Exploring a phage-based real-time PCR assay for diagnosing Acinetobacter baumannii bloodstream infections with high sensitivity

Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics

Bacteriophages, as abundant and specific agents, hold significant promise as a solution to combat the growing threat of antimicrobial resistance. Their unique ability to selectively lyse bacterial cells without harming humans makes them a compelling alternative to traditional antibiotics and point-of-care diagnostics. The article reviews the current landscape of diagnostic technologies, identify gaps and highlight emerging possibilities demonstrates a comprehensive approach to advancing clinical diagnosis of microbial pathogens and covers an overview of existing phage-based bioassays. Overall, the provided data in this review effectively communicates the potential of bacteriophages in transforming therapeutic and diagnostic paradigms, offering a holistic perspective on the benefits and opportunities they present in combating microbial infections and enhancing public health.

Phage amplification coupled with loop-mediated isothermal amplification (PA-LAMP) for same-day detection of viable Salmonella Enteritidis in raw poultry meat

Salmonella Enteritidis is the main serotype responsible for human salmonellosis in the European Union. One of the main sources of Salmonella spp. in the food chain are poultry products, such as eggs or chicken meat. In recent years, molecular methods have become an alternative to culture dependent methods for the rapid screening of Salmonella spp. In this work, the strain S. Enteritidis S1400, and previously isolated and characterized bacteriophage PVP-SE2, were used to develop and evaluate a same-day detection method combining Phage Amplification and Loop-mediated isothermal amplification (PA-LAMP) to specifically detect viable S. Enteritidis in chicken breast. This method is based on the detection of the phage DNA rather than bacterial DNA. The virus is added to the sample during pre-enrichment in buffered peptone water, where it replicates in the presence of viable S. Enteritidis. The detection of phage DNA allows, on the one hand to detect viable bacteria, since viruses only replicate in them, and on the other hand to increase the sensitivity of the method since for each infected S. Enteritidis cell, hundreds of new viruses are produced. Two different PA-LAMP detection strategies were evaluated, a real time fluorescence and a naked-eye detection. The present method could down to 0.2 fg/μL of pure phage DNA and a concentration of viral particles of 2.2 log PFU/mL. After a short Salmonella recovery step of 3 h and a co-culture of 4 h of the samples with phage particles, both real-time fluorescence and naked-eye method showed a LoD95 of 6.6 CFU/25 g and a LoD50 of 1.5/25 g in spiked chicken breast samples. The entire detection process, including DNA extraction and LAMP analysis, can be completed in around 8 h. In the current proof-of-concept, the novel PA-LAMP obtained comparable results to those of the reference method ISO 6579, to detect Salmonella Enteritidis in poultry meat.

CRISPR/Cas12a-mediated Enzymatic recombinase amplification for rapid visual quantitative authentication of halal food

Economically motivated adulteration (EMA) has become a concern in food safety. We propose a CRISPR/Cas12a Mediated Enzymatic Recombinase Amplification detection system (CAMERA) that integrates Enzymatic Recombinase Amplification (ERA) and Cas12a cleavage to detect halal food adulteration. We designed and screened crRNA targeting CLEC, a porcine-specific nuclear single-copy gene, and optimized the reagent concentrations and incubation times for the ERA and Cas12a cleavage steps. CAMERA was highly specific for pork ingredients detection. The DNA concentration and fluorescence signal intensity relationship was linear at DNA concentrations of 20-0.032 ng/μL. CAMERA detected as few as two CLEC copies and quantified samples with porcine DNA content as low as 5% within 25 min. The system could be operated in a miniaturized working mode that requires no technical expertise or professional equipment, making CAMERA a valuable tool in resource-limited areas for the qualitative and quantitative detection of pork ingredients in halal food.

Developing a multiplex PCR-based assay kit for bloodstream infection by analyzing genomic big data

BACKGROUND

In recent years, the incidence of bloodstream infections (BSI) has increased, the composition of pathogenic bacteria has changed, and drug resistance among bacteria has gradually increased due to the widespread use of interventional techniques, broad-spectrum antibacterial drugs, hormones, and immunosuppressive agents. Here, we have developed a multiplex PCR assay kit for the detection of pathogens (14 Gram-negative bacteria, 15 Gram-positive bacteria, and 4 fungi) in whole blood from patients with BSI using five-color fluorescent multiplex PCR followed by capillary electrophoresis. Our assay exhibits a diagnosis of higher quality and an improved detection rate for common pathogens.

METHODS

A local genome DNA database of 33 pathogenic bacteria was constructed. Next, "Exhaustive" primer search of the full coding sequence of the reference genomes of these bacteria was performed. Panels with minimal interactions between primers and amplicons were selected by random sampling and testing by a recursive algorithm. Primers and Mg²⁺ concentrations and PCR reaction procedures were optimized to maximize the detection efficacy.

RESULTS

The LOD of the kit was determined as 100 copies/μl. Using clinical samples, results generated by this kit and regular blood culture method were found to be 95.08% consistent. Additionally, six pathogens which were unidentifiable by blood culture were successfully detected by this kit.

CONCLUSION

Our study provided a bioinformatics approach to the challenge of primer design in multiplex PCR, and combined with optimized wet lab practice, a multiplex PCR-based assay kit for BSI with higher sensitivity and accuracy than blood culture was produced.

Bactericidal Synergism between Phage YC#06 and Antibiotics: a Combination Strategy to Target Multidrug-Resistant Acinetobacter baumannii In Vitro and In Vivo

Phage-antibiotic combination (PAC) therapy is a potential new alternative to treat infections caused by pathogenic bacteria, particularly those caused by antibiotic-resistant bacteria. In the present study, phage YC#06 against highly multidrug-resistant Acinetobacter baumannii 4015 was isolated, identified, and characterized. Compared with antibiotics alone, the time-kill experiments in vitro showed that YC#06 and antibiotic mixtures that include the chloramphenicol, imipenem, and cefotaxime combination could produce phage-antibiotic synergy (PAS), which reduced the ultimate effective concentration of antibiotics. No phage-resistant bacteria have been isolated during the whole time-kill experiments in vitro. Of note, PAS was dose dependent, requiring a moderate phage dose to achieve maximum PAS effect. In addition, PAS could effectively inhibit biofilm formation and remove mature biofilms in vitro. Furthermore, PAS between the combination of YC#06 and antibiotic mixtures in vivo was validated using a zebrafish infection model. Overall, the results of this study demonstrate that PAC could be a viable strategy to treat infection caused by high-level multidrug-resistant Acinetobacter baumannii or other drug-resistant bacteria through switching to other types of phage and antibiotic mixtures.

IMPORTANCE The treatment of multidrug-resistant bacterial infection is an urgent clinical problem. The combination of bacteriophages and antibiotics could produce synergistic bactericidal effects, which could reduce the emergence of antibiotic resistance and antibiotic consumption in antibiotic-sensitive bacteria, restore efficacy to antibiotics in antibiotic-resistant bacteria, and prevent the occurrence of phage-resistant bacteria. Phage-antibiotic combination (PAC) might be a potential new alternative for clinical treatment of multidrug-resistant bacterial infections.

Evaluation of a direct phage DNA detection-based Taqman qPCR methodology for quantification of phage and its application in rapid ultrasensitive identification of Acinetobacter baumannii

Background

Rapid phage enumeration/quantitation and viable bacteria determination is critical for phage application and treatment of infectious patients caused by the pathogenic bacteria.

Methods

In the current study, a direct phage DNA detection-based Taqman qPCR methodology for quantification of phage P53 and rapid ultrasensitive identification of Acinetobacter baumannii (A. baumannii) was evaluated.

Results

The assay was capable of quantifying P53 phage DNA without DNA extraction and the detection limit of the assay was 550 PFU/mL. The agreement bias between the quantitative results of three different phage concentrations in this assay and double agar overlay plaque assay were under 3.38%. Through the built detection system, down to 1 log CFU/mL of viable A. baumannii can be detected within 4 h in A. baumannii spiked swab and bronchoalveolar lavage fluid samples. Compared with the Taqman qPCR that targets the conserved sequence of A. baumannii, the sensitivity of the assay built in this study could increase four orders of magnitude.

Conclusions

The methodology offers a valid alternative for enumeration of freshly prepared phage solution and diagnosis of bacterial infection caused by A. baumannii or other bacterial infection in complicated samples through switching to phages against other bacteria. Furthermore, the assay could offer drug adjustment strategy timely owing to the detection of bacteria vitality.

Phage-based technologies for highly sensitive luminescent detection of foodborne pathogens and microbial toxins: A review

Foodborne pathogens and microbial toxins are the main causes of foodborne illness. However, trace pathogens and toxins in foods are difficult to detect. Thus, techniques for their rapid and sensitive identification and quantification are urgently needed. Phages can specifically recognize and adhere to certain species of microbes or toxins due to molecular complementation between capsid proteins of phages and receptors on the host cell wall or toxins, and thus they have been successfully developed into a detection platform for pathogens and toxins. This review presents an update on phage-based luminescent detection technologies as well as their working principles and characteristics. Based on phage display techniques of temperate phages, reporter gene detection assays have been designed to sensitively detect trace pathogens by luminous intensity. By the host-specific lytic effects of virulent phages, enzyme-catalyzed chemiluminescent detection technologies for pathogens have been exploited. Notably, these phage-based luminescent detection technologies can discriminate viable versus dead microbes. Further, highly selective and sensitive immune-based assays have been developed to detect trace toxins qualitatively and quantitatively via antibody analogs displayed by phages, such as phage-ELISA (enzyme-linked immunosorbent assay) and phage-IPCR (immuno-polymerase chain reaction). This literature research may lead to novel and innocuous phage-based rapid detection technologies to ensure food safety.

Dual-signal lateral flow assay using vancomycin-modified nanotags for rapid and sensitive detection of Staphylococcus aureus

This paper reports a colorimetric-fluorescent dual-signal lateral flow assay (LFA) based on vancomycin (Van)-modified SiO2-Au-QD tags for sensitive and quantitative detection of Staphylococcus aureus (S. aureus). The combination of high-performance Van-tags and detection antibodies integrated into the LFA system produced assays with high sensitivity and specificity. The visualization limit of the colorimetric signal and the detection limit of the fluorescence signal of the proposed method for S. aureus can reach 104 and 100 cells mL-1, respectively.

A universal SERS-label immunoassay for pathogen bacteria detection based on Fe3O4@Au-aptamer separation and antibody-protein A orientation recognition

Rapid, reliable and sensitive detection methods for pathogenic bacteria are strongly demanded. Herein, we proposed a magnetically assisted surface enhanced Raman scattering (SERS)-label immunoassay for the sensitive detection of bacteria by using a universal approach based on free antibody labelling and staphylococcus proteins A (PA)-SERS tags orientation recognition. The SERS biosensor consists of two functional nanomaterials: aptamer-conjugated Fe₃O₄@Au magnetic nanoparticles (MNPs) as magnetic SERS platform for pathogen enrichment and PA modified-SERS tags (Au@DTNB@PA) as a universal probe for target bacteria quantitative detection. After target bacteria enriched, free antibody was used to specific marking target bacteria and provided numerous Fc fragment, which can guide the PA-SERS tags orientation-dependent binding. With this strategy, Fe₃O₄@Au/bacteria/SERS tags sandwich immunocomplexes for most bacteria (expect several species of Staphylococcus) were easy constructed. The limits of detection (LODs) of the proposed assay were found to be 10, 10, and 25 cells/mL for three common pathogens Escherichia coli (E. coli), Listeria monocytogenes (L. mono), and Salmonella typhimurium (S. typhi), respectively, in real food samples. The universal method also exhibits the advantages of rapid, robust, and easy to operate, suggesting its great potential for food safety monitoring and infectious diseases diagnosis.

A Proof of Principle for the Detection of Viable Brucella spp. in Raw Milk by qPCR Targeting Bacteriophages

Brucellosis is still a global health issue, and surveillance and control of this zoonotic disease in livestock remains a challenge. Human outbreaks are mainly linked to the consumption of unpasteurized dairy products. The detection of human pathogenic Brucella species in food of animal origin is time-consuming and laborious. Bacteriophages are broadly applied to the typing of Brucella isolates from pure culture. Since phages intracellularly replicate to very high numbers, they can also be used as specific indicator organisms of their host bacteria. We developed a novel real-time PCR (qPCR) assay targeting the highly conserved helicase sequence harbored in all currently known Brucella-specific lytic phages. Quality and performance tests determined a limit of detection of <1 genomic copy/µL. In raw milk artificially contaminated with Brucella microti, Iz_v phages were reliably detected after 39 h of incubation, indicating the presence of viable bacteria. The qPCR assay showed high stability in the milk matrix and significantly shortened the time to diagnosis when compared to traditional culture-based techniques. Hence, our molecular assay is a reliable and sensitive method to analyze phage titers, may help to reduce the hands-on time needed for the screening of potentially contaminated food, and reveals infection risks without bacterial isolation.

Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review

Bacteria will likely become our most significant enemies of the 21st century, as we are approaching a post-antibiotic era. Bacteriophages, viruses that infect bacteria, allow us to fight infections caused by drug-resistant bacteria and create specific, cheap, and stable sensors for bacteria detection. Here, we summarize the recent developments in the field of phage-based methods for bacteria detection. We focus on works published after mid-2017. We underline the need for further advancements, especially related to lowering the detection (below 1 CFU/mL; CFU stands for colony forming units) and shortening the time of analysis (below one hour). From the application point of view, portable, cheap, and fast devices are needed, even at the expense of sensitivity.

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.

Bacteriophages as Potential Tools for Detection and Control of Salmonella spp. in Food Systems

The global problem of antibiotic resistance in bacteria is quickly developing in most antibiotics used in hospitals and livestock. Recently, the infections with multi-drug resistant (MDR) bacteria become a major cause of death worldwide. Current antibiotics are not very effective in treating MDR Salmonella infections, which have become a public health threat. Therefore, novel approaches are needed to rapidly detect and effectively control antibiotic-resistant pathogens. Bacteriophages (phages) have seen renewed attention for satisfying those requirements due to their host-specific properties. Therefore, this review aims to discuss the possibility of using phages as a detection tool for recognizing bacterial cell surface receptors and an alternative approach for controlling antibiotic-resistant pathogens in food systems.

Continuous-Flow Separation and Efficient Concentration of Foodborne Bacteria from Large Volume Using Nickel Nanowire Bridge in Microfluidic Chip

Separation and concentration of target bacteria has become essential to sensitive and accurate detection of foodborne bacteria to ensure food safety. In this study, we developed a bacterial separation system for continuous-flow separation and efficient concentration of foodborne bacteria from large volume using a nickel nanowire (NiNW) bridge in the microfluidic chip. The synthesized NiNWs were first modified with the antibodies against the target bacteria and injected into the microfluidic channel to form the NiNW bridge in the presence of the external arc magnetic field. Then, the large volume of bacterial sample was continuous-flow injected to the channel, resulting in specific capture of the target bacteria by the antibodies on the NiNW bridge to form the NiNW–bacteria complexes. Finally, these complexes were flushed out of the channel and concentrated in a lower volume of buffer solution, after the magnetic field was removed. This bacterial separation system was able to separate up to 74% of target bacteria from 10 mL of bacterial sample at low concentrations of ≤10² CFU/mL in 3 h, and has the potential to separate other pathogenic bacteria from large volumes of food samples by changing the antibodies.