Ecology and evolution of antimicrobial resistance in bacterial communities

Role of gut microbiome in suppression of cancers

The pathogenesis of cancer is closely related to the disruption of homeostasis in the human body. The gut microbiome plays crucial roles in maintaining the homeostasis of its host throughout lifespan. In recent years, a large number of studies have shown that dysbiosis of the gut microbiome is involved in the entire process of cancer initiation, development, and prognosis by influencing the host immune system and metabolism. Some specific intestinal bacteria promote the occurrence and development of cancers under certain conditions. Conversely, some other specific intestinal bacteria suppress the oncogenesis and progression of cancers, including inhibiting the occurrence of cancers, delaying the progression of cancers and boosting the therapeutic effect on cancers. The promoting effects of the gut microbiome on cancers have been comprehensively discussed in the previous review. This article will review the latest advances in the roles and mechanisms of gut microbiome in cancer suppression, providing a new perspective for developing strategies of cancer prevention and treatment.

Risk factors associated with community colonization of extended-spectrum cephalosporin-resistant Enterobacterales from an antibiotic resistance in communities and hospitals (ARCH) study, Guatemala

Colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) in communities may contribute to proliferation of resistance genes and drug-resistant community and hospital infections. Previous work in the Western Highlands of Guatemala found that approximately 46% of the population is colonized with these bacteria, setting the stage to identify factors that are associated with increased odds of ESCrE colonization. Stool samples and questionnaire data were collected from randomly selected participants in the catchment area of the third largest tertiary hospital in Guatemala. Logistic regression path analysis was used for this cross-sectional study to identify potential direct and indirect risk factors for colonization with ESCrE. Participants (N = 951) had a higher odds of ESCrE colonization if they had exposure to a healthcare facility within 30 days of enrollment (OR: 2.12, 95% CI = 1.19-3.77), if they resided in urban areas (OR: 1.93, 95% CI 1.09-3.42), if they did not have a service to remove household trash (OR: 1.99, 95% CI 1.11-3.58), and if the household reported drinking water from non-bottled sources (OR:1.53, 95% CI 1.0-2.33). Antibiotic self-medication was not significantly associated with the risk of colonization (OR: 1.16, 95% CI 0.65-2.06). Multiple transmission-related factors were associated with increased likelihood of ESCrE colonization, but the cross-sectional nature of this study does not distinguish factors that are correlated with an individual's risk for colonization whence exposed. Assessing risk factors associated with colonization with antibiotic resistant bacteria may be useful for identifying mitigation strategies and evaluating the effectiveness of interventions against antibiotic resistance in community settings.

The Sec secretion system enhances GtfB secretion and exopolysaccharide production to promote the formation of Streptococcus mutans persisters induced by cationic antimicrobials

Bacterial persistence-caused antibacterial tolerance and recurrent infections are critical for clinical treatments. Streptococcus mutans persisters have been reported to enhance bacterial cariogenicity and tolerance to multi-antimicrobial agents, yet their formation mechanisms remain unclear. Here, we investigated the crucial role of the Sec secretion system in persister formation induced by dimethylamino dodecyl methacrylate (DMADDM) and chlorhexidine. DMADDM treated biofilms significantly increased exopolysaccharide (EPS) production and formed a large amount of persisters, while fewer persisters were formed in less EPS produced medium, indicating the important role of EPS in persistence. Persisters significantly upregulated the expressions of gtfB and the Sec secretion system. The Sec secretion system has been previously proposed to secret GtfB. Therefore, nine key gene-knockout mutants of the Sec secretion system and their complementary strains were constructed, including yidC1, yidC2, secY, secA, secE, secG, yajC, ftsY and ffH, respectively; ΔgtfB was also constructed for EPS defect control. ΔyidC2, ΔsecY, ΔsecA and ΔffH significantly decreased the expression and secretion of GtfB, then reduced the amounts of EPS, indicating that these four components from the Sec secretion system were the key proteins responsible for GtfB secretion. Moreover, all Sec secretion system mutants and ΔgtfB reduced persister formation in DMADDM and chlorhexidine induced biofilms, indicating that the Sec secretion system regulates gtfB expression and EPS production, thereby influencing persister formation. Our findings indicated the key roles of the Sec secretion system in S. mutans persistence and suggested that the Sec secretion system and EPS production were key targets to removing biofilms and overcome bacterial persistence.

Polyhexamethylene Biguanide Nanoparticles Inhibit Biofilm Formation by Mastitis-Causing Staphylococcus aureus

Staphylococcus aureus is a mastitis pathogen that compromises cow health and causes significant economic losses in the dairy industry. High antimicrobial resistance and biofilm formation by S. aureus limit the efficacy of conventional treatments. This study evaluated the potential of polyhexamethylene biguanide nanoparticles (PHMB NPs) against mastitis-causing S. aureus. PHMB NPs showed low toxicity to bovine mammary epithelial cells (MAC-T cells) at concentrations up to four times higher than the minimum inhibitory concentration (1 µg/mL) against S. aureus. In Experiment 1, PHMB NPs significantly reduced biofilm formation by S. aureus by 50% at concentrations ≥1 µg/mL, though they showed limited efficacy against preformed biofilms. In Experiment 2, using an excised teat model, PHMB NPs reduced S. aureus concentrations by 37.57% compared to conventional disinfectants (chlorhexidine gluconate, povidone-iodine, and sodium dichloroisocyanurate), though limited by short contact time. These findings highlight the potential of PHMB NPs for the control of S. aureus growth and biofilm formation.

Effect of host microenvironment and bacterial lifestyles on antimicrobial sensitivity and implications for susceptibility testing

Bacterial infections remain a major global health issue, with antimicrobial resistance (AMR) worsening the crisis. However, treatment failure can occur even when bacteria show antibiotic susceptibility in diagnostic tests. We explore factors such as phenotypic resilience, bacterial lifestyles such as biofilms, and differences between laboratory tests and real infection sites, highlighting the need for improved platforms to better predict treatment outcomes, and reviewing emerging technologies aimed at improving susceptibility testing.

Unraveling the dual role in enhancing methane production and mitigating antibiotic resistance gene spread in anaerobic co-digestion of microalgae and waste activated sludge

Waste activated sludge (WAS) is a double-edged sword - a recognized repository for antibiotic resistance genes (ARGs) but also a renewable substrate for methane production. Developing effective WAS treatment strategies is therefore of both ecological and practical importance. In this study, we proposed an anaerobic co-digestion approach of WAS and microalgae Chlorella sp. at a 1:2 ratio (MAcoD-1:2). Results showed that MAcoD-1:2 notably increased cumulative methane production by 52.7 %. Co-digestion also demonstrated a significant increase in the abundance of hydrolyzing acidifying bacteria Candidatus_Promineofilum (12.25 %) and methanogenic archaea Methanothrix (61.2 %). This microbial shift suggested that cosubstrates availability fostered a stable bacterial community structure and synergistic metabolic interactions, thus enhancing methane production. Metagenomic analysis revealed a significant reduction in both ARGs and mobile genetic elements in MAcoD-1:2. Notably, substrate level regulation was found to drive restructuring of microbial communities and metabolic patterns. Investigation showed that the Embden-Meyerhof-Parnas pathways were significantly inhibited while the pentose phosphate pathway was promoted, which constrained the cellular energy budget available for ARG horizontal transfer. Partial least squares path modelling (PLS-PM) further substantiated these findings, revealing methane metabolism negatively affected ARGs (-4.52), whereas confirming its positive correlation with methane production (0.22). Our findings provided distinctive perspectives on WAS resource utilization and novel technologies to inhibit the spread of ARGs.

Water-saving irrigation suppresses on soil-crop pathogenicity: Insight on the co-host of virulence factors and antibiotic resistance genes

Water-saving irrigation is increasingly being prioritized in agricultural production activities to conserve water resources and increase crop productivity. Yet, how water-saving irrigation affects soil-crop pathogenic, primarily involving in the prevalence of virulence factors (VFs) and antibiotic resistance genes (ARGs), remains unclear. Here we investigated the variations in the abundance of VFs and ARGs in the soil-crop system under different irrigation intensities, and explored the underlying mechanisms on suppressing the dissemination of ARGs and VFs. The results showed that irrigation intensities (50 %, 75 % and 100 % irrigation water, hereafter IW50, IW75 and IW100) did not significantly affect soil VFs and ARGs abundance, but was closely associated with their occurrences in roots and leaves. Water-saving irrigation (IW 50 and IW75) clearly reduced the proliferation of VFs and ARGs in crops, especially TEP, PhoP, basS, and evgS genes decreased by more than 80 % compared to recommended irrigation usage (IW100). And, the co-hosts largely contributed to the reduction of VFs and ARGs abundance. The network analysis demonstrated that the increase in negative interactions between co-hosts and non-cohosts after water-saving irrigation resulted in the decrease of co-hosts colonization. Further, the decline in H2O-O2, carbon and nitrogen metabolic functional genes indicated that water-saving irrigation can inhibit the microbial ability to utilize those resources, thus decreasing VFs and ARGs proliferation. Finally, we determined that IW75 was most beneficial for VFs and ARGs reduction and tomato production. The outcome deepened the understanding of suppression on the spread of VFs and ARGs by water-saving irrigation, thereby providing valuable guidance for sustainable water-efficient agricultural practices.

Antimicrobial Resistance (AMR) Development Map: A Conceptual Map and a Tool to Support Economic Evaluation of AMR Interventions

INTRODUCTION

Antimicrobial resistance (AMR) is a complex, inter-sectoral and international problem. Economic evaluation (EE) methods offer systematic, evidence-driven approaches to inform policy decisions about which AMR interventions to fund. EE of AMR interventions is complicated owing to diffuse effects, complex mechanics of the problem and high levels of uncertainty. Current AMR EE literature restricts the analytical scope, potentially resulting in omissions of effects that may limit the utility of EE to inform policy decisions. We aimed to systemise the key evolutionary and ecological processes of AMR to elucidate the paths through which AMR interventions impact population health and healthcare costs to support EE design and to support decision makers in understanding the limitations of EE evidence for decision-making.

METHODS

A conceptual map and a corresponding tool were developed on the basis of a literature review in consultation with experts across the relevant disciplines of molecular biology, infectious disease modelling, health economics and ecology.

RESULTS

The AMR development map: (1) distils the key AMR processes and process drivers behind AMR development and maps the available types of AMR interventions to AMR process drivers; (2) proposes a way to conceptualise the spatial scope of analysis through considering the connectivity of the wider ecosystem and (3) outlines the key dimensions that AMR burden and intervention effects could be measured across. An AMR development map tool was developed to support conceptual modelling, with the focus on the choice of scope in the EE of AMR interventions, and an illustrative case study was provided.

DISCUSSION

This work summarises the key underlying biological principles of AMR development to provide mechanistical grounding for considering the scope of effects of AMR interventions and the appropriate system of analysis to support conceptual modelling in EE of AMR interventions. In addition, this map can facilitate the identification of effects that cannot be considered or quantified, thus enabling transparency about these omissions within decision-making.

Altered Cell Viability, Morphology, and Motility under Ciprofloxacin Stress Influence the Transport and Resistance of Bacteria in Saturated Porous Media

The ubiquitous occurrence of antibiotics in the environment induces various stress responses of microbes and increases the risk of the emergence and spread of antimicrobial resistance (AMR). In this study, the transport and retention of Shewanella oneidensis cells in saturated porous media was investigated under different levels of ciprofloxacin (CIP) stress. Exposing to lethal CIP stress caused significant viability loss and stimulated cell transport due to increasing hydrophilicity and decreasing surface roughness. While exposure to sublethal CIP stress did not affect MR-1's viability, elongation of cells promoted their retention in sand columns via straining and orientation effects. The elongated cells likely adopted an end-on configuration to minimize repulsive interaction energy when approaching sand surfaces and deposited in a side-on position due to local surface roughness and charge heterogeneity of sands. The more diminished breakthrough of MR-1 cells in redox-active media was ascribed to their improving extracellular electron transfer and energy taxis activities under sublethal CIP stress. Moreover, the retention of elongated cells in porous media facilitated the de novo emergence of a resistant gyrase mutant, whose remobilization might exacerbate the AMR dissemination.

Particulate matter continuum as distinct colonization niches for antibiotic resistome, mobilome and virulence factor genes in wastewater: Insights from full size-fractionated partitioning

Particulate matter continuum is recognized for its significant role as a colonization niche for microorganisms, along with antibiotic resistome, mobilome, and virulence factor genes (VFGs). However, potential particle size effects on the dynamics of these bioactive pollutants in WWTPs is largely unknown. Hence, we used filtration membranes to fractionate particulate matter in wastewater into five size-fractions (< 0.2, 0.2 - 0.8, 0.8 - 3.0, 3.0 - 10.0, > 10.0 μm). The results showed that the diversity and abundances of antibiotic resistance genes (ARGs) and VFGs varied across these fractions. Notably, the particle range of 0.8 - 3.0 μm exhibited the highest relative abundances of ARGs (0.71) and MGEs (0.41), indicating that this size-fraction was their hotspots. Moreover, the relative abundances of phyla, such as Acidobacteria (0 - 11.73 %), Chloroflexi (0 - 11.03 %) and Patescibacteria (0.033 - 35.95 %) varied across the size-fractions. The differentiation of ARGs might be attributed to the diversity and structures of bacterial communities colonizing in different size-fractions. Furthermore, it was revealed that the size-fractions (< 3.0 μm) cannot be effectively removed by the treatment units. The removal efficiencies of size-fractionated ARGs are treatment process-specific. It highlights the need to adopt specific technologies to remove size-fractionated ARGs.

Selective pressures for public antibiotic resistance

The rapid increase of antibiotic-resistant pathogens is severely limiting our current treatment possibilities. An important subset of the resistance mechanisms conferring antibiotic resistance have public effects, allowing otherwise susceptible bacteria to also survive antibiotic treatment. As susceptible bacteria can survive treatment without bearing the metabolic cost of producing the resistance mechanism, there is potential to increase their relative frequency in the population and, as such, select against resistant bacteria. Multiple studies showed that this altered selection for resistance is dependent on various environmental and treatment parameters. In this review, we provide a comprehensive overview of their most important findings and describe the main factors impacting the selection for resistance. In-depth understanding of the driving forces behind selection can aid in the design and implementation of alternative treatments which limit the risk of resistance development.

Cutting-edge tools for unveiling the dynamics of plasmid-host interactions

The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.

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.

Hierarchical activation of resistance genes under tetracyclines selective pressure in complex microbial community

The pervasive use of antibiotics exerts selective pressure in both natural and anthropogenic environments, driving the propagation and evolution of antibiotic resistance genes (ARGs) in microbial communities. Understanding the succession of resistome under varying antibiotic stresses is crucial for mitigating the spread of ARGs. This study investigates the succession of resistome under exposure to four structurally different tetracyclines (TC) across concentrations ranging from environmental to clinical levels. A clear hierarchical activation of ARGs was observed, starting with the upregulation of multidrug and TC-specific efflux pump genes, followed by those involved in TC inactivation and ribosomal protection. By identifying the specific thresholds of transcriptional onset times and critical TC concentration ranges that triggered ARG abundance increases, it was found that all ARGs as a whole did not significantly increase when TC concentrations were maintained below 10-5 of the initial minimum inhibitory concentration (MIC0) within 2 h. Similarly, high-risk TC resistance genes do not proliferate when TC concentrations were kept below 10-3 × MIC0 within 24 h. These findings provide quantifiable benchmarks for concentration-time thresholds that can inform the establishment of environmental discharge limits and guide the implementation of targeted treatment technologies to mitigate ARG dissemination.

Synergistic activity of menadione in combination with colistin against colistin-susceptible and colistin-resistant Gram-negative bacteria

OBJECTIVE

Antibiotic resistance poses a formidable challenge, especially with the emergence of multidrug-resistant Gram-negative bacteria. Colistin serves as a last-resort antibiotic to combat multidrug-resistance, but it is limited by its nephrotoxicity and rising resistance. This study introduces menadione, a synthetic form of vitamin K, as a potential adjuvant to enhance colistin's efficacy against both susceptible and resistant strains of Gram-negative bacteria.

METHODS

Through checkerboard dilution assays, we demonstrate that menadione significantly lowers the MICs of colistin, with fractional inhibitory concentration indices ranging from 0.031 to 0.375. Furthermore, synergistic effects were confirmed via time-kill kinetics, indicating effective bacterial growth inhibition. The study also explores the mechanism underlying this synergy, revealing that menadione in combination with colistin disrupts the bacterial outer membrane, reduces the proton motive force and adenosine triphosphate content, and amplify the production of reactive oxygen species, contributing to bacterial cell death.

RESULTS

Menadione was shown to prevent the evolution of colistin resistance.

CONCLUSIONS

This research highlights the potential of using menadione as a colistin adjuvant to combat antibiotic-resistant Gram-negative bacteria, providing a promising approach to extend the utility of existing antibiotics in clinical settings.

Environmental peracetic acid increases antibiotic resistance in Streptococcus Suis

Disinfectants in the environment have important impacts on the occurrence of antibiotic resistant bacteria, posing a new threat to public health. Streptococcus suis (S. suis) can survive in the environment for three months and carries antibiotic resistance genes. However, it remains unclear whether disinfectants directly induce antibiotic resistance in S. suis. Here, we conducted induction experiments on the S. suis standard strain (CVCC609) with eight disinfectants at different concentrations and investigated their effects on the antibiotic resistance mechanism of S. suis. The results showed that only 64 mg L-1 peracetic acid (PAA) led to an increase (8-fold) in S. suis resistance to tiamulin (TIA) with genetic stability. The treatment also induced significant changes in the morphology and capsule of the mutant strains, as well as triggered an increase in reactive oxygen species and biofilms in bacterial cells, resulting in an emergency response. Moreover, PAA significantly decreased the cell membrane permeability and led to slight changes in the adenosine triphosphate level. The key differentially expressed genes are closely related to these resistance mechanisms. These results reveal the co-selection mechanism of S. suis resistance to PAA and TIA, and highlight the importance of standardized application of disinfectants in livestock and poultry farming.

Effect of antibiotics on diverse aquatic plants in aquatic ecosystems

The widespread presence of antibiotics in aquatic ecosystems, mainly due to their use in medicine and veterinary practices, poses a significant environmental challenge. Aquatic plants play a vital role in maintaining ecosystem stability, but their responses to antibiotics vary by species, influenced by differences in their traits and interactions with environmental factors. However, the specific ways antibiotics affect these plants remain poorly understood. In this study, we conducted a meta-analysis of 167 peer-reviewed studies to investigate the mechanisms of antibiotic uptake and their effects on different types of aquatic plants-submerged, emergent, and floating. Our analysis shows that antibiotics, particularly common ones like sulfonamides, tetracyclines, and quinolones, impact aquatic plants through multiple pathways. Submerged and floating plants often face widespread, direct exposure, resulting in "full-coverage" impacts, while emergent plants experience mixed exposure patterns, affecting both submerged and aerial parts and leading to "partial-coverage" impacts. These findings provide a foundation for phytoremediation strategies, enabling the rational selection and management of aquatic plant types to mitigate antibiotic pollution. Our study underscores the ecological risks posed by antibiotic contamination in aquatic ecosystems and offers a theoretical framework for developing effective restoration strategies.

Disruption of Pseudomonas aeruginosa quorum sensing influences biofilm formation without affecting antibiotic tolerance

The opportunistic bacterial pathogen Pseudomonas aeruginosa is a leading cause of antimicrobial resistance-related deaths, and novel antimicrobial therapies are urgently required. P. aeruginosa infections are difficult to treat due to the bacterium's propensity to form biofilms, whereby cells aggregate to form a cooperative, protective structure. Autolysis, the self-killing of bacterial cells, and the bacterial cell-to-cell communication system, quorum sensing (QS), play essential roles in biofilm formation. Strains of P. aeruginosa that have lost the lasI/R QS system commonly develop in patients, and previous studies have characterized distinctive autolysis phenotypes in these strains. Yet, the underlying causes and implications of these autolysis phenotypes remain unknown. This study confirmed these autolysis phenotypes in the PA14 QS mutant strains, ΔlasI and ΔlasR, and investigated the consequences of QS loss and associated autolysis on biofilm formation and antibiotic susceptibility. QS mutants exhibited delayed biofilm formation but ultimately surpassed the wild-type (WT) in biofilm mass. However, the larger biofilm mass of the QS mutants was not reflected in higher live-cell numbers, indicating an altered biofilm structure. Nevertheless, QS mutant biofilms were not more susceptible to antibiotics than the WT. Artificial supplementation of ΔlasI with a QS signal molecule (autoinducer) restored the strain's QS system without the associated costs of QS, enabling ΔlasI to achieve higher pre-treatment and post-treatment live-cell numbers. Overall, the lack of QS functioning was not detrimental to biofilm antibiotic tolerance, though the artificial disruption of QS may reduce the advantages of QS mutants within in vivo mixed-strain populations. Much remains to be understood regarding the regulation and induction of the autolysis phenotypes observed in these strains, and future research to fully elucidate the control and consequences of autolysis may offer potential for novel antimicrobial therapies.

Microbial evaluation of Melaleuca alternifolia essential oil for its antifungal activity against Trichophyton violaceum and its synergistic effects with ITZ and KTZ

This study was designed to evaluate the effects of Melaleuca alternifolia essential oil for its antifungal activity as mono-therapeutic agent, and in combination with current antifungal agents, like itraconazole and ketoconazole. To assess the significance of TTO (Tea Tree Oil), ITZ (Itraconazole) and KTZ (Ketoconazole), for in vitro susceptibility pattern of dermatophyte, which was obtained from the cases of clinically examined dermatophytosis, attending the dermatology outpatient department of Sheikh Zayed Hospital. The tea tree essential oil was extracted through steam distillation method using 500 g of fresh Melaleuca alternifolia leaves from Lawrence Garden and obtained the yield of 3 mL that comes to be 0.6%. Trichophyton violaceum grown on SDA Sabouraud dextrose agar ager plates for 48 h were tested for fungicidal activity using equal quantity of TTO employing well method technique. In a comparative study assessing the minimum fungicidal concentration (MFC) of ITZ and KTZ, the MFC of KTZ was found to be greater than the MFC of ITZ because the solution of same concentration produced lesser inhibition zones in case of ITZ as compared to KTZ. In another study to ascertain the synergistic effects of TTO with ITZ, it was established that TTO significantly potentiated the effect of azoles in combination therapy reducing the MFC of ITZ up to 8 folds from 4 to 0.07 ug/mL. In yet another study to cross check the synergistic effects of TTO with KTZ in combination therapy. It was positively found that TTO potentiated the fungicidal activity of KTZ, reducing the MFC of KTZ up to 8 folds from 0.25 to 0.03 μg/mL. Comparing the synergistic effects of TTO with ITZ and TTO with KTZ in combination therapies the inhibition zones produced by TTO with KTZ are found to be prominently biggest. Hence Synergy of TTO with KTZ is most proficient because it reduces the MFC of azole maximally while potentiating the fungicidal activity of KTZ.

Assessing the potential for non-digestible carbohydrates toward mitigating adverse effects of antibiotics on microbiota composition and activity in an in vitro colon model of the weaning infant

Environmental factors like diet and antibiotics modulate the gut microbiota in early life. During weaning, gut microbiota progressively diversifies through exposure to non-digestible carbohydrates (NDCs) from diet, while antibiotic perturbations might disrupt this process. Supplementing an infant's diet with prebiotic NDCs may mitigate the adverse effects of antibiotics on gut microbiota development. This study evaluated the influence of supplementation with 2-fucosyllactose (2'-FL), galacto-oligosaccharides (GOS), or isomalto/malto-polysaccharides containing 87% of α(1→6) linkages (IMMP-87), on the recovery of antibiotic-perturbed microbiota. The TIM-2 in vitro colon model inoculated with fecal microbiota of 9-month-old infants was used to simulate the colon of weaning infants exposed to the antibiotics amoxicillin/clavulanate or azithromycin. Both antibiotics induced changes in microbiota composition, with no signs of recovery in azithromycin-treated microbiota within 72 h. Moreover, antibiotic exposure affected microbiota activity, indicated by a low valerate production, and azithromycin treatment was associated with increased succinate production. The IMMP-87 supplementation promoted the compositional recovery of amoxicillin/clavulanate-perturbed microbiota, associated with the recovery of Ruminococcus, Ruminococcus gauvreauii group, and Holdemanella. NDC supplementation did not influence compositional recovery of azithromycin-treated microbiota. Irrespective of antibiotic exposure, supplementation with 2'-FL, GOS, or IMMP-87 enhanced microbiota activity by increasing short-chain fatty acids production (acetate, propionate, and butyrate).

Antibiotic-mediated microbial community restructuring is dictated by variability in antibiotic-induced lysis rates and population interactions

It is widely known that faster-growing bacterial cells are more susceptible to many antibiotics. Given this notion, it appears intuitive that antibiotic treatment would enrich slower-growing cells in a clonal population or slower-growing populations in a microbial community, which has been commonly observed. However, experimental observations also show the enrichment of faster-growing subpopulations under certain conditions. Does this apparent discrepancy suggest the uniqueness about different growth environments or the role of additional confounding factors? If so, what could be the major determinant in antibiotic-mediated community restructuring? Combining modeling and quantitative measurements using a barcoded heterogeneous E. coli library, we show that the outcome of antibiotic-mediated community restructuring can be driven by two major factors. One is the variability among the clonal responses of different subpopulations to the antibiotic; the other is their interactions. Our results suggest the importance of quantitative measurements of antibiotic responses in individual clones in predicting community responses to antibiotics and addressing subpopulation interactions.

Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities

Understanding factors influencing community resilience to disturbance is critical for mitigating harm at various scales, including harm from medication to gut microbiota and harm from human activity to global biodiversity, yet there is a lack of data from large-scale controlled experiments. Factors expected to boost resilience include prior exposure to the same disturbance and dispersal from undisturbed patches. Here we set up an in vitro system to test the effect of disturbance pre-exposure and dispersal represented by community mixing. We performed a serial passage experiment on a 23-species bacterial model community, varying pre-exposure history and dispersal rate between three metacommunity patches subjected to different levels of disturbance by the antibiotic streptomycin. As expected, pre-exposure caused evolution of resistance, which prevented decrease in species abundance. The more abundant the pre-exposed species had been in the undisturbed community, the less the entire community changed. Pre-exposure of the most dominant species also decreased abundance change in off-target species. In the absence of pre-exposure, increasing dispersal rates caused increasing spread of the disturbance across the metacommunity. However, pre-exposure kept the metacommunity close to the undisturbed state regardless of dispersal rate. Our findings demonstrate that pre-exposure is an important modifier of ecological resilience in a metacommunity setting.

Genome restructuring and lineage diversification of Cryptococcus neoformans during chronic infection of human hosts

Classified as a critical public health threat by the World Health Organization, Cryptococcus neo-formans infections with significant morbidity and mortality. Reports of cryptococcosis persistence, relapse, and reinfection date back to the 1950s, yet the factors driving chronic infections remain poorly understood. A major challenge is the scarcity of serial patient specimens and detailed medical records to study the simultaneous evolution of the pathogen and host health status. This study provides the first genomic and phenotypic analysis of in-host evolution of C. neoformans during chronic infections lasting over a year in six immunocompromised patients. We find fungal genome evolution during persistent infection is characterized by large-scale genome restructuring and increasing genomic heterogeneity. Phenotypic changes show diversification in virulence traits and antifungal susceptibility. Genotypically and phenotypically distinct sub-lineages arise and co-persist within the same tissues, consistent with a model of diversifying selection and niche partitioning in the complex environment of human hosts.

Spatial population dynamics of bacterial colonies with social antibiotic resistance

Bacteria frequently inhabit surface-attached communities where rich "social" interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of Enterococcus faecalis, an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland-the inoculated region that microbes inhabit prior to range expansion-which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.

Turning antagonists into allies: Bacterial-fungal interactions enhance the efficacy of controlling Fusarium wilt disease

Intense microbial competition in soil has driven the evolution of resistance mechanisms, yet the implications of such evolution on plant health remain unclear. Our study explored the conversion from antagonism to coexistence between Bacillus velezensis (Bv) and Trichoderma guizhouense (Tg) and its effects on Fusarium wilt disease (FWD) control. We found a bacilysin transmembrane transporter (TgMFS4) in Tg, critical during cross-kingdom dialogue with Bv. Deleting Tgmfs4 (ΔTgmfs4) mitigated Bv-Tg antagonism, reduced bacilysin import into Tg, and elevated its level in the coculture environment. This increase acted as a feedback regulator, limiting overproduction and enhancing Bv biomass. ΔTgmfs4 coinoculation with Bv demonstrated enhanced FWD control relative to wild-type Tg (Tg-WT). In addition, the Tg-WT+ Bv consortium up-regulated antimycotic secretion pathways, whereas the ΔTgmfs4+ Bv consortium enriched the CAZyme (carbohydrate-active enzyme) family gene expression in the rhizosphere, potentiating plant immune responses. This study elucidates the intricacies of bacterial-fungal interactions and their ramifications for plant health.

Pooled Antibiotic Susceptibility Testing for Polymicrobial UTI Performs Within CLSI Validation Standards

BACKGROUND/OBJECTIVES

Urinary tract infections (UTIs) pose an increasing risk of antimicrobial resistance, and novel diagnostic tests have been developed to address the limitations of standard urine culture in these cases. It is important that these novel tests be validated for agreement and error rates against the standard antibiotic susceptibility testing (AST) methods.

METHODS

Polymicrobial (≥two non-fastidious microorganisms) consecutive clinical urine specimens submitted for UTI diagnostic testing were included in this analysis. Specimens were tested with Pooled Antibiotic Susceptibility Testing (P-AST) and with broth microdilution/disk diffusion (BMD/DD) in parallel. Performance characteristics, such as essential agreement (EA%), very major errors (VMEs), and major errors (MEs), were assessed using Clinical and Laboratory Standards Institute (CLSI) standards. Specimens with P-AST-resistant and BMD/DD consensus-sensitive results were assessed for heteroresistance. Real-world clinical sample data were used to assess associations between increasing organism counts and average "sensitive" antibiotic count per sample.

RESULTS

The essential agreement between P-AST and standard isolate AST was ≥90%, VMEs were <2.0%, and MEs were <3.0%, meeting the CLSI guidelines for AST verification and validation studies. When heteroresistance was accounted for, overall VMEs and MEs were both <1.5%. The presence of additional non-fastidious organisms dropped the number of average "sensitive" antibiotics from 9.8 with one organism to 2.5 with five or more organisms. The presence of fastidious organisms did not have any meaningful impact.

CONCLUSIONS

P-AST, a component of the Guidance® UTI assay (Pathnostics, Irvine, CA, USA), performed within CLSI standards for AST in polymicrobial UTI diagnostic urine specimens.

Pharmacodynamics of interspecies interactions in polymicrobial infections

The pharmacodynamic response of bacterial pathogens to antibiotics can be influenced by interactions with other bacterial species in polymicrobial infections (PMIs). Understanding the complex eco-evolutionary dynamics of PMIs and their impact on antimicrobial treatment response represents a step towards developing improved treatment strategies for PMIs. Here, we investigated how interspecies interactions in a multi-species bacterial community affect the pharmacodynamic response to antimicrobial treatment. To this end, we developed an in silico model which combined agent-based modeling with ordinary differential equations. Our analyses suggest that both interspecies interactions, modifying either drug sensitivity or bacterial growth rate, and drug-specific pharmacological properties drive the bacterial pharmacodynamic response. Furthermore, lifestyle of the bacterial population and the range of interactions can influence the impact of species interactions. In conclusion, this study provides a foundation for the design of antimicrobial treatment strategies for PMIs which leverage the effects of interspecies interactions.

Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms

Background

Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.

Materials and Methods

In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.

Results

Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.

Conclusion

Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.

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.

Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance

Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.

IMPORTANCE

Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.

Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.

Therapeutic potential of Chromolaena odorata, Vernonia amygdalina, and Cymbopogon citratus against pathogenic Bacteria

Antimicrobial resistance poses a global public health threat, compelling the search for alternative treatments, especially in resource-limited settings. The increasing ineffectiveness of traditional antibiotics has intensified the need to explore medicinal plants as viable therapeutic options. This study sought to compare the efficacy of certain medicinal plants used in Owerri, Nigeria, for treating pathogenic bacteria against traditional commercial antibiotics. We tested graded concentrations (25 mg/ml, 50 mg/ml, 75 mg/ml, and 100 mg/ml) of ethanolic extracts of Awolowo leaf (Chromolaena odorata), Bitter leaf (Vernonia amygdalina), and Lemon grass leaf (Cymbopogon citratus) against Salmonella spp, Klebsiella spp, Escherichia coli, and Staphylococcus aureus employing the agar well diffusion method to measure zones of inhibition. Commercial antibiotics studied included: Pefloxacin, Gentamycin, Ampiclox, Zinnacef, Amoxicillin, Rocephin, Ciprofloxacin, Streptomycin, Septrin and Erythromycin, Sparfloxacin Amoxicillin, Augmentin, and Tarivid. Each experiment was conducted in triplicate to ensure accuracy and reproducibility. Results were analyzed descriptively and presented as mean zones of inhibition and standard deviations. One to three plant species exhibited antibacterial activities (zones of inhibition) across 25-100 mg/ml concentrations. In contrast, some or all antibiotics only exhibited antibacterial activities at 100 mg/ml concentration (none at 25-75 mg/ml concentrations). Zones of inhibition (10.3-14.1 mm) of all three plant species against E.coli and Klebsiella at 100 mg/ml concentration were higher than those of 8-10 antibiotics. C. odorata had shown high zones of inhibition of 11.8 and 11.0 mm against Salmonella spp. and S. aureus at 100 mg/ml concentration, which were higher than those of eight antibiotics. The other two plant species (C. citratus and V. amygdalina) had exhibited low zones of inhibition against Salmonella spp. and S. aureus, which were higher than those of 3 or 4 antibiotics at 100 mg/ml concentration. In general, the antibacterial activities of the three plant species across 25-100 mg/ml concentrations were higher than those of many antibiotics. To a large extent, the efficacy of medicinal plant extracts across different concentrations against bacterial strains was higher than that of many antibiotics. Those plant species have therefore shown some potential to be used as alternative or complementary therapeutics to antibiotics in addressing antibiotic resistance. Since the promising findings were based on an in vitro study, we recommend clinical trials to establish safe and effective doses of those plant extracts in humans.

Drug delivery dynamics dictate evolution of bacterial antibiotic responses

Microbes inhabit natural environments that are remarkably dynamic. Therefore, microbes harbor regulated genetic mechanisms to sense shifts in conditions and induce the appropriate responses. Recent studies suggest that the initial evolution of microbes occupying new niches favors mutations in regulatory pathways. However, it is not clear how this evolution is affected by how quickly conditions change (i.e. dynamics), or which mechanisms are commonly used to implement new regulation. Here, we perform experimental evolution on continuous cultures of Escherichia coli carrying the tetracycline resistance tet operon to identify specific mutations that adapt drug responses to different dynamic regimens of drug administration. We find that cultures evolved under gradually increasing tetracycline concentrations show no mutations in the tet operon, but instead a predominance of fine-tuning mutations increasing the affinity of an alternative efflux pump AcrB to tetracycline. When cultures are instead periodically exposed to large drug doses, all populations evolved transposon insertions in repressor TetR, resulting in loss of regulation and constitutive expression of efflux pump TetA. We use a mathematical model of the dynamics of antibiotic responses to show that sudden exposure to large drug concentrations overwhelm regulated responses, which cannot induce resistance fast enough, resulting in selection for constitutive expression of resistance. These results help explain the frequent loss of regulation of antibiotic resistance by pathogens evolved in clinical environments. Our experiment supports the notion that initial evolution in new ecological niches proceeds largely through regulatory mutations and suggests that transposon insertions are the main mechanism driving this process.

In vitro and in silico effect of meldrum's acid-derived compounds on Staphylococcus aureus strains as NorA efflux pump inhibitors

The misuse of antibiotics has led to an alarming increase in bacterial strains resistant to these drugs. Efflux pumps, which expel antibiotics from bacterial cells, have emerged as one of the key mechanisms of bacterial resistance. In the quest to combat and mitigate bacterial resistance, researchers have turned their attention to efflux pump inhibitors as a potential solution. Meldrum's acid, a synthetic molecule widely utilized in the synthesis of bioactive compounds, has garnered significant interest in this regard. Hence, this study aims to investigate the antibacterial activity and evaluate the efficacy of three derivatives of meldrum's acid in inhibiting efflux mechanisms, employing both in silico and in vitro approaches. The antibacterial activity of the derivatives was assessed through rigorous broth microdilution testing. While the derivatives themselves did not exhibit direct antibacterial activity, they demonstrated remarkable potential in potentiating the effects of antibiotics. Additionally, fluorescence emission assays using ethidium bromide (EtBr) revealed fluorescence levels comparable to the positive control, indicating a possible blockade of efflux pumps. Molecular docking studies conducted in silico further supported these findings by revealing binding interactions similar to norfloxacin and CCCP, known efflux pump inhibitors. These results underscore the potential of meldrum's acid derivatives as effective inhibitors of efflux pumps. By inhibiting these mechanisms, the derivatives hold promise in enhancing the effectiveness of antibiotics and combatting bacterial resistance. This study contributes valuable insights into the development of novel strategies to address the pressing issue of bacterial resistance and paves the way for further research and exploration in this field.

Prevalence and antibiotic resistance patterns of Pseudomonas aeruginosa and Acinetobacter baumannii strains isolated from chicken droppings on poultry farms in Gondar city, Northwest Ethiopia

Background

Pseudomonas aeruginosa and Acinetobacter baumannii are common nosocomial pathogens in hospital settings. Recently, they have also been found in non-hospital environments, such as poultry farms. While most studies in Ethiopia have focused on these bacteria's antibiotic resistance patterns in hospitals, information regarding their prevalence and resistance in veterinary settings, particularly poultry farms, is limited. This study aimed to assess the prevalence and antibiotic resistance patterns of P. aeruginosa and A. baumannii isolated from chicken droppings on poultry farms.

Methods

A cross-sectional study was conducted from March 2022 to June 2022. A total of 87 poultry farms were included in this study, and pooled chicken dropping samples were collected. The samples were subsequently transferred to buffered peptone water and cultured on MacConkey agar. Species of the isolates were identified via routine biochemical tests, including oxidase, catalase, urease, Simon's citrate, sulfide indole motility medium, triple sugar iron agar and growth at temperatures of 37 °C and 42 °C. The Kirby-Bauer disk diffusion technique was used for antibiotic susceptibility testing. The data were entered into EpiData version 4.6 and then exported to SPSS version 26 for analysis. Fisher's exact test was used to observe an appropriate association between independent variables and the occurrence of isolates. The results are presented in the text, figures and tables.

Results

Among the 87 poultry farms, 41 (47.1 %) were positive for Pseudomonas and Acinetobacter. Among these strains, 24 (27.6 %) P. aeruginosa strains and 13 (14.9 %) A. baumannii strains were recovered. P. aeruginosa showed complete resistance to tetracycline (24, 100.0 %) and trimethoprim-sulfamethoxazole (24, 100.0 %). Additionally, there was a high rate of resistance to ciprofloxacin (13, 54.2 %) and amikacin (12, 50.0 %). Similarly, 13 (100.0 %) A. baumannii isolates were resistant to tetracycline, and 12 (92.3 %) were resistant to trimethoprim-sulfamethoxazole. However, both isolates presented lower resistance rates to piperacillin-tazobactam (4, 9.8 %) and cefepime (7, 17.1 %). Both A. baumannii and P. aeruginosa exhibited multidrug resistance in 10/13 (76.9 %) and 16/24 (66.7 %) of the strains, respectively. The overall prevalence of multidrug resistance in this study was 28/41 (68.3 %).

Conclusion

This study demonstrated that poultry farms may be potential reservoirs for P. aeruginosa and A. baumannii, including antibiotic-resistant strains. This is a significant concern to public health because poultry farmers may be contaminated, increasing their dissemination to the community. Therefore, poultry farmers should improve sanitation and reduce the misuse and overuse of antibiotics at poultry farms.

Soil Amoebae Are Unexpected Hotspots of Environmental Antibiotics and Antibiotic Resistance Genes

Antibiotic resistance poses a significant threat to human health. While most studies focus on bacteria, interactions between antibiotics and other crucial microbial groups like protists remain uncertain. This study investigates how protists interact with antibiotics and examines how these interactions impact the fate of resistance genes. It reveals that amoebae exhibit high resistance to eight high-risk environmental antibiotics, accumulating significant quantities within their cells. Wild amoeboid strains from distant locations carry substantial antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), with significant heterogeneity within a single species. Amoeboid symbionts and pathogens predominantly carry these genes. Paraburkholderia symbionts have reduced genomes and fewer resistance genes compared to free-living strains, while amoeba-endogenous Stenotrophomonas maltophilia does not exhibit a significantly reduced genome size. This suggests that the amoeboid hosts serve as a temporary medium facilitating its transmission. In summary, the study unveils that soil amoebae represent unexpected hotspots for antibiotics and resistance genes. Future research should assess the effects of antibiotics on often-overlooked protists and explore their role in spreading ARGs and MRGs in ecosystems. Incorporating protists into broader antibiotic resistance research is recommended, highlighting their significance within a One Health perspective.

Contribution of the infection ecosystem and biogeography to antibiotic failure in vivo

The acquisition of antibiotic resistance in bacteria, though a deeply concerning international issue, is reasonably well-understood at a mechanistic level. Less well-understood is why bacteria that are sensitive in vitro to well-established and widely-used antibiotics sometimes fail to respond to these agents in vivo. This is a particularly common problem in chronic, polymicrobial infection scenarios. Here, we discuss this in vitro-in vivo disconnect from the perspective of the bacterium, focusing in particular on how infection micro/macro-environment, biogeography, and the presence of co-habiting species affect the response to antibiotics. Using selected exemplars, we also consider interventions that might improve treatment outcomes, as well as ecologically 'eubiotic' approaches that have less of an impact on the patient's commensal microflora. In our view, the accrued data strongly suggest that we need a more comprehensive understanding of the in situ microbiology at infection sites.

The evolution of reduced facilitation in a four-species bacterial community

Microbial evolution is typically studied in monocultures or in communities of competing species. But microbes do not always compete and how positive inter-species interactions drive evolution is less clear: Initially facilitative communities may either evolve increased mutualism, increased reliance on certain species according to the Black Queen Hypothesis (BQH), or weaker interactions and resource specialization. To distinguish between these outcomes, we evolved four species for 44 weeks either alone or together in a toxic pollutant. These species initially facilitated each other, promoting each other's survival and pollutant degradation. After evolution, two species (Microbacterium liquefaciens and Ochrobactrum anthropi) that initially relied fully on others to survive continued to do so, with no evidence for increased mutualism. Instead, Agrobacterium tumefaciens and Comamonas testosteroni (Ct) whose ancestors interacted positively, evolved in community to interact more neutrally and grew less well than when they had evolved alone, suggesting that the community limited their adaptation. We detected several gene loss events in Ct when evolving with others, but these events did not increase its reliance on other species, contrary to expectations under the BQH. We hypothesize instead that these gene loss events are a consequence of resource specialization. Finally, co-evolved communities degraded the pollutant worse than their ancestors. Together, our results support the evolution of weakened interactions and resource specialization, similar to what has been observed in competitive communities.

Unravelling a Latent Pathobiome Across Coral Reef Biotopes

Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.

Screening and identification of phytochemicals from Acorus calamus L. to overcome NDM-1 mediated resistance in Klebsiella pneumoniae using in silico approach

Klebsiella pneumoniae is a potent human pathogen and a prevalent ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Considerably, K. pneumoniae becomes a major clinical problem due to numerous AMR genes [extended-spectrum β-lactamase, plasmid-mediated AmpC, carbapenemases, tigecycline resistance, and New Delhi Metallo-β-lactamase-1 (NDM-1)] and can hydrolyze the majority of β-lactam antibiotics. Hence, targeting NDM-1 could be an effective approach to eradicate K. pneumoniae pathogenesis. A plethora of reports suggests that the plant compounds possess an anti-microbial activity and their utilization could be a promising strategy to develop novel antibiotics. Our study utilized the hydromethanolic leaves extract of Acorus calamus L. (AC) to target NDM-1 containing K. pneumonia using an in silico approach. At first, we determined the phytochemical composition of AC using GC-HRMS. Further, the phytoconstituents were screened against the NDM-1 (PDB ID: 3ZR9) of K. pneumoniae through molecular docking studies. Our results revealed the compounds from AC such as (2R,4S,6R,7S,8R,9S,13S)-16-hydroxy-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icos-1(12)-ene-6,2'-oxane]-11-one (-9.5 kcal/mol), 4,4,5,8-tetramethyl-2,3-dihydrochromen-2-ol (-6.6 kcal/mol), 5-chloro-2-(2,4-dichloro phenoxy)phenol (-6.0 kcal/mol), [(3S,3aS,6R,6aS)-3-nitrooxy-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-6-yl] nitrate (-5.7 kcal/mol), 4-(3-hydroxyprop-1-enyl)-2-methoxyphenol (-5.6 kcal/mol), and (E)-3-(2,4-dimethoxyphenyl)prop-2-enoic acid (-5.6 kcal/mol) possess substantial docking scores against NDM-1. Therefore, our study concludes that phytochemicals of AC may inhibit NDM-1-mediated resistance in K. pneumoniae and could be an alternative therapeutic strategy for targeting NDM-1-containing K. pneumoniae.

Spatial population dynamics of bacterial colonies with social antibiotic resistance

Bacteria frequently inhabit surface-attached communities where rich "social" interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of E. faecalis , an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland-the inoculated region that microbes inhabit prior to range expansion-, which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.

Significance

Interactions between bacteria are common, particularly in the crowded surface-associated communities that occur anywhere from natural ecosystems to the human body to medical devices. Antibiotic resistance can be influenced by these "social" interactions, making it difficult to predict how spatial communities respond to antibiotic. Here, we show that complex spatial arrangements emerge when initially randomly distributed populations of antibiotic-resistant and -sensitive E. faecalis , a microbial pathogen, are exposed to antibiotic. Using mathematical models and experiments, we show how local competition and dynamic-range cross-protection drive pattern formation. As a result, these spatially structured populations respond differently to antibiotics than well-mixed communities. Our findings elucidate how "social" antibiotic resistance affects spatially structured bacterial communities, a step towards predicting and controlling resistance.

Miniature Robots for Battling Bacterial Infection

Micro/nanorobots have shown great promise for minimally invasive bacterial infection therapy. However, bacterial infections usually form biofilms inside the body by aggregation and adhesion, preventing antibiotic penetration and increasing the likelihood of recurrence. Moreover, a substantial portion of the infection happens in those hard-to-access regions, making delivery of antibiotics to infected sites or tissues difficult and exacerbating the challenge of addressing bacterial infections. Micro/nanorobots feature exceptional mobility and controllability, are able to deliver drugs to specific sites (targeted delivery), and enhance drug penetration. In particular, the emergence of bioinspired microrobot surface design strategies have provided effective alternatives for treating infections, thereby preventing the possible development of bacterial resistance. In this paper, we review the recent advances in design, mechanism, and actuation modalities of micro/nanorobots with exceptional antimicrobial features, highlighting active therapy strategies for bacterial infections and derived complications at various organs, from the laboratory bench to in vivo applications. The current challenges and future research directions in this field are summarized. Those breakthroughs in micro/nanorobots offer a huge potential for clinical translation for bacterial infection therapy.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile

BACKGROUND

Aquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance.

RESULTS

The taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site.

CONCLUSIONS

Our results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities' risk for antibiotic resistance, and that a human-influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.

From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance

Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.

Interplay of virulence factors shapes ecology and treatment outcomes in polymicrobial infections

Polymicrobial infections, caused by a community of multiple micro-organisms, are often associated with increased infection severity and poorer patient outcomes. The design of improved antimicrobial treatment strategies for PMIs can be supported by an understanding of their ecological and evolutionary dynamics. Bacterial species present in polymicrobial infections can produce virulence factors to inhibit host immune responses, such as neutrophil recruitment and phagocytosis. The presence of virulence factors can indirectly affect other bacterial species acting as a type of host-mediated interspecies interaction. The aim of this study was to assess how bacterial virulence factors targeting neutrophil function influence ecology and treatment outcomes of PMIs. An agent-based model was constructed which describes a dual-species bacterial population in the presence of neutrophils and a bacteriostatic drug. Our analysis has revealed unforeseen dynamics of the interplay of multiple virulence factors acting as interspecies interaction. We found that the distribution of two phagocytosis-inhibiting virulence factors amongst species can impact whether they have a mutually protective effect for both species. The addition of a virulence factor inhibiting neutrophil recruitment was found to reduce the protective effect of phagocytosis-inhibiting virulence factors. Furthermore we demonstrate the importance of virulence strength of a species relative to other virulent species to determine the fate of a species. We conclude that virulence factors are an important driver of population dynamics in polymicrobial infections, and may be a relevant therapeutic target for treatment of polymicrobial infections.

Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms

Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.

Upper respiratory microbial communities of healthy populations are shaped by niche and age

BACKGROUND

Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.

RESULTS

We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS

In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.

A novel PhoPQ-potentiated mechanism of colistin resistance impairs membrane integrity in Pseudomonas aeruginosa

Polymicrobial communities are often recalcitrant to antibiotic treatment because interactions between different microbes can dramatically alter their responses and susceptibility to antimicrobials. However, the mechanisms of evolving antimicrobial resistance in such polymicrobial environments are poorly understood. We previously reported that Mg2+ depletion caused by the fungus Candida albicans can enable Pseudomonas aeruginosa to acquire significant resistance to colistin, a last-resort antibiotic targeting bacterial membrane. Here, we dissect the genetic and biochemical basis of this increased colistin resistance. We show that P. aeruginosa cells can acquire colistin resistance using three distinct evolutionary trajectories involving mutations in genes involved in lipid A biosynthesis, lipid A modifications that are dependent on low Mg2+, and a putative Mg2+ transporter, PA4824. These mutations confer colistin resistance by altering acyl chains, hydroxylation, and aminoarabinose modification of lipid A moieties on the bacterial outer membrane. In all cases, enhanced colistin resistance initially depends on the low Mg2+-responsive PhoPQ pathway, which potentiates the evolution of resistance mutations and lipid A modifications that do not occur without Mg2+ depletion. However, the PhoPQ pathway is not required to maintain high colistin resistance in all cases. In most cases, the genetic and biochemical changes associated with these novel forms of colistin resistance also impair bacterial membrane integrity, leading to fitness costs. Our findings provide molecular insights into how nutritional competition drives a novel antibiotic resistance mechanism and its ensuing fitness tradeoffs.

Bacterial outer membrane vesicles increase polymyxin resistance in Pseudomonas aeruginosa while inhibiting its quorum sensing

The persistent emergence of multidrug-resistant bacterial pathogens is leading to a decline in the therapeutic efficacy of antibiotics, with Pseudomonas aeruginosa (P. aeruginosa) emerging as a notable threat. We investigated the antibiotic resistance and quorum sensing (QS) system of P. aeruginosa, with a particular focused on outer membrane vesicles (OMVs) and polymyxin B as the last line of antibiotic defense. Our findings indicate that OMVs increase the resistance of P. aeruginosa to polymyxin B. The overall gene transcription levels within P. aeruginosa also reveal that OMVs can reduce the efficacy of polymyxin B. However, both OMVs and sublethal concentrations of polymyxin B suppressed the transcription levels of genes associated with the QS system. Furthermore, OMVs and polymyxin B acted in concert on the QS system of P. aeruginosa to produce a more potent inhibitory effect. This suppression was evidenced by a decrease in the secretion of virulence factors, impaired bacterial motility, and a notable decline in the ability to form biofilms. These results reveal that OMVs enhance the resistance of P. aeruginosa to polymyxin B, yet they collaborate with polymyxin B to inhibit the QS system. Our research contribute to a deeper understanding of the resistance mechanisms of P. aeruginosa in the environment, and provide new insights into the reduction of bacterial infections caused by P. aeruginosa through the QS system.