Distribution of smf-1, rmlA, spgM and rpfF genes among Stenotrophomonas maltophilia isolates in relation to biofilm-forming capacity

Revealing sRNA expression profiles of NDM-5-producing CRKP and explore the role of sRNA207 in NDM-5-producing CRKP resistance

New Delhi metallo-beta-lactamase-5 (NDM-5)-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) is characterized by high virulence, high morbidity, and mortality, and the detection rate in children has increased in recent years. Therefore, it is urgent to develop new therapeutic targets and strategies. Non-coding small RNA (sRNA)-mediated RNA-based therapies offer a new direction for the treatment of bacterial infections, especially resistant bacteria. This study first analyzed the transcriptional expression profiles of NDM-5-producing CRKP and Carbapenem-susceptible Klebsiella pneumoniae (CSKP) isolates from the clinic by RNA-seq. A total of 4,623 genes were obtained, of which 307 genes were differentially expressed in NDM-5-producing CRKP, and these differentially expressed genes are mainly related to metabolism. Then, by analyzing the length and secondary structure of genes that could not match the reference gene and non-redundant protein database, we obtained 268 sRNAs, of which 13 sRNAs were differentially expressed in NDM-5-producing CRKP. After the expression level of differentially expressed sRNA was verified by RT-PCR to be consistent with that of RNA-seq, we chose sRNA207 as our research target. By knockdown of sRNA207 and smf-1 (the predicted target mRNA of sRNA207) in the strain, we found that increased expression of sRNA207 promoted biofilm formation by stabilizing expression of smf-1, which in turn affected the resistance of NDM-5-producing CRKP to carbapenems. This provides a new approach to treat CRKP infection.

IMPORTANCE

sRNAs form a regulatory network that regulates bacterial virulence, drug resistance, and other functions by targeting mRNAs. However, sRNA expression profile and function of NDM-5-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) are still unknown. In this study, we analyzed the sRNA expression profiles of NDM-5-producing CRKP obtained from clinical by referring to the methods of previous articles. A total of 268 candidates sRNAs were obtained, of which 248 were newly discovered. More importantly, 13 sRNAs were differentially expressed in NDM-5-producing CRKP compared with CSKP. We knocked down sRNA207 in NDM-5-producing CRKP to validate its effect on smf-1, biofilm, and resistance of strains. We also confirmed the role of smf-1 in biofilm formation and drug resistance of NDM-5-producing CRKP by constructing smf-1-knockdown strain. The results suggest that smf-1 is the target gene of sRNA207. Increased expression of sRNA207 in NDM-5-producing CRKP stabilizes smf-1 expression, which in turn affects the resistance of the strains through biofilm formation.

Preparation and Optimization of Hydrophilic Modified Pullulan Encapsulated Tetracycline for Significant Antibacterial and Anti-Biofilm Activity Against Stenotrophomonas maltophilia Isolates

Stenotrophomonas maltophilia (S. maltophilia), resistant to antibiotics, is a hazardous illness and a well-known worldwide public health issue. The present investigation included the preparation of formulations of tetracycline encapsulated in pullulan (referred to as HM-PULL-Tetracycline). The study aimed to assess the effectiveness of these formulations against strains of S. maltophilia in terms of their antimicrobial and anti-biofilm properties. The physicochemical characteristics of HM-PULL-Tetracycline were analyzed using a field scanning electron microscope, X-ray dispersion, Zeta potential, and dynamic light scattering analysis. The antibacterial and anti-biofilm activity was assessed using minimal biofilm inhibitory concentration and broth micro-dilution. In addition, the biocompatibility of HM-PULL-Tetracycline was assessed by investigating its cytotoxicity on the human diploid fibroblasts (HDF) normal cell line using the MTT test. The HM-PULL-Tetracycline formulation successfully prevented biofilm formation, measuring 179.7±2.66 nm in size and with an encapsulation efficiency of 84.86±3.14 %. It exhibited a biofilm growth inhibition rating of 69 % and significantly down-regulated the expression of the smf-1, rpfF, rmlA, and spgM biofilm genes in S. maltophilia strains (p<0.05). Furthermore, the HM-PULL-Tetracycline formulation exhibited a 4 to 6-fold increase in antibacterial efficacy compared to unbound tetracycline. The HM-PULL-Tetracycline formulation demonstrated cell viability of over 90 % at all doses tested against HDF normal cells. The findings of the current investigation demonstrate that HM-PULL-Tetracycline enhances the bactericidal and anti-biofilm properties without causing harm to healthy human cells. This suggests that Could be a promising approach for medication administration.

Susceptibility of clinical isolates of novel pathogen Stenotrophomonas sepilia to novel benzoquinolizine fluoroquinolone levonadifloxacin

Background

Stenotrophomonas sepilia, identified in 2021, is part of the Stenotrophomonas maltophilia complex (Smc) and shares high genomic identity with S. maltophilia. Resistance to levofloxacin, the recommended fluoroquinolone for S. maltophilia, is being increasingly reported. Recent studies indicate that levonadifloxacin, a novel benzoquinolizine, may be more effective. This study evaluates the antimicrobial efficacy of levofloxacin and levonadifloxacin against clinical isolates of S. sepilia.

Objectives

To assess the antibacterial effectiveness of levofloxacin and levonadifloxacin against novel pathogen S. sepilia.

Methods

A total of 116 S. maltophilia isolates, identified by MALDI-TOF MS, were collected from five centres across India. S. sepilia was confirmed by PCR using primers targeting a unique genomic sequence (NCBI accession number LXXZ00000000.1). Minimum inhibitory concentrations (MICs) of levonadifloxacin and levofloxacin were determined by using the microbroth-dilution method and Etest as per CLSI guidelines. The levofloxacin breakpoint was used to interpret MICs of levonadifloxacin.

Results

Among a total of 116 circulating S. maltophilia isolates collected, 46 were identified as S. sepilia, representing a prevalence rate of (∼40%), thus highlighting its significance as an important pathogen within the Smc. Both levofloxacin and levonadifloxacin demonstrated a 98% inhibition rate against the 46 S. sepilia tested. Only one S. sepilia isolate resistant to levofloxacin showed intermediate susceptibility to levonadifloxacin, which consistently had lower MICs.

Conclusions

Levofloxacin and levonadifloxacin show similar susceptibility rates against S. sepilia, with levonadifloxacin exhibiting lower MICs. Further studies are required to establish clinical utility of levonadifloxacin in managing these infections.

Evaluation of the therapeutic effect of a novel bacteriophage in the healing process of infected wounds with Klebsiella pneumoniae in mice

OBJECTIVE

Bacterial wound infections have recently become a threat to public health. The emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae highlights the need for a new treatment method. The effectiveness of bacteriophages has been observed for several infections in animal models and human trials. In this study, we assessed the effectiveness of bacteriophages in the treatment of wound infections associated with MDR and biofilm-producing K. pneumoniae and compared its effectiveness with that of gentamicin.

METHODS

A lytic phage against MDR K. pneumoniae was isolated and identified. The effectiveness of phages in the treatment of wound infection in mice was investigated and its effectiveness was compared with gentamicin.

RESULTS

The results showed that the isolated phage belonged to the Drexlerviridae family. This phage acts like gentamicin and effectively eliminates bacteria from wounds. In addition, mice in the phage therapy group were in better physical condition.

CONCLUSION

Our results demonstrated the success of phage therapy in the treatment of mice wounds infected with K. pneumoniae. These results indicate the feasibility of topical phage therapy for the safe treatment of wound infections.

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.

StM171, a Stenotrophomonas maltophilia Bacteriophage That Affects Sensitivity to Antibiotics in Host Bacteria and Their Biofilm Formation

Stenotrophomonas maltophilia mainly causes respiratory infections that are associated with a high mortality rate among immunocompromised patients. S. maltophilia exhibits a high level of antibiotic resistance and can form biofilms, which complicates the treatment of patients infected with this bacterium. Phages combined with antibiotics could be a promising treatment option. Currently, ~60 S. maltophilia phages are known, and their effects on biofilm formation and antibiotic sensitivity require further examination. Bacteriophage StM171, which was isolated from hospital wastewater, showed a medium host range, low burst size, and low lytic activity. StM171 has a 44kbp dsDNA genome that encodes 59 open-reading frames. A comparative genomic analysis indicated that StM171, along with the Stenotrophomonas phage Suso (MZ326866) and Xanthomonas phage HXX_Dennis (ON711490), are members of a new putative Nordvirus genus. S. maltophilia strains that developed resistance to StM171 (bacterial-insensitive mutants) showed a changed sensitivity to antibiotics compared to the originally susceptible strains. Some bacterial-insensitive mutants restored sensitivity to cephalosporin and penicillin-like antibiotics and became resistant to erythromycin. StM171 shows strain- and antibiotic-dependent effects on the biofilm formation of S. maltophilia strains.

Evaluation of ethanol and EDTA concentrations in the expression of biofilm-producing smf-1, rpfF genes in XDR clinical isolates of Stenotrophomonas maltophilia

BACKGROUND

Stenotrophomonas maltophilia is able to cause infections in immunocompromised patients, and the treatment of this opportunistic pathogen is complicated due to its virulence factors, antibiotic resistance, and the ability of the bacteria to produce biofilm. The main goals of this study were to assess the susceptibility of extensively drug-resistant (XDR) isolates to ethanol and EDTA, and evaluating the synergistic effect of these disinfectants, and also survey the effect of exposure to sub-inhibitory concentrations of ethanol and EDTA on the expression of biofilm-producing smf-1, rpfF genes.

RESULTS

The results showed that EDTA significantly increased the effectiveness of the ethanol and have a synergistic effect. All of the 10 XDR isolates included in the current study harbored smf-1 and rpfF genes and produced biofilm. After exposure to MIC, sub-MIC, synergism, and sub-synergism of ethanol and EDTA, the expression of smf-1 and rpfF genes was repressed significantly.

CONCLUSION

In the current study, it was indicated that the expression of biofilm-producing genes was repressed when bacteria are exposed to different concentrations of ethanol and EDTA. Future studies should include more complex microbial communities residing in the hospitals, and more disinfectants use in hospitals. Expression of other virulence genes in different conditions is suggested.

Construction and application of a new CRISPR/Cas12a system in Stenotrophomonas AGS-1 from aerobic granular sludge

Aerobic granular sludge (AGS) is a microbial aggregate with a biofilm structure. Thus, investigating AGS in the aspect of biofilm and microbial attachment at the genetic level would help to reveal the mechanism of granule biofilm formation. In this work, a two-plasmid clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas)12a genome editing system was constructed to identify attachment genes for the first time in Stenotrophomonas AGS-1 from AGS. One plasmid contained a Cas12a cassette driven by an arabinose-inducible promoter, and another contained the specific crRNA and homologous arms (HAs). Acidaminococcus sp. Cas12a (AsCas12a) was adopted and proven to have mild toxicity (compared to Cas9) and strong cleavage activity for AGS-1. CRISPR/Cas12a-mediated rmlA knockout decreased attachment ability by 38.26%. Overexpression of rmlA in AGS-1 resulted in an increase of 30.33% in attachment ability. These results showed that the modulation of rmlA was an important factor for the biofilm formation of AGS-1. Moreover, two other genes (xanB and rpfF) were knocked out by CRISPR/Cas12a and identified as attachment-related genes in AGS-1. Also, this system could achieve point mutations. These data indicated that the CRISPR/Cas12a system could be an effective molecular platform for attachment gene function identification, which would be useful for the development of AGS in wastewater treatment.

The Relationship between the Biofilm Genes and Antibiotic Resistance in Stenotrophomonas maltophilia

Objectives

Today, Stenotrophomonas maltophilia (S. maltophilia) is a major opportunistic pathogen among hospitalized or immunocompromised patients. Antibiotic-resistant clinical isolates are increasing in several parts of the world. Various antibiotic-resistance and biofilm-forming genes are identified in this bacterium. Its capacity to form biofilms is an important virulence factor that may impact antibiotic-resistance patterns. In the current study, we evaluated the biofilm-formation capacity, antibiotic-resistance profile, and prevalence of biofilm-forming genes as well as antibiotic resistance genes among S. maltophilia isolates.

Materials and Methods

In this cross-sectional study, 94 clinical S. maltophilia isolates were recovered from four tertiary-care hospitals in Iran between 2021 and 2022. The presence of the selected antibiotic-resistance genes and biofilm-forming genes was examined by polymerase chain reaction (PCR). The ability of biofilm formation was examined by microtiter plate assay. The Kirby-Bauer disc diffusion method was used to evaluate the trimethoprim-sulfamethoxazole (TMP-SMX), levofloxacin, and minocycline resistance.

Results

S. maltophilia is mainly isolated from bloodstream infections. Notably, 98.93% of isolates were biofilm producers, of which 19.35%, 60.22%, and 20.43% produced strong, moderate, and weak biofilm, respectively. The frequency of biofilm genes was 100%, 97.88%, 96.80%, and 75.53% for spgM, rmlA, smf-1, and rpfF, respectively. Isolates with the genotype of smf-1+/rmlA+/spgM+/rpfF+ were mostly strong biofilm producers. Among the antibiotic-resistance genes, the Smqnr, L1, and sul1 had the highest prevalence (76.59%, 72.34%, and 64.89), respectively. Antimicrobial susceptibility evaluation showed 1.06%, 3.19%, and 6.3% resistance to minocycline, TMP-SMX, and levofloxacin.

Conclusion

The results of the current study demonstrated that S. maltophilia isolates differ in biofilm-forming ability. Moreover, smf-1, rmlA, and spgM genes were presented in all strong biofilm producers. Although the overall resistance rate to the evaluated antibiotics was high, there was no statistically significant relation between antibiotic resistance and the type of biofilm.

Chemical constituents of Aspergillus udagawae isolated from the soil of the Xingren coal areas and their antibacterial activities

A new helvolic acid derivative (1), together with nine known compounds (2-10) were isolated from the metabolites of Aspergillus udagawae MST1-10 with the bioassay-guided fractionation method. Their structures were identified on the basis of spectroscopic analysis. The absolute configuration of compound 1 was elucidated through NOESY and ECD spectra. Compound 2 displayed significant antibacterial activities against Stenotrophomonas maltophilia with MIC value of 2 μg/mL (Trimethoprim, MIC = 64 μg/mL), and with biofilm inhibition rates of 96.41%, 87.77%, and 41.70% at 4MIC, 2MIC, and MIC, respectively.

The prevalence of colistin resistance in clinical Stenotrophomonas maltophilia isolates worldwide: a systematic review and meta-analysis

While trimethoprim-sulfamethoxazole (TMP-SMX) is the first-line therapy of Stenotrophomonas maltophilia infections, colistin is one of the therapeutic options in cases of allergy or resistance to TMP-SMX. However, understanding the global status of resistance to colistin amongst S. maltophilia isolates could be helpful for appropriate antibiotic prescription. This study aimed to conduct a systematic review and meta-analysis to examine the prevalence of colistin resistance in clinical S. maltophilia isolates worldwide. According to eligibility criteria, a total of 61 studies were included in the analysis. The pooled prevalence for colistin resistance was 42% (95% CI: 35-49%), ranging from 0.1 to 97%. Subgroups analysis indicated that, the pooled prevalence of colistin resistance was 44% (95% CI: 29-60%) in 15 studies during 2000-2010, and it was estimated to be 41% (95% CI: 33-50%) in 46 articles from 2011 to 2021. It was 46% (95% CI: 35-58%) in the studies that used broth microdilution method, and 39% (95% CI: 30-49%) in the studies with other used methods. The resistance rate in Asian countries was 45% (95% CI: 31-60%), in European countries was 45% (95% CI: 34-56%) and in the countries of North and South America was 33% (95% CI: 20-46%). Our review showed notable resistance to colistin in clinical S. maltophilia isolates. Given the estimated resistance rates, alternative antibiotics could be preferred to treat serious infections due to S. maltophilia.

In Vitro Activity of Fosfomycin on Multidrug-Resistant Strains of Klebsiella pneumoniae and Klebsiella oxytoca Causing Urinary Tract Infection

With the emergence of multi-drug resistant strains among Klebsiella isolates, the use of old drugs such as fosfomycin has been considered. In this context, we investigated the effect of fosfomycin on biofilm-producing Klebsiella pneumoniae and Klebsiella oxytoca strains isolated from ICU patients. A total of 90 isolates of Klebsiella pneumoniae and 30 isolates of Klebsiella oxytoca were collected from the ICU ward. All isolates were confirmed by biochemical and genotypic methods. Antibiotic susceptibility testing was performed by disc diffusion method and for fosfomycin and colistin, minimum inhibitory concentration (MIC) was done using micro broth dilution. The presence of the beta-lactamase encoding genes, biofilm-related genes, and fosfomycin resistance-related genes was detected by PCR. Finally, for fosfomycin-resistant isolates, we determined the sequence type by the MLST method. Sensitivity rate to fosfomycin in Klebsiella pneumoniae and Klebsiella oxytoca isolates was 92.2% and 100%, respectively. Fosfomycin was the most active antimicrobial agent with 96% sensitivity among all tested antibiotics. All tested isolates could produce biofilm. The frequency of biofilm-related genes for Klebsiella pneumoniae was as follows: 95.5% fimH, 86.6% mrkD, 77.7% mrkA, and 50% wcaG. The frequency of these genes for Klebsiella oxytoca was as follows: 56.6% fimA, 46.6% mrkA, 93.3% matB, and 90% pilQ. Only 4.4% of Klebsiella pneumoniae isolates showed resistance to fosfomycin, and the fosA gene was detected in all of them. Our results showed that fosfomycin effectively inhibits multidrug-resistant (MDR) strains of Klebsiella pneumoniae and Klebsiella oxytoca.

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.

Myxinidin-Derived Peptide against Biofilms Caused by Cystic Fibrosis Emerging Pathogens

Chronic lung infections in cystic fibrosis (CF) patients are triggered by multidrug-resistant bacteria such as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. The CF airways are considered ideal sites for the colonization and growth of bacteria and fungi that favor the formation of mixed biofilms that are difficult to treat. The inefficacy of traditional antibiotics reinforces the need to find novel molecules able to fight these chronic infections. Antimicrobial peptides (AMPs) represent a promising alternative for their antimicrobial, anti-inflammatory, and immunomodulatory activities. We developed a more serum-stable version of the peptide WMR (WMR-4) and investigated its ability to inhibit and eradicate C. albicans, S. maltophilia, and A. xylosoxidans biofilms in both in vitro and in vivo studies. Our results suggest that the peptide is able better to inhibit than to eradicate both mono and dual-species biofilms, which is further confirmed by the downregulation of some genes involved in biofilm formation or in quorum-sensing signaling. Biophysical data help to elucidate its mode of action, showing a strong interaction of WMR-4 with lipopolysaccharide (LPS) and its insertion in liposomes mimicking Gram-negative and Candida membranes. Our results support the promising therapeutic application of AMPs in the treatment of mono- and dual-species biofilms during chronic infections in CF patients.

Stenotrophomonas maltophilia and Its Ability to Form Biofilms

In the last ten years, Stenotrophomonas maltophilia has gained increasing interest as an important agent of infection, which is why it has come to be recognized as a serious cause of nosocomial infections related to bloodstream infections, pneumonia, and cancer, mainly in patients with intensive care, and is associated with high mortality rates in immunocompromised patients, with prolonged hospital stays and extensive use of antimicrobials. The importance of this microorganism lies in its low pathogenicity, high multiresistance to various antibiotics, and frequent and persistent isolation in predisposed patients. In addition, few studies have evaluated its epidemiology and clinical relevance. The pathogenesis of biofilms lies mainly in the fact that they can generate persistent chronic infections that are difficult to eradicate. To this extent, it is important to make the characteristics of the biofilm formation behavior of Stenotrophomonas maltophilia known and generate more knowledge about its colonization or infection in humans through this review, which discusses more recent information.

Stenotrophomonas maltophilia: Genotypic Characterization of Virulence Genes and The Effect of Ascorbic Acid on Biofilm Formation

Stenotrophomonas maltophilia is an environmental bacterium that has gained a lot of attention, as a nosocomial pathogen associated with significant mortality rates. Biofilm formation is considered the corner stone for establishing infections in many bacteria including S. maltophilia. The aim of this study was the genotypic characterization of the different virulence-associated genes and the investigation of the effect of ascorbic acid on S. maltophilia biofilm formation. A total of 20 S. maltophilia isolates from different sources were included in this study. Genes encoding different virulence factors were investigated genotypically. These included stmPr1, stmPr2, smlt3773 locus, smf-1, rpfF, rmlA and spgM. Biofilm formation was investigated phenotypically. The effect of ascorbic acid on biofilm formation was investigated using MIC as well as sub-inhibitory concentrations. Many of the isolates harbored both serine proteases genes stmPr-1 and stmPr-2. Fourteen (70%) of the 20 isolates carried stmPr-1 and 15 (75%) had stmPr-2. Most of the isolates (95%) possessed smlt-3773 locus. Genes linked to biofilm formation such as smf-1, rpfF, rmlA and spgM, were found in (90%), (45%), (85%) and (30%) of the isolates, respectively. Phenotypically, all S. maltophilia isolates (100%) were biofilm producers. Fifteen (75%) were strong biofilm producers and 5 (25%) were moderate biofilm producers. In attempts to seek a non-chemotherapeutic alternative that can hinder biofilm formation without provoking antimicrobial resistance, the results, herein, showed that ascorbic acid inhibits biofilm formation in a dose-dependent manner.