Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes

The rapid diagnosis of pathogenic infections plays a vital role in disease prevention, control, and public health safety. Recombinase-aided amplification (RAA) is an innovative isothermal nucleic acid amplification technology capable of fast DNA or RNA amplification at low temperatures. RAA offers advantages such as simplicity, speed, precision, energy efficiency, and convenient operation. This technology relies on four essential components: recombinase, single-stranded DNA-binding protein (SSB), DNA polymerase, and deoxyribonucleoside triphosphates, which collectively replace the laborious thermal cycling process of traditional polymerase chain reaction (PCR). In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) system, a groundbreaking genome engineering tool, has garnered widespread attention across biotechnology, agriculture, and medicine. Increasingly, researchers have integrated the recombinase polymerase amplification system (or RAA system) with CRISPR technology, enabling more convenient and intuitive determination of detection results. This integration has significantly expanded the application of RAA in pathogen detection. The step-by-step operation of these two systems has been successfully employed for molecular diagnosis of pathogenic microbes, while the single-tube one-step method holds promise for efficient pathogen detection. This paper provides a comprehensive review of RAA combined with CRISPR-Cas and its applications in pathogen detection, aiming to serve as a valuable reference for further research in related fields.

Silver Nanoparticles of Artemisia sieberi Extracts: Chemical Composition and Antimicrobial Activities

BACKGROUND

Artemisia sieberi (mugwort) is a member of the daisy family Asteraceae and is widely propagated in Saudi Arabia. A. sieberi has historical medical importance in traditional societies. The current study aimed to assess the antibacterial and antifungal characteristics of the aqueous and ethanolic extracts of A. sieberi. In addition, the study investigated the effect of silver nanoparticles (AgNPs) synthesized from the A. sieberi extract.

METHODS

The ethanolic and aqueous extracts and AgNPs were prepared from the shoots of A. sieberi. The characteristics of AgNPs were assessed by UV-visible spectroscopy, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and dynamic light scattering (DLS). The antibacterial experiments were performed against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa. The fungal species used were Candida parapsilosis, Candida krusei, Candida famata, Candida rhodotorula, and Candida albicans. The antibacterial and antifungal characteristics were evaluated by measuring the diameter of growing organisms in Petri dishes treated with different concentrations of either extracts or AgNPs compared to the untreated controls. Furthermore, TEM imaging was used to investigate any ultrastructure changes in the microbes treated with crude extracts and AgNO₃.

RESULTS

The ethanolic and aqueous extracts significantly decreased the growth of E. coli, S. aureus, and B. subtilis (p < 0.001), while P. aeruginosa was not affected. Unlike crude extracts, AgNPs had more substantial antibacterial effects against all species. In addition, the mycelial growth of C. famata was reduced by the treatment of both extracts. C. krusei mycelial growth was decreased by the aqueous extract, while the growth of C. parapsilosis was affected by the ethanolic extract and AgNPs (p < 0.001). None of the treatments affected the growth of C. albicans or C. rhodotorula. TEM analysis showed cellular ultrastructure changes in the treated S. aureus and C. famata compared to the control.

CONCLUSION

The biosynthesized AgNPs and extracts of A. sieberi have a potential antimicrobial characteristic against pathogenic bacterial and fungal strains and nullified resistance behavior.

Akkermansia muciniphila Associated with Improved Linear Growth among Young Children, Democratic Republic of the Congo

To investigate the association between enteric pathogens, fecal microbes, and child growth, we conducted a prospective cohort study of 236 children <5 years of age in rural eastern Democratic Republic of the Congo. We analyzed baseline fecal specimens by quantitative PCR and measured child height and weight at baseline and growth at a 6-month follow-up. At baseline, 66% (156/236) of children had >3 pathogens in their feces. We observed larger increases in height-for-age-z-scores from baseline to the 6-month follow-up among children with Akkermansia muciniphila in their feces (coefficient 0.02 [95% CI 0.0001-0.04]; p = 0.04). Children with Cryptosporidium in their feces had larger declines in weight-for-height/length z-scores from baseline to the 6-month follow-up (coefficient -0.03 [95% CI -0.05 to -0.005]; p = 0.02). Our study showed high prevalence of enteric pathogens among this pediatric cohort and suggests A. muciniphila can potentially serve as a probiotic to improve child growth.

Biofloc Microbiome With Bioremediation and Health Benefits

The biofloc system has recently attracted great attention as a cost-effective, sustainable, and environmentally friendly technology and expected to contribute toward human food security (Zero Hunger SDG 2). It is also expected that this endeavor can be adopted widely because of its characteristics of zero water exchange and reduced artificial feeding features. In the biofloc system, the flocs which are generally formed by aggregation of heterotrophic microorganisms, serve as natural bioremediation candidates. These microbes effectively maintain water quality by utilizing the nutrient wastes, mostly originated from digested, unconsumed, and metabolic processes of feed. Additionally, the flocs are important sources of nutrients, mainly a protein source, and when these are consumed by aquaculture animals they improve the growth performance, immunity, and disease tolerance of host against pathogenic microbial infection. Here in this review, we focus on recent advances that could provide a mechanistic insight on how the microbial community developed in the biofloc system helps in the bioremediation process and enhances the overall health of the host. We have also tried to address the possible role of these microbial communities against growth and virulence of pathogenic microbes.

Pathogenic Microbes Increase Plant Dependence on Arbuscular Mycorrhizal Fungi: A Meta-Analysis

Numerous studies have confirmed that arbuscular mycorrhizal fungi (AMF) can promote plant nitrogen and phosphorus absorption, and prime systemic plant defense to plant pathogenic microbes. Despite that, the information on the interaction between AMF and plant pathogenic microbes is limited, especially the influence of plant pathogenic microbes on the effect of AMF promoting plant growth. In this study, 650 independent paired-wise observations from 136 published papers were collected and used to calculate the different effect of AMF with plant pathogenic microbes (DAPP) in promoting plant growth through meta-analysis. The results showed that AMF had a higher effect size on plant growth with pathogenic microbes comparing to without pathogenic microbes, including the significant effects in shoot and total fresh biomass, and shoot, root, and total dry biomass. The results of the selection models revealed that the most important factor determining the DAPP on plant dry biomass was the harm level of plant pathogenic microbes on the plant dry biomass, which was negatively correlated. Furthermore, the change of AMF root length colonization (RLC) was the sub-important factor, which was positively correlated with the DAPP. Taken together, these results have implications for understanding the potential and application of AMF in agroecosystems.

An Eco-Friendly Approach to the Control of Pathogenic Microbes and Anopheles stephensi Malarial Vector Using Magnesium Oxide Nanoparticles (Mg-NPs) Fabricated by Penicillium chrysogenum

The discovery of eco-friendly, rapid, and cost-effective compounds to control diseases caused by microbes and insects are the main challenges. Herein, the magnesium oxide nanoparticles (MgO-NPs) are successfully fabricated by harnessing the metabolites secreted by Penicillium chrysogenum. The fabricated MgO-NPs were characterized using UV-Vis, XRD, TEM, DLS, EDX, FT-IR, and XPS analyses. Data showed the successful formation of crystallographic, spherical, well-dispersed MgO-NPs with sizes of 7-40 nm at a maximum wavelength of 250 nm. The EDX analysis confirms the presence of Mg and O ions as the main components with weight percentages of 13.62% and 7.76%, respectively. The activity of MgO-NPs as an antimicrobial agent was investigated against pathogens Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, and Candida albicans, and exhibited zone of inhibitions of 12.0 ± 0.0, 12.7 ± 0.9, 23.3 ± 0.8, 17.7 ± 1.6, and 14.7 ± 0.6 mm respectively, at 200 µg mL-1. The activity is decreased by decreasing the MgO-NPs concentration. The biogenic MgO-NPs exhibit high efficacy against different larvae instar and pupa of Anopheles stephensi, with LC50 values of 12.5-15.5 ppm for I-IV larvae instar and 16.5 ppm for the pupa. Additionally, 5 mg/cm2 of MgO-NPs showed the highest protection percentages against adults of Anopheles stephensi, with values of 100% for 150 min and 67.6% ± 1.4% for 210 min.

Endophytic Bacteria Enterobacter hormaechei Fabricated Silver Nanoparticles and Their Antimicrobial Activity

Antimicrobial resistance (AMR), one of the greatest issues for humankind, draws special attention to the scientists formulating new drugs to prevent it. Great emphasis on the biological synthesis of silver nanoparticles (AgNPs) for utilization in single or combinatorial therapy will open up new avenues to the discovery of new antimicrobial drugs. The purpose of this study was to synthesize AgNPs following a green approach by using an endophytic bacterial strain, Enterobacter hormaechei, and to assess their antimicrobial potential against five pathogenic and four multidrug-resistant (MDR) microbes. UV-Vis spectroscopy, fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX), and zeta potential (ζ) were used to characterize the synthesized AgNPs. Endophytic E. hormaechei-mediated AgNPs (Eh-AgNPs) were represented by a strong UV-Vis absorbance peak at 418 nm within 5 min, forming spherical and polydispersed nanoparticles in the size range of 9.91 nm to 92.54 nm. The Eh-AgNPs were moderately stable with a mean ζ value of -19.73 ± 3.94 mV. The presence of amine, amide, and hydroxyl functional groups was observed from FTIR analysis. In comparison to conventional antibiotics, the Eh-AgNPs were more effective against Bacillus cereus (ATCC 10876) and Candida albicans (ATCC 10231), exhibiting 9.14 ± 0.05 mm and 8.24 ± 0.05 mm zones of inhibition (ZOIs), respectively, while displaying effective inhibitory activity with ZOIs ranging from 10.98 ± 0.08 to 13.20 ± 0.07 mm against the MDR bacteria. Eh-AgNP synthesis was rapid and eco-friendly. The results showed that Eh-AgNPs are promising antimicrobial agents that can be used in the development and formulation of new drugs to curb the menace of antimicrobial resistance in pathogenic and MDR microbes.

Silver Nanoparticles Synthesized by Using the Endophytic Bacterium Pantoea ananatis are Promising Antimicrobial Agents against Multidrug Resistant Bacteria

Antibiotic resistance is one of the most important global problems currently confronting the world. Different biomedical applications of silver nanoparticles (AgNPs) have indicated them to be promising antimicrobial agents. In the present study, extracellular extract of an endophytic bacterium, Pantoea ananatis, was used for synthesis of AgNPs. The synthesized AgNPs were characterized by UV⁻Vis spectroscopy, FTIR, transmission electron microscopy (TEM), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX), and Zeta potential. The antimicrobial potential of the AgNPs against pathogenic Staphylococcus aureus subsp. aureus (ATCC 11632), Bacillus cereus (ATCC 10876), Escherichia coli (ATCC 10536), Pseudomonas aeruginosa (ATCC 10145) and Candida albicans (ATCC 10231), and multidrug resistant (MDR) Streptococcus pneumoniae (ATCC 700677), Enterococcus faecium (ATCC 700221) Staphylococcus aureus (ATCC 33592) Escherichia coli (NCTC 13351) was investigated. The synthesized spherical-shaped AgNPs with a size range of 8.06 nm to 91.32 nm exhibited significant antimicrobial activity at 6 μg/disc concentration against Bacillus cereus (ATCC 10876) and Candida albicans (ATCC 10231) which were found to be resistant to conventional antibiotics. The synthesized AgNPs showed promising antibacterial efficiency at 10 µg/disc concentration against the MDR strains. The present study suggests that AgNPs synthesized by using the endophytic bacterium P. ananatis are promising antimicrobial agent.

Microbes, Transmission Routes and Survival Outside the Body

Microbes like bacteria, virus, parasites and fungi may naturally colonize skin and mucous membranes without any sign of illness, for a longer or shorter period, in all humans, animals, fish, parasites, plants and all other living beings. Some types may be more invasive in human tissue than others. Many microbes are free-living in the environment—in water, soil and air and on equipment—as a part of the normal microbial flora on the Earth. Most of them are not dangerous and live in peaceful symbiosis with other living beings and may also be transferred between living species, from man to animal or man to plants and environment—and vice versa. New and old human pathogenic microbes are increasing all over the world. Some agents, like drug-resistant bacteria and highly pathogenic viruses, are more dangerous than others, and some microbes may cause chronic devastating diseases. Transmission routes depend on the robustness of the microbe in the environment, virulence, infectious dose, anatomical site in the body, etc. Pathogenic microbes are spread by contact, air, water, food, beverages, contaminated equipment and environment and are more seldom vector-borne, by insects or animals. The following chapter is focused on the most frequent pathogenic microbes, their preselected localization in the body, transmission routes and survival in the environment.