Search Results (49)

Cronobacter sakazakii is a rare, life-threatening neonatal pathogen. In this study, we profiled antimicrobial resistance genes (ARGs), plasmid replicons, virulence genes, sequence types (STs), and core-genome phylogeny across all publicly available clinical C. sakazakii genomes from the United States (n = 116). All isolates harbored exclusively chromosomally encoded bla_CSA variants. IncFIB and rep cluster 574 co-occurred in 93.1% of isolates as a conserved backbone among 17 replicon types. Among 49 virulence genes, 13 formed a universal core (flagellar motility and type VI secretion); accessory genes such as the yersiniabactin cluster were sporadic. ARG, plasmid replicon, and virulence gene contents were strongly structured by ST, dominated by ST4, ST1, ST8, and ST13. Stratified testing shows most pairwise associations were confounded by clonal lineage, except the IncFIB-rep cluster 574 co-carriage and an IncFII-hcp/tssD association, significant after ST stratification but not multiple testing correction. Core-genome phylogenetics identified 16 clusters, from a large ST4-dominated group to nine singletons, corroborated by ST monophyly; a genomically identical ST1 pair, nine years apart, indicated long-term clonal persistence. Ancestral state reconstruction distinguished stable single acquisitions from features with repeated turnover. Core-genome and gene-content phylogenies demonstrated substantial discordance despite significant overall correlation. These findings provide a genomic framework for clinical C. sakazakii population structure in the United States. Full article

Yersinia enterocolitica is a psychrotrophic foodborne bacterium that can proliferate at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns about food safety and public health. However, genomic data on Y. enterocolitica isolates from South Korea are limited, despite the increasing use of whole-genome sequencing (WGS) in bacterial surveillance. Herein, 91 Y. enterocolitica isolates recovered from chicken, pork, beef, and duck samples collected nationwide in 2024 were analyzed using WGS to elucidate their genomic diversity and genomic features. Phylogenomic analysis predicted all isolates as biotype 1A (sub-biotype 1Aa) and revealed substantial genetic diversity, comprising 27 sequence types and 43 core-genome types. Pan-genome analysis identified 11,230 gene clusters, revealing an open pan-genome in which accessory and unique gene clusters were assigned to predicted functional categories associated with metabolism, defense mechanisms, and stress responses. Although the canonical virulence plasmid pYV was absent, conserved chromosomal virulence-associated genes involved in adhesion (yapE), invasion (inv), secretion, and enterotoxicity (ystB) were detected. Antimicrobial resistance genes were predominantly intrinsic, particularly blaA and vat(F), whereas acquired resistance genes were identified sporadically. These findings provide a genomic baseline for biotype 1A Y. enterocolitica isolates recovered from animal-source foods in South Korea. The functional and public health significance of the detected virulence-associated loci requires further phenotypic investigation. Full article

Fusarium oxysporum f. sp. radicis-cucumerinum (Forc) V03-2g and Fusarium oxysporum f. sp. radicis-lycopersici (Forl) ZUM2407 both cause foot and root rot in cucumber, but differ in host range. Forc V03-2g possesses Secreted in Xylem (SIX) effector genes, whereas Forl ZUM2407 does not, raising questions about their distinct infection strategies on this host. Using comparative transcriptomic analysis (in cucumber at 7 and 14 days post-inoculation (dpi) and in tomato at 2 dpi) we show that Forl ZUM2407 induces a delayed defense response in cucumber compared to Forc V03-2g. In turn, Forc V03-2g rapidly activates accessory chromosome effectors on cucumber, while Forl ZUM2407 initially deploys core chromosome genes, activating distinct from Forc V03-2g accessory genes only by 14 dpi. Thereby, Forc V03-2g and Forl ZUM2407 use distinct accessory gene repertoires (unique to each strain) and distinct core gene transcription strategies to infect the same host. Full article

Wastewater treatment plants represent a primary source of environmental dissemination of multidrug-resistant (MDR) bacteria, underscoring the urgent need for in-depth investigation of these organisms. While the resistome of MDR bacteria has been extensively studied, there remains a critical gap in understanding the role of plasmid-borne genes encoding adaptive metabolic functions. We isolated two MDR strains from municipal wastewater, Klebsiella sp. KOS9 and Pseudomonas veronii Yu15, both exhibiting resistance to antibiotics, including ampicillin, cefazolin, kanamycin, streptomycin, erythromycin, chloramphenicol, tetracycline, and ciprofloxacin. The plasmids of these strains harbored genes encoding aliphatic amidases, as well as antibiotic resistance genes (ARGs) and enzymes involved in glycogen and dTDP-L-rhamnose biosynthesis, which may contribute to virulence. In Klebsiella sp. KOS9 a single acetamidase operon, was found on the megaplasmid, along with copper and silver resistance genes. P. veronii Yu15 harbored an operon containing the acetamidase and formamidase genes on the chromosome, as well as a phylogenetically distant acetamidase operon on the conjugative megaplasmid. Both strains exhibit acetamidase activity and P. veronii Yu15 was able to utilize acetamide and formamide as sole nitrogen sources. The occurrence of ARGs and adaptive accessory genes on plasmids likely enhances the competitiveness and environmental flexibility of these MDR bacteria. Full article

The remarkable ecological success of fungi is supported by their capacity for rapid and often reversible molecular responses to fluctuating environments. While conventional evolutionary theory has largely emphasized mutation and selection as central drivers of adaptation, many environmentally responsive fungal traits are also shaped by molecular processes that generate reversible phenotypic variation on ecological or developmental timescales. This review synthesizes current knowledge on reversible genetic and epigenetic mechanisms underlying fungal phenotypic plasticity by integrating insights from programmed genetic rearrangements such as mating-type switching, transposable element activity, variation in tandem repeats and the behavior of accessory chromosomes, together with dynamic epigenetic processes including histone modifications, DNA methylation, chromatin remodeling and RNA mediated regulation. Together, these mechanisms form an interconnected framework that enables rapid and, in many cases, reversible phenotypic diversification, although their consequences range from transient regulatory shifts to partially or fully irreversible sequence-level changes. We highlight the molecular machinery that governs reversibility and its evolutionary implications for fungal pathogenesis, symbiosis, and biotechnology. By uniting genetic and epigenetic perspectives, this review advances a holistic framework in which reversibility is treated as a key property of fungal phenotypic plasticity, helping fungi balance stability with flexibility under environmental challenge. Understanding these mechanisms provides new insights into fungal evolution, and opens new avenues for antifungal intervention and the rational design of industrially valuable fungal strains. Full article

Campylobacter jejuni is a major zoonotic pathogen that circulates among birds, livestock, humans, and environmental reservoirs, yet the genomic mechanisms that enable persistence and transmission across divergent hosts remain incompletely understood. Here, we sequenced 61 C. jejuni isolates recovered from multiple host-associated sources in Shenzhen, China, from 2016 to 2023, and analyzed them together with 312 dereplicated publicly available high-quality reference genomes. Phylogenomic analyses resolved three major clades, including one avian-restricted clade and two clades showing frequent cross-host occurrence. Human-associated isolates displayed lower coding density than mammal-associated isolates and significantly higher proteome-level carbon and nitrogen demands than avian-associated isolates. Comparative genomic analyses further revealed strong host-associated divergence in chromosome-encoded, plasmid-encoded, and horizontally acquired gene repertoires. In human-derived isolates, 11 dataset-specific human-unique KEGG genes and 48 human-unique virulence-associated genes were identified, and human-associated strains showed the strongest multidrug-resistance signal across both chromosome-encoded and mobile-gene compartments. Resistance-associated functions enriched in human-associated genomes included antibiotic inactivation, efflux-mediated resistance, target protection/replacement/alteration, reduced permeability, and nutrient-acquisition-associated resistance. By contrast, core host-interaction loci remained under strong purifying selection, indicating that major human-associated traits were linked more closely to mobile gene acquisition than to extensive mutation-driven diversification. Together, these findings support a proposed genome-partition framework of host adaptation in C. jejuni, in which relatively stable chromosomal backgrounds are complemented by rapid plasmid- and horizontal-transfer-mediated acquisition of high-impact accessory genes. Full article

Serratia marcescens is a highly adaptable Gammaproteobacterium with broad ecological distribution and growing clinical importance. Advances in whole-genome sequencing (WGS) and pangenome analysis reveal extensive genomic plasticity, driven by mobile genetic elements (MGEs) such as plasmids, transposons, integrons, prophages, and extracellular vesicles, which collectively accelerate virulence and antimicrobial resistance (AMR) evolution. S. marcescens displays a dynamic accessory genome enriched in resistance and virulence determinants, supporting persistence in diverse environments, including hospital water systems. Clinically, S. marcescens is an emerging opportunistic pathogen associated with severe healthcare-associated infections, ICU outbreaks, and multidrug-resistant “superbug” phenotypes. Its resistome includes intrinsic AmpC β-lactamase, broad efflux systems, and chromosomal determinants conferring resistance to β-lactams, polymyxins, and multiple additional drug classes, while acquired ESBLs and carbapenemases urther limit therapeutic options. Integrating genomic, evolutionary, and clinical insights underscores the urgent need for improved surveillance, mechanistic understanding, and targeted interventions against carbapenem-resistant S. marcescens (CRSM). Full article

Fusarium is a diverse genus of filamentous fungi that has long been recognized for its importance in plant disease and food security. Beyond its agricultural impact, a growing number of studies now show that Fusarium species can also act as opportunistic pathogens in animals and humans. This review synthesizes current knowledge on Fusarium biology by integrating perspectives from plant pathology, veterinary science, and medical mycology. We examine how shared virulence mechanisms, environmental reservoirs, and genomic plasticity—including accessory chromosomes and horizontal gene transfer—facilitate adaptation across plant, animal, and human hosts. We also consider the role of environmental change in shaping the distribution and pathogenic potential of this genus. By bringing together evidence that is often scattered across disciplines, this review emphasizes the need to move beyond host-specific views and highlights Fusarium as a useful model for understanding fungal adaptability and cross-kingdom pathogenicity within a One Health framework. Full article

Elsinoe fawcettii is a devastating citrus pathogen worldwide, yet high-quality genomic resources are lacking, limiting insights into its adaptive mechanisms. Seventeen strains collected from 13 host species across 5 Chinese provinces were confirmed as E. fawcettii by multi-loci (ITS, rpb2, tef1-α) phylogenetic and morphological analyses. A near-telomere-to-telomere (near-T2T) genome for representative strain FJ-Y-3 was constructed using integrated PacBio and Hi-C sequencing. The 24.40 Mb assembly was organized into 11 chromosomes with exceptional completeness (BUSCO: 97.1%) and continuity (scaffold N50: 2.18 Mb). Pan-genome analysis revealed a closed structure, with core genes representing 77.19% of the total, suggesting evolutionary adaptation through fine-regulation of conserved elements rather than extensive gene content variation. Accessory genes were significantly enriched in terpenoid/polyketide metabolism, cell surface remodeling, and xenobiotic degradation, underscoring metabolic plasticity. Whole-genome resequencing showed single-nucleotide polymorphisms as the dominant variant, with ~60% residing in regulatory regions, implicating cis-regulation as a key adaptive mechanism. This work provides a high-quality genome and multi-omics framework for E. fawcettii, establishing a crucial molecular foundation for understanding pathogen adaptation and developing sustainable disease management strategies. Full article

Listeria monocytogenes is a major foodborne pathogen, responsible for severe listeriosis outbreaks associated with contaminated foods. This study reports the comparative genomic analysis of three novel L. monocytogenes strains C5, A2D9 and A2D10, obtained from dairy and clinical sources. Hybrid genome sequencing with Oxford-Nanopore and Illumina technologies provided high-quality complete chromosomes. Phylogenomic analysis revealed a highly conserved core genome alongside accessory genome diversity. Strain C5 belonged to sequence type ST2, while A2D9 and A2D10 were assigned to ST155 and ST1, respectively. All strains exhibited close genomic relatedness to isolates from dairy animals and/or the dairy environment. Functional analysis identified conserved metabolic functions across all genomes. A total of 40 virulence genes were detected, including the LIPI-1 island in all strains and the LIPI-3 operon exclusively in A2D10, indicating a potential hypervirulent phenotype consistent with its ST1 background and the associated fatal clinical outcome. All strains exhibited similar antimicrobial resistance profiles typical of L. monocytogenes and diverse defense systems. The newly sequenced strains provide a valuable resource for functional analyses of the mechanisms underlying adaptation of L. monocytogenes to diverse environments. Full article

There is increasing research interest in the ORF3 accessory protein of PEDV as a critical element for viral virulence. Here, wild type ORF3 (ORF3_wt) gene was constructed in pEGFP-C1 vector. Additionally, two truncation mutants, ORF3-N (1-98 amino acids [aa]) and ORF3-C (99-224 aa) were inserted in the same vector. Results of ORF3 expression revealed early cytoplasmic localization but 12 h after transfection, ORF3 accumulated around the nucleus, especially ORF3-N. This caused chromosome condensation and morphological distortion that culminated in cell death. In comparison with the native cells expressing GFP alone, ORF3wt-induced lethality was 6.61% above baseline while ORF3- C expression resulted in moderate increase in cell death (0.64%). ORF3-N was affected the most with 220.32% increased lethality. It was, therefore, inferred that the ORF3 gene encodes a protein that causes nuclear damage, distorts cell morphology and leads to cell death. Furthermore, the role of the protein could be inherent in the N-terminal domain, which consists of the transmembrane domains. These findings underpin the importance of ORF3 gene expression in the host and are rudimental insights for further exploration into the mechanistic interactions of ORF3 and the host, as well as a possible role in pathogenesis in PEDV and other coronaviruses. Full article

Stenotrophomonas maltophilia (S. maltophilia) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on S. maltophilia infections in recent years, and the species is becoming a public health concern. Many studies have focused on profiling and pangenome of the species, particularly on their antibiotic resistance and virulence genes. However, there is a lack of studies on mobile genetic elements (MGEs), a subset of pangenome that significantly contributes to the diversity, stability, and plasticity of a population. In this study, 20 genomes of S. maltophilia were downloaded from the NCBI Genome database. The genomes were subjected to profiling of MGEs, their impact on the population structures, and the evaluation of evolutionary trends of the core genomes. The cataloguing of MGEs indicated active horizontal gene transfer events in the S. maltophilia’s population. Multiple virulence and drug resistance genes were predicted within and outside of the MGEs. We observed multiple chromosomal rearrangements in the genomes, most likely caused by MGEs, affecting up to approximately 50% of a single genome sequence. A high number of linkage disequilibrium sites were also predicted in the core genomes. This study provides insights into stability in the core and plasticity in the accessory regions in the S. maltophilia population. Full article

Fusarium oxysporum f. sp. vasinfectum (Fov) is a devastating cotton pathogen. Australian Fov strains are distinguished by their ability to infect plants without nematode interaction and are genetically distinct from global Fov, classified into two vegetative compatibility groups (VCG-01111 and VCG-01112). Here, we present chromosome-level genome assemblies of a historical isolate for each Australian Fov VCG. The end-to-end gapless genome assemblies demonstrate high contiguity and completeness, with 97.7% BUSCO completeness for both isolates. Phylogenetic analysis indicates that the Australian Fov lineages diverged from other known Fov genomes over 3.6 million years ago, while VCG-01111 and VCG-01112 separated approximately 1.1 million years ago. Comparative genomics analysis identified four accessory chromosomes unique to the Australian isolates. Functional annotations revealed 14,495 and 15,342 genes in VCG-01111 and VCG-01112, respectively, with accessory chromosomes containing significantly fewer genes than core chromosomes. Ortholog analysis uncovered unique gene clusters enriched in key metabolic pathways, pathogenicity, and cell division processes. Additionally, we identified several novel lineage-specific peptides unique to each Australian isolate. This comprehensive genomic characterization provides the first insights into the unique evolutionary history of Australian Fov, distinguishing them from global Fov races. Our findings lay the foundation for understanding the genetic factors underlying their exceptional virulence, which makes Australian Fov among the most aggressive cotton pathogens worldwide. Full article

An EBSL-encoding plasmid, pESBL-PH, was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. The plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long reads and illumina short reads, yielding a fully closed plasmid, pESBL-PH-2018. pESBL-PH-2018 was queried against the complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, which was downloaded on 16 July 2024. To identify structurally similar plasmids, strict thresholds were applied, including a mash similarity ≥0.98. This returned 61 plasmids belonging to 13 unique sequence types (STs) hosts. The plasmids were detected from 13 unique countries, dating from 2012 to 2023. The AMR region of the plasmids varied. Interestingly IS26-mediated tandem amplification of resistance genes, including the ESBL gene bla_CTX-M-15 was identified in two independent strains, raising their copy number to three. Furthermore, the genomic background of strains carrying a pESBL-PH-2018-like plasmid were analyzed, revealing truncation of the chromosomal ompK36 porin gene and carbapenem resistance gene carriage on accessory plasmids in 17.85% and 26.78% of strains with a complete chromosome available. This analysis reveals the widespread dissemination of an ESBL-encoding plasmid in a background of resistance-encoding strains, requiring active surveillance. Full article

The host specificity of Fusarium oxysporum (Fox) formae speciales has been reported to be linked to effector proteins known as Secreted in Xylem (SIX). These genes are associated with the non-autonomous mobile element miniature impala (mimp), normally distributed on the accessory chromosomes. The pattern of mimp associated with effector genes has been used to predict candidate effector profiles which characterize Fox formae speciales. In this study, we demonstrate the pathogenicity of strains Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407 and Fusarium oxysporum f.sp. radicis-cucumerinum (Forc) V03-2g in a common host plant (cucumber) and compare their genomes. The Forl ZUM2407 genome lacks SIX genes and their homologs, in contrast to Forc V03-2g. We predicted the total number of mimp elements in the genome of Forl ZUM2407 to be three-fold less than that of Forc V03-2g (10 and 36 copies, respectively). The mimp distribution pattern in Forl ZUM2407 was completely different from that present in Forc V03-2g. Candidate effector profile analysis did not predict that Forl ZUM2407 was able to infect cucumber plants like Forc V03-2g. Therefore, we assume that Forl ZUM2407 has a different type of genome organization associated with pathogenicity, whose effector profile cannot be described using the mimp-based approach. Full article