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Diagnostics
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Diagnosis of Bacterial Pathogens
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Diagnosis of Bacterial Pathogens

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (31 May 2019) | Viewed by 93451

Special Issue Editor

Dr. Sabine Dittrich

E-Mail Website1 Website2
Guest Editor
1. Foundation for Innovative New Diagnostics (FIND), Campus Biotech Building B2 Level 0, 9 Chemin des Mines, 1202 Geneva, Switzerland
2. Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
Interests: diagnostic; public health; infectious diseases; non-malarial fevers; Rickettsial pathogens; resource limited; diagnosis; low and middle income countries; Emerging infections

Special Issue Information

Dear Colleagues,

Bacterial infections are responsible for a large disease burden globally with a wide range of syndromes, from fevers without a focus to severe meningitis. These clinical manifestations are caused by a multitude of bacterial pathogens like Streptococcus spp. and Pseudomonas spp. both contributing to the pneumonia disease burden, or Vibrio cholera and Salmonella spp. which is responsible for diarrheal diseases in certain parts of the world. Globally the bacterial pathogen that causes the most death is Mycobacterium tuberculosis—the causative agent of TB—particularly in less well-resourced settings. However, while TB is a major killer, it is clear that a wide range of bacterial pathogens are in fact responsible for mortality and morbidity around the world. Some pathogens are well-known, others are newly or re-emerging agents like Orientia tsutsugamushi or Burkholderia pseudomallei. While the transmission of pathogens varies depending on the species (food/water contamination, soil transmitted, and vector borne or person-to-person) the diagnostic challenge—to pin-point the causative agent in a timely manner—exists for nearly all of them. As such, the field of bacterial pathogen diagnosis particularly interesting and puzzling.

In light of this, it is essential that we build a holistic understanding of the bacterial ecosystem and natural history, to improve timely diagnosis and patient care, particularly in times of rising antimicrobial resistance levels and global warming. To contribute to the knowledge base on diagnosis of bacterial pathogens, the following topics will be considered:

  • Simple tools to address AMR
  • Sample processing and innovative approaches to improve the latter
  • One Health approach to diagnostic of bacterial infections
  • Innovative approaches to understand infection vs carriage

Dr. Sabine Dittrich
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. Diagnostics is an international peer-reviewed open access semimonthly 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.

Keywords

  •  Bacteria
  •  Diagnosis
  •  Diagnostic
  •  Natural history of infection
  •  Intracellular
  •  Emerging
  •  Point of care
  •  Microbiology
  •  Antimicrobial resistance
  •  AMR
  •  Surveillance
  •  Quality
  •  Co-infections
  •  Severe
  •  Non-malarial
  •  Identification
  •  Typing

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Published Papers (7 papers)

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Research

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9 pages, 2316 KiB  
Article
Development of Rapid Extraction Method of Mycobacterium avium Subspecies paratuberculosis DNA from Bovine Stool Samples
by Sören Hansen, Marco Roller, Lamia M. A. Alslim, Susanne Böhlken-Fascher, Kim Fechner, Claus-Peter Czerny and Ahmed Abd El Wahed
Diagnostics 2019, 9(2), 36; https://doi.org/10.3390/diagnostics9020036 - 29 Mar 2019
Cited by 11 | Viewed by 9195
Abstract
The rapid identification of Mycobacterium avium subspecies paratuberculosis (MAP) infected animals within the herd is essential for preventing the spread of the disease as well as avoiding human exposure. Although culture is seen as the gold standard, there are various molecular assays available [...] Read more.
The rapid identification of Mycobacterium avium subspecies paratuberculosis (MAP) infected animals within the herd is essential for preventing the spread of the disease as well as avoiding human exposure. Although culture is seen as the gold standard, there are various molecular assays available i.e., polymerase chain reaction (PCR) or isothermal amplification technique (recombinase polymerase amplification (RPA)) for the detection of MAP. The accuracy of the molecular assays is highly dependent on the DNA extraction method. In order to establish a rapid point of need system for the detection of MAP DNA from stool samples, we developed a rapid DNA extraction protocol (MAP DNA SpeedXtract) specified for use in combination with the RPA. The whole procedure from “sample in” to “result out” was conducted in a mobile suitcase laboratory. The DNA extraction is based on reverse purification by magnetic beads, which reduces the required technical demand. The MAP DNA SpeedXtract was performed within 25 min and only three pipetting steps were needed. The amplification and detection time were 20 min in RPA. The sensitivity and specificity of the developed protocol in comparison with the lab-based silica membrane column extraction and real-time PCR were 90.9% (n = 22) and 100% (n = 23), respectively. In conclusion, we established a rapid and reliable protocol for the extraction and detection of MAP DNA. All reagents are cold chain independent. The entire setup is ideal for point of need identification of MAP infected cases. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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12 pages, 221 KiB  
Article
Defining System Requirements for Simplified Blood Culture to Enable Widespread Use in Resource-Limited Settings
by Peter J. Dailey, Jennifer Osborn, Elizabeth A. Ashley, Ellen Jo Baron, David A. B. Dance, Daniela Fusco, Caterina Fanello, Yukari C. Manabe, Margaret Mokomane, Paul N. Newton, Belay Tessema, Chris Isaacs and Sabine Dittrich
Diagnostics 2019, 9(1), 10; https://doi.org/10.3390/diagnostics9010010 - 11 Jan 2019
Cited by 29 | Viewed by 8170
Abstract
Bacterial blood stream infections (BSI) are a common cause of mortality and morbidity globally. As the causative agents and the resulting treatment decisions vary, near-patient testing and surveillance tools are necessary to monitor bacterial causes and resistance to antimicrobial agents. The gold standard [...] Read more.
Bacterial blood stream infections (BSI) are a common cause of mortality and morbidity globally. As the causative agents and the resulting treatment decisions vary, near-patient testing and surveillance tools are necessary to monitor bacterial causes and resistance to antimicrobial agents. The gold standard to identify BSIs is blood culture (BC), a methodology not widely available in resource-limited settings. The aim of the study was to map out a target product profile of a simplified BC system (SBCS) to inform product development efforts. To identify the desired characteristics of a SBCS, we enlisted a small group of specialists working in Africa and Asia. Questions were used to understand challenges and how these constraints inform system requirements. The specialists were infectious disease physicians, public health/clinical microbiologists, clinical researchers, and technology experts with different geographical backgrounds. All suggested that BC should ideally be available at the district hospital level. Many of the same operational challenges, such as limited availability of culture bottles, electricity and internet connectivity, profuse dust, the lack of ambient temperature control, and human capacity constraints were identified across the different regions. BCs, although the accepted gold standard for diagnosis of BSIs, are not widely available outside of reference/research centers in Africa and Asia. To extend the reach of this important tool, it is crucial to engage product developers and academic research partners to develop accessible alternatives. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
9 pages, 673 KiB  
Article
Enhanced Systemic Response of Matrix Metalloproteinases and Their Regulators in Campylobacter and Salmonella Patients
by Anna Nilsson, Taina Tervahartiala, David Lennebratt, Anders Lannergård, Timo Sorsa and Hilpi Rautelin
Diagnostics 2018, 8(4), 82; https://doi.org/10.3390/diagnostics8040082 - 13 Dec 2018
Cited by 5 | Viewed by 4461
Abstract
Campylobacters are major enteropathogens worldwide with a substantial financial burden. Matrix metalloproteinases (MMPs) are proteolytic metalloendopeptidases with ability to modify immune response and shown to be upregulated in patients with several tissue destructive diseases, including infections. We measured here serum concentrations of MMP-8 [...] Read more.
Campylobacters are major enteropathogens worldwide with a substantial financial burden. Matrix metalloproteinases (MMPs) are proteolytic metalloendopeptidases with ability to modify immune response and shown to be upregulated in patients with several tissue destructive diseases, including infections. We measured here serum concentrations of MMP-8 and MMP-9 together with their regulators myeloperoxidase (MPO), human neutrophil elastase (HNE), and tissue inhibitor of metalloproteinases (TIMP)-1 in 80 Campylobacter and 25 Salmonella patients as well as in 27 healthy controls. Paired serum samples were available for 73 and 23 patients, respectively. When the initial serum samples were compared to those from controls, both Campylobacter and Salmonella patients showed elevated concentrations of all biomarkers tested (p ≤ 0.037). In the follow-up samples, collected about 25 days afterwards, MMP-8 levels of Campylobacter patients had already turned to normal but all the other biomarkers still showed elevated, although from the initial levels significantly dropped, levels. For the follow-up samples of Salmonella patients, only MMP-9 and MPO levels were at a significantly higher level than in controls. It remains to be studied if the systematically enhanced neutrophil-derived proteolytic and oxidative stress, induced by Campylobacter infection as shown here and persisting for several weeks, is important for the development of late sequelae. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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7 pages, 472 KiB  
Communication
Triplex Real-Time PCR without DNA Extraction for the Monitoring of Meningococcal Disease
by Melissa J. Whaley, Laurel T. Jenkins, Fang Hu, Alexander Chen, Seydou Diarra, Rasmata Ouédraogo-Traoré, Claudio T. Sacchi and Xin Wang
Diagnostics 2018, 8(3), 58; https://doi.org/10.3390/diagnostics8030058 - 30 Aug 2018
Cited by 4 | Viewed by 4534
Abstract
Detection of Neisseria meningitidis has become less time- and resource-intensive with a monoplex direct real-time PCR (drt-PCR) to amplify genes from clinical specimens without DNA extraction. To further improve efficiency, we evaluated two triplex drt-PCR assays for the detection of meningococcal serogroups AWX [...] Read more.
Detection of Neisseria meningitidis has become less time- and resource-intensive with a monoplex direct real-time PCR (drt-PCR) to amplify genes from clinical specimens without DNA extraction. To further improve efficiency, we evaluated two triplex drt-PCR assays for the detection of meningococcal serogroups AWX and BCY. The sensitivity and specificity of the triplex assays were assessed using 228 cerebrospinal fluid (CSF) specimens from meningitis patients and compared to the monoplex for six serogroups. The lower limit of detection range for six serogroup-specific drt-PCR assays was 178–5264 CFU/mL by monoplex and 68–2221 CFU/mL by triplex. The triplex and monoplex showed 100% agreement for six serogroups and the triplex assays achieved similar sensitivity and specificity estimates as the monoplex drt-PCR assays. Our triplex method reduces the time and cost of processing CSF specimens by characterizing six serogroups with only two assays, which is particularly important for testing large numbers of specimens for N. meningitidis surveillance. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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Review

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17 pages, 2425 KiB  
Review
Current and Emerging Methods of Antibiotic Susceptibility Testing
by Zeeshan A. Khan, Mohd F. Siddiqui and Seungkyung Park
Diagnostics 2019, 9(2), 49; https://doi.org/10.3390/diagnostics9020049 - 3 May 2019
Cited by 261 | Viewed by 42392
Abstract
Antibiotic susceptibility testing (AST) specifies effective antibiotic dosage and formulates a profile of empirical therapy for the proper management of an individual patient’s health against deadly infections. Therefore, rapid diagnostic plays a pivotal role in the treatment of bacterial infection. In this article, [...] Read more.
Antibiotic susceptibility testing (AST) specifies effective antibiotic dosage and formulates a profile of empirical therapy for the proper management of an individual patient’s health against deadly infections. Therefore, rapid diagnostic plays a pivotal role in the treatment of bacterial infection. In this article, the authors review the socio-economic burden and emergence of antibiotic resistance. An overview of the phenotypic, genotypic, and emerging techniques for AST has been provided and discussed, highlighting the advantages and limitations of each. The historical perspective on conventional methods that have paved the way for modern AST like disk diffusion, Epsilometer test (Etest), and microdilution, is presented. Several emerging methods, such as microfluidic-based optical and electrochemical AST have been critically evaluated. Finally, the challenges related with AST and its outlook in the future are presented. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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12 pages, 611 KiB  
Review
The Basics and the Advancements in Diagnosis of Bacterial Lower Respiratory Tract Infections
by Stephanie Noviello and David B. Huang
Diagnostics 2019, 9(2), 37; https://doi.org/10.3390/diagnostics9020037 - 3 Apr 2019
Cited by 26 | Viewed by 9736
Abstract
Lower respiratory tract infections (LRTIs) are the leading infectious cause of death and the sixth-leading cause of death overall worldwide. Streptococcus pneumoniae, with more than 90 serotypes, remains the most common identified cause of community-acquired acute bacterial pneumonia. Antibiotics treat LRTIs with [...] Read more.
Lower respiratory tract infections (LRTIs) are the leading infectious cause of death and the sixth-leading cause of death overall worldwide. Streptococcus pneumoniae, with more than 90 serotypes, remains the most common identified cause of community-acquired acute bacterial pneumonia. Antibiotics treat LRTIs with a bacterial etiology. With the potential for antibiotic-resistant bacteria, defining the etiology of the LRTI is imperative for appropriate patient treatment. C-reactive protein and procalcitonin are point-of-care tests that may differentiate bacterial versus viral etiologies of LRTIs. Major advancements are currently advancing the ability to make rapid diagnoses and identification of the bacterial etiology of LRTIs, which will continue to support antimicrobial stewardship, and is the focus of this review. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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Other

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16 pages, 3775 KiB  
Tutorial
Understanding Real-Time Fluorescence Signals from Bacteria and Wound Tissues Observed with the MolecuLight i:XTM
by Monique Y. Rennie, Danielle Dunham, Liis Lindvere-Teene, Rose Raizman, Rosemary Hill and Ron Linden
Diagnostics 2019, 9(1), 22; https://doi.org/10.3390/diagnostics9010022 - 26 Feb 2019
Cited by 85 | Viewed by 13324
Abstract
The persistent presence of pathogenic bacteria is one of the main obstacles to wound healing. Detection of wound bacteria relies on sampling methods, which delay confirmation by several days. However, a novel handheld fluorescence imaging device has recently enabled real-time detection of bacteria [...] Read more.
The persistent presence of pathogenic bacteria is one of the main obstacles to wound healing. Detection of wound bacteria relies on sampling methods, which delay confirmation by several days. However, a novel handheld fluorescence imaging device has recently enabled real-time detection of bacteria in wounds based on their intrinsic fluorescence characteristics, which differ from those of background tissues. This device illuminates the wound with violet (405 nm) light, causing tissues and bacteria to produce endogenous, characteristic fluorescence signals that are filtered and displayed on the device screen in real-time. The resulting images allow for rapid assessment and documentation of the presence, location, and extent of fluorescent bacteria at moderate-to-heavy loads. This information has been shown to assist in wound assessment and guide patient-specific treatment plans. However, proper image interpretation is essential to assessing this information. To properly identify regions of bacterial fluorescence, users must understand: (1) Fluorescence signals from tissues (e.g., wound tissues, tendon, bone) and fluids (e.g., blood, pus); (2) fluorescence signals from bacteria (red or cyan); (3) the rationale for varying hues of both tissue and bacterial fluorescence; (4) image artifacts that can occur; and (5) some potentially confounding signals from non-biological materials (e.g., fluorescent cleansing solutions). Therefore, this tutorial provides clinicians with a rationale for identifying common wound fluorescence characteristics. Clinical examples are intended to help clinicians with image interpretation—with a focus on image artifacts and potential confounders of image interpretation—and suggestions of how to overcome such challenges when imaging wounds in clinical practice. Full article
(This article belongs to the Special Issue Diagnosis of Bacterial Pathogens)
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