Biofilm establishment, biofilm persister cell formation, and relative gene expression analysis of type II toxin-antitoxin system in Klebsiella pneumoniae

Investigating the effects of zinc oxide and titanium dioxide nanoparticles on the formation of biofilm and persister cells in Klebsiella pneumoniae

The biofilm formation in klebsiella pneumoniae isolates poses a significant problem as it can result in treatment failure and the development of chronic infections. These biofilms act as protective barriers, rendering the bacteria resistant to antibiotics. Additionally, persister cells, which make up a small fraction of the bacterial population, have the ability to enter a dormant state after treatment with high doses of antibiotics. These persister cells play a crucial role in the high level of biofilm-mediated tolerance to antibiotics. The present study aimed to investigate the impact of Zinc oxide (ZnO) and titanium dioxide (TiO2) nanoparticles on the formation of biofilm and persister cells in K. pneumoniae. The minimum inhibitory concentration (MIC) of colistin in K. pneumoniae ATCC 13883 was determined using the microdilution method. The formation of persister cells was evaluated by introducing sub-MIC of colistin. Subsequently, the MIC of ZnO NPs and TiO2 NPs in these persister cells was assessed using the microdilution method. Furthermore, the effects of nanoparticles on the expression levels of biofilm-associated genes were analyzed using real-time polymer chain reaction (PCR). The MIC values for colistin, ZnO, and TiO2 were determined at 2, 12.5, and 6.25 μg/mL, respectively. In the presence of nanoparticles, biofilm formation decreased. Real-time PCR results showed the messenger RNA (mRNA) level of mrkH and fimH were decreased and the expression of luxS and mazF were increased. Biofilm formation of K. pneumoniae ATCC 1383 was inhibited in response to nanoparticles. According to the results of the present study use of nanoparticles may help control multidrug-resistant (MDR) infections in hospitalized patients.

GNAT toxin may have a potential role in Pseudomonas aeruginosa persistence: an in vitro and in silico study

Aims: Persistent cells are primarily responsible for developing antibiotic resistance and the recurrence of Pseudomonas aeruginosa. This study investigated the possible role of GNAT toxin in persistence. Materials & methods: P. aeruginosa was exposed to five MIC concentrations of ciprofloxacin. The expression levels of target genes were assessed. The GNAT/HTH system was bioinformatically studied, and an inhibitory peptide was designed to disrupt this system. Results: Ciprofloxacin can induce bacterial persistence. There was a significant increase in the expression of the GNAT toxin during the persistence state. A structural study of the GNAT/HTH system determined that an inhibitory peptide could be designed to block this system effectively. Conclusion: The GNAT/HTH system shows promise as a novel therapeutic target for combating P. aeruginosa infections.

Inhibitory Effects of Carvacrol on Biofilm Formation in Colistin Heteroresistant Acinetobacter baumannii Clinical Isolates

BACKGROUND

The ability of bacteria to form biofilm is an essential strategy for creating stable infections. This issue is more critical in Acinetobacter bauamannii as a hospital pathogen. Today, the control of biofilm formation and solutions to prevent or remove biofilm is being developed. Carvacrol has been considered an anti-biofilm compound in significant bacteria. This study investigated the anti-biofilm effect of Carvacrol on biofilm formation in clinical colistin heteroresistant isolates of A. baumannii.

METHODS

22 clinical strains of A. baumannii were collected from Motahari Hospital in Tehran, Iran, in 2019. Biochemical and genotypic methods confirmed these isolates. Colistin heteroresistance was determined by the Standard PAP method. Carvacrol's antibacterial and anti-biofilm activity was determined according to the standard protocol.

RESULTS

About 12 isolates were considered strong biofilm producers and were used for analysis. Six isolates had hetero-resistance to colistin. Carvacrol at a 512 g/ml concentration showed the best antibacterial activity against all isolates. The sub-MIC of Carvacrol (256 g/ml) reduced the biofilm formation capacity, which was statistically significant (p < 0.05).

CONCLUSION

The results of this study showed that sub-MIC of Carvacrol has anti-biofilm effects in clinical A.baumannii colistin hetero-resistance isolates.

Zinc oxide nanoparticles impact the expression of the genes involved in toxin-antitoxin systems in multidrug-resistant Acinetobacter baumannii

The aim of this study was to investigate the effect of zinc oxide nanoparticles (ZnO-NPs) on the expression of genes involved in toxin-antitoxin (TA) systems in multidrug-resistant (MDR) Acinetobacter baumannii. Seventy clinical isolates of A. baumannii were collected from variuos clinical samples. Antimicrobial susceptibility test was determined by disk diffusion. Type II TA system-related genes including GNAT, XRE-like, hipA, hipB, hicA, hicB were screened using polymerase chain reaction (PCR). ZnO-NPs prepared and characterized by field emission scanning electron microscopy and X-ray diffraction. MIC of ZnO-NPs of A. baumannii isolates was performed using the microdilution method. The expression of type II TA systems-related genes were assessed with and without exposure to ZnO-NPs using real-time PCR. The highest rate of resistance and sensitivity was observed against cefepime (77.14%), and ampicillin/sulbactam (42.85%), respectively. All A. baumannii isolates were considered as MDR. In this study, three TA loci were identified for A. baumannii including GNAT/XRE-like, HicA/HicB, and HipA/HipB and their prevalence was 100%, 42%, and 27.1%, respectively. There was no significant relationship between the prevalence of these systems and the origin of A. baumannii. Our data showed significant correlations between the presence of HicA/HicB system and resistance to ceftazidime, meropenem, imipenem, and cefepime (p < 0.05), and the presence of HipA/HipB system and resistance to ceftazidime, meropenem, imipenem, and cefepime (p < 0.05). In presence of ZnO-NPs, the expression of all studied genes decreased. GNAT and hicB showed the highest and lowest expression changes by 2.4 folds (p < 0.001) and 1.3 folds (p < 0.05), respectively. This study demonstrates the promising potential of nanoparticles to impact the expression of the genes involved in TA Systems. So, the application of ZnO-NPs may be helpful to design target-based strategies towards MDRs pathogens for empowered clinical applications by microbiologists and nanotechnologists.

In silico Study of the Proteins Involved in the Persistence of Brucella spp

BACKGROUND

One of the major problems with Brucella infections is its tendency to become chronic and recurrent, providing a hindrance to the management of this infection. It has been proposed that chronicity is greatly affected by a phenomenon called persistence in bacteria. Several mechanisms are involved in bacterial persistence, including the type II toxin-antitoxin system, the SOS and oxidative and stringent responses.

METHODS

In this in silico study, these persistence mechanisms in Brucella spp. were investigated.

RESULTS

The structure and the interactions between modules involved in these systems were designed, and novel peptides that can interfere with some of these important mechanisms were developed.

CONCLUSION

Since peptide-based therapeutics are a new and evolving field due to their ease of production, we hope that peptides developed in this study, as well as the information about the structure and interactions of modules of persistence mechanisms, can further be used to design drugs against Brucella persister cells in the hope of restraining the chronic nature of Brucellosis.

Bacterial survivors: evaluating the mechanisms of antibiotic persistence

Bacteria withstand antibiotic onslaughts by employing a variety of strategies, one of which is persistence. Persistence occurs in a bacterial population where a subpopulation of cells (persisters) survives antibiotic treatment and can regrow in a drug-free environment. Persisters may cause the recalcitrance of infectious diseases and can be a stepping stone to antibiotic resistance, so understanding persistence mechanisms is critical for therapeutic applications. However, current understanding of persistence is pervaded by paradoxes that stymie research progress, and many aspects of this cellular state remain elusive. In this review, we summarize the putative persister mechanisms, including toxin-antitoxin modules, quorum sensing, indole signalling and epigenetics, as well as the reasons behind the inconsistent body of evidence. We highlight present limitations in the field and underscore a clinical context that is frequently neglected, in the hope of supporting future researchers in examining clinically important persister mechanisms.

Antibiofilm Synergistic Activity of Streptomycin in Combination with Thymol-Loaded Poly (Lactic-co-glycolic Acid) Nanoparticles against Klebsiella pneumoniae Isolates

Background. Thymol is an important component of essential oils found in the oil of thyme, is extracted mainly from Thymus vulgaris, and was shown to act synergistically with streptomycin against Klebsiella pneumoniae biofilms. Additionally, thymol could be encapsulated into poly (lactic-co-glycolic acid) (PLGA) nanoparticles to overcome issues related to its low water solubility and high volatility. The present study aimed to investigate the antibiofilm activity of thymol-loaded PLGA nanoparticles (Thy-NPs) alone and in combination with streptomycin against biofilms of K. pneumoniae isolates. Methods. The broth microdilution method was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The antibiofilm activities were determined by the safranin dye assay. The synergistic effect of Thy-NPs with streptomycin was assessed by the checkerboard method. The kinetic study of the biofilm biomass and time-kill assay were further performed. Results. Thy-NPs exhibited the highest antibacterial activity against K. pneumoniae isolates, with MIC values ranging from 1 to 8 µg/mL. Additionally, Thy-NPs showed the highest antibiofilm activity against K. pneumoniae isolates with minimal biofilm inhibitory concentration (MBIC) and minimal biofilm eradication concentration (MBEC) values ranging from 16 to 64 µg/mL and from 32 to 128 µg/Ml, respectively. The combination treatment combining Thy-NPs with streptomycin showed a synergistic effect against the inhibition of biofilm formation and eradication of biofilms of K. pneumoniae isolates with fractional inhibitory concentration index values ranging from 0.13 to 0.28. In addition, the MBIC and MBEC values of streptomycin against K. pneumoniae isolates were dramatically reduced (up to 128-fold) in combination with Thy-NPs, suggesting that Thy-NPs would enhance the antibiofilm activity of streptomycin. The biomass and time-kill kinetics analysis confirmed the observed synergistic interactions and showed the bactericidal activity of streptomycin in combination with Thy-NPs. Conclusions. Our results indicate that the synergistic bactericidal effect between streptomycin and Thy-NPs could be a promising approach in the control of biofilm-associated infections caused by K. pneumoniae.

Prevalence of colistin resistance of Klebsiella pneumoniae isolates in Iran: a systematic review and meta-analysis

Objective

Klebsiella pneumoniae is a gram-negative pathogen common cause of nosocomial infections. Colistin is a last resort antibiotic to treat infections caused by K. pneumoniae. In recent years, the resistance rate to colistin has increased in K. pneumoniae. This study evaluated the prevalence of colistin resistance of K. pneumoniae isolates in Iran using a systematic review and meta-analysis.

Method

A systematic search was performed for relevant articles until August 2021 in the following database: PubMed, Scopus, SID and Google Scholar. The pooled prevalence of colistin resistance in clinical K. pneumoniae isolates analyzed using Comprehensive Meta-Analysis Software (CMA).

Results

Finally, 19 articles with appropriate criteria were included in the meta-analysis. Our results showed 6.9% of the pooled prevalence of colistin resistance in clinical K. pneumoniae isolates in Iran. The results of subgroup analysis demonstrated increase resistance of colistin from 4.8%; (95% CI 1.5–13.9%) in 2013–2018 to 8.2%; (95% CI 3.4–18.6%), in 2019–2021. Also, the results of our study showed a strong association between the carbapenem producing K. pneumoniae and increased resistance to colistin.

Conclusions

This study showed a high prevalence of colistin resistance in K. pneumoniae isolates. It is recommended that regular evaluation be performed to control colistin resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00520-8.

Isolation of Persister Cell within the Biofilm and Relative Gene Expression Analysis of Type II Toxin-antitoxin System in Pseudomonas aeruginosa Isolates in the Exponential and Stationary Phases

OBJECTIVES

Chronic infections and treatment failure are concerning issues in patients with Pseudomonas aeruginosa infections. Persister cell formation in biofilm is considered a key reason for antibiotic resistance and treatment failure. Thus, in this study, the expression of TA type II system genes (relBE, Xre-COG5654, vapBC, and Xre-GNAT) in persister cells of biofilm was evaluated in the presence of ciprofloxacin and colistin antibiotics during exponential and stationary phases.

METHODS

The impacts of ciprofloxacin and colistin were examined on persister cell formation of biofilm during the exponential and stationary phases of P. aeruginosa strains through colony count method at different time intervals in the presence of 5-fold MIC of ciprofloxacin and colistin. Furthermore, the expression of relBE, Xre-COG5654, vapBC, and Xre-GNAT genes in P. aeruginosa strains underwent antibiotic treatment for 3.5 hours during the exponential and stationary phases via qRT-PCR.

RESULTS

Formation of persister cells was observed in the biofilms by P. aeruginosa strains in the presence of 5-fold MIC of ciprofloxacin and colistin when compared with the control group after 3.5 hours of incubation during both exponential and stationary phases. The number of persister cells of biofilm was higher in the stationary phase than in the exponential phase. According to the findings of qRT-PCR, ciprofloxacin and colistin may induce persister cells through enhancing the expression of type II TA systems during stationary and exponential phases.

CONCLUSION

The result of this study indicated that ciprofloxacin and colistin have the potential to increase persister cells formation in biofilm through influencing the expression of type II TA systems.

Antibiotic tolerance in biofilm persister cells of Staphylococcus aureus and expression of toxin-antitoxin system genes

The ability of Staphylococcus aureus to form biofilm and persister cells is the main cause of recurrent infections. This study aimed to evaluate the expression of toxin-antitoxin (TA) systems in persister cells within S. aureus biofilms. Time-dependent variation in the persister population present in biofilms of S. aureus was examined after treatment with bactericidal antibiotics. Then, the relative expression level of type II TA system (mazF, relE1, and relE2), type I TA system (sprG), and clpP protease genes in S. aureus strains were assessed by Real _Time PCR. Among the sixteen isolates, two isolates were found to be the strongest biofilm producers. The established biofilm of these isolates showed a comparable biphasic pattern at the lethal dose of the antibiotics. The expression level of TA system genes was increased and strain-specific expression patterns were observed under antibiotics stress conditions. Persisters within a biofilm may establish a reservoir for relapsing infection and could contribute to treatment failures. Hence, the possible role of the TA systems should be considered in biofilm and persister cell formation.

Evaluation of gene expression and protein structural modeling involved in persister cell formation in Salmonella Typhimurium

Persisters are phenotypic variants of the bacterial population that survive against lethal doses of bactericidal antibiotics.These phenotypes are created in numerous bacterial species, including those of clinical significance, such as Salmonella Typhimurium. Since persister cells are associated with the failure of antibiotic treatment and infection recurrence, it is crucial to identify the mechanisms that influence the formation of these cells. The aim of this study is to investigate the persister cell formation and expression analysis as well as to predict the 3D structure of the genes involved in the production of persister cells. The presence of persisters in S. Typhimurium was determined by time dependent killing of different types of bactericidal antibiotics and expression of genes associated with persister cell formation which was assessed five hours after the addition of antibiotics by the qRT-PCR. Indeed, the 3D structural model of the proteins studied was predicted by performing several computational methods of retrieved primary protein sequences. The results of the study showed that the S. Typhimurium produced high levels of persister cells in the exposure of bactericidal antibiotics. Furthermore, qRT-PCR resulted in the fact that the expression of related genes was different depending on the type of antibiotic. Overall, this study provides information on the creation of persister cells and the role of different genes in the formation of these cells and structure of proteins involved in the production of persister cells in S. Typhimurium.