Advances in the Microbiology of Stenotrophomonas maltophilia

Emergence of colistin-resistant Stenotrophomonas maltophilia with high virulence in natural aquatic environments

The presence of Stenotrophomonas maltophilia in aquatic environments poses great health risks to immunocompromised individuals because of its multidrug resistance and resultant high mortality. However, a significant gap exists in the isolation and understanding of colistin-resistant S. maltophilia in aquatic environments. In this study, nine colistin-resistant S. maltophilia strains isolated from natural lakes were explored, and their phylogenetic relationship, biofilm formation, virulence, and antibiotic resistance profiles and underlying genetic determinants were assessed. After genome analysis, besides known multi-locus sequence typing (MLST) of ST532, new assigned ST965 and ST966 which phylogenetically clustered into soil isolates were found firstly. All the isolates exhibited resistance to multiple antibiotics, including aminoglycosides, beta-lactams, tetracyclines, and even colistin, with the highest minimum inhibitory concentration (MIC) against colistin reaching 640 mg/L. Comparative genomic analysis revealed aph(3')-Iic, blaL1, tetT, phoP, mcr-3, arnA, pmrE, and efflux pump genes as the genetic determinants underlying this multidrug resistance. Notably, the biofilm-forming capacities of the newly discovered ST965 and ST966 isolates were significant stronger than those of the known ST532 isolates (p < 0.01), resulting in the death of over 50 % of the Galleria mellonella population within 1 day of injection. The ST965 isolates demonstrated the highest virulence against G. mellonella, followed by the ST966 isolates and ST532 isolates which was phylogenetically clustered with clinical isolates, indicating that the novel S. maltophilia strains of ST965 and ST966 may pose considerable health risks to humans. Our findings provide insights into colistin-resistant S. maltophilia in aquatic environments and raise concerns about the health risks posed by the newly assigned sequence types of colistin-resistant S. maltophilia with potential high virulence in natural aquatic environments.

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB

Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli, indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase.IMPORTANCEStenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa. We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Stenotrophomonas maltophilia contributes to smoking-related emphysema through IRF1-triggered PANoptosis of alveolar epithelial cells

Cigarette smoke (CS), the main source of indoor air pollution and the primary risk factor for respiratory diseases, contains chemicals that can perturb microbiota through antibiotic effects. Although smoking induces a disturbance of microbiota in the lower respiratory tract, whether and how it contributes to initiation or promotion of emphysema are not well clarified. Here, we demonstrated an aberrant microbiome in lung tissue of patients with smoking-related COPD. We found that Stenotrophomonas maltophilia (S. maltophilia) was expanded in lung tissue of patients with smoking-related COPD. We revealed that S. maltophilia drives PANoptosis in alveolar epithelial cells and represses formation of alveolar organoids through IRF1 (interferon regulatory factor 1). Mechanistically, IRF1 accelerated transcription of ZBP1 (Z-DNA Binding Protein 1) in S. maltophilia-infected alveolar epithelial cells. Elevated ZBP1 served as a component of the PANoptosome, which triggered PANoptosis in these cells. By using of alveolar organoids infected by S. maltophilia, we found that targeting of IRF1 mitigated S. maltophilia-induced injury of these organoids. Moreover, the expansion of S. maltophilia and the expression of IRF1 negatively correlated with the progression of emphysema. Thus, the present study provides insights into the mechanism of lung dysbiosis in smoking-related COPD, and presents a potential target for mitigation of COPD progression.

Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing

University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.

A novel thermostable YtnP lactonase from Stenotrophomonas maltophilia inhibits Pseudomonas aeruginosa virulence in vitro and in vivo

Infections caused by multidrug-resistant pathogens are one of the biggest challenges facing the healthcare system today. Quorum quenching (QQ) enzymes have the potential to be used as innovative enzyme-based antivirulence therapeutics to combat infections caused by multidrug-resistant pathogens. The main objective of this research was to describe the novel YtnP lactonase derived from the clinical isolate Stenotrophomonas maltophilia and to investigate its antivirulence potential against multidrug-resistant Pseudomonas aeruginosa MMA83. YtnP lactonase, the QQ enzyme, belongs to the family of metallo-β-lactamases. The recombinant enzyme has several advantageous biotechnological properties, such as high thermostability, activity in a wide pH range, and no cytotoxic effect. High-performance liquid chromatography analysis revealed the activity of recombinant YtnP lactonase toward a wide range of N-acyl-homoserine lactones (AHLs), quorum sensing signaling molecules, with a higher preference for long-chain AHLs. Recombinant YtnP lactonase was shown to inhibit P. aeruginosa MMA83 biofilm formation, induce biofilm decomposition, and reduce extracellular virulence factors production. Moreover, the lifespan of MMA83-infected Caenorhabditis elegans was prolonged with YtnP lactonase treatment. YtnP lactonase showed synergistic inhibitory activity in combination with gentamicin and acted additively with meropenem against MMA83. The described properties make YtnP lactonase a promising therapeutic candidate for the development of next-generation antivirulence agents.

Phylogenomic, structural, and cell biological analyses reveal that Stenotrophomonas maltophilia replicates in acidified Rab7A-positive vacuoles of Acanthamoeba castellanii

Acanthamoeba species are clinically relevant free-living amoebae (FLA) ubiquitously found in soil and water bodies. Metabolically active trophozoites graze on diverse microbes via phagocytosis. However, functional studies on Rab GTPases (Rabs), which are critical for controlling vesicle trafficking and maturation, are scarce for this FLA. This knowledge gap can be partly explained by the limited genetic tools available for Acanthamoeba cell biology. Here, we developed plasmids to generate fusions of A. castellanii strain Neff proteins to the N- or C-termini of mEGFP and mCherry2. Phylogenomic and structural analyses of the 11 Neff Rab7 paralogs found in the RefSeq assembly revealed that eight of them had non-canonical sequences. After correcting the gene annotation for the Rab7A ortholog, we generated a line stably expressing an mEGFP-Rab7A fusion, demonstrating its correct localization to acidified macropinocytic and phagocytic vacuoles using fluorescence microscopy live cell imaging (LCI). Direct labeling of live Stenotrophomonas maltophilia ESTM1D_MKCAZ16_6a (Sm18) cells with pHrodo Red, a pH-sensitive dye, demonstrated that they reside within acidified, Rab7A-positive vacuoles. We constructed new mini-Tn7 delivery plasmids and tagged Sm18 with constitutively expressed mScarlet-I. Co-culture experiments of Neff trophozoites with Sm18::mTn7TC1_Pc_mScarlet-I, coupled with LCI and microplate reader assays, demonstrated that Sm18 underwent multiple replication rounds before reaching the extracellular medium via non-lytic exocytosis. We conclude that S. maltophilia belongs to the class of bacteria that can use amoeba as an intracellular replication niche within a Stenotrophomonas-containing vacuole that interacts extensively with the endocytic pathway.IMPORTANCEDiverse Acanthamoeba lineages (genotypes) are of increasing clinical concern, mainly causing amoebic keratitis and granulomatous amebic encephalitis among other infections. S. maltophilia ranks among the top 10 most prevalent multidrug-resistant opportunistic nosocomial pathogens and is a recurrent member of the microbiome hosted by Acanthamoeba and other free-living amoebae. However, little is known about the molecular strategies deployed by Stenotrophomonas for an intracellular lifestyle in amoebae and other professional phagocytes such as macrophages, which allow the bacterium to evade the immune system and the action of antibiotics. Our plasmids and easy-to-use microtiter plate co-culture assays should facilitate investigations into the cellular microbiology of Acanthamoeba interactions with Stenotrophomonas and other opportunistic pathogens, which may ultimately lead to the discovery of new molecular targets and antimicrobial therapies to combat difficult-to-treat infections caused by these ubiquitous microbes.

Emerging importance of multidrug-resistant Stenotrophomonas maltophilia infections in neonatal intensive care unit in a tertiary center in Turkey

OBJECTIVE

Stenotrophomonas maltophilia is an emerging multi-drug resistant, opportunistic pathogen in the neonatal intensive care unit (NICU). In this study, we aimed to assess the incidence, clinical features, antibiotic susceptibility, and treatment options of S. maltophilia infection among the healthcare-associated infections (HAIs) in the neonatal unit.

METHODS

In this study, the patients who were hospitalized in the NICU between January 2020 and December 2021 with S. maltophilia isolated from clinical samples were included. Demographic, clinic features, and microbiological findings of the patients were retrospectively evaluated by using the medical records. The samples (lower respiratory tract, urine, peritoneal fluid) were first examined microscopically by gram preparation and cultured. Antibiotic susceptibility tests were performed according to the recommendations of The European Committee on Antimicrobial Susceptibility Testing (EUCAST) for TMP-SMX.

RESULTS

S. maltophilia was isolated in 38 clinical samples of the 20 patients who were hospitalized at the NICU between January 2020 and December 2021. A total of 40 % (n = 8) of samples from different patients were accepted as colonization. Ventilator-associated pneumonia was determined in 55 % (n = 11), and urinary tract infection in 5 % (n = 1). S. maltophilia-associated bacteremia was not detected in any of the cases. The TMP-SMX susceptibilities of the strains were as it follows: 3 (15 %) were resistant (R), 7 (28 %) were susceptible (S), and 10 (47 %) were susceptible-increased exposure (I). Three of these patients were given dual antibiotics therapy (levofloxacin plus TMP-SMX) and nine of them were given only TMP-SMX. The most common hospital-acquired infectious agents are Gram negative microorganisms (51 %), followed by coagulase negative staphylococci (CNS), Staphylococcus aureus (24 %) and S. maltophilia (24 %).

CONCLUSION

Increasing TMP-SMX resistance and specific drug and dosage-related problems in the neonatal unit are important problems in treatment management.

The Mla system and its role in maintaining outer membrane barrier function in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia are ubiquitous Gram-negative bacteria found in both natural and clinical environments. It is a remarkably adaptable species capable of thriving in various environments, thanks to the plasticity of its genome and a diverse array of genes that encode a wide range of functions. Among these functions, one notable trait is its remarkable ability to resist various antimicrobial agents, primarily through mechanisms that regulate the diffusion across cell membranes. We have investigated the Mla ABC transport system of S. maltophilia, which in other Gram-negative bacteria is known to transport phospholipids across the periplasm and is involved in maintaining outer membrane homeostasis. First, we structurally and functionally characterized the periplasmic substrate-binding protein MlaC, which determines the specificity of this system. The predicted structure of the S. maltophilia MlaC protein revealed a hydrophobic cavity of sufficient size to accommodate the phospholipids commonly found in this species. Moreover, recombinant MlaC produced heterologously demonstrated the ability to bind phospholipids. Gene knockout experiments in S. maltophilia K279a revealed that the Mla system is involved in baseline resistance to antimicrobial and antibiofilm agents, especially those with divalent-cation chelating activity. Co-culture experiments with Pseudomonas aeruginosa also showed a significant contribution of this system to the cooperation between both species in the formation of polymicrobial biofilms. As suggested for other Gram-negative pathogenic microorganisms, this system emerges as an appealing target for potential combined antimicrobial therapies.

Complete genome sequence of Stenotrophomonas maltophilia complex strain STEN00241

We report here the complete, closed genome sequence of Stenotrophomonas maltophilia complex strain STEN00241, which was isolated from patient sputum. The genome is a single contig with a total length of 4,751,329 nucleotides and a GC content of 66.5%.

A guide to Stenotrophomonas maltophilia virulence capabilities, as we currently understand them

The Gram-negative pathogen Stenotrophomonas maltophilia causes a wide range of human infections. It causes particularly serious lung infections in individuals with cystic fibrosis, leading to high mortality rates. This pathogen is resistant to most known antibiotics and harbors a plethora of virulence factors, including lytic enzymes and serine proteases, that cause acute infection in host organisms. S. maltophilia also establishes chronic infections through biofilm formation. The biofilm environment protects the bacteria from external threats and harsh conditions and is therefore vital for the long-term pathogenesis of the microbe. While studies have identified several genes that mediate S. maltophilia's initial colonization and biofilm formation, the cascade of events initiated by these factors is poorly understood. Consequently, understanding these and other virulence factors can yield exciting new targets for novel therapeutics.

Stenotrophomonas maltophilia complex: insights into evolutionary relationships, global distribution and pathogenicity

Introduction

Stenotrophomonas maltophilia complex (Smc) comprises opportunistic Gram-negative bacilli responsible for various nosocomial infections. Limited data exists concerning its evolutionary lineage, global prevalence and pathogenicity.

Methods

We conducted an extensive genomic analysis on 734 Smc genomes, of which 90 were newly sequenced and isolated from different patients. The species composition and evolutionary relationships of Smc were examined using core protein sequence analysis. Pathogenicity evaluation was used by assays for swimming motility, biofilm formation and identification of virulence factors. The broth microdilution method was used to evaluate the drug resistance spectrum of clinical isolates.

Results

Phylogenetic analyses delineated 24 species-level clades, dominated by S. maltophilia (42.8%), S. sepilia (13.6%) and S. geniculata (9.9%). Geographically, strains were primarily distributed in Europe (34.2%), Asia (33.7%) and North America (24.0%), with intricate global distribution patterns. Meanwhile, 154 virulence-associated genes and 46 antimicrobial resistance genes within Smc were identified. These genes encoded span various functions, including motility, adherence, toxin, RND antibiotic efflux pumps, beta-lactamases and aminoglycoside-modifying enzymes. Moreover, significant variations were indicated in swimming motility and biofilm-forming capability across the different species, with S. sepilia exhibiting superior levels of both traits. Additionally, no statistically significant discrepancy was detected among Smc species to other antibiotics, despite the fact that all S. geniculata isolates were resistant to Ceftazidime and much higher than other species.

Conclusion

Our findings indicate the need to pay increased attention to other mainstream species of Smc besides S. maltophilia in order to better manage Smc-related infections and tailor effective treatment strategies.

Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates

Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.

The type VI secretion system of the emerging pathogen Stenotrophomonas maltophilia complex has antibacterial properties

IMPORTANCE

Infections with the opportunistic pathogen Stenotrophomonas maltophilia complex can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the type VI secretion system (T6SS) allows S. maltophilia complex to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia complex. The T6SS may confer survival advantages to S. maltophilia complex isolates in polymicrobial communities in both environmental settings and during infections.

Comparative genomics analysis of Stenotrophomonas maltophilia strains from a community

Background

Stenotrophomonas maltophilia is a multidrug-resistant (MDR) opportunistic pathogen with high resistance to most clinically used antimicrobials. The dissemination of MDR S. maltophilia and difficult treatment of its infection in clinical settings are global issues.

Methods

To provide more genetic information on S. maltophilia and find a better treatment strategy, we isolated five S. maltophilia, SMYN41-SMYN45, from a Chinese community that were subjected to antibiotic susceptibility testing, biofilm formation assay, and whole-genome sequencing. Whole-genome sequences were compared with other thirty-seven S. maltophilia sequences.

Results

The five S. maltophilia strains had similar antibiotic resistance profiles and were resistant to β-lactams, aminoglycosides, and macrolides. They showed similar antimicrobial resistance (AMR) genes, including various efflux pumps, β-lactamase resistance genes (blaL1/2), aminoglycoside resistance genes [aac(6'), aph(3'/6)], and macrolide-resistant gene (MacB). Genome sequencing analysis revealed that SMYN41-SMYN45 belonged to sequence type 925 (ST925), ST926, ST926, ST31, and ST928, respectively, and three new STs were identified (ST925, ST926, and ST928).

Conclusion

This study provides genetic information by comparing genome sequences of several S. maltophilia isolates from a community of various origins, with the aim of optimizing empirical antibiotic medication and contributing to worldwide efforts to tackle antibiotic resistance.

Stenotrophomonas maltophilia Belonging to Novel Sequence Types ST473 and ST474 in Wild Birds Inhabiting the Brazilian Amazonia

Stenotrophomonas maltophilia is an opportunistic human pathogen associated with nosocomial and community-acquired infections. We have conducted a microbiological and genomic surveillance study of broad-spectrum cephalosporin- and carbapenem-resistant Gram-negative bacteria colonizing wild birds inhabiting the Brazilian Amazonia. Strikingly, two S. maltophilia strains (SM79 and SM115) were identified in Plain-throated antwren (Isleria hauxwelli) passerines affected by Amazonian fragmentation and degradation. Noteworthy, SM79 and SM115 strains belonged to new sequence types (STs) ST474 and ST473, respectively, displaying resistance to broad-spectrum β-lactams, aminoglycosides and/or fluoroquinolones. In this regard, resistome analysis confirmed efflux pumps (smeABC, smeDEF, emrAB-tolC and macB), blaL1 and blaL2, aph(3')-IIc and aac(6')-Iak, and Smqnr resistance genes. Comparative phylogenomic analysis with publicly available S. maltophilia genomes clustered ST473 and ST474 with human strains, whereas the ST474 was also grouped with S. maltophilia strains isolated from water and poultry samples. In summary, we report two novel sequence types of S. maltophilia colonizing wild Amazonian birds. The presence of opportunistic multidrug-resistant pathogens in wild birds, from remotes areas, could represent an ecological problem since these animals could easily promote long-distance dispersal of medically important antimicrobial-resistant bacteria. Therefore, while our results could provide a baseline for future epidemiological genomic studies, considering the limited information regarding S. maltophilia circulating among wild animals, additional studies are necessary to evaluate the clinical impact and degree of pathogenicity of this human opportunistic pathogen in wild birds.

Construction of a CRISPR Interference System for Gene Knockdown in Stenotrophomonas maltophilia AGS-1 from Aerobic Granular Sludge

To identify the function of attachment genes involved in biofilm formation in Stenotrophomonas maltophilia AGS-1 isolated from aerobic granular sludge, an effective gene molecular tool is needed. We developed a two-plasmid CRISPRi system in Stenotrophomonas maltophilia AGS-1. One plasmid expressed dCas9 protein with the l-arabinose inducible promoter, and the other plasmid contained the sgRNA cassette complementary to the target gene. Under control of the araC-inducible promoter, this system exhibited little leaky basal expression and highly induced expression that silenced endogenous and exogenous genes with reversible knockdown. This system achieved up to 211-fold suppression for mCherry expression on the nontemplate strand compared to the template strand (91-fold). The utility of the developed CRISPRi platform was also characterized by suppressing the xanA and rpfF genes. The expression of these two genes was rapidly depleted and the adhesion ability decreased, which demonstrated that the modulation of either gene was an important factor for biofilm formation of the AGS-1 strain. The system also tested the ability to simultaneously silence transcriptional suppression of multiple targeted genes, an entire operon, or part of it. Lastly, the use of CRISPRi allowed us to dissect the gene intricacies involved in flagellar biosynthesis. Collectively, these results demonstrated that the CRISPRi system was a simple, feasible, and controllable manipulation system of gene expression in the AGS-1 strain.

Stenotrophomonas maltophilia: An Urgent Threat with Increasing Antibiotic Resistance

Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can cause many infections, such as chronic pulmonary infections in patients with cystic fibrosis and infections in immunocompromised patients with hematology-oncology diseases. Because of its remarkable and increasing antimicrobial resistance, the treatment of S. maltophilia infections is quite challenging. Meanwhile, the prevalence of S. maltophilia infections is increasing in recent decades. S. maltophilia is usually considered to be of low virulence but has numerous virulence factors involved in the pathogenesis of infections caused by S. maltophilia. By revealing its pathogenesis associated with virulence factors and molecular mechanisms of antimicrobial resistance, many existing or potential therapeutic strategies have been developed. However, because of the limited treatment options, new strategies are urgently needed. Here, we review the recent progresses in research on S. maltophilia which may help to develop more effective treatments against this increasing threat.

Risk factors for mortality in intensive care unit patients with Stenotrophomonas maltophilia pneumonia in South Korea

BACKGROUND

Stenotrophomonas maltophilia has been increasingly recognized as an opportunistic pathogen associated with high morbidity and mortality. Data on the prognostic factors associated with S. maltophilia pneumonia in patients admitted to intensive care unit (ICU) are lacking.

METHODS

We conducted a retrospective analysis of data from 117 patients with S. maltophilia pneumonia admitted to the ICUs of two tertiary referral hospitals in South Korea between January 2011 and December 2022. To assess risk factors associated with in-hospital mortality, multivariable logistic regression analyses were performed.

RESULTS

The median age of the study population was 71 years. Ventilator-associated pneumonia was 76.1% of cases, and the median length of ICU stay before the first isolation of S. maltophilia was 15 days. The overall in-hospital mortality rate was 82.1%, and factors independently associated with mortality were age (odds ratio [OR], 1.05; 95% confidence interval [CI], 1.00-1.09; P=0.046), Sequential Organ Failure Assessment (SOFA) score (OR, 1.21; 95%; CI, 1.02-1.43; P=0.025), corticosteroid use (OR, 4.19; 95% CI, 1.26-13.91; P=0.019), and polymicrobial infection (OR, 95% CI 0.07-0.69). However, the impact of appropriate antibiotic therapy on mortality was insignificant. In a subgroup of patients who received appropriate antibiotic therapy (n=58), antibiotic treatment modality-related variables, including combination or empirical therapy, also showed no significant association with survival.

CONCLUSIONS

Patients with S. maltophilia pneumonia in ICU have high mortality rates. Older age, higher SOFA score, and corticosteroid use were independently associated with increased in-hospital mortality, whereas polymicrobial infection was associated with lower mortality. The effect of appropriate antibiotic therapy on prognosis was insignificant.

Time-course transcriptome analysis of lungs from mice infected with inhaled aerosolized Stenotrophomonas maltophilia

Background

Stenotrophomonas maltophilia (SMA) has emerged as an important pathogen capable of causing an opportunistic and nosocomial infection. We performed RNA sequencing (RNA-seq) of lung tissues from mice with pulmonary SMA infection over time via aerosolized intratracheal inhalation to investigate transcription profile changes in SMA-infected lungs.

Methods

A mouse model of acute lethal SMA pneumonia was established in this study using aerosolized intratracheal inhalation, laying the groundwork for future SMA research. RNA-seq was then used to create a transcriptional profile of the lungs of the model mice at 0, 4, 12, 24, 48, and 72 hours post-infection (hpi). Mfuzz time clustering, weighted gene coexpression network analysis (WGCNA), and Immune Cell Abundance Identifier for mouse (ImmuCellAI-mouse) were used to analyze RNA-seq data.

Results

A gradual change in the lung transcriptional profile was observed, which was consistent with the expected disease progression. At 4 hpi, the expression of genes related to the acute phase inflammatory response increased, as predicted abundance of innate immune cells. At this stage, an increased demand for energy was also observed, including an increase in the expression of genes involved in circulation, muscle function and mitochondrial respiratory chain function. The expression of genes associated with endoplasmic reticulum stress (ERS) and autophagy increased at 24 hpi. Unlike the number of natural killer (NK) cells following most bacterial lung infections, the abundance of NK cells decreased following infection with SMA. The expression levels of Cxcl10, Cd14, Gbp5, Cxcr2, Tnip1, Zc3h12a, Egr1, Sell and Gbp2 were high and previously unreported in SMA pneumonia, and they may be important targets for future studies.

Conclusions

To our knowledge, this is the first study to investigate the pulmonary transcriptional response to SMA infection. The findings shed light on the molecular mechanisms underlying the pathogenesis of SMA pneumonia, which may aid in the development of therapies to reduce the occurrence of SMA pulmonary infection.

Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis

Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.

First case of persistent Stenotrophomonas maltophilia bacteraemia due to septic thrombosis successfully treated with a cefiderocol-containing regimen

INTRODUCTION

There is scarce evidence in literature of what should be the best antimicrobial treatment for bloodstream infections (BSIs) sustained by Stenotrophomonas maltophilia, a peculiar pathogen that intrinsically withstands to most of the available antibiotics.

RESULTS AND CONCLUSION

Here, we describe a challenging case of a persistent S. maltophilia BSI due to septic thrombosis successfully treated with the addition of the novel siderophore cephalosporin cefiderocol to an only partially effective levofloxacin regimen. Additionally, an intra-lock therapy with trimethoprim/sulfamethoxazole was selected as a strategy to prevent recurrence of infection since complete source control was not possible. The serum bactericidal assay was also used to corroborate the in vivo efficacy of the adopted combination therapy.

Global prevalence and distribution of antibiotic resistance among clinical isolates of Stenotrophomonas maltophilia: A systematic review and meta-analysis

OBJECTIVES

Stenotrophomonas maltophilia (S. maltophilia), an opportunistic pathogen, causes infection in patients undergoing immunosuppressive therapy, mechanical ventilation, or catheters and in long-term hospitalized patients. Due to its extensive resistance to various antibiotics and chemotherapeutic agents, S. maltophilia is challenging to treat. Using case reports, case series, and prevalence studies, the current study provides a systematic review and meta-analysis of antibiotic resistance profiles across clinical isolates of S. maltophilia.

METHODS

A systematic literature search was performed for original research articles published in Medline, Web of Science, and Embase databases from 2000 to 2022. Statistical analysis was performed using STATA 14 software to report antibiotic resistance of S. maltophilia clinical isolates worldwide.

RESULTS

223 studies (39 case reports/case series and 184 prevalence studies) were collected for analysis. A meta-analysis of prevalence studies demonstrated that the most antibiotic resistance worldwide was to levofloxacin, trimethoprim-sulfamethoxazole (TMP/SMX), and minocycline (14.4%, 9.2%, and 1.4%, respectively). Resistance to TMP/SMX (36.84%), levofloxacin (19.29%), and minocycline (1.75%) were the most prevalent antibiotic resistance types found in evaluated case reports/case series studies. The highest resistance rate to TMP/SMX was reported in Asia (19.29%), Europe (10.52%), and America (7.01%), respectively.

CONCLUSION

Considering the high resistance to TMP/SMX, more attention should be paid to patients' drug regimens to prevent the emergence of multidrug-resistant S. maltophilia isolates.

Ocular Bacterial Infections: A Ten-Year Survey and Review of Causative Organisms Based on the Oklahoma Experience

Ocular infections can be medical emergencies that result in permanent visual impairment or blindness and loss of quality of life. Bacteria are a major cause of ocular infections. Effective treatment of ocular infections requires knowledge of which bacteria are the likely cause of the infection. This survey of ocular bacterial isolates and review of ocular pathogens is based on a survey of a collection of isolates banked over a ten-year span at the Dean McGee Eye Institute in Oklahoma. These findings illustrate the diversity of bacteria isolated from the eye, ranging from common species to rare and unique species. At all sampled sites, staphylococci were the predominant bacteria isolated. Pseudomonads were the most common Gram-negative bacterial isolate, except in vitreous, where Serratia was the most common Gram-negative bacterial isolate. Here, we discuss the range of ocular infections that these species have been documented to cause and treatment options for these infections. Although a highly diverse spectrum of species has been isolated from the eye, the majority of infections are caused by Gram-positive species, and in most infections, empiric treatments are effective.

In vitro activities of antimicrobial combinations against planktonic and biofilm forms of Stenotrophomonas maltophilia

Objectives

To investigate the in vitro activity of antibiotic combinations against Stenotrophomonas maltophilia isolates and their associated biofilms.

Methods

Thirty-two S. maltophilia clinical isolates with at least twenty-five different pulsotypes were tested. The antibacterial activity of various antibiotic combinations against seven randomly selected planktonic and biofilm-embedded S. maltophilia strains with strong biofilm formation was assessed using broth methods. Extraction of bacterial genomic DNA and PCR detection of antibiotic resistance and biofilm-related genes were also performed.

Results

The susceptibility rates of levofloxacin (LVX), fosfomycin (FOS), tigecycline (TGC) and sulfamethoxazole-trimethoprim (SXT) against 32 S. maltophilia isolates were 56.3, 71.9, 71.9 and 90.6%, respectively. Twenty-eight isolates were detected with strong biofilm formation. Antibiotic combinations, including aztreonam-clavulanic (ATM-CLA) with LVX, ceftazidime-avibactam (CZA) with LVX and SXT with TGC, exhibited potent inhibitory activity against these isolates with strong biofilm formation. The antibiotic resistance phenotype might not be fully caused by the common antibiotic-resistance or biofilm-formation gene.

Conclusion

S. maltophilia remained resistant to most antibiotics, including LVX and β-lactam/β-lactamases; however, TGC, FOS and SXT still exhibited potent activity. Although all tested S. maltophilia isolates exhibited moderate-to-strong biofilm formation, combination therapies, especially ATM-CLA with LVX, CZA with LVX and SXT with TGC, exhibited a higher inhibitory activity for these isolates.

Stenotrophomonas maltophilia natural history and evolution in the airways of adults with cystic fibrosis

Introduction

Stenotrophomonas maltophilia is an opportunistic pathogen infecting persons with cystic fibrosis (pwCF) and portends a worse prognosis. Studies of S. maltophilia infection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution of S. maltophilia in a large Canadian cohort of 321 pwCF over a 37-year period.

Methods

One-hundred sixty-two isolates from 74 pwCF (23%) were typed by pulsed-field gel electrophoresis, and shared pulsotypes underwent whole-genome sequencing.

Results

S. maltophilia was recovered at least once in 82 pwCF (25.5%). Sixty-four pwCF were infected by unique pulsotypes, but shared pulsotypes were observed between 10 pwCF. In chronic carriage, longer time periods between positive sputum cultures increased the likelihood that subsequent isolates were unrelated. Isolates from individual pwCF were largely clonal, with differences in gene content being the primary source of genetic diversity objectified by gene content differences. Disproportionate progression of CF lung disease was not observed amongst those infected with multiple strains over time (versus a single) or amongst those with shared clones (versus strains only infecting one patient). We did not observe evidence of patient-to-patient transmission despite relatedness between isolates. Twenty-four genes with ≥ 2 mutations accumulated over time were identified across 42 sequenced isolates from all 11 pwCF with ≥ 2 sequenced isolates, suggesting a potential role for these genes in adaptation of S. maltophilia to the CF lung.

Discussion

Genomic analyses suggested common, indirect sources as the origins of S. maltophilia infections in the clinic population. The information derived from a genomics-based understanding of the natural history of S. maltophilia infection within CF provides unique insight into its potential for in-host evolution.

Assessment of the relative benefits of monotherapy and combination therapy approaches to the treatment of hospital-acquired Stenotrophomonas maltophilia pneumonia: a multicenter, observational, real-world study

PURPOSE

Stenotrophomonas maltophilia is a Gram-negative pathogen that most commonly causes hospital-acquired infections that can be extremely challenging to treat, contributing to underrecognized mortality throughout the world. The relative benefits of monotherapy as compared to combination therapy in patients diagnosed with S. maltophilia pneumonia, however, have yet to be established.

METHODS

Data from 307 patients diagnosed with S. maltophilia hospital-acquired pneumonia (HAP) across four Chinese teaching hospitals from 2016 to 2022 were retrospectively analyzed.

RESULTS

Of the analyzed patients, 55.7% (171/307) were administered combination definitive therapy, with a 30-day all-cause mortality rate of 41.0% (126/307). A propensity score weighting analysis revealed that compared with monotherapy, combination definitive therapy was associated with a comparable 30-day mortality risk in the overall patient cohort (OR 1.124, 95% CI 0.707-1.786, P = 0.622), immunocompetent patients (OR 1.349, 95% CI 0.712-2.554, P = 0.359), and patients with APACHE II scores < 15 (OR 2.357, 95% CI 0.820-6.677, P = 0.111), whereas it was associated with a decreased risk of death in immunocompromised patients (OR 0.404, 95% CI .170-0.962, P = 0.041) and individuals with APACHE II scores ≥ 15 (OR 0.494, 95% CI 0.256-0.951, P = 0.035).

CONCLUSION

The present data suggest that when treating S. maltophilia-HAP, immunocompromised patients and individuals with APACHE II scores ≥ 15 may potentially benefit from combination therapy.

The Type VI Secretion System of the Emerging Pathogen Stenotrophomonas maltophilia has Antibacterial Properties

Antagonistic behaviors between bacterial cells can have profound effects on microbial populations and disease outcomes. Polymicrobial interactions may be mediated by contact-dependent proteins with antibacterial properties. The Type VI Secretion System (T6SS) is a macromolecular weapon used by Gram-negative bacteria to translocate proteins into adjacent cells. The T6SS is used by pathogens to escape immune cells, eliminate commensal bacteria, and facilitate infection. Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that causes a wide range of infections in immunocompromised patients and infects the lungs of patients with cystic fibrosis. Infections with the bacterium can be deadly and are challenging to treat because many isolates are multidrug-resistant. We found that globally dispersed S. maltophilia clinical and environmental strains possess T6SS genes. We demonstrate that the T6SS of an S. maltophilia patient isolate is active and can eliminate other bacteria. Furthermore, we provide evidence that the T6SS contributes to the competitive fitness of S. maltophilia against a co-infecting Pseudomonas aeruginosa isolate, and that the T6SS alters the cellular organization of S. maltophilia and P. aeruginosa co-cultures. This study expands our knowledge of the mechanisms employed by S. maltophilia to secrete antibacterial proteins and compete against other bacteria.

IMPORTANCE

Infections with the opportunistic pathogen Stenotrophomonas maltophilia can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the T6SS allows S. maltophilia to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia . The T6SS may confer survival advantages to S. maltophilia isolates in polymicrobial communities in both environmental settings and during infections.

Stenotrophomonas maltophilia Infections: A Systematic Review and Meta-Analysis of Comparative Efficacy of Available Treatments, with Critical Assessment of Novel Therapeutic Options

Stenotrophomonas maltophilia (SM) represents a challenging pathogen due to its resistance profile. A systematic review of the available evidence was conducted to evaluate the best treatment of SM infections to date, focusing on trimethoprim/sulfamethoxazole (TMP/SMX), fluoroquinolones (FQs), and tetracycline derivatives (TDs).

MATERIALS

PubMed/MEDLINE and Embase were searched from inception to 30 November 2022. The primary outcome was all-cause mortality. Secondary outcomes included clinical failure, adverse events, and length of stay. A random effects meta-analysis was performed. This study was registered with PROSPERO (CRD42022321893).

RESULTS

Twenty-four studies, all retrospective, were included. A significant difference in terms of overall mortality was observed when comparing as a monotherapy TMP/SMX versus FQs (odds ratio (OR) 1.46, 95% confidence interval (CI) 1.15-1.86, I² = 33%; 11 studies, 2407 patients). The prediction interval (PI) did not touch the no effect line (1.06-1.93), but the results were not robust for the unmeasured confounding (E-value for point estimate of 1.71). When comparing TMP/SMX with TDs, the former showed an association with higher mortality but not significant and with a wide PI (OR 1.95, 95% CI 0.79-4.82, PI 0.01-685.99, I² = 0%; 3 studies, 346 patients). Monotherapies in general exerted a protective effect against death opposed to the combination regimens but were not significant (OR 0.71, 95% CI 0.41-1.22, PI 0.16-3.08, I² = 0%; 4 studies, 438 patients).

CONCLUSIONS

Against SM infections, FQs and, possibly, TDs seem to be reasonable alternative choices to TMP/SMX. Data from clinical trials are urgently needed to better inform therapeutic choices in this setting by also taking into account newer agents.

Osteomyelitis due to Stenotrophomonas maltophilia treated with trimethoprim-sulfamethoxazole monotherapy

Stenotrophomonas maltophilia is an opportunistic infection commonly encountered in various systems of the human body and has been noted to be a rare cause of osteomyelitis. This report examines a rare case of osteomyelitis of the foot caused by S. maltophilia from a poorly managed foot wound and highlights the successful treatment of this condition with trimethoprim-sulfamethoxazole monotherapy.

Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait

Stenotrophomonas maltophilia is a species with immensely broad phenotypic and genotypic diversity that could widely distribute in natural and clinical environments. However, little attention has been paid to reveal their genome plasticity to diverse environments. In the present study, a comparative genomic analysis of S. maltophilia isolated from clinical and natural sources was systematically explored its genetic diversity of 42 sequenced genomes. The results showed that S. maltophilia owned an open pan-genome and had strong adaptability to different environments. A total of 1612 core genes were existed with an average of 39.43% of each genome, and the shared core genes might be necessary to maintain the basic characteristics of those S. maltophilia strains. Based on the results of the phylogenetic tree, the ANI value, and the distribution of accessory genes, genes associated with the fundamental process of those strains from the same habitat were found to be mostly conserved in evolution. Isolates from the same habitat had a high degree of similarity in COG category, and the most significant KEGG pathways were mainly involved in carbohydrate and amino acid metabolism, indicating that genes related to essential processes were mostly conserved in evolution for the clinical and environmental settings. Meanwhile, the number of resistance and efflux pump gene was significantly higher in the clinical setting than that of in the environmental setting. Collectively, this study highlights the evolutionary relationships of S. maltophilia isolated from clinical and environmental sources, shedding new light on its genomic diversity.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

Genotypic Diversity, Antibiotic Resistance, and Virulence Phenotypes of Stenotrophomonas maltophilia Clinical Isolates from a Thai University Hospital Setting

Stenotrophomonas maltophilia is a multidrug-resistant organism that is emerging as an important opportunistic pathogen. Despite this, information on the epidemiology and characteristics of this bacterium, especially in Thailand, is rarely found. This study aimed to determine the demographic, genotypic, and phenotypic characteristics of S. maltophilia isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand. A total of 200 S. maltophilia isolates were collected from four types of clinical specimens from 2015 to 2016 and most of the isolates were from sputum. In terms of clinical characteristics, male and aged patients were more susceptible to an S. maltophilia infection. The majority of included patients had underlying diseases and were hospitalized with associated invasive procedures. The antimicrobial resistance profiles of S. maltophilia isolates showed the highest frequency of resistance to ceftazidime and the lower frequency of resistance to chloramphenicol, levofloxacin, trimethoprim/sulfamethoxazole (TMP/SMX), and no resistance to minocycline. The predominant antibiotic resistance genes among the 200 isolates were the smeF gene (91.5%), followed by bla_L1 and bla_L2 genes (43% and 10%), respectively. Other antibiotic resistance genes detected were floR (8.5%), intI1 (7%), sul1 (6%), mfsA (4%) and sul2 (2%). Most S. maltophilia isolates could produce biofilm and could swim in a semisolid medium, however, none of the isolates could swarm. All isolates were positive for hemolysin production, whereas 91.5% and 22.5% of isolates could release protease and lipase enzymes, respectively. In MLST analysis, a high degree of genetic diversity was observed among the 200 S. maltophilia isolates. One hundred and forty-one sequence types (STs), including 130 novel STs, were identified and categorized into six different clonal complex groups. The differences in drug resistance patterns and genetic profiles exhibited various phenotypes of biofilm formation, motility, toxin, and enzymes production which support this bacterium in its virulence and pathogenicity. This study reviewed the characteristics of genotypes and phenotypes of S. maltophilia from Thailand which is necessary for the control and prevention of S. maltophilia local spreading.

Test Performance and Potential Clinical Utility of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel

The test performance and potential clinical utility of the ePlex blood culture identification Gram-negative (BCID-GN) panel was evaluated relative to matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry on bacterial isolates and conventional antimicrobial susceptibility testing. The majority (106/108, 98.1%) of GN bacteria identified by MALDI were on the BCID-GN panel, and valid tests (107/108, 99.1%) yielded results on average 26.7 h earlier. For all valid tests with on-panel organisms, the positive percent agreement was 102/105 (97.2%) with 3 false negatives and the negative percent agreement was 105/105. Chart review (n = 98) showed that in conjunction with Gram stain results, negative pan-Gram-positive (GP) markers provided the opportunity to discontinue GP antibiotic coverage in 63/98 (64.3%) cases on average 26.2 h earlier. Only 8/12 (66.7%) Enterobacterales isolates with resistance to third-generation cephalosporins harbored the CTX-M gene. In contrast, 8/8 CTX-M⁺ samples yielded a resistant isolate. Detection of 1 Stenotrophomonas maltophilia (18 h), 1 OXA23/48⁺ Acinetobacter baumannii (52.4 h), and 3 CTX-M⁺ Enterobacterales isolates on ineffective treatment (47.1 h) and 1 on suboptimal therapy (72.6 h) would have additionally enabled early antimicrobial optimization in 6/98 (6.1%) patients. IMPORTANCE The GenMark Dx ePlex rapid blood culture diagnostic system enables earlier time to identification of antimicrobial-resistant Gram-negative bacteria causing bloodstream infections. Its ability to rule out Gram-positive bacteria enabled early discontinuation of unnecessary antibiotics in 63/98 (64.3%) cases on average 26.2 h earlier. Detection of bacteria harboring the CTX-M gene as well as early identification of highly resistant bacteria such as Stenotrophomonas maltophilia and Acinetobacter baumannii enabled optimization of ineffective therapy in 6/98 (6.1%) patients. Its implementation in clinical microbiology laboratories optimizes therapy and improves patient care.

Efficacy in Galleria mellonella Larvae and Application Potential Assessment of a New Bacteriophage BUCT700 Extensively Lyse Stenotrophomonas maltophilia

In recent years, Stenotrophomonas maltophilia (S. maltophilia) has become an important pathogen of clinically acquired infections accompanied by high pathogenicity and high mortality. Moreover, infections caused by multidrug-resistant S. maltophilia have emerged as a serious challenge in clinical practice. Bacteriophages are considered a promising alternative for the treatment of S. maltophilia infections due to their unique antibacterial mechanism and superior bactericidal ability compared with traditional antibiotic agents. Here, we reported a new phage BUCT700 that has a double-stranded DNA genome of 43,214 bp with 70% GC content. A total of 55 ORFs and no virulence or antimicrobial resistance genes were annotated in the genome of phage BUCT700. Phage BUCT700 has a broad host range (28/43) and can lyse multiple ST types of clinical S. maltophilia (21/33). Furthermore, bacteriophage BUCT700 used the Type IV fimbrial biogenesis protein PilX as an adsorption receptor. In the stability test, phage BUCT700 showed excellent thermal stability (4 to 60°C) and pH tolerance (pH = 4 to 12). Moreover, phage BUCT700 was able to maintain a high titer during long-term storage. The adsorption curve and one-step growth curve showed that phage BUCT700 could rapidly adsorb to the surface of S. maltophilia and produce a significant number of phage virions. In vivo, BUCT700 significantly increased the survival rate of S. maltophilia-infected Galleria mellonella (G. mellonella) larvae from 0% to 100% within 72 h, especially in the prophylactic model. In conclusion, these findings indicate that phage BUCT700 has promising potential for clinical application either as a prophylactic or therapeutic agent. IMPORTANCE The risk of Stenotrophomonas maltophilia infections mediated by the medical devices is exacerbated with an increase in the number of ICU patients during the Corona Virus Disease 2019 (COVID-19) epidemic. Complications caused by S. maltophilia infections could complicate the state of an illness, greatly extending the length of hospitalization and increasing the financial burden. Phage therapy might be a potential and promising alternative for clinical treatment of multidrug-resistant bacterial infections. Here, we investigated the protective effects of phage BUCT700 as prophylactic and therapeutic agents in Galleria mellonella models of infection, respectively. This study demonstrates that phage therapy can provide protection in targeting S. maltophilia-related infection, especially as prophylaxis.

Comparative Proteomic Analysis of Protein Patterns of Stenotrophomonas maltophilia in Biofilm and Planktonic Lifestyles

Stenotrophomonas maltophilia is a clinically relevant bacterial pathogen, particularly in cystic fibrosis (CF) patients. Despite the well-known ability to form biofilms inherently resistant to antibiotics and host immunity, many aspects involved in S. maltophilia biofilm formation are yet to be elucidated. In the present study, a proteomic approach was used to elucidate the differential protein expression patterns observed during the planktonic-to-biofilm transition of S. maltophilia Sm126, a strong biofilm producer causing chronic infection in a CF patient, to identify determinants potentially associated with S. maltophilia biofilm formation. In all, 57 proteins were differentially (3-fold; p < 0.01) expressed in biofilm cells compared with planktonic counterparts: 38 were overexpressed, and 19 were down-expressed. It is worth noting that 34 proteins were exclusively found in biofilm, mainly associated with quorum sensing-mediated intercellular communication, augmented glycolysis, amino acid metabolism, biosynthesis of secondary metabolites, phosphate signaling, response to nutrient starvation, and general stress. Further work is warranted to evaluate if these proteins can be suitable targets for developing anti-biofilm strategies effective against S. maltophilia.

Characterization of Antibiotic-Resistant Stenotrophomonas Isolates from Painted Turtles Living in the Wild

Stenotrophomonas maltophilia is a ubiquitous multidrug-resistant opportunistic pathogen commonly associated with nosocomial infections. The purpose of this study was to isolate and characterize extended-spectrum beta-lactamase (ESBL) producing bacteria from painted turtles (Chrysemys picta) living in the wild and captured in southeastern Wisconsin. Fecal samples from ten turtles were examined for ESBL producing bacteria after incubation on HardyCHROM™ ESBL agar. Two isolates were cultivated and identified by 16S rRNA gene sequencing and whole genome sequencing (WGS) as Stenotrophomonas sp. 9A and S. maltophilia 15A. They were multidrug-resistant, as determined by antibiotic susceptibility testing. Stenotrophomonas sp. 9A was found to produce an extended spectrum beta-lactamase (ESBL) and both isolates were found to be carbapenem-resistant. EDTA-modified carbapenem inactivation method (eCIM) and the modified carbapenem inactivation method (mCIM) tests were used to examine the carbapenemase production and the test results were negative. Through WGS several antimicrobial resistance genes were identified in S. maltophilia 15A. For example a chromosomal L1 β-lactamase gene, which is known to hydrolyze carbapenems, a L2 β-lactamase gene, genes for the efflux systems smeABC and smeDEF and the aminoglycosides resistance genes aac(6')-lz and aph(3')-llc were found. An L2 β-lactamase gene in Stenotrophomonas sp. 9A was identified through WGS.

Antibiofilm and antimicrobial activity of curcumin-chitosan nanocomplexes and trimethoprim-sulfamethoxazole on Achromobacter, Burkholderia, and Stenotrophomonas isolates

BACKGROUND

Non-fermenting Gram-negative Achromobacter xylosoxidans, Burkholderia cepacia complex, and Stenotrophomonas maltophilia species cause healthcare-associated infections, often showing resistance to first-line drugs such as trimethoprim-sulfamethoxazole (TMP-SXT). The aim of this study was to determine the effect of curcumin-chitosan nanocomplexes on biofilm-producing clinical isolates of non-fermenting Gram-negative bacilli.

METHODS

A. xylosoxidans, B. cepacia complex, and S. maltophilia clinical isolates were identified by MALDI-TOF mass spectrometry. Antimicrobial susceptibility was determined by broth microdilution. Curcumin (Cur), chitosan (Chi), and sodium tripolyphosphate (TPP) were encapsulated by ionotropic gelation in magnetic nanoparticles (MNP) and were assessed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR). Biofilm inhibition and eradication by Cur-Chi-TPP-MNP with TMP-SXT was assessed.

RESULTS

Cur-Chi-TPP-MNP in combination with TMP-SXT showed biofilm inhibition activity in A. xylosoxidans (37.5 µg/mL), B. cepacia (18.75 µg/mL), and S. maltophilia (4.69-18.75 µg/mL) and low biofilm eradication activity in all three strains (150 - 300 µg/mL).

CONCLUSIONS

Cur-Chi-TPP-MNP in combination with TMP-SXT was able to inhibit biofilm and in lower effect to eradicate established biofilms of clinical isolates of A. xylosoxidans, B. cepacia complex, and S. maltophilia species. Our results highlight the need to assess these potential treatment options to be used clinically in biofilm-associated infections.

Stenotrophomonas maltophilia promotes lung adenocarcinoma progression by upregulating histone deacetylase 5

Introduction

Lung cancer is the leading cause of cancer death worldwide, and lung adenocarcinoma (LADC) is the most common lung cancer. Lung cancer has a distinct microbiome composition correlated with patients' smoking status. However, the causal evidence of microbial impacts on LADC is largely unknown.

Methods

We investigated microbial communities' differences in Formalin-Fixed Paraffin-Embedded tissues of ever-smoke (n = 22) and never-smoke (n = 31) patients with LADC through bacterial 16S rRNA gene high-throughput sequencing. Then nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-induced lung cancer mouse model and A549 cells were used to study the effect of Stenotrophomonas maltophilia (S. maltophilia) in LADC.

Results and Discussion

We found a significant increase of genus Stenotrophomonas in LADC tissues of patients with primary tumor size greater than 3 cm and never-smoker patients. We further found that intratracheal infection with S. maltophilia promoted tumor progression in the NNK-induced lung cancer mouse model. We performed RNA-seq analysis on lung tissues and found that S. maltophilia treatment drove inflammation and upregulated tumor associated cell signaling, including Apelin signaling pathway. Mechanistically, histone deacetylase 5 (HDAC5) gene expression was significantly upregulated in S. maltophilia treated groups, and was required for S. maltophilia induced cell proliferation and migration in LADC cell line A549. Therefore, we provide in vivo and in vitro evidence to demonstrate that S. maltophilia promotes LADC progression, in part, through HDAC5.

Cefiderocol for Stenotrophomonas maltophilia prosthetic joint infection: a case report

Treatment of Stenotrophonomas maltophilia infections is difficult due to its predilection to form biofilms and susceptibility to a limited number of antibiotics. We report a case of S. maltophilia-associated periprosthetic joint infection successfully treated with a combination of the novel therapeutic agent, cefiderocol, and trimethoprim-sulfamethoxazole after debridement and implant retention.

Characterization of three Stenotrophomonas strains isolated from different ecosystems and proposal of Stenotrophomonas mori sp. nov. and Stenotrophomonas lacuserhaii sp. nov

Stenotrophomonas spp. have primarily been reported as non-pathogenic, plant-probiotic bacteria, despite the presence of some opportunistic human pathogens in the genus. Here, three Gram-stain negative, rod-shaped, non-spore-forming bacteria, designated as strains CPCC 101365^T, CPCC 101269^T, and CPCC 101426 were isolated from surface-sterilized medicinal plant roots of a mulberry plant in Chuxiong of the Yunnan Province, freshwater from Erhai Lake in the Yunnan Province, and sandy soils in the Badain Jaran desert in Inner Mongolia Autonomous Region, China, respectively. The 16S rRNA gene sequences analysis of these isolates in comparison with sequences from the GenBank database indicated that they belong to the genus Stenotrophomonas, with nucleotide similarities of 96.52-99.92% to identified Stenotrophomonas members. Phylogenetic analysis based on 16S rRNA gene and genome sequences confirmed that the isolates are members of the genus Stenotrophomonas. Values for genomic average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; < 70%) indicated that strains CPCC 101365^T and CPCC 101269^T were well-differentiated from validly described Stenotrophomonas species, while strain CPCC 101426 shared high ANI (97.7%) and dDDH (78.3%) identity with its closest phylogenetic neighbor, Stenotrophomonas koreensis JCM 13256^T. The three genomes were approximately 3.1-4.0 Mbp in size and their G + C content ranged in 66.2-70.2%, with values slightly differing between CPCC 101365^T (3.4 Mbp; 70.2%), CPCC 101269^T (4.0 Mbp; 66.4%), and CPCC 101426 (3.1 Mbp; 66.2%). Genes encoding enzymes involved in the biosynthesis of indole-3-acetic acid (IAA) and siderophores were identified in the genomes of the three isolates, suggesting that these strains might serve roles as plant-growth promoting microorganisms. The polar lipid fractions of the three isolates primarily comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The predominant cellular fatty acid was iso-C₁₅: ₀, with moderate amounts of antesio-C_{15: 0}, iso-C_{11: 0}, iso C_{17: 1} ɷ9c/C_{16: 0} 10-methyl, iso-C_{14: 0}, and C_{16: 1} ɷ7c/C_{16: 1} ɷ6c. These results indicated that polyphasic characteristics of strains CPCC 101365^T and CPCC 101269^T differed from other identified Stenotrophomonas species and that strain CPCC 101426 was affiliated with the species Stenotrophomonas koreensis. Accordingly, two novel species of the genus Stenotrophomonas were consequently proposed, corresponding to Stenotrophomonas mori sp. nov. (type strain CPCC 101365^T = DY006^T = KCTC 82900^T) and Stenotrophomonas lacuserhaii sp. nov. (type strain CPCC 101269^T = K32^T = KCTC 82901^T).

Highlights

Members of the genus Stenotrophomonas, and particularly Stenotrophomonas maltophilia, are opportunistic human pathogens, but not enough research has evaluated the identification of environmental Stenotrophomonas spp. However, most Stenotrophomonas spp. serves as plant-probiotic bacteria.In this study, we obtained and characterized three Stenotrophomonas strains from different ecosystems. Based on phenotypic differences, chemotaxonomic properties, ANI and dDDH identity values, and phylogenetic analyses, two novel Stenotrophomonas species are proposed for the strains identified here. The encoding genes related to plant-growth promotion in the genomes of the newly recovered Stenotrophomonas spp. were retrieved. Follow-on experiments confirmed that these strains produced the important plant hormone IAA. Thus, these Stenotrophomonas spp. could considerably contribute to shaping and maintaining ecological stability in plant-associated environments, particularly while acting as plant-probiotic microorganisms.

Alterations of the gut microbiota and short chain fatty acids in necrotizing enterocolitis and food protein-induced allergic protocolitis infants: A prospective cohort study

Background

Even though presenting with similar clinical manifestations, necrotizing enterocolitis (NEC) and food protein-induced allergic protocolitis (FPIAP) have completely different treatments and prognosis. Our study aimed to quantify and evaluate differences in gut microbiota and short chain fatty acids (SCFAs) between infants with NEC and FPIAP to better identify these two diseases in clinical settings.

Methods

A total of 43 infants with NEC or FPIAP in Children's Hospital of Chongqing Medical University, China between December 2020 and December 2021 were enrolled. Stool samples were prospectively collected and froze. Infants defined as NEC were those who presented with clinical courses consistent with NEC and whose radiographs fulfilled criteria for Bell's stage 2 or 3 NEC, while those who were healthy in appearance and had blood in the stool (visible or may be microscopic), had normal bowel sounds in physical examination, were resolved after eliminating the causative food, and/or had recurrence of symptoms after oral food challenge (OFC) were defined as FPIAP. Primers specific for bacterial 16S rRNA genes were used to amplify and pyrosequence fecal DNA from stool samples. Gas chromatography-mass spectrometry (GC-MS) technology was used to determine the concentrations of SCFAs.

Results

Among the 43 infants, 22 were diagnosed with NEC and 21 were diagnosed with FPIAP. The microbial community structure in NEC infant stools differed significantly from those in FPIAP infant stools. NEC infants had significantly higher proportion of Actinobacteria and reduced proportion of Bacteroidetes compared with FPIAP infants, and the proportions of Halomonas, Acinetobacter, Bifidobacterium, and Stenotrophomonas in NEC infants were significantly higher than that of FPIAP infants. In addition, infants with NEC had significantly lower levels of acetic acid, propionic acid, butyric acid, isovaleric acid, and total SCFAs, and higher level of hexanoic acid as compared to the infants of the FPIAP group.

Conclusions

The differences of gut microbiota composition and concentrations of SCFAs might represent suitable biomarker targets for early identification of NEC and FPIAP.

Antibacterial Screening of Isoespintanol, an Aromatic Monoterpene Isolated from Oxandra xylopioides Diels

The incidence of nosocomial infections, as well as the high mortality and drug resistance expressed by nosocomial pathogens, especially in immunocompromised patients, poses significant medical challenges. Currently, the efficacy of plant compounds with antimicrobial potential has been reported as a promising alternative therapy to traditional methods. Isoespintanol (ISO) is a monoterpene with high biological activity. Using the broth microdilution method, the antibacterial activity of ISO was examined in 90 clinical isolates, which included 14 different species: (Escherichia coli (38), Pseudomonas aeruginosa (12), Klebsiella pneumoniae (13), Acinetobacter baumannii (3), Proteus mirabilis (7), Staphylococcus epidermidis (3), Staphylococcus aureus (5), Enterococcus faecium (1), Enterococcus faecalis (1), Stenotrophomonas maltophilia (2), Citrobacter koseri (2), Serratia marcescens (1), Aeromonas hydrophila (1), and Providencia rettgeri (1). MIC90 minimum inhibitory concentration values ranged from 694.3 to 916.5 µg/mL and MIC50 values from 154.2 to 457.3 µg/mL. The eradication of mature biofilms in P. aeruginosa after 1 h of exposure to ISO was between 6.6 and 77.4%, being higher in all cases than the percentage of biofilm eradication in cells treated with ciprofloxacin, which was between 4.3 and 67.5%. ISO has antibacterial and antibiofilm potential against nosocomial bacteria and could serve as an adjuvant in the control of these pathogens.

Effects of Free or Immobilized Bacterium Stenotrophomonas acidaminiphila Y4B on Glyphosate Degradation Performance and Indigenous Microbial Community Structure

The overuse of glyphosate has resulted in serious environmental contamination. Thus, effective techniques to remove glyphosate from the environment are required. Herein, we isolated a novel strain Stenotrophomonas acidaminiphila Y4B, which completely degraded glyphosate and its major metabolite aminomethylphosphonic acid (AMPA). Y4B degraded glyphosate over a broad concentration range (50-800 mg L^-1), with a degradation efficiency of over 98% within 72 h (50 mg L^-1). Y4B degraded glyphosate via the AMPA pathway by cleaving the C-N bond, followed by degradation of AMPA and subsequent metabolism. Y4B demonstrated strong competitiveness and substantially accelerated the degradation of glyphosate in different soils, degrading 71.93 and 89.81% of glyphosate (400 mg kg^-1) within 5 days in sterile and nonsterile soils, respectively. The immobilized cells of Y4B were more efficient than their free cells and they displayed excellent biodegradation efficiency in a sediment-water system. Taken together, Y4B is an ideal degrader for the bioremediation of glyphosate-contaminated sites.

Antibiotic Susceptibility and Minimum Inhibitory Concentration for Stenotrophomonas maltophilia Ocular Infections

Stenotrophomonas maltophilia (S. maltophilia) is a Gram-negative, opportunistic pathogen that can lead to ocular infections, such as keratitis and endophthalmitis. The purpose of this study was to determine the antibiotic susceptibility and minimum inhibitory concentrations (MICs) of S. maltophilia isolates from ocular infections and to evaluate the differences in antibiotic MICs between keratitis and endophthalmitis isolates. The disc diffusion method revealed that S. maltophilia isolates exhibited 91% susceptibility to levofloxacin and moxifloxacin and 61% susceptibility to trimethoprim−sulfamethoxazole (TMP−SMX). The E-test indicated that S. maltophilia isolates exhibited 40%, 100%, 72%, 91%, 91%, and 93% susceptibility to ceftazidime, tigecycline, TMP−SMX, levofloxacin, gatifloxacin, and moxifloxacin, respectively. The MIC90 values of amikacin, ceftazidime, cefuroxime, tigecycline, TMP−SMX, levofloxacin, gatifloxacin, and moxifloxacin were >256, >256, >256, 3, >32, 1, 2, and 0.75 µg/mL, respectively. The geometric mean MICs of ceftazidime, TMP−SMX, levofloxacin, gatifloxacin, and moxifloxacin were significantly lower for the keratitis isolates than for the endophthalmitis isolates (p = 0.0047, 0.003, 0.0029, 0.0003, and 0.0004, respectively). Fluoroquinolones showed higher susceptibility and lower MICs for the S. maltophilia isolates when compared with other antibiotics. Fluoroquinolones can be recommended for treating S. maltophilia ocular infections. Tigecycline and TMP−SMX could be alternative antibiotics for S. maltophilia ocular infections.

Antibacterial contact-dependent proteins secreted by Gram-negative cystic fibrosis respiratory pathogens

Cystic fibrosis (CF) is a genetic disease that affects almost 100 000 people worldwide. CF patients suffer from chronic bacterial airway infections that are often polymicrobial and are the leading cause of mortality. Interactions between pathogens modulate expression of genes responsible for virulence and antibiotic resistance. One of the ways bacteria can interact is through contact-dependent systems, which secrete antibacterial proteins (effectors) that confer advantages to cells that harbor them. Here, we highlight recent work that describes effectors used by Gram-negative CF pathogens to eliminate competitor bacteria. Understanding the mechanisms of secreted effectors may lead to novel insights into the ecology of bacteria that colonize respiratory tracts and could also pave the way for the design of new therapeutics.

Epidemiology, Mechanisms of Resistance and Treatment Algorithm for Infections Due to Carbapenem-Resistant Gram-Negative Bacteria: An Expert Panel Opinion

Antimicrobial resistance represents a serious threat for global health, causing an unacceptable burden in terms of morbidity, mortality and healthcare costs. In particular, in 2017, carbapenem-resistant organisms were listed by the WHO among the group of pathogens for which novel treatment strategies are urgently needed. Fortunately, several drugs and combinations have been introduced in recent years to treat multi-drug-resistant (MDR) bacteria. However, a correct use of these molecules is needed to preserve their efficacy. In the present paper, we will provide an overview on the epidemiology and mechanisms of resistance of the most common MDR Gram-negative bacteria, proposing a treatment algorithm for the management of infections due to carbapenem-resistant bacteria based on the most recent clinical evidence.