Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry

Proteomic profile of multidrug-resistant Serratia marcescens under meropenem challenge

Serratia marcescens is an opportunistic bacterium implicated in the prevalence of serious nosocomial infections and increased outbreaks in Intensive Care Units (ICUs) and Neonatal Intensive Care Units (NICUs). S. marcescens strains are resistant to several antimicrobial classes and express numerous virulence factors that promote pathogenicity. In the present study, the proteomic profile of the multidrug-resistant (MDR) S. marcescens clinical isolate challenged with the antimicrobial meropenem was evaluated. The proteins obtained were analyzed using liquid chromatography coupled with tandem mass spectrometry (LC-MSE). A total of 199 induced proteins were identified revealing that multidrug-resistant S. marcescens promotes increasing of proteins related to energy metabolism and efflux pump and decreases synthesis of proteins related to oxidative stress response and cell mobility upon meropenem challenge, shedding some light on the relationship between expressed proteins and bacterial pathogenicity after antimicrobial induction.

Genetic basis of carbapenem-resistant clinical Serratia marcescens in Japan

OBJECTIVE

To investigate the genetic basis of carbapenem resistance in clinical Serratia marcescens isolates collected from patients in Japan between 1994 and 2016. A total of 5135 clinical isolates of S. marcescens were recovered from different medical centres across Japan, identified in central laboratories, and tested for antimicrobial agents using the broth microdilution method.

METHODS

All the isolates that showed intermediate or resistant phenotypes for at least one carbapenem antibiotic were confirmed by antimicrobial susceptibility testing and for carbapenemase production by the modified carbapenem inactivation method. Furthermore, full genetic characterization was performed by whole genome sequencing for all the isolates.

RESULTS

Based on our findings, 27 isolates (0.53%) exhibited resistance to ertapenem and/or meropenem. Among these, 10 isolates were phenotypically confirmed as carbapenemase producers using the modified carbapenem inactivation method test. The isolates were resistant to a wide range of antibiotics including β-lactams (48.1%-100%), two fluoroquinolones (77.8%-88.9%), tigecycline and minocycline (70.4% each), and sulfamethoxazole-trimethoprim (55.6%). Whole-genome sequencing was conducted on all carbapenem-resistant strains, uncovering blaIMP in eight isolates, comprising seven with blaIMP-1 and one with blaIMP-11, alongside multiple antimicrobial resistance determinants. Importantly, the phylogenomic comparison with international S. marcescens isolates revealed genetic relatedness and potential cross-border transmission events.

CONCLUSIONS

Our findings underscore the importance of enhanced surveillance and infection control measures to mitigate the dissemination of multidrug-resistant pathogens, emphasizing the need for international collaboration and coordinated efforts to address antimicrobial resistance on a global scale.

Potential and application of tandem mass spectrometry (MS/MS) in the analysis and identification of novel bacteriocins: a review

Bacteriocins are antimicrobial peptides synthesised ribosomally by Gram-positive or Gram-negative bacteria to gain a competitive advantage. The majority of bacteriocins are derived from Gram-positive bacteria, with lactic acid bacteria being the most common source. Because they are considered ‘natural’, there is currently significant development of bacteriocins for application as food preservative agents. As a preservative agent, bacteriocin activity is highly dependent on purity, down to the amino acid profile and sequence. Therefore, bacteriocin identification is important. Currently, MS is a cutting-edge tool in bacteriocin identification. This method has high selectivity, sensitivity and resolution. To the best of our knowledge, systematic reviews focusing on the application of MS for bacteriocin identification are currently limited. In light of this, the objective of this study is to provide a comprehensive review and summary of MS technologies in bacteriocin research, with a particular focus on the discovery and characterisation of novel sources of bacteriocin. Additionally, studies related to the discovery of bacteriocins from various sources, their role as antimicrobial agents, and their synthesis are emphasised. Thus, this study presents a comprehensive analysis of the advantages, limitations, and future perspectives of the methods employed.

Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications

Antimicrobial peptides (AMPs) constitute a group of small molecular peptides that exhibit a wide range of antimicrobial activity. These peptides are abundantly present in the innate immune system of various organisms. Given the rise of multidrug-resistant bacteria, microbiological studies have identified AMPs as potential natural antibiotics. In the context of antimicrobial resistance across various human pathogens, AMPs hold considerable promise for clinical applications. However, numerous challenges exist in the detection of AMPs, particularly by immunological and molecular biological methods, especially when studying of newly discovered AMPs in proteomics. This review outlines the current status of AMPs research and the strategies employed in their development, considering resent discoveries and methodologies. Subsequently, we focus on the advanced techniques of mass spectrometry for the quantification of AMPs in diverse samples, and analyzes their application, advantages, and limitations. Additionally, we propose suggestions for the future development of tandem mass spectrometry for the detection of AMPs.

Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach

Micrococcus luteus, also known as M. luteus, is a bacterium that inhabits mucous membranes, human skin, and various environmental sources. It is commonly linked to infections, especially among individuals who have compromised immune systems. M. luteus is capable of synthesizing the enzyme superoxide dismutase (SOD) as a component of its protective response to reactive oxygen species (ROS). This enzyme serves as a promising target for drug development in various diseases. The current study utilized a subtractive genomics approach to identify potential therapeutic targets from M. luteus. Additionally, genome mining was employed to identify and characterize the biosynthetic gene clusters (BGCs) responsible for the production of secondary metabolites in Bacillus licheniformis (B. licheniformis), a bacterium known for its production of therapeutically relevant secondary metabolites. Subtractive genomics resulted in identification of important extracellular protein SOD as a drug target that plays a crucial role in shielding cells from damage caused by ROS. Genome mining resulted in identification of five potential ligands (secondary metabolites) from B. licheniformis such as, Bacillibactin (BAC), Paenibactin (PAE), Fengycin (FEN), Surfactin (SUR) and Lichenysin (LIC). Molecular docking was used to predict and analyze the binding interactions between these five ligands and target protein SOD. The resulting protein-ligand complexes were further analyzed for their motions and interactions of atoms and molecules over 250 ns using molecular dynamics (MD) simulation analysis. The analysis of MD simulations suggests, Bacillibactin as the probable candidate to arrest the activities of SOD. All the five compounds reported in this study were found to act by directly/indirectly interacting with ROS molecules, such as superoxide radicals (O2-) and hydrogen peroxide (H2O2), and transforming them into less reactive species. This antioxidant activity contributes to its protective effects against oxidative stress-induced damage in cells making them likely candidate for various applications, including in the development of antioxidant-based therapies, nutraceuticals, and functional foods.

Impact of metal exposure on environmentally isolated Serratia marcescens' growth, oxidative-stress resistance, biofilm formation, and proliferation in eukaryotic co-culture models

Environmental metals can be noxious to the surrounding biota, indirectly impact freshwater habitats, and also impact microbiological communities. In this study, zinc (Zn) (55.5 mg/kg), manganese (Mn) (863.4 mg/kg) and lead (Pb) (17.5 mg/kg) levels measured in Houston watershed flood plain soil samples were higher than environmental agencies' thresholds. To investigate the effects of metal exposures, an environmentally isolated Serratia marcescens (SME), etiological agent of endocarditis and respiratory infections, and its reference strain (SMR) were exposed to Pb, Zn, and Mn, and subsequent oxidative stress responses and biofilm production were measured. Not surprisingly, SME was less sensitive to all 3 metal exposures than was SMR. Interestingly, SME produced increased biofilm and was more resistant to oxidative stress in the presence of Zn and Pb than SMR. In a 6 h lung infection model using BAES-2B cells, SME exhibited greater proliferation than SMR in all metal challenges. Similarly, in our HT29 gut infection model, SME out-proliferated SMR when challenged with Pb and Mn following the 6 h infection. Taken together, SME was better able to withstand environmental stressors than SMR, suggesting increased virulence potential of this opportunistic human pathogen.