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Key Points Stenotrophomonas spp. are found throughout the environment, particularly in close association with plants. Currently, the genus comprises eight validly described species: Stenotrophomonas maltophilia , Stenotrophomonas nitritireducens , Stenotrophomonas rhizophila , Stenotrophomonas acidaminiphila , Stenotrophomonas chelatiphaga , Stenotrophomonas koreensis , Stenotrophomonas terrae and Stenotrophomonas humi . Stenotrophomonas spp. have an important ecological role in the nitrogen and sulphur cycles and several Stenotrophomonas spp. can engage in beneficial interactions with plants, promoting growth and protecting plants from attack. These bacteria can degrade many xenobiotic compounds and so have the potential to be agents for bioremediation. S. maltophilia is the only species of Stenotrophomonas that is known to cause human disease and is a cause of bacteraemia, septicaemia and severe lung infections in patients with cystic fibrosis. S. maltophilia has also been shown to possess a cell–cell signalling system that is mediated by a diffusible signal factor and is involved in modulating the production of extracellular protease, biofilm behaviour and virulence. Determination of the genome sequences of clinical and endophytic S. maltophilia strains has formed the basis for functional genomic analyses to test the contribution of specific functions to the tenacity of these bacteria in colonization, their broad resistance to antibiotics and their ability to enter into close associations with plants and humans. Bacteria from the genus Stenotrophomonas are found in a wide range of different environments. Here, Ryan et al . compare the recently sequenced genomes of two different Stenotrophomonas species to highlight the possible genetic basis of adaptation to these different niches. The genus Stenotrophomonas comprises at least eight species. These bacteria are found throughout the environment, particularly in close association with plants. Strains of the most predominant species, Stenotrophomonas maltophilia , have an extraordinary range of activities that include beneficial effects for plant growth and health, the breakdown of natural and man-made pollutants that are central to bioremediation and phytoremediation strategies and the production of biomolecules of economic value, as well as detrimental effects, such as multidrug resistance, in human pathogenic strains. Here, we discuss the versatility of the bacteria in the genus Stenotrophomonas and the insight that comparative genomic analysis of clinical and endophytic isolates of S. maltophilia has brought to our understanding of the adaptation of this genus to various niches.

Stenotrophomonas spp. are increasingly recognized as opportunistic pathogens with high levels of antimicrobial resistance (AMR). Despite their clinical importance, genomic diversity within the genus remains underexplored, particularly in Thailand and Southeast Asia. Ten Stenotrophomonas strains were isolated from diverse clinical specimens at Songklanagarind Hospital, Thailand, in 2023. Whole genome sequencing was performed using MGISEQ 2000 platform. Genome-based classification was assessed via average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH). Functional annotation was conducted using RAST and COG databases. Pan-genome structure, AMR/virulence genes, and phenotypic traits (biofilm and hemolysis) were investigated. The genomes ranged from 4.11 to 5.05 Mb with 66.02–66.84% GC content. While 16S rRNA gene sequences showed high similarity to type strains, ANI and dDDH analyses clearly differentiated the ten studied strains from validly published species and grouped them into five putative novel genospecies. The pan-genome was open, with only 21.6% core, 1.5% soft-core and 76.9% accessory/unique genes, indicating high plasticity. Functional annotation revealed enrichment in genes related to regulation, metabolism, and cell envelope biogenesis, reflecting metabolic flexibility and environmental adaptability. AMR profiling showed conserved aminoglycoside-modifying enzymes, β-lactamase bla L1 and efflux pumps across all strains. Phenotypically, all strains exhibited multidrug resistance but remained uniformly susceptible to cotrimoxazole, the current treatment of choice. Virulence genes for adhesion, hemolysin, proteases, and biofilm were conserved, consistent with observed α-hemolysis and moderate-to-strong biofilm formation. This study reveals substantial genomic and functional diversity among ten Stenotrophomonas strains, highlighting five putative novel genospecies and underscoring the importance of continued surveillance and accurate identification for effective clinical management strategies.

Five autotrophic strains isolated from non-photosynthetic microbial communities (NPMCs), which were screened from oceans with high CO sub(2) fixing capability, were identified as Ochrobactrum sp. WH-2, Stenotrophomonas sp. WH-11, Ochrobactrum sp. WH-13, Castellaniella sp. WH-14, and Sinomicrobium oceani WH-15. The CO sub(2) fixation pathways of all these strains were Calvin-Benson-Bassham pathway. These strains could metabolize multifarious organic compounds, which allowed switching them to autotrophic culture after enrichment in heterotrophic culture. The central composite response surface method indicated that these strains possessed many interactive effects, which increased the CO sub(2) fixing efficiency of a combined community composed of these strains by 56 %, when compared with that of the single strain. Furthermore, another combined community composed of these autotrophic strains and NPMC had richer interactive relationships, with CO sub(2) fixing efficiency being 894 % higher than that of the single strain and 148 % higher than the theoretical sum of the CO sub(2) fixing efficiency of each of its microbial components. The interaction between strictly heterotrophic bacteria in NPMC and isolated autotrophic strains played a crucial role in improving the CO sub(2) fixing efficiency, which not only eliminated self-restraint of organic compounds generated during the growth of autotrophic bacteria but also promoted its autotrophic pathway.

Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.

Drinking-water distribution systems (DWDS) impose ecological pressures shaped by oligotrophy, surface attachment, hydraulic fluctuation, and residual disinfectants. These conditions may favor stress-tolerant and biofilm-capable microorganisms, including members of the Stenotrophomonas maltophilia complex. Although this complex is clinically relevant because of intrinsic multidrug resistance and opportunistic pathogenic potential, the strain-level genomic features that may support persistence in disinfectant-managed water systems remain incompletely characterized. We applied an integrated genome-resolved framework to Stenotrophomonas sp. NG-SM01, a drinking-water isolate assigned to the S. maltophilia complex genomospecies Sgn4. Hybrid sequencing was used to generate a closed genome assembly, followed by phylogenomics and MLST for taxonomic placement, pangenome analysis for gene-content context, and genomic-island mapping to identify candidate accessory regions. Functional profiling included BacMet screening for metal/biocide tolerance-associated loci and genome-scale metabolic reconstruction using gapseq. Phenotypic assays assessed crystal-violet biofilm biomass and acute hydrogen peroxide (H₂O₂) survival as a general oxidative-stress proxy. NG-SM01 clustered within the Sgn4 genomospecies of the S. maltophilia complex and formed a strongly supported sister lineage to its closest available reference genome, GCF_025642255.1 (UFboot = 100). MLST confirmed a newly curated guaA allele ( guaA -909), and the allelic profile was assigned ST1409. Disk diffusion showed limited inhibition by several antimicrobial agents; however, categorical interpretation using S. maltophilia -specific CLSI criteria was applied only to levofloxacin and trimethoprim–sulfamethoxazole, both of which were susceptible. Genomic-island analysis highlighted two candidate loci potentially relevant to stress adaptation: GI_6, carrying an EPS/envelope-remodeling cassette including algL and a GT26-family glycosyltransferase within a panel-restricted architecture, and GI_4, an IME-associated region located near SOS-response genes including recA , recX , and lexA . NG-SM01 formed reproducible moderate biofilm biomass under static microtiter conditions and showed plateau-like survival dynamics during acute H₂O₂ exposure. BacMet screening prioritized Tier-1 metal/biocide tolerance-associated signals, including CzcR-like and AdeL-like regulators and a YfeB-like transport component, while gapseq reconstruction predicted broad transport capacity, including 1,920 transporter entries, of which 23% were metal-related. This single-isolate study identifies genomic and phenotypic features potentially relevant to persistence in a drinking-water S. maltophilia complex Sgn4 isolate. The combined evidence supports a hypothesis-generating “Switch–Shield” framework, in which stress-response regulation and mobilome-associated plasticity may represent a candidate “switch,” while EPS/envelope remodeling may represent a candidate protective “shield.” However, direct causality between GI_4/GI_6 and the observed phenotypes was not demonstrated. Future validation using transcriptomics, mutant-based assays, and DWDS-mimetic free-chlorine or chloramine exposure models, including flow/pipe reactors with detachment and shedding measurements, will be required to test this model.

The membrane-associated F sub(1)F sub(0)-ATP synthase of bacteria plays a vital role in the production of energy molecule, i.e. adenosine triphosphate (ATP). However, under alkaline conditions, ATP synthesis in bacteria is not thermodynamically feasible due to external high pH. Various studies reported motifs in ATP synthase c-subunit as alkaliphile-specific features for adaptation under alkaline condition. Some conserved residues in alkaliphiles were observed in Stenotrophomonas species DL18 isolated from Indian alkaline Soda Lake, Lonar, which has pH 10.5. The above-mentioned specific amino acid features in the studied alkaliphile may involve proton translocating mechanism for ATP synthesis. The studied motifs of F sub(1)F sub(0)-ATP synthase c-subunit of Stenotrophomonas species DL18 have GXGXGXA in the inner helix and GXXDXXF in the outer helix. The overall interacting residues of the c-subunit structure may be responsible for the ATP synthesis in particular pH conditions.

is a prominent genus owing to its dual nature. Species of this genus have many applications in industry and agriculture as plant growth-promoting rhizobacteria and microbial biological control agents, whereas species such as are considered one of the leading gram-negative multi-drug-resistant bacterial pathogens because of their high contribution to the increase in crude mortality and significant clinical challenge. Pathogenic species and most clinical isolates belong to the complex (SMc). However, a strain highly homologous to was isolated from a patient with pulmonary tuberculosis (TB), which aroused our interest, as belongs to a relatively distant clade from SMc and there have been no human association reports. The pathogenicity, immunological and biochemical characteristics of 610A2 were systematically evaluated. 610A2 is a new species of genus , which is named as sp. nov. for its obvious brown water-soluble pigment. 610A2 is pathogenic and caused significant weight loss, pulmonary congestion, and blood transmission in mice because it has multiple virulence factors, haemolysis, and strong biofilm formation abilities. In addition, the cytokine response induced by this strain was similar to that observed in patients with TB, and the strain was resistant to half of the anti-TB drugs. The pathogenicity of 610A2 may not be weaker than that of . Its isolation extended the opportunistic pathogenic species to all 3 major clades of the genus , indicating that the clinical importance of species of other than and potential risks to biological safety associated with the use of require more attention.

Multiple antibiotic resistance mechanisms, including two β-lactamases, L1, a metallo-β-lactamase, and L2, a class A cephalosporinase, make S. maltophilia naturally multidrug resistant. Thus, infections caused by S. maltophilia pose a big therapeutic challenge. Our study aims to understand the microbiological and molecular characteristics of S. maltophilia isolates recovered from human sources. A highlight of the resistance profile of this collection is the excellent activity of the ceftazidime-avibactam and aztreonam combination. We hope this result prompts controlled and observational studies to add clinical data on the utility and safety of this therapy. We also identify 35 and 43 novel variants of L1 and L2, respectively, some of which harbor novel substitutions that could potentially affect substrate and/or inhibitor binding. We believe our results provide valuable knowledge to understand the epidemiology of this species and to advance mechanism-based inhibitor design to add to the limited arsenal of antibiotics active against this pathogen. Stenotrophomonas maltophilia is a Gram-negative, nonfermenting, environmental bacillus that is an important cause of nosocomial infections, primarily associated with the respiratory tract in the immunocompromised population. Aiming to understand the population structure, microbiological characteristics and impact of allelic variation on β-lactamase structure and function, we collected 130 clinical isolates from across the United States. Identification of 90 different sequence types (STs), of which 63 are new allelic combinations, demonstrates the high diversity of this species. The majority of the isolates (45%) belong to genomic group 6. We also report excellent activity of the ceftazidime-avibactam and aztreonam combination, especially against strains recovered from blood and respiratory infections for which the susceptibility is higher than the susceptibility to trimethoprim-sulfamethoxazole, considered the “first-line” antibiotic to treat S. maltophilia . Analysis of 73 bla L1 and 116 bla L2 genes identified 35 and 43 novel variants of L1 and L2 β-lactamases, respectively. Investigation of the derived amino acid sequences showed that substitutions are mostly conservative and scattered throughout the protein, preferentially affecting positions that do not compromise enzyme function but that may have an impact on substrate and inhibitor binding. Interestingly, we detected a probable association between a specific type of L1 and L2 and genomic group 6. Taken together, our results provide an overview of the molecular epidemiology of S. maltophilia clinical strains from the United States. In particular, the discovery of new L1 and L2 variants warrants further study to fully understand the relationship between them and the β-lactam resistance phenotype in this pathogen. IMPORTANCE Multiple antibiotic resistance mechanisms, including two β-lactamases, L1, a metallo-β-lactamase, and L2, a class A cephalosporinase, make S. maltophilia naturally multidrug resistant. Thus, infections caused by S. maltophilia pose a big therapeutic challenge. Our study aims to understand the microbiological and molecular characteristics of S. maltophilia isolates recovered from human sources. A highlight of the resistance profile of this collection is the excellent activity of the ceftazidime-avibactam and aztreonam combination. We hope this result prompts controlled and observational studies to add clinical data on the utility and safety of this therapy. We also identify 35 and 43 novel variants of L1 and L2, respectively, some of which harbor novel substitutions that could potentially affect substrate and/or inhibitor binding. We believe our results provide valuable knowledge to understand the epidemiology of this species and to advance mechanism-based inhibitor design to add to the limited arsenal of antibiotics active against this pathogen.

This study aimed to evaluate the biofilm formation and disinfectant tolerance of Stenotrophomonas maltophilia strains originated from hospitalized patients during the COVID-19 pandemic. Nine strains were isolated from different clinical departments at a hospital in Brazil, were identified by VITEK®2, Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, 16S rRNA sequencing, and 23S rRNA PCR. Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR), Fourier-transform infrared (FTIR) spectroscopy, antimicrobial susceptibility testing, and biofilm formation and disinfectant tolerance tests were applied. ERIC-PCR, FTIR, and VITEK®2 results exhibited no correlation between the strains, indicating different origins in the Hospital. Most strains expressed resistance to several antibiotics but minocycline and cefiderocol, which were therefore regarded as optimistic therapy options. All strains produced biofilms on polystyrene and most of them (n = 7) on stainless-steel surfaces. The sodium hypochlorite 0.5% was shown to be the most efficient disinfectant for biofilm eradication. Biofilm formation and tolerance to disinfectants analysis indicated the requirement for efficient cleaning protocols to eliminate S. maltophilia contamination.

Abstract Stenotrophomonas maltophilia is an emerging global opportunistic pathogen that causes nosocomial infections. We demonstrated that the superoxide stress-sensing transcriptional regulator SoxR directly modulated the expression of an operon encompassing sodA1 (encoding manganese-containing superoxide dismutase) and fre (encoding putative flavin reductase) by directly binding to the operator site, which was located between the −35 and −10 motifs of the sodA1 promoter. It is known that upon exposure to the superoxide generators/redox-cycling drugs, the SoxR, which is bound to the operator site, became oxidized. This oxidation causes a conformational change of SoxR to an active form, enabling the upregulation of sodA1–fre gene expression. A ΔsodA1 was constructed, and the mutant showed enhanced sensitivity to the redox-cycling drugs, including menadione, plumbagin, and methyl viologen (paraquat), relative to its parental strain K279a. Thus, sodA1 may play a role in the survival of S. maltophilia under superoxide stress during either its saprophyte stage (e.g. exposure to redox-cycling drugs) or host–pathogen interactions. sodA1 may play a role in the survival of Stenotrophomonasmaltophilia under superoxide stress during either its saprophyte stage (e.g. exposure to redox-cycling drugs) or host–pathogen interactions.