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PubMed2025

Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective.

INTRODUCTION: Antibiotic resistance, particularly carbapenem-resistant Klebsiella pneumoniae (CRKP), poses significant clinical and environmental threats, especially in urban aquatic ecosystems and hospital wastewaters. OBJECTIVES: This study aims to analyze the epidemiological and genomic features of CRKP isolates in urban aquatic environments and evaluate their public health and environmental impacts. METHODS AND RESULTS: Water samples were collected from 113 rivers and 3 hospitals in China, Sri Lanka, and Nepal to isolate carbapenem-resistant Klebsiella spp. isolates. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics analyses were performed to characterize resistance phenotypes, antibiotic resistance genes (ARGs), and evolutionary trends. Big data analysis further elucidated the genomic characteristics of CRKP in global water sources, and Galleria mellonella larvae were used to assess virulence. Statistical analysis validated the findings. A total of 192 carbapenem-resistant Klebsiella spp. isolates were identified from urban aquatic ecosystems in China (n = 60) and Nepal (n = 132), with CRKP (n = 161) being the predominant species. All CRKP isolates exhibited a multidrug-resistant phenotype, yet significant differences in resistance profiles and associated ARGs were observed between isolates from the two countries. Nine carbapenem resistance genes (CRGs) were detected, with blaNDM-1 being the most prevalent (57.8 %). Correlation analysis revealed a strong association between these CRGs and multiple Inc-type plasmids. Global genomic analysis of CRKP from water sources across eight countries identified ten distinct CRGs across 45 serotypes, with KL64 being the most predominant. Notably, carbapenem-resistant hypervirulent Klebsiella pneumoniae was detected in water samples from Nepal. CONCLUSION: Our findings highlight significant regional disparities in CRKP prevalence and ARG dissemination across urban aquatic environments, with Nepal showing the highest prevalence, particularly in untreated rivers. China exhibited lower prevalence but distinct resistance gene profiles, while no CRKP was detected in Sri Lanka, underscoring the impact of environmental management and healthcare infrastructure on ARG spread.

Humans↗
PubMed2024

Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.

Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.

Humans↗
PubMed2026

Virome metatranscriptomic profiling of birch pollen reveals a diverse viral community.

INTRODUCTION: Viruses are increasingly recognized as integral components of plant-associated biological systems. However, their occurrence and diversity in the reproductive tissues of woody plants remain poorly understood. Birch (Betula spp.) produces large quantities of wind-dispersed pollen that can travel over long distances and may harbour viruses or virus-derived nucleic acids originating from the host plant and/or its associated microbiota. METHODS: We investigated the virome of birch pollen collected from trees growing in central and suburban Berlin, Germany. Metatranscriptomic analyses were performed on pooled pollen samples collected in 2020. These analyses were complemented by RT-PCR screening of individually processed pollen samples collected in 2025 from resampled trees. Primer walking was additionally used to recover an extended genome sequence of a pollen-associated birch toti-like virus. RESULTS: Multiple virus-associated contigs were identified in both pooled metatranscriptomic datasets. These included sequences corresponding to the cherry leaf roll virus (CLRV), the birch idaeovirus (BIV) and the birch toti-like virus (BTLV), as well as additional virus-like contigs provisionally assigned to lineages related to the Orthototiviridae, Botourmiaviridae, Endornaviridae, and Chrysoviridae families. RT-PCR analysis of individually processed pollen samples confirmed the continued detection of CLRV, BIV, and BTLV within the Berlin sampling framework. A near-complete genome sequence was recovered from a pollen-derived BTLV isolate from Berlin, showing high amino acid sequence identity to a recently described leaf-derived BTLV isolate from the United States. DISCUSSION: These findings demonstrate that birch pollen harbours a diverse assemblage of plant- and/or microbiome-associated viruses and expand the known tissue distribution and geographic range of BTLV. More broadly, they establish pollen as an underexplored ecological niche for virome research and provide a foundation for future studies on the ecology, transmission dynamics, and epidemiological significance of pollen-associated and pollen-transmitted viruses.

Betula↗
PubMed2026

Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.

Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.

Soil Microbiology↗
PubMed2026

Heavy-metal stress shapes habitat-specific microbial survival strategies in estuarine environments.

Estuarine ecosystems face increasing heavy metal pollution from rapid urbanization and industrialization, yet the microbial adaptive strategies to multiple metal stressors across different habitats remain poorly understood. This study investigated the diversity and composition of bacterial and fungal communities across free-living (FL), particle-attached (PA), and sediment (SE) fractions from three estuaries with varying heavy metal contamination, and further investigated functional adaptations of bacterial communities. High-throughput amplicon sequencing revealed habitat-specific communities, with SE hosting the highest alpha diversity and enrichment of metal-resistant genera such as Woeseia and Sva1033. Environmental filtering, particularly by Zn, was the dominant driver shaping bacterial assemblages across all habitats, whereas fungal communities displayed greater stochastic assembly patterns. Analysis of 44 high-quality bacterial metagenome-assembled genomes (MAGs) revealed diverse metal resistance genes (cusA, znuB, and zntA), along with enriched metabolic pathways for carbon, nitrogen, and sulfur cycling. Notably, both active efflux/oxidative stress defense and indirect immobilization mechanisms were observed across all habitats, but their relative importance differed: FL and PA communities exhibited a greater reliance on active metal efflux (czcAB) and oxidative stress defense (trxAB) to maintain intracellular homeostasis, whereas SE communities displayed a stronger genomic potential for sulfate reduction (dsrAB) that may contribute to metal immobilization through sulfide precipitation. This metabolic partitioning highlights the complementary roles of different habitats in mediating metal toxicity and biogeochemical cycling, providing new insights into microbial resilience in polluted estuaries and underscoring the urgency of addressing heavy-metal contamination in these critical ecosystems.

Estuaries↗
PubMed2026

Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed that diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N₂O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.

Nitrous Oxide↗
PubMed1977

Human ecology in understanding environmental health problems.

The role of human ecology in understanding of environmental health problems is discussed, and the importance of study on "regional" ecosystems is emphasized in consideration of recent arguments on theoretical frame work of human ecology. After brief conceptual discussion on "regional" ecosystems, the environmental health on hunter-gatherer populations, and then, the influence of agricultural development is discussed in relation to the "closedness" of regional ecosystems. Finally, by an example, e.g. islanders on small islands of southern Japan, the differentiation of economic activities by island is shown as the most important regulating factor for the accumulation of mercury in islanders.

Agriculture↗
PubMed2026

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.

BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored. RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes. CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.

Plasmids↗
PubMed2026

Whole Genome Characterization of Klebsiella Strains in European Hedgehogs and Human Nosocomial Settings Identified Shared Sequence Types, Antimicrobial Resistance Genes and Plasmids.

INTRODUCTION: Klebsiella pneumoniae is a pathogen associated with healthcare-acquired infections and antimicrobial resistance (AMR) to beta-lactams and carbapenems. Although wild animals are not typically exposed to antibiotics, they can harbour resistant strains. The European hedgehog (Erinaceus europaeus) is increasingly found in urban areas, where it interacts with humans and livestock. Studies have identified concerning levels of AMR in hedgehogs, including Extended-Spectrum β-Lactam (ESBL) and carbapenems-resistant Klebsiella pneumoniae strains. METHODS: This study focuses on Klebsiella spp. isolated in hedgehogs from urban areas, using whole-genome sequencing (WGS). We compared these isolates with openly available strains isolated from humans in the same region with the objective to have a thorough understanding of ST, AMR gene, and plasmid overlap between human and environmental compartments. RESULTS: High AMR gene levels, including the carbapenemase blaOXA-48, were found in the hedgehog population. Notably, human nosocomial clones, including ST307 and ST392, globally distributed sequence types also found in wildlife, were identified in both hedgehogs and humans. The presence of conjugative plasmids, including IncFIB(K) and IncL1 types, was identified in both hedgehogs and humans, highlighting plasmid dissemination as a significant factor in AMR spread. CONCLUSIONS: Although no direct transmission from wildlife to hospital settings has been conclusively demonstrated, our findings suggest that hedgehogs may play a role in bridging environmental and healthcare environments. The study underscores the need for further investigation into multidrug-resistant Klebsiella spp. and other resistant bacteria in wildlife to better understand their potential role in the dissemination of resistance genes across ecosystems.

Animals↗