Additional regulatory activities of MrkH for the transcriptional expression of the Klebsiella pneumoniae mrk genes: Antagonist of H-NS and repressor

Nanocomposites against Pseudomonas aeruginosa biofilms: Recent advances, challenges, and future prospects

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that causes life-threatening and persistent infections in immunocompromised patients. It is the culprit behind a variety of hospital-acquired infections owing to its multiple tolerance mechanisms against antibiotics and disinfectants. Biofilms are sessile microbial aggregates that are formed as a result of the cooperation and competition between microbial cells encased in a self-produced matrix comprised of extracellular polymeric constituents that trigger surface adhesion and microbial aggregation. Bacteria in biofilms exhibit unique features that are quite different from planktonic bacteria, such as high resistance to antibacterial agents and host immunity. Biofilms of P. aeruginosa are difficult to eradicate due to intrinsic, acquired, and adaptive resistance mechanisms. Consequently, innovative approaches to combat biofilms are the focus of the current research. Nanocomposites, composed of two or more different types of nanoparticles, have diverse therapeutic applications owing to their unique physicochemical properties. They are emerging multifunctional nanoformulations that combine the desired features of the different elements to obtain the highest functionality. This review assesses the recent advances of nanocomposites, including metal-, metal oxide-, polymer-, carbon-, hydrogel/cryogel-, and metal organic framework-based nanocomposites for the eradication of P. aeruginosa biofilms. The characteristics and virulence mechanisms of P. aeruginosa biofilms, as well as their devastating impact and economic burden are discussed. Future research addressing the potential use of nanocomposites as innovative anti-biofilm agents is emphasized. Utilization of nanocomposites safely and effectively should be further strengthened to confirm the safety aspects of their application.

Genomic surveillance of carbapenem-resistant Klebsiella pneumoniae reveals a prolonged outbreak of extensively drug-resistant ST147 NDM-1 during the COVID-19 pandemic in the Apulia region (Southern Italy)

OBJECTIVES

The recent worldwide spread of New Delhi metallo-beta-lactamase-producing Klebsiella pneumoniae (NDM-KP) in health-care settings remains a concern. The aim of the study was to describe an outbreak of extensively drug-resistant ST147 NDM-1-KP in the Apulia region of Southern Italy that occurred between 2020 and 2022 through genomic surveillance of carbapenem-resistant Enterobacterales.

METHODS

A total of 459 carbapenem-resistant KP isolates collected from patients hospitalised with bloodstream infections were tested using a commercial multiplex real-time polymerase chain reaction to identify carbapenemase genes. A subset of 27 isolates was subjected to whole-genome sequencing. Core-genome multilocus sequence typing was performed by analysing a panel of 4884 genes.

RESULTS

Molecular testing revealed that 104 (22.6%) isolates carried the carbapenemase NDM gene. Phylogenetic analysis of the 27 isolates subjected to whole-genome sequencing revealed high genetic relatedness among strains. All isolates were resistant to all first-line antibiotics. Virulome analysis identified the ybt locus, the two well-recognised virulence factors iucABCDiutA and rmpA, and the genes encoding the type 3 pilus virulence factor. Plasmids IncFIB(pkPHS1), IncFIB(pNDM-Mar), IncFIB(pQil), IncHI1B(pNDM-MAR), IncR, and Col(pHAD28) were identified in all isolates. Moreover, further analysis identified the IncFIB-type plasmid carrying the NDM-1 genes.

CONCLUSION

The increasing circulation of extensively drug-resistant NDM-1 ST147 KP strains in Southern Italy in recent years is worrisome, because these clones pose a real risk, particularly in hospital settings. Genomic surveillance is a crucial tool for early identification of emerging threats such as the spread of high-risk pathogens. Rapid infection control measures and antimicrobial stewardship are key to preventing further spread of hypervirulent KP strains.

The Biological and Regulatory Role of Type VI Secretion System of Klebsiella pneumoniae

Bacteria communicate with their surroundings through diverse secretory systems, and the recently discovered Type VI Secretion System (T6SS) has gained significant attention. Klebsiella pneumoniae (K. pneumoniae), an opportunistic pathogen known for causing severe infections in both hospital and animal settings, possesses this intriguing T6SS. This system equips K. pneumoniae with a formidable armory of protein-based weaponry, enabling the delivery of toxins into neighboring cells, thus granting a substantial competitive advantage. Remarkably, the T6SS has also been associated with K. pneumoniae's ability to form biofilms and acquire resistance against antibiotics. However, the precise effects of the T6SS on K. pneumoniae's functions remain inadequately studied, despite research efforts to understand the intricacies of these mechanisms. This comprehensive review aims to provide an overview of the current knowledge regarding the biological functions and regulatory mechanisms of the T6SS in K. pneumoniae.

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.

Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database

Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.

A protein containing the DUF1471 domain regulates biofilm formation and capsule production in Klebsiella pneumoniae

BACKGROUND/PURPOSE

Biofilms formed by Klebsiella pneumoniae on medical devices increase infection risk. Fimbriae and capsule polysaccharides (CPSs) are important factors involved in biofilm formation. KP1_4563 in K. pneumoniae NTUH-K2044, a small protein containing the DUF1471 domain, was reported to inhibit type 3 fimbriae function. In this study, we aimed to determine whether the KP1_4563 homolog is conserved in each K. pneumoniae isolate and what role it has in Klebsiella biofilms.

METHODS

The genomes of K. pneumoniae NTUH-K2044, CG43, MGH78578, KPPR1 and STU1 were compared. The KP1_4563 homolog in K. pneumoniae STU1 was named orfX. Biofilms of wild-type and orfX mutant strains from K. pneumoniae STU1 and one clinical isolate, 83535, were quantified. Transcription levels of the type 3 fimbrial genes, mrkA and mrkH, were investigated by RT-qPCR. MrkA of the wild-type and orfX mutant were observed by Western blotting. The morphology of bacterial cells was observed by transmission electron microscopy (TEM). Bacterial CPSs were quantified.

RESULTS

The gene and upstream region of orfX were conserved among the five K. pneumoniae isolates. Deletion of orfX enhanced Klebsiella biofilm formation. However, the amount of mRNA from mrkA and mrkH and the level of MrkA protein were not different between the wild type and orfX mutant. In contrast, the amount of CPS in orfX mutants was increased, compared to their parental strains, STU1 and 83535.

CONCLUSION

The role of orfX is speculated to be conserved in most K. pneumoniae isolates. OrfX negatively controlled biofilm formation by reducing CPS, not type 3 fimbriae, production.

Conserved FimK Truncation Coincides with Increased Expression of Type 3 Fimbriae and Cultured Bladder Epithelial Cell Association in Klebsiella quasipneumoniae

Klebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its type 1 and type 3 fimbriae have not been studied. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well conserved between Escherichia coli and K. pneumoniae apart from fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that K quasipneumoniae strain KqPF9 cultured bladder epithelial cell association and invasion are dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as cultured bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52. Finally, we show that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and cultured bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation. IMPORTANCE K. quasipneumoniae is often indicated as the cause of opportunistic infections, including urinary tract infection, which affects >50% of women worldwide. However, the virulence factors of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment in vitro. We observe clear differences in bladder epithelial cell attachment and regulation of type 3 fimbriae between uropathogenic K. pneumoniae and K. quasipneumoniae that coincide with a structural difference in the fimbrial regulatory gene fimK.

Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring bla KPC- 2 or bla NDM- 1

Objectives

Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) is a major cause of infections in transplanted patients and has been associated with high mortality rates in this group. There is a lack of information about the Brazilian structure population of CP-Kp isolated from transplanted patients. By whole-genome sequencing (WGS), we analyzed phylogeny, resistome, virulome of CP-Kp isolates, and the structure of plasmids encoding bla_KPC–2 and bla_NDM–1 genes.

Methods

One K. pneumoniae isolated from each selected transplanted patient colonized or infected by CP-Kp over a 16-month period in a hospital complex in Porto Alegre (Brazil) was submitted for WGS. The total number of strains sequenced was 80. The hospital complex in Porto Alegre comprised seven different hospitals. High-resolution SNP typing, core genome multilocus sequence typing (cgMLST), resistance and virulence genes inference, and plasmid reconstruction were performed in 80 CP-Kp.

Results

The mortality rate of CP-Kp colonized or infected transplanted inpatients was 21.3% (17/80). Four CP-Kp epidemic clones were described: ST11/KPC-2, ST16/KPC-2, and ST15/NDM-1, all responsible for interhospital outbreaks; and ST437/KPC-2 affecting a single hospital. The average number of acquired resistance and virulence genes was 9 (range = 2–14) and 27 (range = 6–36), respectively. Two plasmids carrying the bla_KPC–2 were constructed and belonged to IncN and IncM types. Additionally, an IncFIB plasmid carrying the bla_NDM–1 was described.

Conclusion

We detected intrahospital and interhospital spread of mobile structures and international K. pneumoniae clones as ST11, ST16, and ST15 among transplanted patients, which carry a significant range of acquired resistance and virulence genes and keep spreading across the world.

Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

Background

Klebsiella pneumoniae (KP) is an opportunistic pathogen that mainly causes respiratory and urinary tract infections. The frequent occurrence of simultaneously virulent and multiple drug-resistant isolates led WHO to include this species in the list of top priorities for research and development of therapeutic alternatives. The comprehensive knowledge of the molecular mechanisms underlying KP virulence may lead to the proposal of more efficient and specific drugs. One of its virulence factors is the Type VI Secretion System (T6SS), which contributes to bacterial competition, cell invasion and in vivo colonisation. Despite the few studies showing the involvement of T6SS in KP pathogenesis, little is known concerning the regulation of its expression. The understanding of regulatory mechanisms may give more clues about the function of the system and the possibilities of future interference in this process. This work aimed to standardise the annotation of T6SS genes in KP strains and identify mechanisms of their transcriptional regulation through computational predictions.

Results

We analyzed the genomes of Kp52.145, HS11286 and NTUH-K2044 strains to perform a broad prediction and re-annotation of T6SS genes through similarity searches, comparative and linear discriminant analysis. 38 genes were found in Kp52.145, while 29 in HS11286 and 30 in NTUH-K2044. Genes coding for iron uptake systems are encoded in adjacencies of T6SS, suggesting that KP T6SS might also play a role in ion import.

Some of the T6SS genes are comprised in syntenic regions. 17 sigma 70-dependent promoter regions were identified in Kp52.145, 12 in HS11286 and 12 in NTUH-K2044. Using VirtualFootprint algorithm, binding sites for 13 transcriptional regulators were found in Kp52.145 and 9 in HS11286 and 17 in NTUH-K2044. Six of them are common to the 3 strains: OxyR, H-NS, RcsAB, GcvA, Fis, and OmpR.

Conclusions

The data presented herein are derived from computational analysis. Although future experimental studies are required to confirm those predictions, they suggest that KP T6SS might be regulated in response to environmental signals that are indeed sensed by the bacteria inside the human host: temperature (H-NS), nutrition-limitation (GcvA and Fis), oxidative stress (OxyR) and osmolarity (RscAB and OmpR).

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5885-9) contains supplementary material, which is available to authorized users.

Phosphorylated OmpR Is Required for Type 3 Fimbriae Expression in Klebsiella pneumoniae Under Hypertonic Conditions

OmpR/EnvZ is a two-component system that senses osmotic signals and controls downstream gene expression in many species of Enterobacteriaceae. However, the role of OmpR/EnvZ in Klebsiella pneumoniae remains unknown. In this study, we found that production of MrkA, the major subunit of type 3 fimbriae, was decreased under hypertonic conditions. A deletion mutant of ompR and a site-directed mutant with a single amino acid substitution of aspartate 55 to alanine (D55A), which mimics the unphosphorylated form of OmpR, markedly reduced MrkA production under hypertonic conditions. These results indicate that K. pneumoniae type 3 fimbriae expression is activated by the phosphorylated form of OmpR (OmpR∼P). Although no typical OmpR∼P binding site was found in the P_mrkA sequence, mrkA mRNA levels and P_mrkA activity were decreased in the ΔompR and ompR_D55A strains compared with the wild type (WT) strain, indicating that OmpR∼P mediates type 3 fimbriae expression at the transcriptional level. Previous reports have demonstrated that a cyclic-di-GMP (c-di-GMP) related gene cluster, mrkHIJ, regulates the expression of type 3 fimbriae. We found that both the ompR and ompR_D55A mutants exhibited decreased mrkHIJ mRNA levels, intracellular c-di-GMP concentration, and bacterial biofilm amount, but increased total intracellular phosphodiesterase activity in response to hypertonic conditions. These results indicate that OmpR∼P regulates type 3 fimbriae expression to influence K. pneumoniae biofilm formation via MrkHIJ and modulation of intracellular c-di-GMP levels. Taken together, we herein provide evidence that OmpR∼P acts as a critical factor in the regulation of the c-di-GMP signaling pathway, type 3 fimbriae expression, and biofilm amount in K. pneumoniae in response to osmotic stresses.

The association of surface adhesin genes and the biofilm formation among Klebsiella oxytoca clinical isolates

Bacterial adhesins mediate the attachment and biofilm production leading to the persistence of colonized strains. The aim of this study was evaluation of the association of surface adhesin genes with the biofilm formation among Klebsiella oxytoca isolates. Among 50 isolates of K. oxytoca from patients with antibiotic-associated diarrhoea, the susceptibility test, MIC (according to CLSI 2016) and phenotypic biofilm formation (with microtitre tissue-plate assay) were performed. The presence of adhesins was investigated using PCR. Thirty-three (66%) isolates produced moderate-level biofilms, but none of them exhibited strong biofilm formation. The presence of adhesins was as follows: fimA, 60% (n = 30), mrkA, 42% (n = 21), matB, 96% (n = 48) and pilQ, 92% (n = 46). The biofilm formation was related to the presence of fimA (odds ratio (OR) 0.8571, 95% CI 1.733–6.267, p <0.0001), mrkA (OR 0.2462, 95% CI 2.723–4.622, p 0.001), matB (OR 0.4521, 95% CI 1.353–5.332, p 0.008) and pilQ (OR 0.1481, 95% CI 1.691–6.117, p <0.0001). The npsB toxin-encoding gene was detected among 46 (92%) isolates. Resistance to non-β-lactam antibiotics was significantly associated with the presence of adhesin-encoding genes. The presence of adhesins and the capsular encoding gene was significantly associated with biofilm formation among K. oxytoca isolates. The presence of surface adhesin-encoding genes was significantly associated with the biofilm formation and also with resistance to non-β-lactam antibiotics among K. oxytoca clinical isolates. In addition, biofilm production was not significantly associated with β-lactam resistance among the isolates.