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Results for “co-selection mechanisms”

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PubMed2026

Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.

Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D₂O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42%-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a two- to three-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.

Soil Microbiology↗

PubMed2026

Narasin used as a feed additive in conventional rearing of broilers can co-select for vancomycin-resistant Enterococcus faecium through the NarAB ionophore resistance mechanisms.

OBJECTIVES: To investigate the role of the NarAB resistance mechanism in the selection of vancomycin-resistant Enterococcus faecium (VREfm) and assess the impact of ionophore feed additives, particularly narasin, on the emergence of VREfm in broiler chickens. MATERIALS AND METHODS: Three isogenic E. faecium strains with different antimicrobial resistance determinants were created by mutagenesis and conjugation and used in a controlled animal experiment. Ross 308 broiler chickens were inoculated with either a rifampicin-resistant, a rifampicin- and vancomycin-resistant or a rifampicin-, vancomycin- and narasin-resistant strain and fed diets supplemented with selected ionophores. Bacterial populations were analysed on selective Slanetz and Bartley agar to determine the presence and selection of VREfm and other vancomycin-resistant species. Bacterial inoculation strains and isolates were whole genome sequenced for species identification and to identify genetic resistance mechanisms. RESULTS: Narasin was shown to select for VREfm in broilers, with NarAB being essential for co-selection. Intrinsically vancomycin-resistant Pediococcus acidilactici and Enterococcus gallinarum were identified as part of the broilers' vancomycin-resistant resident microbiota. Notably, among the P. acidilactici isolates that were susceptibility tested, strains resistant to both vancomycin and narasin were only found in broilers fed narasin, supporting that narasin promotes the growth of narasin-resistant populations. CONCLUSION: Narasin use in broiler feed can co-select for vancomycin-resistant bacteria, including VREfm, through the NarAB mechanism. These findings emphasize the concerns associated with the use of particular ionophores in poultry and suggest that vancomycin and narasin resistance may be more widespread in the broiler microbiota than previously recognized. Further research is needed to understand the implications for antimicrobial resistance and human health.

Animals↗

PubMed2026

Genomic Insights into Mammaliicoccus sciuri from Subclinical Bovine Mastitis to Unveil Key Resistance, Virulence, Biofilm and Adaptation Traits.

The Mammaliicoccus sciuri (M. sciuri), is recognized as a reservoir of antimicrobial resistance (AMR) genes, poses challenges in the Indian dairy sector where antibiotic use is poorly regulated. This study aimed to genomically characterize M. sciuri (formerly Staphylococcus sciuri) isolates recovered from subclinical mastitis (SCM) cattle milk. A total of 128 composite (quarter-wise pooled) milk samples were collected from 199 households (HH) across 16 epiunits /villages in four blocks of Chikkaballapur district, Karnataka, India. Of these, 36 milk samples (28.13%, 36/128; 95% CI: 21.06–36.46%) were diagnosed with SCM using the California Mastitis Test (CMT) and bacteriological culture yielded 113 isolates (88.28%; 113/128; 95% CI: 81.56–92.77%) were phenotypically identified as Staph spp. Through molecular technique PCR targeting the gap gene, two isolates (1.77%; 2/113; 95% CI: 0.49–6.22%) from Hosuru and Gattamaranahalli epiunits were confirmed as M. sciuri and both isolates were mecA-positives indicating methicillin resistance. Whole genome sequencing (WGS) identified 36–37 resistance genes (mecA and blaZ), conferring resistance to β-lactams, macrolides, fluoroquinolones and aminoglycosides. Horizontal gene transfer (HGT) was evidenced by diverse mobile genetic elements (MGEs) such as SCCmec variants, insertion sequences, transposons (IS3, IS6, IS256, and IS1182) and plasmids (Rep1, Rep13, RepUS5 and RepUS43). Virulence profiling uncovered biofilm-associated genes (ica, bap) and heavy metal resistance operons (ars, cop, znu) suggesting mechanisms for environmental persistence and co-selection of resistance traits. Phylogenetic analysis of 99 global isolates revealed host-and geography-specific clustering with Indian isolates occupying distinct evolutionary niches. These findings highlights its possible role as an AMR reservoir and also in bovine mastitis.

Animals↗

PubMed2026

Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.

The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40 ± 41.67 TPM, P < 0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.

Antibiotic resistance gene↗

PubMed2026

Global lessons from antibiotic resistance: Metformin-hydrolysing genes in transposable elements, a new threat for type II diabetic patients?

OBJECTIVES: To investigate the evolutionary origin, genomic mobility, and potential dissemination of metformin-hydrolysing genes (mfmAB), and to assess whether environmental selection by metformin pollution may drive the emergence of transferable pharmaceutical-degrading traits analogous to antibiotic resistance. METHODS: Large-scale comparative genomics was performed using publicly available bacterial genomes carrying mfmAB homologs. Phylogenomic reconstruction, average nucleotide identity analysis, genomic context comparison, plasmid characterization, and insertion sequence mapping were used to infer evolutionary history and identify mechanisms of horizontal gene transfer. RESULTS: mfmAB homologs were identified in twelve Aminobacter and three Pseudomonas genomes within a conserved ∼8.2 kb gene cluster. Phylogenomic analyses showed that metformin-degrading capacity emerged independently in multiple Aminobacter lineages across distinct continents, consistent with convergent evolution under anthropogenic selective pressure. Genomic comparisons indicated a chromosomal origin of mfmAB, followed by mobilization onto conjugative plasmids through IS1182-mediated transposition. In Pseudomonas, additional IS3/IS6-mediated transposition events integrated mfmAB into diverse plasmid backbones, frequently within composite transposons also encoding guanylurea and biguanide degradation pathways (guuH, bguH). These findings reveal a dynamic modular assembly of metabolic functions facilitating adaptation to pharmaceutical pollutants. CONCLUSIONS: Metformin pollution appears to promote the emergence and mobilization of pharmaceutical-degrading genes through mechanisms paralleling antibiotic resistance evolution. Although no clinical impact has yet been demonstrated, the potential spread of such genes into human-associated microbiomes and their possible co-selection with antibiotic resistance determinants represent an emerging One Health concern. Environmental surveillance of pharmaceutical-degrading genes is warranted to anticipate future threats to drug efficacy.

Convergent evolution↗

PubMed2025

Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.).

Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome-wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad-sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co-selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE-1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole-3-pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement.

Arachis↗

PubMed2026

Soil erosion and landscape elevation as unnoticed determinants of environmental antibiotic resistance distribution.

Climate change is reshaping the global antibiotic resistance gene (ARG) landscape through geomorphological processes that remain largely overlooked in the One Health framework. This critical review synthesises evidence on how soil erosion and landscape elevation gradients redistribute, select for, and disseminate ARGs across terrestrial and aquatic ecosystems. Erosion physically removes and transports ARG-bearing microbes, depletes nutrients, and co-selects for resistance via heavy metal exposure and horizontal gene transfer, creating source-sink dynamics that connect eroding hillslopes to downstream water bodies and food systems. Elevation gradients impose abiotic stressors-declining temperature, elevated UV radiation, and shifting pH-that drive microbial community reassembly through environmental selection and dispersal limitation, with emerging evidence linking bacterial competition at high altitude to enhanced multidrug efflux and resistome complexity. The review identifies critical knowledge gaps, including unquantified ARG mass fluxes across erosion-deposition gradients, unresolved dispersal-versus-selection mechanisms along elevation transects, and the absence of integrated One Health surveillance linking environmental ARG reservoirs to clinical outcomes. A synthesis of global case studies illustrates how these processes converge across diverse landscapes. The review concludes with a mechanistic research agenda-including reciprocal transplant experiments, landscape connectivity modelling, and cross-sectoral surveillance-needed to translate these emerging drivers into actionable climate-AMR mitigation policy.

Drug Resistance, Microbial↗

PubMed2026

Co-occurrence of biofilm formation, acid tolerance, and antibiotic resistance in environmental Escherichia coli associated with lettuce.

BACKGROUND: Environmental niches represent important reservoirs of Escherichia coli with stress-adaptation traits that support persistence outside the host. Contaminated irrigation water and soils can facilitate transfer to fresh produce, where bacterial survival may reduce the effectiveness of downstream control measures. This study investigated the co-occurrence of biofilm formation, acid tolerance, and antibiotic resistance (AR) in environmental E. coli and their contribution to persistence along the farm-to-produce continuum. RESULTS: Eighteen E. coli isolates recovered from irrigation water, soil, and lettuce were characterized using phenotypic assays and genome-based analyses. Most isolates remained susceptible to the majority of tested antibiotics, with multidrug resistance observed in only 11.1% of isolates. In contrast, moderate-to-strong biofilm formation was widespread (83.3%), and several isolates exhibited reduced susceptibility to acetic acid at concentrations relevant to household washing practices. Genotypic screening revealed a broad distribution of adhesion, iron acquisition, biofilm-associated, and plasmid-borne resistance determinants, indicating substantial functional diversity. Significant positive associations were observed between acid tolerance, biofilm formation, and antibiotic resistance, suggesting co-occurrence of stress-adaptation phenotypes rather than definitive evolutionary convergence. While antibiotic resistance phenotypes showed strong concordance with corresponding resistance genes, biofilm formation and acid tolerance were not associated with specific genetic determinants, supporting a multifactorial basis of these traits. CONCLUSIONS: These findings demonstrate that environmental E. coli can combine multiple stress-adaptation mechanisms that enhance persistence across agricultural and food-associated environments, even in the absence of high-risk resistance profiles. The observed co-occurrence of phenotypic traits highlights the potential for co-selection under environmental pressures and underscores the limitations of relying solely on downstream decontamination strategies. Effective risk mitigation requires integrated, preventive approaches targeting pre-harvest contamination and environmental reservoirs.

Biofilms↗