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PubMed2026

Whole-genome profiling of antimicrobial resistance and virulence determinants in extensively-drug resistant Pseudomonas aeruginosa isolates causing ventilator associated pneumonia in Egypt.

Among critically ill ICU patients under prolonged mechanical ventilation, Pseudomonas aeruginosa is one of the most common cause of ventilator-associated pneumonia (VAP), with antimicrobial pressure leading to emergence of multidrug, extensively drug and pandrug-resistant (PDR) strains. In Egypt, very little genomic data exist on P. aeruginosa associated with VAP. This study aimed at characterizing the antimicrobial resistance (AMR) determinants, virulence repertoire, MGEs, and sequence types of two highly drug-resistant Pseudomonas aeruginosa isolates, including one pandrug-resistant colistin-resistant isolate and one extensively drug-resistant colistin-susceptible isolate from respiratory tract of Egyptian ICU patients suffering from VAP. The two isolates were identified conventionally and confirmed to the species level using MALDI-TOF MS. Antibiotic susceptibility was assessed using the VITEK-2 Compact system and the broth microdilution method. Genome analysis was performed using PATRIC, ResFinder, CARD, and Mobile Element Finder. For both isolates, resistance was found to all antibiotics routinely tested, however, one isolate had high-level colistin resistance (MIC > 64 µg/mL), while the other isolate was still colistin susceptible. Whole-genome sequencing identified two rare sequence types, ST2023 and ST2685, both 6.5-7.6 Mb in size with a 66% GC content. The presence of 21 MGEs in the SRR36105565 genome shows that it has high genomic flexibility, including a broader resistome than other strains, such as blaVIM-2 and OXA variants, aminoglycoside-modifying enzymes, crpP, and disinfectant-resistance markers. Both isolates retained large virulence determinants including Type III and Type VI secretion systems, alginate regulation genes, quorum-sensing networks, and siderophore biosynthesis clusters. It also represents one of the first genomic studies of VAP associated PDR P. aeruginosa from Egypt. The combination of widespread AMR with intact virulence supports the potential value of future genomic surveillance efforts and improved antimicrobial stewardship in local ICUs.

Pneumonia, Ventilator-Associated↗

PubMed2026

[Genes determining virulence factors of Escherichia coli strains isolated from prostate secretions patients with chronic bacterial prostatitis].

UNLABELLED: The aim of the work is to characterize virulence genes of E. coli strains isolated from prostate secretions patients with chronic bacterial prostatitis. MATERIALS AND METHODS: Escherichia coli were isolated from the prostate secretions of men of reproductive age (20-45 years) with chronic bacterial prostatitis using a generally accepted bacteriological method, the type was determined using MALDI-TOF mass spectrometry, virulence genes were PCR and sequencing. RESULTS: The genomes of the studied strains contain genes encoding groups of virulence factors: adhesins, toxins, capsule antigens, siderophores, invasins, and anti-immunity of the macroorganism. Itwas shown that the genes of adhesins, siderophores, and immune system counteraction factors prevailed in E. coli. CONCLUSION: Further studies of E. coli strains using genome-wide sequencing and proteomics technologies are needed. The accumulation of the obtained data will make it possible to use virulence genes as diagnostic markers in patients with chronic prostatitis, indicating the presence of infection.

Humans↗

PubMed2026

A rapid molecular assay for the detection of hypervirulent Klebsiella pneumoniae in the context of antimicrobial resistance surveillance.

Hypervirulent Klebsiella pneumoniae (hvKP) represents an emerging clinical and public-health concern, particularly as hypervirulence increasingly converges with multidrug resistance. Current diagnostic approaches rely on phenotypic assays, such as the string test, or on whole-genome sequencing (WGS), both of which have limitations in specificity, turnaround time, standardization, and feasibility for routine surveillance. To address this gap, we developed a multiplex real-time PCR assay targeting key hvKP-associated virulence loci, including siderophore systems, hypermucoviscosity regulators, and additional markers linked to invasive potential. The assay was evaluated on 110 K. pneumoniae clinical isolates and 9 positive blood cultures, using WGS and the string test as comparators. The molecular panel demonstrated high concordance with WGS for principal virulence determinants, correctly identifying all high-virulence (score 4) profiles, and most intermediate profiles. Against WGS, the assay yielded a sensitivity of 82% and a specificity of 73%; performance against the string test was 96% and 87%, respectively. Direct testing from blood culture pellets yielded results consistent with both WGS and DNA-based PCR for the limited number of targets detected, supporting the technical feasibility of this approach. However, broader validation is needed to confirm performance in this specimen type. Overall, this multiplex PCR assay provides a targeted molecular screening approach for the rapid identification of hvKP-associated virulence profiles. Its agreement with genomic data supports its potential utility as an accessible complement to WGS for hvKP surveillance, although further workflow optimization will be required before broader routine implementation.IMPORTANCEThe global emergence of hypervirulent and multidrug-resistant K. pneumoniae represents a major public-health threat, as the convergence of virulence and antimicrobial resistance dramatically limits therapeutic options and increases the likelihood of severe, invasive, and potentially untreatable infections. Rapid identification of essential virulence determinants is therefore critical for timely clinical management and for preventing onward transmission. However, current diagnostic approaches are either insufficiently sensitive or require substantial resources, limiting their routine use. By providing a rapid and targeted molecular assay capable of detecting the principal loci associated with hypervirulent K. pneumoniae and by demonstrating the preliminary feasibility of its use directly on blood culture pellets previously identified as Klebsiella spp. by MALDI-TOF MS, this work provides a pragmatic approach for early virulence profiling. Implementation of such assays can significantly enhance epidemiological surveillance, support tailored patient management, and reduce the spread of high-risk K. pneumoniae lineages in both community and healthcare environments.

Klebsiella pneumoniae↗

PubMed2026

Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces.

The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.

Animals↗

PubMed2026

Genomic Characterisation of Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter hormaechei Clinical Isolates from Nigeria: Evidence of Resistance, Virulence, and Putative Plasmid-Mediated Gene Sharing.

The global proliferation of carbapenem-resistant Enterobacterales (CRE) constitutes one of the most urgent public health threats, yet high-resolution genomic data from sub-Saharan Africa remain critically scarce. We applied whole-genome sequencing (WGS) and comparative phylogenomics to characterise antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs) in three carbapenem-resistant clinical isolates originating from three tertiary hospitals (selected from a broader surveillance collection spanning four facilities) in Osun State, southwestern Nigeria. We purposively selected three isolates, two Klebsiella pneumoniae subsp. pneumoniae (K22, ST411; K31, ST17) and one Enterobacter hormaechei subsp. steigerwaltii (K32, ST45) from a broader surveillance collection of 27 carbapenem-non-susceptible Enterobacterales, to represent phenotypically and genotypically divergent lineages. Resistome analysis revealed extensive plasmid-associated β-lactam and aminoglycoside resistance in K31 (including blaCTX-M-15, blaOXA-1, and blaTEM-1). K32 harboured an intrinsic chromosomal blaACT-17 AmpC gene, while IS26 and ISEcp1 insertion sequences, consistent with transposon-mediated mobilisation, flanked its acquired aminoglycoside and sulfonamide resistance cassettes. K22 lacked detected acquired carbapenemase, ESBL, or plasmid-mediated AmpC genes, indicating that its carbapenem-resistant phenotype may involve non-carbapenemase mechanisms such as porin alteration or efflux-mediated reduced susceptibility; however, this mechanism requires confirmation by direct ompK35/ompK36 sequence analysis and/or phenotypic outer membrane protein profiling. Virulome profiling identified a broader repertoire of siderophore, adhesion, and biofilm genes in both K. pneumoniae isolates than in E. hormaechei. Phylogenomic analysis demonstrated that K22 and K31 cluster within the broader K. pneumoniae population framework but represent distinct high-risk lineages (ST411 and ST17) rather than a single clonal outbreak. Analysis also identified a shared plasmid backbone between K31 and K32, supporting interspecies horizontal gene transfer. These descriptive genomic findings identify clinically relevant resistance and virulence determinants in three purposively selected carbapenem-resistant Enterobacterales from Nigerian tertiary-care hospitals. The detection of shared resistance elements between K. pneumoniae and E. hormaechei suggests possible plasmid-mediated gene sharing. Still, larger WGS studies with long-read sequencing and patient-level epidemiological data are required to define transmission and dissemination patterns.

Nigeria↗

PubMed2026

The Small Noncoding RNA, RsaC, Is Essential for Staphylococcus aureus Virulence.

BACKGROUND: Bacterial small noncoding RNAs (sRNAs) play critical roles in virulence, stress adaptation, and host-pathogen interactions. Transcriptomic analyses during infection can help reveal pathogen-derived sRNAs required for pathogenesis, providing valuable insights for the development of novel therapeutic strategies. However, the low abundance of pathogen biomass within the host tissues poses a significant challenge for such analyses. METHODS: We employed 2-step cell disruption to enrich Staphylococcus aureus cells from infected mouse organs and conducted RNA sequencing (RNA-seq) analysis to examine staphylococcal sRNAs expressed during infection. qRT-PCR was used to confirm the gene expression. A knockout mutant of highly expressed sRNA, RsaC, was generated, and RNA-seq under in vivo as well as in vitro aerobic and anaerobic conditions were compared between the wild-type and ΔrsaC strains. Virulence of S. aureus was assessed using both mouse and silkworm survival assays. RESULTS: We identified RsaC as one of the most highly expressed sRNAs in mouse organs with consistent increment over time postinfection. Through gene disruption and complementation, we demonstrated that RsaC is an independent virulence determinant required for full pathogenicity of S. aureus in a murine infection model. In addition, RsaC influenced gene expression in response to oxygen availability and host-associated stress. Further analysis revealed that mutation of 2 genes downregulated in ΔrsaC in vivo, NWMN_RS03420 (sodium: proton antiporter) and NWMN_RS12015 (hypothetical protein), reduced S. aureus virulence in a silkworm model. CONCLUSIONS: These findings identify RsaC as a novel independent virulence determinant that supports S. aureus adaptation within the host.

Animals↗

PubMed2026

Comparative genomic analysis of Streptococcus parasuis and Streptococcus suis reveals mobile element-associated enrichment of antimicrobial resistance and lack of detectable same-MGE colocalization with virulence-associated genes within stable species boundaries.

Streptococcus suis is a major porcine pathogen and a zoonotic agent that causes meningitis and septicemia in humans. Streptococcus parasuis, a recently recognized close relative, remains poorly characterized with regard to its clinical significance and genomic features. In this study, we generated a single-contig closed genome assembly with genome-wide DNA methylation profiles for S. parasuis strain A1, isolated from a diseased pig in Xinjiang, China, and complemented in silico genomic predictions with isolate-level experimental validation of antimicrobial resistance (AMR) genotypes, virulence genotypes, and phenotypic susceptibility for this reference strain. Using this high-quality genome as a reference anchor, we performed comparative genomic analyses across 195 streptococcal genomes, comprising 15 S. parasuis and 180 S. suis strains, to distinguish genome-level co-occurrence of resistance and virulence determinants from their physical colocalization on the same mobile genetic element (MGE).Species boundaries remained clearly delineated at the genomic level, with a median interspecies average nucleotide identity (ANI) of approximately 86.0%, compared with intraspecies ANI medians of 97.5% for S. parasuis and 96.2% for S. suis. Pangenome analysis identified 12,693 gene clusters, of which 1086 were core clusters, and functional annotation revealed significant differences in accessory gene repertoires between the two species. Within this stable genomic framework, S. parasuis genomes carried a higher AMR gene burden; strain A1 harbored 10 AMR genes, multiple virulence-associated genes, three genomic islands, and eight prophage regions. For strain A1, PCR validation confirmed six AMR genes and six virulence genes, and disk diffusion testing demonstrated a multidrug-resistant phenotype consistent with the genotypic profile.Among 235 predicted mobile elements, 19 harbored AMR genes and seven carried Virulence Factor Database (VFDB) homologs, but none carried both categories simultaneously. This finding reflects a lack of detectable same-MGE colocalization under the applied annotation and assembly framework; it should not be interpreted as evidence of biological physical decoupling. Under a random-placement model, the expected number of co-carrying regions was only 0.57, and the probability of observing zero co-carrying regions was P = 0.55. This negative result should be interpreted with caution, given the limited number of cargo-bearing regions and the predominantly draft status of most genomes. Furthermore, the A1 genome contained multiple restriction-modification systems, showed depletion of several methylation motif families in mobile regions, and had limited CRISPR spacer matching evidence, suggesting prior exposure to the relevant sequence space. None of the genomes met our predefined criteria for whole-genome convergence.Collectively, our results support a model in which S. parasuis accumulates AMR-related genes in a modular fashion via mobile elements within stable species boundaries, with no detectable same-MGE colocalization of AMR and virulence determinants under our analytical pipeline. These findings imply that AMR surveillance strategies for this species should prioritize tracking mobile genetic elements rather than inferring wholesale genomic convergence toward S. suis.

Streptococcus suis↗

PubMed2026

Host life-history strategy is a critical determinant of virulent phage infection propensity.

Bacteriophages shape microbial communities through two major lifestyles: virulent (obligately lytic) and temperate (capable of lysogeny). Prevailing phage ecology frameworks focus on how environmental conditions, host density, and physiological state modulate infection modality. This perspective overlooks how host traits exert selective pressure on the distribution of virulent and temperate lifestyles across bacterial species, which limits understanding of phage ecology. To address this critical knowledge gap, we adopt a host-centric, trait-based perspective and use 5821 complete bacterial genomes to build a host life-history space predominantly defined by genome size, metabolic capacity, and growth rate potential. After mapping phage lifestyle association signals, prophage burden formed a continuous gradient across this space. Also, virulent phage association was positively correlated with prophage burden, revealing a nested structure of lifestyle signals. Functional trait analysis identified enrichment of resource-acquisition modules underlying both temperate and virulent associations. Overall, these findings indicate that phage lifestyle is significantly influenced by host life-history strategies, highlighting fast-growing, metabolically versatile hosts as favorable targets for virulent phage isolation and biocontrol applications.

Bacteriophages↗

PubMed2026

Genomic and virulence characteristics of Staphylococcus aureus isolates from foodborne outbreak cases.

This study aimed to investigate the genomic characteristics, enterotoxin production, and antimicrobial resistance profiles of Staphylococcus aureus isolates associated with foodborne outbreaks. A total of 19 bacterial isolates were collected from foodborne outbreaks in Guizhou Province, China between 2014 and 2023. Following biochemical identification, all isolates were confirmed as S. aureus. Phylogenetic analysis divided the 19 strains into seven branches. Enterotoxin production was detected using standard microbiological techniques and immunoassays. Antimicrobial susceptibility was evaluated using the broth microdilution method. Whole-genome sequencing and subsequent bioinformatic analyses were conducted to characterize virulence genes, antimicrobial resistance genes, multilocus sequence typing (MLST) genotypes, and phylogenetic relationships among the isolates. This study found that all strains produced classical staphylococcal enterotoxins, with staphylococcal enterotoxin (SEA) showing the highest detection rate (63.16%). Virulence gene profiling revealed widespread presence of hlb, hlgA, nuc, clfB, spa, and set genes. All strains were resistant to penicillin, with high resistance rates for erythromycin and cefoxitin. Multidrug resistance occurred in 11 of the 19 strains, and 22 resistance genes were identified. MLST analysis showed that ST6 and ST59 were the dominant types, with ST59 methicillin-resistant S. aureus (MRSA) strains displaying stronger resistance and more virulence determinants. These findings provide insights into the virulence, resistance, and molecular epidemiology of S. aureus strains involved in foodborne outbreaks, and may provide useful information for future surveillance and risk assessment.

Staphylococcus aureus↗

PubMed2026

Sungouiella purgamenti sp. nov., a yeast isolated from hospital wastewater in Brazil: a taxogenomic analysis.

Yeasts recovered from wastewater of a public hospital in Minas Gerais state, Brazil, included a single isolate representing a putative novel species. Sequence analysis of the ITS-5.8S region and the D1/D2 domains of the LSU rRNA gene placed this yeast within the genus Sungouiella, close to Sungouiella thailandica. Phylogenomic inference based on 1,849 single-copy orthologues from Sungouiella species with available genomes confirmed that strain UFMG-CM-Y7468 forms a distinct lineage with S. thailandica as its closest known relative. The name Sungouiella purgamenti sp. nov. (MycoBank MB 863665) is proposed, with CBS 19634 designated as the holotype. The isolate was able to grow at 37 °C, showed susceptibility to most antifungal agents tested, except for itraconazole with an MIC of 0.5 mg l-1, within the dose-dependent range, and exhibited strong extracellular protease activity. However, S. purgamenti showed a genomic toolkit consistent with a stress-tolerant and environmentally versatile lifestyle, while no specific or unique virulence determinants were identified based on genome content alone.

Brazil↗

PubMed2025

Strain-level differences in Gardnerella urinary tract persistence and pathogenesis are consistent with comparative phylogenomic analyses.

BACKGROUND: Gardnerella is a genus of gram variable anaerobic bacteria that is commonly present in the female urogenital tract, especially during bacterial vaginosis (BV). BV is linked with increased risk of urinary tract infections (UTI) and Gardnerella has been frequently detected in urine collected directly from the bladder. Understanding the contribution of Gardnerella to urogenital pathogenesis has been complicated by its genetic heterogeneity and a shortage of data from in vivo models. Recently, a clinical isolate of Gardnerella displayed covert pathogenesis in a mouse urinary tract inoculation model, triggering urothelial exfoliation and promoting UTI by uropathogenic E. coli. Data from clinical studies suggests differential association of Gardnerella phylogenetic clades with BV or urogenital infections. In vitro data has demonstrated heterogeneity in the presence and expression of putative virulence determinants between Gardnerella strains. This study was designed to compare diverse Gardnerella strains in vivo to identify genomic variation associated with urinary tract persistence and pathogenesis. METHODS: Eighteen Gardnerella clinical isolates from each of the four main phylogenetic clades were individually inoculated transurethrally into female C57BL/6 mice. Bacteriuria was monitored by quantitative culturing of Gardnerella in urine. Pathologic features were assessed by immunofluorescent and histological staining of bladder tissues. Pan-genome phylogenetic analyses were performed on the 18 Gardnerella isolates used for mouse infections to identify accessory genes that were associated with observable in vivo phenotypes, including long and short-term persistence, urothelial exfoliation and bladder edema. Genes that were significantly associated to phenotype were then matched against a pangenome analysis of 291 publicly available Gardnerella genomes to determine the conservation of these putative colonization and virulence factors across the genus. RESULTS: Gardnerella strains displayed clear differences in persistence and pathogenesis in the mouse bladder that were congruent with phylogeny. Clade 2 strains were more persistent in the urinary tract whereas strains from the other three clades either caused transient bacteriuria or were undetectable. Strains from clade 2 and 4 induced urothelial exfoliation while edema was triggered by strains from clades 2, 3 and 4. Pangenome analyses revealed 45 genes that were associated with in vivo persistence and pathogenicity. Among the wider 291 publicly available genomes, clade 2 strains encoded more of the genes associated with bacteriuria phenotypes compared to strains in the other three clades. Exfoliation-associated genes were present in most clade 4 strains. Clade 3 strains lack most of the in vivo-associated genes, whereas clade 1 strains were more heterogenous. CONCLUSIONS: This study provides in vivo evidence for differential urinary tract colonization and pathogenesis by strains from different clades/species within the genus Gardnerella and identifies new putative persistence and virulence factors. Utilizing the in vivo data from tested strains, pangenome analyses predicts that clade 2 Gardnerella are the most likely to persist in the urinary tract and that clades 2 and 4 have the highest uropathogenic potential. These findings inform future targeted screening and treatment approaches aimed at limiting harmful Gardnerella urinary tract exposures.

Journal Article↗

PubMed2026

First characterization of Staphylococcus felis in diabetic foot osteomyelitis: from intracellular persistence to phage treatment.

Staphylococcus felis is a coagulase-negative Staphylococcus (CoNS) primarily associated with the feline microbiota and only rarely reported in human disease. Here, we report its implication in diabetic foot osteomyelitis, and provide the first comprehensive characterization of its pathogenic potential. Two isolates (NSF001 and NSF002), recovered 5 months apart from bone biopsies of the same patient, were analyzed for growth kinetics, biofilm formation, and intracellular persistence in macrophages and osteoblasts. Both isolates proliferated efficiently, produced robust biofilm, and persisted within host cells, most markedly in osteoblasts. In a zebrafish embryo infection model, both isolates caused significant mortality, confirming their pathogenic potential in vivo. Whole-genome sequencing revealed conserved virulence determinants, a narrow resistome, and strain-specific genomic variations affecting genes involved in virulence regulation, phage defense, and iron acquisition. The lytic phage SAVM02, previously characterized for activity against other Staphylococcus species, effectively inhibited S. felis growth in vitro and conferred protection in vivo against lethal infection. Notably, the two sequential isolates differed in their in vivo virulence and phage susceptibility, paralleling these within-host microevolutionary changes and illustrating bacterial adaptation during chronic infection. Altogether, this study establishes S. felis as a CoNS capable of intracellular persistence, biofilm formation, and in vivo virulence in chronic human infection. Our findings also highlight the therapeutic potential of lytic phages against virulent CoNS species and support further investigation of phage therapy for chronic staphylococcal infections.IMPORTANCECoagulase-negative staphylococci (CoNS) are increasingly recognized as genuine agents of chronic infection, yet the pathogenic capacity of most individual species remains undefined. Staphylococcus felis, a commensal of cats only exceptionally reported in humans, had never been implicated in a chronic human infection. Here, we describe two sequential S. felis isolates recovered from bone biopsies of a patient with diabetic foot osteomyelitis and show that this species combines biofilm formation, intracellular persistence in macrophages and osteoblasts, and lethality in a zebrafish embryo model. Whole-genome comparison of the two isolates uncovered microevolutionary changes, most notably in iron-acquisition and genome-defense loci, that paralleled differences in virulence and phage susceptibility. These findings extend the list of CoNS capable of causing invasive human disease and provide a rationale for lytic phage therapy against emerging, difficult-to-treat staphylococcal pathogens.

Staphylococcus felis↗

PubMed2026

Whole-genome surveillance supports hazard profiling of Escherichia coli lineages in recycled water treatment systems.

UNLABELLED: The use of treated wastewater is increasingly important for sustainable water management under a changing climate, yet conventional monitoring based on Escherichia coli enumeration provides limited insight into strain diversity and associated public health hazards. Here, we applied longitudinal whole-genome sequencing (WGS) to 180 E. coli isolates collected across the treatment continuum of a recycled water facility, from influent to final effluent. Genomic analysis revealed extensive strain-level heterogeneity, comprising 88 sequence types across eight phylogroups, with greater diversity in influent than in treated effluent. Phylogenetic comparisons with contextual Australian genomes indicated clustering with strains associated with companion animals, wild birds, humans, and livestock, suggesting multiple potential source reservoirs rather than a single dominant origin, although source contributions were not definitive. Despite a >90% reduction in total E. coli loads, isolates recovered from upstream and downstream stages exhibited broadly comparable virulence factor and antimicrobial resistance gene (ARG) profiles, suggesting that, within the cultured isolate collection, reductions in abundance exceeded shifts in genomic composition. To assess operational relevance, we prototyped a genomics-informed hazard framework integrating virulence determinants, ARGs, plasmid-associated mobility, and reuse-specific exposure context. Using this framework, 92.8% of isolates were classified as low hazard, and 7.2% as moderate hazard, with no isolates meeting criteria for high or critical hazard classifications. These findings demonstrate that genomic profiling of indicator organisms can reveal population structure and hazard heterogeneity not captured by conventional enumeration alone, and can provide a practical basis for incorporating genomic information into hazard-informed monitoring of recycled water systems. IMPORTANCE: Routine recycled water monitoring relies largely on culture-based E. coli counts, which indicate regulatory compliance but provide limited insight into strain diversity, persistence, and genomic characteristics relevant to public health. Using longitudinal whole-genome sequencing, we show that genetically distinct E. coli lineages, including isolates carrying combinations of virulence and antimicrobial resistance determinants, can persist through advanced treatment despite substantial reductions in overall E. coli loads. While most isolates were classified as low genomic hazard and no high- or critical-hazard isolates were detected, these findings demonstrate that conventional enumeration alone cannot distinguish between genetically diverse lineages with differing hazard potential in highly treated systems. By integrating genomic data into a hazard classification framework, this study demonstrates an applied approach to contextualize E. coli detections and distinguish low-risk background populations from isolates with elevated genomic hazard profiles. This work supports the use of genomic profiling of indicator organisms to improve surveillance, inform treatment performance assessment, and enable more risk-based management of recycled water systems.

Escherichia coli↗

PubMed2026

From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.

A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.

Animals↗

PubMed2026

A plasmid-associated immunoglobulin-binding protein in Acinetobacter baumannii.

BACKGROUND: Acinetobacter baumannii is a critical global health threat due to multidrug resistance and high mortality. Although antimicrobial resistance mechanisms are well characterised, the virulence determinants that drive severe infections remain poorly understood. METHODS: We screened 89 carbapenem-resistant clinical isolates of A. baumannii for virulence in animal infection models and combined comparative genomics with functional assays to identify virulence factors. An immunoglobulin-binding protein from A. baumannii (ImbA) encoded on the type D plasmid was selected and characterised. Protein-immunoglobulin interactions were analysed by pull-down and biolayer interferometry. Additional ImbA inhibition of IgG-Fcγ receptor binding by flow cytometry were tested. Protective efficacy was evaluated in mice using vaccination or anti-ImbA antibodies. FINDINGS: A type D plasmid was consistently linked to high virulence in clinical isolates. The deletion of plasmid-encoded ImbA attenuated virulence. ImbA bound murine IgA and IgG with high affinity. The binding to the Fc region of IgG disrupted IgG-Fcγ receptor interactions. Vaccination with recombinant ImbA improved survival and reduced bacterial dissemination in female mice with anti-ImbA antibodies partially protecting against lethal infection. Bacterial burdens in the blood were reduced in treated groups. INTERPRETATION: Our study demonstrates ImbA as an unrecognised plasmid-encoded virulence factor in A. baumannii. By intercepting host immunoglobulins, ImbA drives immune evasion and hypervirulence. Blocking ImbA by vaccination and antibody therapy restored host defence and improved outcomes in female mice, highlighting ImbA as a non-antibiotic therapeutic target with potential against multidrug-resistant A. baumannii. FUNDING: Bio&Medical Technology Development Program of the National Research Foundation (NRF), funded by the Korean government (MSIT) (No. RS-2023-00219213); Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program.

Animals↗

PubMed1978

[Hyaluronidase in meningococcus].

A total of 204 meningococcus strains were tested for the presence of hyaluronidase, and 45.5% of the strains were found to contain it. Strains penetrating into the cerebrospinal fluid were the ones which largely produced the enzyme (in 83% of the cases). The enzyme was revealed only in 25.5% of the strains habituating on the nasopharyngeal mucosa. Hyaluronidase was mostly found in the meningococcus strains referred to the serological group A; strains of other serological groups and ungrouped strains produced the enzyme in 23.7% of the case only. There was no correlation between the capacity to form hyaluronidase and the virulence determinable in intraperitoneal infection of mice.

Hyaluronoglucosaminidase↗

PubMed2026

The AAA+ chaperone ClpB contributes to stress tolerance and pathogenesis in Mycoplasma bovis.

ClpB, an ATP-dependent molecular chaperone belonging to the Hsp100/Clp subfamily of AAA+ ATPases, plays a crucial role in protein disaggregation, thereby enhancing bacterial survival under stress conditions. Despite its well-conserved function in prokaryotes, the specific contributions of ClpB to the pathogenesis of the ruminant pathogen Mycoplasma bovis remain largely unexplored. In this study, we identified and functionally characterized a ClpB homolog in M. bovis. Biochemical assays confirmed that the recombinant ClpB protein exhibits intrinsic ATPase activity and, in cooperation with the DnaK chaperone system, efficiently mediates protein disaggregation in vitro. Through genome-wide transposon mutagenesis of the M. bovis HB0801 strain, we generated ClpB-deficient mutants that maintained normal growth kinetics and morphology at 37 °C but exhibited significant growth defects under thermal and oxidative stress conditions. Phenotypic analysis demonstrated that ClpB disruption attenuated key virulence traits, including impaired adhesion to host cells, marked reduction in biofilm formation, diminished pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) expression in BoMac cells. Furthermore, the reduced virulence of the ClpB mutant was investigated by DIA proteomic analyses, which revealed that the ClpB mutant strain altered distinct protein expression patterns related to proteostasis, including phosphotransferase system, serine-type peptidase activity, serine hydrolase activity, and chaperone-mediated protein folding that contribute to the stress response and virulence. These findings collectively demonstrate that ClpB serves as a multifunctional virulence determinant in M. bovis, orchestrating stress adaptation, host-pathogen interactions, and pathogenic potential through modulation of both protein quality control systems and virulence-associated pathways.

Mycoplasma bovis↗

PubMed1979

Capsular K1 polysaccharide of Escherichia coli: relationship to virulence in newborn rats and resistance to phagocytosis.

The virulence of Escherichia coli strains for newborn rats was related to opsonic requirements of the strains, sensitivity to the bactericidal activity of serum, and K1 capsular polysaccharide content. K1 E. coli strains were more virulent than non-K1 strains after intraperitoneal injection in newborn rats (P less than 0.05) and were more resistant to phagocytosis than non-K1 strains when the classical complement pathway was blocked with Mg-ethyleneglycoltetraacetic acid (P less than 0.0005). Sensitivity to the bactericidal activity of serum was similar among K1 and non-K1 E. coli strains. Two groups of K1 E. coli strains were defined on the basis of opsonic requirements. Group I strains were efficiently opsonized by the alternative complement pathway, while group II strains required the classical complement pathway for opsonization. Group I strains had less detectable K1 polysaccharide in the washed whole cell fraction than group II strains (10.3 versus 18.9 microgram of K1 polysaccharide per 10(10) colony-forming units) and were less virulent than group II strains (mortality, 44 versus 77%, P less than 0.05). The K1 capsular polysaccharide appears to play an important role in determining virulence in newborn rats and opsonic requirements of these strains, but does not contribute to the sensitivity of strains to the bactericidal activity of serum.

Animals↗