Evolution of Multi-Resistance to Vancomycin, Daptomycin, and Linezolid in Methicillin-Resistant Staphylococcus aureus Causing Persistent Bacteremia

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.

A simple and rapid colorimetric detection of Staphylococcus aureus relied on the distance-dependent optical properties of silver nanoparticles

The quick and accurate diagnosis of pathogens has appeared as a pressing issue in clinical diagnostics, environmental monitoring, and food safety. The available assays are suffering from limited capacities in simple, fast, low-cost, and on-site detection to increase prevention and proper treatment. Herein, we address these challenges by developing a simple, speedy, affordable, and ultrasensitive nanoplasmonic biosensor for colorimetric detection of cDNA from staphylococcal RNA relying on the distance-dependent optical features of silver nanostructures for the measurement of color variations and spectral shifts owing to the plasmon coupling generated by the cross-linking accumulation of AgNPs. The method described utilizes silver nanoparticles (AgNPs) immobilized with two different single-stranded oligonucleotides (ssDNA1 and ssDNA2) that specifically recognize the target DNA. Sandwich hybridization of target DNA with ssDNA1 and ssDNA2 induced color variations and spectral shifts of AgNPs, whereas test samples without the target DNA remained yellow as the initial color of colloidal silver. The designed nanoplasmonic biosensor demonstrated high specificity with the detection limit (LOD) of ∼1.8 amol target DNA (∼106 molecules per test) in the broad linear dynamic range from 0.01 to 100 nM, and LOD down to a few cells was attained for amplified bacterial nucleic acids and a linear range from 102 CFU mL-1 to 107 CFU mL-1. The sensing approach showed great potential for the timely diagnosis of pathogens in low-density samples, and it has considerable merits over traditional culture approaches and qPCR techniques.

Fish Epidermal Mucus as a Source of Diverse Therapeutical Compounds

Microbes are helpful and destructive to human health and other living organisms. Microbes can be eliminated by using antibiotics against them, but their capability to resist regularly encountering antibiotics makes them more injurious. Microbes can adjust and adapt according to the chemicals used against them and become antibiotic resistant. Thus, the requirement for novel antimicrobial compounds increases with time to treat antibiotic-resistant microbes. Fish epidermal mucus encounters various pathogens present in their surrounding environment. It has become a rich source of novel antimicrobial compounds mainly antimicrobial peptides that can be used against various antibiotic-resistant pathogenic microbes. Compounds extracted from epidermal mucus can be used synergistically with other antibiotics or resistance modifying agents to inhibit the growth of resistant microbes. Fishes are consumed as a protein-rich food source worldwide and contribute to the world economy. Diseases in fish cause significant losses in the economic benefits exploited by fishermen and industries based on fisheries products. This paper will review compounds from fish epidermal mucus and their use to control the growth of antibiotic-resistant or non-resistant pathogenic microbes of humans and fishes. So, to increase fisheries' economic benefits and decrease infections involving resistant microbes.

Study of the antibacterial effects of the starch-based zinc oxide nanoparticles on methicillin resistance Staphylococcus aureus isolates from different clinical specimens of patients from Basrah, Iraq

This study aimed to assess the efficacy of starch-based zinc oxide nanoparticles (ZnO-NPs) against methicillin-resistant Staphylococcus aureus (MRSA) isolates from clinical specimens in Basrah, Iraq. In this cross-sectional study, 61 MRSA were collected from different clinical specimens of patients in Basrah city, Iraq. MRSA isolates were identified using standard microbiology tests, cefoxitin disc diffusion and oxacillin salt agar. ZnO-NPs were synthesized in three different concentrations (0.1 M, 0.05 M, 0.02 M) by the chemical method using starch as the stabilizer. Starch-based ZnO-NPs were characterized using ultraviolet-visible spectroscopy (UV-Vis), X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), energy dispersive X-ray spectroscopy (EDS), and transmission electron microscopy (TEM). The antibacterial effects of particles were investigated by the disc diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the most effective starch-based ZnO-NPs were determined using a broth microdilution assay. The UV-Vis of all concentrations of starch-based ZnO-NPs exhibited a strong absorption band at 360 nm which was characteristic of the ZnO-NPs. XRD assay confirmed the representative hexagonal wurtzite phase of the starch-based ZnO-NPs, and their purity and high crystallinity. The spherical shape with a diameter of 21.56 ± 3.42 and 22.87 ± 3.91 was revealed for the particles by FE-SEM and TEM, respectively. EDS analysis confirmed the presence of zinc (Zn) (61.4 ± 0.54%) and oxygen (O) (36 ± 0.14%). The 0.1 M concentration had the highest antibacterial effects (mean ± SD of inhibition zone = 17.62 ± 2.65 mm) followed by the 0.05 M concentration (16.03 ± 2.24 mm) and the 0.02 M concentration (12.7 ± 2.57 mm). The MIC and the MBC of the 0.1 M concentration were in the range of 25-50 µg/mL and 50-100 µg/mL, respectively. Infections caused by MRSA can be treated with biopolymer-based ZnO-NPs as effective antimicrobials.

Linezolid-resistance Staphylococcus aureus – Prevalence, Emerging Resistance Mechanisms, Challenges and Perspectives

Staphylococcus aureus, an opportunistic pathogen, can root several infections viz skin and tissue infections, bacteraemia, food poisoning, pneumonia, and many other clinical conditions with some variations of virulence factors. In treatment of infections, caused by this Gram-positive pathogen, several antibiotics are being used importantly Methicillin and Vancomycin. This pathogen has high capability of antibiotic resistance development and had evolved new strains such as Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin-resistant Staphylococcus aureus (VRSA). Meta-analysis in Ethiopia showed that pooled prevalence of MRSA in environment, food, animal, and human was 54%, 77%, 15%, and 38% respectively (2022). Risk of MRSA isolates from burn ICU was 55 % higher (2018). In Bangladesh, 37.1% isolates from frozen meat chicken (2021) were identified as MRSA. This problem is being dealt with a novel drug called Linezolid which has been proved effective against both MRSA and VRSA. Exacerbating the situation, this pathogen has shown resistance against this unprecedented drug by means of a number of drug resistance mechanisms. Its prevalence has been reporting since the adoption of the drug, but with a minute ratio at one time/place to the very high percentage at another time/place. This inconsistent prevalence must not be ignored, and its surveillance should be augmented as antibiotic treatment is critical for fighting against microbial infections. This review highlights the worldwide reports in which Staphylococcus aureus of either wildtype or Methicillin or Vancomycin resistance that have shown resistance to Linezolid drug for the past 2 decades. At the same time where incidences of Linezolid Resistant Staphylococcus aureus (LRSA) indications are reporting, there is a call for comprehensive strategies to overcome this challenge of antibiotic resistance.

A Structurally Characterized Staphylococcus aureus Evolutionary Escape Route from Treatment with the Antibiotic Linezolid

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the oxazolidinone family, of which linezolid is the first member to see regular use in the clinic. Here, we report a short time scale selection experiment in which strains of MRSA were subjected to linezolid treatment. Clonal isolates which had evolved a linezolid-resistant phenotype were characterized by whole-genome sequencing. Linezolid-resistant mutants were identified which had accumulated mutations in the ribosomal protein uL3. Multiple clones which had two mutations in uL3 exhibited resistance to linezolid, 2-fold higher than the clinical breakpoint. Ribosomes from this strain were isolated and subjected to single-particle cryo-electron microscopic analysis and compared to the ribosomes from the parent strain. We found that the mutations in uL3 lead to a rearrangement of a loop that makes contact with Helix 90, propagating a structural change over 15 Å away. This distal change swings nucleotide U2504 into the binding site of the antibiotic, causing linezolid resistance. IMPORTANCE Antibiotic resistance poses a critical problem to human health and decreases the utility of these lifesaving drugs. Of particular concern is the "superbug" methicillin-resistant Staphylococcus aureus (MRSA), for which treatment of infection requires the use of last-line antibiotics, including linezolid. In this paper, we characterize the atomic rearrangements which the ribosome, the target of linezolid, undergoes during its evolutionary journey toward becoming drug resistant. Using cryo-electron microscopy, we describe a particular molecular mechanism which MRSA uses to become resistant to linezolid.

In-Human Multiyear Evolution of Carbapenem-Resistant Klebsiella pneumoniae Causing Chronic Colonization and Intermittent Urinary Tract Infections: A Case Study

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a frequent pathogen of the urinary tract, but how CRKP adapts in vivo over time is unclear. We examined 10 CRKP strains from a patient who experienced chronic colonization and recurrent urinary tract infections over a period of 4.5 years. We performed whole-genome sequencing and phenotypic assays to compare isolates that had evolved relative to the first isolate collected and to correlate genetic and phenotypic changes over time with the meropenem-containing regimen received. Phylogenetic analysis indicated that all 10 strains originated from the same sequence type 258 (ST258) clone and that three sublineages (SL) evolved over time; strains from two dominant sublineages were selected for detailed analysis. Up to 60 new mutations were acquired progressively in genes related to antibiotic resistance, cell metabolism, and biofilm production over time. Doubling of meropenem MICs, increases in biofilm production and bla_KPC expression, and altered carbon metabolism occurred in the latter strains from the last sublineage compared to the initial strain. Subinhibitory meropenem exposure in vitro significantly induced or maintained high levels of biofilm production in colonizing isolates, but isolates causing infection were unaffected. Despite acquiring different mutations that affect carbon metabolism, overall carbon utilization was maintained across different strains. Together, these data showed that isolated urinary CRKP evolved through multiple adaptations affecting carbon metabolism, carbapenem resistance, and biofilm production to support chronic colonization and intermittent urinary tract infections. Our findings highlight the pliability of CRKP in adapting to repeated antibiotic exposure and should be considered when developing novel therapeutic and stewardship strategies. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) can cause a variety of infections such as recurrent urinary tract infections (rUTI) with the ability to change with the host environment over time. However, it is unclear how CRKP adapts to the urinary tract during chronic infections and colonization. Here, we studied the evolution of CRKP strains from a patient who experienced chronic colonization and recurrent UTIs over a period of 4.5 years despite multiple treatment courses with meropenem-containing regimens. Our findings show the flexibility of CRKP strains in developing changes in carbapenem resistance, biofilm production, and carbon metabolism over time, which could facilitate their persistence in the human body for long periods of time in spite of repeated antibiotic therapy.

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium

The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.

New Antimicrobial Bioactivity against Multidrug-Resistant Gram-Positive Bacteria of Kinase Inhibitor IMD0354

Multidrug-resistant pathogens pose a serious threat to human health. For decades, the antibiotic vancomycin has been a potent option when treating Gram-positive multidrug-resistant infections. Nonetheless, in recent decades, we have begun to see an increase in vancomycin-resistant bacteria. Here, we show that the nuclear factor-kappa B (NF-κB) inhibitor N-[3,5-Bis(trifluoromethyl)phenyl]-5-chloro-2-hydroxybenzamide (IMD0354) was identified as a positive hit through a Caenorhabditis elegans–methicillin-resistant Staphylococcus aureus (MRSA) infection screen. IMD0354 was a potent bacteriostatic drug capable of working at a minimal inhibitory concentration (MIC) as low as 0.06 µg/mL against various vancomycin-resistant strains. Interestingly, IMD0354 showed no hemolytic activity at concentrations as high as 16 µg/mL and is minimally toxic to C. elegans in vivo with 90% survival up to 64 µg/mL. In addition, we demonstrated that IMD0354′s mechanism of action at high concentrations is membrane permeabilization. Lastly, we found that IMD0354 is able to inhibit vancomycin-resistant Staphylococcus aureus (VRSA) initial cell attachment and biofilm formation at sub-MIC levels and above. Our work highlights that the NF-κB inhibitor IMD0354 has promising potential as a lead compound and an antimicrobial therapeutic candidate capable of combating multidrug-resistant bacteria.

Retracted Article: Functional disruption of staphylococcal accessory regulator A from Staphylococcus aureus by silver ions

It was identified that SarA in S. aureus is a target of Ag⁺, which further expanded the antibacterial mechanism of Ag⁺.