Isolation and Whole Genome Sequence Analysis of Alcaligenes and Chromobacterium Strains with Antimicrobial Activity Against ESKAPE Pathogen Relatives

Differential anti-microbial secondary metabolites in different ESKAPE pathogens explain their adaptation in the hospital setup

The two-component system (TCS) helps bacteria sense and respond to environmental stimuli through histidine kinases and response regulators. TCSs are the largest family of multistep signal transduction processes, and they are involved in many important cellular processes such as antibiotic resistance, pathogenicity, quorum sensing, osmotic stress, and biofilms. Here, we perform the first comprehensive study to highlight the role of TCSs as potential drug targets against ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) pathogens through annotation, mapping, pangenomic status, gene orientation, and sequence variation analysis. The distribution of the TCSs is group specific with regard to Gram-positive and Gram-negative bacteria, except for KdpDE. The TCSs among ESKAPEE pathogens form closed pangenomes, except for Pseudomonas aeruginosa Furthermore, their conserved nature due to closed pangenomes might make them good drug targets. Fitness score analysis suggests that any mutation in some TCSs such as BaeSR, ArcBA, EvgSA, and AtoSC, etc., might be lethal to the cell. Taken together, the results of this pangenomic assessment of TCSs reveal a range of strategies deployed by the ESKAPEE pathogens to manifest pathogenicity and antibiotic resistance. This study further suggests that the conserved features of TCSs might make them an attractive group of potential targets with which to address antibiotic resistance.IMPORTANCE The ESKAPEE pathogens are the leading cause of health care-associated infections worldwide. Two-component systems (TCSs) can be used as effective targets against pathogenic bacteria since they are ubiquitous and manage various vital functions such as antibiotic resistance, virulence, biofilms, quorum sensing, and pH balance, among others. This study provides a comprehensive overview of the pangenomic status of the TCSs among ESKAPEE pathogens. The annotation and pangenomic analysis of TCSs show that they are significantly distributed and conserved among the pathogens, as most of them form closed pangenomes. Furthermore, our analysis also reveals that the removal of the TCSs significantly affects the fitness of the cell. Hence, they may be used as promising drug targets against bacteria.

The effect of greenness on ESKAPE pathogen reduction and its heterogeneity across global climate zones and urbanization gradient

Escaping mechanisms of ESKAPE pathogens from antibiotics and their targeting by natural compounds

Antimicrobial resistance has persisted as a global threat with increasing associated numbers of morbidity and mortality. ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) were termed by the Infectious Diseases Society of America as a group of bacteria with rapid antibiotic resistance development. The aim of the study was to describe the extent and resistance patterns of ESKAPE pathogens isolated in pus swabs from patients admitted at Muhimbili National Hospital, Tanzania. A retrospective cross-sectional study was performed in August 2019. A total of 75 admitted patients with open wounds and surgical site infections were recruited. Files were analyzed to collect microbiology laboratory data and relevant patient data. A total of 76 clinically significant bacteria were isolated of which 52 bacteria were categorized as ESKAPE pathogens. The most common bacteria isolated were 25% (n = 19/76) P. aeruginosa and 17.1% S. aureus. A high level of antibiotic resistance was shown in all ESKAPE and non-ESKAPE pathogens. The Gram-negative bacteria of ESKAPE pathogens were further analyzed comparing 3rd generation cephalosporin and carbapenems resistance patterns. A. baumannii showed the highest resistance towards 3rd generation cephalosporin and carbapenems. In addition, P. aeruginosa showed high resistance to 3rd generation cephalosporins with 89.5% resistance, with E. coli showing high resistance to carbapenems with 50.0% resistance. The burden of ESKAPE pathogens is high in pus swabs obtained from admitted patients at Muhimbili National Hospital. The results showed high antibiotic resistance within ESKAPE and non-ESKAPE pathogens including the "last resort" antibiotics: 3rd generation cephalosporin and carbapenems.

The emergence of antibiotic-resistant bacteria, particularly the most hazardous pathogens, namely Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE)-pathogens pose a significant threat to global health. Current antimicrobial therapies, including those targeting biofilms, have shown limited effectiveness against these superbugs. Nanoparticles, specifically silver nanoparticles (AgNPs), have emerged as a promising alternative for combating bacterial infections. In this study, two types of AgNPs with different physic-chemical properties were evaluated for their antimicrobial and antibiofilm activities against clinical ESKAPE strains. Two types of silver nanoparticles were assessed: spherical silver nanoparticles (AgNPs-1) and cubic-shaped silver nanoparticles (AgNPs-2). AgNPs-2, characterized by a cubic shape and higher surface-area-to-volume ratio, exhibited superior antimicrobial activity compared to spherical AgNPs-1. Both types of AgNPs demonstrated the ability to inhibit biofilm formation and disrupt established biofilms, leading to membrane damage and reduced viability of the bacteria. These findings highlight the potential of AgNPs as effective antibacterial agents against ESKAPE pathogens, emphasizing the importance of nanoparticle characteristics in determining their antimicrobial properties. Further research is warranted to explore the underlying mechanisms and optimize nanoparticle-based therapies for the management of infections caused by antibiotic-resistant bacteria.

Antibiotic (antibacterial) resistance is a serious global problem and the need for new treatments is urgent. The current antibiotic discovery model is not delivering new agents at a rate that is sufficient to combat present levels of antibiotic resistance. This has led to fears of the arrival of a 'post-antibiotic era'. Scientific difficulties, an unfavourable regulatory climate, multiple company mergers and the low financial returns associated with antibiotic drug development have led to the withdrawal of many pharmaceutical companies from the field. The regulatory climate has now begun to improve, but major scientific hurdles still impede the discovery and development of novel antibacterial agents. To facilitate discovery activities there must be increased understanding of the scientific problems experienced by pharmaceutical companies. This must be coupled with addressing the current antibiotic resistance crisis so that compounds and ultimately drugs are delivered to treat the most urgent clinical challenges. By understanding the causes of the failures and successes of the pharmaceutical industry's research history, duplication of discovery programmes will be reduced, increasing the productivity of the antibiotic drug discovery pipeline by academia and small companies. The most important scientific issues to address are getting molecules into the Gram-negative bacterial cell and avoiding their efflux. Hence screening programmes should focus their efforts on whole bacterial cells rather than cell-free systems. Despite falling out of favour with pharmaceutical companies, natural product research still holds promise for providing new molecules as a basis for discovery.

Evolutionary and in silico guided development of novel peptide analogues for antibacterial activity against ESKAPE pathogens

The aim of this study was to test the antimicrobial, anti-adhesive and anti-biofilm activities of a rhamnolipid extracted from Pseudomonas aeruginosa UKMP14T previously isolated from oil contaminated soil in Malaysia against ESKAPE (i.e. multidrug resistant) pathogens. Zones of inhibition in an agar well diffusion assay were observed at 50μg mL-1 concentrations of rhamnolipid for all the ESKAPE bacteria. The MIC and MBC values ranged between 7.81-62.5µg mL-1 and 31.25-1000µg mL-1, respectively. Percent killing was recorded to be more than 90% except for Klebsiella pneumoniae (86.84%). Furthermore, anti-adhesion studies showed that there was 76% hindrance in attachment of E. faecium and 91% in Acinetobacter baumannii at 4xMIC. The highest inhibition in adhesion was found at 4xMIC, which was 46% for A. baumannii and 62% for Enterococcus faecium. Finally, the anti-biofilm capability of the rhamnolipid was determined which ranged between 25%-76% in A. baumannii and 35%-88% in E. faecium. To the best of our knowledge, this is the first study to include research on antimicrobial, anti-adhesive and anti-biofilm activities of rhamnolipid from the local isolate P. aeruginosa UKMP14T against ESKAPE bacteria. Obtained results suggest that this rhamnolipid can be exploited commercially for the production of novel antibiotics.

This study aimed to determine the antimicrobial activity of ethanol-extracts obtained from Ocimum gratissimum L. (clove or African basil, Lamiaceae) and O. santum L. (holy basil) against some microorganisms present in oral cavity related to either medical or dental disease. Antimicrobial properties of both ethanol-extracts of Ocimum species against Streptococcus mutans KPSK2, S. pyogenes ATCC 19615, Staphylococcus aureus ATCC 16794, and Candida albicans ATCC 10231 were primarily determined by agar disk diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal or fungicidal concentration (MBC or MFC) of these herbal extracts were further determined by broth micro-dilution method. Ethanol-extracts of O. sanctum L. and O. gratissimum L. inhibited the growth of all tested microorganisms in various degrees ranging from the strongest antimicrobial activity of O. sanctum against S. pyogenes [MIC at 0.19% (w/v); MBC at 0.78% (w/v)] to the least inhibitory activity of O. gratissimum against C. albicans [MIC at 12.5% (w/v); undetectable MFC]. The ethanol-extract of O. sanctum showed stronger antimicrobial property against the tested bacteria and fungus than O. gratissimum. The ethanol-extracts of both Ocimum species showed stronger antibacterial than antifungal activity. However, the ethanol-extract of O. gratissimum even at a high concentration of 50% (w/v) was unable to eliminate the tested fungus. Ethanol-extracts of Ocimum species contain effective antibacterial and antifungal properties that may be beneficial for further development of antimicrobial agents in medical and dental fields.

The United States GAIN (Generating Antibiotic Incentives Now) Act is a call to action for new antibiotic discovery and development that arises from a ground swell of concern over declining activity in this therapeutic area in the pharmaceutical sector. The GAIN Act aims to provide economic incentives for antibiotic drug discovery in the form of market exclusivity and accelerated drug approval processes. The legislation comes on the heels of nearly two decades of failure using the tools of modern drug discovery to find new antibiotic drugs. The lessons of failure are examined herein as are the prospects for a renewed effort in antibiotic drug discovery and development stimulated by new investments in both the public and private sector.

Antibacterial activity of medicinal plants against ESKAPE: An update

ESKAPE pathogens and associated quorum sensing systems: New targets for novel antimicrobials development

Background: The excessive use of antibiotics has posed a global threat and challenge to the emergence of drug resistance in pathogenic bacteria. Various innovative methods, including using naturally occurring compounds to weaken antibacterial activity, are under investigation to address this issue. Nutmeg seeds are commonly used as spices in culinary applications and traditional medicine, as they are known for their stomachic, analgesic, and stimulant properties. Aim: The primary objective of the present work was to assess the antimicrobial activity of the flower extract of Myristica fragrans post purification process by Thin Layer Chromatography (TLC) and Column Chromatography. Methods: The column fractions were then assessed for their antimicrobial activity against ESKAPE pathogens, followed by the characterisation of the bioactive compounds by Fourier Transform Infrared Spectroscopy (FTIR) and Gas Chromatography Mass Spectrometry (GC-MS) analysis. Result: The characterisation analysis resulted in a compound called elemicin, a phenyl propene compound with a high yield of 62%. The second phase of the study involved the Minimal Inhibitory Concentration (MIC) determination and biofilm inhibition of elemicin against ESKAPE pathogens, along with the toxicity study on MRC-5 cell lines with signs of no toxicity, obtaining an IC50 value of 194.889 ug/ml. Conclusion: This present study of the characterisation of the bioactive compounds from the flower extract of M. fragrans was conducted for the first time. There have been no earlier studies pertaining to this, and the results exhibited by the bioactive compound as potent biofilm inhibitors and antimicrobial agents are worth mentioning and can be further extrapolated to translational research. Major Findings: The analytical process of characterisation of the crude extract of M. fragrans was a major finding in the present study where 6 different fractions were separated and each identified via GC-MS technique. The identification of 3 potent antibacterial compounds namely elemicin, p-Menth-1-en-4-ol and p-Cymene with a good yield and low cytotoxicity was a breakthrough in the study which could be further extrapolated to translational research.

PurposeThis study aimed at identifying the main antimicrobial resistance of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli) pathogens in a Romanian infectious diseases hospital. This antimicrobial resistance is a global threat, having high rates of multidrug resistance and limited treatment options.Patients and MethodsThis retrospective study (2016–2020) assessed the antimicrobial resistance of ESKAPE pathogens isolated from the patient’s biological samples. The microbiological diagnosis was performed by classical culture methods. The antimicrobial susceptibility analysis used the Kirby–Bauer disk-diffusion method and the method of minimum inhibiting concentration with the automated Vitek, according to the CLSI (Clinical and Laboratory Standards Institute) standards.ResultsIncluded in this study were 4293 bacterial isolates: 67% Gram-negative bacilli, 31% Gram-positive cocci and 2% other morphotinctorial bacteria. ESKAPE pathogens were found in 97% of the bacterial isolates strains; E. coli (38.26%) and Staphylococcus aureus (26%) were the most prevalent. Most bacterial strains were isolated from urine cultures (45.6%), skin and soft tissue secretions/collections (35.9%) and also blood cultures (4.2%). Increased antimicrobial resistance was observed for methicillin-resistant Staphylococcus aureus (MRSA)s, extended spectrum beta-lactamase producing (ESBL) Enterobacterales, carbapenem-resistant (CR) Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae. No vancomycin resistance was found for Enterococcus faecium. The highest prevalence rates of multidrug resistance were found in methicillin-resistant Staphylococcus aureus (86.6%), Acinetobacter baumannii (36.8%), Pseudomonas aeruginosa (29.1%) and Klebsiella pneumoniae (24.4%).ConclusionESKAPE pathogens are frequently isolated in the infectious diseases hospital, with main antimicrobial resistance: ESBL, MRSA and CR. The local antimicrobial resistance pattern is essential in updating the local protocols and for appropriately prescribing antibiotics. Streamlining microbiological diagnosis and aligning with the European standards for antimicrobial susceptibility testing are necessary steps in harmonizing the regional network for good antimicrobial resistance control practices.