Search Results (222)

A novel lytic bacteriophage, XAN_XB1, was isolated from hospital wastewater through host bacterial enrichment and evaluated for its potential in controlling multidrug-resistant Stenotrophomonas maltophilia infections. Transmission electron microscopy revealed that XAN_XB1 has a long tail, possessing an icosahedral head of ~80 nm in diameter and a tail measuring ~150 nm in length. It produced clear plaques of 0.5–1 mm on host bacterial lawns. Host range analysis demonstrated its ability to infect multiple multidrug-resistant S. maltophilia isolates. Biological characterization showed that the phage is chloroform-insensitive, retains strong lytic activity across a wide temperature (4–60 °C) and pH (3.0–10.0) range, and achieves more rapid host suppression under higher multiplicity of infection (MOI). Whole-genome sequencing determined a ~47 kb double-stranded DNA genome encoding 71 predicted open reading frames, with no known virulence or antibiotic resistance genes. Phylogenetic analysis of MCP and terminase large subunit sequences placed XAN_XB1 in a unique Caudoviricetes, with ANI values below the 95% ICTV threshold verifying its status as a novel phage species. The XAN_XB1 therapy significantly alleviates S. maltophilia infection-induced severe pulmonary inflammatory lesions, high mortality, elevated serum inflammatory factors and massive pulmonary bacterial colonization in male BALB/c mice, confirming its favorable therapeutic effect on such infections. Collectively, these results reveal that is an efficacious candidate for therapeutic development against S. maltophilia infections. Full article

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥90%, contamination ≤5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia. Full article

Background/Objectives: Stenotrophomonas maltophilia is an opportunistic pathogen causing severe infections, particularly in patients with cystic fibrosis (CF). Its intrinsic multidrug resistance and biofilm-forming capacity complicate treatment. Although biofilms are generally associated with antimicrobial tolerance, the relationship between biofilm formation and planktonic antibiotic resistance in S. maltophilia remains poorly understood. This study investigated the association between antibiotic resistance profiles and biofilm production in clinical isolates from CF and non-CF patients. Methods: A total of 86 clinical isolates (40 from CF airways and 46 from non-CF patients) were analyzed. Susceptibility to seven antibiotics was assessed by disk diffusion, and multidrug resistance profiles were defined using standard criteria. Biofilm formation was quantified after 24 h using a crystal violet microtiter plate assay and categorized by using a semiquantitative scale. Results: High resistance rates were observed, particularly to meropenem (87.2%), ciprofloxacin (80.2%), and rifampicin (72.1%). CF isolates exhibited significantly higher resistance to piperacillin/tazobactam and a greater prevalence of multidrug resistance. Biofilm formation was detected in 94.2% of isolates, with strong or powerful producers predominating. However, CF isolates formed significantly less biofilm than non-CF isolates. Notably, resistance to piperacillin/tazobactam and meropenem was associated with reduced biofilm biomass and a lower proportion of high biofilm producers. Across all isolates, an inverse correlation was observed between the number of antibiotic resistances and biofilm biomass. These trends persisted after stratification by clinical origin, although some comparisons did not reach statistical significance. Conclusions: This study reveals an unexpected inverse relationship between planktonic antibiotic resistance and biofilm-forming capacity in S. maltophilia. Enhanced biofilm production may represent an alternative persistence strategy in more antibiotic-susceptible strains, with important implications for infection management and therapeutic failure. Full article

Blood culture remains the gold standard for identifying bloodstream infections caused by bacteria and fungi. Isolation of the culprit microorganism onto agar plates also facilitates antimicrobial susceptibility testing. The purpose of this study was to determine the contamination rates, pathogen profile, and antimicrobial resistance in a secondary healthcare setting in a two-year timeframe. In this study, data regarding blood cultures of the years 2023 and 2024 were retrospectively analyzed to address the above questions. Blood cultures were incubated for seven days before being discarded as negative. The percentage of positive blood cultures for both years was 14.3%. Most positive cultures contained Gram-positive cocci, with a prevalence of coagulase-negative Staphylococci. In descending order, 72.72% were coagulase-negative Staphylococci, 15.15% were Staphylococcus aureus, and 12.12% were Streptococci. One strain of S. aureus was methicillin-resistant (MRSA), and one strain of Enterococcus faecium was vancomycin-resistant (VRE). Of the Gram-negative rods, 78.3% were Enterobacterales. Of these, Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were the top pathogens. The remainder comprised eight strains of Pseudomonas aeruginosa, four strains of Acinetobacter baumannii (one pandrug-resistant), three strains of Stenotrophomonas maltophilia, one strain of Sphingomonas paucimobilis, and one strain of Campylobacter jejuni. The isolated fungi comprised Candida parapsilosis, Candida glabrata, and Candida tropicalis. Of the isolated Escherichia coli strains, 39.5% were resistant to ciprofloxacin regardless of origin (outpatient or hospitalized patients). Outpatient samples were taken in a Hemodialysis Unit that collaborates with our laboratory, obtained from patients with fever or other signs of infection. Distinguishing true bacteremia from contamination remains challenging. The contamination rate in our study was quite high at 5.3%. Since there is no dedicated phlebotomy team in our healthcare setting, in light of our results, educational courses have been conducted to demonstrate the best practices for sample collection. Full article

Background: Stenotrophomonas maltophilia is an intrinsically multidrug-resistant, biofilm- forming, non-fermenter increasingly implicated in hospital-acquired infections. Evidence from non-cystic fibrosis populations, especially in the Middle East, remains sparse. Methods: We conducted a retrospective observational cohort study at a tertiary academic center (Al-Khobar, Saudi Arabia) spanning 1 May 2001–30 April 2023. Hospitalized adults (≥18 years) with culture-confirmed, clinically diagnosed S. maltophilia infection and ≥72 h of antibiotic therapy were included. The primary outcome was all-cause mortality (14-day, 30-day, 1-year). Secondary outcomes were clinical response, microbiological eradication, and infection recurrence. Predictors of 30-day mortality were assessed using multivariable logistic regression; 14-day mortality was analyzed by Kaplan–Meier/log-rank according to susceptibility-guided versus alternative therapy. Results: Of 539 patients with positive cultures, 436 met the inclusion criteria. Mean age was 60.5 ± 19.3 years; 62.2% were male. Most infections were hospital-acquired (92.9%); pneumonia composed 64.7% and bloodstream infection 15.4%. Polymicrobial growth occurred in 55.5% (predominantly Gram-negative co-isolation). Susceptibility was 95.1% to trimethoprim–sulfamethoxazole, 76.4% to levofloxacin, and 43.6% to ceftazidime. Mortality at 14 days, 30 days, and 1 year was 22.8%, 37.9%, and 57.2%, respectively. On multivariable modelling, intensive care unit (ICU) admission, leukocytosis, neutrophilia, anemia, and thrombocytopenia independently predicted 30-day mortality. Susceptibility-guided therapy was associated with improved 14-day survival (log-rank p = 0.033). Conclusions: In this large, long-running non-cystic fibrosis cohort, host acuity and early alignment of treatment to susceptibility data were dominant drivers of outcome. High polymicrobial burden and limited reliably active agents underscore the need for meticulous stewardship, robust infection prevention, and cautious interpretation of S. maltophilia antimicrobial susceptibility testing. Full article

Stenotrophomonas maltophilia bloodstream infection (SM-BSI) carries high mortality and limited therapeutic options. We conducted a single-center retrospective cohort of adults with first SM-BSI (2018–2024) to describe treatment patterns and identify factors associated with survival. Demographic, clinical, and microbiological data were extracted and analyzed. Forty-three patients were included (median age: 63 years; 61% male). Appropriate antimicrobial therapy was given to 74%; trimethoprim–sulfamethoxazole-based regimens were used in 61%; and combination therapy in 23%. The median time from BSI to treatment initiation was 4 days (IQR: 3–5) and the treatment duration averaged 7 days (IQR: 0–12). Thirty-day mortality was 37% (16/43). The survival analysis found that a 14–21-day course was associated with better 30-day survival than a 7–13-day course (0/9 vs. 5/15 deaths; log-rank p = 0.045), whereas monotherapy and combination therapy did not differ (p = 0.855). Multidrug resistance was linked to worse survival (log-rank p = 0.001). In multivariable models for 30-day mortality, only active treatment (aHR: 0.14; 95% CI: 0.02–0.88) and microbiological cure (aHR: 0.08; 95% CI: 0.01–0.47) remained independently protective. These data suggest that outcomes in SM-BSI are driven primarily by the receipt of appropriate therapy and achievement of microbiological clearance, reinforcing the need for prompt source control, optimized antimicrobial treatment, and continued development of novel therapeutic strategies to improve outcomes in this challenging infection. Full article

Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host–microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa—including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica—was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization. Full article

Antagonistic endophytes are one of the most effective methods for crop disease biocontrol. This study reports on a convenient method termed ‘Targeted Identification of Disease-resistant Endophytes’ (TIDRE), which combines the isolation of culturable endophytic isolates from plant tissues with the screening of phytopathogen-antagonistic microbes. In addition to the direct discovery of endophytes with resistance to specific phytopathogens, the TIDRE method also facilitates the screening of endophyte-based disease-resistant crop lines. Using the TIDRE protocol, we successfully isolated endophytic bacterial strains with antagonistic activity against the pathogenic fungus Fusarium oxysporum from a traditional Chinese medicinal herb Panax notoginseng. These candidate bacteria included three Bacillus subtilis strains, a Stenotrophomonas maltophilia strain, a Pantoea brenneri strain, and a Bacillus sp. strain. Furthermore, we identified grapevine cutting clones with strong resistance to three fungal pathogens: Botrytis cinerea, F. solani, and F. graminearum, by using the TIDRE protocol. The endophytic bacterial strains (Bacillus) isolated from the highly resistant grapevine clones confer significant antagonistic effects against the fungal pathogens. Compared to existing methods, TIDRE offers superior speed and efficiency, and great potential for advancing the development and utilization of beneficial endophytic resources in sustainable agriculture. Full article

Fresh produce represents a key interface in the One Health continuum, connecting environmental, agricultural and clinical settings where opportunistic bacteria can circulate. Among them, Stenotrophomonas comprises an environmental genus of growing concern due to its multidrug resistance and rising clinical relevance. To investigate their diversity and pathogenic potential, nineteen isolates from vegetables, irrigation water and hospital sources were characterized by MLST, growth kinetics, biofilm formation, antimicrobial susceptibility assays and whole-genome sequencing. Phylogenetic analyses grouped 12 isolates within the Stenotrophomonas maltophilia complex (SMC) (clinical S. maltophilia (n = 7) and environmental S. geniculata (n = 4) and S. sepilia (n = 1)) and seven non-SMC isolates, including S. indicatrix (n = 5) and two unclassified clinical strains. Environmental S. geniculata and S. sepilia isolates showed robust growth at 37 °C and biofilm formation comparable to clinical lineages. Genomic analyses further revealed shared mobile loci (afaD, fhaB, zot) and homologous plasmids between environmental and clinical isolates, suggesting a connected gene pool. The identification of environmental strains with virulence-associated traits and clinical-like phenotypes supports fresh produce as a potential reservoir and transmission route for opportunistic Stenotrophomonas, underscoring the need for integrated surveillance across the food–health interface. Full article

Background/Objectives: Stenotrophomonas maltophilia (SM) is a significant cause of hospital-acquired infections in immunocompromised and critical care patients. This study investigates the impact of combining ceftazidime/avibactam (CZA) with conventional antibiotics on SM obtained from various sources in planktonic and biofilm cell cultures. Methods: Using broth microdilution, the MICs of different antibiotics, including CZA, were determined on 37 SM strains. CZA’s bactericidal and synergistic effectiveness were examined through in vitro time–kill curve tests with tigecycline (TGC), chloramphenicol (CHL), levofloxacin (LVX), colistin (CS), and amikacin (AMK). In addition, synergistic activity was investigated against SM biofilm cell cultures, and antibiotic Mutant Prevention Concentrations (MPCs) were tested against SM isolates. Results: Compared to ceftazidime (CAZ), CZA was four times more efficient against 37 SM strains. Unlike TGC and CHL, CS, AMK, and CZA had 2–4 times higher MBCs than MICs. All studied antibiotics were bactericidal at 1× or 4× MIC doses against SM bacteria, except for CZA. The combinations of CZA with LVX and CZA with AMK or CS demonstrated synergistic effects in four out of seven (57%) strains and in three out of seven (43%) strains, respectively, when tested at doses equivalent to the MIC. Moreover, all antibiotic combinations with CZA showed a synergistic effect at dosages four times the MIC. Additionally, CZA and the tested drugs synergistically inhibited SM biofilm formation, and MPC values were 8–16 times the MIC. Conclusions: The results of this study indicate that combining CZA with LVX and CS was more effective against SM strains. These combinations might provide alternatives for treating SM pathogens in both planktonic and biofilm cell cultures. Full article

Background: The Songnen Plain in China contains soda saline–alkaline soil, wherein salinity and alkalinity severely constrain crop productivity. Alfalfa (Medicago sativa L.) is a forage legume that has adapted to moderate saline–alkaline conditions, but how its rhizosphere microbial community facilitated this adaptation remains unclear. Methods: Using 16S rRNA gene sequencing, we compared alfalfa rhizosphere bacteria in saline–alkaline soil (AS) and control soil. Bacteria isolated from AS were screened for plant growth-promoting traits, with the most effective strains validated in pot experiments involving 50 mM NaHCO₃. Results: Compared with the control soil bacterial community, the AS bacterial community was significantly enriched with Methylomirabilota and unclassified bacteria (phylum level), with the genus RB41 identified as the most discriminative biomarker. Gene functions predicted using PICRUSt2 reflected the responsiveness of this community to environmental stressors. Inoculations with Pseudomonas laurentiana strain M73 and Stenotrophomonas maltophilia strain M81, which were isolated from AS, significantly improved alfalfa growth and health under NaHCO₃ stress. Conclusions: Saline–alkaline conditions in the Songnen Plain reshape the alfalfa rhizosphere bacterial community, enriching for specific taxa and potentially enhancing microbial functions associated with stress resistance. Strains M73 and M81 can effectively promote stress tolerance, making them useful microbial resources for improving soil conditions. Full article

The gut microbiome regulates multiple physiological processes of the host and plays a significant role in the adaptation of wild animal hosts to extreme environments. The saxaul sparrow (Passer ammodendri) is a typical bird species found in the northwest of China, characterized by its strong adaptability to extreme environments. Studying it can help reveal the microbial adaptation mechanisms of the host to extreme environments. Therefore, we conducted a comparative analysis of the intestinal microbial community characteristics and functions of the saxaul sparrow in high-altitude (Pamir Plateau) and desert (Tazhong Town) habitats in Xinjiang. The results of full-length 16S rRNA sequencing and species annotation indicated that the bacterial species composition (relative abundance > 0.1%) of the intestinal microbiota community of the saxaul sparrow was Candidatus Arthromitus sp. SFB rat Yit, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, and Klebsiella pneumoniae, in sequence. In addition, Lysinibacillus sphaericus is a unique strain specific to the Tazhong group, while Stenotrophomonas maltophilia has a much higher abundance in the Tazhong group than in the Pamir Plateau group. It is worth noting that both groups of samples contain potential opportunistic pathogenic bacteria, such as Escherichia coli and Klebsiella pneumoniae. The Shannon index of the Pamir Plateau group was lower than that of the Tazhong Town group (p = 0.0026), indicating that the intestinal microbial diversity of the Pamir Plateau group was lower than that of the Tazhong Town group. However, there was no significant difference in the ACE index between the two groups and it was not statistically significant (p > 0.05). The Beta diversity analysis revealed that the distance between the two groups of samples was considerable (p = 0.001), indicating a significant separation. The functional annotation results indicated that the Pamir Plateau group exhibited enhanced capabilities in carbohydrate metabolism, energy metabolism, and DNA damage repair, while the Tazhong Town group demonstrated enhanced lipid metabolism and detoxification abilities. These findings will help reveal the possible impact of the living environment on the composition and function of the intestinal microbiota of the saxaul sparrow, fill the gap in comparative studies of the intestinal microbiota characteristics of the saxaul sparrow in two extreme environments, and provide new theoretical support for subsequent related research. Full article

Stenotrophomonas maltophilia is considered one of the emerging bacterial agents causing healthcare-associated infections (HAIs) in hospital environments. This microorganism has been identified as multidrug-resistant, capable of forming mature biofilms—an ability that promotes adherence to surfaces and invasive medical devices, favoring persistence in hospital environments and the potential to generate outbreaks. The aim of this study was to characterize S. maltophilia strains isolated from HAI cases at the Hospital Juárez de México and to determine the presence of hidden outbreaks. Antibiotic resistance profiles were determined, along with the typing of 20 genes associated with virulence factors and the assessment of the ability to form mature biofilms on inert surfaces. Finally, sequence type (ST) was obtained through multilocus sequence typing (MLST) analysis, and a phylogenetic tree was constructed to determine the clonal diversity of the isolates. All strains showed uniform resistance to β-lactam antibiotics tested while remaining sensitive to fluoroquinolones, phenicols, tetracyclines, and trimethoprim/sulfamethoxazole. Some isolates exhibited adherent activity, with the “strong biofilm-former” phenotype predominating. Sixteen virulence-related genes were heterogeneously detected, revealing broad genetic diversity. MLST analysis grouped the isolates into nine ST related to infection cases reported in others countries. Phylogenetic analyses demonstrated the presence of three potential clones distributed across Internal Medicine and the Pediatric Intensive Care Unit. These results highlight the importance of investigating S. maltophilia as an HAI-associated pathogen that remains understudied. Full article

Stenotrophomonas maltophilia (S. maltophilia) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on S. maltophilia infections in recent years, and the species is becoming a public health concern. Many studies have focused on profiling and pangenome of the species, particularly on their antibiotic resistance and virulence genes. However, there is a lack of studies on mobile genetic elements (MGEs), a subset of pangenome that significantly contributes to the diversity, stability, and plasticity of a population. In this study, 20 genomes of S. maltophilia were downloaded from the NCBI Genome database. The genomes were subjected to profiling of MGEs, their impact on the population structures, and the evaluation of evolutionary trends of the core genomes. The cataloguing of MGEs indicated active horizontal gene transfer events in the S. maltophilia’s population. Multiple virulence and drug resistance genes were predicted within and outside of the MGEs. We observed multiple chromosomal rearrangements in the genomes, most likely caused by MGEs, affecting up to approximately 50% of a single genome sequence. A high number of linkage disequilibrium sites were also predicted in the core genomes. This study provides insights into stability in the core and plasticity in the accessory regions in the S. maltophilia population. Full article

Stenotrophomonas maltophilia is a nosocomial pathogen that is resistant to many broad-spectrum antibiotics. This study aimed to evaluate the in vitro synergy of trimethoprim/sulfamethoxazole (SXT) combined with levofloxacin (LEV) or ceftazidime (CAZ) using checkerboard and gradient diffusion methods. Between 2016 and 2021, 20 S. maltophilia strains (five SXT-resistant and 15 SXT-susceptible strains) were collected from various clinical settings. Their susceptibility to SXT, LEV, and CAZ was assessed using both checkerboard and gradient diffusion synergy tests. The gradient diffusion method was performed using commercial strip-based tests (Liofilchem^®). It should be noted that the gradient diffusion method has not been standardized by the Clinical and Laboratory Standards Institute (CLSI) for synergy testing and is considered for research purposes only. In the checkerboard method, the SXT + LEV combination showed synergy in one strain and an additive effect in 19 strains; the SXT + CAZ combination exhibited synergy in eight strains and an additive effect in 12 strains. In the gradient diffusion method, the SXT + LEV combination showed synergy in one strain and an additive effect in 19 strains; the SXT + CAZ combination exhibited synergy in five strains, an additive effect in 14 strains, and antagonism in one strain. A correlation between the two methods was observed in 90% of SXT + LEV combinations and 65% of SXT + CAZ combinations. Both checkerboard and gradient diffusion methods yielded similar results, indicating their reliability in determining antibiotic combinations. Given the observed synergy, CAZ combinations may be effective for treating SXT-resistant strains. Full article