Reduction of the fitness cost of antibiotic resistance caused by chromosomal mutations under poor nutrient conditions

Evolution and distribution of antibiotic resistance genes in submerged macrophytes and biofilm systems: From seasonal monitoring to mesocosm experiments

The aquatic ecosystem has been extensively investigated as a hotspot for the spread of antibiotic resistance genes (ARGs); yet, the evolution and distribution of ARGs profiles in submerged macrophytes biofilms and surrounding water remained unclear. In this study, the dynamic distribution and seasonal variations of microbial communities and ARGs profiles were investigated, alongside their assembly processes and mutual interactions. Bacitracin and multidrug resistance genes were predominant, constituting more than 60% of the total ARGs abundance. The deterministic processes (<65%), influenced by the physicochemical properties of the river environment, governed the assembly and composition of ARGs profiles, exhibiting significant seasonal variation. The peak diversity (21 types) and abundance (0.316 copy ratios) of ARGs were detected during the summer. Proteobacteria and Actinobacteria were the dominant bacterial phyla, accounting for 38.41-85.50% and 4.03-27.09% of the microbial community, respectively. Furthermore, Proteobacteria, especially genera such as Acinetobacter, Burkholderia, and Pseudomonas, with various resistance sequences, were the primary carriers of multiple ARGs. Notably, the genetic exchanges between biofilms and surrounding water facilitated the further propagation of high-risk ARGs, posing greater ecological risks. Redundancy analysis indicated that the total nitrogen and temperature in water determined the fate of pathogenic-resistant species. These findings provided theoretical support for the mitigation of ARGs contamination in aquatic environments.

Transmission mechanism of antibiotic resistance genes and their differences between water and sediment in the Weihe River Basin

Antibiotic resistance genes (ARGs) are emerging microbial pollutants that are regulated by many factors and pose potential threats to aquatic environments. In this study, we used network analysis, correlation analysis, and constructed models based on metagenomic sequencing results to explore the spatial patterns, impact mechanisms, transmission risks and differences in ARGs in the water and sediment of the Weihe River Basin. The findings revealed notable disparities in ARGs, mobile genetic elements (MGEs), and bacterial communities. In the sediment, the abundance of ARGs was considerably greater than that in water. Moreover, the percentage of ARGs shared by the two components reached a value of 85.8%. Through network analysis, it was determined that the presence of 16 MGEs and 20 bacterial phyla was strongly associated with ARGs (R2 > 0.7, P < 0.05). The Mantel test showed that abiotic factors including DO, pH, nutrients, and heavy metals played important roles in the distribution of ARGs (P < 0.05). A structural equation model revealed that the key factors influencing the distribution of ARGs in water were bacterial diversity and environmental parameters (standardized effects of -0.730 and -0.667), and those in sediment were bacterial diversity and MGEs (standardized effects of -0.751 and 0.851). Neutral modeling indicated that deterministic processes played an important role in the assembly of ARGs in the water of the Weihe River Basin, and stochastic processes were dominant in the sediment. There was a highly significant positive linear correlation between ARGs and pathogens, and there was more complex co-occurrence in the water than in the sediment (R2 > 0.9, P < 0.05), with stronger migration and transmission occurring. Exploring ARGs in large-scale watersheds is immensely important for elucidating their traits and transmission mechanisms and consequently paving the way for the formulation of efficient strategies to mitigate resistance threats.

Seasonal meropenem resistance in Acinetobacter baumannii and influence of temperature-driven adaptation

BACKGROUND

Recognition of seasonal trends in bacterial infection and drug resistance rates may enhance diagnosis, direct therapeutic strategies, and inform preventive measures. Limited data exist on the seasonal variability of Acinetobacter baumannii. We investigated the seasonality of A. baumannii, the correlation between temperature and meropenem resistance, and the impact of temperature on this bacterium.

RESULTS

Meropenem resistance rates increased with lower temperatures, peaking in winter/colder months. Nonresistant strain detection exhibited temperature-dependent seasonality, rising in summer/warmer months and declining in winter/colder months. In contrast, resistant strains showed no seasonality. Variations in meropenem-resistant and nonresistant bacterial resilience to temperature changes were observed. Nonresistant strains displayed growth advantages at temperatures ≥ 25 °C, whereas meropenem-resistant A. baumannii with β-lactamase OXA-23 exhibited greater resistance to low-temperature (4 °C) stress. Furthermore, at 4 °C, A. baumannii upregulated carbapenem resistance-related genes (adeJ, oxa-51, and oxa-23) and increased meropenem stress tolerance.

CONCLUSIONS

Meropenem resistance rates in A. baumannii display seasonality and are negatively correlated with local temperature, with rates peaking in winter, possibly linked to the differential adaptation of resistant and nonresistant isolates to temperature fluctuations. Furthermore, due to significant resistance rate variations between quarters, compiling monthly or quarterly reports might enhance comprehension of antibiotic resistance trends. Consequently, this could assist in formulating strategies to control and prevent resistance within healthcare facilities.

Interaction with a phage gene underlie costs of a β-lactamase

The fitness cost of an antibiotic resistance gene (ARG) can differ across host strains, creating refuges that allow the maintenance of an ARG in the absence of direct selection for its resistance phenotype. Despite the importance of such ARG-host interactions for predicting ARG dynamics, the basis of ARG fitness costs and their variability between hosts are not well understood. We determined the genetic basis of a host-dependent cost of a β-lactamase, blaTEM-116*, that conferred a significant cost in one Escherichia coli strain but was close to neutral in 11 other Escherichia spp. strains. Selection of a blaTEM-116*-encoding plasmid in the strain in which it initially had a high cost resulted in rapid and parallel compensation for that cost through mutations in a P1-like phage gene, relAP1. When the wild-type relAP1 gene was added to a strain in which it was not present and in which blaTEM-116* was neutral, it caused the ARG to become costly. Thus, relAP1 is both necessary and sufficient to explain blaTEM-116* costs in at least some host backgrounds. To our knowledge, these findings represent the first demonstrated case of the cost of an ARG being influenced by a genetic interaction with a phage gene. The interaction between a phage gene and a plasmid-borne ARG highlights the complexity of selective forces determining the maintenance and spread of ARGs and, by extension, encoding phage and plasmids in natural bacterial communities.IMPORTANCEAntibiotic resistance genes (ARGs) play a major role in the increasing problem of antibiotic resistance in clinically relevant bacteria. Selection of these genes occurs in the presence of antibiotics, but their eventual success also depends on the sometimes substantial costs they impose on host bacteria in antibiotic-free environments. We evolved an ARG that confers resistance to penicillin-type antibiotics in one host in which it did confer a cost and in one host in which it did not. We found that costs were rapidly and consistently reduced through parallel genetic changes in a gene encoded by a phage that was infecting the costly host. The unmutated version of this gene was sufficient to cause the ARG to confer a cost in a host in which it was originally neutral, demonstrating an antagonism between the two genetic elements and underlining the range and complexity of pressures determining ARG dynamics in natural populations.

Sub-inhibitory antibiotic treatment selects for enhanced metabolic efficiency

Bacterial growth and metabolic rates are often closely related. However, under antibiotic selection, a paradox in this relationship arises: antibiotic efficacy decreases when bacteria are metabolically dormant, yet antibiotics select for resistant cells that grow fastest during treatment. That is, antibiotic selection counterintuitively favors bacteria with fast growth but slow metabolism. Despite this apparent contradiction, antibiotic resistant cells have historically been characterized primarily in the context of growth, whereas the extent of analogous changes in metabolism is comparatively unknown. Here, we observed that previously evolved antibiotic-resistant strains exhibited a unique relationship between growth and metabolism whereby nutrient utilization became more efficient, regardless of the growth rate. To better understand this unexpected phenomenon, we used a simplified model to simulate bacterial populations adapting to sub-inhibitory antibiotic selection through successive bottlenecking events. Simulations predicted that sub-inhibitory bactericidal antibiotic concentrations could select for enhanced metabolic efficiency, defined based on nutrient utilization: drug-adapted cells are able to achieve the same biomass while utilizing less substrate, even in the absence of treatment. Moreover, simulations predicted that restoring metabolic efficiency would re-sensitize resistant bacteria exhibiting metabolic-dependent resistance; we confirmed this result using adaptive laboratory evolutions of Escherichia coli under carbenicillin treatment. Overall, these results indicate that metabolic efficiency is under direct selective pressure during antibiotic treatment and that differences in evolutionary context may determine both the efficacy of different antibiotics and corresponding re-sensitization approaches.IMPORTANCEThe sustained emergence of antibiotic-resistant pathogens combined with the stalled drug discovery pipelines highlights the critical need to better understand the underlying evolution mechanisms of antibiotic resistance. To this end, bacterial growth and metabolic rates are often closely related, and resistant cells have historically been characterized exclusively in the context of growth. However, under antibiotic selection, antibiotics counterintuitively favor cells with fast growth, and slow metabolism. Through an integrated approach of mathematical modeling and experiments, this study thereby addresses the significant knowledge gap of whether antibiotic selection drives changes in metabolism that complement, and/or act independently, of antibiotic resistance phenotypes.

Determining the spatiotemporal variation, sources, and ecological processes of antibiotic resistance genes in a typical lake of the middle reaches of the Yangtze River

Antibiotic resistance genes (ARGs) are emerging environmental pollutants, influenced by complex regulatory factors. River-lake systems act as natural reservoirs for ARGs and provide an ideal model for studying their regulatory mechanisms. This study employed high-throughput quantitative PCR, high-throughput sequencing, correlation analyses, and model predictions to investigate the dynamics of ARGs and their influencing factors in Liangzi Lake, located in the mid-reaches of the Yangtze River. The research specifically centered on three environmental components: lake water, sediment, and river water. Results indicated that the ARGs from eight major antibiotic classes, displaying distinct seasonal distribution patterns. In comparison to the sediment, the water phase demonstrated a higher diversity of ARGs, with the highest level of ARGs sharing observed between lake and river waters (approximately 83.7 %). Furthermore, seasonal variations significantly influenced the distributions of both ARGs and bacterial communities. The diversity of ARGs was highest during the summer and autumn, and specific bacterial species exhibited robust correlations with ARGs (including matA/mel, aac (6')-Ib-03, and blaROB). It is worth noting that environmental attributes and bacterial diversity had the most substantial impact on the dynamic changes in ARGs. Lastly, source tracking analysis pinpointed that sediment as the primary source of ARGs in lake water, constituting 45 % to 48 % of the total ARGs. Our study provides a comprehensive analysis of ARGs and their influencing factors in the river-lake system of the middle reaches of the Yangtze River, with Liangzi Lake as a representative case.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

Nothing makes sense in drug resistance except in the light of evolution

Our ability to fight infectious diseases is being increasingly compromised due to the emergence and spread of pathogens that become resistant to one or several drugs. This phenomenon is ubiquitous among pathogens and has parallels in cancer treatment. Given the urgency of the problem, there is a need for a paradigm shift in drug therapy toward one in which the objective to prevent the evolution of drug resistance is considered alongside the main objective of eliminating the infection or tumor. Here, I stress the importance of considering an evolutionary perspective to achieve this goal, and review recent advances in this direction, including therapies that exploit the fitness trade-offs of resistance.

Fructose-enabled killing of antibiotic-resistant Salmonella enteritidis by gentamicin: Insight from reprogramming metabolomics

Salmonella enterica is a food-borne pathogen that poses a severe threat to both poultry production and human health. Antibiotics are critical for the initial treatment of bacterial infections. However, the overuse and misuse of antibiotics results in the rapid evolution of antibiotic-resistant bacteria, and the discovery and development of new antibiotics are declining. Therefore, understanding antibiotic resistance mechanisms and developing novel control measures are essential. In the present study, GC-MS-based metabolomics analysis was performed to determine the metabolic profile of gentamicin sensitive (SE-S) and resistant (SE-R) S. enterica. Fructose was identified as a crucial biomarker. Further analysis demonstrated a global depressed central carbon metabolism and energy metabolism in SE-R. The decrease in the pyruvate cycle reduces the production of NADH and ATP, causing a decrease in membrane potential, which contributes to gentamicin resistance. Exogenous fructose potentiated the effectiveness of gentamicin in killing SE-R by promoting the pyruvate cycle, NADH, ATP and membrane potential, thereby increasing gentamicin intake. Further, fructose plus gentamicin improved the survival rate of chicken infected with gentamicin-resistant Salmonella in vivo. Given that metabolite structures are conserved across species, fructose identified from bacteria could be used as a biomarker for breeding disease-resistant phenotypes in chicken. Therefore, a novel strategy is proposed for fighting against antibiotic-resistant S. enterica, including exploring molecules suppressed by antibiotics and providing a new approach to find pathogen targets for disease resistance in chicken breeding.

Pervasive genotype-by-environment interactions shape the fitness effects of antibiotic resistance mutations

The fitness effects of antibiotic resistance mutations are a major driver of resistance evolution. While the nutrient environment affects bacterial fitness, experimental studies of resistance typically measure fitness of mutants in a single environment only. We explored how the nutrient environment affected the fitness effects of rifampicin-resistant rpoB mutations in Escherichia coli under several conditions critical for the emergence and spread of resistance-the presence of primary or secondary antibiotic, or the absence of any antibiotic. Pervasive genotype-by-environment (GxE) interactions determined fitness in all experimental conditions, with rank order of fitness in the presence and absence of antibiotics being strongly dependent on the nutrient environment. GxE interactions also affected the magnitude and direction of collateral effects of secondary antibiotics, in some cases so drastically that a mutant that was highly sensitive in one nutrient environment exhibited cross-resistance to the same antibiotic in another. It is likely that the mutant-specific impact of rpoB mutations on the global transcriptome underpins the observed GxE interactions. The pervasive, mutant-specific GxE interactions highlight the importance of doing what is rarely done when studying the evolution and spread of resistance in experimental and clinical work: assessing fitness of antibiotic-resistant mutants across a range of relevant environments.

Occurrence, distribution and their correlation with different parameters of antibiotics and antibiotic resistance genes in lakes of China: A review

The exposure of antibiotics and antibiotic resistance genes (ARGs) as potential threats to the environment has raised global concern. This study provides discussion on the emergence and distribution of antibiotics and ARGs in lakes. The correlation of critical water quality parameters with antibiotics and ARGs are evaluated along with their integrative potential ecological risk. Sulfonamides (∼67.18 ng/L) and quinolones (∼77.62 ng/L) were the dominant antibiotics distributed in the aqueous phase, while the quinolones and tetracyclines were the primary contamination factors in the sediment phase. The temporal and spatial distribution revealed that the antibiotic concentrations were significantly lower in summer than other seasons and the lakes in Hebei and Jiangsu provinces exhibited the highest antibiotic pollution. The detection frequency and relative abundance of sul1 gene have been the highest among all detected ARGs. Moreover, ARGs in lakes were driven by several factors, with bacterial communities and mobile genetic elements that prevailed the positive distribution of ARGs. Antibiotics have been identified as critical factors in inducing the propagation of ARGs, which could be further enhanced by chemical contaminants (e.g., heavy metals and nutrients). Involving the risk assessment strategies, research attention should be paid on three antibiotics (ofloxacin, sulfamethoxazole and erythromycin) to strengthen the policy and management of Baiyangdian Lake and East Dongting Lake. This review analysis will provide in-depth understanding to the researchers and policy-makers in formulation of strategies for remediation of antibiotic contamination in the lakes.

Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.

Combined antimicrobial effect of phage-derived endolysin and depolymerase against biofilm-forming Salmonella Typhimurium

This study was designed to evaluate the antimicrobial activity of phage-derived endolysin (LysPB32) and depolymerase (DpolP22) against planktonic and biofilm cells of Salmonella Typhimurium (STKCCM). Compared to the control, the numbers of STKCCM were reduced by 4.3 and 5.9 log, respectively, at LysPB32 and LysPB32 + DpolP22 in the presence of polymyxin B (PMB) after 48-h incubation at 37 °C. LysPB32 + DpolP22 decreased the relative fitness (0.8) and the cross-resistance of STKCCM to chloramphenicol (CHL), cephalothin (CEP), ciprofloxacin (CIP), and tetracycline (TET) in the presence of PMB. The MICtrt/MICcon ratios of CHL, CEP, CIP, PMB, and TET were between 0.25 and 0.50 for LysPB32 + DpolP22 in the presence of PMB. These results suggest that the application of phage-encoded enzymes with antibiotics can be a promising approach for controlling biofilm formation on medical and food-processing equipment. This is noteworthy in that the application of LysPB32 + DpolP22 could increase antibiotic susceptibility and decrease cross-resistance to other antibiotics.

Improvement of carbon source composition reduces antibiotic resistance genes in the ectopic fermentation system

Effectively reduce antibiotic resistance genes (ARGs) in ectopic fermentation system (EFS) is essential for practical production. In this study, three experiments were performed to explore how to remove ARGs in EFS effectively. Results demonstrated that ARGs were easily enriched in rice-husk-sawdust padding; simultaneous addition of laccase and cellulase suppressed the ARGs, mainly by increasing soluble carbohydrate concentration and promoting humic acid concentration; addition of corn stalks into rice-husk-sawdust decreased the abundance of ARGs by improving the carbon source structure and enhancing cellulase activity. In conclusion, the present study provides a guidance to reduce the threat of ARGs in EFS, which paved a potential pathway to safely utilize manure resources.

Epistasis decreases with increasing antibiotic pressure but not temperature

Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (G × E), gene-by-gene (G × G or epistatic) or gene-by-gene-by-environment (G × G × E) interactions. We quantified G × G × E effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single-nucleotide ABR mutations previously identified to vary in the extent of G × E effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found G × G interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Assessment of the potential of phage-antibiotic synergy to induce collateral sensitivity in Salmonella Typhimurium

This study was designed to evaluate the synergistic effect of phage and antibiotic on the induction of collateral sensitivity in Salmonella Typhimurium. The synergistic effects of Salmonella phage PBST32 combined with ciprofloxacin (CIP) against S. Typhimurium KCCM 40253 (ST^KCCM) were evaluated using a fractional inhibitory concentration (FIC) assay. The CIP susceptibility of ST^KCCM was increased when combined with PBST32, showing 16-fold decrease at 7 log PFU/mL. The combination of 1/2 × MIC of CIP and PBST32 (CIP[1/2]+PBST32) effectively inhibited the growth of ST^KCCM up to below the detection limit (1.3 log CFU/mL) after 12 h of incubation at 37 °C. The significant reduction in bacterial swimming motility was observed for PBST32 and CIP[1/4]+PBST32. The CIP[1/4]+PBST32 increased the fitness cost (relative fitness = 0.57) and decreased the cross-resistance to different classes of antibiotics. ST^KCCM treated with PBST32 alone treatment exhibited the highest coefficient of variation (90%), followed by CIP[1/4]+PBST32 (75%). These results suggest that the combination of PBST32 and CIP can be used to control bacterial pathogens.

Field-realistic dose of cefotaxime enhances potential mobility of β-lactam resistance genes in the gut microbiota of zebrafish (Danio rerio)

With large amounts of cephalosporin end up in natural ecosystems, water has been acknowledged as the large reservoir of β-lactam resistance over the past decades. However, there is still insufficient knowledge available on the function of the living organisms to the transmission of antibiotic resistance. For this reason, in this study, using adult zebrafish (Danio rerio) as animal model, exposing them to environmentally relevant dose of cefotaxime for 150 days, we asked whether cefotaxime contamination accelerated β-lactam resistance in gut microbiota as well as its potential transmission. Results showed that some of β-lactam resistance genes (βRGs) were intrinsic embedded in intestinal microbiome of zebrafish even without antibiotic stressor. Across cefotaxime treatment, the abundance of most βRGs in fish gut microbiome decreased apparently in the short term firstly, and then increased with the prolonged exposure, forming distinctly divergent βRG profiles with antibiotic-untreated zebrafish. Meanwhile, with the rising concentration of cefotaxime, the range of βRGs' host-taxa expanded and the co-occurrence relationships of mobile genetics elements (MGEs) with βRGs intensified, indicating the enhancement of βRGs' mobility in gut microbiome when the fish suffered from cefotaxime contamination. Furthermore, the path of partial least squares path modeling (PLS-PM) gave an integral assessment on the specific causality of cefotaxime treatment to βRG profiles, showing that cefotaxime-mediated βRGs variation was most ascribed to the alteration of MGEs under cefotaxime stress, followed by bacterial community, functioning both direct influence as βRG-hosts and indirect effects via affecting MGEs. Finally, pathogenic bacteria Aeromonas was identified as the critical host for multiple βRGs in fish guts, and its β-lactam resistance increased over the duration time of cefotaxime exposure, suggesting the potential spreading risks for the antibiotic-resistant pathogens from environmental ecosystems to clinic. Overall, our finding emphasized cefotaxime contamination in aquatic surroundings could enhance the β-lactam resistance and its transmission mobility in fish bodies.

Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment

Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.

Cyclic AMP and biofilms reveal the synergistic proliferation strategy of Pseudomonas aeruginosa and Escherichia coli under the costimulation of high concentrations of microplastics and enrofloxacin

Microplastics (MPs) provide attachment sites for biofilm formation of microorganisms, which can promote their resistance to environmental stress has been proved. However, the effect of MPs on synergy survival among microorganisms under antibiotic stress remains unclear. In the present study, the proliferation of Escherichia coli and Pseudomonas aeruginosa was assessed under enrofloxacin stress with the influence of MPs. Here, MPs reduced the growth speed of E. coli and enhanced that of P. aeruginosa, especially at 12 h, but the final value of OD₆₀₀ and CFU of both bacteria not be influenced. E. coli was enrofloxacin sensitive (MIC = 0.25 μg/mL), and a high MP concentration in the presence of enrofloxacin notably enhanced the biofilm formation ability of P. aeruginosa, but proliferation decreased. In the coculture system, the proliferation of E. coli (increased 1.42-fold) and P. aeruginosa (increased 1.06-fold) both increased under enrofloxacin stress (0.25 μg/mL) with high-concentration MP addition. P. aeruginosa may provide the biofilm matrix for E. coli to resist the stress of enrofloxacin. The high concentration of cyclic AMP secreted by E. coli may slightly inhibited biofilm formation, leading to a decrease in the fitness cost of P. aeruginosa; thus, the proliferation of P. aeruginosa increased. The present study is the first to show that MP combined with antibiotics stimulates the metabolic cooperation of bacteria to promote proliferation.

Dynamic distribution and driving mechanisms of antibiotic resistance genes in a human-intensive watershed

Accelerated urbanization has promoted urban watersheds as important reservoirs of antibiotic resistance genes (ARGs); yet the biogeographical patterns and driving mechanisms of ARGs at the watershed scale remain unclear. Here, we examined the dynamic distribution of ARGs in a human-intensive watershed (including city, river and lake systems) over different seasons in a temperate region, as well as revealed the key factors shaping ARGs dynamics through structural equation models (SEMs). High diversity and abundance of ARGs were detected in sediments and surface water, with aminoglycoside, beta-lactamase and multidrug resistance genes dominating. PCoA showed distinct ARGs variations between the two phases. Seasonal changes and regional functions had significant impacts on the distribution patterns of ARGs. More diverse ARGs were detected in winter, while higher ARGs abundances were observed in spring and summer. The city system showed the highest level of ARGs contamination and was mainly derived from wastewater and human/animal feces based on SourceTracker analysis and ARGs indicators. Notably, watershed restoration could significantly mitigate the ARGs pollution status and improve biodiversity in the aquatic environment. Network analysis identified several hub ARGs and bacterial genera, which helped to infer potential bacterial hosts carrying ARGs. Furthermore, ARGs indicators provided insights to trace ARGs sources. SEMs indicated that bioavailable heavy metals and nutrients can greatly shape ARGs dynamics in regions with high-intensity human activities, while the microbial community and MGEs dominate the fate of ARGs in less human-impacted regions. More attention should be given to control heavy metals and nutrients to curb the spread of ARGs. Overall, this study highlights the environmental fate of ARGs and provides novel strategies to mitigate ARGs pollution in the human-intensive watershed.

Potential impact factors on the enhancement of antibiotic resistance in a lake environment

There is considerable concern regarding antibiotic resistance in the water environment due to antibiotic residues from anthropogenic origins. The low antibiotic concentration in the water environment may promote the selection of antibiotic resistance. However, it is unclear how environmental factors affect resistance selection. We investigated the proliferation of quinolone-susceptible faecal bacteria (E. coli) exposed to low norfloxacin concentration (ng/L) at variable temperatures, exposure times, and carbon concentrations, simulating the conditions of the water environment. The induction of antibiotic resistance in thirteen E. coli isolates was more likely to occur at 37 °C. However, resistance also occurred at temperatures as low as 25 °C, provided a longer exposure time of 5 days. These results suggest that antibiotic resistance is more likely to be induced in regions where temperatures may reach 25-37 °C, such as tropical regions.

Decreased thermal niche breadth as a trade-off of antibiotic resistance

Evolutionary theory predicts that adaptations, including antibiotic resistance, should come with associated fitness costs; yet, many resistance mutations seemingly contradict this prediction by inducing no growth rate deficit. However, most growth assays comparing sensitive and resistant strains have been performed under a narrow range of environmental conditions, which do not reflect the variety of contexts that a pathogenic bacterium might encounter when causing infection. We hypothesized that reduced niche breadth, defined as diminished growth across a diversity of environments, can be a cost of antibiotic resistance. Specifically, we test whether chloramphenicol-resistant Escherichia coli incur disproportionate growth deficits in novel thermal conditions. Here we show that chloramphenicol-resistant bacteria have greater fitness costs at novel temperatures than their antibiotic-sensitive ancestors. In several cases, we observed no resistance cost in growth rate at the historic temperature but saw diminished growth at warmer and colder temperatures. These results were consistent across various genetic mechanisms of resistance. Thus, we propose that decreased thermal niche breadth is an under-documented fitness cost of antibiotic resistance. Furthermore, these results demonstrate that the cost of antibiotic resistance shifts rapidly as the environment changes; these context-dependent resistance costs should select for the rapid gain and loss of resistance as an evolutionary strategy.

Mutation of rpoB Shifts the Nutrient Threshold Triggering Myxococcus Multicellular Development

The ability to perceive and respond to environmental change is essential to all organisms. In response to nutrient depletion, cells of the soil-dwelling δ-proteobacterium Myxococcus xanthus undergo collective morphogenesis into multicellular fruiting bodies and transform into stress-resistant spores. This process is strictly regulated by gene networks that incorporate both inter- and intracellular signals. While commonly studied M. xanthus reference strains and some natural isolates undergo development only in nutrient-poor conditions, some lab mutants and other natural isolates commit to development at much higher nutrient levels, but mechanisms enabling such rich medium development remain elusive. Here we investigate the genetic basis of rich medium development in one mutant and find that a single amino acid change (S534L) in RpoB, the β-subunit of RNA polymerase, is responsible for the phenotype. Ectopic expression of the mutant rpoB allele was sufficient to induce nutrient-rich development. These results suggest that the universal bacterial transcription machinery bearing the altered β-subunit can relax regulation of developmental genes that are normally strictly controlled by the bacterial stringent response. Moreover, the mutation also pleiotropically mediates a tradeoff in fitness during vegetative growth between high vs. low nutrient conditions and generates resistance to exploitation by a developmental cheater. Our findings reveal a previously unknown connection between the universal transcription machinery and one of the most behaviorally complex responses to environmental stress found among bacteria.

Role of Efflux Pump-Mediated Antibiotic Resistance in Quorum Sensing-Regulated Biofilm Formation by Salmonella Typhimurium

This study was designed to assess the influence of efflux pump activity on the biofilm formation in Salmonella Typhimurium. Salmonella enterica subsp. enterica serovar Typhimurium ATCC 19585 (STWT) and clinically isolated S. Typhimurium CCARM 8009 (STCI) were treated with ceftriaxone (CEF), chloramphenicol (CHL), ciprofloxacin (CIP), erythromycin (ERY), norfloxacin (NOR), and tetracycline (TET) in autoinducer-containing media in the absence and presence of phenylalanine-arginine β-naphthylamide (PAβN) to compare efflux pump activity with biofilm-forming ability. The susceptibilities of STWT and STCI were increased in the presence of PAβN. ERY+PAβN showed the highest decrease in the minimum inhibitory concentration (MIC) of ERY from 256 to 2 μg/mL against STWT and STCI. The antimicrobial activity of NOR against planktonic cells was significantly increased in the presence of PAβN, showing the lowest numbers of STWT (3.2 log CFU/cm2), and the TET+PAβN effectively inhibited the growth of STCI (5.2 log CFU/cm2). The lowest biofilm-forming abilities were observed at NOR+PAβN against STWT (biofilm-forming index, BFI < 0.41) and CEF+PAβN against STCI (BFI = 0.32). The bacteria swimming motility and relative fitness varied depending on the antibiotic and PAβN treatments. The motility diameters of STWT were significantly decreased by NOR+PAβN (6 mm) and TET+PAβN (15 mm), while the lowest motility of STCI was observed at CIP+PAβN (8 mm). The significant decrease in the relative fitness levels of STWT and STCI was observed at CIP+PAβN and NOR+PAβN. The PAβN as an efflux pump inhibitor (EPI) can improve the antimicrobial and anti-biofilm efficacy of antibiotics against S. Typhimurium. This study provides useful information for understanding the role of efflux pump activity in quorum sensing-regulated biofilm formation and also emphasizes the necessity of the discovery of novel EPIs for controlling biofilm formation by antibiotic-resistant pathogens.

The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing

Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere

Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.

Removal of antibiotic-resistant genes during drinking water treatment: A review

Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.

Fitness reduction of antibiotic resistome by an extra carbon source during swine manure composting

This study employed high-throughput quantitative polymerase chain reaction to evaluate the effects of specific co-substrate and additive on the fitness of antibiotic resistome during swine manure composting. The results showed that corncob particle as a co-substrate significantly reduced the relative abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) simultaneously. The diversity of ARGs was also reduced more effectively by corncob addition. Brick granule as an additive reduced the concentrations of bioavailable Cu and Zn. However, the relative abundances of ARGs and MGEs were not reduced by the addition of brick granule subsequently. Redundancy analysis indicated a negative effect of the C content and positive effects of class I integrase gene (intI) and bioavailable metals on the variation of the relative abundance of ARGs (p < 0.01). The Procrustes test showed a higher goodness-of-fit between the relative abundance of ARGs and 16S rRNA genes (r = 0.8166; p < 0.0001). Our results suggests that the effect of corncob particle on the relative abundance of ARGs was achieved by driving the changes in physicochemical properties and microbial communities. This study confirmed the hypothesis of fitness cost and demonstrated the contribution of extra C source to ARG attenuation during composting.

Metabonomics reveals an alleviation of fitness cost in resistant E. coli competing against susceptible E. coli at sub-MIC doxycycline

High concentrations of antibiotics may induce bacterial resistance mutations and further lead to fitness costs by reducing growth of resistant bacteria. However, antibiotic concentrations faced by bacteria are usually low in common environments, which leads to questions about how resistant bacteria with fitness costs regulate metabolism to coexist or compete with susceptible bacteria during sublethal challenge. Our study revealed that a low proportion (< 15%) of resistant bacteria coexisted with susceptible bacteria due to the fitness cost without doxycycline. However, the cost for the resistant strain decreased at a doxycycline concentration of 1 mg/L and even disappeared when the doxycycline concentration was 2 mg/L. Metabonomics analysis revealed that bypass carbon metabolism and biosynthesis of secondary metabolites were the primary metabolic pathways enriching various upregulated metabolites in resistant bacteria without doxycycline. Moreover, the alleviation of fitness cost for resistant bacteria competed with susceptible bacteria at 1 mg/L doxycycline was correlated with the downregulation of the biomarkers pyruvate and pilocarpine. Our study offered new insight into the metabolic mechanisms by which the fitness cost of resistant mutants was reduced at doxycycline concentrations as low as 1 mg/L and identified various potential metabolites to limit the spread of antimicrobial resistance in the environment.

Accumulation of antibiotic resistance genes in full-scale drinking water biological activated carbon (BAC) filters during backwash cycles

Biological activated carbon (BAC) filtration, a process widely used in drinking water treatment, was recently reported to harbor antibiotic resistance genes (ARGs). This emerging contamination is poorly understood. This study was conducted to investigate the occurrence of ARGs and bacterial community in full-scale BAC filters during the backwash cycle using high-throughput qPCR and high-throughput sequencing. A total of 178 ARGs were detected in all biofilm samples, with relative abundance ranging from 0.1 to 1.37 copies per 16S rRNA and absolute abundance ranging from 4.48 × 10⁷ to 3.09 × 10⁹ copies/g carbon. Biofilms sampled from different filters shared most detected ARGs and dominant genera including Bryobacter, Pedomicrobium, Reyranella, and Terrimonas, though their bacterial community structure differed significantly. After backwashing, the relative ARGs abundance increased by 1.5- to 3.8-folds and the absolute ARGs abundance increased by 0.90- to 1.12-logs in all biofilm samples during filter ripening, indicating that ARGs accumulated in filters during this period. Redundancy analysis suggested that such ARGs accumulation was mainly driven by horizontal gene transfer in winter, but highly correlated with the increasing relative abundance of genera Bryobacter and Acidibacter in summer. It was observed that 80.6 %-89.3% of the detected ARGs persisted in the filters despite of the backwashing. Given the high richness and relative abundance of ARGs in BAC filter and the ineffectiveness of backwashing in ARG removal, more stringent downstream disinfection strategies are deserved and more research is necessary to assess potential human health risks due to the persistence of ARGs in drinking water.

River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus)

Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10^-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.

The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage

Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.

The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39

Application of supplementary drugs which increase susceptibility of pathogenic bacteria to antibiotics is a promising yet unexplored approach to overcome the global problem of multidrug-resistant infections. The discovery of a new drug, an iodine-containing nano-molecular complex FS-1, which has proven to improve susceptibility to antibiotics in various pathogens, including MRSA strain Staphylococcus aureus ATCC BAA-39TM, allowed studying this phenomenon. Chromosomal DNA and total RNA samples extracted from the FS-1 treated strain (FS) and from the negative control (NC) cultures were sequenced by PacBio SMRT and Ion Torrent technologies, respectively. PacBio DNA reads were used to assemble chromosomal DNA of the NC and FS variants of S. aureus BAA-39 and to perform profiling of epigenetically modified nucleotides. Results of transcriptional profiling, variant calling and detection of epigenetic modifications in the FS variant were compared to the NC variant. Additionally, the genetic alterations caused by the treatment of S. aureus BAA-39 with FS-1 were compared to the results of a similar experiment conducted with another model organism, E. coli ATCC BAA-196. Several commonalities in responses of these phylogenetically distant microorganisms to the treatment with FS-1 were discovered, which included metabolic transition toward anaerobiosis and oxidative/osmotic stress response. S. aureus culture appeared to be more sensitive to FS-1 due to a higher penetrability of cells by iodine bound compounds, which caused carbonyl stress associated with nucleotide damaging by FS-1, abnormal epigenetic modifications and an increased rate of mutations. It was hypothesized that the disrupted pattern of adenine methylated loci within methicillin-resistance chromosome cassettes (SCCmec) may promote excision of this antibiotic resistance determinant from chromosomes while the altered pattern of cytosine methylation was behind the adaptive gene regulation in the culture FS. The selection against the antibiotic resistance in bacterial populations caused by abnormal epigenetic modifications exemplifies possible mechanisms of antibiotic resistance reversion induced by iodine-containing compounds. These finding will facilitate development of therapeutic agents against multidrug-resistant infections.

Pollution profiles of antibiotic resistance genes associated with airborne opportunistic pathogens from typical area, Pearl River Estuary and their exposure risk to human

To reveal the selective pressures of near-shore human activities on marine and continental bioaerosols, the pollution profile and potential exposure risk of airborne pathogens and antibiotic-resistance genes (ARGs) in Pearl River Estuaries (113.52 ^oE, 22.69 ^oN), a transitional zone between marine and continental environments, were fully explored. The results showed that the total bacteria among bioaerosols varied largely with average pollution levels of 1.86 × 10⁵ and 4.35 × 10⁴ cfu m^-3 in spring and summer, respectively, and were high than those of airborne fungi. The predominant aerodynamic diameters of bioaerosols were in respirable size range (<4.7 µm), and the microbes communities' diversity and abundance varied significantly. Besides, many opportunistic pathogenic bacteria (Burkholderia-Paraburkholderia, Staphylococcus and Acinetobacter) and fungi (Alternaria, Penicillium and Cladosporium) were dominant in bioaerosol samples. Of 21 ARGs subtypes detected, the tetracycline resistance gene tetA was the most abundant, followed by aminoglycoside resistance gene and mobile genetic elements. Correlation analysis revealed that the changes of pathogens community contributed significantly to the prevalence of ARGs in bioaerosol. Based on the average daily dose rates of microorganisms and human direct intake of ARGs, health risk of bioaerosols from the Pearl River Estuaries were also evaluated. In summary, the presence of opportunistic pathogens and diversity of ARGs strengthens the call to consider the bioaerosol in air quality monitoring and risk assessment in the future.

Drinking water biofiltration: Behaviour of antibiotic resistance genes and the association with bacterial community

Antibiotic resistance genes (ARGs) are being detected in drinking water frequently, constituting a major public health issue. As a typical drinking water treatment process, the biofilter may harbour various ARGs due to the filter biofilms established during the filtration process. The objective of this study was to investigate the behaviour of ARGs (bla_CTX-M, bla_OXA-1, bla_TEM, ermB, tetA, tetG, tetQ, tetW, tetX, sul 1, sul 2, dfrA1 and dfrA12) and their possible association with bacteria in a bench-scale biofiltration system. The impact of filter media on horizontal gene transfer (HGT) was also explored using a model conjugative plasmid, RP1. The biofiltration system comprised four types of biofilters, including sand, granular activated carbon (GAC), GAC sandwich, and anthracite-sand biofilters. Results showed that although the absolute abundance of ARGs decreased (0.97-log reduction on average), the ARGs' abundance normalised to bacterial numbers showed an increasing trend in the filtered water. Biofilms collected from the surface layer revealed the lowest relative abundance of ARGs (p < 0.01) compared to the deeper layer biofilms, indicating that the proportion of ARG-carrying bacteria was greater in the lower position. Most chosen ARG numbers correlated to Proteobacteria, Acidobacteria and Nitrospirae phyla, which accounted for 51.9%, 5.2% and 2.0% of the biofilm communities, respectively. GAC media revealed the highest transfer frequency (2.60 × 10^-5), followed by anthracite (5.31 × 10^-6) and sand (2.47 × 10^-6). Backwashing can reduce the transferability of RP1 plasmid significantly in biofilms but introduces more transconjugants into the planktonic phase. Overall, the results of this study could enhance our understanding of the prevalence of ARGs in drinking water biofiltration treatment.

Effectiveness of Antibiotic Combination Treatments to Control Heteroresistant Salmonella Typhimurium

This study was designed to assess the interactions between antibiotics in combination treatments of Salmonella enterica serovar Typhimurium in association with the development of antibiotic heteroresistance. Salmonella Typhimurium ATCC 19585 (ST^WT), ciprofloxacin (CIP)-induced S. Typhimurium ATCC 19585 (ST^CIP), and clinically isolated antibiotic-resistant S. Typhimurium CCARM 8009 (ST^CLI) treated with antibiotic alone (cephalothin [CEP], CIP, ceftriaxone [CEF], and tobramycin [TOB]) and combination antibiotics (CEP-CIP and CEF-TOB) were used to compare the antibiotic susceptibility, resistance fitness, and cross-resistance. The susceptibilities of ST^WT, ST^CIP, and ST^CLI to CEP were not significant differences between CEP and CEP-CIP treatments, whereas those of ST^WT, ST^CIP, and ST^CLI to TOB were significant differences between TOB and CEF-TOB treatments. The interactions between CEP and CIP in the combination treatment showed mutually synergistic activities against ST^WT and ST^CLI. For the CEF-TOB combination treatments, TOB helped enhance the antibiotic activity of CEF against ST^WT, showing directional synergistic effect. The CEF-TOB combination treatment increased bactericidal activity against ST^WT, ST^CIP, and ST^CLI without causing injured cells. The combination antibiotic treatments (CEP-CIP and CEF-TOB) increased the fitness cost (relative fitness = 0.7) and decreased the cross-resistance of ST^WT, ST^CIP, and ST^CLI when exposed to different classes of antibiotics. This study provides new insight for designing combination antibiotic regimens that can synergistically enhance the antimicrobial activity against antibiotic-resistant Salmonella and inhibit the emergence of cross-resistance to different classes of antibiotics.

Co-selection and stability of bacterial antibiotic resistance by arsenic pollution accidents in source water

Frequent heavy-metal pollution accidents severely deteriorated the source water quality of drinking water treatment plants (DWTP). Limited data have explicitly addressed the impact of these incidents on bacterial antibiotic resistance (BAR). In present study, we investigated the shift of antibiotic resistome caused by heavy metal pollution incidents via simulating an arsenic shock loading [As (III)], along with the associated risks imposed on drinking water systems. The results indicated that a quick co-selection of antibiotic resistant bacteria (ARB) was achieved after exposure to 0.2-1 mg/L As (III) for only 6 h, meanwhile, there was an increase of relative abundance of antibiotic resistance genes (ARGs) and mobile genetic elements. Most of the co-selected BAR could be maintained for at least 4 days in the absence of As (III) and antibiotics, implying that the pollution in source water possibly contributed to the preservation and proliferation of antibiotic resistance determinants in the subsequent DWTP. Bacterial community structure analysis showed a strong correlation between bacterial community shift and BAR promotion, and enrichment of opportunistic bacteria (e.g. Escherichia-Shigella, Empedobacter sp. and Elizabethkingia sp.). The results indicated a potential epidemiological threat to the public due to accident-level arsenic contamination in the source water. This study gave insight into understanding the source water pollution accidents from the perspective of bio-hazard and biological risks, and highlighted a neglected important source of BAR in drinking water systems.

Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment

With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.

Soft sweep development of resistance in Escherichia coli under fluoroquinolone stress

We employed a stepwise selection model for investigating the dynamics of antibiotic-resistant variants in Escherichia coli K-12 treated with increasing concentrations of ciprofloxacin (CIP). Firstly, we used Sanger sequencing to screen the variations in the fluoquinolone target genes, then, employed Illumina NGS sequencing for amplicons targeted regions with variations. The results demonstrated that variations G81C in gyrA and K276N and K277L in parC are standing resistance variations (SRVs), while S83A and S83L in gyrA and G78C in parC were emerging resistance variations (ERVs). The variants containing SRVs and/or ERVs were selected successively based on their sensitivities to CIP. Variant strain 1, containing substitution G81C in gyrA, was immediately selected following ciprofloxacin exposure, with obvious increases in the parC SRV, and parC and gyrA ERV allele frequencies. Variant strain 2, containing the SRVs, then dominated the population following a 20× increase in ciprofloxacin concentration, with other associated allele frequencies also elevated. Variant strains 3 and 4, containing ERVs in gyrA and parC, respectively, were then selected at 40× and 160× antibiotic concentrations. Two variants, strains 5 and 6, generated in the selection procedure, were lost because of higher fitness costs or a lower level of resistance compared with variants 3 and 4. For the second induction, all variations/indels were already present as SRVs and selected out step by step at different passages. Whatever the first induction or second induction, our results confirmed the soft selective sweep hypothesis and provided critical information for guiding clinical treatment of pathogens containing SRVs.

Low nutrient levels as drinking water conditions can reduce the fitness cost of efflux pump-mediated ciprofloxacin resistance in Pseudomonas aeruginosa

The long-term persistence of antibiotic resistance in the environment, especially in drinking water, is a public health concern. Expression of an efflux pump, an important mechanism of resistance to antibiotics, usually confers a fitness cost in bacteria. In this study, we aimed to determine why antibiotic resistance conferred by overexpression of an efflux pump persisted in low-nutrient environments (TOC < 10 mg/L) such as drinking and source water in which antibiotic selective pressure might be very low or even absent. Competition experiments between wild-type Pseudomonas aeruginosa and ciprofloxacin-resistant mutants revealed that the fitness cost of ciprofloxacin resistance significantly decreased (p < 0.05) under low-nutrient (0.5 mg/L total organic carbon (TOC)) relative to high-nutrient (500 mg/L TOC) conditions. Mechanisms underlying this fitness cost were analyzed. The mexD gene expression in resistant bacteria (cip_3 strain) was significantly lower (p < 0.05) in low-nutrient conditions, with 10 mg/L TOC ((8.01 ± 0.82)-fold), than in high-nutrient conditions, with 500 mg/L TOC ((48.89 ± 4.16)-fold). Moreover, rpoS gene expression in resistant bacteria ((1.36 ± 0.13)-fold) was significantly lower (p < 0.05) than that in the wild-type strain ((2.78 ± 0.29)-fold) under low-nutrient conditions (10 mg/L TOC), suggesting a growth advantage. Furthermore, the difference in metabolic activity between the two competing strains was significantly smaller (p < 0.05) in low-nutrient conditions (5 and 0.5 mg/L TOC). These results suggest that nutrient levels are a key factor in determining the persistence of antibiotic resistance conferred by efflux pumps in the natural environment with trace amounts or no antibiotics.

Effect of Environment on the Evolutionary Trajectories and Growth Characteristics of Antibiotic-Resistant Escherichia coli Mutants

The fitness cost to bacteria of acquisition of resistance determinants is critically under-investigated, and the identification and exploitation of these fitness costs may lead to novel therapeutic strategies that prevent the emergence of antimicrobial resistance. Here we used Escherichia coli and amoxicillin–clavulanic acid (AMC) resistance as a model to understand how the artificial environments utilized in studies of bacterial fitness could affect the emergence of resistance and associated fitness costs. Further, we explored the predictive value of this data when strains were grown in the more physiologically relevant environments of urine and urothelial organoids. Resistant E. coli isolates were selected for following 24-h exposure to sub-inhibitory concentrations of AMC in either M9, ISO, or LB, followed by growth on LB agar containing AMC. No resistant colonies emerged following growth in M9, whereas resistant isolates were detected from cultures grown in ISO and LB. We observed both within and between media-type variability in the levels of resistance and fitness of the resistant mutants grown in LB. MICs and fitness of these resistant strains in different media (M9, ISO, LB, human urine, and urothelial organoids) showed considerable variation. Media can therefore have a direct effect on the isolation of mutants that confer resistance to AMC and these mutants can exhibit unpredictable MIC and fitness profiles under different growth conditions. This preliminary study highlights the risks in relying on a single culture protocol as a model system to predict the behavior and treatment response of bacteria in vivo and highlights the importance of developing comprehensive experimental designs to ensure effective translation of diagnostic procedures to successful clinical outcomes.

Development of de novo resistance in Salmonella Typhimurium treated with antibiotic combinations

This study was designed to evaluate the evolution of antibiotic resistance in Salmonella enterica serovar Typhimurium treated with the combination of antibiotics. The experimental evolution of antibiotic resistance of S. Typhimurium was evaluated either under single antibiotic (kanamycin, KAN; penicillin, PEN; erythromycin, ERY) or in combination of two antibiotics (KAN + PEN or KAN + ERY) as measured by fractional inhibitory concentrations (FICs), stepwise resistance selection, cross-resistance evaluation, resistance fitness and relative gene expression. KAN + PEN and KAN + ERY showed the synergistic effect against S. Typhimurium (FIC index < 0.5). KAN + ERY delayed the induction of de novo mutations in S. Typhimurium. The cross-resistance of S. Typhimurium to all antibiotics except ERY and tetracycline was observed in KAN and PEN alone. The fitness cost was lower in single antibiotic treatments than combinations. The highest relative fitness was 0.91 in PEN, followed by KAN (0.84) and ERY (0.78), indicating the low fitness costs in single antibiotic treatments. The overexpression of efflux pump-related genes (acrA and acrB), outer membrane-related gene (ompC) and adherence-related gene (csgD) were observed in the single antibiotic treatments. Our results suggest that KAN + PEN and KAN + ERY could be used as a potential therapeutic treatment by decreasing the evolution of antibiotic resistance in S. Typhimurium and reusing conventional antibiotics.

Organic carbon: An overlooked factor that determines the antibiotic resistome in drinking water sand filter biofilm

Biofilter, an essential water treatment process, is reported to be the harbor of bacterial antibiotic resistance genes (ARGs). Due to the oligotrophic characteristic of source water, filter biofilm is largely influenced by the concentration of organic carbon. The objective of this study was to investigate the effect of organic carbon concentration on shaping bacterial antibiotic resistome in filter biofilm. Our study was based on pilot-scale sand filters, and we investigated the antibiotic resistome using high-throughput qPCR. A total of 180 resistance genes from eight categories of antibiotics were detected in 15 biofilm samples of three sand filters. The results indicated that higher concentration of influent organic carbon led to lower diversity of bacterial community and richness of antibiotic resistance genes (ARGs) in biofilm. We discovered a negative correlation (p ≤ 0.01) between the richness of ARGs and the corresponding TOC level. Moreover, the absolute abundance of ARGs was positively correlated (p ≤ 0.05) with the abundance of 16S rRNA gene and was determined by the organic carbon concentration. Sand filters with gradient influent organic carbon concentration led to the formation of different antibiotic resistomes and canonical correspondence analysis (CCA) indicated that difference in bacterial community composition was likely the main reason behind this difference. We also observed a similar trend in the relative abundance of ARGs, which increased with the depth of sand filters. However, this trend was more pronounced in filters with low organic carbon concentrations. Overall, this study revealed that the organic carbon concentration determined the absolute abundance of ARGs and also shaped the diversity and relative abundance of ARGs in drinking water sand filters. These results may provide new insights into the mechanism of persistent bacterial antibiotic resistance in drinking water treatment.