Microbiology laboratories play a critical role in the diagnosis and management of infectious diseases. However, recent advancements aimed at reducing human workload and minimizing time loss are gaining popularity. Artificial intelligence (AI) technologies, particularly machine learning (ML) and deep learning (DL), have been reported to contribute significantly to microbial laboratory diagnostics. Through this approach, molecular methods, genetic sequencing, microbiological meta-analyses, and related fields benefit from faster and more accurate analytic capabilities. In addition to diagnostic applications, AI is increasingly used in genomics, metagenomics, antimicrobial resistance (AMR) prediction, and drug and vaccine discovery, enabling more comprehensive and data-driven microbiological analysis. This review comprehensively evaluates current AI applications in microbiology, highlighting their advantages, limitations, and implementation challenges. It further examines the suitability of different AI methodologies for specific laboratory tasks and compares AI-driven approaches with conventional expert-based practices. Finally, the study emphasizes the complementary roles of AI systems and human expertise, underscoring their synergistic potential to improve diagnostic accuracy, efficiency, and clinical decision-making.
Precise characterization of Escherichia coli isolates plays a crucial role in the treatment and prevention of diseases in animal production. The classical diagnostic approach to define pathotypes of E. coli relies on detection of virulence genes. However, by targeting a limited set of genetic markers, routine PCR-based approaches may hinder the detection of atypical pathogenic isolates, especially in bacteria with high genomic plasticity. Genomic approaches were used to characterize a hybrid ETEC/ExPEC E. coli strain isolated from lambs submitted for necropsy over the course of six months, during an investigation of persistent neonatal mortality. Most lambs submitted for necropsy showed lesions suggestive of a septicemia. Routine PCR analysis detected genes encoding two ETEC-associated toxins but none of the ExPEC-associated virulence genes commonly targeted in routine diagnostics. Whole-genome sequencing revealed a diverse set of virulence genes, consistent with the hybrid nature of the strain. Genes encoding toxins were located on plasmids, while ExPEC-associated virulence factors were found to be chromosomally encoded. Genomic analyses revealed rapid antimicrobial resistance evolution, driven by plasmid acquisition. This case highlights how horizontal gene transfer promotes the development of hybrid pathotype and facilitates resistance genes acquisition, compromising traditional diagnostic approaches and treatment. ExPEC strains are particularly difficult to identify due to their diverse and ill-defined virulence markers, which are not always targeted by standard genotyping tests. Emergence of atypical E. coli strains such as those with hybrid pathotypes reinforces the need for more comprehensive methods such as whole-genome sequencing in veterinary diagnostics.
Canine transmissible venereal tumor (CTVT), also known as transmissible venereal sarcoma, is a naturally occurring, contagious neoplasm primarily transmitted by the transfer of viable tumor cells during mating. Although the disease is widely distributed worldwide, epidemiological and clinicopathological data from Central Asia remain scarce. This study aimed to characterize the epizootological distribution, clinical manifestations, hematological and biochemical alterations, microbiological findings, and morphological features of CTVT in dogs presented to a Veterinary Diagnostic Center in Astana, Kazakhstan. A prospective observational study was conducted from February 2024 to February 2025. A total of 2,500 dogs were screened, and 425 dogs with tumor-like lesions underwent clinical, laboratory, cytological, histopathological, and microbiological investigations. Twenty-three dogs with confirmed CTVT were included in the final analysis. Animals were categorized according to the presence (n = 13) or absence (n = 10) of purulent complications. Clinical examination, complete blood count, serum biochemical analysis, cytological evaluation using smear-imprint and fine-needle aspiration techniques, histopathological assessment, and microbiological testing were performed. Statistical analyses included Student's t-test, Mann-Whitney U test, Fisher's exact test, and odds ratio estimation, with significance set at p < 0.05. CTVT accounted for 23 of 425 tumor-bearing dogs (5.4%). The disease was more frequently observed in males (73.9%) and in dogs aged 1.5-5 years (65.2%). Mixed-breed dogs represented the largest affected group (47.8%). Clinically, all dogs exhibited friable genital masses accompanied by hemorrhagic discharge, while purulent exudation occurred in 56.5% of cases. Extragenital involvement was identified in 8.7% of dogs. Animals with purulent complications showed significantly elevated heart rate and respiratory rate (p < 0.001), leukocytosis, reduced hemoglobin concentration, and lower hematocrit values. Biochemical analysis revealed increased concentrations of urea, creatinine, alanine aminotransferase, aspartate aminotransferase, bilirubin, and alkaline phosphatase in dogs with purulent lesions. Cytological examination demonstrated round tumor cells with eccentrically positioned nuclei, coarse chromatin, prominent nucleoli, abundant cytoplasmic vacuoles forming a characteristic "string-of-pearls" pattern, and marked mitotic activity. Histopathological findings confirmed the diagnosis and supported the observed cytomorphological features. This study provides the first comprehensive clinicopathological, epizootological, microbiological, and morphological characterization of CTVT in dogs from Kazakhstan. Male sex, reproductive age, and inadequate reproductive control were associated with disease occurrence. Cytoplasmic vacuolization and high mitotic activity were reliable morphological indicators of CTVT. The findings provide valuable baseline data to improve diagnosis, surveillance, and disease management strategies in Central Asia.
The gut-brain axis (GBA) represents a paradigm shift in veterinary neuropharmacology, offering novel approaches for managing neurological and behavioural disorders in companion animals. This review synthesizes current evidence on the bidirectional communication between the gut microbiome and the central nervous system, examining the neural, endocrine, immune, and metabolic pathways that facilitate this dialogue. We explore the unique aspects of canine and feline microbiomes and their implications for species-specific drug development and critically evaluate emerging pharmacological strategies, including psychobiotics, prebiotics, synbiotics and faecal microbiota transplantation (FMT), highlighting their clinical applications in conditions ranging from anxiety and aggression to cognitive dysfunction and epilepsy. This narrative review followed established guidelines for evidence synthesis in veterinary medicine. A comprehensive literature search was performed using PubMed, Google Scholar and Scopus databases covering publications from January 2011 to March 2026. While promising results have been demonstrated with specific strains, such as Bifidobacterium longum BL999 and Lactiplantibacillus plantarum PS128, significant challenges remain. These include methodological limitations in microbiome research, the predominance of correlative over causal evidence and the need for standardized diagnostic tools. Future directions must prioritize large-scale longitudinal studies, robust clinical trials and advanced multi-omics approaches to establish causal mechanisms and develop personalized, microbiome-targeted therapies. Realizing this potential requires a shift from correlative data to causal mechanisms, from a one-size-fits-all approach to species-specific therapeutics and from rodent models to rigorous trials in dogs and cats.
This study characterized the bacterial epidemiology and antimicrobial resistance profiles of 448 isolates recovered from feline urine cultures in Rio de Janeiro, Brazil, between 2020 and 2024. Antimicrobial susceptibility was assessed by disk diffusion and interpreted according to CLSI VET01S and Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST) breakpoints. Escherichia coli was the predominant pathogen (45.1%), followed by Proteus spp. (16.3%) and Klebsiella spp. (12.5%). Resistance to antimicrobials recommended as first-line options by the ISCAID guidelines was frequent among E. coli isolates, including trimethoprim-sulfamethoxazole (57.2%), cephalexin (52.5%), and amoxicillin-clavulanate (43.9%). Veterinary fluoroquinolones showed moderate resistance (enrofloxacin 28.5%, marbofloxacin 20.9%), while nitrofurantoin resistance reached 37.7%. Third-generation cephalosporins and carbapenems retained the highest activity (ceftazidime 13.2%; meropenem 0%). Multidrug resistance (MDR) was observed in 55.8% of all isolates, with the highest prevalence in Proteus spp. (79.5%) and E. coli (57.9%). Resistance to third-generation cephalosporins was detected in 22.8% of E. coli isolates, and carbapenem resistance was detected in 5 isolates from different species. These findings indicate that resistance to first-line agents is common in feline uropathogens in this setting and support the routine use of urine culture and antibiotic susceptibility testing to guide antimicrobial therapy.
Antimicrobial resistance (AMR) in swine poses a threat to animal health and food safety. Escherichia coli is commonly used as an indicator organism for AMR surveillance; however, comparative data across anatomical sites in swine remain limited in countries with intensive antimicrobial use, such as Vietnam. This study aims to characterize phenotypic AMR and multidrug resistance (MDR) in E. coli isolated from faecal and uterine samples of swine in Northern Vietnam and to compare AMR patterns between sample types and across seasons. Samples submitted to a veterinary diagnostic laboratory in Northern Vietnam between February 2023 and November 2024 were cultured for E. coli. Isolates were tested for antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. The tested antimicrobials represented five major classes: β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and folate-pathway inhibitors. Descriptive analyses and logistic regression models assessed AMR and MDR profiles and associations with sample type and season. A total of 211 E. coli isolates (96 faecal and 115 uterine) were identified. High resistance was observed to ampicillin (96.7%), tetracycline (95.7%), gentamicin (80.1%), sulfamethoxazole/trimethoprim (80.1%), and enrofloxacin (73.5%). Significantly higher odds of AMR were observed in faecal isolates for ceftiofur, enrofloxacin, norfloxacin, and sulfamethoxazole/trimethoprim (odds ratios: 1.38-4.62). Higher odds of resistance to ceftiofur and gentamicin were observed during the winter months. High AMR was observed in E. coli from swine in Northern Vietnam, with faecal isolates having a significantly higher resistance than uterine isolates, likely reflecting selection pressure in the intestinal tract or differences between commensal and extraintestinal E. coli populations.
Preweaning diarrhea and intestinal inflammation represent leading causes of morbidity and economic loss in modern dairy calf production systems, causing impaired growth performance, increased mortality, and substantial veterinary costs that collectively constrain farm profitability. Faecalibacterium duncaniae, a key butyrate-producing commensal bacterium, is consistently depleted in diarrheic dairy calves, yet its protective effects on the ruminant intestinal epithelium remain mechanistically understood. In this study, a long-term expandable ruminant colonic organoid model was used to investigate the effects of F. duncaniae-derived metabolites under inflammatory conditions induced by tumor necrosis factor-α (TNF-α). TNF-α stimulation caused epithelial injury characterized by elevated inflammatory cytokine expression, impaired barrier function, and increased epithelial permeability. Treatment with F. duncaniae cell-free supernatant markedly attenuated inflammatory responses, restored epithelial proliferation, and preserved tight junction integrity, as evidenced by reduced permeability and increased expression of barrier-related proteins. Transcriptomic analysis further indicated suppression of inflammation-associated signaling pathways, including chemokine signaling and NF-κB pathways, accompanied by enrichment of energy metabolism and epithelial repair pathways, thereby creating a molecular environment conducive to epithelial barrier improvement and repair. In addition, comparison with the bacterial culture medium and the single metabolite sodium butyrate (NaB) further supported the role of F. duncaniae-derived metabolites in barrier repair. Collectively, these findings demonstrate that F. duncaniae-derived metabolites protect intestinal epithelial integrity under inflammatory stress and provide mechanistic and translational support for microbiota-targeted nutritional strategies to improve gut health in dairy calves, thereby establishing a foundation for the development of postbiotic-based interventions aimed at reducing diarrhea incidence, decreasing antimicrobial dependence, and enhancing growth efficiency and long-term productivity in dairy systems. Dairy calves are highly susceptible to severe impacts from diarrhea and intestinal inflammation before weaning, leading to malnutrition, dehydration, and even death. The costs associated with enteritis, including mortality, productivity losses, and treatment expenses, have been rising annually. Therefore, the treatment and prevention of enteritis are of paramount importance. Faecalibacterium duncaniae, a beneficial bacterium that produces butyrate, plays a crucial role in maintaining gut health. However, its specific protective mechanisms in intestinal inflammation remain poorly understood. This study reveals the molecular mechanisms by which F. duncaniae metabolites protect the intestinal barrier under inflammatory stress, providing valuable insights into how microbiota-based nutritional interventions can enhance gut health in neonatal and preweaning dairy calves. These strategies may offer innovative approaches to managing calf intestinal diseases, improving their health and growth, and enhancing overall productivity in dairy farming.
The advancement of synthetic biology and the rise of antimicrobial resistance have led to the development of bacteriophage therapy for more than antibacterial applications. This review focuses on applications to multidrug-resistant infections, biofilm diseases, cancer research, veterinary medicine and animal production. Recent research suggests phages can be used in combination with antibiotics to enhance treatment of large multidrug resistant pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae. This could also help to restore antibiotic sensitivity by making bacteria change resistance related structures or mechanisms. Despite this, there are several challenges for the use of phage therapy prior to its widespread clinical application, including phage resistance, difference in patient response, unknown pharmacokinetic parameters, immune issues, and unclear regulatory guidelines. Additionally, in some cases, phages could also play a role in horizontal gene transfer, raising further safety concerns. Beyond antimicrobial therapy, phage display platforms derived from M13, T7 and λ phages have enabled the identification of tumor-targeting peptides, the development of immunomodulatory constructs, and targeted delivery of therapeutic molecules. Over 100 clinical cases and 44 registered trials support the generally favorable safety profile of personalized phage therapy, and highlight the need for better treatment standardization, controlled clinical evaluation, and better regulatory processes. Additionally, engineered phages expressing biofilm degrading enzymes represent promising tools for disrupting matrix-embedded bacterial communities associated with chronic infections and medical devices. In summary, CRISPR-based engineering and genome refactoring highlight the potential of phage-based therapeutics as complements to conventional antimicrobial therapy, although their broader use depends on overcoming biological, clinical, and regulatory challenges.
Aqueous deficient dry eye disease (ADDE) results from a quantitative reduction in aqueous tears. We sought to determine the clinical effect of autologous mesenchymal stromal cell (MSC) injections into the region of the lacrimal gland and the gland of the third eyelid in immunomodulatory-dependent ADDE-affected dogs. Dogs (n = 4) were enrolled that met the inclusion criteria for ADDE (consistent clinical signs combined with Schirmer tear test I [STT-I] value < 15 mm/min, responsive to topical immunomodulatory therapy, and documented drop in STT-I after cessation of therapy). By applying these stringent criteria, there was a high failure rate for inclusion. Autologous MSCs were harvested, expanded, and unilaterally injected after cessation of immunomodulatory therapy. Examinations, ophthalmic diagnostics, clinical scoring, and owner surveys were performed at regular intervals post-injection. No adverse ocular events were associated with the MSC injections. There were variable responses between dogs, with one dog exhibiting an immediate increase in STT-I that remained elevated (5.5-fold increase); two dogs had a smaller and temporary increase in STT-I over baseline (0.6-0.7-fold increases), and one dog had no increases detected over the initial 6 months. Repeated injections did not improve clinical or diagnostic values. Autologous MSC injections were well-tolerated in dogs with ADDE. Results were variable in this small sample size. Despite initial improvement in 3 of 4 dogs, the positive response was variable in magnitude of response and duration of effect. Repeated injections did not sustain this response. Future studies using conditioned MSCs and/or exosomal therapy are warranted.
Airborne transmission contributes substantially to the spread of avian respiratory viruses, yet standardized and field-validated air sampling methods remain limited. Although significant efforts focus on improving the detection of avian influenza virus on farms, the rapid identification of other prevalent avian respiratory viruses is essential. This study systematically assessed the performance of cellulose-based, polytetrafluoroethylene (PTFE), and gelatin filters for capturing and recovering avian metapneumovirus (aMPV), infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), and Newcastle disease virus (NDV). Laboratory assays using viral dilutions spiked onto filter surfaces were conducted to optimize elution conditions and to compare viral titer losses across different filter types. PTFE and gelatin filters consistently achieved the highest viral recovery rates in laboratory conditions and were subsequently field-tested in a commercial breeding hen farm. Under these conditions, using both impactor-based air samplers and passive sampling, the optimized PTFE and gelatin filters enabled early detection of low-pathogenicity IBV strains in environmental samples, even in the absence of clinical signs. This demonstrates the sensitivity of the approach for identifying low-level viral circulation. Individual hen sampling and qPCR assays confirmed the presence of IBV GI-12 and IBV G1-13 in cloacal swabs, while inoculation of embryonated eggs demonstrated viable virus in a subset of cloacal samples. Collectively, these findings demonstrate that appropriate filter selection and sample processing protocols are essential for reliable environmental viral detection. They support implementing air sampling as a practical component of routine surveillance and biosecurity programs against prevalent avian respiratory viruses beyond influenza.
Atlantic cod possess a unique immune system due to the loss of the MHC II antigen-presenting system and an extreme expansion of the MHC class I repertoire. Additional modifications are demonstrated within the innate immune system with losses and expansions of Toll-like receptor (TLR) genes. While Atlantic cod has lost its mammalian orthologs for plasma membrane localized TLRs, such as TLR1/6 and TLR2, it has expanded its intracellular TLRs including TLR7, -8, and -9. It has been hypothesized that teleost-specific TLR1-family related members TLR14 and TLR25 localize at the plasma membrane with the potential function to recognize bacterial surface components, compensating for the loss of cell surface TLRs. In this study, we have investigated the intracellular localization and function of Atlantic cod TLR14 and TLR25 using super-resolution microscopy in an Atlantic cod cell line and primary cells. Our results show that these TLRs localize to endolysosomes, and colocalize with LysoTracker, Rab5, and Rab7. Interestingly, TLR14 is also present at the plasma membrane, suggesting a function at the cell surface. In cells infected with Francisella noatunensis subsp. noatunensis (Fnn), these TLRs colocalize with the internalized bacteria. While the localization of both TLR14 and TLR25 to late endosomal compartments increases upon infection with Fnn, only TLR25 relocates to the perinuclear region and triggers up-regulation of the pro-inflammatory cytokines IL-6 and IL-18. Overall, our findings provide novel insight into the function of teleost-specific TLRs in Atlantic cod which indicates that these TLRs employ different strategies for microbial detection and activation.
Odor emissions from animal waste represent a persistent challenge in livestock production, with implications for animal welfare, environmental quality, and the societal sustainability of farming. These emissions are primarily driven by volatile organic compounds (VOCs) generated through microbial degradation of feces and urine, including ammonia, sulfur-containing compounds, volatile fatty acids, and aromatic metabolites. Conventional odor control strategies rely largely on physical, chemical, or management-based approaches, which often provide inconsistent or short-term mitigation and raise concerns regarding cost and sustainability. Advances in microbiome research have highlighted the central role of gut-associated and manure-associated microbial communities in shaping VOC production, positioning microbiome engineering as a promising novel biological alternative for odor mitigation. This review synthesizes current knowledge on microbiome-based strategies targeting VOCs in animal waste, including dietary modification, probiotic and functional microbial consortia approaches, as well as post-excretion bioaugmentation. This review evaluates also the microbial basis, health and biosecurity relevance, and practical limitations of these mitigation strategies. While microbiome engineering shows considerable potential, its effectiveness remains highly context dependent, and broader adoption is constrained by variability across production systems and limited farm-scale validation. Future interventions will require mechanism-driven research, standardized methodologies, and integration within comprehensive waste management frameworks to support sustainable livestock production.
Photocatalytic degradation of perfluorooctanoic acid (PFOA) has drawn great attention in the past. These studies have focused on developing high-efficacy photocatalysts and understanding the reaction mechanisms and structure-performance relationships. However, the photocatalytic degradation efficacy and kinetics under environmentally relevant conditions and the reduced toxicological impact of degraded PFAS products are lacking. To fill in this gap, we developed a photocatalytic system to deconstruct perfluorooctanoic acid (PFOA) under ambient conditions using sunlight as a renewable energy source. We evaluated the degradation pathway and reaction mechanisms using high-resolution mass spectrometry (LC/MS-MS) and product portfolio. The photocatalytic degradation of PFOA in environmental water matrices was set up over a two-week period using natural sunlight outdoors. The toxicity of degraded products was assessed in parallel using duckweed, or Lemna minor as a representative ecotoxicological assay during the same time course. Degraded products containing shorter carbon chain PFAS such as perfluoroheptanoic acid (PFHpA, C7) and perfluorohexanoic acid (PFHxA, C6) showed significantly reduced toxicity to L. minor, compared to untreated PFOA water. In the day and night cycles of PFOA photocatalytic treatment using natural sunlight, the measured toxicity of the photocatalytic reaction system continued to decline during the two-week period. However, the concentrations of measured PFAS, including degraded products of PFHpA and PFHxA, remained stable after six days for a period of 2 weeks. Our study suggested another potential detoxification mechanism exists with prolonged treatment, which leads to continuously reduced toxicity. Our results highlighted the need for a systematic approach combining analytical chemistry for degradation mechanisms and ecotoxicological models to perform time-dependent toxicological assessments of PFAS destruction.
Neonatal calf diarrhoea (NCD) is a major cause of morbidity and mortality in cattle worldwide, with group A rotaviruses (RVA) recognised as a principal viral aetiological agent. Despite extensive genotyping studies, the relationship between RVA genotypes, segmental phylogenetic patterns, lineage-level diversity, and intestinal pathology in fatal cases remains poorly defined, particularly in Türkiye. In this study, RVA strains detected in fatal NCD cases were investigated through integrated molecular characterisation of the VP7, VP4, and VP6 genes and histopathological examination of small intestinal tissues. Phylogenetic analyses revealed G6-P[1]-I2 and G8-P[1]-I2 genotype constellations and demonstrated segment-specific phylogenetic incongruence, with discordant clustering patterns between VP7 and VP4/VP6 gene segments, consistent with reassortment. Notably, G8 strains clustered within multi-host-associated lineages, including bovine-like human and caprine RVA strains, suggesting potential interspecies transmission dynamics, whereas G6 strains were associated with more host-restricted bovine lineages. Histopathological findings, including villus atrophy, epithelial desquamation, crypt necrosis, and lymphoid depletion, were consistent across cases and showed no genotype-associated differences. These findings highlight reassortment as a key driver of bovine RVA evolution and demonstrate that lineage-level diversity may reflect host adaptation and cross-species transmission processes. The integration of molecular epidemiology with pathological assessment provides a more comprehensive understanding of RVA-associated disease. It supports the need for coordinated surveillance of bovine and multi-host RVA populations.
Mobile colistin resistance determinants (mcr) in ESBL-producing Enterobacterales represent a public health concern, given the renewed reliance on colistin as a last-resort agent for multidrug-resistant Gram-negative infections. To resolve the genetic context and transferability of colistin resistance in an ESBL-producing Enterobacter mori isolate (SH93I1) recovered from seafood (MIC of 8 mg/L). We characterized the location, genetic environment and mobility of the colistin resistance determinant in SH93I1 using hybrid whole-genome sequencing (short- and long-read data), comparative genomics, in vitro conjugation to Escherichia coli MG1655 and gene cloning in E. coli DH5α. E. mori SH93I1 carried a novel mcr allele, designated mcr-11.1 according to current classification criteria. The allele shared 91% nucleotide identity and 93% predicted amino acid identity with mcr-9.1. mcr-11.1 was located on a 328 kb non-typeable conjugative plasmid that also carried blaCTX-M-14. The mcr-11.1 region formed a 25.5 kb segment bracketed by IS3-family elements and included wbuC-qseBC-vapBC and the arnBCADTEF operon. Conjugation experiments confirmed plasmid transfer, with co-transfer of resistance phenotypes; however, colistin MICs were not increased in the E. coli MG1655 transconjugants or in E. coli DH5α strains expressing mcr-11.1, alone or with wbuC and qseBC. We describe mcr-11.1 on a large conjugative plasmid in E. mori from seafood, with evidence consistent with mobilization of a chromosomal fragment from L. adecarboxylata. Although mcr-11.1 did not increase colistin MICs in E. coli, its presence on a multidrug-resistance plasmid highlights the potential for dissemination under co-selection and future adaptation in clinically relevant hosts.
Shiga toxin-producing Escherichia coli (STEC) represent a genetically diverse group of pathogens whose virulence is largely driven by mobile genetic elements (MGEs), including plasmids and bacteriophages. While horizontal gene transfer is central to STEC evolution, the extent to which virulence-associated MGEs circulate within natural reservoirs remains poorly understood. In this study, we investigated the diversity, distribution and lineage associations of MGEs in a collection of 73 E. coli strains isolated from cattle in France, a major reservoir for pathogenic STEC. Using both short-read and long-read whole-genome sequencing, we characterized plasmid content, prophage repertoires and stx-encoding phages and examined their relationships with strain phylogeny. We observed a high diversity of plasmids, with individual strains carrying up to four large plasmids, alongside an even greater diversity of prophages. Despite this diversity, some associations were identified between specific virulence plasmid groups, Stx phage types and defined pathogroups or lineages. These patterns were supported by the congruence between core-genome and accessory-genome phylogenies, suggesting long-term evolutionary coupling rather than frequent exchange of entire MGEs. In contrast, some non-virulence plasmids were broadly distributed, consistent with more general selective advantages. Notably, we identified enterohaemorrhagic E. coli strains (stx- and eae-positive strains) in atypical phylogenetic backgrounds, highlighting the capacity for virulence determinants to emerge in diverse lineages, while underscoring the constraints that limit their stable establishment, as their long-term persistence appears limited to specific genetic backgrounds. Together, our findings indicate that the circulation of virulence-associated MGEs in the bovine reservoir is constrained by ecological and evolutionary factors.
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Aeromonas species are important opportunistic pathogens in freshwater aquaculture, including Polish fish farms, where outbreak-associated isolates have been assigned to local provisional serogroups. Among these, PGO1 is frequently detected, but the structural and genetic diversity of the corresponding O-specific polysaccharides remains poorly understood. Here, we characterized Aeromonas sobria strain K221, a PGO1 isolate recovered from common carp during an outbreak of motile Aeromonas infection/septicaemia. The O-specific polysaccharide (OPS), isolated from LPS, was analysed by chemical methods and 1H/13C NMR spectroscopy, and its O-repeating unit was identified as a linear pentasaccharide containing β-GlcpNAc, 2-O-acetylated α-Rhap, and α-Abep residues. Bioinformatic analysis of the O-antigen gene cluster (OGC) revealed gene content consistent with the OPS structure and supported functional assignment of the biosynthesis locus, including a putative α-1,3-CDP-abequosyltransferase. Both the OPS and its OGC differed from those of other recently characterized PGO1 strains, indicating that K221 represents a distinct variant within this serogroup. The occurrence of 2-substituted abequose, not previously reported in Aeromonas O-polysaccharides or as a 2-substituted residue in bacterial O-polysaccharides, highlights an unusual structure-biosynthesis relationship. These findings reveal greater structural and genetic diversity within the Aeromonas PGO1 serogroup than previously recognized and expand current knowledge of bacterial O-specific carbohydrate polymers.
Escherichia coli is predominantly an intestinal commensal; however, avian pathogenic E. coli (APEC) causes colibacillosis in poultry. The APEC pathotype lacks a clear genetic definition, further complicated by its opportunistic nature. To compare the genomic characteristics of avian pathogenic and commensal E. coli, isolates from diseased and healthy broiler flocks in Sweden were analysed, collected between 2022 and 2024. Clinical isolates (n=202) were collected at necropsy from 40 flocks during colibacillosis outbreaks, and non-clinical isolates (n=109) were obtained from litter using sock sampling in 60 unaffected flocks. Whole-genome sequencing was performed to determine sequence types (STs), serotypes, phylogroups, virulence-associated genes (VAGs) and to identify ColV plasmids. A five-gene APEC marker panel targeting plasmid-associated virulence genes (iutA, hlyF, iss, iroN and ompT) was used to classify isolates as APEC or non-APEC, and high-risk clones were identified according to the APECtyper scheme. Clinical isolates comprised 22 STs and 25 serotypes and were dominated (59%) by the ST23 O78:H4 clone within phylogroup C. Non-clinical isolates were more diverse (44 STs, 67 serotypes), primarily within phylogroups A (48%) and B1 (33%), with no clone predominating. Clinical isolates carried significantly more VAGs (P<0.001). Overall, 97% of clinical isolates were identified as APEC, all of which carried a ColV plasmid. Among non-clinical isolates, 28% were APEC, of which 80% were ColV-positive. However, clinical APEC isolates carried significantly more ColV-associated virulence gene clusters than non-clinical APEC isolates (P<0.001). Only 5% of non-APEC isolates were ColV-positive. High-risk clones were restricted to clinical APEC isolates (63%). These findings indicate that colibacillosis in Swedish broilers was largely driven by a dominant APEC clone during the study period, highlighting the need for coordinated surveillance and targeted control of high-risk clones. The presence of VAG reservoirs among isolates from unaffected flocks, together with the limitations of marker-based APEC typing, supports integrated frameworks combining lineage, VAG profiles and plasmid content for more reliable APEC identification and pathogenicity assessment.
Increasing incidence and accelerating antimicrobial resistance have made gonorrhoea a major global health challenge. As ceftriaxone stands as the only reliably effective option, the development of new therapies is increasingly urgent. This meta-analysis evaluates the efficacy and safety of oral antibiotics, gepotidacin and zoliflodacin, which target bacterial type II DNA topoisomerases and represent novel therapeutic options for uncomplicated gonorrhoea. A search of CENTRAL, Embase, PubMed, and Web of Science to 10 July 2025 identified randomised controlled trials comparing zoliflodacin or gepotidacin with ceftriaxone-based therapy for uncomplicated gonorrhoea. The primary outcome was microbiological cure in the micro-ITT population across urogenital, rectal, and pharyngeal sites. Risk of bias was assessed using Cochrane RoB 2.0. Risk ratios were pooled using random-effects meta-analysis, with heterogeneity assessed by I2 and certainty of evidence evaluated using GRADE. Across three RCTs, urogenital microbiological cure rates were high in both groups (92% vs 94%). No significant differences were found between oral topoisomerase II inhibitors and ceftriaxone-based therapy for urogenital, rectal, or pharyngeal cure, although confidence intervals for extragenital outcomes remained wide. Adverse events were similar between groups. Preliminary evidence from a limited number of randomised controlled trials suggests that oral bacterial topoisomerase II inhibitors may represent promising treatment options for uncomplicated gonorrhoea. However, the current evidence remains limited, and further adequately powered clinical trials and post-approval surveillance are required to confirm their long-term efficacy, safety, and resistance implications.