1 Introduction

Resistance to chemotherapeutic treatment or prophylaxis has been regularly observed not only in bacteria but also in fungi, viruses, protozoa, and other parasites; hence, these bacteria are referred to as “microbial superbugs” [1]. According to the WHO [2], antibiotic resistance is a major threat to world health because of the staggering number of lives it claims each year [3]. Superbug microorganisms, which have evolved to withstand antibiotics, do so through a series of physiological changes, thereby aiding in the neutralization of antibiotics in the bacterial/fungal cell wall. The drug's target site, the regulation of inflow and efflux pumps, drug-metabolizing enzymes and pathways, etc., could all be affected. To treat these MDR bacteria, therapeutic techniques that can directly target and change the pathways that contribute to their resistance need to be developed [4].

In response, the discovery of several chemical substances, also known as phytochemicals, in plants has led to the identification of better alternatives to industrially synthesized antimicrobial drugs for which superbugs have developed resistance. These findings suggest a promising future for ethno-phytophenolic compounds in the world of microbiology and pharmacology if critically explored, as they could lead to novel research in developing a new pharmaceutical approach to tackling and altering the underlying mechanisms of drug resistance targets in microbial superbugs [3, 4]. Phytochemicals, which have therapeutic potential and mediate the treatment of ailments and diseases, can be found in many different plant components, including flowers, leaves, roots, bark, stems, roots, and seeds [3, 5].

Thymus vulgaris, also known in local Nigerian dialect as Efirin-aja (Yoruba), and Nchanwu (Igbo) has been shown to be effective against a wide range of bacteria and fungi, making it a viable option for treating a number of different infectious disorders and serving a number of other uses [5]. Phytochemical screening of Piper nigrum, also known in local Nigerian dialet as Iyere (Yoruba), and Oziza (Igbo) exhibited the presence of numerous secondary metabolites in the plant that exhibit antibacterial activity over time, depending on the dose and technique of extraction utilized [6]. In addition, extracts and phytoconstituents of Annona muricata also known in local Nigerian dialet as Gishiri (Yoruba), and Ehuru or Ehiri (Igbo) and Nigella sativa also known in local Nigerian dialet as Isalube funfun (Yoruba) essential oils have been shown to possess antimicrobial activity, among many other beneficial properties [7]. The advantageous activities and variety of useful biomedical applications of A. muricata are associated with its enrichment of secondary metabolites, mainly phenolic acids, acetogenins, alkaloids, terpenoids, and flavonoids, which are inherently found in its leaves and fruits [8, 9]. Having established the ethno-medicinal potency of plant bioactive compounds, with a major focus on Piper nigrum, Annona muricata, Thymus vulgaris and Nigella sativa as substitutes for the increasing resistance of superbugs to antimicrobial pharmaceutical drugs, a paradigm shift to plant chemicals is needed to revolutionize therapeutic strategies effective at combating infectious diseases, thereby improving quality of health and increasing life expectancy. The aim of this review study is to ascertain the potential of phytophenolic derivatives as ameliorative agents against microbial superbug bacterial and fungal pathogens mainly responsible for or implicated in nosocomial infections.

Multidrug-resistant (MDR) bacteria pose a significant threat to public health due to their ability to withstand multiple antibiotics, making infections caused by them challenging to treat. The rise of MDR bacteria is a global concern, with various studies highlighting the mechanisms behind their resistance and the impact on healthcare systems. González‐Villarreal et al. [10] emphasized the molecular mechanisms driving multidrug resistance in clinically relevant enteropathogenic bacteria, underscoring the severe illnesses and economic burden they impose on healthcare. This resistance is further compounded by the overuse and misuse of antibiotics, inadequate infection control measures, and global movement of people and goods, as discussed by Daoud and Dropa, [11]. The consequences of infections with antibiotic-resistant bacteria are dire, with Cassini et al. [12] estimating nearly 5 million deaths worldwide in 2019 associated with bacterial resistance, including 1.27 million directly attributable to MDR bacteria.

The statistics surrounding MDR bacteria paint a grim picture of the impact on mortality rates, particularly in hospital settings where nosocomial infections caused by antibiotic-resistant bacteria lead to high mortality rates. Huguet et al. [13] highlights that infections due to MDR bacteria are responsible for one death every 15 min in the United States, emphasizing the urgency of addressing this issue. Alkofide et al. [14] further supports this by noting that over 70% of bacteria causing hospital-acquired infections are resistant to commonly used antimicrobial agents, indicating a critical need for effective treatment strategies against MDR bacteria.

The complexity of MDR bacteria extends beyond their resistance mechanisms to the challenges they pose in clinical settings. Donkor et al. [15] found high rates of multidrug resistance among Gram-negative bacteria isolated from bloodstream infections in Ghana, with significant resistance to third-generation cephalosporins and fluoroquinolones. This observation was also supported by the need for the regulation of over-the-counter prescription of antipseudomonal and antienterococcal quinolone drugs for the management of nosocomial infections owing to the spread of QnrS and QnrB genes by horizontal gene transfer and selective pressure in clinical settings as inferred by Bayode et al. [16] who studied the multiple antibiotic resistance (MAR) index and detection of quinolone-resistant genes in the bacterial consortium of urine specimens from clinical settings in Nigeria. Owing to the current lack of clinical knowledge and self medication, this underscores the difficulty in treating infections caused by MDR bacteria, leading to poorer patient outcomes and increased healthcare costs in Nigeria. Moreover, Yan et al. [17] highlights the evolution of sophisticated resistance mechanisms by pathogens, contributing to the rapid spread of MDR bacteria and complicating treatment strategies.

The dynamics of MDR bacteria colonization and transmission are crucial aspects to consider in combating their spread. Kantele et al. [18] suggested that international travel plays a significant role in the acquisition of multidrug-resistant Gram-negative strains, emphasizing the need for global efforts to address this issue. Additionally, the role of environmental factors in the spread of MDR bacteria is evident in the study by Kwansa-Bentum et al. [19], which explores the effects of plant extracts on multidrug-resistant bacteria, highlighting the potential of alternative antimicrobial strategies. The prevalence of multidrug-resistant bacteria presents a formidable challenge to healthcare systems worldwide, with high mortality rates associated with difficult-to-treat nosocomial infections. Understanding the molecular mechanisms of resistance, addressing the global spread of MDR bacteria, and developing effective treatment strategies are essential in combating this growing public health threat.

The selection of Thymus vulgaris, Piper nigrum, Nigella sativa, and Annona muricata for the study on combating antibiotic resistance in microbial "superbugs" is a strategic choice based on their known efficacy and potential as natural remedies against nosocomial infections. Thymus vulgaris, commonly known as thyme, has been extensively studied for its antimicrobial properties. Research by Kryvtsova et al. [20] highlights the antimicrobial and antibiofilm properties of T. vulgaris essential oil against clinical isolates of opportunistic infections, showcasing its potential in combating resistant bacteria. This underscores the rationale behind including T. vulgaris in the study, as its bioactive compounds have demonstrated effectiveness against a range of microbial pathogens.

Piper nigrum, black pepper, is another plant species chosen for its potential antimicrobial properties. While not as extensively studied as T. vulgaris, black pepper has shown promise in antimicrobial applications. Kováčová et al. [21] demonstrated the antibacterial activity of silver nanoparticles synthesized using extracts from P. nigrum, indicating its potential as an antibacterial agent. This evidence supports the inclusion of P. nigrum in the study, as it offers a unique source of phytochemicals that may aid in combating antibiotic resistance in microbial superbugs.

Nigella sativa, black seed, has a long history of medicinal use and is renowned for its diverse therapeutic properties. Studies by Khalil et al. [22] and Mekky, [23] emphasized the medicinal value of N. sativa, showcasing its potential in various applications, including food science and antimicrobial activity. The bioactive components of N. sativa, such as thymoquinone, have been attributed to its antimicrobial effects, making it a valuable candidate for combating antibiotic resistance [24]. The inclusion of N. sativa in the study aligns with its reputation as a potent natural remedy with broad-spectrum antimicrobial properties. The study by Abdulrahman et al. [25] on the effects of N. sativa in COVID-19 patients highlights the importance of exploring traditional remedies for modern healthcare challenges.

Annona muricata, commonly known as soursop, is the fourth plant species chosen for its potential in managing nosocomial infections. Studies on A. muricata have revealed the presence of novel antineoplastic metabolites in its extracts, highlighting its potential as a source of potent antioxidant and therapeutic agents Gavamukulya et al. [26]. The antibacterial activity of A. muricata extracts against biofilm-forming MRSA further underscores its efficacy in combating antibiotic-resistant bacteria [27].

The selection of Thymus vulgaris, Piper nigrum, Nigella sativa, and Annona muricata for the study on combating antibiotic resistance in microbial "superbugs" is grounded in their historical uses, documented antimicrobial properties, and potential synergistic effects with conventional treatments. By elucidating the mechanisms of action of phytophenols from these plant species, the study aims to provide insights into novel strategies for managing nosocomial infections and addressing the escalating threat of antibiotic-resistant superbugs.

The utilization of natural secondary metabolites from Nigella sativa, Piper nigrum, Thymus vulgaris, and Annona muricata for medicinal and remedial applications in managing nosocomial diseases is crucial due to their therapeutic properties and historical significance in traditional medicine. These plant species have been extensively studied for their bioactive compounds, which exhibit a wide range of pharmacological activities beneficial for combating nosocomial infections.

Similarly, research on N. sativa has demonstrated its antimicrobial properties, making it a valuable candidate for managing bacterial infections. The antibacterial activity of N. sativa leaves' extracts against a variety of bacteria highlights its potential in addressing common bacterial diseases [28]. Moreover, the hypoglycemic, hypolipidemic, and antioxidant activities of Nigella sativa make it a promising natural remedy for conditions like diabetes [29]. These findings emphasized the importance of exploring the therapeutic potential of Nigella sativa in combating nosocomial infections.

Piper nigrum, known for its antimicrobial properties, offers another valuable source of secondary metabolites for medicinal applications. The antibacterial activity of silver nanoparticles synthesized using P. nigrum extracts showcases its potential as an antibacterial agent. The modulatory effect of P. nigrum extracts on selected antibiotics against biofilm-forming MRSA further highlights its role in enhancing the efficacy of conventional antibiotics [27]. These studies support the preference for utilizing P. nigrum in the management of nosocomial infections.

Thymus vulgaris, commonly known as thyme, is renowned for its antimicrobial properties, making it a valuable resource for combating infectious diseases. Research on T. vulgaris essential oil has demonstrated its antimicrobial and antibiofilm properties against clinical isolates, indicating its potential in addressing opportunistic infections. The inclusion of T. vulgaris in medicinal formulations can provide synergistic effects with conventional treatments, enhancing the efficacy of antimicrobial therapies as reported by Tacconelli et al. [30].

The preference for utilizing natural secondary metabolites from Nigella sativa, Piper nigrum, Thymus vulgaris, and Annona muricata in medicinal and remedial applications for nosocomial diseases' management stems from their well-documented pharmacological activities, including antimicrobial, antioxidant, and therapeutic properties. These plant species offer a rich source of bioactive compounds that can aid in combating antibiotic resistance and addressing the challenges posed by nosocomial infections, making them valuable assets in the field of natural medicine.

1.1 Pharmacological potential and biochemical derivatives of Nigella sativa, Piper nigrum, Thymus vulgaris, and Annona muricata

The use of biochemical derivatives of medicinal plants has considerably improved drug research and infectious disease management. Currently, 60% of all antibacterial and anticancer drugs on the market are derived from plants [31]. Nigella sativa has been used for millennia in traditional Arabic medicine and is one of the first known herbal remedies. The seeds of N. sativa contain oil, protein, carbohydrates, fiber, and saponins. The essential oil of Nigella sativa contains nigellone, thymoquinone, and thymohydroquinone; the fixed oil contains arachidonic, linoleic, oleic, almitoleic, palmitic, stearic, myristic, sterole, and eicosadenoic acids [32]. In addition to its culinary use, Piper nigrum is widely used in traditional medicine across a number of nations. Several nations typically cultivate Thymus vulgaris L. for commercial use to harvest its dried leaves, plant extracts, plant oil, and oleoresins [33]. Due to its broad aromaticity, Thymus vulgaris L. is utilized commercially as a flavoring ingredient in the food industry [34]. Along with its application for flowering and decorative purposes, it is also employed for the preservation of meat, poultry, and fish [35]; [36]. Furthermore, A. muricata is a plethora of medicinal plants that have been widely studied in recent years due to its pharmacological potential. In folklore treatment, various A. muricata plant parts have been used as potential cures for a number of ailments, such as arthritis, and they have been reported to be useful for treating diabetes, inflammation, spasm, and cancer [37]; [8].

1.2 Antimicrobial, anti-inflammatory, and immunomodulatory properties of Nigella sativa, Piper nigrum, Thymus vulgaris and Annona muricata

Nigella sativa has been used for a variety of ailments in traditional Arabic herbal medicine, including pyrexia, conjunctivitis, dermatitis, internal bleeding, and gastrointestinal disorders [38]. The potential of its crude leaf extracts to boost the activity of intrinsic enzymes with antioxidant properties, such as glutathione peroxidase and catalase, can be attributed to some of these effects. Additionally, the oil also alters B-cell-dependent immunological pathways, influences the production of prostaglandins, cytokines, and chemokines, and scavenges free radicals [39].

Many diseases have been treated or managed using various P. nigrum components, including flowers, seeds, fruits, and leaves [40]. The Asia region has the most reports on the traditional use of P. nigrum. Additionally, menstrual abnormalities such as menorrhagia, oligomenorrhea, hypomenorrhea, and dysmenorrhea are among the maladies that P. nigrum has been applied for treatment [40]. In addition to being used to treat fever, jaundice, and snake bites, Piper nigrum has also been used to treat skin conditions such as scabies, itch, bed sores, and boils [40]. Babayemi et al. [41] also confirmed the potency of phytophenolic compounds comprising phytol, octadecanoic acid, and n-hexadecanoic acid elucidated via chromatographic studies due to inherent inhibitory upshot on nosocomial wound MDR bacterial pathogens including Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. Thymus vulgaris, due to its wide range of pharmacological qualities, has a variety of ethno-medicinal uses. The plant is largely used for its healing and disinfecting properties on wounds [33]. Ancient Europeans employed the antibacterial properties of this plant's aerial parts for fumigation, skin, and respiratory ailments [5]. Satyal et al. [42] has demonstrated the antibacterial activity of T. vulgaris for virulent, common MDR strains of bacteria and fungal pathogens. Benameur et al. [43] suggested that plants can reduce bacterial adsorption and the formation of biofilm matrices. Furthermore, Thymus vulgaris L. is thought to possess antibacterial, astringent, carminative, tonic, and anthelminthic properties. Due to its ability to combat intestinal diseases and infestations caused by ascarids, hookworms, fungi, yeasts, and bacteria, the plant has become quite well known [5]. Additionally, thyme can also be used to manage dermatological conditions such as rheumatoid arthritis, sciatica, greasy skin, dermatitis, and bug bites [5]. According to Tian et al. [44], Thymus vulgaris L. alleviates the neurological problems caused by bites and stings. The red variety of Thymus vulgaris L. oil and T. vulgaris L. oil is used to cure bodily aches and skin conditions. Recent research on anti-inflammatory agents has shown that Thymus vulgaris L. is effective at reducing oxidative stress and cell-mediated immunity [45].

Annona muricata, popularly known as soursop, is a plant fruit found in tropical and subtropical parts of the world. In Africa, India, and tropical America, A. muricata has been widely used customarily against an assortment of human illnesses and diseases. Over the years, the leaves, fruits, seeds, and bark of A. muricata have been used in traditional medicines in various cultures and from various Nations [46]. As a consequence, it has become widely known and used for hypoglycemic, hypotensive, and hypolipidemic treatments [47,48,49]. Takahashi et al. [50] previously reported the antimicrobial properties of A. muricata, although its mechanism of action is not fully understood. Thus, the plant fruit A. muricata has attracted increased amounts of attention due to its potential to treat viral infections, and new therapeutic agents against microbial activity are becoming a focus of research [51]. Nícolas et al. [52] have demonstrated that A. muricata possesses a broad spectrum of antibacterial activity against both gram-negative and gram-positive bacteria, and bacterial membranes have been identified as the primary targets of A. muricata. To further corroborate the antimicrobial properties of A. muricata, as reported by Campos et al. [9], Takahashi et al. [50] reported significant antifungal activity against fluconazole-, itraconazole-, and anidulafungin-resistant C. albicans.

1.3 Microbial inhibition profile of Thymus vulgaris, Piper nigrum, Nigella sativa, and Annona muricata on nosocomial infection-causing bacteria, fungi and viruses

Nigella sativa, commonly known as Black Cumin, has been extensively studied for its antibacterial properties against various microbial pathogens. Research by Tiji et al. [53] highlighted the antimicrobial activity of Moroccan Nigella sativa extracts, showing MIC values ranging from micrograms to milligrams per milliliter against different pathogens. Specifically, the MIC for Staphylococcus aureus was found to be 0.96 mg/mL, for Bacillus cereus 0.5 mg/mL, and for Escherichia coli 0.68 mg/mL. This indicates the potency of Nigella sativa in inhibiting the growth of these bacteria at relatively low concentrations.

Denizkara et al. [54] provides information on determining MIC and MBC values for antimicrobial agents. In this context, the MIC and MBC values of purified aqueous extract against Staphylococcus aureus bacteria were reported as 35.15 and 23.39 µg/mL, respectively. This finding aligns with the concept of assessing the inhibitory and bactericidal concentrations of compounds, similar to the approach taken with Piper nigrum by Sanad et al. [55] who discussed the use of ciprofloxacin as a reference to determine MIC and MBC values against selected strains. The MIC/MBC values of ciprofloxacin were reported as 2.9/5.9 μM. This observation highlights the importance of understanding the potency of antimicrobial agents through MIC and MBC assessments, which can be applied to evaluate the efficacy of compounds from Piper nigrum.

Sirimongkolvorakul and Jasancheun, [56] presents the MIC and MBC values of Piper nigrum ethanol extract against Staphylococcus aureus, with MIC and MBC reported as 0.13 and 0.52 mg/mL, respectively. This inference aligns with the concept of determining the inhibitory and bactericidal concentrations of natural extracts, similar to the evaluation of compounds from Piper nigrum.

Thyme essential oil inhibited the adherence of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus saprophyticus in the presence of sucrose, with minimum adherence inhibitory concentrations ranging from 0.78–3.12 μL/mL as reported by Gedikoğlu et al. [57]. Thyme essential oil showed potent inhibitory activity against methicillin-resistant Staphylococcus aureus (MRSA) strains when combined with the antimicrobial clindamycin, with MIC ranges between 125–500 μg/mL [58]. Mohsenipour and Hassanshahian, [59] reported inhibitory effect of Thymus vulgaris essential oil extracts on bacteria with MIC values ranging from 64 to 512 μg/mL against the planktonic form and biofilm structures of human pathogenic bacteria comprising Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus saprophyticus. In a study by Jalal et al. [60], biosynthesized silver nanoparticles showed promising MIC values ranging from 156.25 to 1,250 µg/mL against various Candida species. Although this study did not specifically involve Annona muricata, it sheds light on the efficacy of silver nanoparticles against fungal pathogens, including Candida species, which are relevant in the context of antifungal activity. Additionally, the MBC values for MDR Pseudomonas aeruginosa strains were reported by Murad, [61], with the bacterial strain showing an MBC of 0.5 mg/mL and the MDR strain exhibiting an MBC of 1 mg/mL. This information underscores the challenge posed by MDR strains and the need for effective antimicrobial agents like Annona muricata to address such infections. The study by Gavamukulya et al. [26] have explored the antineoplastic and cytotoxic activities of Annona muricata extracts, indicating the presence of compounds with potential antiviral properties. These findings lay the groundwork for investigating the effectiveness of Annona muricata against viruses responsible for nosocomial infections, highlighting its broad-spectrum therapeutic potential.

Moreover, the study by Bitar et al. [62] delves into the anti-inflammatory effects of Annona muricata through the inactivation of the NALP3 inflammasome. This mechanism of action suggests that Annona muricata may possess immunomodulatory properties that could be beneficial in combating viral infections by regulating the inflammatory response, which is crucial in managing nosocomial viral outbreaks. Furthermore, the research by Vignera et al. [63] on the use of ellagic acid and Annona muricata to improve semen quality in men with high-risk papillomavirus infection hints at the potential antiviral effects of Annona muricata. This study underscores the ability of compounds derived from Annona muricata to modulate viral infections, indicating a promising avenue for exploring its antiviral activity against nosocomial pathogens.

1.4 Evaluation of the antibacterial potential of Nigella sativa and Annona muricata against Salmonella serotypes, MRSA, VRSA, and other multidrug-resistant pathogens

Well diffusion tests and tube dilution methods were used to examine the antibacterial activity of N. sativa oil and crude extracts against the growth of six Salmonella serotypes, namely, Salmonella paratyphi, S. typhi, S. enteritidis, S. typhimurium, S. Heidelberg, and S. agona [64, 65]. Using drug sensitivity testing, it was determined that the synthetic antibiotics ceftriaxone and ciprofloxacin were ineffective against all of the Salmonella strains examined. The oil extract made only 90% of the resistant Salmonella strains vulnerable to treatment, whereas the crude extract made all of them susceptible. In another study, the well diffusion technique was used to investigate the effects of various doses of black cumin seed oil on MRSA strains that had been obtained from diabetic wounds. Each strain had been in contact with the oil for a different amount of time [65]. Another in vitro investigation revealed that 819.2 g/ml N. sativa ethanol extract was necessary to kill vancomycin-resistant Staphylococcus aureus (VRSA). The agar-well diffusion method was utilized to obtain all five clinical isolates. The average inhibitory zone for all five VRSA isolates was 22.2 mm when treated with an ethanol extract at 20 mg/ml [66].

Solomon-Wisdom et al. [67] reported the antimicrobial potential of soursop against gram-positive and gram-negative bacteria, which was comparable to that of the standard antibiotic streptomycin. The bioactivity of soursop was dependent on the kind of extract used. Additionally, Mutakin et al. [68] reported that combining an ethanol extract and antibiotic treatment increased the potency of antibiotics against multidrug-resistant strains of E. coli and S. aureus. Further investigations by Nicolas et al. [52], such as bacterial killing assays, bacterial abundance, and membrane viability analysis via fluorescent probes, as well as nucleotide leakage and outer membrane permeability assays, demonstrated the bioactivity of Annona muricata against both Gram-negative and Gram-positive bacteria. The minimal inhibitory concentration (MIC) assay showed that E. faecalis, S. typhimurium and S. aureus were the most susceptible bacteria to A. muricata, while the minimum bactericidal concentration (MBC) was shown for S. typhimurium, S. aureus and P. aeruginosa; in this order, these bacteria species were the most susceptible to soursop [52]. Gavamukulya et al. [37] suggested that the probable mechanism was due to the synergistic action of Annona muricata phytoactives, such as alkaloids, flavonoids, and polyphenols. This submission was corroborated by Campos et al. [9], as their investigation through UPLC-ESI–MS/MS also revealed the presence of similar phytochemicals, suggesting their synergetic action in nucleotide leakage and that bacterial membranes are primary targets of this extract.

1.5 Evaluation of the antifungal potential of Thymus vulgaris and Annona muricata against Candida, Cryptococcus, Aspergillus, and other pathogenic fungi

Essential thyme oil has been proven to be effective against a wide variety of fungal species, including Sclerotinia spp., Botrytis spp., Phytophthora spp., Pythium spp., Fusarium spp., Alternaria spp., and Cladobotryum spp. The sensitivity of these fungi was studied using a circumferential growth inhibition assay, and the results showed that the ED50 values for all investigated species ranged from 9.3 to 18.0%, with inhibitory values ranging from 13.9 to 41.4 mm at a 5% dosage (p ≤ 0.05) [69]. Additionally, a total of 76 C. difficile and 183 C. albicans clinical isolates were analyzed in this study. For each of the isolates, researchers determined an MIC and MFC ranging from 0.04 to 22.9 mg/mL. Thyme oil slowed fungal growth early in the time-kill test. Thyme oil plus sorbitol, a low-dose osmoprotectant (MIC = 0.08 mg/ml; p ≤ 0.05), had a synergistic effect on fungal development [70]. The antifungal effects of thymol at 64 mg/l and 128 mg/ml were significantly greater than those of conventional antibiotics (p ≤ 0.05). Thymol increases pmk-1 and sec-1 gene expression to enhance the p38 MAPK biophysical pathway; this route inhibits C. albicans proliferation [71]. Scalas et al. [72] investigated fluconazole (FLC), itraconazole (ITC), and voriconazole (VRC) for the treatment of Cryptococcus neoformans. The MIC and MFC ranged from 56 to 1.12 mg/ml VRC. However, at doses between 0.02 and 0.08 mg/ml, thymol had significant effects (p ≤ 0.05) in a single antifungal test conducted by Scalas et al. [72]. Evidence shows that thyme oil inhibits fungal development in both the vapor and liquid phases. The mycelial growth of Aspergillus flavus was completely inhibited at doses of 20 and 400 g/ml. In addition, 10 g/ml thyme oil reduced aflatoxin production by 97.0% in the liquid phase and 56.4% in the vapor phase (p ≤ 0.05) as observed by Pinto et al. [73]. A number of studies have shown the fungicidal potency of soursop against Candida species [74, 75]. However, the mechanism of action, especially for multidrug-resistant strains, has yet to be established. Recently, Campos et al. [9] evaluated the effect of the ethanol extract of A. muricata on multidrug-resistant C. albicans. The MIC revealed the fungistatic effect of A. muricata against C. albicans, which was found to be resistant to fluconazole and itraconazole. Annona muricata reduced fungal growth by 58% and cell density by 65%. Additionally, the study further revealed that after treatment with the ethanol extract, soursop affects the fungal plasma membrane and cell wall, which significantly affects and reduces the viability of the cell. Phyto-constituents such as alkaloids, flavonoids, acetogenins, phenolic acids, benzofurans, and disaccharides were detected by UFLC-QTOF-MS as major bioactive components [9].

1.6 Evaluation of the antiviral potential of Thymus vulgaris and Annona muricata against Influenza Virus, HIV-1, Dengue Virus, Herpes Simplex Virus, and SARS-CoV-2

Thyme oil, in both its liquid and vapor forms, has been found to be effective against the influenza virus. While the vapor phase showed only weak activity, the liquid phase completely inhibited viral growth at a concentration of 3.1 g/ml, far outperforming the control (canola oil) [40]. Researchers have also examined the effects of hemaglutinin on two main surface proteins, neuraminidase (NA) and hemagglutinin (HA), and found that HA was significantly suppressed. Additionally, a TC50 value of 14.34 l/ml (p ≤ 0.05) indicated that 50% of the culture was lost [72]. The antiviral activities of P-cymene, terpinen-4-ol, terpineol, terpinen, thymol, citral, and 1, 8-cineole were investigated. The noncytotoxic dose of citral ranged from 20 g/ml to 1250 g/ml in RC-37 kidney cells. The IC50 of 1, 8-cineole was 1200 g/mL. Thyme oil inhibited viral replication by > 96% (p ≤ 0.05) compared to that of other monoterpenes [76]. Feriotto et al. [77] studied the Tat protein, which helps transcribe the viral genome of Thymus vulgaris L. Essential oil works with other substances; long terminal repeat (LTR) transcription of HIV-1 requires the Tat protein and the Tat/TAR-RNA complex [77]. With respect to the electrochemical impedance shift assay, this molecule revealed a significant inhibitory potential (3–6 g/ml) compared to that of the control (EMIE). This dynamic was replicated in a study investigating antiviral activity against Tat-induced HIV-1 LTR transcription; the results showed 50% inhibitory activity (RT50 = 0.83 g/ml), which is a significant modulatory potential that reduces viral expression by 52% (p ≤ 0.05) [77]. Posttreatment, an aqueous extract of soursop (A. muricata) showed antiviral activity against dengue virus type 2, with 0.20 mg/mL being the EC50 value for A. muricata tested against DENV-2. Additionally, the selectivity index (SI) of soursop, an antiviral compound, was greater than 12.5 [78], suggesting that soursop is a potential antiviral agent because any antimicrobial compound with an SI greater than 10 (SI > 10) could be established as a potential antiviral agent. In another study by Balderrama-Carmona et al. [79], bacteriophage surrogates were used to evaluate the antiviral effect of an acidified ethanol extract (AEE) of A. muricata. This antiviral evaluation revealed a dose-dependent effect of soursop. An increase in the contact time and dose of the AEE extract led to a decrease in viral replication. The greatest reduction in phage yield was reported at a concentration of 1 mg/ml AEE and with a contact time greater than 30 min, with values of 7 and 4 log10 PFU/ml for Av-05 and Av-08, respectively. A similar concentration of 1 mg/mL was reported by Padmaa et al. [80] for the MIC of the ethanol extract of soursop against HSV-1. In the 1990s, Padmaa et al. [80] investigated the effects of soursop on herpes simplex virus-1 (HSV-1). This in vitro investigation using standard strains and wild clinical isolates revealed the inhibition of the cytopathic effect of HSV-1 on Vero cells, suggesting the potential of A. muricata for preventing HSV-1 infection.

More than 200 bioactive compounds have been identified, isolated, and studied from A. muricata; these principal compounds are phenols, alkaloids, acetogenins, and flavonoids [81], which have been reported for their antiviral activity. Rutin, a major component of soursop (Annona muricata), reportedly interacts with multiple viral proteins. Current in silico and in vivo investigations have reported that rutin, a major bioactive compound, inhibits the replication of SARS-CoV and SARS-CoV-2 (COVID-19). Angiotensin-converting enzyme 2 (ACE 2) is the receptor that binds to the SARS-CoV-2 glycoprotein and can cause membrane fusion and viral infection. However, Balderrama-Carmona et al. [48] reported that rutin potentially inhibits ACE2, which further suppresses the entry of SARS-CoV-2. Elmi et al. [81] reported that polyphenol bioactive compounds interfere with HIV-1 replication at an early stage of the virus. In essence, these bioactive compounds inhibit virus entry into host cells, thus reducing viral RNA levels, which indicates the virucidal activity of polyphenols found in plants.

2 Resistance mechanisms and connections in microbial superbugs responsible for nosocomial infections

Nosocomial, or hospital-acquired, infections caused by multidrug-resistant (MDR) "superbug" pathogens have developed various resistance mechanisms that allow them to evade the effects of commonly used antibiotics. Understanding the resistance mechanisms and connections within microbial superbugs responsible for nosocomial infections requires an exploration of the pathways through which these pathogens evade conventional treatments. The emergence of multidrug-resistant Gram-negative bacteria (MDR-GNB) poses a significant challenge in healthcare settings, as these pathogens exhibit resistance to vital antibiotics, including broad-spectrum penicillins, fluoroquinolones, aminoglycosides, and β-lactams as reported by Ahmed et al. [82]. The resistance mechanisms employed by these superbugs often involve intricate genetic adaptations that confer the ability to withstand the effects of multiple antimicrobial agents, leading to treatment failures and increased mortality rates.

One of the key players in nosocomial infections is Acinetobacter baumannii, a pathogen known for its carbapenem resistance. Carbapenem-resistant Acinetobacter baumannii (CRAB) strains have become increasingly prevalent in healthcare settings, posing a significant threat to patient safety [83]. The resistance mechanisms in Acinetobacter baumannii often involve the production of carbapenemases, enzymes that hydrolyze carbapenem antibiotics, rendering them ineffective against the bacteria. This resistance mechanism highlights the adaptability of superbugs in evading the effects of potent antibiotics, leading to persistent infections and treatment challenges.

Moreover, the use of antimicrobial peptides and the CRISPR/Cas9 system has been proposed as a potential therapeutic approach against multidrug-resistant pathogens. Antimicrobial peptides offer a novel strategy to combat nosocomial infections by targeting bacterial membranes and disrupting essential cellular functions [84]. The CRISPR/Cas9 system, known for its gene-editing capabilities, provides a promising avenue for developing targeted therapies against multidrug-resistant microbes, offering precision in combating resistant strains [84].

In the context of nosocomial infections, the presence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant threat to patient safety. MRSA contamination in healthcare settings, particularly on frequently touched objects as formites, contributes to the spread of infections and challenges infection control measures [85]. The ability of MRSA to persist on surfaces for extended periods underscores the importance of stringent hygiene practices and effective disinfection strategies to prevent nosocomial transmission.

The prevalence of nosocomial infections caused by multidrug-resistant organisms highlights the urgent need for novel antimicrobial strategies. Nanomaterials, such as silver nanoparticles, have shown promise as multimodal photothermal agents against superbugs, offering a potential solution to combat antibiotic resistance [86]. The unique properties of nanomaterials enable targeted antimicrobial effects, providing a versatile approach to addressing nosocomial infections caused by multidrug-resistant pathogens.

2.1 Resistant mechanisms of key MDR bacteria-causing nosocomial infections

The resistance mechanisms and connections within microbial superbugs responsible for nosocomial infections are multifaceted and dynamic, requiring a comprehensive understanding of the genetic, biochemical, and environmental factors that contribute to antimicrobial resistance. By exploring novel therapeutic approaches, such as antimicrobial peptides, gene-editing technologies, and nanomaterial-based strategies, researchers aim to develop innovative solutions to combat the growing threat of multidrug-resistant superbugs in healthcare settings. The key resistance mechanisms and the associated "superbug" pathogens responsible for nosocomial infections are summarized in Table 1.

Table 1 The key resistance mechanisms and the associated "superbug" pathogens responsible for nosocomial infections
Full size table

2.1.1 Enzymatic inactivation by nosocomial bacterial pathogens

Certain bacteria, such as Enterobacteriaceae and Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli produce enzymes that can chemically modify and inactivate antibiotics. Examples include β-lactamases that hydrolyze β-lactam antibiotics like penicillins and carbapenems [87]; [88]; [89]. Aminoglycoside-modifying enzymes that acetylate, phosphorylate or adenylate aminoglycoside antibiotics comprising Streptomycin, Kanamycin, Gentamicin, Tobramycin, Netilmicin, Amikacin, Arbekacin and Plazomicin [90].

The presence of additional classes of antibiotics, such as aminoglycosides, reveals a distinct resistance mechanism. The biosynthetic pathway has ceased because the modified products lack the ability to bind to ribosomes and thus have a much lower affinity for RNA [33]; [91]. Acetyltransferase, adenylyltransferase, and phosphotransferase are three metabolic enzymes responsible for inactivating these antimicrobial medicines. The amino groups of aminoglycosides use these enzymes for site remodeling of aminoglycoside resistance genes (aac6'la and aac6'lb) (Fig. 1), which encode these enzymes [3]. One of the five apramycin-resistant dairy bacterial isolates, Escherichia coli J62-1, produced the aac (1) enzyme as described previously [92].

Fig. 1
figure 1

The protein synthesizing enzyme DNA gyrase, the deconstruction and remodeling enzymes that superbugs use are both inhibited by the phytochemicals found in plants. In addition to lowering efflux pump activity, they can selectively target porins for vascular permeability. Phytochemicals are able to disrupt the superbug's target sites before those sites may be modified

Full size image

2.1.2 Target modification by nosocomial bacterial pathogens

Pathogens can alter the molecular targets of antibiotics, preventing the drugs from binding effectively. Altered penicillin-binding proteins (PBPs) in methicillin-resistant Staphylococcus aureus (MRSA) was reported by Sousa et al. [90]. Mutations in DNA gyrase and topoisomerase IV that confer resistance to fluoroquinolones in Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Acinetobacter baumannii, Enterobacter species and Citrobacter freundii as reported by Sousa et al. [90].

2.1.3 Reduced drug accumulation by nosocomial bacterial pathogens

Bacteria can reduce the intracellular concentration of antibiotics through increased efflux pump activity that actively expels drugs out of the cell, as seen in Pseudomonas aeruginosa and Acinetobacter baumanni as reported by Xia et al. [88]; Walsh et al. [89]. Decreased porin expression, limiting drug entry into the bacterial cell, observed in Gram-negative bacteria comprising Escherichia coli, Klebsiella pneumoniae, Enterobacter aerogenes, Acinetobacter baumannii and Neisseria meningitidis was also reported by Xiao et al. [87]; Xia et al. [88]; Walsh et al. [89].

2.1.4 Bypass of metabolic pathways by nosocomial bacterial pathogens

Some bacteria comprising Staphylococcus aureus and Neisseria meningitidis can bypass the metabolic pathways targeted by certain antibiotics, rendering the drugs ineffective. The overproduction of the target enzyme to overcome inhibition by antimetabolite drugs like sulfonamides which are antimetabolite drugs that target the enzyme dihydropteroate synthase (DHPS) in Campylobacter jejuni and Streptococcus pneumoniae was reported by Sousa et al. [90], as well as the development of alternative metabolic pathways that do not require the targeted enzyme in Pseudomonas species, Zymomonas mobilis, Vibrio cholerae and Escherichia coli also reported by Sousa et al. [90].

These resistance mechanisms, often combined in a single pathogen, contribute to the emergence and spread of "superbug" infections in healthcare settings, posing significant challenges to effective treatment and control.

2.1.5 Enzymatic inactivation of antibiotics by nosocomial bacterial pathogens to evade beta-lactams and glycopeptides

It comprises destructive and modifying enzymes [3]. Bacteria chemically destroy antibiotics to escape being killed by them, changing their chemical composition. Beta-lactamases attach to the beta-lactam ring of penicillins, cephalosporins, and carbapenems, degrading them [40, 93, 94]. In earlier studies, the antibacterial effects of baicalein restored the efficacy of the beta-lactam antibiotics tetracycline and ciprofloxacin against MRSA by blocking NorAEP [95]. Bayode et al. [16] reported that Penicillins, cephalosporins, monobactams, and carbapenems are among the antibiotics of the beta-lactam class that inactivate glycopeptide transpeptidases to prevent the formation of bacterial cell walls. Bitter leaves (Vernonia amydalina) also demonstrate potent antimicrobial activity via their inherent phytochemicals (polyphenol family) that inhibit the beta-lactamase enzymes responsible for the pathogenicity of Enterobacteriaceae infections, as reported by [94].

2.1.6 The potential of porin-targeting phenolics in combating antibiotic resistance in gram-negative bacteria-causing nosocomial infections

Porins govern active diffusion across lipid bilayers [96]. Gram-negative bacteria are vulnerable to porin-targeting phenolics. By altering their porins, bacteria can evade antimicrobial agents [96] (Fig. 1). Gram-negative bacteria employ this method to avoid antibiotics [96]. Additionally, polyphenol families found naturally in bitter leaves (Vernonia amygdalina) have shown strong antibacterial activity by inhibiting the beta-lactamase enzymes responsible for the pathogenicity of Enterobacteriaceae infections [94].

2.1.7 Modification of drug-binding sites as mechanism of antibiotic resistance in nosocomial bacterial pathogens

One type of drug resistance is the modification of drug-binding sites. This form of resistance develops when an antibacterial agent's specific targeting site is modified in a way that prevents the agent from reacting with the bacterium. As a consequence, the effectiveness of antibacterial compounds is greatly diminished [96]. Antibiotic-resistant bacteria may have multiple methods of resistance, one of which involves peptidyltransferase modification of the treatment site. Epigenetic modification of this enzyme at a specific amino acid residue reduces antibiotic selectivity to the action site peptidyltransferase [96] (Fig. 1). Clinical isolates of Staphylococcus aureus that have developed resistance to antimicrobial agents almost always do so by employing this resistance mechanism.

2.2 Phenolic compounds as efflux pump inhibitors to combat antibiotic resistance in nosocomial pathogens

The phenol group, which is connected to numerous regions of each molecule, gave rise to the name phenolic class of phytochemical compounds. Phenolics are a diverse group of bioactive, naturally occurring substances that are widely used in medicine. In several ways, these substances, which are bioactive molecules, contribute significantly to improving antibiotic action against bacteria that have developed resistance [97]. Some of the most important strategies for treating this disease include lowering efflux pump (EP) activity and functioning as multidrug efflux inhibitors (MEIs). The efficacy of these substances for efflux pump inhibition (EPI) against pathogenic bacteria has been encouraging. Natural phenolic compounds have antimicrobial properties beyond their capacity to obstruct efflux pumps. Numerous phenolic compounds have been discovered thus far, each with a unique mode of action [97]. Among plant families, the Fabaceae family possesses the most phenolic chemical byproducts [98]. Maximizing the combinatorial effect of phytonutrients with failed antibiotics, which reportedly restores optimal antibacterial activity, is pertinent as supported by Brown, [99]; Porras et al. [100].

When produced at sufficiently high concentrations, phenolic compounds show promising EPI activity against pathogenic germs, increasing the efficacy of antibiotics by inhibiting the development of resistance [101]. Phenolics’ antibacterial action can be attributed to two main processes namely by chemical interference with the creation or operation of key components of bacteria and by side-stepping of well-established antibacterial resistance mechanisms. Cell wall phenolics target multiple enzymes, including dihydrofolate reductase, urease, and sortase A [33]. Understanding the systems of resistant bacteria is crucial for finding solutions to slow the development of antibiotic resistance. These systems typically involve strengthening the efflux pump, eliminating antibacterial agents using neutralizing enzymes, distorting antibiotics using modifying enzymes, and evolving target structures in the bacterium that have lower resistance to antibacterial recognition [3, 35]. Recently, Lawani et al. [1] reported that employing alternative compounds such as phytochemicals alone or in combination with other antibacterial agents appears to be an effective and safe strategy for battling microbial superbug pathogens implicated in nosocomial infections.

2.3 Phenolic compounds as efflux pump inhibitors for the inhibition of DNA gyrase and antibiotic resistance nosocomial bacterial pathogens

Anthraquinones [102], chebulinic acid [103], and tannic acid found in Nigella sativa (Curmin), Piper nigrum (Black Pepper), Annona muricata (Soursop) are all phenolic compounds that have inhibitory effects on DNA gyrase [104]. Epigallocatechin Gallate (ECG) found in Nigella sativa, Piper nigrum (Black Pepper) has the propensity to inhibit β-lactamase activity [105] (Table 2), Annona muricata has the potential to block the B subunit of DNA gyrase from connecting to ATP [106]. Chebulinic acid was identified as the most effective bioactive component in a virtual screening against quinolone-resistant mutations of Mycobacterium tuberculosis DNA gyrase [107]. However, the results can be evaluated only via in silico prediction because no in vitro experimental research has been conducted. An in vitro study examined the DNA gyrase inhibitor chebulinic acid and its antituberculosis potential as Haloemodins are semisynthetic anthraquinone esters. These agents prevented the entry of vancomycin-resistant Enterococcus faecalis DNA gyrase and MRSA. Various halogenated analogs of the plant-derived chemical emodin have high activity against bacterial DNA gyrase [104]. Among bacteria, five efflux pump (EP) families are found in most Gram-positive and Gram-negative bacteria [108].

Table 2 Bioactive machinery of plant-derived phenolics in bacterial superbugs
Full size table

The RND family of Gram-negative bacteria is a trimeric complex spanning both membranes. Some of the most well-known EPs are members of the MFS family and include Staphylococcus aureus NorA and Streptococcus pneumoniae PmrA. It has been determined that this family of EPs is the most prevalent among these microbes. This antibiotic resistance has been detected in S. aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Candida albicans, among others [109]. Ferreira et al. [110] studied the EPI action of this medication against Arcobacter butzleri and Arcobacter cryaerophilus. Baicalein, a phytophenol from Nigella sativa and tetracycline prevented efflux pump (EP) from killing E. coli, a prominent betalactamase-producing bacteria as affirmed by Cho et al. [111] and Fujita et al. [112] as illustrated in (Table 2). The results revealed that this drug could inhibit MRSA EPs by decreasing NorA protein production. Gholamnezhad et al. [40] also investigated antibiotic-flavonoid fusions for MRSA. The hybrid compounds had increased antibacterial stability and activity, confirming their dual mode of action [113].

2.4 Mechanisms of action, chemotherapeutic synergy, metabolic pathways and antioxidant properties of phytophenolic derivatives as potential antimicrobials

The genetic and genomic differences related to the potential ameliorative effects of phytophenolic derivatives on microbial superbugs and their synergistic selectivity for chemotherapeutics can be elucidated by elucidating the mechanisms of antibiotic resistance, interactions with cellular pathways, and antioxidant properties. The origins and evolution of antibiotic resistance have been extensively studied over the past few decades, leading to the urgent need for action. This phenomenon is particularly relevant in the context of microbial superbugs, where the mechanisms of antibiotic resistance play a crucial role in persistence and virulence [92].

Phytophenols have been shown to interact with muscle proteins, modifying their structural characteristics and textural properties in food products. This interaction may also have implications for the mechanisms of action of phytophenolic derivatives on microbial superbugs, especially in terms of disrupting microbial cell membranes or metabolic pathways [147]. Furthermore, a review of tumor-associated macrophages (TAMs) and TAM-based antitumor nanomedicines provides insights into the molecular mechanisms and nanodrug delivery systems based on TAMs. This finding is relevant because it sheds light on the potential mechanisms of action of phytophenolic derivatives on microbial superbugs, especially in the context of nanomedicine and targeted drug delivery [148].

In addition, studies of microbial infections caused by quorum quenching have elucidated the underlying mechanisms and implications of quorum quenching, which could be relevant for understanding how phytophenolic derivatives may interfere with microbial communication and virulence factors [149]. Moreover, the inhibition of hazardous compound formation in muscle foods by antioxidative phytophenols highlights the potential of phytophenolic derivatives for mitigating the production of carcinogenic compounds, which could be extrapolated to their effects on microbial superbugs [150]. Phytophenolic bioactive substances can disrupt regular cellular membrane communication, cause cellular components to coagulate, and alter different cellular pathways, all of which might eventually result in microbial death.

The study of the effectiveness of Lactobacillus and phytophenols in reducing high-fat diet-induced mTOR activation in rats provides insights into the modulation of cellular pathways by phytophenols, which could be relevant for understanding their effects on microbial cells [151]. The synthesis of a cardanol-based levelling agent as a biodegradable alternative to synthetic surfactants underscores the potential of plant-derived and biodegradable surfactants, which could have implications for the development of phytophenolic derivatives as antimicrobial agents [152, 153].

The opioid receptor activation that triggers the downregulation of cAMP improves the effectiveness of anticancer drugs, highlighting the potential for synergistic effects between phytophenolic derivatives and chemotherapeutics in combating cancer cells [154]. The radical scavenging activity of dietary phytophenols in combination with coantioxidants provides insights into the antioxidant properties of phytophenolic derivatives, which could be relevant in understanding their potential mechanisms of action against microbial superbugs [155].

3 Conclusions

Phytoactives, which are chemicals derived from plants, have been used to treat a wide variety of infectious diseases, with encouraging results. They have even shown antibacterial activity against a good number of human infections. A few of these chemicals not only exhibited antibacterial effects but also altered bacterial resistance to antimicrobial agents. Antimicrobial polyphenols have shown promise, but additional research is needed to confirm their activity pathways and stability. The move from in vitro to in vivo drug testing has hindered the development of new phytochemicals to attack microbial superbugs.