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Wahid B, Tiwana MS. Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics. Future Microbiol 2024; 19:811-824. [PMID: 38900594 PMCID: PMC11290765 DOI: 10.2217/fmb-2023-0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/01/2024] [Indexed: 06/22/2024] Open
Abstract
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.
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Affiliation(s)
- Braira Wahid
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton VIC Australia
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2
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Paul SS. Phage engineering for development of diagnostic tools. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:91-101. [PMID: 37739561 DOI: 10.1016/bs.pmbts.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The bacteriophages rely on the host cell to provide energy and resources for their own replication. Antibody-based diagnostic tests rely on the antibody and the biomarker interactions. Since, most of these diagnostic tools employ the use of antibodies; hence, they require intensive storage protocols at cold conditions and incur high time and capital cost due to their production and purification process. Phage-based diagnostics can overcome this limitation. Bacteriophages, have been used as emerging tools for the detection of various pathogens. Rapid phage-mediated detection assays have become commercial diagnostic tools. Conventional method and new cloning approaches have been followed to specifically detect a disease- causing microbial strains. This review discusses use of Phage typing as diagnostic tools, phage-based detection methods, and their usage for signal amplification. Design rules for reporter phage engineering are also discussed followed by different engineering platforms for phage genome editing. We also discuss recent examples of how phage research is influencing the recent advances in the development of phage-based diagnostics for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays.
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3
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Braun P, Raab R, Bugert JJ, Braun S. Recombinant Reporter Phage rTUN1:: nLuc Enables Rapid Detection and Real-Time Antibiotic Susceptibility Testing of Klebsiella pneumoniae K64 Strains. ACS Sens 2023; 8:630-639. [PMID: 36719711 PMCID: PMC9972469 DOI: 10.1021/acssensors.2c01822] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The emergence of multi-drug-resistant Klebsiella pneumoniae (Kp) strains constitutes an enormous threat to global health as multi-drug resistance-associated treatment failure causes high mortality rates in nosocomial infections. Rapid pathogen detection and antibiotic resistance screening are therefore crucial for successful therapy and thus patient survival. Reporter phage-based diagnostics offer a way to speed up pathogen identification and resistance testing as integration of reporter genes into highly specific phages allows real-time detection of phage replication and thus living host cells. Kp-specific phages use the host's capsule, a major virulence factor of Kp, as a receptor for adsorption. To date, 80 different Kp capsule types (K-serotypes) have been described with predominant capsule types varying between different countries and continents. Therefore, reporter phages need to be customized according to the locally prevailing variants. Recently, we described the autographivirus vB_KpP_TUN1 (TUN1), which specifically infects Kp K64 strains, the most predominant capsule type at the military hospital in Tunis (MHT) that is also associated with high mortality rates. In this work, we developed the highly specific recombinant reporter phage rTUN1::nLuc, which produces nanoluciferase (nLuc) upon host infection and thus enables rapid detection of Kp K64 cells in clinical matrices such as blood and urine. At the same time, rTUN1::nLuc allows for rapid antibiotic susceptibility testing and therefore identification of suitable antibiotic treatment in less than 3 h.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
| | - Rene Raab
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
| | | | - Simone Braun
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
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Ding Y, Huang C, Chen M, Wang J, Shao Y, Wang X. Rapid and simultaneous detection of viable S. aureus and its penicillin susceptibility by phage amplification techniques in different food matrices. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Yang X, Wang Y, Liu Y, Huang J, Wei X, Tan Q, Zeng X, Ying X, Li S. Rapid, ultrasensitive, and highly specific identification of Brucella abortus utilizing multiple cross displacement amplification combined with a gold nanoparticles-based lateral flow biosensor. Front Microbiol 2022; 13:1071928. [PMID: 36523830 PMCID: PMC9744775 DOI: 10.3389/fmicb.2022.1071928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 10/28/2023] Open
Abstract
Brucella abortus (B. abortus) as an important infectious agent of bovine brucellosis cannot be ignored, especially in countries/regions dominated by animal husbandry. Thus, the development of an ultrasensitive and highly specific identification technique is an ideal strategy to control the transmission of bovine brucellosis. In this report, a novel detection protocol, which utilizes multiple cross displacement amplification (MCDA) combined with a gold nanoparticles-based lateral flow biosensor (AuNPs-LFB) targeting the BruAb2_0168 gene was successfully devised and established for the identification of B. abortus (termed B. abortus-MCDA-LFB). Ten specific primers containing engineered C1-FAM (carboxyfluorescein) and D1-biotin primers were designed according to the MCDA reaction mechanism. These genomic DNA extracted from various bacterial strains and whole blood samples were used to optimize and evaluate the B. abortus-MCDA-LFB assay. As a result, the optimal reaction conditions for the B. abortus-MCDA-LFB assay were 66°C for 40 min. The limit of detection of the B. abortus-MCDA-LFB was 10 fg/μl (~3 copies/μl) for genomic DNA extracted from pure cultures of B. abortus isolate. Meanwhile, the B. abortus-MCDA-LFB assay accurately identified all tested B. abortus strains, and there was no cross-reaction with non-B. abortus pathogens. Moreover, the detection workflow of the B. abortus-MCDA-LFB assay for whole blood samples can be completed within 70 min, and the cost of a single test is approximately 5.0 USD. Taken together, the B. abortus-MCDA-LFB assay is a visual, fast, ultrasensitive, low-cost, easy-to-operate, and highly specific detection method, which can be used as a rapid identification tool for B. abortus infections.
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Affiliation(s)
- Xinggui Yang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Yue Wang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Ying Liu
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Junfei Huang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Xiaoyu Wei
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Qinqin Tan
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Xiaoyan Zeng
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xia Ying
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Shijun Li
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, China
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6
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Luo J, Liu M, Wang P, Li Q, Luo C, Wei H, Hu Y, Yu J. 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. BMC Infect Dis 2022; 22:523. [PMID: 35672689 PMCID: PMC9172196 DOI: 10.1186/s12879-022-07493-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
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.
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Affiliation(s)
- Jun Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China. .,Central Laboratory, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, 443003, China. .,Yichang Central People's Hospital, Yichang, China.
| | - Min Liu
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.,Yichang Central People's Hospital, Yichang, China
| | - Peng Wang
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.,Yichang Central People's Hospital, Yichang, China
| | - Qianyuan Li
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.,Yichang Central People's Hospital, Yichang, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.,Yichang Central People's Hospital, Yichang, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Yuanyuan Hu
- Medical College, China Three Gorges University, Yichang, 443002, China.
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
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Sozhamannan S, Hofmann ER. The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. Viruses 2020; 12:v12121393. [PMID: 33291831 PMCID: PMC7762055 DOI: 10.3390/v12121393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Accurate pathogen detection and diagnosis is paramount in clinical success of treating patients. There are two general paradigms in pathogen detection: molecular and immuno-based, and phage-based detection is a third emerging paradigm due to its sensitivity and selectivity. Molecular detection methods look for genetic material specific for a given pathogen in a sample usually by polymerase chain reaction (PCR). Immuno-methods look at the pathogen components (antigens) by antibodies raised against that pathogen specific antigens. There are different variations and products based on these two paradigms with advantages and disadvantages. The third paradigm at least for bacterial pathogen detection entails bacteriophages specific for a given bacterium. Sensitivity and specificity are the two key parameters in any pathogen detection system. By their very nature, bacteriophages afford the best sensitivity for bacterial detection. Bacteria and bacteriophages form the predator-prey pair in the evolutionary arms race and has coevolved over time to acquire the exquisite specificity of the pair, in some instances at the strain level. This specificity has been exploited for diagnostic purposes of various pathogens of concern in clinical and other settings. Many recent reviews focus on phage-based detection and sensor technologies. In this review, we focus on a very special group of pathogens that are of concern in biodefense because of their potential misuse in bioterrorism and their extremely virulent nature and as such fall under the Centers for Disease and Prevention (CDC) Category A pathogen list. We describe the currently available phage methods that are based on the usual modalities of detection from culture, to molecular and immuno- and fluorescent methods. We further highlight the gaps and the needs for more modern technologies and sensors drawing from technologies existing for detection and surveillance of other pathogens of clinical relevance.
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Affiliation(s)
- Shanmuga Sozhamannan
- National Security Science & Technology, Management Advisory Services, Logistics Management Institute, 7940 Jones Branch Drive, Tysons, VA 22102, USA;
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense (CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), 110 Thomas Johnson Drive, Suite 250, Frederick, MD 21702, USA
| | - Edward R. Hofmann
- EXCET, Inc., 6225 Brandon Ave #360, Springfield, VA 22150, USA
- US Army Combat Capabilities Development Command, Chemical Biological Center, 8908 Guard St, E3831, Edgewood, MD 21010, USA
- Correspondence:
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A Proof of Principle for the Detection of Viable Brucella spp. in Raw Milk by qPCR Targeting Bacteriophages. Microorganisms 2020; 8:microorganisms8091326. [PMID: 32878169 PMCID: PMC7565414 DOI: 10.3390/microorganisms8091326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 01/15/2023] Open
Abstract
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, Izv 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.
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Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments. Viruses 2020; 12:v12090944. [PMID: 32858938 PMCID: PMC7552063 DOI: 10.3390/v12090944] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Fast and reliable detection of bacterial pathogens in clinical samples, contaminated food products, and water supplies can drastically improve clinical outcomes and reduce the socio-economic impact of disease. As natural predators of bacteria, bacteriophages (phages) have evolved to bind their hosts with unparalleled specificity and to rapidly deliver and replicate their viral genome. Not surprisingly, phages and phage-encoded proteins have been used to develop a vast repertoire of diagnostic assays, many of which outperform conventional culture-based and molecular detection methods. While intact phages or phage-encoded affinity proteins can be used to capture bacteria, most phage-inspired detection systems harness viral genome delivery and amplification: to this end, suitable phages are genetically reprogrammed to deliver heterologous reporter genes, whose activity is typically detected through enzymatic substrate conversion to indicate the presence of a viable host cell. Infection with such engineered reporter phages typically leads to a rapid burst of reporter protein production that enables highly sensitive detection. In this review, we highlight recent advances in infection-based detection methods, present guidelines for reporter phage construction, outline technical aspects of reporter phage engineering, and discuss some of the advantages and pitfalls of phage-based pathogen detection. Recent improvements in reporter phage construction and engineering further substantiate the potential of these highly evolved nanomachines as rapid and inexpensive detection systems to replace or complement traditional diagnostic approaches.
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10
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Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review. Viruses 2020; 12:v12080845. [PMID: 32756438 PMCID: PMC7472331 DOI: 10.3390/v12080845] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/09/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
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.
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Development and validation of immunoassay for whole cell detection of Brucella abortus and Brucella melitensis. Sci Rep 2020; 10:8543. [PMID: 32444793 PMCID: PMC7244763 DOI: 10.1038/s41598-020-65347-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/16/2020] [Indexed: 01/30/2023] Open
Abstract
Brucella is alpha-2 Proteobacteria mainly responsible for multi-factorial bacterial zoonotic disease brucellosis with low concentration (10–100 CFU) required to establish the infection. In this study, we developed sandwich ELISA with detection range of 102 to 108 cells mL−1 and limit of detection at 103 cells mL−1 by employing polyclonal rabbit IgG (capture antibody, 10 µg mL−1) and mice IgG (detection antibody, 50 µg mL−1) antibody for its detection. Surface Plasmon Resonance evaluated the interaction of detection antibody with whole cell spiked serum samples at LOD of 102 cells mL−1 along with non co-operative interaction of protein albumin. Further, kinetic evaluation study using detection antibody against cell envelope antigen was performed whereby, Equilibrium Dissociation Constant (KD) and Maximum Binding Capacity (Bmax) were found to be 16.48 pM and 81.67 m° for Brucella abortus S99 and 0.42 pM and 54.50 m° for Brucella melitensis 16 M, respectively. During interference study, sandwich ELISA assay cross-reacted with either of the polyclonal antibody of above Brucella species. Upon validation, no cross-reactivity observed with bacteria-closely related to Brucella. In conclusion, developed semi-quantitative sandwich immunoassay is sensitively rapid in whole cell detection of Brucella and will be useful in development of detection assays from environmental and clinical matrices.
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12
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Phage-Mediated Molecular Detection (PMMD): A Novel Rapid Method for Phage-Specific Bacterial Detection. Viruses 2020; 12:v12040435. [PMID: 32290520 PMCID: PMC7232155 DOI: 10.3390/v12040435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial infections pose a challenge to human health and burden the health care system, especially with the spread of antibiotic-resistant populations. To provide effective treatment and improved prognosis, effective diagnostic methods are of great importance. Here we present phage-mediated molecular detection (PMMD) as a novel molecular method for the detection and assessment of bacterial antibiotic resistance. This technique consists of a brief incubation, of approximately ten minutes, of the biological sample with a natural bacteriophage (phage) targeting the bacteria of interest. This is followed by total RNA extraction and RT-PCR. We applied this approach to Staphylococcus aureus (SA), a major causative agent of human bacterial infections. PMMD demonstrated a high sensitivity, rapid implementation, and specificity dependent on the phage host range. Moreover, due to the dependence of the signal on the physiological state of the bacteria, PMMD can discriminate methicillin-sensitive from methicillin-resistant SA (MSSA vs. MRSA). Finally, we extended this method to the detection and antibiotic sensitivity determination of other bacteria by proving PMMD efficacy for Bacillus anthracis.
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Li X, Zhao C, Liu Y, Li Y, Lian F, Wang D, Zhang Y, Wang J, Song X, Li J, Yang Y, Xu K. Fluorescence signal amplification assay for the detection of B. melitensis 16M, based on peptide-mediated magnetic separation technology and a AuNP-mediated bio-barcode assembled by quantum dot technology. Analyst 2019; 144:2704-2715. [PMID: 30864589 DOI: 10.1039/c9an00028c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the Brucella spp. are facultative intracellular bacteria that can cause global brucellosis, a zoonotic disease. Herein, a novel fluorescence signal amplification (FSA) method for the rapid detection of B. melitensis 16M was developed based on peptide-mediated magnetic separation (PMS) technology and Au nanoparticle (AuNP)-mediated bio-barcode assay technology assembled by quantum dots (QDs). The PMS technology was used to specifically capture and isolate B. melitensis 16M from food. The immunomagnetic bead-B. melitensis 16M bioconjugates (IMBs-B. melitensis 16M) were then identified by IgY on the surface of AuNPs and the oligonucleotide chains on the surface of the gold nanoparticles were hybridized with bio-barcodes assembled by quantum dots (QD-probe2). The IMB/B. melitensis 16M/IgY-AuNP-probe1/QD-probe2 bioconjugates were concentrated by magnetic separation. Therefore, as the concentration of B. melitensis 16M in the sample increased, the unbound QD-probe2 in the supernatant reduced, and the B. melitensis 16M in the sample could be indirectly measured by detecting the fluorescence in the supernatant. This FSA method can detect B. melitensis 16M concentration in the range of 10 to 106 cfu ml-1 without pre-enrichment, and the limit of detection (LOD) is as low as 10 cfu ml-1 with high specificity. Furthermore, the proposed method for the detection of B. melitensis 16M has a LOD of 1.07 × 102 cfu ml-1 and a linear range from 102 to 107 cfu ml-1 in milk, and a LOD of 1.72 × 102 cfu ml-1, and a linear range from 102 to 106 cfu ml-1 in lamb leach. In addition, this method takes less than 3 h to perform. Thus, the assay that was developed in this study shows promise for rapid, sensitive, and specific detection of B. melitensis 16M.
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Affiliation(s)
- Xinxin Li
- School of Public Health of Jilin University, Changchun, Jilin 130021, P. R. China.
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Characterization of circulating miRNA signature in water buffaloes (Bubalus bubalis) during Brucella abortus infection and evaluation as potential biomarkers for non-invasive diagnosis in vaginal fluid. Sci Rep 2019; 9:1945. [PMID: 30760784 PMCID: PMC6374377 DOI: 10.1038/s41598-018-38365-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/15/2018] [Indexed: 12/12/2022] Open
Abstract
Brucellosis is an infectious disease caused by bacteria from the Brucella genus that can be transmitted to humans through contact with infected animals or contaminated animal products. Brucellosis also causes financial losses in animal production. Ruminants are highly susceptible to brucellosis, and the causative agent water buffaloes (Bubalus bubalis) is Brucella abortus. Circulating microRNAs (miRNAs) are cropping up as promising biomarkers for several infectious diseases. The goals of this study were to characterize the serum miRNA signature associated with brucellosis in water buffaloes and investigate the miRNAs’ potential use as biomarkers in vaginal fluids. Next Generation Sequencing was used to assess miRNA expression profiles in Brucella-positive and Brucella-negative blood sera; dysregulated miRNAs in blood serum and vaginal fluids were validated using RT-qPCR. ROC curves were generated to evaluate the diagnostic value of miRNAs for Brucella. GO and KEGG pathway enrichment analyses were exploited to investigate the biological functions of dysregulated miRNAs. The results showed that 20 miRNAs were modulated, of which, 12 were upregulated and 8 were downregulated. These findings were corroborated by RT-qPCR, and ROC curves indicated that the miRNAs can serve as potential biomarkers for Brucella. GO and KEGG pathway analyses pointed out that some of these miRNAs are related to immune response and apoptosis. These results provided an overview of miRNA expression profiles and highlighted potential biomarkers for Brucella infection in water buffaloes. We also demonstrated the potential of vaginal fluids in studies involving microRNA detection. Further functional and mechanistic studies of these miRNAs may improve our understanding of the biological processes involved in Brucella infection and host immune response.
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15
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Hinkley TC, Singh S, Garing S, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. A phage-based assay for the rapid, quantitative, and single CFU visualization of E. coli (ECOR #13) in drinking water. Sci Rep 2018; 8:14630. [PMID: 30279488 PMCID: PMC6168599 DOI: 10.1038/s41598-018-33097-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/21/2018] [Indexed: 01/06/2023] Open
Abstract
Drinking water standards in the United States mandate a zero tolerance of generic E. coli in 100 mL of water. The presence of E. coli in drinking water indicates that favorable environmental conditions exist that could have resulted in pathogen contamination. Therefore, the rapid and specific enumeration of E. coli in contaminated drinking water is critical to mitigate significant risks to public health. To meet this challenge, we developed a bacteriophage-based membrane filtration assay that employs novel fusion reporter enzymes to fully quantify E. coli in less than half the time required for traditional enrichment assays. A luciferase and an alkaline phosphatase, both specifically engineered for increased enzymatic activity, were selected as reporter probes due to their strong signal, small size, and low background. The genes for the reporter enzymes were fused to genes for carbohydrate binding modules specific to cellulose. These constructs were then inserted into the E. coli-specific phage T7 which were used to infect E. coli trapped on a cellulose filter. During the infection, the reporters were expressed and released from the bacterial cells following the lytic infection cycle. The binding modules facilitated the immobilization of the reporter probes on the cellulose filter in proximity to the lysed cells. Following substrate addition, the location and quantification of E. coli cells could then be determined visually or using bioluminescence imaging for the alkaline phosphatase and luciferase reporters, respectively. As a result, a detection assay capable of quantitatively detecting E. coli in drinking water with similar results to established methods, but less than half the assay time was developed.
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Affiliation(s)
- Troy C Hinkley
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States
| | - Sangita Singh
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, United States
| | - Spencer Garing
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Anne-Laure M Le Ny
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Kevin P Nichols
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, United States
| | - Joey N Talbert
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, United States
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States.
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Luo J, Jiang M, Xiong J, Li J, Zhang X, Wei H, Yu J. Exploring a phage-based real-time PCR assay for diagnosing Acinetobacter baumannii bloodstream infections with high sensitivity. Anal Chim Acta 2018; 1044:147-153. [PMID: 30442396 DOI: 10.1016/j.aca.2018.09.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/14/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022]
Abstract
In the present study, we developed a phage-based real-time quantitative PCR (qPCR) methodology for sensitive diagnosis of bloodstream infection (BSI) caused by Acinetobacter baumannii (A. baumannii). An isolated A. baumannii phage p53 was used for Taqman qPCR through detecting phage replication in live A. baumannii cells in serum samples. At the phage concentration of 103 PFU/mL, the sensitive detection of A. baumannii (down to 10 CFU in 100 μL serum) has been obtained within 4 h in spiked serum samples without bacteria isolation and DNA extraction. Subsequent testing of 22 simulated serum samples spiked by different strains has shown that the results from the phage-based Taqman qPCR method have 100% agreement with the spiked concentrations of the bacteria. The assay built in this study, gathering all the advantages for detections of high rapidity, high sensitivity, good specificity, being able to detect only live bacteria not dead bacteria and no DNA extraction or purifications, can be developed to detecting other bacterial pathogens in serum or other complicated samples through switching to other types of phages and realize the rapid and sensitive detection of bacteria in BSI, which would potentially be applied for fast diagnosis in sepsis clinically.
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Affiliation(s)
- Jun Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China; University of Chinese Academy of Sciences, Beijing 100039, China; The First College of Clinical Medical Science, China Three Gorges University, Yichang, China; Yichang Central People's Hospital, China
| | - Mengwei Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jin Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Junhua Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China; The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
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18
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Richter Ł, Janczuk-Richter M, Niedziółka-Jönsson J, Paczesny J, Hołyst R. Recent advances in bacteriophage-based methods for bacteria detection. Drug Discov Today 2017; 23:448-455. [PMID: 29158194 DOI: 10.1016/j.drudis.2017.11.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022]
Abstract
Fast and reliable bacteria detection is crucial for lowering the socioeconomic burden related to bacterial infections (e.g., in healthcare, industry or security). Bacteriophages (i.e., viruses with bacterial hosts) pose advantages such as great specificity, robustness, toughness and cheap preparation, making them popular biorecognition elements in biosensors and other assays for bacteria detection. There are several possible designs of bacteriophage-based biosensors. Here, we focus on developments based on whole virions as recognition agents. We divide the review into sections dealing with phage lysis as an analytical signal, phages as capturing elements in assays and phage-based sensing layers, putting the main focus on development reported within the past three years but without omitting the fundamentals.
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Affiliation(s)
- Łukasz Richter
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marta Janczuk-Richter
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | | | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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19
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Viruses of Microbes. Viruses 2017; 9:v9090263. [PMID: 28930187 PMCID: PMC5618029 DOI: 10.3390/v9090263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 01/15/2023] Open
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