbreen in High Arctic Svalbard. Herein, we investigated the resistance and tolerance of Pseudomonas sp. B14-6 against aminoglycosides at various temperatures. This bacterium was resistant to streptomycin and susceptible to apramycin, gentamicin, kanamycin, and tobramycin. The two putative aminoglycoside phosphotransferase genes aph1 and aph2 were the most likely contributors to streptomycin resistance. Notably, unlike the mesophilic Pseudomonas aeruginosa PA14, this cold-adapted bacterium demonstrated reduced susceptibility to all tested aminoglycosides in a temperature-dependent manner. Pseudomonas sp. B14-6 at a lower temperature formed the persister cells that shows tolerance to the 100-fold minimum inhibitory concentration (MIC) of gentamicin, as well as the partially tolerant cells that withstand 25-fold MIC gentamicin. The temperature-dependent gentamicin tolerance appears to result from reduced metabolic activity. Lastly, the partially tolerant Pseudomonas sp. B14-6 cells could slowly proliferate under the bactericidal concentrations of aminoglycosides. Our results demonstrate that Pseudomonas sp. B14-6 has a characteristic ability to form cells with a range of tolerance, which appears to be inversely proportional to its growth rate.

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.

Progress Report: Antimicrobial Drug Discovery in the Resistance Era

Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.

Impact of flooding on urban soils: Changes in antibiotic resistance and bacterial community after Hurricane Harvey

Major perturbations in soil and water quality are factors that can negatively impact human health. In soil environments of urban areas, changes in antibiotic-resistance profiles may represent an increased risk of exposure to antibiotic-resistant bacteria via oral, dermal, or inhalation routes. We studied the perturbation of antibiotic-resistance profiles and microbial communities in soils following a major flooding event in Houston, Texas, caused by Hurricane Harvey. The main objective of this study was to examine the presence of targeted antibiotic-resistance genes and changes in the diversity of microbial communities in soils a short time (3-5 months) and a long time (18 months) after the catastrophic flooding event. Using polymerase chain reaction, we surveyed fourteen antibiotic-resistance elements: intI1, intI2, sul1, sul2, tet(A) to (E), tet(M), tet(O), tet(W), tet(X), and bla_CMY-2. The number of antibiotic-resistance genes detected were higher in short-time samples compared to samples taken a long time after flooding. From all the genes surveyed, only tet(E), bla_CMY-2, and intI1 were prevalent in short-time samples but not observed in long-time samples; thus, we propose these genes as indicators of exogenous antibiotic resistance in the soils. Sequencing of the V3-V4 region of the bacterial 16S rRNA gene was used to find that flooding may have affected bacterial community diversity, enhanced differences among bacterial lineages profiles, and affected the relative abundance of Actinobacteria, Verrucomicrobia, and Gemmatimonadetes. A major conclusion of this study is that antibiotic resistance profiles of soil bacteria are impacted by urban flooding events such that they may pose an enhanced risk of exposure for up to three to five months following the hurricane. The occurrence of targeted antibiotic-resistance elements decreased eighteen months after the hurricane indicating a reduction of the risk of exposure long time after Harvey.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

Study of indiscriminate distribution of restrained antimicrobial resistome of different environmental niches

Prophylactic usage and high persistent nature of several antibiotics have put selective pressure on the native microbial population that led to the emergence, propagation, and persistence of antibiotic resistance in nature. The surveillance of antibiotic resistome pattern and identification of points of intervention throughout the different environmental habitats will help to break the flow of antibiotic resistance from environmental bacteria to human pathogens. The present study compares the occurrence, diversity, and abundance of ARGs in industrial sludge, wetland sludge, and sediment sample contaminated with pharmaceutical discharge. Metagenomes were mined for the presence of ARGs against the ResFinder 3.2 database using BLASTn program. Pharmaceutical sample (2.52%) showed high degree of ARG abundance and richness as compared with ETP sludge (2.28%) and wetland sludge samples (1.29%). The modern resistome pattern represented by critically important resistance genes against tetracycline (tetA, tetC, tetW, tetT, and tetS/M) and quinolone (qnrS, qnrVC, and qnrD) was identified in pharmaceutical sediment sample. However, effluent treatment plant (ETP) sludge sample showed abundance of multidrug efflux pumps indicating the presence of primitive resistome profile. In conclusion, the indiscriminate distribution pattern of antibiotic resistance genes in three selected environmental sites suggests enrichment and distribution of environmental niche-driven resistance. The study also suggests effluent discharge site from pharmaceutical industries and ETPs as pivotal points of intervention for the mitigation of antibiotic resistance.

The Antibiotic Resistome: A Guide for the Discovery of Natural Products as Antimicrobial Agents

The use of life-saving antibiotics has long been plagued by the ability of pathogenic bacteria to acquire and develop an array of antibiotic resistance mechanisms. The sum of these resistance mechanisms, the antibiotic resistome, is a formidable threat to antibiotic discovery, development, and use. The study and understanding of the molecular mechanisms in the resistome provide the basis for traditional approaches to combat resistance, including semisynthetic modification of naturally occurring antibiotic scaffolds, the development of adjuvant therapies that overcome resistance mechanisms, and the total synthesis of new antibiotics and their analogues. Using two major classes of antibiotics, the aminoglycosides and tetracyclines as case studies, we review the success and limitations of these strategies when used to combat the many forms of resistance that have emerged toward natural product-based antibiotics specifically. Furthermore, we discuss the use of the resistome as a guide for the genomics-driven discovery of novel antimicrobials, which are essential to combat the growing number of emerging pathogens that are resistant to even the newest approved therapies.

Listeria monocytogenes isolates from Western Cape, South Africa exhibit resistance to multiple antibiotics and contradicts certain global resistance patterns

Food-borne disease outbreaks are common and offer valuable insights into the causes, impacts, and mechanisms underlying food pathogens. This also serves as a good foundation to validate the performance of current best practice control methods, for example antibiotics, that are used in the fight against food pathogens. Listeriosis outbreaks, caused by Listeria monocytogenes, is no exception. In 2018, South Africa experienced the largest global listeriosis outbreak recorded to date. However, despite the scale of this outbreak, information on the bacterium and its resistance towards antibiotics is still severely lacking. Furthermore, until now it remained to be determined whether L. monocytogenes antibiotic resistance patterns in South Africa mirror resistance patterns elsewhere in the world. The aim of this study was therefore to evaluate the efficacy of antibiotics that are currently used against L. monocytogenes. Using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) disc diffusion method, L. monocytogenes isolates (n = 177) from diverse origins in the Western Cape, South Africa (clinical, food, and environment) were tested for susceptibility against five different antibiotics, namely ampicillin, erythromycin, chloramphenicol, gentamicin, and tetracycline. Isolates were collected over a period of two years (2017-2019). All isolates were susceptible to ampicillin, the currently recommended antibiotic, while a large number of isolates were resistant to chloramphenicol, erythromycin, and tetracycline. Also, patterns of resistance observed here are different to patterns observed elsewhere. The findings of this study demonstrate that it is imperative to continuously monitor the efficacy of currently recommended antibiotics, since resistance patterns can quickly develop when such antibiotics are overutilized, and secondly, that it is crucial to assess local antibiotic resistance patterns in conjunction with global patterns, since the latter is not necessarily generalizable to local scales.

Prevalence of ESBL-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae in treated wastewater: a comparison with nosocomial infection surveillance

The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae (CRE) is a worldwide health threat. Monitoring of these resistant bacteria in the environment can provide regional prevalence reflecting both healthy and infected populations, although the quantitative monitoring of those resistant bacteria, especially CRE, is difficult due to their low proportion in the total Enterobacteriaceae population and the possible interference by autochthonous species with intrinsic resistance. In this study, these resistant bacteria in treated wastewater were quantified at 12 different treatment plants. The proportions of cefotaxime-resistant and ESBL-producing E. coli in the total E. coli population in the chlorinated effluents in Tokyo were 5.7 and 5.3%, respectively. The estimated proportion of CRE was 0.007% with the constituting species of Klebsiella spp. and Enterobacter spp., although the conditions during the first incubation may have affected the estimation even after the correction by the proportion of resistant population in the isolates. The observed resistant proportions in this study were lower than those in the surveillance on nosocomial infection not only for inpatients but also for outpatients, and higher than those in the veterinary monitoring.

Carbapenem resistant Enterobacteriaceae from port areas in São Paulo State (Brazil): Isolation and molecular characterization

Coastal areas with important economic activities have high levels of contamination by metals, pathogenic bacteria, among other contaminants. The emergence of antibiotic-resistant bacteria is a global problem of public health. Carbapenem resistant Enterobacteriaceae (CRE) are a serious threat. The occurrence of carbapenem resistant bacteria was investigated in waters and sediments of a Brazilian coastal area, characterized by high levels of contamination. The samples of water and sediment were collected in two areas of the coast of São Paulo (Brazil). The study involved the characterization of the molecular mechanisms associated with the carbapenem resistance phenotype. No genes were detected for β-lactamases but the absence and/or presence of mutations in outer membrane proteins (OMPs) may justify the detected phenotype. The presented results show the need for further studies that allow a review of the current legislation and the importance of the reevaluation of monitoring policies of these environments.

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

Metallo-β-lactamases (MBLs) degrade a broad spectrum of β-lactam antibiotics, and are a major disseminating source for multidrug resistant bacteria. Despite many biochemical studies in diverse MBLs, molecular understanding of the roles of residues in the enzyme's stability and function, and especially substrate specificity, is lacking. Here, we employ deep mutational scanning (DMS) to generate comprehensive single amino acid variant data on a major clinical MBL, VIM-2, by measuring the effect of thousands of VIM-2 mutants on the degradation of three representative classes of β-lactams (ampicillin, cefotaxime, and meropenem) and at two different temperatures (25°C and 37°C). We revealed residues responsible for expression and translocation, and mutations that increase resistance and/or alter substrate specificity. The distribution of specificity-altering mutations unveiled distinct molecular recognition of the three substrates. Moreover, these function-altering mutations are frequently observed among naturally occurring variants, suggesting that the enzymes have continuously evolved to become more potent resistance genes.

Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes

Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.

Co-Existence of mcr-1 and bla NDM-5 in an Escherichia coli Strain Isolated from the Pharmaceutical Industry, WWTP

Abstract

The emergence of the plasmid-borne colistin-resistant gene (mcr-1) poses a great threat to human health. What is worse, the recent observations of the co-existence of mcr-1 with other antimicrobial resistance genes in some bacteria cause further concern. Here, we present the first report of a wild Escherichia coli strain that co-carries an mcr-1 encoding phage-like IncY plasmid (pR15_MCR-1) and a bla_NDM-5 encoding IncX3 plasmid (pR15_NDM-5) from a pharmaceutical industry, wastewater treatment plant, in China. This study highlights the spreading of E. coli carrying both mcr-1 and bla_NDM-5 genes in the pharmaceutical industry.

Importance

Escherichia coli strains that carry both mcr-1 and bla_NDM-5 genes are of great health concern and are already found in humans and animals worldwide, yet there is a paucity of observations of this resistant strain in the environment. Here we present the first isolation of an E. coli strain (R15) that co-carries mcr-1 and bla_NDM-5 genes from a wastewater treatment plant in China. Whole-genome sequencing indicated that R15 harbored two plasmids, pR15_MCR-1 and pR15_NDM-5, that carry mcr-1 and bla_NDM-5, respectively. The observation of this wild-derived E. coli strain that carries mcr-1 and bla_NDM-5 genes simultaneously calls for the urgency to improve monitoring and reducing its further spreading.