Multi-regional transcriptomics reveals robust consensus subtypes beyond tumor heterogeneity of breast cancer.

Molecular typing, biofilm characteristics and biofilm-targeted inhibition strategies of Streptococcus equi subsp. zooepidemicus isolated from donkey endometritis.

Harnessing AI and bioinformatics to combat methicillin-resistant staphylococcus aureus: Innovations in genomic surveillance, diagnosis, and therapeutic development.

Methicillin-resistant Staphylococcus aureus (MRSA) is a common bacterial pathogen responsible for hospital- and community-acquired infections and typically exhibits a β-hemolytic phenotype. Notably, MRSA with an incomplete hemolytic phenotype (SIHP-MRSA) has been reported in few studies and has been shown to display altered virulence and resistance to last-resort antibiotics. However, the detailed genotypic and phenotypic characteristics of SIHP-MRSA clinical isolates remain unclear. This study aims to analyze the genotypic and phenotypic characteristics of SIHP-MRSA clinical isolates using a large sample size and to explore potential molecular mechanisms underlying the incomplete hemolytic phenotype, altered biofilm production capability, and elevated antimicrobial resistance of SIHP-MRSA. MRSA clinical isolates were obtained from patients admitted to the Affiliated Hospital of Inner Mongolia Medical University during 2010-2024, and hemolytic patterns were visually assessed on blood agar plates. Multilocus sequence typing (MLST), staphylococcal protein A (spa) typing, and staphylococcal cassette chromosome mec (SCCmec) typing were used to characterize the molecular genotypes of SIHP-MRSA isolates, whereas PCR was used to identify the distribution of virulence genes. Mutations in the agrA gene among SIHP-MRSA isolates were identified via Sanger sequencing. Biofilm formation capabilities were assessed using Congo red agar and crystal violet staining, while antimicrobial resistance profiles were determined using the VITEK-2 Compact system and the broth microdilution method. Among 1,122 MRSA clinical isolates analyzed in this study, 28.5% (320/1,122) were classified as SIHP-MRSA. The majority of isolates were isolated from lower respiratory tract samples (61.8%), followed by whole blood (9.0%) and secretions (8.5%). Molecular typing results indicated that ST5-t2460-II (85.6%, 274/320) and ST59-t437-IVa (10.3%, 33/320) were the dominant clones. Among these isolates, 21.5% (69/320) carried the pvl gene and 56.8% (182/320) carried tsst-1. Notably, 35 isolates carried both pvl and tsst-1 genes, primarily belonging to ST5-t2460-II (93.5%, 29/31). Overall, 13.4% (43/320), 45.9% (147/320), and 40.6% (130/320) of SIHP-MRSA isolates were classified as weak, moderate, and strong biofilm producers, respectively. The agrA-I238K mutation occurred in 89.7% (287/320) of isolates, and 57.1% (164/287) and 61.3% (176/287) of isolates exhibited reduced susceptibility to teicoplanin and daptomycin, respectively. Elevated teicoplanin MICs (≥ 2µg/mL) and daptomycin MICs (≥ 1µg/mL) were significantly more frequent in SIHP-MRSA isolates with the agrA-I238K mutation than in isolates with a complete hemolytic phenotype (SCHP-MSRA) (P = 0.007). This study is the first to report a high prevalence of SIHP-MRSA in a tertiary teaching hospital in China and to describe its genotypic diversity. These isolates showed enhanced biofilm formation, reduced susceptibility to daptomycin and teicoplanin, strong nosocomial transmission potential, and higher carriage rates of pvl and tsst-1 virulence genes. The significant genotypic and phenotypic features of SIHP-MRSA identified in this study highlight the previously neglected clinical significance of this MRSA subtype and emphasize the need for further exploration into its pathogenicity among vulnerable populations and its underlying molecular mechanisms.

Objectives Although K64-type carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) has been reported, its molecular characteristics remain unclear. This study aimed to characterize the phenotypic and molecular features of K64 putative hypervirulent CR- K. pneumoniae (phvKp).. Methods Two K64 putative hypervirulent CR- K. pneumoniae isolates were recovered from a patient in the emergency intensive care unit of a Chinese teaching hospital. Antimicrobial susceptibility testing was performed using broth microdilution method. Multilocus sequence typing (MLST) was used for molecular typing. Virulence was assessed using a mouse infection model, and whole-genome sequencing was performed to analyze resistance and virulence genes. Results Both isolates were resistant to aztreonam, cephalosporins, carbapenems, quinolones, and aminoglycosides, but susceptible to trimethoprim/sulfamethoxazole, colistin, tigecycline, and ceftazidime/avibactam. MLST identified both isolates as ST11. The mouse infection model showed elevated virulence of two clinical isolates, which was significantly higher than that of the classical non-hypervirulent reference strain ATCC 13883. Genomic analysis identified 133 virulence- and pathogen-associated genes, including those involved in fimbriae synthesis, iron acquisition, and enterobactin production. Both isolates harbored the rmpA gene, but string tests were negative. Sequence alignment revealed >80% similarity among 13 rmpA-harboring IncHI1B plasmids. Conclusions K64 ST11-type phvKp has emerged in China, exhibiting multidrug resistance and putative hypervirulence characteristics. The increase in virulence of K.pneumoniae involves multiple factors, and these factors act independently or the synergistic effect leads to elevated virulence potential.

This study aimed to explore the culturable bacterial community in healthy volunteers, with a focus on the staphylococcal population. First, 120 bacterial isolates were collected from conjunctival swabs of 49 healthy volunteers (aged 18 to 77 years). Isolates were characterized by phenotypic analyses, and 68 of them were confirmed as staphylococci by MALDI-TOF/MS and a multiplex PCR assay. The Staphylococcus strains (n = 68) were tested for resistance to the most relevant clinical antibiotics. Clonal relationships among isolates were evaluated by pulsed-field gel electrophoresis (PFGE), and the presence of mecA and mecC, as well as pvl genes, was investigated. Staphylococcus aureus (74%) was the major identified species, followed by Staphylococcus epidermidis (19%) and Staphylococcus xylosus (7%). A high incidence of resistance was detected against gentamicin (64%), erythromycin (62%), and penicillin (51%). Moreover, 33 isolates (48%) exhibited multidrug-resistant phenotypes, and the two S. epidermidis strains harbouring the mec genes exhibited the highest resistance. A marked heterogeneity among isolates, mostly for S. aureus and S. epidermidis, was revealed, clustering them into 20 and 4 genotypes, respectively. The prevalence of the same clones, isolated from different volunteers, across the three species, and the different phenotypic resistance patterns within the same PFGE type, was observed. These findings corroborate that staphylococci constitute a significant component of the ocular microbiota in healthy individuals; however, their exhibited antimicrobial resistance profiles are of concern.

Daptomycin-resistant Staphylococcus capitis: mechanisms, molecular epidemiology, and clinical aspects.

Nosocomial infections are a major health problem worldwide. The increasing time patients spend in hospitals has led to an increase in mortality. Acinetobacter baumannii is an opportunistic pathogen that is a significant factor in nosocomial infections. The main aim of the current study was to investigate biofilm and pathogenicity-related genes among multidrug-resistant A. baumannii strains (n = 54) obtained from patients with respiratory infections. ERIC-PCR was also used to determine their molecular typing correlation. Disk diffusion and MIC methods were used to test antibiotic susceptibility. Biofilm formation was evaluated using crystal violet staining and SEM imaging. In this study, 96.30% of isolates formed biofilms, and 59.25% were strong biofilm producers. The most prevalent biofilm-related genes were pgaC (98.15%), pgaB (92.6%), and pgaA (79.6%), followed by epsA and ompA (74.1%). The isolates demonstrated high resistance to imipenem (100%), cefotaxime (98.15%), followed by cefepime, ceftazidime, levofloxacin, and piperacillin/tazobactam (96.3%). The presence of antibiotic-resistant genes was as follows: blaOXA-58 (20.4%), blaOXA-23 (5.55%), aacC1 (50.0%), aphA6 (45.45%), sulⅡ (63.25%), and sulⅠ (32.65%). The sulⅢ gene was not detected. A dendrogram based on UPGMA revealed significant genetic diversity among the 54 A. baumannii strains. Twenty-two ERIC types were identified, with 14 unique types and 8 common types. This study illuminates a concerning rise in antibiotic resistance and the widespread presence of resistance genes in A. baumannii strains. Furthermore, the high ability of these isolates to form biofilms likely contributes to their enhanced resistance, further complicating eradication efforts. Molecular typing demonstrated considerable genetic diversity.

Platelet transfusion refractoriness (PTR) represents a major challenge in the transfusion support of patients with severe thrombocytopenia, particularly those with hematologic malignancies, intensive chemotherapy, or hematopoietic stem cell transplantation. Although nonimmune mechanisms account for the majority of cases, immune-mediated PTR caused by alloantibodies against platelet antigens, most commonly human leukocyte antigen (HLA) class I molecules, remains clinically important. This review summarizes current knowledge on the definition, mechanisms, diagnostic evaluation, and management of immune PTR. The immunologic basis of platelet destruction in immune PTR involves several mechanisms mediated by anti-HLA antibodies, including Fc receptor-dependent phagocytosis, complement activation, and antibody-induced platelet activation. Diagnostic evaluation integrates clinical assessment with laboratory detection of HLA antibodies, molecular HLA typing, and platelet crossmatching. Clinical management primarily relies on the provision of compatible platelet products, including HLA-matched platelets, antibody-specific antigen-negative platelet units, or crossmatched platelet concentrates. In selected cases, additional testing for antibodies against human platelet antigens (HPAs) may be required. Preventive strategies such as leukoreduction have substantially reduced the incidence of alloimmunization, although immune PTR continues to occur in a subset of transfusion-dependent patients. Emerging strategies aimed at improving transfusion outcomes include approaches to reduce platelet immunogenicity, development of HLA-deficient platelets, and pharmacologic interventions targeting antibody-mediated platelet clearance. A better understanding of the mechanisms underlying immune PTR may help refine diagnostic algorithms and expand therapeutic options for patients requiring long-term platelet transfusion support.

Nanoparticles (NPs) have attracted increasing attention because of their antimicrobial properties. This study aimed to evaluate the antibacterial and antibiofilm activities of nickel oxide (NiO) nanoparticles against representative uropathogenic Escherichia coli (UPEC) O-serotypes isolated from patients with urinary tract infections (UTIs) and characterized by ERIC-PCR typing. A total of 153 UPEC isolates were characterized by PCR-based O-serogrouping and ERIC-PCR typing. NiO nanoparticles were synthesized using the sol-gel method. The antibacterial and antibiofilm activities of NiO nanoparticles were evaluated against one representative biofilm-forming isolate from each ERIC type using the broth microdilution and microtiter plate methods, respectively. Among the 153 UPEC isolates, seven O-serogroups, O2, O4, O6, O8, O15, O16, and O25, were detected, with O25 being the most prevalent. ERIC-PCR analysis classified the isolates into 19 distinct clusters (E1-E19) at an 80% similarity threshold, comprising 13 common types (each containing ≥ 2 isolates) and 6 unique (singleton) types. No significant association was observed between O-serogroups and ERIC-PCR clusters (p > 0.05). NiO nanoparticles exhibited antibacterial and antibiofilm activity against 19 representative UPEC isolates, with MIC values ranging from 250 to 500µg/mL and significant inhibition of biofilm formation at concentrations of 125-500µg/mL (p = 0.001). Biofilm inhibition was also observed at sub-MIC concentrations. NiO nanoparticles demonstrated in vitro antibacterial and antibiofilm activity against 19 representative UPEC isolates. However, broader isolate screening and comprehensive toxicity and in vivo studies are required to further evaluate the antimicrobial activity and potential applicability of NiO nanoparticles.

Tularemia, caused by Francisella tularensis, is a zoonotic disease with various sources, transmission routes, and geographically different clinical signs. Diagnosis is challenging due to nonspecific symptoms, highlighting the importance of laboratory testing for accurate detection, effective outbreak management, and targeted treatment. Recent improvements have enhanced the accuracy of sensitive and specific immunological and molecular methods. Techniques such as enzyme-linked immunosorbent assay, immunochromatography, microagglutination tests, indirect immunofluorescence assays, and PCR continue to be key detection tools. Molecular typing methods such as whole-genome sequencing, single-nucleotide polymorphism analysis, multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and matrix-assisted laser desorption ionization-time of flight enable precise genetic characterization of F. tularensis strains. These methods improve understanding of phylogeny, strain diversity, and transmission routes, while supporting outbreak investigations. This review aims to provide a comprehensive overview of current laboratory methods for diagnosing and typing tularemia as well as their application in clinical and research settings.

Investigation of environmental bacterial contamination associated with distilled water in a neonatal formula preparation unit.

Objective: To analyze the occurrence and distribution of high-level microsatellite instability (MSI-H) in precancerous lesions and histological subtypes of endometrial cancer, to compare the concordance rate between mismatch repair protein deficiency (dMMR) and MSI-H, to investigate the incidence of minimal microsatellite shift in the development of endometrial cancer, and to explore potential solutions for accurate MSI-H diagnosis. Methods: A total of 848 endometrial lesion samples that underwent molecular typing at the Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University from January 2023 to January 2024 were collected, including 93 cases of atypical endometrial hyperplasia (AEH) and 755 cases of endometrial carcinoma. Microsatellite status, MMR protein expression, and gene mutations (MMR, POLE, etc.) were analyzed by histology, IHC, and NGS. Microsatellite status was determined by calculating the MSI-score based on 34 microsatellite loci. An MSI-score<0.3 was defined as microsatellite stable (MSS),≥0.3 as microsatellite instability-high (MSI-H), and 0.3±0.05 as the equivocal range. Simultaneously, a visualization graph was established for minimal microsatellite shift analysis and identification. Results: The 848 lesions included 93 cases of AEH, 442 cases of low-grade endometrioid carcinoma (G1-G2), 143 cases of high-grade endometrioid carcinoma (G3), 20 cases of clear cell carcinoma, 20 cases of carcinosarcoma, 16 cases of mixed adenocarcinoma, 12 cases of dedifferentiated/undifferentiated carcinoma, and 102 cases of other types (including 94 serous carcinomas, 6 mesonephric-like adenocarcinomas, and 2 gastric-type mucinous adenocarcinomas). The results showed that the incidence of dMMR in AEH was 4.3%, and MSI-H was 3.2%, significantly lower than the 24.9% and 23.0% in endometrial cancer, respectively (P<0.001). All the 102 cases of other types, including serous carcinoma, were pMMR/MSS. The overall concordance rate between dMMR and MSI-H was 90.6%, but it varied between 75% and 100% across different stages and histological subtypes. In molecular subtyping, the concordance rate was 75% for AEH and carcinosarcoma, 87.5% for dedifferentiated/undifferentiated carcinoma, 91.5% for high-grade endometrioid carcinoma, and 100% for other high-grade carcinomas, while the POLE-mutated subtype had the lowest concordance rate of 66.7%, significantly lower than the 93.1% overall concordance rate for the MSI-H subtype (P<0.001). In MSI-H cases, up to 84.5% of endometrial cancer cases exhibited minimal microsatellite shift in at least one locus, with 67.8% showing shifts in≥3 loci. Through analysis of 34 microsatellite loci and visualization, 20 cases (11.5% of 174 MSI-H cases) were identified as borderline (MSI-score=0.3±0.05), considered diagnostically challenging. Among these, MLH1-/PMS2- co-loss accounted for 12/20 cases, with half (6/12) harboring MLH1 mutations; isolated MSH6 loss accounted for 6/20 cases, with 5 of these harboring MSH6 mutations. The 20 minimal shift MSI-H cases shared all pathological features of typical MSI-H endometrial cancer. Conclusions: The incidence and distribution of MSI-H show significant differences across histological subtypes between endometrial precancerous lesions and endometrial carcinomas. The overall concordance between dMMR and MSI-H is good, but varies across different disease stages, histological types, and molecular subtypes. Minimal microsatellite shift is commonly detected in MSI-H cases, and some cases are difficult to interpret due to their classification within the equivocal range. Increasing the number of microsatellite loci, combined with visualization graph comparison and integration of mismatch repair protein immunophenotype and histological features, can effectively improve the accuracy of MSI-H interpretation.

Surveillance of antimalarial drug efficacy is essential for drug policy in the fight against malaria. This includes clinical trials of drug efficacy, molecular marker typing and ex vivo/in vitro drug susceptibility tests such as 50% inhibitory concentration (IC50) assay. The goal of this review was to elaborate on the variance in the IC50 assay across labs in sub-Saharan Africa (sSA) where malaria is endemic. We systematically reviewed 71 articles, published between 2015 and 2025, evaluating IC50 in sSA where only 56 were performed in labs in Western (WA), Central (CA), East (EA) and Southern Africa (SA). The IC50 values of the major antimalarial drugs, including dihydroartemisinin (DHA), lumefantrine (LUM), mefloquine (MFQ), amodiaquine (AMD), chloroquine (CQ), piperaquine (PPQ), artesunate (ATS), artemisinin (ART) and quinine (QN), were reported. An F-test performed on the IC50 values from WA and EA, where ex vivo assays were conducted, revealed a statistically significant variation (P value <0.05) in the IC50 values of some major antimalarials (DHA, CQ, LUM and AMD). The geometric means for DHA, CQ, LUM and AMD in WA versus EA were 2.46 versus 2.21, 83.15 versus 34.34, 10.06 versus 10.47, and 10.63 versus 17.61 nM, respectively. The overall ex vivo IC50 values of CQ were generally below the known resistance thresholds. Differences in drug reconstitution solvents, the range of drug concentrations, period of drug exposure (48 or 72 h), and curve-fitting tools and assay methods were observed. These differences together could account for the variance in IC50 values across sSA. We therefore recommend regional harmonization of the IC50 protocol for antimalarial drug efficacy surveillance and formation of a regional quality assessment network of malaria IC50 labs, as a step towards reliable data sharing and integration into strategic plans for malaria elimination.

Vancomycin-resistant enterococci (VRE) represent a major challenge in healthcare settings due to limited therapeutic options and the emergence of resistance to last-line agents. Accurate detection of resistance mechanisms and understanding the molecular epidemiology of circulating strains are essential for effective surveillance and infection control. A total of 192 non-duplicate Enterococcus isolates (103 VRE and 89 vancomycin-susceptible isolates) recovered from clinical specimens between 2018 and 2022 were analyzed. Antimicrobial susceptibility testing was performed using broth microdilution (BMD) as the reference method and compared with automated and gradient-based methods. Resistance genes associated with vancomycin and linezolid resistance were investigated by in-house PCR and sequencing. Clonal relatedness of VRE isolates was assessed using AP-PCR, PFGE, and MLST. Among VRE isolates, vanA was the predominant resistance determinant, while a single isolate carried vanB. Importantly, vanA was also detected in three phenotypically vancomycin-susceptible E. faecalis isolates, consistent with vancomycin-variable enterococci. Linezolid resistance was identified in three isolates (1.6%); two E. faecalis isolates harbored the transferable optrA gene, representing the first report of optrA-positive E. faecalis causing human infections in Türkiye, while one E. faecium isolate showed linezolid resistance in the absence of the investigated resistance genes. Tigecycline resistance was uncommon. Daptomycin retained in vitro activity with higher MIC₅₀/ MIC₉₀ values in E. faecium, whereas oritavancin MIC values were higher among E. faecalis isolates. The BD Phoenix system demonstrated high categorical agreement with BMD for vancomycin and teicoplanin but generated major and very major errors for linezolid susceptibility testing. Molecular typing revealed extensive genetic diversity among VRE isolates, with 35 AP-PCR genotypes, PFGE-confirmed clustering including one predominant clone, and the identification of 11 novel MLST sequence types (ST2994-ST3004). This study provides insight into the resistance landscape and genetic diversity of clinical Enterococcus isolates. The detection of vancomycin-variable enterococci and transferable linezolid resistance determinants underscores the need for integrated phenotypic and molecular approaches to ensure accurate resistance detection and effective surveillance.

Bee sting-induced hypervirulent Klebsiella pneumoniae infection causing fulminant necrotizing fasciitis: case report and narrative review.

Exploration of virulence and resistance profiles of newly emerging MDR B. cereus in wild birds, as the first report in Egypt.

This study aimed to investigate the infection status, serotype distribution, drug resistance, and molecular typing characteristics of Salmonella in food-borne diarrhea patients in Chifeng, China, from 2022 to 2024. Fecal samples were collected from diarrhea patients for Salmonella isolation and molecular serotype identification. The isolates were tested using the microbroth dilution method and pulsed-field gel electrophoresis (PFGE) to assess drug susceptibility and perform molecular typing. Statistical analysis was conducted using the SPSS 25.0 software. Salmonella was detected in 52 of the 737 fecal samples, yielding a positive detection rate of 7.06% (52/737). A total of 52 Salmonella strains were isolated, predominantly Salmonella Typhimurium and Salmonella Enteritidis, which accounted for 40.38% (21/52) and 21.15% (11/52), respectively. Additionally, 5 other serotypes were identified: S. Kentucky, S. Dublin, S. Liverpool, S. Vilshaw, and S. Paratyphoid A. Notably, 48 strains (92.31%, 48/52) exhibited resistance to at least one antibiotic, with resistance rates exceeding 50% for ampicillin, streptomycin, tetracycline, and nalidixic acid. The rate of multiple drug resistance reached 86.54% (45/52). Cluster analysis of the 52 Salmonella strains revealed 39 band types with similarity indices ranging from 50.1% to 100%. Notably, a higher similarity coefficient indicated greater similarity in drug resistance phenotypes among the strains. The detection rate of Salmonella among food-borne diarrhea patients in Chifeng from 2022 to 2024 was notably high. The predominant serotypes were S. Typhimurium and S. Enteritidis. The PFGE band types were relatively diverse, and the strains exhibited significant drug resistance, including multiple drug resistance.

Bordetella pertussis: emerging epidemiology, diagnosis and management.

To describe the serological and molecular characteristics of a rare Gerbich-negative phenotype detected in a Peruvian patient. The Gerbich blood group (Ge) system includes high-prevalence antigens (Ge2, Ge3, Ge4) encoded by the GYPC gene. Absence of these antigens is extremely rare and has been reported mainly in Melanesian and Middle Eastern populations. To our knowledge, no molecularly confirmed cases have been reported in Peru. A 65-year-old Peruvian man scheduled for orthopaedic surgery underwent pretransfusion testing, including an indirect antiglobulin test, antibody identification using Low Ionic Strength Solution (LISS)/Coombs column agglutination cards at 37°C, papain-treated reagent red cells, a direct antiglobulin test, autocontrol, differential alloadsorptions and neutralization studies. Anti-Ge2 reference serum (IBGRL 4370) and molecular analysis of GYPC were performed. Pretransfusion testing showed panagglutination with 2+ reactions in all reagent red cells; no reaction was observed with papain-treated cells. The direct antiglobulin test, autocontrol and additional serological studies were negative. The antibody titre was 1:8. No reactivity was observed with anti-Ge2, and molecular analysis identified the GE*01.-03.02 allele, responsible for the Gerbich phenotype (Ge:-2,-3,4). This report describes a rare Gerbich-negative phenotype in a Peruvian patient and highlights the importance of molecular typing for transfusion management.