Antibiotic resistance and its cost: is it possible to reverse resistance?

Leveraging strain competition to address antimicrobial resistance with microbiota therapies

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

Isolation and characterization of Salmonella Typhimurium SL1344 variants with increased resistance to different stressing agents and food processing technologies

In this study, resistant variants of Salmonella enterica serovar Typhimurium SL1344 to different stressors were selected. In addition, a genetic and phenotypic study was performed to explore the mechanisms underlying the acquisition of resistance. We isolated 4 variants with increased stable resistance to acid, osmotic stress, high hydrostatic pressure (HHP) and Ultraviolet-C light (UV-C) after repeated rounds of exposure to these agents and outgrowth of survivors. A PEF-resistant variant (SL1344-RS), previously isolated by Sagarzazu et al. (2013), was also included in the analysis. The results indicated that the isolated variants showed resistance to at least one other agent. This increased resistance, in general terms, had a fitness cost in growth, and exerted a variable impact on virulence (mainly in cell adhesion capacity), increased antibiotic resistance but did not influence in biofilm formation capacity. Whole Genome Sequencing (WGS) analysis allowed us to identify the genetic changes responsible for these phenotypic differences, and revealed that in 3 out of the 5 variants (including SL1344-RS) a mutation was found in hnr gene, an anti-sigma factor that promotes RpoS proteolysis. Hence the expression of several rpoS-regulated genes was quantified and found higher in these variants. This increase in RpoS activity would explain the lower growth rates observed in these 3 variants, as it would lead to increased transcription of genes involved in growth arrest and resistance to various types of stress. However, further analysis of a set of 22 additional Salmonella strains obtained from different culture collections indicated that a direct relationship between RpoS activity and stress resistance might not exist within Salmonella.

"Acceptable" concentrations of enrofloxacin in food lead to reduced enrofloxacin susceptibility in a mouse model of gastrointestinal Klebsiella pneumoniae

Concentrations of antimicrobials up to 1,000-fold lower than the minimum inhibitory concentration can select for antimicrobial resistance. This generates the hypothesis that the low concentrations of antimicrobials allowed in our food could select for resistance. We assessed if the dose of enrofloxacin allowed in food by the European Medicines Agency (6.2 µg/kg) could decrease susceptibility to enrofloxacin in a strain of Klebsiella pneumoniae colonizing the gastrointestinal tracts of Specific Opportunistic Pathogen-Free Naval Medical Research Institute (NMRI) mice. We found that one-tenth of this dose given daily was able to increase the K. pneumoniae enrofloxacin MIC 8-fold (from 0.047 µg/mL to 0.38 µg/mL). Our findings suggest the need for studies to assess if the same could occur in humans.IMPORTANCEAntimicrobial-resistant infections are responsible for over a million deaths a year. Reducing antimicrobial resistance requires addressing all the sources of unnecessary antimicrobial exposure. Because the antimicrobial concentration in our food frequently approaches or exceeds the maximum allowed limits, it is crucial to ensure that the legal concentrations of antimicrobials in food do not induce antimicrobial resistance. We found that enrofloxacin doses, 10 times lower than those classified as safe, could increase enrofloxacin MICs 8-fold in K. pneumoniae in the gastrointestinal tracts of mice. These findings suggest that we need to consider the induction of antimicrobial resistance when defining safe concentrations of antimicrobials in our food.

Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes

Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.

Emerging threats: Listeria monocytogenes with acquired multidrug resistance from food in China, 2012-2022

Listeria monocytogenes is a foodborne pathogen that poses threat to food safety and public health. Generally, the rates of resistance to clinically important antibiotics in L. monocytogenes are low. This study aimed to investigate the prevalence and genetic characteristics of L. monocytogenes with acquired multidrug resistance (MDR) in food samples from China between 2012 and 2022. Of 8344 isolates collected, 34 (0.41 %) were identified as acquired MDR. The majority of acquired MDR isolates (n = 31, 92.3 %) belonged to hypovirulent clonal complex (CC) 9 (Lineage II, IIc), including 3 sequence types (ST) (ST9, n = 29; ST2458, n = 1; ST9-1LV, n = 1), which has remained dominant over the past decade. In 2022, three additional acquired MDR clones emerged: CC87/ST87 (Lineage I, IIb), CC8/ST8 (Lineage II, IIa), and CC155/ST705 (Lineage II, IIa), with CC87/ST87 and CC8/ST8 being notably associated with human listeriosis in Asia. The rep25_2_M640p00130 plasmid was the most common mobile genetic element among these acquired MDR isolates, consistently harboring seven types of antibiotic resistance genes, including aminoglycosides (ant(6)-Ia; aph(3')-III), trimethoprim (dfrG), macrolides, lincosamides and streptogramin B (MLSb) (erm(B)), lincosamides (lnu(B)), pleuromutilins, lincosamides and streptogramin A (PLSA) (lsa(E)), tetracyclines (tet(S)), and phenicols (catA), and flanked on one side by IS1216E. However, the diversity of acquired MDR-carrying plasmids increased from 2017 to 2022, with an increased prevalence among replicons including rep26_2_repA, rep26_4_repA, and rep26_1_pli0070/rep32_1_pli0023. Importantly, compared to the dominant hypovirulent CC9, which contained premature stop codons in the internalin gene inlA associated with adhesion and invasion, the newly emerged acquired MDR L. monocytogenes CC8/ST8 and CC155/ST705 maintained intact inlA gene and exhibited stronger adhesion and invasion phenotype in Caco-2 cells. These findings emphasize the need for continuous surveillance of acquired MDR L. monocytogenes, particularly the virulent CC8/ST8 and CC155/ST705, to mitigate risks to food safety and human health.

Antimicrobial effects, and selection for AMR by non-antibiotic drugs in a wastewater bacterial community

Antimicrobial resistance (AMR) is a major threat to human, animal, and crop health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals, at environmentally relevant concentrations. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. There is a significant knowledge gap in understanding a range of NAD concentrations, (including lower µg/L concentrations found in the environment) on mixed bacterial communities containing a diverse mobile resistome. Here, we determined the antimicrobial effect and selective potential of diclofenac, metformin, and 17-β-estradiol, NADs that are commonly found environmental pollutants, in a complex bacterial community using a combination of culture based, metagenome, and metratranscriptome approaches. We found that diclofenac, metformin, and 17-β-estradiol at 50 µg/L, 26 µg/L, and 24 µg/L respectively, significantly reduced growth of a bacterial community although only 17-β-estradiol selected for an AMR marker using qPCR (from 7 µg/L to 5400 µg/L). Whole metagenome sequencing indicated that there was no clear selection by NADs for antibiotic resistance genes, or effects on community composition. Additionally, increases in relative abundance of some specific metal resistance genes (such as arsB) were observed after exposure to diclofenac, metformin, and 17-β-estradiol. These results indicate that environmentally relevant concentrations of NADs are likely to affect community growth, function, and potentially selection for specific metal resistance genes.

IS26-mediated cointegration generates a plasmid co-harbouring blaIMP-4 and blaKPC-2 in Klebsiella pneumoniae

BACKGROUND

This study aims to explore the phenotypic and genotypic characteristics of a plasmid that co-harbours blaIMP-4 and blaKPC-2 in a carbapenem-resistant Klebsiella pneumoniae.

METHODS

Strain K194 was isolated from a 60-year-old patient. Species identification was performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, followed by antibiotic susceptibility testing. Antimicrobial resistance genes were detected and S1-pulsed-field gel electrophoresis with Southern blot experiments were performed to identify plasmids. Whole-genome sequencing was executed with the Illumina and Oxford Nanopore platforms.

RESULTS

K. pneumoniae K194 was resistant to multiple antibiotics, including carbapenems. This strain carried both blaIMP-4 and blaKPC-2 on a single 163 kb plasmid (pK194-P2). pK194-P2 was capable of conjugation with an efficiency of 3.4 × 10-7 in vitro conjugation experiments. Whole-genome analysis confirmed that pK194-P2 was a novel plasmid and had both IncFII- and IncN-type replicons. Sequence alignment revealed direct repeats of the sequences (GCCCAAGG) flanking a 109-kb region bounded by two copies of IS26. In vitro, evolution experiments showed that blaKPC-2 in pK194-P2 could be stably maintained in the transconjugants after 10 days of passage, while blaIMP-4 could be lost during repeated laboratory passage. Whole-genome sequencing and alignment of two blaIMP-4-negative plasmids with pK194-P2 revealed that they had a deletion of 81 or 94 kb adjacent to IS26.

CONCLUSIONS

Our study reports a novel plasmid co-harbouring blaIMP-4 and blaKPC-2 in K. pneumoniae, and highlights the potential role of IS26-mediated cointegration and deletion in plasmid formation and evolution.

MXene and Near-Infrared Carbon Dots Co-Encapsulated Hydrogel Facilitates Infected Bone Defect Reconstruction

Inadequate bone differentiation and intractable biofilm formation due to stubborn bacterial infection complicate infected bone defect repair. Adding harmful antibiotics into scaffolds not only promotes multidrug-resistant bacteria but also decreases bone repair effect. Furthermore, dynamic monitor of scaffolds' degradation is crucial for achieving visualized bone defect repair, however, currently reported biomaterials do not have imaging tracing capabilities. On this basis, this work develops a scaffold material with triple functionality for visualized therapy of infected bone defects: antibacterial, osteogenesis, and near-infrared (NIR) imaging capabilities. Single-layer Ti3C2Tx with broad-spectrumantibacterial activity and negatively charged carbon dots (CDs) with osteogenic activity are synthesized for infected bone defect repair. To validate antibacterial and osteogenic activities in vivo, 3D injectable hydrogels encapsulated with Ti3C2Tx and CDs (CD/Ti3C2Tx/GelMA) are constructed. NIR imaging is used to monitor the degradation process of CD/Ti3C2Tx/GelMA hydrogels in infected bone defect models, which indicated that CDs are completely released from hydrogels in about 30 days. Owing to the continuous release of Ti3C2Tx and CDs, the obtained CD/Ti3C2Tx/GelMA hydrogels can efficiently promote the repair of infected bone defects within 60 days. These findings develop a new biomaterial with great performance for visualized antibacterial and osteogenic therapy of infected bone defects.

The new strategies for high efficiency removal of antibiotics and antibiotic resistance genes by direct bio-drying of biogas slurry: Microbiological mechanisms

High levels of antibiotics and antibiotic resistance genes (ARGs) still exist in biogas slurry after anaerobic digestion of cow manure. In this study, direct bio-drying strategies of cow manure biogas slurry without solid-liquid separation for the removal of antibiotics and ARGs were explored. The results showed that, after direct bio-drying of biogas slurry, the moisture contents decreased to 25.2 %-31.5 %. The maximum temperatures of the piles reached 76.1-77.4 °C, which is close to ultra-high temperatures (>80 °C). Direct biogas slurry bio-drying (CK treatment) achieved efficient removal of antibiotics, ARGs, and mobile genetic elements (MGEs) (95.4 %, 98.6 % and 86.7 % removal, respectively). Compared to the CK treatment, molecular membrane covering (MMC) alone was the most effective in further significantly decreasing the antibiotic concentration and the abundance of ARGs and MGEs in the final bio-dried samples, followed by food waste hydrochar (FHC) addition alone. Methanogenic archaea were identified as potential hosts for ARGs based on Network analysis. FHC addition-MMC increased the abundance of potential hosts for ARGs and promoted the expression of microbial methane metabolism function relative to the CK treatment during the later stages of bio-drying, thereby decreasing the removal efficiency of ARGs. The results of structural equation model and redundancy analysis showed that MGEs had the most significant direct effect on ARGs and moisture content had the highest relative contribution to changes in ARGs. In summary, direct bio-drying strategies were able to efficiently remove antibiotics and ARGs from cow manure biogas slurry and also achieve biological dewatering of the biogas slurry.

Brief antibiotic use drives human gut bacteria towards low-cost resistance

Understanding the relationship between antibiotic use and the evolution of antimicrobial resistance is vital for effective antibiotic stewardship. Yet, animal models and in vitro experiments poorly replicate real-world conditions1. To explain how resistance evolves in vivo, we exposed 60 human participants to ciprofloxacin and used longitudinal stool samples and a new computational method to assemble the genomes of 5,665 populations of commensal bacterial species within participants. Analysis of 2.3 million polymorphic sequence variants revealed 513 populations that underwent selective sweeps. We found convergent evolution focused on DNA gyrase and evidence of dispersed selective pressure at other genomic loci. Roughly 10% of susceptible bacterial populations evolved towards resistance through sweeps that involved substitutions at a specific amino acid in gyrase. The evolution of gyrase was associated with large populations that decreased in relative abundance during exposure. Sweeps persisted for more than 10 weeks in most cases and were not projected to revert within a year. Targeted amplification showed that gyrase mutations arose de novo within the participants and exhibited no measurable fitness cost. These findings revealed that brief ciprofloxacin exposure drives the evolution of resistance in gut commensals, with mutations persisting long after exposure. This study underscores the capacity of the human gut to promote the evolution of resistance and identifies key genomic and ecological factors that shape bacterial adaptation in vivo.

Changing climate and socioeconomic factors contribute to global antimicrobial resistance

Climate change poses substantial challenges in containing antimicrobial resistance (AMR) from a One Health perspective. Using 4,502 AMR surveillance records involving 32 million tested isolates from 101 countries (1999-2022), we analyzed the impact of socioeconomic and environmental factors on AMR. We also established forecast models based on several scenarios, considering antimicrobial consumption reduction, sustainable development initiatives and different shared socioeconomic pathways under climate change. Our findings reveal growing AMR disparities between high-income countries and low- and middle-income countries under different shared socioeconomic pathway scenarios. By 2050, compared with the baseline, sustainable development efforts showed the most prominent effect by reducing AMR prevalence by 5.1% (95% confidence interval (CI): 0.0-26.6%), surpassing the effect of antimicrobial consumption reduction. Key contributors include reducing out-of-pocket health expenses (3.6% (95% CI: -0.5 to 21.4%)); comprehensive immunization coverage (1.2% (95% CI: -0.1% to 8.2%)); adequate health investments (0.2% (95% CI: 0.0-2.4%)) and universal access to water, sanitation and hygiene services (0.1% (95% CI: 0.0-0.4%)). These findings highlight the importance of sustainable development strategies as the most effective approach to help low- and middle-income countries address the dual challenges of climate change and AMR.

Ceftolozane/tazobactam use and emergence of resistance: a 4-year analysis of antimicrobial susceptibility in Pseudomonas aeruginosa isolates in a tertiary hospital

Background

Ceftolozane/tazobactam (C/T) was temporarily withdrawn from December 2020 to February 2022: this forced unavailability created the conditions to study how drug discontinuation might influence Pseudomonas aeruginosa (PA) resistance reversibility in a real-life setting.

Methods

Clinically relevant PA isolates collected between January 1st 2019 and February 22nd 2023 with a C/T susceptibility test available were included. Changes in PA antibiotic susceptibility towards C/T and other antibiotics were examined in three different periods (period A, March-December 2019 and March-December 2020, C/T available; period B, March-December 2021, C/T withdrawn; period C, March-December 2022, C/T reintroduced), also considering the overall consumption rate through the Defined Daily Dose per 100 bed-days per year.

Results

Seven hundred and fifty-one PA isolates were included. A statistically significant reduction of C/T resistance rate was observed when C/T became unavailable, followed by a subsequent increase with its reintroduction (period A 25.1% vs. period B 5.3% vs. period C 10.0%, p < 0.001). A concomitant reduction of resistance rates towards other antibiotics was recorded, consistent with antibiotic consumptions and antimicrobial stewardship programs implementation. A subgroup of 22 patients presented a C/T-resistant isolate after a previous susceptible one; only 4 patients had received a prior C/T treatment.

Conclusion

The unavailability of C/T created the conditions to analyze the practical application of the theory of fitness cost to maintain resistance. A subsequent increase after a first reduction in C/T resistance rate was observed, probably due to persistence of resistant isolates and antibiotic selective pressure. Continuous monitoring of antibiotic use and evolving resistance is essential.

Epistasis-mediated compensatory evolution in a fitness landscape with adaptational tradeoffs

The evolutionary adaptation of an organism to a stressful environment often comes at the cost of reduced fitness. For example, resistance to antimicrobial drugs frequently reduces growth rate in the drug-free environment. This cost can be compensated without loss in resistance by mutations at secondary sites when the organism evolves again in the stress-free environment. Here, we analytically and numerically study evolution on a simple model fitness landscape to show that compensatory evolution can occur even in the presence of the stress and without the need for mutations at secondary sites. Fitness in the model depends on two phenotypes-the null-fitness defined as the fitness in the absence of stress, and the resistance level to the stress. Mutations universally exhibit antagonistic pleiotropy between the two phenotypes, that is they increase resistance while decreasing the null-fitness. Initial adaptation in this model occurs in a smooth region of the landscape with a rapid accumulation of stress resistance mutations and a concurrent decrease in the null-fitness. This is followed by a second, slower phase exhibiting partial recovery of the null-fitness. The second phase occurs on the rugged part of the landscape and involves the exchange of high-cost resistance mutations for low-cost ones. This process, which we call exchange compensation, is the result of changing epistatic interactions in the genotype as evolution progresses. The model provides general lessons about the tempo and mode of evolution under universal antagonistic pleiotropy with specific implications for drug resistance evolution.

The fitness connection of antibiotic resistance

More than three decades ago multidrug-resistant (MDR) clones of the pathogens: Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Clostridioides difficile, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii have started to disseminate across wide geographical areas. A characteristic feature of all these MDR lineages is the carriage of some mutations in the quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV which besides conferring resistance to fluoroquinolones are associated with a fitness benefit. Several lines of evidence strongly suggest that extra fitness conferred by these mutations facilitated the dissemination of the international MDR lineages. MDR pathogens require extra energy to cover the fitness cost conferred by the excess antibiotic resistance gene cargo. However, extra energy generated by upgraded metabolic activity was demonstrated to increase the uptake of antibiotics enhancing susceptibility. Accordingly, MDR bacteria need additional positive fitness schemes which, similarly to the QRDR advantage, will not compromise resistance. Some of these, not clone-specific effects are large genomes, the carriage of low-cost plasmids, the transfer of plasmid genes to the chromosome, the application of weak promoters in integrons and various techniques for the economic control of the activity of the integrase enzyme including a highly sophisticated system in A. baumannii. These impacts - among others - will confer a fitness advantage promoting the spread of MDR pathogens. However, even the potential of extra fitness generated by the combined effect of various schemes is not without limit and virulence-related genes or less relevant antibiotic resistance gene cargoes will often be sacrificed to permit the acquisition of high-priority resistance determinants. Accordingly major MDR clone strains are usually less virulent than susceptible isolates. In summary, a fitness approach to the research of antibiotic resistance is very useful since the fitness status of MDR bacteria seem to profoundly impact the capacity to disseminate in the healthcare setting.

Discovery of novel thiazole-pleuromutilin derivatives with potent antibacterial activity

A series of novel thiazole-pleuromutilin derivatives were designed and synthesized, and their antibacterial activities were evaluated. Most of the synthesized derivatives showed good activity against Gram-positive bacteria, among which compound h19 was more prominent and had the strongest antibacterial activity against MRSA. Compound h19 was selected for further evaluation of bacterial time-kill kinetics, and the results demonstrated its highly promising efficacy in inhibiting MRSA growth. Moreover, h19 exhibited a superior post-antibiotic effect (PAE) value and a lower possibility for bacterial resistance development compared to tiamulin. Docking studies demonstrated the strong affinity of h19 for the 50S ribosomal subunit with a binding free energy of -10.6 kcal/mol. The cytotoxic assay indicated that h19 had low cytotoxicity on both HEK293T and HepG2 cells (IC50 > 200 μM). In MRSA systemic-infected mouse model, h19 improved survival rates, reduced the bacterial load, and alleviated pathological changes in the lungs of the infected mice, which exhibited a more potent antibacterial efficacy compared to tiamulin. Compound h19 also displayed low oral toxicity with an LD50 value more than 2000 mg/kg.

Effects of Cigarette-Derived Compounds on the Spread of Antimicrobial Resistance in Artificial Human Lung Sputum Medium, Simulated Environmental Media, and Wastewater

BACKGROUND

Antimicrobial resistance (AMR) and smoking of tobacco products are two of the most important threats to global human health. Both are associated with millions of deaths every year. Surprisingly, the immediate interactions between these two threats remain poorly understood.

OBJECTIVES

We aimed to elucidate the effect of toxic compounds from cigarette smoke, ashes, and filters on the spread of antibiotic resistance genes in human lung and environmental microbiomes.

METHODS

Conjugation experiments using donor and recipient strain pairs of either Pseudomonas putida or Escherichia coli and AMR-encoding plasmids were conducted under exposure to different concentrations of cigarette smoke condensate in lung sputum medium, as well as cigarette ash and filter leachate in environmental media. We further measured reactive oxygen species (ROS) production of the donor strain under exposure to the cigarette-derived compounds to explore whether stress experienced by the bacteria could be one of the underlying mechanisms of change in plasmid transfer frequencies. Furthermore, used cigarette filters were submerged in a wastewater stream for several weeks, and the colonizing communities were analyzed using high-throughput sequencing and high-throughput quantitative polymerase chain reaction and compared with communities colonizing unused control filters.

RESULTS

Exposure to cigarette smoke condensate at relevant concentrations resulted in > 2 -fold higher transfer rates of a multidrug-resistance-encoding plasmid in artificial lung sputum medium. This was associated with higher ROS production as part of the bacterial stress response when exposed to cigarette-derived toxicants. Similar results were obtained for cigarette ash leachate in an environmental medium. Further, used cigarette filters were colonized by different microbial communities compared with unused filters. Those communities were significantly enriched with potential human pathogens and AMR.

DISCUSSION

The results of this study suggest that cigarette-derived compounds can indeed promote the spread of AMR within simulated human lung and environmental conditions. This study highlights that the consumption of cigarettes has not only direct but may also have indirect adverse effects on human health by promoting AMR. https://doi.org/10.1289/EHP14704.

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii

The proliferation of multi-drug resistant (MDR) bacteria is driven by the global spread of epidemic lineages that accumulate antimicrobial resistance genes (ARGs). Acinetobacter baumannii, a leading cause of nosocomial infections, displays resistance to most frontline antimicrobials and represents a significant challenge to public health. In this study, we conduct a comprehensive genomic analysis of over 15,000 A. baumannii genomes to identify a predominant epidemic super-lineage (ESL) accounting for approximately 70% of global isolates. Through hierarchical classification of the ESL into distinct lineages, clusters, and clades, we identified a stepwise evolutionary trajectory responsible for the worldwide expansion and transmission of A. baumannii over the last eight decades. We observed the rise and global spread of a previously unrecognized Clade 2.5.6, which emerged in East Asia in 2006. The epidemic of the clade is linked to the ongoing acquisition of ARGs and virulence factors facilitated by genetic recombination. Our results highlight the necessity for One Health-oriented research and interventions to address the spread of this MDR pathogen.

Industrialization drives the gut microbiome and resistome of the Chinese populations

Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that Escherichia coli genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.

IMPORTANCE

As China experiences rapid but uneven industrialization, understanding its effect on people's gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.

Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens

The increase in antimicrobial resistance presents a major challenge in treating bacterial infections, underscoring the need for innovative drug discovery approaches and novel inhibitors. Bacterial RNA polymerase (RNAP) has emerged as a crucial target for antibiotic development due to its essential role in transcription. RNAP is a molecular motor, and its function relies heavily on the dynamic shifts between multiple conformational states. While biochemical and structural experimental methods offer crucial insights into static RNAP-drug interactions, they fall short in capturing the dynamics at a molecular level. By integrating experimental data with advanced computational techniques like Markov State Models (MSMs), Generalized Master Equation (GME) Models and other machine-learning models constructed from molecular dynamics (MD) simulations, researchers can elucidate novel cryptic pockets that open transiently for antibiotic compounds and gain a more nuanced and comprehensive understanding of RNAP-drug interactions. This integrated approach not only deepens our fundamental knowledge but also enables more targeted and efficient antibiotic design strategies. In this Perspective, we highlight how this synergy between experimental and computational methods has the potential to open new pathways for innovative drug design and combination therapies that may help turn the tide in the ongoing battle against antibiotic-resistant bacteria.

Proteins from Microalgae: Nutritional, Functional and Bioactive Properties

Microalgae have emerged as a sustainable and efficient source of protein, offering a promising alternative to conventional animal and plant-based proteins. Species such as Arthrospira platensis and Chlorella vulgaris contain protein levels ranging from 50% to 70% of their dry weight, along with a well-balanced amino acid profile rich in essential amino acids such as lysine and leucine. Their cultivation avoids competition for arable land, aligning with global sustainability goals. However, the efficient extraction of proteins is challenged by their rigid cell walls, necessitating the development of optimized methods such as bead milling, ultrasonication, enzymatic treatments, and pulsed electric fields. These techniques preserve functionality while achieving yields of up to 96%. Nutritional analyses reveal species-dependent digestibility, ranging from 70 to 90%, with Spirulina platensis achieving the highest rates due to low cellulose content. Functionally, microalgal proteins exhibit emulsifying, water-holding, and gel-forming properties, enabling applications in baking, dairy, and meat analogs. Bioactive peptides derived from these proteins exhibit antioxidant, antimicrobial (inhibiting E. coli and S. aureus), anti-inflammatory (reducing TNF-α and IL-6), and antiviral activities (e.g., Dengue virus inhibition). Despite their potential, commercialization faces challenges, including regulatory heterogeneity, high production costs, and consumer acceptance barriers linked to eating habits or sensory attributes. Current market products like Spirulina-enriched snacks and Chlorella tablets highlight progress, but food safety standards and scalable cost-effective extraction technologies remain critical for broader adoption. This review underscores microalgae's dual role as a nutritional powerhouse and a source of multifunctional bioactives, positioning them at the forefront of sustainable food and pharmaceutical innovation.

Assessing the threat of Yersinia pestis harboring a multi-resistant IncC plasmid and the efficacy of an antibiotic targeting LpxC

Self-transmissible IncC plasmids rapidly spread multidrug resistance in many medically important pathogens worldwide. A large plasmid of this type (pIP1202, ~80 Kb) has been isolated in a clinical isolate of Yersinia pestis, the agent of plague. Here, we report that pIP1202 was highly stable in Y. pestis-infected mice and fleas and did not reduce Y. pestis virulence in these animals. Although pIP1202 inflicted a fitness cost in fleas (but not in mice) when the insects fed on blood containing a mixture of plasmid-free and plasmid-bearing strains, such a co-infection scenario has never been reported in nature, indicating that pIP1202 could persist in Y. pestis strains. Despite being resistant to commonly used antibiotic treatments, we show that plague caused by Y. pestis harboring the pIP1202 plasmid is effectively cured by LPC-233-a potent inhibitor of the essential LpxC enzyme in the lipid A biosynthetic pathway. Taken as a whole, our data highlight the alarming threat posed by Y. pestis harboring multidrug-resistant IncC plasmids that may persist in wild animals as a reservoir for long periods without antibiotic pressure and illuminate the impact of antibiotics with a novel mode of action against such a biothreat.

De novo acquisition of antibiotic resistance in six species of bacteria

Bacteria can become resistant to antibiotics in two ways: by acquiring resistance genes through horizontal gene transfer and by de novo development of resistance upon exposure to non-lethal concentrations. The importance of the second process, de novo build-up, has not been investigated systematically over a range of species and may be underestimated as a result. To investigate the DNA mutation patterns accompanying the de novo antibiotic resistance acquisition process, six bacterial species encountered in the food chain were exposed to step-wise increasing sublethal concentrations of six antibiotics to develop high levels of resistance. Phenotypic and mutational landscapes were constructed based on whole-genome sequencing at two time points of the evolutionary trajectory. In this study, we found that (1) all of the six strains can develop high levels of resistance against most antibiotics; (2) increased resistance is accompanied by different mutations for each bacterium-antibiotic combination; (3) the number of mutations varies widely, with Y. enterocolitica having by far the most; (4) in the case of fluoroquinolone resistance, a mutational pattern of gyrA combined with parC is conserved in five of six species; and (5) mutations in genes coding for efflux pumps are widely encountered in gram-negative species. The overall conclusion is that very similar phenotypic outcomes are instigated by very different genetic changes. The outcome of this study may assist policymakers when formulating practical strategies to prevent development of antimicrobial resistance in human and veterinary health care.IMPORTANCEMost studies on de novo development of antimicrobial resistance have been performed on Escherichia coli. To examine whether the conclusions of this research can be applied to more bacterial species, six species of veterinary importance were made resistant to six antibiotics, each of a different class. The rapid build-up of resistance observed in all six species upon exposure to non-lethal concentrations of antimicrobials indicates a similar ability to adjust to the presence of antibiotics. The large differences in the number of DNA mutations accompanying de novo resistance suggest that the mechanisms and pathways involved may differ. Hence, very similar phenotypes can be the result of various genotypes. The implications of the outcome are to be considered by policymakers in the area of veterinary and human healthcare.

Quantitative analysis of relationship between mutation rate and speed of adaptation under antibiotic exposure in Escherichia coli

Mutations are the ultimate source of biological evolution that creates genetic variation in populations. Mutations can create new advantageous traits but can also potentially interfere with pre-existing organismal functions. Therefore, organisms may have evolved mutation rates to appropriate levels to maintain or improve their fitness. In this study, we aimed to experimentally quantify the relationship between the mutation rate and evolution of antibiotic resistance. We conducted an evolution experiment using 12 Escherichia coli mutator strains with increased mutation rates and five antibiotics. Our results demonstrated that the rate of adaptation generally increased with higher mutation rates, except in a single mutator strain with the highest mutation rate, which exhibited a significant decline in evolutionary speed. To further elucidate these findings, we developed a simple population dynamics model that successfully recapitulated the observed dependence of adaptation speed on mutation rate. These findings provide important insights into the evolution of mutation rate accompanied by the evolution.

Selective pressure of various levels of erythromycin on the development of antibiotic resistance

This study evaluated microbial fitness under selective pressure of various erythromycin concentrations and the development of resistance genes in Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis). Eight different concentrations of erythromycin were applied to the environment of erythromycin-resistant strains. The development of erythromycin resistance genes and gene expression were evaluated with plate counting method (PCM), fluorescence in situ hybridization (FISH), and quantitative polymerase chain reaction (qPCR). The results indicated that bacterial growth and adaptation were influenced by bacterial fitness in response to different levels of erythromycin concentrations. Furthermore, the concentration at one minimum inhibitory concentration (1x MIC) was the most effective concentration to select for antibiotic resistance for E.coli, while 4x MIC was the most effective concentration to select for antibiotic resistance for E. faecalis. Total cell densities, measured by qPCR, FISH, and PCM, decreased with increasing erythromycin concentrations. Conversely, resistant bacteria and erythromycin ribosome methylase (erm) gene abundance increased with sub-MIC erythromycin concentrations. Methylated 23S rRNA decreased with increasing erythromycin concentrations. In summary, erythromycin-resistant E. coli and E. faecalis strains adapted to the selective pressure of varying erythromycin concentrations by acquiring and proliferating antibiotic-resistant genes. These results indicate that the development of antibiotic resistance is closely linked to antibiotic concentrations and highlight the significance of selective windows in the emergence and persistence of antibiotic resistance under varying antibiotic concentrations.

Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440

Beyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug-and-play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for Pseudomonas putida), a framework to optimise genetic circuit performance by means of (i) chromosome-location-based differential gene expression and (ii) subsequent fitness improvement through evolutionary engineering if needed. Using gene expression strength and cell-to-cell variation, we characterised 10 P. putida chromosomal loci (ppLPS) to show that genome context rather than distance to ORI is the main factor driving differential expression performance. We further contextualised ppLPS gene expression against well-known chromosomal integration sites and plasmids displaying different copy numbers. GENIO supports comprehensive exploration of the gene expression space across P. putida's genome while unlocking performance optimization of complex heterologous metabolic pathways through evolutionary engineering. To demonstrate the usability of GENIO, we restored P. putida's aromatic hydrocarbon metabolism by (de)constructing the toluene/m-xylene catabolic pathway coded in the pWW0 plasmid. We also showed that engineering complex phenotypes requires accurate contextualisation of the synthetic pathways involved, a process that benefits from biological robustness.

Fitness Burden for the Stepwise Acquisition of First- and Second-Line Antimicrobial Reduced-Susceptibility in High-Risk ESKAPE MRSA Superbugs

Background: The fitness costs (FCs) of antimicrobial resistance (AMR) are crucial issues in antimicrobial resistance (AMR) onset, spread, and, consequently, public health. In Staphylococcus aureus, AMR can induce significant FCs due to slow growth, low competitiveness, and virulence. Here, we investigated the genomics and FCs emerging for progressively acquiring daptomycin (DAP) and glycopeptide (GLY) reduced susceptibility in MRSA. Methods: Genomics was carried out using Illumina-MiSeq Whole-genome sequencing and bioinformatics. The biological FCs of isogenic MRSA strain pairs progressively acquiring DAP and GLY-reduced susceptibility, under DAP/GLY mono or combined therapy, were performed by in-vitro independent and competitive mixed growth, phenotypic in-vitro virulence analysis, and in-vivo G. mellonella larvae killing. Results: Genomics evidenced four different extremely resistant high-risk clones, i.e., ST-5 N315 HA-MRSA, ST-398 LA-MRSA, ST-22 USA-100 HA-EMRSA-15, and ST-1 MW2 CA-MRSA. In-vitro fitness assays revealed slow growth, lower competitiveness, and reduced virulence, predominantly in Galleria mellonella killing ability, in DAP-S hGISA, DAP-R GSSA, DAP-R hGISA, and DAP-R GISA strains. Conclusions: The occurrence of glycopeptide and daptomycin reduced susceptibility conferred increasing FCs, paid as a gradual reduction in virulence, competitiveness, and slow growth performance.

Iron oleate containing lipid nanoparticles prepared by gradient solvent diffusion method for oxidative stress dependent antibacterial therapy

This study was designed to assess the efficacy of iron oleate lipid nanoparticles (IO-LNPs) in inducing Fenton reaction as a therapeutic approach for bacterial infections caused by Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), both of which are common pathogens in skin wound infections. IO-LNPs were synthesized using the gradient solvent diffusion method, followed by characterization of their particle size, polydispersity index (PDI), zeta potential, and morphology. In vitro antibacterial assays were conducted to evaluate the inhibitory effects of IO-LNPs on bacterial growth; the impact on bacterial viability was confirmed via live/dead staining assays. Furthermore, the mechanism underlying the antibacterial activity of IO-LNPs was investigated. Lastly, in vivo antibacterial studies were performed in a mouse model infected with S. aureus to evaluate the efficacy of IO-LNPs. The results indicated that the IO-LNPs synthesized via the gradient solvent diffusion method possessed a particle size of 114 ± 2 nm, a PDI of 0.198, and a zeta potential of -12.3 ± 1.73 mV. The IO-LNPs demonstrated a significant reduction in the viability of S. aureus and E. coli, effectively inhibiting the formation of biofilms by these bacteria and disrupting pre-existing biofilms. Crucially, in the skin infection model, IO-LNPs significantly inhibited the growth of S. aureus and accelerated wound healing. By day 13, the wound area in the 90 % minimum inhibitory concentration (MIC90) group had decreased to 6.53 %. Collectively, these findings suggest that IO-LNPs, as a novel antibacterial agent, can effectively inhibit bacterial growth and disrupt biofilms by inducing Fenton reaction, thereby demonstrating considerable potential against antibiotic-resistant bacterial infections. This study establishes a theoretical foundation for the development of new treatment modalities for skin wound infections.

Deterministic, stochastic and fractional mathematical approaches applied to AMR

In this work, we study the qualitative properties of a simple mathematical model that can be applied to the reversal of antimicrobial resistance. In particular, we analyze the model from three perspectives: ordinary differential equations (ODEs), stochastic differential equations (SDEs) driven by Brownian motion, and fractional differential equations (FDEs) with Caputo temporal derivatives. Finally, we address the case of Escherichia coli exposed to colistin using parameters from the literature in order to assess the validity of the qualitative properties of the model.

The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation

The history of clinical resistance to tetracycline antibiotics is characterized by cycles whereby the deployment of a new generation of drug molecules is quickly followed by the discovery of a new mechanism of resistance. This suggests mechanism-specific selection by each tetracycline generation; however, the evolutionary dynamics of this remain unclear. Here, we evaluate 24 recombinant Escherichia coli strains expressing tetracycline resistance genes from each mechanism (efflux pumps, ribosomal protection proteins, and enzymatic inactivation) in the context of each tetracycline generation. We employ a high-throughput barcode sequencing protocol that can discriminate between strains in mixed culture and quantify their relative abundances. We find that each mechanism is preferentially selected for by specific antibiotic generations, leading to their expansion. Remarkably, the minimum inhibitory concentration associated with individual genes is secondary to resistance mechanism for inter-mechanism relative fitness, but it does explain intra-mechanism relative fitness. These patterns match the history of clinical deployment of tetracycline drugs and resistance discovery in pathogens.

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health

BACKGROUND

Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of penicillin in the early 1940s, has been proposed as a primary contributor to the cumulative alteration of microbiota over generations. However, the mechanistic link between the antibiotics-altered microbiota and chronic conditions remains unclear.

RESULTS

In this study, we discovered that variants of the key beneficial gut microbe, Akkermansia muciniphila, were selected upon exposure to penicillin. These variants had mutations in the promoter of a TEM-type β-lactamase gene or pur genes encoding the de novo purine biosynthesis pathway, and they exhibited compromised abilities to mitigate host obesity in a murine model. Notably, variants of A. muciniphila are prevalent in the human microbiome worldwide.

CONCLUSIONS

These findings highlight a previously unknown mechanism through which antibiotics influence host health by affecting the beneficial capacities of the key gut microbes. Furthermore, the global prevalence of A. muciniphila variants raises the possibility that these variants contribute to global epidemics of chronic conditions, warranting further investigations in human populations. Video Abstract.

A comprehensive analysis of antimicrobial resistance of clinical emm89 Streptococcus pyogenes in Japan

Objectives

Streptococcus pyogenes is involved in a wide range of diseases, including pharyngitis and life-threatening invasive infections. Increasing prevalence of antimicrobial resistance (AMR) has been reported worldwide in various bacteria, limiting the use of antibiotics in infection cases. The present study investigated the AMR of most prevalent S. pyogenes emm types, including emm89 strains in Japan.

Methods

A total of 368 previously identified S. pyogenes isolates (311 emm89 strains and 57 of other emm types), which were previously isolated from patients with invasive and non-invasive infections throughout Japan, were used in the analyses. The minimum inhibitory concentrations of seven antibiotics, including penicillin-G, azithromycin (AZM) and clindamycin, were determined, and whole-genome sequences of AMR-associated genes were screened.

Results

We identified 47 resistant strains, of which 91.49% (43/47) were resistant to AZM and/or clindamycin. A strong correlation was observed between non-invasive phenotypes and AMR. Whole-genome analysis indicated the wide distribution of three AMR-related genes, ermT, folP and lmrP, among the emm89 strains. Additionally, tetO was detected in tetracycline-resistance and soxS and mel was detected in chloramphenicol-resistance only in emm4 strains.

Conclusions

The high prevalence of S. pyogenes resistance to AZM and/or clindamycin poses a threat to public health in Japan; thus, the development of next-generation antimicrobial therapies is imperative.

A supramolecular diazapyrene radical assembly with NIR absorption for selective photothermal antibacterial activity

A supramolecular radical assembly that can be induced in situ by facultative anaerobic bacteria has been reported and used for selective near-infrared (NIR) photothermal antibacterial action. Herein, we report the synthesis of a water-soluble diazapyrene derivative (DAPNP), which could be in situ initiated into the corresponding radicals by facultative anaerobic bacteria, such as E. coli or S. aureus. The introduction of cucurbit[10]uril (CB[10]) alters the stacking mode of the diazapyrene radical cations, resulting in a redshift of their characteristic absorption peak from the visible region to the NIR region. Under 660 nm laser irradiation, the in situ-induced supramolecular radical assembly exhibits great photothermal conversion properties and achieves highly efficient antibacterial activity (up to 98%). In contrast, with the aerobic B. subtilis it is difficult to induce the formation of diazapyrene radical cations in situ and maintain good activity under light irradiation. In addition, DAPNP@CB[10] exhibits excellent biocompatibility and has great potential as an intelligent photothermal material for antibacterial applications.

Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response

BACKGROUND

Fluoroquinolones are indispensable antibiotics used in treating bacterial infections in both human and veterinary medicine. However, resistance to these drugs presents a growing challenge. The SOS response, a DNA repair pathway activated by DNA damage, is known to influence resistance development, yet its role in fluoroquinolone resistance is not fully understood. This study aims to unfold the mechanisms of fluoroquinolone resistance by investigating the impact of the SOS response on bacterial adaptation.

RESULTS

We exposed Escherichia coli to four fluoroquinolones-ciprofloxacin, enrofloxacin, levofloxacin, and moxifloxacin. Using a recA knockout mutant, deficient in the SOS response, as a control, we assessed how the presence or absence of this pathway affects resistance development. Our findings demonstrated that the rate of resistance evolution varied between the different fluoroquinolones. Ciprofloxacin, enrofloxacin, and moxifloxacin exposures led to the most evident reliance on the SOS response for resistance, whereas levofloxacin exposed cultures showed less dependency. Whole genome analysis indicated distinct genetic changes associated with each fluoroquinolone, highlighting potential different pathways and mechanisms involved in resistance.

CONCLUSIONS

This study shows that the SOS response plays a crucial role in resistance development to certain fluoroquinolones, with varying dependencies per drug. The characteristic impact of fluoroquinolones on resistance mechanisms emphasizes the need to consider the unique properties of each antibiotic in resistance studies and treatment strategies. These findings are essential for improving antibiotic stewardship and developing more effective, tailored interventions to combat resistance.

An eco-evolutionary perspective on antimicrobial resistance in the context of One Health

The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.

Overcoming Nanosilver Resistance: Resensitizing Bacteria and Targeting Evolutionary Mechanisms

The rapid spread of antimicrobial resistance poses a critical threat to global health and the environment. Antimicrobial nanomaterials, including silver nanoparticles (AgNPs), are being explored as innovative solutions; however, the emergence of nanoresistance challenges their effectiveness. Understanding resistance mechanisms is essential for developing antievolutionary strategies. AgNPs exhibit diverse resistance mechanisms, and our findings reveal a dynamic transition between these mechanisms: from flagellin-mediated AgNP precipitation (state I) to activation of the copper efflux pump (CusCFBA) system (state II). We designed targeted physicochemical interventions to counteract these mechanisms. Energy supply blocking was effective for state I, while for state II, neutralizing intracellular acidic pH significantly reduced resistance. These strategies reduced nanoresistance/tolerance by up to 10,000-fold. Additionally, resistance evolution can be completely halted by disrupting the energy supply using carbonyl cyanide 3-chlorophenylhydrazone and overactivating sigma E, one of the key envelope stress regulators that govern resistance transitions. Our findings provide practical strategies to overcome nanoresistance, offering a groundbreaking approach to enhance nanoantimicrobials' efficacy in medical therapies and combat resistance evolution.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BACKGROUND

The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS

Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION

The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.

Antimicrobial susceptibility and genomic characterization of Vibrio cholerae non-O1/non-O139 isolated from clinical and environmental samples in Jiaxing City, China

Non-O1/non-O139 (NOVC) strains inhabit aquatic environments and sporadically induce human illnesses. This study involved the virulence and antimicrobial genetic characterization of 176 NOVC strains, comprising 25 from clinical samples and 151 from environmental sources, collected between 2021 and 2023. The antimicrobial susceptibility of the examined NOVC population was predominantly high, exhibiting only poor susceptibility to colistin, with 89.2% resistance. The examination of virulence genes revealed that the majority of strains were positive for glucose metabolism (als gene) (169/176, 96.0%). Through multilocus sequence typing, the 176 NOVC strains were categorised into 121 sequence types, 79 of which were novel. NOVC strains demonstrate significant genetic variability and frequently engage in recombination. This work offers genetic characterization of the pathogenicity and antimicrobial resistance of a NOVC community. Our findings offer insights that may aid in the development of preventative and treatment methods for this pathogen.

Uncovering a cryptic Streptococcus suis endemic post-outbreak: Evidence of host switching to humans

Streptococcus suis (S. suis) is a neglected and emerging pathogen that leads to severe economic losses in swine industry. Despite its epidemic potential, the zoonotic threat posed by S. suis remains underappreciated, even after the unprecedented Sichuan outbreak, which highlighted its ability to cause fatal human infections. Understanding of the dynamics and evolution of this pathogen in human populations is crucial for preventing future outbreaks. Our study revealed the emergence of highly pathogenic S. suis lineages in Zhejiang Province following the Sichuan outbreak, showing an increasingly specialized lifestyle that has persisted for nearly two decades. Phylogenetic analysis traced the zoonotic transmission of this pathogen back to a livestock lineage in the Netherlands prior to 1990, which eventually led to the Sichuan outbreak lineage in 2005 and its subsequent spread to Zhejiang the same year. Two independent evolved sub-lineages were identified in Zhejiang, suggesting a cryptic, regional endemicity following the Sichuan outbreak. Furthermore, the accumulation of lineage-specific resistance and metabolic acclimation after divergence from the Sichuan population suggested potential regional evolutionary shifts in S. suis. These new findings could help inform future intervention strategies and guide public health policies.

Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya

Antibiotics can trigger antimicrobial resistance and microbiome alterations. Reducing pathogen exposure and undernutrition can reduce infections and antibiotic use. We assess effects of water, sanitation, handwashing (WSH) and nutrition interventions on caregiver-reported antibiotic use in Bangladesh and Kenya, longitudinally measured at three timepoints among birth cohorts (ages 3-28 months) in a cluster-randomized trial. Over 50% of children used antibiotics at least once in the 90 days preceding data collection. In Bangladesh, the prevalence of antibiotic use was 10-14% lower in groups receiving WSH (prevalence ratio [PR] = 0.90 (0.82-0.99)), nutrition (PR = 0.86 (0.78-0.94)), and nutrition+WSH (PR = 0.86 (0.79-0.93)) interventions. The prevalence of using antibiotics multiple times was 26-35% lower in intervention arms. Reductions were largest when the birth cohort was younger. In Kenya, interventions did not affect antibiotic use. In this work, we show that improving WSH and nutrition can reduce antibiotic use. Studies should assess whether such reductions translate to reduced antimicrobial resistance.

Membrane anchoring of New Delhi metallo-β-lactamase-1 alters the fitness of Escherichia coli and increases its susceptibility to colistin by inducing outer membrane destabilization

New Delhi metallo-β-lactamase-1 (NDM-1)-producing bacteria are resistant to nearly all available β-lactam antibiotics and have become a public health threat. Antibiotic resistance often carries fitness costs, which typically manifest as a reduced bacterial growth rate. Here, we investigated the mechanism of fitness cost in NDM-1-producing bacteria. Our findings revealed that strains expressing blaNDM-1 exhibited a significant growth defect under high osmotic stress. This fitness cost was attributed to the anchoring of NDM-1 to the bacterial outer membrane via its leader peptide, which destabilized the outer membrane. Replacing the membrane-anchoring residue Cys26 in the leader peptide with alanine not only restored outer membrane stability but also ameliorated the bacterial fitness cost. Furthermore, the anchoring of NDM-1 to the membrane increased bacterial susceptibility to the membrane-disrupting antibiotic colistin, both in vitro and in vivo, as confirmed in engineered and clinically isolated strains. In conclusion, membrane anchoring of NDM-1 increased the permeability of the bacterial outer membrane, thereby reducing the fitness of NDM-1-producing bacteria and enhancing their susceptibility to colistin. These results not only elucidate the mechanism of fitness cost associated with NDM-1 but also provide new insights into the rational use of colistin to combat infections caused by NDM-1-producing bacteria.

Cell-Penetrating Peptide Induced Superstructures Triggering Highly Efficient Antibacterial Activity

To endow non-antibacterial molecules with highly efficient bactericide activity is an important but challenging issue. Herein, a kind of cell-penetrating peptide octa-arginine (R8) is found to be effective in activating antibacterial ability when assembling with anionic surfactant sodium dodecyl sulfate (SDS), while individual R8 or SDS shows poor or no antibacterial ability. By combined electrostatic, hydrogen bond, and hydrophobic interactions, R8 and SDS associate into wormlike micelle and lamellar structure by forming supramolecular self-assembling units, depending on their charge ratio (CR). The lamellar aggregates show particularly high antibacterial activities against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus). Interestingly, E. coli and S. aureus are killed by membrane-disrupting and membrane-penetrating mechanisms, respectively. Furthermore, in vivo experiments evidence that the R8/SDS lamellar aggregates accelerate the recovery of bacteria-infected wounds, wherein the reduced inflammation and promoted angiogenesis are clearly presented. This study proves that highly efficient bactericidal activity is triggered by the synergistic action of penetrating peptide and anionic amphiphiles, thus providing a new strategy to realize highly efficient and targetable antibacterial application.

Determination of the De Novo Minimum Selection Concentration of Trimethoprim In Vivo for Escherichia coli Using Galleria mellonella: A Pilot Study

We investigated whether the maximum residual levels of trimethoprim permitted in food (Acceptable Daily Intake-ADI) could select for de novo trimethoprim resistance in Escherichia coli in vivo. We designed chronic infection models of E. coli in Galleria mellonella and exposed them to sub-ADI doses of trimethoprim through a single-dosing regimen. The emergence of trimethoprim resistance was determined by isolating the target bacteria on selective agar plates, followed by species confirmation using MALDI-TOF mass spectrometry. The minimum inhibitory concentration (MIC) was assessed via the E-test to determine E. coli susceptibility to trimethoprim. Notably, exposure to as low as one-tenth of the ADI dose through a single-dosing regimen resulted in the selection of trimethoprim-resistant E. coli. Our findings indicate that trimethoprim doses ten-fold lower than the established ADI threshold could induce resistance to trimethoprim in E. coli. These results highlight the importance of considering antimicrobial resistance induction as a key factor when determining ADI levels in food.

Increased risk of antibiotic resistance in surface water due to global warming

As the pace of global warming accelerates, so do the threats to human health, urgent priority among them being antibiotic-resistant infections. In the context of global warming, this review summarises the direct and indirect effects of rising surface water temperatures on the development of bacterial antibiotic resistance. First, the resistance of typical pathogens such as E. coli increased with average temperature. This is not only related to increased bacterial growth rate and horizontal gene transfer frequency at high temperatures but also heat shock responses and cumulative effects. Secondly, the acceleration of bacterial growth indirectly promotes antibiotic residues in surface water, which is conducive to the growth and spread of resistant bacteria. Furthermore, the cascading effects of global warming, including the release of nutrients into the water and the resulting increase of bacteria and algae, indirectly promote the improvement of resistance. Water treatment processes exposed to high temperatures also increase the risk of resistance in surface water. The fitness costs of antibiotic resistance under these dynamic conditions are also discussed, concluding the relationship between various factors and resistance persistence. It was expected to provide a comprehensive basis for mitigating antibiotic resistance in the face of global warming.

Evolutionary trajectories of β-lactam resistance in Enterococcus faecalis strains

Resistance to ampicillin and imipenem in Enterococcus faecalis is infrequent. However, the evolution of resistance can occur through prolonged antibiotic exposure during the treatment of chronic infections. In this study, we conducted a long-term evolution experiment using four genetically diverse strains of E. faecalis with varying susceptibilities to ampicillin and imipenem. Each strain was subjected to increasing concentrations of either ampicillin or imipenem over 200 days, with three independent replicates for each strain. Selective pressure from imipenem led to the rapid selection of highly resistant lineages across all genetic backgrounds, compared to ampicillin. In addition to high resistance, we describe, for the first time, the evolution of a β-lactam-dependent phenotype observed in lineages from all backgrounds. Whole-genome sequencing and bioinformatic analysis revealed mutations in three main functional classes: genes involved in cell wall synthesis and degradation, genes in the walK/R two-component system, and genes in the c-di-AMP pathway. Our analysis identified new mutations in genes known to be involved in resistance as well as novel genes potentially associated with resistance. Furthermore, the newly described β-lactam-dependent phenotype was correlated with the inactivation of c-di-AMP degradation, resulting in high levels of this second messenger. Together, these data highlight the diverse genetic mechanisms underlying resistance to ampicillin and imipenem in E. faecalis. The emergence of high resistance levels and β-lactam dependency underscores the importance of understanding evolutionary dynamics in the development of antibiotic resistance.

IMPORTANCE

Enterococcus faecalis is a major human pathogen, and treatment is frequently compromised by poor response to first-line antibiotics such as ampicillin. Understanding the factors that play a role in susceptibility/resistance to these drugs will help guide the development of much-needed treatments.

Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal

Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.

Advances in the clinical treatment of multidrug-resistant pathogens using polymyxins

OBJECTIVES

Polymyxins are a vital class of antibiotics used to combat multidrug-resistant Gram-negative bacteria. However, their use is limited due to potential nephrotoxicity and the availability of alternative antibiotics. This review aims to examine the properties of polymyxins and the clinical advances in their use for treating infections caused by carbapenem-resistant Gram-negative bacteria (CR-GNB).

METHODS

This review analyses literature on polymyxin properties and various clinical approaches, including intravenous drip infusion, nebulized or dry powder inhalation, and ointment application. Treatment efficacy in terms of bacterial eradication, cure rate and mortality rate are reviewed and evaluated.

RESULTS

Polymyxins have been reintroduced to treat critical infections due to the increasing prevalence of CR-GNB. Clinical trials and studies have confirmed that polymyxins can effectively treat CR-GNB infections when the formulation and administration are appropriate, with acceptable levels of nephrotoxicity.

CONCLUSIONS

In the future, the development of polymyxin formulations will aim to improve their clinical effectiveness while reducing toxicity and side effects and preventing the emergence of polymyxin-resistant strains. Enhanced efficacy and minimized potential side effects can be achieved by developing new polymyxin-delivery systems that provide a smart and controlled release or customized patient administration.

Using digital health technologies to optimise antimicrobial use globally

Digital health technology (DHT) describes tools and devices that generate or process health data. The application of DHTs could improve the diagnosis, treatment, and surveillance of bacterial infection and the prevention of antimicrobial resistance (AMR). DHTs to optimise antimicrobial use are rapidly being developed. To support the global adoption of DHTs and the opportunities offered to optimise antimicrobial use consensus is needed on what data are required to support antimicrobial decision making. This Series paper will explore bacterial AMR in humans and the need to optimise antimicrobial use in response to this global threat. It will also describe state-of-the-art DHTs to optimise antimicrobial prescribing in high-income and low-income and middle-income countries, and consider what fundamental data are ideally required for and from such technologies to support optimised antimicrobial use.

Isolation and Characterization of Antimicrobial Peptides Isolated from Brevibacillus halotolerans 7WMA2 for the Activity Against Multidrug-Resistant Pathogens

Multidrug resistance to pathogens has posed a severe threat to public health. The threat could be addressed by antimicrobial peptides (AMPs) with broad-spectrum suppression. In this study, Brevibacillus halotolerans 7WMA2, isolated from marine sediment, produced AMPs against Gram-positive and Gram-negative bacteria. The AMPs were precipitated by ammonium sulfate 30% (w/v) from culture broth and dialyzed by a 1 kDa membrane. Tryptone Soy Agar (TSA) was used for the cultivation and resulted in the largest bacteria-inhibiting zones under aerobic conditions at 25 °C, 48 h. An SDS-PAGE gel overlay test revealed that strain 7WMA2 could produce AMPs of 5-10 kDa and showed no degradation when held at 121 °C for 30 min at a wide pH 2-12 range. The AMPs did not cause toxicity to HeLa cells with concentrations up to 500 µg/mL while increasing the arbitrary unit up to eight times. The study showed that the AMPs produced were unique, with broad-spectrum antimicrobial ability.

Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains

The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.

Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria

Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.