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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.

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.

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.

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.

represents a group of bacteria that exhibit significant value in industrial and agricultural applications, while also posing pathogenic risks to humans. 704A1 was isolated from a patient with tuberculous pleurisy. Its 16S rRNA sequence showed the highest homology (99.72%) with a strain without defined species classification. It is necessary to clarify the species 704A1 belonging to and its potential pathogenicity to humans. Systematical evaluations including phenotypic and biochemical characteristics, antibiotic susceptibility, genomic sequencing were conducted. The pathogenicity and immunological characteristics were tested by intranasally inoculated C57BL/6J mice. 704A1 is Gram negative rod-shaped bacterium with flagella at single extreme. Showing highly similar with , 704A1 also displayed distinct characteristic peaks in fatty acid profiling and MALDI-TOF analysis. 704A1 was resistance to 21 antibiotics, including four anti-tuberculosis drugs: rifampicin, streptomycin, rifabutin, and cycloserine. The average nucleotide identity (ANI) values of 704A1 compared to defined species ranged from 80.03% to 89.6%, below than both the commonly accepted 95%-96% ANI threshold for prokaryote species and the 95% threshold suggested for . Though no mortality was observed, 704A1 could cause severe consolidation in murine lung tissue and has the ability of hematogenous dissemination. Results supported the classification of 704A1 (=GDMCC 1.4133 ) as a novel species within the genus , for which the name sp. nov. is proposed. 704A1 is a multi-antibiotic resistance strain with potentially stronger pathogenicity than and requires more clinical attention. The isolation of 704A1 underscored the importance of sustained surveillance and taxonomic clarity of species emerging from clinical environments.

Background In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host. Results We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405 T (both are biocontrol agents). We found an overall high degree of sequence similarity between the genomes of all three strains. Despite the notable similarity in potential factors responsible for host invasion and antibiotic resistance, other factors including several crucial virulence factors and heat shock proteins were absent in the plant-associated DSM14405 T . Instead, S. rhizophila DSM14405 T possessed unique genes for the synthesis and transport of the plant-protective spermidine, plant cell-wall degrading enzymes, and high salinity tolerance. Moreover, the presence or absence of bacterial growth at 37°C was identified as a very simple method in differentiating between pathogenic and non-pathogenic isolates. DSM14405 T is not able to grow at this human-relevant temperature, most likely in great part due to the absence of heat shock genes and perhaps also because of the up-regulation at increased temperatures of several genes involved in a suicide mechanism. Conclusions While this study is important for understanding the mechanisms behind the emerging pattern of infectious diseases, it is, to our knowledge, the first of its kind to assess the risk of beneficial strains for biotechnological applications. We identified certain traits typical of pathogens such as growth at the human body temperature together with the production of heat shock proteins as opposed to a temperature-regulated suicide system that is harnessed by beneficials.

Carbapenem antimicrobials are critically important to human health and they are often the only remaining effective antibiotics for treating serious infections. Resistance to these drugs mediated by acquired carbapenemase enzymes is increasingly encountered in gram-negative bacteria and is considered a public health emergency. Animal origin food products are recognized as a potential source of resistant organisms, although carbapenem resistance has only recently been reported. In western countries there are active resistance surveillance programs targeting food animals and retail meat products. These programs primarily target beef, pork and poultry and focus exclusively on E. coli, Salmonella, Campylobacter spp. and Enterococcus spp. This global surveillance strategy does not capture the diversity of foods available nor does it address the presence of resistance gene-bearing mobile genetic elements in non-pathogenic bacterial taxa. To address this gap, a total of 121 seafood products originating in Asia purchased from retail groceries in Canada were tested. Samples were processed using a taxa-independent method for the selective isolation of carbapenem resistant organisms. Isolates were characterized by phenotypic antimicrobial susceptibility testing, PCR and DNA sequencing. Carbapenemase producing bacteria, all blaOXA-48, were isolated from 4 (3.3%) of the samples tested. Positive samples originated from China (n=2) and Korea (n=2) and included squid, sea squirt, clams and seafood medley. Carbapenemase producing organisms found include Pseudomonas, Stenotrophomonas and Myroides species. These findings suggest that non-pathogenic bacteria, excluded from resistance surveillance programs, in niche market meats may serve as a reservoir of carbapenemase genes in the food supply.

Bacterial type IV secretion systems (T4SS) are a highly diversified but evolutionarily related family of macromolecule transporters that can secrete proteins and DNA into the extracellular medium or into target cells. It was recently shown that a subtype of T4SS harboured by the plant pathogen Xanthomonas citri transfers toxins into target cells. Here, we show that a similar T4SS from the multi-drug-resistant opportunistic pathogen Stenotrophomonas maltophilia is proficient in killing competitor bacterial species. T4SS-dependent duelling between S. maltophilia and X. citri was observed by time-lapse fluorescence microscopy. A bioinformatic search of the S. maltophilia K279a genome for proteins containing a C-terminal domain conserved in X. citri T4SS effectors (XVIPCD) identified twelve putative effectors and their cognate immunity proteins. We selected a putative S. maltophilia effector with unknown function (Smlt3024) for further characterization and confirmed that it is indeed secreted in a T4SS-dependent manner. Expression of Smlt3024 in the periplasm of E. coli or its contact-dependent delivery via T4SS into E. coli by X. citri resulted in reduced growth rates, which could be counteracted by expression of its cognate inhibitor Smlt3025 in the target cell. Furthermore, expression of the VirD4 coupling protein of X. citri can restore the function of S. maltophilia ΔvirD4, demonstrating that effectors from one species can be recognized for transfer by T4SSs from another species. Interestingly, Smlt3024 is homologous to the N-terminal domain of large Ca2+-binding RTX proteins and the crystal structure of Smlt3025 revealed a topology similar to the iron-regulated protein FrpD from Neisseria meningitidis which has been shown to interact with the RTX protein FrpC. This work expands our current knowledge about the function of bacteria-killing T4SSs and increases the panel of effectors known to be involved in T4SS-mediated interbacterial competition, which possibly contribute to the establishment of S. maltophilia in clinical and environmental settings.

Stenotrophomonas maltophilia has emerged as an important opportunistic pathogen in the debilitated host. S maltophilia is not an inherently virulent pathogen, but its ability to colonise respiratory-tract epithelial cells and surfaces of medical devices makes it a ready coloniser of hospitalised patients. S maltophilia can cause blood-stream infections and pneumonia with considerable morbidity in immunosuppressed patients. Management of infection is hampered by high-level intrinsic resistance to many antibiotic classes and the increasing occurrence of acquired resistance to the first-line drug co-trimoxazole. Prevention of acquisition and infection depends upon the application of modern infection-control practices, with emphasis on the control of antibiotic use and environmental reservoirs.

In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection–inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.