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Results for “Environmental selection”

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At least 19 recordsLinked to original sources

PubMed2024

Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study.

Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.

Metagenomics↗

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

Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).

Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.

Hybridization, Genetic↗

PubMed2026

From colonization to infection: Genomic evolution of Clostridioides difficile pathogenesis.

Clostridioides difficile is a spore-forming, toxin-producing anaerobe that is a leading cause of healthcare-associated infections. Its success as a pathogen reflects a complex interplay between bacterial evolution, virulence regulation, ecological adaptation, environmental selection, and host susceptibility. Comparative genomics has revealed deep C. difficile lineage diversification, driven by mobile genetic elements and selective pressures from antibiotics and host environments. These events affect strain-specific virulence by shaping the organization and regulation of the pathogenicity toxin loci, metabolic adaptations for nutrient utilization, and enhanced spore resilience. This review integrates evolutionary and genomic perspectives to illustrate how adaptive diversification has sculpted C. difficile pathogenesis and epidemic success.

CP: microbiology↗

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↗

PubMed2025

Multivariate Effects of SNPs on Environmental Streptococcal Mastitis Evaluated With an NGS-Based Association Study Using Targeted Resequencing in the Bovine MHC Region.

Mastitis is an inflammatory reaction caused by bacterial infection of the teat, and a relationship between its onset and cattle major histocompatibility complex (BoLA) region has been reported. However, no comprehensive genetic analysis of mastitis caused by environmental streptococci has been reported. Here, we resequenced the BoLA region using a hybridisation capture target next-generation sequencing (NGS) method to identify disease susceptibility markers mapped to the BoLA region in environmental streptococcal mastitis. This study examined 75 cows with mastitis caused by environmental streptococci selected from 1641 cows with mastitis and 222 healthy cows without mastitis in Japan. Targeted sequences obtained from MiSeq NGS were aligned to the bovine reference genome (ARS-UCD1.2/bosTau9), and 2,920,355 variants were detected within the BoLA region of the 297 Holstein cattle. In an association study using 2264 variants after quality control, the top 20 variants with the lowest P values were selected and assigned to the 18 surrounding candidate genes, and a gene network analysis of these genes resulted in the narrowing down of five candidate genes POU5F1, IER3, GNL1, ABCF1, and PRR3. Multivariate effect analysis of all 6 SNPs associated with these 5 genes revealed that they were significantly correlated with mastitis, indicating that they were useful for classification of mastitis-resistant and mastitis-susceptible cattle. This is the first report to identify SNPs associated with environmental streptococcal mastitis with an NGS-based association study using targeted resequencing in the BoLA region, and understanding host factors may provide important clues for mastitis control.

Animals↗

PubMed2026

Finlay-Wilkinson random regression for yield and yield stability prediction in cereals.

Year-to-year climate variability poses a challenge for agriculture by increasing crop yield variability; therefore, there is a need to identify genotypes that can withstand these fluctuations. With the right selection criteria, genotypes with yield stability across variable environmental conditions can be selected. Methods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability. Our objective was to examine how the number of environments and the variance among those environments affect stability predictions. We also integrate FWRR as a genomic prediction tool for characterizing yield stability, comparing it to the traditional genomic prediction models as a reference. We used three datasets: one highly unbalanced dataset for oats (Avena sativa L.) and two completely balanced datasets with different numbers of environments for barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We fit standard Finlay-Wilkinson (FW) and FWRR models to estimate grain yield and stability under various scenarios. We found that the estimated stability values obtained were similar using balanced datasets for FW or FWRR. FWRR also achieved moderate predictive ability for stability using unbalanced datasets under 10-fold cross-validation (CV1) with new genotypes. In terms of environmental representation, selecting the right set of environments for inclusion in the model was more important than adding more environments. Our results suggest the possibility of using FWRR to select stable genotypes earlier in line development, as well as to design resource-efficient stability-testing schemes.

Hordeum↗

PubMed2025

Annotated genome of the Atlantic dog whelk, Nucella lapillus.

Nucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes them an ideal species to examine isolation by distance and selection across environmental gradients. Here we present the fully annotated genome of N. lapillus generated with Oxford Nanopore Techonology sequencing at ∼37× coverage. The genome assembly is 2.32 Gbp and consists of 2,525 contigs, with an N50 length of 2 Mbp. Repeat annotation identified 2,491 families that cover 67.56% of the genome, which is similar to other gastropods. Despite its large size and high proportion of repeats, the genome is of high quality. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed a score of 96.8%. Functional annotation of the genome produced 45,848 protein-coding genes with a 96.6% BUSCO score. Genomic resources for mollusks lag behind that of other phyla, perhaps because many of their innate characteristics complicate DNA extraction, sequencing, and assembly. This new N. lapillus genome will increase our genomic understanding of the second largest phylum (and the most diverse class within said phylum) and serve as a key resource to advance studies on the organismal biology and population genetics of this iconic species as well as the connection between genomic variation and community-level processes.

Animals↗

PubMed2026

Genetically diverse populations hold the keys to climatic adaptation in the Western barn owl (Tyto alba).

Although local adaptation influences species distributions, its role in driving evolutionary resilience under climate change remains unclear. Current predictive models focus on genetic adaptation to present climates, providing limited insight into future adaptive capacity. We hypothesise that historical responses to climatic shifts can reveal candidate loci for local adaptation in the future. Combining ecological niche modelling and genomic analyses, we investigate spatiotemporal patterns and mechanisms of local adaptation of the Western Palearctic barn owl (Tyto alba). Ecological modelling reveals that barn owls now occupy a broader climatic niche than during the Last Glacial Maximum. Genomic analyses indicate ongoing adaptation, with regions under selection linked to environmental factors across all populations. We find that local adaptation drives evolutionary changes across populations, enabling colonisation of new habitats and shaping responses to climate change in resident populations. We show that standing genetic diversity plays a crucial role in adaptation to past, present, and future environmental shifts.

Animals↗

PubMed2026

Sparse phenotyping for wheat grain yield enabled by multiomics prediction.

Grain yield is a central target in wheat breeding, yet accurately predicting it remains challenging because it depends on many genes and responds strongly to environmental variation. Genomic selection (GS) has improved breeding efficiency by enabling genome-based prediction of genetic merit, but predictability (PA) for grain yield is often limited under stress environments. At the same time, advances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance and may complement genomic information. In this study, we evaluated genomic and phenomic models for predicting grain yield in elite bread wheat lines across irrigated, drought, and heat-stress environments. Using a sparse phenotyping framework, we compared parametric and non-parametric models. PA was evaluated within environments and under cross-environment sparse phenotyping scenarios. Genomic models provided a stable baseline and enabled effective information sharing across environments when phenotypic data were incomplete. Phenomics-only models captured environment-specific plant responses but were more sensitive to environmental context. Multiomics models that integrated genomic and phenomic information consistently achieved the highest PA, with the largest gains observed under stress conditions. Overall, our results demonstrate that integrating genomics and UAV-based phenomics within sparse phenotyping designs offers a practical and scalable approach to improve grain yield prediction in wheat.

Triticum↗

PubMed2025

Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae.

As organisms adapt to environmental changes, natural selection modifies the frequency of nonneutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae, a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.

Animals↗

PubMed2024

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids.

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations.

Journal Article↗

PubMed2025

Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae.

As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae , a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.

Journal Article↗

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

Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.

Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.

Journal Article↗

PubMed2025

The efficacy of a filtered handheld far-ultraviolet disinfection device for decontamination of high-touch surfaces in healthcare settings: a genomic bacterial analysis.

BACKGROUND AND OBJECTIVES: Enhanced environmental disinfection is linked to reduced hospital-acquired infection rates. In this study, we aimed to evaluate the efficacy of an emerging disinfection technology, a filtered far-UV-C handheld (FFUHH) device, for reducing bacterial loads on high-touch surfaces in shared clinical workrooms, and to isolate, identify and characterize clinically significant environmental pathogens. METHODS: We compared samples from high-touch items (dictation device, mouse, armchair, desk, and keyboard) before and after FFUHH treatment. Samples were collected weekly: contact plates for colony counts and swabs before and after intervention on standardized adjacent areas for each surface, respectively. The swabs were enriched and cultured on selective media to isolate pathogens. Environmental samples, as well as clinical samples collected from patients during the study period, were validated using MALDI-TOF and whole genome sequencing. RESULTS: Among the 440 collected plates (220 before and 220 after treatment), the highest mean colony count pre-treatment was detected from armchairs, and the lowest from keyboards. The mean reduction of colony-forming units ranged 53% and 83% and was statistically significant (P < 0.05) across all surfaces except for the keyboard. We characterized multidrug-resistant Staphylococcus epidermidis ST5 and ST16 strains, a carbapenem-resistant Acinetobacter baumannii, and a Klebsiella pneumoniae genetically related to a clinical isolate with a rare sequence type not previously detected in our institution. CONCLUSION: The FFUHH effectively reduced the microbial burden on high-touch surfaces. It can offer an advantage for surface disinfection and an alternative to routinely used biocides.

Humans↗

PubMed2026

Genomic insights into natural selection in recent human history.

For over a century, scientists have debated the extent to which genetic and phenotypic variation among present-day humans is the result of natural selection - in which heritable traits influence survival or reproduction - versus neutral processes such as genetic drift or population history. The initial sequencing of the human genome and subsequent population resequencing studies enabled genome-scale searches for signatures of selection in present-day genomes. This first generation of genome-wide selection scans identified many targets but left open questions about the timing and nature of selection, making it challenging to identify environmental and biological drivers. Recent methodological advances based on reconstructing ancestral recombination graphs have increased the potential power and resolution of selection scans based on present-day genomes, while the availability of new data on ancient DNA has facilitated the direct reconstruction of genetic change through time. However, there is little consensus on how to use these data to detect and interpret signatures of selection, while avoiding confounders. Here, we review the current state of knowledge about the impact of selection on human genomic diversity and highlight conceptual advances in our understanding of human evolution over the past 10,000 years.

Journal Article↗

PubMed2026

Detection of TR34/L98H pan-azole-resistant Aspergillus fumigatus in poultry farm environments.

INTRODUCTION: Poultry farms have been recognized as environments prone to fungal contamination. However, the occurrence of azole-resistant Aspergillus fumigatus and its cytotoxic potential remain insufficiently characterized. This study aimed to characterize the occurrence, cytotoxic potential, and azole-resistance profile ofAspergillus section Fumigati in poultry farms. METHODS: A total of 420 samples, including air (n = 47), electrostatic dust cloths (n = 87), bedding (n = 87), feed (n = 95), swabs (n = 87), workers' masks (n = 2), and broiler breast (n = 15), were obtained. Fungal characterization was performed through culture-based methods (27 °C and 37 °C), followed by azole resistance screening according to EUCAST guidelines. Resistant isolates were subjected to whole-genome sequencing and a targeted analysis of cyp51A mutations. The cytotoxicity potential of fungal isolates and environmental samples was evaluated using selected cell lines representing respiratory organs (human alveolar [A549]) and detoxification organs (swinekidney [SK]/hepatocellular carcinoma [HepG2]). RESULTS: Seven putative Aspergillus fumigatus isolates exhibited pan-azole resistance (MICs: ≥ 2 mg/L ITR/VOR; ≥ 1mg/L for POS). Four isolates carried the TR34/L98H mutation and were recovered from bedding (n = 3) and air (n = 1), suggesting the presence of resistant A. fumigatus in poultry farm matrices. Although 12% of isolates induced toxicity on both cell lines (17/145), no significant association was observed between isolate cytotoxicity and environmental sample toxicity, suggesting that additional biological and chemical components may contribute to the overall toxicological profile of farm environments. DISCUSION: The study highlights the occurrence of azole-resistant A. fumigatus in poultry farms and support integrated surveillance approaches addressing antifungal resistance and environmental exposure risks in poultry production.

Aspergillus fumigatus↗