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Viruses
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Phage-Based Pathogen Detection
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Phage-Based Pathogen Detection

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 39735

Special Issue Editor

Prof. Dr. Lawrence Goodridge

E-Mail Website
Guest Editor
Department of Food Science, University of Guelph, Guelph, ON, Canada
Interests: food microbiology; food safety

Special Issue Information

Dear Colleagues,

Infectious bacterial agents are a major cause of morbidity and mortality worldwide. Diarrheal diseases are responsible for more than half of the global burden of foodborne diseases, causing 550 million people to fall ill and 230,000 deaths every year. In addition, the continued emergence of multidrug-resistant bacterial pathogens is a major public health threat. It is estimated that, by 2050, multidrug-resistant infections could cause up to 10 million deaths annually and cost the global economy US$100 trillion.

Conventional laboratory-based methods of bacterial detection and identification typically have long processing times, can lack sensitivity and specificity, and require specialized equipment and trained users. They are therefore costly and not available in all countries. Typically, specimens (e.g., blood, saliva, urine, or food samples) are collected and shipped to the laboratory for analysis, delaying the time for results to be obtained, and therefore limiting potential treatments or approaches to alleviate food contamination.

The use of bacteriophages (phages) and their products (endolysins, tail proteins) as bacterial diagnostic reagents has several advantages over traditional laboratory-based testing methods. For example, phage-based diagnostics is amenable for field deployment, reduce labor intensiveness, and can distinguish between viable and non-viable bacteria, which is a major shortcoming of current laboratory-based diagnostic methods.

In this Special Issue, we welcome the submission of original research articles and reviews covering, but not limited, to the most current research on the use of phages and/or their components to rapidly detect bacteria.

Prof. Dr. Lawrence Goodridge
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (5 papers)

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Research

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15 pages, 243 KiB  
Article
Development and Evaluation of a Sensitive Bacteriophage-Based MRSA Diagnostic Screen
by Matthew Brown, Wendy Hahn, Bryant Bailey, Alex Hall, Gema Rodriguez, Henriett Zahn, Marcia Eisenberg and Stephen Erickson
Viruses 2020, 12(6), 631; https://doi.org/10.3390/v12060631 - 11 Jun 2020
Cited by 8 | Viewed by 16393
Abstract
Engineered luciferase reporter bacteriophages provide specific, sensitive, rapid and low-cost detection of target bacteria and address growing diagnostic needs in multiple industries. Detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization and antibiotic susceptibility play a critical supportive role in preventing hospital-acquired infections and [...] Read more.
Engineered luciferase reporter bacteriophages provide specific, sensitive, rapid and low-cost detection of target bacteria and address growing diagnostic needs in multiple industries. Detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization and antibiotic susceptibility play a critical supportive role in preventing hospital-acquired infections and facilitating antibiotic stewardship. We describe the development and evaluation of a novel phage-based MRSA diagnostic screen for nasal swab specimens. The screen utilizes two luciferase reporter phages capable of recognizing genetically-diverse Staphylococcus aureus. The beta-lactam antibiotic cefoxitin is included to differentiate between resistant (MRSA) and susceptible organisms. The screen positively identified 97.7% of 390 clinical MRSA isolates at low bacterial concentrations. At higher inoculums, 93.5% of 123 clinical non-MRSA Staphylococcus aureus yielded appropriate negative results. Although cross-reactivity of the phage cocktail was observed with other staphylococcal and bacillus species, these false positives were absent under selective conditions. MRSA remained detectable in the presence of 38 distinct competing species and was accurately identified in 100% of 40 spiked nasal specimens. Thus, this six-hour screen sensitively detected MRSA both in vitro and in human nasal matrix. Full article
(This article belongs to the Special Issue Phage-Based Pathogen Detection)
13 pages, 2810 KiB  
Article
Phage-Mediated Molecular Detection (PMMD): A Novel Rapid Method for Phage-Specific Bacterial Detection
by Francisco Malagon, Luis A. Estrella, Michael G. Stockelman, Theron Hamilton, Nimfa Teneza-Mora and Biswajit Biswas
Viruses 2020, 12(4), 435; https://doi.org/10.3390/v12040435 - 11 Apr 2020
Cited by 12 | Viewed by 3444
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Phage-Based Pathogen Detection)
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Review

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18 pages, 1998 KiB  
Review
The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It’s Going
by Shanmuga Sozhamannan and Edward R. Hofmann
Viruses 2020, 12(12), 1393; https://doi.org/10.3390/v12121393 - 4 Dec 2020
Cited by 5 | Viewed by 3412
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Phage-Based Pathogen Detection)
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25 pages, 1694 KiB  
Review
Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments
by Susanne Meile, Samuel Kilcher, Martin J. Loessner and Matthew Dunne
Viruses 2020, 12(9), 944; https://doi.org/10.3390/v12090944 - 26 Aug 2020
Cited by 43 | Viewed by 10030
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Phage-Based Pathogen Detection)
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22 pages, 1118 KiB  
Review
Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review
by Jan Paczesny, Łukasz Richter and Robert Hołyst
Viruses 2020, 12(8), 845; https://doi.org/10.3390/v12080845 - 3 Aug 2020
Cited by 42 | Viewed by 5923
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. [...] Read more.
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. Full article
(This article belongs to the Special Issue Phage-Based Pathogen Detection)
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