Specific phenotypic, genomic, and fitness evolutionary trajectories toward streptomycin resistance induced by pesticide co-stressors in Escherichia coli

Proline mitigates antibiotic resistance evolution induced by ciprofloxacin at environmental concentrations

Antibiotics-induced resistance development in the environment has emerged as a critical issue under the 'one health' framework. Although there have been approaches to control antibiotic resistance evolution in clinical settings, they are rarely applicable in environmental contexts. Amino acids can affect the metabolic states of bacteria and potentially influence their resistance evolution. In this study, we screened 18 amino acids and identified proline as an efficient agent capable of mitigating ciprofloxacin-induced resistance of a soil-isolated Escherichia coli by over 50 % during a 24-day evolutionary experiment. Using transcriptomics and 13C metabolic flux analysis, we revealed the evolution mitigation mechanism of proline, which mainly involves down-regulated gene expressions and reduced metabolic flux of the TCA cycle, thereby decreasing NADH production, proton motive force, and uptake of ciprofloxacin. Based on single-cell RNA-seq, proline also reduced the size of resistant subgroups in the evolved E. coli population. Based on soil microcosm experiments, proline not only reduced the overall antibiotic resistance but also increased community diversity and robustness (optimal dosage: 5 mg/kg). Moreover, proline's evolution mitigation potentials likely extend to other antibiotics (e.g., streptomycin) and populations (e.g., Pseudomonas and Serratia spp.). Overall, proline addition holds promising potentials for mitigating antibiotic resistance in diverse antibiotics-polluted environments.

Synergistic effects of quaternary ammonium compounds and antibiotics on the evolution of antibiotic resistance

The usage of quaternary ammonium compounds (QACs) as disinfectants has surged dramatically during the COVID-19 pandemic and thereafter. QACs can promote antimicrobial resistance, but the combined effects of QACs and antibiotics in driving resistance evolution were yet revealed. This study aimed to evaluate antibiotic resistance of wastewater microorganisms under coexposure to typical antibiotics and the most widely used QAC, dodecyl dimethyl benzyl ammonium chloride (DDBAC). DDBAC exhibited synergistic effects with multiple antibiotics (ampicillin, azithromycin, ciprofloxacin, kanamycin, polymyxin B) in enhancing activated sludge resistance by 1.53-6.67 folds, compared with antibiotics exposure alone. DDBAC-ampicillin coexposure enriched multidrug and aminoglycoside ARGs with relatively high horizontal gene transfer potential. The synergistic mechanism was further explored using sludge-isolated pathogenic E. coli. DDBAC at 1-10 mg/L alone did not induce notable resistance, but synergized with ampicillin on enhancing resistance by 6.56-22.90 folds. Based on mutation analysis and transcriptomics, DDBAC-enhanced resistance evolution was attributable to efflux pump upregulation, target modification, and inhibition of ATP synthesis (a less reported mechanism). Five DDBAC-induced, resistance-conferring mutant genes were highly enriched in globally collected E. coli strains from wastewater outflow (n = 537) than soil/sediments (n = 714, p < 0.05). Considering the strong adsorption and persistence of QACs, their coexistence with antibiotics poses elevated antimicrobial resistance risks, particularly in wastewater treatment systems with long solid retention time and sewage sludge applied farmland.

Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance

Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, are thought to rely on the emergence of spontaneous mutations or lateral gene transfer from a reservoir of pre-existing variants within the surrounding environment. These variants then become fixed in the population upon exposure to selective pressures. Here, we show that multiple distinct wild-type (WT) substrains of the highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly to the potent herbicide methyl viologen (MV). Genome sequencing revealed that the mutations responsible for adaptation to MV were already present prior to selection in the genomes of the unadapted parental strains at low allelic frequencies. This indicates that chromosomal polyploidy in bacteria can provide cells with a reservoir of conditionally beneficial mutations that can become rapidly enriched and fixed upon selection. MV-resistant strains performed oxygenic photosynthesis less efficiently than WTs when MV was absent, suggesting trade-offs in cellular fitness associated with the evolution of MV resistance and a possible role for balancing selection in the maintenance of these alleles under ecologically relevant growth conditions. Resistance was associated with reduced intracellular accumulation of MV. Our results indicate that genome polyploidy plays a role in the rapid adaptation of some bacteria to stressful conditions, which may include xenobiotics, nutrient limitation, environmental stresses, and seasonal changes.

Effects of Temperature on Resistance to Streptomycin in Xanthomonas arboricola pv. pruni

Xanthomonas arboricola pv. pruni (Xap) causes the shot hole disease of stone fruits and almonds. This bacterium is a damaging, widespread pathogen distributed across the major stone fruit producing regions of the world. To control shot hole disease, antibiotics such as streptomycin are mainly used. However, as concerns about antibiotic resistance increase, many restrictions are placed on the use of antibiotics. Additionally, it has been reported that the rise in temperature due to climate change affects disease occurrence and ecology. Therefore, in this study, we determined the minimum inhibitory concentration (MIC) of streptomycin for Xap at an optimal growth temperature of 28°C and investigated the changes in MIC and the occurrence frequency of resistant bacteria at 10°C, 25°C and 30°C. The results of this study showed that the MIC was 30 µg/ml at 28°C. In addition, when the change in streptomycin resistance concentration due to temperature was confirmed, we found that the resistance concentration decreased to 10 µg/ml at 30°C. When the occurrence of resistance according to concentration and temperature conditions was investigated, the occurrence frequency of resistant strains was found to be the highest at 50 µg/ml. In the case of temperature, the occurrence frequency of resistant strains was confirmed to be high at 30°C. These results provide basic data for further reducing the problem of antibiotic resistance by suggesting the possibility of changes in the occurrence of streptomycin-resistant strains depending on the antibiotic treatment environment.

Experiment to Demonstrate Pesticide-Induced Antimicrobial Resistance (AMR): An Emerging Health Threat

Background Pesticides, including insecticides, herbicides, and fungicides, are essential for global food production, boosting crop yields, and preventing disease transmission. However, their excessive and improper use raises concerns about potential long-term consequences, affecting microbial ecosystems and fostering antimicrobial resistance. Materials and methods The objective of the study was to identify the effect of the pesticide compound (Imidacloprid 17.1% w/w) on the ATCC Escherichia coli. An experiment was conducted on ATCC Escherichia coli 27852. A 0.5 McFarland suspension of the strain was incubated in the presence of a pesticide compound (Imidacloprid 17.1% w/w) at a dilution of 1:4, 1:8, and 1:16. at 370C. Antibiotic susceptibility for cefoxitin, ciprofloxacin, ceftazidime, amikacin, and imipenem was determined via the Kirby-Bauer disk diffusion test at intervals of 24 hours, 48 hours, seven days, and 21 days. The results were then compared to the standard zone of inhibition diameter for ATCC Escherichia coli 27852 by Clinical and Laboratory Standards Institute (CLSI) guidelines. Results No bacterial growth was detected at pesticide dilutions of 1:1 and 1:2, indicating their inability to tolerate high pesticide concentrations. However, growth became evident at a 1:4 dilution and beyond, with mutants thriving within the inhibition zone. The experiment caused significant alterations in the inhibition zone sizes for all antibiotics, especially notable with imipenem, amikacin, and ceftazidime compared to the initial zone size for ATCC Escherichia coli 27852. Conclusion Our study concludes that the pesticide (Imidacloprid 17.1% w/w) significantly influences antibiotic resistance, especially with carbapenems, aminoglycosides, and cephalosporins in the tested groups at various concentrations and durations of exposure.

Fitness Costs of Antibiotic Resistance Impede the Evolution of Resistance to Other Antibiotics

Antibiotic resistance is a major threat to global health, claiming the lives of millions every year. With a nearly dry antibiotic development pipeline, novel strategies are urgently needed to combat resistant pathogens. One emerging strategy is the use of sequential antibiotic therapy, postulated to reduce the rate at which antibiotic resistance evolves. Here, we use the soft agar gradient evolution (SAGE) system to carry out high-throughput in vitro bacterial evolution against antibiotic pressure. We find that evolution of resistance to the antibiotic chloramphenicol (CHL) severely affects bacterial fitness, slowing the rate at which resistance to the antibiotics nitrofurantoin and streptomycin emerges. In vitro acquisition of compensatory mutations in the CHL-resistant cells markedly improves fitness and nitrofurantoin adaptation rates but fails to restore rates to wild-type levels against streptomycin. Genome sequencing reveals distinct evolutionary paths to resistance in fitness-impaired populations, suggesting resistance trade-offs in favor of mitigation of fitness costs. We show that the speed of bacterial fronts in SAGE plates is a reliable indicator of adaptation rates and evolutionary trajectories to resistance. Identification of antibiotics whose mutational resistance mechanisms confer stable impairments may help clinicians prescribe sequential antibiotic therapies that are less prone to resistance evolution.

Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil

Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Low-Level Cefepime Exposure Induces High-Level Resistance in Environmental Bacteria: Molecular Mechanism and Evolutionary Dynamics

Antibiotics exert selective pressures on clinically relevant antibiotic resistance. It is critical to understand how antibiotic resistance evolves in environmental microbes exposed to subinhibitory concentrations of antibiotics and whether evolutionary dynamics and emergence of resistance are predictable. In this study, Comamonas testosteroni isolated from wastewater activated sludge were subcultured in a medium containing 10 ng/mL cefepime for 40 days (∼300 generations). Stepwise mutations were accumulated, leading to an ultimate 200-fold increase in the minimum inhibitory concentration (MIC) of cefepime. Early stage mutation in DNA polymerase-encoding gene dnaE2 played an important role in antibiotic resistance evolution. Diverse resistance mechanisms were employed and validated experimentally, including increased efflux, biofilm formation, reduced antibiotic uptake, and drug inactivation. The cefepime minimal selective concentrations (MSCs) and relative fitness of susceptible, intermediate, and resistant mutants were determined. Agent-based modeling of the modified Moran process enabled simulations of resistance evolution and predictions of the emergence time and frequency of resistant mutants. The unraveled cefepime resistance mechanisms could be employed by broader bacteria, and the newly developed model is applicable to the predictions of general resistance evolution. The improved knowledge facilitates the assessment, prediction, and mitigation of antibiotic resistance progression in antibiotic-polluted environments.

Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella

Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for in vitro evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.

Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence

Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the "Lactobacterin" probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.