The aim of this study is to detect the carbapenemase type and to determine the in vitro effects of ceftazidime/avibactam-colistin, ceftazidime/avibactam-meropenem and ceftazidime/avibactam-tigecycline combinations against Carbapenem-Resistant Klebsiella pneumoniae (CRKP) isolates. A total of 35 CRKP isolates were included to the study. The minimum inhibitory concentrations of ceftazidime/avibactam, meropenem, colistin and tigecycline were determined by broth dilution method. Synergistic effects of ceftazidime/avibactam-colistin, ceftazidime/avibactam-meropenem and ceftazidime/avibactam-tigecycline were investigated by microdilution checkerboard method. Carbapenemase genes (blaOXA-48, blaNDM, blaKPC, blaIMP, blaVIM) were detected by multiplex PCR. All of the isolates were resistant to meropenem, whereas 77.1% of the isolates were resistant to ceftazidime/avibactam and 14.3% of the isolates were resistant to colistin.The carbapenemase genes of the CRKP isolates were determined as 17 OXA-48+NDM, 9 KPC, 6 OXA-48, 1 NDM, 1 KPC+NDM and 1 KPC+OXA-48. Ceftazidime/avibactam-colistin, ceftazidime/avibactam-meropenem and ceftazidime/avibactam-tigecycline combinations were synergistic against 5.7% (2/35), 17.1% (6/35), and 5.7% (2/35) of the isolates, respectively. Ceftazidime/avibactam-meropenem was the most effective synergistic combination in our study, showing synergism in 17.1% of isolates, however, the synergistic effect varied depending on the CRKP isolate tested.
This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.
Acinetobacter baumannii is a major cause of hospital-acquired infections and has emerged as a critical multidrug-resistant (MDR) pathogen with limited therapeutic options. In this study, two MDR clinical isolates from a tertiary care hospital in Chennai, India, selected based on their strong biofilm-producing capacity, were subjected to whole-genome sequencing (WGS) to characterize their resistome, virulome, and genomic features. Both isolates exhibited resistance to β-lactams, carbapenems, aminoglycosides, fluoroquinolones, and trimethoprim-sulfamethoxazole, while remaining susceptible to tigecycline and colistin. Genomic analysis identified key carbapenemase genes blaOXA-23, blaOXA-51, and blaOXA-144 along with additional resistance determinants including blaADC-76 and blaPER-7, aminoglycoside-modifying enzymes (ant(3″)-Ia and aph(6)), tetracycline resistance genes (tet(A), tet(B), and tet(R)), macrolide resistance gene msr(E), sulfonamide resistance gene sul1, and chloramphenicol efflux gene cmlA5. Fluoroquinolone resistance was associated with mutations in the quinolone resistance determining regions, including an S81L substitution in gyrA and multiple substitutions in parC. Virulence profiling revealed biofilm-associated genes, including bap and the pgaABC operon, along with genes linked to motility and metabolic fitness. Phylogenomic analysis showed close relatedness between the isolates and reference strains, and multilocus sequence typing (MLST) assigned both isolates to sequence type ST1051, indicating a shared clonal background. The genomes also harbored diverse mobile genetic elements, prophage regions, and siderophore-associated biosynthetic gene clusters, reflecting high genomic plasticity. Overall, this study highlights the coexistence of multiple resistance and virulence determinants in biofilm-forming MDR A. baumannii, emphasizing the importance of genome-based surveillance for monitoring high-risk strains in clinical settings.
The present study aimed to evaluate the in vitro activity of ceftazidime-avibactam (CZA), imipenem-cilastatin-relebactam (IMR), meropenem-vaborbactam (MEV), cefiderocol (CFDC), and plazomicin (PLZ), against nosocomial carbapenem-resistant Pseudomonas aeruginosa (CRPA) (n = 40), carbapenem-resistant Acinetobacter baumannii (CRAB) (n = 56), and Stenotrophomonas maltophilia (n = 50) isolates from Bulgaria (2014-2023). Antimicrobial susceptibility testing, polymerase chain reaction screening for antimicrobial resistance (AMR) determinants, and whole-genome sequencing were performed. In CRPA, blaNDM-1 (20%), blaVIM-2 (5%), and blaVIM-4 (2.5%) metallo-β-lactamase (MBL)-encoding genes were detected. Both P. aeruginosa and S. maltophilia showed absolute susceptibility to CFDC, and 78.6% of the tested A. baumannii isolates were also susceptible. All CFDC-resistant (MIC values in the range of 4-64 mg L-1) CRAB isolates (12 out of 56) were positive for blaPER-1 (n = 12) and acquired class D carbapenemase genes, as follows: blaOXA-23-like (n = 7), blaOXA-24/40-like (n = 1), and blaOXA-23-like + blaOXA-24/40-like (n = 4). Only 22.5-25% of CRPA isolates revealed susceptibility to the combined β-lactam (BL)-β-lactamase inhibitor (BLI) antimicrobials. Equal PLZ MIC50 values were reported against P. aeruginosa and A. baumannii (8 mg L-1), but higher MIC90 values against CRAB (>256 vs. 16 mg L-1). MBL-producing CRPA demonstrated absolute resistance to all BL-BLI preparations, whereas non-MBL-producing isolates possessed significantly higher susceptibility (P < 0.05), ranging from 31% (for CZA and IMR) to 34.5% (MEV). In conclusion, the emergence of MBL-positive P. aeruginosa and the associated ineffectiveness of the novel BL-BLI combinations, as well as the relatively high proportion of CFDC-resistant A. baumannii isolates, are alarming. Therefore, continuous surveillance of AMR concerning newly approved antibiotics should be the mainstay of multifaceted global and national "One Health" strategies and infection control stewardship practices in hospital settings.
The relationship between gut microbiota dysbiosis and bone mineral density (BMD) in hemodialysis patients, mediated through immune-metabolic pathways, remains to be fully elucidated. In this single-center prospective cross-sectional study, 165 maintenance hemodialysis patients were included to evaluate the independent association between gut microbiota composition and BMD, quantify the mediating roles of immune markers and gut-derived metabolites, and assess the effect modification by nursing-modifiable factors. Fecal samples underwent 16S rRNA sequencing and functional prediction. Inflammatory cytokines (IL-6, TNF-α), gut-derived metabolites (indoxyl sulfate, butyrate), and BMD via dual-energy X-ray absorptiometry (DXA) were measured. Gut microbiota community structure significantly differed across BMD tertiles (R2 = 0.033, P = 0.003). After full adjustment, principal coordinate 1 (PCoA-PC1, beta-diversity) was negatively associated with femoral neck BMD, while the Shannon diversity index showed a positive association (both P < 0.05). We identified 15 differentially abundant genera between high and low BMD groups. Functional prediction revealed short-chain fatty acid pathways were positively associated with BMD, while indole/p-cresol pathways showed negative associations. Mediation analysis demonstrated that immune markers and gut-derived metabolites collectively explained 45.71% of the microbiota-BMD relationship. Nursing factors significantly modified this association, with the negative relationship strengthened by low fiber intake, severe constipation, proton pump inhibitor use, and inadequate dialysis (Kt/V < 1.4). In conclusion, gut microbiota dysbiosis is independently associated with lower BMD in hemodialysis patients, partially mediated through immune-inflammatory pathways and gut-derived metabolites. Dietary fiber optimization, constipation management, prudent proton pump inhibitor prescribing, and dialysis adequacy represent actionable nursing targets to mitigate gut-mediated bone loss in this vulnerable population.
This study evaluated the reliability of different laboratory methods for detecting resistance to glycopeptide antibiotics-vancomycin and teicoplanin-in clinical Staphylococcus aureus and coagulase-negative staphylococci (CoNS) isolates. While automated systems are widely used in clinical microbiology laboratories due to their efficiency and ease of use, they may yield inaccurate results when assessing glycopeptide susceptibility. A total of 87 previously collected clinical isolates (22 S. aureus and 65 CoNS), initially identified as resistant to at least one of the vancomycin or teicoplanin by an automated system, were retrospectively analyzed. All isolates were stored at -80 °C and retested using three methods: the same automated system (following the manufacturer's protocol), the gradient diffusion method, and the reference broth microdilution (BMD) method. Interpretations were made according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Upon re-evaluation, all isolates were found to be susceptible to vancomycin and teicoplanin using the BMD method. The automated system yielded 100% concordance with BMD for vancomycin and 77% for teicoplanin, while the gradient method produced similar findings. Notably, five S. aureus isolates (23%) remained resistant to teicoplanin according to both the automated system and the gradient method but were susceptible by BMD. These results emphasize that automated systems, although practical, may lead to overestimation of glycopeptide resistance. Therefore, when resistance is suspected, especially to teicoplanin, confirmatory testing with the BMD reference method is essential to ensure accurate interpretation and avoid misclassification.
The present study aimed to investigate the resistome of four trimethoprim-sulfamethoxazole (SXT)-resistant Stenotrophomonas maltophilia complex (Smc) isolates from Bulgarian hematopoietic stem cell transplantation (HSCT) recipients and to subject them to phylogenomic analysis involving all sul1-positive strains of the identified species with available genomes worldwide. Preliminary identification by MALDI-TOF mass spectrometry determined all four isolates as S. maltophilia. The sources of isolation were stools (SM175, SM176, and SM179) and urine (SM178). SM176 and SM178 also showed high-level levofloxacin resistance. All isolates demonstrated in vitro susceptibility to minocycline and cefiderocol. Whole-genome sequencing (WGS) assigned SM175, SM176, and SM178 as Stenotrophomonas forensis. Two types of class 1 integrons were detected in the four isolates, namely SM175 and SM179 carried empty integrons, whereas SM176 and SM178 carried a gene cassette (3,748 bp in length) consisting of aac6'-Ib-cmlB-blaOXA-9. Alignment against public databases revealed that this cassette has not been found in Stenotrophomonas species so far, but it was present in Pseudomonas aeruginosa and Enterobacterales. Phylogenomic analysis of our assembled sequences, together with all 26 sul1-positive S. maltophilia and S. forensis genomes, indicated that S. maltophilia SM179 was not part of any S. maltophilia cluster. SM175, SM176, and SM178 were closely related (differences of 35-101 SNPs). To the best of our knowledge, this is the first report of SXT-resistant Smc isolates from post-HSCT patients with hematological malignancies in Bulgaria, which presents WGS-based resistome and phylogenomic analyses. We also report on the first sul1-containing S. forensis clinical isolates. Our findings reveal high global heterogeneity of sul1-positive S. maltophilia.
Products of avian origin are one of the major Salmonella reservoirs, responsible for serious public health concerns. Transmission and pathogenicity are mainly caused by molecular mechanisms, including chromosomal and plasmid-encoded virulence factors. This study aimed to perform phenotypic identification, antibiotic resistance profiling against 15 antibiotics, and characterization of virulence factors of 80 Salmonella strains (30 from human and 50 from poultry), collected in Annaba and Constantine regions in Algeria.Antibiogram analysis and simplex PCR revealed complete resistance to four antibiotics: Ampicillin, Penicillin, Cephalotin and Cephoxetin. In addition, four virulence genes (spvA, spiC, spvC and pefA) were detected. These genes were identified in isolates from both avian and human origins, with variations in their distrubition frequencies. This study highlights the significant role of avian-derived Salmonella as a reservoir of antibiotic resistance and virulence genes, posing a serious threat to public health.Antibiotic resistance profiling revealed that avian isolates exhibited complete resistance (100%) to ampicillin, penicillin and cephalothin, followed by a high resistance rate of 98% to cefalexin and ceftriaxone. Moderate resistance levels, ranging from 76% to 46%, were observed against streptomycin, tetracycline, trimethoprim-sulfamethoxazole, ciprofloxacin, kanamycin and nalidixic acid. In contrast, low resistance rates were reported for gentamicin, amikacin, and chloramphenicol, at 20%, 18%, and 16%, respectively.On the other hand, human isolates showed complete resistance (100%) to ampicillin, penicillin, cephalothin and cefalexin. Moderate resistance (76%-46%) was observed against ceftriaxone, kanamycin, cefotaxime, gentamicin, trimethoprim-sulfamethoxazole, nalidixic acid, streptomycin, and chloramphenicol. Low resistance levels were detected for tetracycline, ciprofloxacin, and amikacin, at 26%, 20%, and 6.6%, respectively.These findings along with the widespread presence of virulence genes (spvA, spiC, spvC, and pefA) in both human and poultry isolates, underscore the potential for cross-species transmission and the urgent need for enhanced surveillance. The regional findings from Annaba and Constantine emphasize the importance of stricter antibiotic use policies in poultry farming.
The etiological diagnosis of peripheral pulmonary infectious lesions (PPILs) is challenging due to the limitations of conventional microbiological methods (CMMs). This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid (BALF) obtained via radial endobronchial ultrasound (r-EBUS) for PPILs. This single-center, retrospective diagnostic accuracy study enrolled 110 patients with PPILs who underwent r-EBUS-guided BALF between January 2023 and December 2024. BALF samples were subjected to both mNGS and CMMs. The final diagnosis was established by two senior pulmonologists based on a comprehensive review of all clinical data. The diagnostic performance of mNGS and CMMs was compared against this final diagnosis. A definitive diagnosis was established in all 110 patients, with 68 cases identified as infectious lesions and 42 as non-infectious. The sensitivity of mNGS for detecting pathogens in infectious lesions was significantly higher than that of CMMs (89.7% vs. 47.1%, P < 0.001). The overall diagnostic accuracy of mNGS was also superior to CMMs (90.9% vs. 66.4%, P < 0.001). Among patients with positive mNGS results, clinical management was altered in 73.8% of cases based on the findings. mNGS uniquely identified pathogens in 31 cases that were missed by CMMs. For patients with PPILs, mNGS analysis of BALF samples obtained via r-EBUS demonstrates significantly greater diagnostic sensitivity and accuracy than conventional methods. This approach has a substantial impact on clinical decision-making, facilitating targeted antimicrobial therapy and representing a powerful tool in the diagnostic workflow for peripheral pulmonary infections.
Carbapenem-resistant Enterobacterales (CRE) infections are difficult to treat and are associated with high morbidity and mortality. Therefore, it is important to rapidly identify the carriers. This study aimed to investigate the clinical and microbiological risk factors associated with CRE colonization, infection, and mortality rates in adult intensive care unit (ICU) patients. A retrospective cohort analysis was performed in the adult ICU of Selahaddin Eyyubi State Hospital, Diyarbakır, Türkiye, between October 2022 and February 2024. Rectal swabs were obtained at ICU admission and weekly thereafter. Based on clinical, laboratory, and microbiological findings, the patients were categorized into colonized or infected groups. Demographic parameters, comorbidities, device use, previous antibiotic exposure, and mortality were analyzed using logistic regression, Kaplan-Meier survival estimates, and Cox proportional hazard modeling. Of the 420 patients, 69 (16.4%) were CRE-positive, 46 (66.7%) remained colonized, and 23 (33.3%) developed infections. The most frequent isolates were Klebsiella pneumoniae (63.8%) and Escherichia coli (36.2%). Independent risk factors for colonization included male sex, prolonged hospitalization, pulmonary or cerebrovascular disease, and prior exposure to β-lactam/β-lactamase inhibitors or cephalosporin antibiotics. CRE infection was related to prior β-lactam/β-lactamase inhibitor and carbapenem use. Mortality was 65.2% in the colonized-infected group versus 13% in those with colonization alone (P < 0.001). Overall survival was similar for CRE-positive and CRE-negative patients, but infected patients had higher mortality rates than colonized patients. CRE colonization in ICU patients poses a substantial risk once infection develops and is closely associated with broad-spectrum antibiotic exposure. These findings support routine rectal CRE screening as a key tool for identifying high-risk patients and informing antibiotic stewardship strategies aimed at preventing progression to fatal infections and improving survival.
Vancomycin-intermediate Staphylococcus aureus (VISA) strains represent a serious public health concern. It is crucial to investigate the genetic diversity, biofilm formation, and virulence analysis of VISA isolated from hospitalized patients. During the two-year study period, 42 VISA were obtained from 520 S. aureus isolates collected from various clinical samples, corresponding to a prevalence of 8.1%, as determined by the broth microdilution method. These VISA isolates were further characterized using biofilm formation, antimicrobial susceptibility tests, SCCmec typing, spa typing, multilocus sequence typing (MLST), and PCR analysis for detecting resistance (erm(B), tet(M), mecC, msr(B), mecA, mupA, vanA, aac(6')-Ie/aph(2˝), mupB, msr(A), erm(C), erm(A), vanB, ant(4')-Ia, and aph(3')-IIIa), biofilm (clfA, clfB, fnbA, fnbB, ebp, cna and bap) and virulence (eta, etb, pvl, and tst) genes. Our results indicated that the 42 VISA isolates belonged to three clonal complexes, including CC8 (78.6%), CC22 (11.9%), and CC5 (9.5%). The vast majority of S. aureus isolates belonged to CC8/ST239-SCCmec III/t037 (42.9%). Our result revealed that PVL-positive strains belonged to CC/ST5-SCCmec IV/t002 (9.5%), CC/ST8-SCCmec IV/t008 (19%), and CC/ST22-SCCmec IV/t790 (7.1%) while TST-positive isolates belonged to CC8/ST239-SCCmec III/t030 (9.5%) and CC8/ST239-SCCmec III/t037 (35.7%). The majority of HLMUPR isolates belonged to CC8/ST239-SCCmec III/t037 (14.3%), followed by CC/ST8-SCCmec IV/t008 (7.1%), CC8/ST239-SCCmec III/t030 (4.8%), and CC/ST5-SCCmec IV/t002 (2.4%) lineages carrying mupA. The highest frequency of VISA strain with iMLSB phenotype belonged to the CC8/ST239-SCCmec III/t037 (11.9%) clonal lineage. The study highlights that genetic diversity and characteristics of the VISA strains should be closely and continuously monitored. Besides that, importance of measures to prevent the transmission of VISA to treat such infection were urgently needed.
Invasive fungal infections caused by resistant Candida species are a global public health problem. Increasing antifungal resistance makes antifungal susceptibility tests (AFST) crucial, necessitating rapid methods. This study aims to determine the fluconazole and anidulafungin susceptibility profiles of clinical Candida strains using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and compare the results with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference broth microdilution method to assess the accuracy and reproducibility of MALDI-TOF MS in evaluating in vitro antifungal susceptibility. The susceptibilities of 40 Candida glabrata isolates for anidulafungin and fluconazole, and 40 Candida albicans and 40 Candida parapsilosis isolates for fluconazole were tested. Candida isolates were incubated for 3 h at two different antifungal concentrations ("maximum" and "breakpoint" concentrations) and a drug-free control (Anidulafungin: 16, 0.06, and 0 mg L-1; Fluconazole: 256, 16, and 0 mg L-1). MALDI-TOF MS spectra from these concentrations were used to create composite correlation index (CCI) matrices for each isolate. The strains with the "mean CCI of the breakpoint/maximum concentration" of which was higher than the "mean CCI of the breakpoint/null concentration" were classified as susceptible. Classifications defined by the MS-AFST method were compared to those based on the EUCAST broth microdilution method. The overall agreement between MS-AFST and EUCAST AFST ranged from 60% to 85%, highest for C. glabrata and anidulafungin. The reproducibility of the MS-AFST assay ranged from 45% to 75%, highest for C. parapsilosis and fluconazole. The study suggests that the MALDI-TOF MS method for assessing antifungal susceptibility in Candida strains is promising but requires further improvements for enhancing the accuracy and reproducibility.
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant challenge globally. This study reports on a ceftazidime-avibactam resistant KPC-35 producing K. pneumoniae strain from a patient with cerebral hemorrhage undergoing ceftazidime-avibactam (CZA) treatment. In this study, three K. pneumoniae strains were isolated from blood samples of a patient after intracerebral hemorrhage. Broth microdilution, checkerboard assays, and time-kill assays were employed to evaluate antimicrobial susceptibility and combination regimens. Whole-genome sequencing (WGS) was used to investigate the genetic characteristics of the three K. pneumoniae strains. The results showed that, K. pneumoniae KP29870 strain belonged to ST15, it was KPC-35 positive and exhibited a 16-fold higher minimum inhibitory concentration (MIC) of CZA (32 vs 1-2 mg L-1) but significantly lower MICs of imipenem (2 vs ≥ 16 mg L-1) and meropenem (1 vs ≥ 16 mg L-1), compared to the other two K. pneumoniae strains, that harboured KPC-2. CZA resistant K. pneumoniae remained highly susceptible to aztreonam-avibactam (MIC 0.03/4 mg L-1). The single base mutation (T503C) resulted in the substitution of leucine with proline at Ambler amino acid position 169 (L169P), corresponding to an evolution from blaKPC-2 to blaKPC-35. Checkerboard and time-kill assays demonstrated synergistic antibacterial effects for CZA combined with imipenem, meropenem, or with aztreonam against KPC-35 positive K. pneumoniae. This is the first report in China of a K. pneumoniae ST15 strain harboring blaKPC-35 emerging from a blaKPC-2-positive ancestor during CZA treatment. The new β-lactamase inhibitor combination such as aztreonam-avibactam monotherapy or CZA combined with carbapenems or with aztreonam represents promising treatment strategies against such KPC mutants. We recommend prompt susceptibility testing and KPC genotyping if resistance emergence is suspected during CZA therapy.
Lack of standardized criteria for discontinuing contact precautions (CP) in patients colonized or infected with multidrug-resistant bacteria (MDRB) can prolong isolation and strain healthcare resources. This retrospective cohort study aimed to assess the safety of a protocol-guided CP discontinuation strategy and identify risk factors for MDRB reacquisition. The study evaluated 88 adult patients under CP who met an institutional protocol for CP discontinuation between 2018 and 2023. The protocol required: no active infection; no antibiotic use in the preceding seven days; no drains or open wounds; no diarrhea; a negative culture from the initial site of MDRB identification; and a subsequent confirmatory negative screening (culture and/or PCR). Patients were followed for one year after CP discontinuation to assess MDRB reacquisition, defined as a new positive specimen for the same species. Potential risk factors for reacquisition were analyzed using multivariable Cox regression. At the one-year follow-up, MDRB reacquisition occurred in 17% (15/88) of patients. The reacquired pathogens included carbapenem-resistant Enterobacterales (9/50), methicillin-resistant Staphylococcus aureus (6/30), and vancomycin-resistant Enterococcus spp. (0/8). Independent risk factors for reacquisition were chronic obstructive pulmonary disease (HR 5.76, 95% CI 1.34-24.81), shorter duration of isolation (HR 0.98 per day, 95% CI 0.97-0.99), frequent hospitalizations (HR 1.75 per admission, 95% CI 1.07-2.88), and central venous catheterization (HR 13.04, 95% CI 2.63-64.69). Protocol-guided CP discontinuation was associated with a low rate of MDRB reacquisition and appears safe in appropriately selected patients. This approach may reduce unnecessary isolation in eligible patients, though high-risk individuals require closer monitoring.
Accurate and rapid identification of carbapenemase-producing Gram-negative bacteria is essential for appropriate antimicrobial therapy and infection control. This study compared the diagnostic performance of two multiplex lateral flow immunoassays, the NG-Test CARBA 5 (NG) and a Colloidal Gold Immunoassay (CGI), for the detection of major carbapenemases in clinical isolates of Klebsiella pneumoniae and Pseudomonas aeruginosa. A total of 100 non-duplicate carbapenem-resistant isolates collected in 2024 were included. An in-house polymerase chain reaction assay targeting blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48-like genes served as the reference standard.Overall, the NG assay demonstrated higher sensitivity than the CGI assay, while both tests showed excellent specificity. For OXA-48-like enzymes, both assays exhibited 100% specificity and 89.6% sensitivity. Detection of NDM was more sensitive with NG (96.9%) than with CGI (87.7%), whereas both maintained 100% specificity. For KPC detection, NG achieved 100% sensitivity, while CGI showed a markedly lower sensitivity (73.7%). Diagnostic performance was generally superior in K. pneumoniae compared with P. aeruginosa, and both assays showed reduced sensitivity in isolates co-harboring multiple carbapenemase genes.These findings indicate that although both lateral flow assays are rapid and practical tools for routine laboratory use, their performance may vary depending on the carbapenemase type and local epidemiology. Molecular confirmation remains essential, particularly in settings with a high prevalence of multiple carbapenemase-producing isolates.
Patients with advanced non-small cell lung cancer (NSCLC) are prone to lower respiratory tract infection (LRTI) during immune checkpoint inhibitor (ICI) treatment, but the pathogen spectrum and clinical impact remain unclear. This study provides comprehensive microbiological characterization of pathogen spectrum, molecular resistance mechanisms, and prognostic significance of LRTI during ICI treatment in patients with advanced NSCLC. A single-center retrospective cohort design was adopted, and 903 patients with advanced NSCLC who first received PD-1 or PD-L1 inhibitor treatment between January 1, 2019 and November 30, 2023 were included. Molecular characterization of resistant isolates was performed using PCR and sequencing for ESBL genes (blaCTX-M, blaSHV, blaTEM), carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48, blaOXA-23), and mecA, with multilocus sequence typing (MLST) for clonality analysis. Competing risk models estimated cumulative incidence of first LRTI; time-dependent Cox models evaluated associations with overall survival (OS) and progression-free survival (PFS). Among 903 patients, 176 (19.49%) developed LRTI during ICI treatment. Among 243 infection episodes, any phenotypic resistance was identified in 31 episodes (12.76%). Of 24 available resistant isolates, molecular characterization revealed blaCTX-M-15 as the predominant ESBL determinant (87.5%), blaKPC-2 and blaNDM-1 in CRE, blaVIM-2 and blaIMP-4 in CRPA, and blaOXA-23 in CRAB. MLST identified high-risk clones: K. pneumoniae ST11 (n = 3) and ST15 (n = 2), E. coli ST131 (n = 2), Pseudomonas aeruginosa ST235 (n = 3), A. baumannii ST2 (n = 6), and MRSA ST239 (n = 2). Older age, male sex, higher ECOG score, stage IV disease, COPD, ILD, baseline corticosteroid exposure, and higher NLR were associated with increased infection risk (all P < 0.05). First LRTI was independently associated with worse OS (HR = 1.78) and PFS (HR = 1.41). Fungal infection (HR = 2.48), mixed infection (HR = 2.34), resistance-associated infection (HR = 2.61), and severe infection (HR = 2.96) indicated worst prognosis. LRTI during ICI treatment in advanced NSCLC carries substantial burden and is associated with poor prognosis. Molecular characterization reveals that resistant infections are driven by established epidemic clones (ST2 CRAB, ST11 CRKP, ST235 CRPA, ST131 ESBL-EC), highlighting the need for enhanced infection control and targeted antimicrobial strategies in this vulnerable population.
The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.
This study reports on a multidrug-resistant (MDR) Acinetobacter baumannii isolate identified through microbiological surveillance of rectal swabs from a patient admitted to an intensive care unit (ICU) of a public hospital in Pernambuco, Brazil, in 2022. Bacterial identification and antimicrobial susceptibility testing were performed using the VITEK® automated system, and species confirmation was carried out by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of antibiotic resistance genes, including blaKPC, blaIMP, blaVIM, blaNDM, blaSPM, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and mcr-1 to mcr-10, was investigated by polymerase chain reaction (PCR). The A. baumannii isolate exhibited resistance to all tested antimicrobials and demonstrated strong biofilm-forming capacity. Molecular analysis revealed the presence of blaNDM-1, blaOXA-23 and blaOXA-58 genes, representing a concerning genetic combination associated with carbapenem resistance. The A. baumannii isolate exhibited resistance to polymyxin B but lacked mcr-1 to mcr-10 genes. Asymptomatic colonization of MDR A. baumannii in a patient at ICU underscores the risk of possible infection that may become invasive. These findings highlight the importance of continuous microbiological surveillance to monitor the dissemination of MDR pathogens in hospital environments.
Diarrhea is one of the leading infectious diseases, causing the greatest health burden in most developing countries, with Clostridioides difficile-associated diarrhea being the primary cause of hospital-acquired diarrhea. Given the demonstrated mortality associated with diarrhea and its consequences and the significant association between C. difficile and diarrhea, this study aimed to investigate the ribotype distribution of C. difficile isolated from patients with diarrhea in Ahvaz, Iran. From May to November of 2025, 50 patients with diarrhea were admitted to the hospital. The tpi gene was amplified by the PCR method to detect C. difficile isolates. The other method was a real-time PCR to identify C. difficile isolates from stool samples. The two diagnostic methods applied in this study were comparable. PCR was used to investigate the presence of C. difficile toxin genes. Among the 12 positive isolates, the tcdA gene was detected in 6/12 (50%) of the isolates. Additionally, 6/12 (50%) of the isolates was detected the tcdB gene. 1/12 C. difficile isolate was resistant to vancomycin, but all isolates were susceptible to metronidazole and fidaxomicin. Ribotype 001 was the most dominant (n = 4, 33.3%), with ribotype 126 representing the second most common at 25% (n = 3). Ribotype 070 (n = 2, 16.7%), 084 (n = 2, 16.7%), and 078 (n = 1, 8.3%) were detected at lower frequencies. The detection of toxin-producing genes in some isolates is also an indication of the bacterium's significant virulence potential. The findings indicated the need for ongoing surveillance of C. difficile and the antibiotic resistance characteristics in hospital settings.
The prognostic utility of plasma endotoxemia, marked by elevated lipopolysaccharide (LPS) and often associated with gut barrier dysfunction, remains undefined in acute ischemic stroke (AIS) patients with type 2 diabetes. In this single-center prospective cohort of 300 AIS patients with diabetes, we measured early admission plasma LPS and assessed its correlation with stroke severity and inflammatory markers, and its independent association with 90-day unfavorable functional outcome (modified Rankin Scale 3-6). Compared to the good outcome group, patients with poor outcomes had significantly higher LPS levels. Log-transformed LPS levels positively correlated with baseline NIHSS score, high-sensitivity C-reactive protein, and white blood cell count. After multivariable adjustment for age, NIHSS, HbA1c, atrial fibrillation, estimated glomerular filtration rate, and other covariates, each standard deviation increase in log-LPS was independently associated with an increased risk of 90-day unfavorable outcome (odds ratio 1.86, 95% CI 1.39-2.48). A clear dose-response relationship was observed, with the risk of poor outcome and mortality rising across LPS quartiles. Adding LPS to a basic clinical prediction model improved the area under the curve from 0.79 to 0.83, enhanced risk reclassification, and provided greater net clinical benefit across a range of decision thresholds. In conclusion, early admission plasma endotoxemia is an independent predictor of 90-day functional outcome in AIS patients with diabetes and improves conventional risk stratification. This finding positions LPS as a clinically accessible biomarker that is associated with poor recovery in acute ischemic stroke.