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.
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.
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.
This study compared liquid chromatography-mass spectrometry (LC-MS), micro-bioassay (MBa), and enzyme-linked immunosorbent assay (ELISA) for quantification of lincomycin (10 mg/kg BW) in porcine serum and evaluated lincomycin pharmacokinetic (PK) data in healthy piglets also co-infected with Actinobacillus pleuropneumoniae and Pasteurella multocida. All methods satisfied standard bioanalytical validation criteria, including low limits of detection and quantification, acceptable intra-assay imprecision and error, and strong linearity across clinically relevant concentration ranges. Serum concentrations measured by MBa and ELISA showed high correlation with LC-MS in both healthy and infected models (Pearson r ≥ 0.97, low bias on Bland-Altman analysis); they produced comparable PK parameters (Cmax, Tmax, area under the curve [AUC], clearance, and mean residence time), indicating suitability for PK/pharmacodynamic (PD)-based dose optimization. PK analysis demonstrated rapid absorption after intramuscular administration and disease-associated alterations in selected distribution and disposition parameters. AUC and clearance were nearly similar across analytical methods and largely consistent between software platforms (WinNonlin and PKSolver). Thus, lower-cost MBa and ELISA-combined with freely available PKSolver-can generate robust, decision-relevant PK/PD data for lincomycin in swine, providing a practical framework for antimicrobial dose refinement and stewardship in resource-limited veterinary and farm settings.
Osteoarticular infection is an emerging complication of sporotrichosis, often leading to a significant increase in morbidity and longer treatment. We conducted a retrospective cohort study of osteoarticular sporotrichosis (OS) in southeastern Brazil (2014-2024) using clinical, epidemiological, and molecular data. Among 252 patients, 20 (7.9%) had OS, including 10 (4%) with osteomyelitis. The median age of patients with OS was 58 years (IQR 39-64; range 18-83) and 55% were male. Hypertension (45%), diabetes (40%), alcohol use (40%), smoking (40%), and HIV infection (15%) were the most frequent conditions identified. Cutaneous lesions occurred in 95% of cases, and 90% of patients presented with arthralgia and edema. Multifocal OS was observed in 50% of cases, most commonly affecting the knees, fingers, and wrists. The mean time to diagnosis was 14.2 months. Most patients were treated with itraconazole combined with amphotericin B; 13 required surgical intervention, including 2 amputations. The mean treatment duration was 21 months. Multisystem involvement due to sporotrichosis was observed in 45% of cases, including pulmonary involvement. Mortality was 15%. Diabetes (OR = 4.11; 95% CI, 1.50-11.38; p = 0.006) was independently associated with OS. OS is associated with substantial morbidity and prolonged treatment. Diabetes may increase the risk of OS, while delayed diagnosis jeopardizes outcomes, underscoring the need for early management.
A case of chronic proliferative rhinitis (CPR) associated with Salmonella enterica subsp. diarizonae serovar 61:(k):1,5,(7) (SED) is described in a 3-year-old ewe from the university teaching farm in Transylvania, Romania. Clinical examination revealed bilateral seromucous nasal discharge and visible proliferative masses within both nasal cavities. Infrared thermography demonstrated increased heat emission over the nasal region, consistent with active inflammation. Computed tomography imaging showed marked proliferative invasion within the ventral nasal turbinates. Histopathology and immunohistochemistry confirmed chronic proliferative rhinitis characterized by fibrovascular tissue proliferation, epithelial cell hyperplasia, and mixed inflammatory cell infiltrate, predominated by lymphocytes, plasma cells and macrophages. SED was isolated as the sole microorganism from nasal swabs and confirmed by serotyping, PCR, and immunohistochemistry. To the authors' knowledge, this is the first documented case of CPR associated with SED in Romania and in Southeastern Europe, highlighting the need to include CPR among the differential diagnoses for adult sheep with chronic upper respiratory disease, and to include SED within its aetiological agents.
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.
Although PD-1 blockade shows strong antitumor efficacy and is being considered for chronic infections including Mycobacterium tuberculosis (M.tb), its influence on early lymphocyte responses to M.tb remains poorly understood. In this study, we characterized the transcriptional and developmental states of pulmonary B and T cells in mice lacking PD-1 after 7 days post-M.tb infection. We found that loss of PD-1 disturbed pulmonary lymphocyte homeostasis, characterized by abnormal regulatory T cell (Tregs) expansion, early exhaustion-like differentiation of cytotoxic T cells, and impaired maturation of memory B cells. These alterations are associated with changes in key transcriptional regulators, including reduced activity of factors promoting effector differentiation (e.g., Runx2, Runx3 in T cells; Tcf4, Pou2f2 in B cells) and upregulation of regulators driving regulatory or suppressive phenotypes (e.g., Ikzf2 in Tregs). Additionally, PD-1 deficiency rewired B-T cell communication with diminished antigen presentation and co-stimulation while amplifying proinflammatory signals. These insights provide a transcriptional blueprint for PD-1-mediated immune balance, with implications for host-directed therapies in tuberculosis.IMPORTANCEWhile PD-1 inhibition can boost protective T cell responses, it has also been linked to increased TB susceptibility. Our study reveals that PD-1 plays a previously unrecognized role in shaping the earliest immune responses to M.tb. In mice lacking PD-1, lung lymphocytes failed to develop in a balanced manner: regulatory T cells expanded excessively, cytotoxic T cells showed signs of early exhaustion, and memory B cell maturation was delayed. These changes disrupted the normal communication between B and T cells, weakening adaptive immunity while amplifying inflammation. By defining PD-1 as a critical organizer of early lymphocyte fate, our findings highlight the risks of indiscriminate PD-1 blockade in infectious contexts and point toward more precise strategies for host-directed TB therapies and vaccine design.
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.
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.
Chlamydia psittaci is an important zoonotic pathogen mainly transmitted to humans through exposure to infected birds or contaminated bird excreta, and infection may range from mild respiratory illness to severe systemic disease. Between 2023 and 2024, 114 samples were collected in Shenzhen, China, including bronchoalveolar lavage fluid (BALF) samples from four laboratory-confirmed psittacosis patients, five tissue samples from one suspected infected parrot, and 105 oropharyngeal and cloacal swabs from parrots in a local bird market. C. psittaci was detected by conventional PCR targeting ompA. Positive samples were subjected to targeted capture sequencing, isolation in McCoy cells, ompA-based genotyping, whole-genome SNP phylogenetic analysis, and intracellular antibiotic inhibition assays. C. psittaci DNA was detected in 42 samples, of which 19 yielded high-quality genomic sequence data. Three isolates were successfully cultured: SZ1 from parrot trachea, SZ2 from parrot small-intestinal mucosa, and SZ3 from BALF from Case 1. Phylogenetic analyses based on ompA and genome-wide SNPs showed that all three isolates belonged to genotype A and clarified their relationships with previously reported strains. No known acquired antimicrobial resistance genes were identified, but nucleotide substitutions were detected at selected loci previously reported to be potentially associated with antimicrobial susceptibility. Comparative intracellular inhibition assays showed different antibiotic response patterns between the parrot-derived isolate SZ1 and the human-derived isolate SZ3; SZ1 showed a less pronounced inhibitory response to doxycycline under the present in vitro conditions, suggesting reduced doxycycline susceptibility rather than confirmed resistance. These findings highlight the value of genomic surveillance and antimicrobial susceptibility monitoring of C. psittaci isolates from both avian reservoirs and human infections, which may support risk assessment and clinical management of psittacosis.
Toxoplasmosis caused by the Apicomplexan parasite Toxoplasma gondii is a significant health threat to immunocompromised individuals and newborns. This parasite has a complex life cycle that is well controlled to achieve optimal transmission and pathogenesis. Acute phase of the disease is caused by rapid proliferation of tachyzoites, which has a highly coordinated and tightly regulated cell cycle to allow parasite propagation. Tachyzoite cell cycle has five partially overlapping phases (G1, S, G2, M and C) with distinct gene expression patterns and cellular activities, yet the underlying regulatory mechanisms are not well understood. In this study, we show that the AP2 family transcription factor AP2XI-3 has important roles in regulating the cell cycle to progress through the G1 phase. Depletion of AP2XI-3 resulted in cell cycle retention at G1, leading to growth inhibition of tachyzoites. RNA-Seq and CUT&Tag analyses revealed that AP2XI-3 regulates the transcription of genes involved in nucleic acid metabolism, RNA biogenesis and processing, which are consistent with the cellular activities of G1 phase in preparing biomass for cell cycle progression. Moreover, AP2XI-3 binds to the conserved DNA motif, TRP-2, a sequence widely distributed in the promoters of genes that exhibit peak expression during the G1 phase. Together, these findings underscore the essential role of AP2XI-3 in the tight regulation of the G1 phase, highlighting its potential as a therapeutic target for drug development.
Staphylococcus aureus (S. aureus) is a well-recognized pathogen known for its multi-drug resistance and diverse virulence mechanisms. Its ability to grow biofilms on implanted medical devices enhances its antimicrobial resistance (AMR) and virulence. Despite its clinical relevance, the underlying genetic basis of S. aureus biofilm formation remains insufficiently characterized, particularly regarding key biofilm-associated genes (BAGs) and their regulatory contributions. This study presents a two-part integrative approach to identify genetic determinants of biofilm formation in 178 Egyptian, clinical S. aureus isolates. The framework integrates a genome-wide association study (GWAS) module with a learning-based classification module. GWAS was conducted using a linear mixed model, while logistic regression was the best-performing model in binary and multiclass classification. Integrating both modules, we identified 20 BAGs as promising determinants of biofilm formation. Protein-protein interaction network and pathway enrichment analyses revealed their involvement in biofilm-related pathways. Of the identified BAGs, nine genes have direct links to biofilm formation in S. aureus or other bacteria, while the rest are linked to AMR, nutrient acquisition, and cell division. This study presents a robust framework for biofilm genomics research, uncovering 20 candidate BAGs that span diverse biological functions and capture the multi-faceted nature of biofilm formation in S. aureus.
Streptococcus suis (S. suis) is an important zoonotic pathogen that leads to serious diseases in pigs and humans, marked by conditions such as meningitis and septicemia. The histidine triad protein (HtP) family plays a significant role in the pathogenicity of S. suis. However, the specific function of HtpsB in the pathogenicity of S. suis remains unclear to date. In this study, we demonstrated that the gene deletion mutant ∆htpsB exhibited significantly reduced pathogenicity compared with SC19, both in vivo and in vitro. This attenuation was particularly evident in its reduced virulence and its impaired ability to disrupt and invade the blood-brain barrier (BBB). Furthermore, the adhesion, invasion, and toxicity of ∆htpsB to human brain microvascular endothelial cells (HBMECs) were diminished. HSPA8 was identified as an interacting partner of HtpsB in HBMECs, suggesting that it mediates the interaction between SS2 and HBMECs. These findings provide an important theoretical basis for a comprehensive analysis of the molecular mechanisms by which S. suis traverses the BBB to cause meningitis.
Vibrio alginolyticus is a frequently implicated species for vibriosis in humans and diverse wildlife, but it has previously been difficult to identify from the closely related and emerging Vibrio diabolicus. Comparisons of both species, including antimicrobial resistance (AMR) and virulence characterizations, are scarce and impeded by intraspecies diversity, minimal genomes, discordant classification methods, and gene databases with limited utility to understudied species. The species identities of 3,442 public domain genomes (SRA files) within the Harveyi clade were re-evaluated using genomic methods. Public genomes identified as V. diabolicus and V. alginolyticus were combined with previously published genomes isolated from humans, sea otters (Enydra lutris), or coastal environments (V. diabolicus n = 88, V. alginolyticus n = 163, Vibrio parahaemolyticus n = 287) for pangenome-wide association studies to identify species-specific gene clusters (95% identification threshold). Additional genome wide associations with isolation source (humans versus sea otters) were investigated, including AMR and virulence related gene clusters. Genomic reclassification identified 29 of 150 misclassified public domain V. alginolyticus genomes, including 26 reclassified as V. diabolicus. In total, 28 previously misclassified V. diabolicus genomes (n = 37 total) were identified, including 10 human-derived strains. GWAS identified 643 and 477 gene clusters specific to V. alginolyticus and V. diabolicus, respectively, while some multilocus sequencing analysis (MLSA) gene clusters were non-specific. Gene clusters (n = 109) associated with either V. alginolyticus isolated from humans or sea otters were identified including one annotated to a multidrug resistance gene (mdtk_1). No V. diabolicus gene clusters were associated with host species after multiple comparison correction, although pre-correction associations related to antimicrobial resistance were detected (cat_1, ampC). The genomic methods of classification presented provide accurate species identification for V. diabolicus and V. alginolyticus beyond current MLSA/MLST schemes, although target species-specific genes were identified that may be useful for improved future schemes. While limited sample size of V. diabolicus hampered the ability to detect host associated markers, the GWAS approach employed provide a reusable framework for discovering insights into host adaptation and prioritizing target genes for future functional AMR and virulence validation experiments in both species.
Non-typhoidal Salmonella (NTS) is a leading cause of foodborne illness globally, with poultry eggs serving as a primary vehicle for human infection. The emergence of antimicrobial resistance (AMR) in Salmonella, particularly to critically important antibiotics, compounds this public health threat. This cross-sectional study, conducted in the Rupandehi district of Nepal, aimed to assess Salmonella prevalence in table eggs and characterize the AMR profiles of recovered isolates. A total of 150 eggs were collected from layer farms (n = 45), retail shops (n = 60) and restaurants (n = 45). Salmonella was isolated using standard culture-based methods, and antimicrobial susceptibility was determined via the Kirby-Bauer disk diffusion method. The overall prevalence of Salmonella was 10.0% (95% CI: 5.6%-16.2%). A statistically significant contamination gradient was observed across the supply chain, with prevalence increasing from 2.2% at farms to 15.0% at retail shops and 11.1% at restaurants (Fisher's exact test, p < 0.05). Logistic regression analysis identified retail shops as a significant risk factor for contamination compared to farms (OR = 7.6). Antimicrobial susceptibility testing of 17 isolates revealed alarmingly high resistance rates to ciprofloxacin (88.2%), tetracycline (76.5%) and ampicillin (70.6%). Furthermore, 58.8% of isolates were multidrug-resistant (MDR). These findings reveal systemic failures in post-farmgate hygiene and underscore the urgent need for integrated One Health interventions, including enhanced surveillance, improved food handling practices and stringent antimicrobial stewardship in the poultry sector to mitigate this pressing public health risk.
African swine fever is a highly contagious disease caused by African swine fever virus (ASFV). The immune evasion capabilities of ASFV are crucial for its efficient replication within cells. As a DNA virus, the molecular mechanisms by which ASFV evades the cGAS-STING pathway have been extensively studied. However, the mechanisms underlying the evasion of dsRNA-activated pathways remain unclear. In this study, we aimed to identify the immunosuppressive function of ASFV E301R protein. We identified that pE301R strongly inhibits retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling and suppresses IFN-I production. pE301R impedes RLR signaling by directly degrading RIG-I, and pharmacological inhibition of autophagy rescued pE301R-induced RIG-I degradation. pE301R degrades RIG-I by promoting its interaction with p62. The siRNA-mediated knockdown of p62 rescued pE301R-mediated RIG-I degradation. In summary, our study demonstrates that pE301R degrades RIG-I via the autophagy pathway, thereby suppressing IFN-I production and aiding ASFV in evading the host's innate immune response. This finding enriches our understanding of the molecular mechanisms underlying the escape of ASFV from the RLR signaling pathway.