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Translational Aspects of Infectious Diseases: From Bench to Bedside
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Translational Aspects of Infectious Diseases: From Bench to Bedside

A special issue of International Journal of Translational Medicine (ISSN 2673-8937).

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 23526

Special Issue Editor

Prof. Dr. Jean-ralph Zahar

E-Mail Website
Guest Editor
1. APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, 93140 Bondy, France
2. IAME, UMR 1137, Sorbonne Université, Université Paris 13, 75005 Paris, France
Interests: infection control; antimicrobial resistance; antimircrobial stewardship; health acquired infection; environmental contamination
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The COVID-19 pandemic has shown us the importance of anticipating infectious risks and the need for responses adapted to each individual’s epidemiological situation. We have debated a lot about the interest of specific measures throughout the period, but beyond that, we have realized the importance of simple but applicable and applied prevention measures. In this future issue, we would like to bring to our readers a cross-sectional reflection including the different actors involved in the control and fight against infectious diseases. The topics discussed will open new horizons not only in the field of prevention, but also in the field of therapy.

I hope that you will join us.

Prof. Dr. Jean-ralph Zahar
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. International Journal of Translational Medicine is an international peer-reviewed open access quarterly 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 1000 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

  • antimicrobial stewardship
  • artificial intelligence
  • contact isolation
  • modelization
  • geography
  • behaviors

Related Special Issue

Published Papers (7 papers)

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Research

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12 pages, 285 KiB  
Article
Brixia Score in Outcomes of Alpha versus Delta Variant of Infection in Pregnant Critical COVID-19 Patients
by Roxana Covali, Demetra Socolov, Ioana Pavaleanu, Mona Akad, Lucian Vasile Boiculese and Razvan Socolov
Int. J. Transl. Med. 2022, 2(1), 66-77; https://doi.org/10.3390/ijtm2010007 - 17 Feb 2022
Cited by 2 | Viewed by 2289
Abstract
Background: Critical COVID-19 patients account for 1.7 to 13% of all pregnant COVID-19 patients. Methods: Patients admitted to the COVID-19 intensive care unit of Elena Doamna Obstetrics and Gynecology University Hospital in Iasi between 1 January and 1 December 2021, with critical forms [...] Read more.
Background: Critical COVID-19 patients account for 1.7 to 13% of all pregnant COVID-19 patients. Methods: Patients admitted to the COVID-19 intensive care unit of Elena Doamna Obstetrics and Gynecology University Hospital in Iasi between 1 January and 1 December 2021, with critical forms of the disease, were included and retrospectively studied. The patients’ age range was 25–44 years in the Alpha group (n = 12) and 27–52 years in the Delta group (n = 9). Results: Most critically ill pregnant COVID-19 patients in the Alpha group delivered when admitted to the intensive care unit, while less than half of those in the Delta group delivered when admitted; the rest were released home and continued their pregnancy normally. There was a significant difference regarding the number of patients released to home care and the number of days after admission when delivery occurred (p = 0.02 and 0.022, respectively). Conclusions: There was no significant difference in maternal and fetal outcomes between the two groups, except for the number of patients released to home care and the number of days after admission when delivery occurred. There was no correlation between any Brixia scores (H, L, A, E) and any maternal or fetal outcomes in both groups. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
9 pages, 2791 KiB  
Article
Artificial Intelligence and Democratization of the Use of Lung Ultrasound in COVID-19: On the Feasibility of Automatic Calculation of Lung Ultrasound Score
by Jorge Camacho, Mario Muñoz, Vicente Genovés, Joaquín L. Herraiz, Ignacio Ortega, Adrián Belarra, Ricardo González, David Sánchez, Roberto Carlos Giacchetta, Ángela Trueba-Vicente and Yale Tung-Chen
Int. J. Transl. Med. 2022, 2(1), 17-25; https://doi.org/10.3390/ijtm2010002 - 13 Jan 2022
Cited by 4 | Viewed by 3418
Abstract
During the COVID-19 pandemic, lung ultrasound has been revealed as a powerful technique for diagnosis and follow-up of pneumonia, the principal complication of SARS-CoV-2 infection. Nevertheless, being a relatively new and unknown technique, the lack of trained personnel has limited its application worldwide. [...] Read more.
During the COVID-19 pandemic, lung ultrasound has been revealed as a powerful technique for diagnosis and follow-up of pneumonia, the principal complication of SARS-CoV-2 infection. Nevertheless, being a relatively new and unknown technique, the lack of trained personnel has limited its application worldwide. Computer-aided diagnosis could possibly help to reduce the learning curve for less experienced physicians, and to extend such a new technique such as lung ultrasound more quickly. This work presents the preliminary results of the ULTRACOV (Ultrasound in Coronavirus disease) study, aimed to explore the feasibility of a real-time image processing algorithm for automatic calculation of the lung ultrasound score (LUS). A total of 28 patients positive on COVID-19 were recruited and scanned in 12 thorax zones following the lung score protocol, saving a 3 s video at each probe position. Those videos were evaluated by an experienced physician and by a custom developed automated detection algorithm, looking for A-Lines, B-Lines, consolidations, and pleural effusions. The agreement between the findings of the expert and the algorithm was 88.0% for B-Lines, 93.4% for consolidations and 99.7% for pleural effusion detection, and 72.8% for the individual video score. The standard deviation of the patient lung score difference between the expert and the algorithm was ±2.2 points over 36. The exam average time with the ULTRACOV prototype was 5.3 min, while with a conventional scanner was 12.6 min. Conclusion: A good agreement between the algorithm output and an experienced physician was observed, which is a first step on the feasibility of developing a real-time aided-diagnosis lung ultrasound equipment. Additionally, the examination time was reduced to less than half with regard to a conventional ultrasound exam. Acquiring a complete lung ultrasound exam within a few minutes is possible using fairly simple ultrasound machines that are enhanced with artificial intelligence, such as the one we propose. This step is critical to democratize the use of lung ultrasound in these difficult times. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
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Review

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6 pages, 248 KiB  
Review
CRISPR-Based Diagnostics for Point-of-Care Viral Detection
by Alexander I. Mosa
Int. J. Transl. Med. 2022, 2(2), 198-203; https://doi.org/10.3390/ijtm2020017 - 1 Jun 2022
Cited by 1 | Viewed by 1827
Abstract
Point-of-care detection of viral infection is required for effective contact-tracing, epidemiological surveillance, and linkage to care. Traditional diagnostic platforms relying on either antigen detection or nucleic amplification are limited by sensitivity and the need for costly laboratory infrastructure, respectively. Recently, CRISPR-based diagnostics have [...] Read more.
Point-of-care detection of viral infection is required for effective contact-tracing, epidemiological surveillance, and linkage to care. Traditional diagnostic platforms relying on either antigen detection or nucleic amplification are limited by sensitivity and the need for costly laboratory infrastructure, respectively. Recently, CRISPR-based diagnostics have emerged as an alternative, combining equipment light workflows with high specificity and sensitivity. However, as a nascent technology, several outstanding challenges to widespread field deployment remain. These include the need for pre-detection amplification of target molecules, the lack of standardization in sample preparation and reagent composition, and only equivocal assessments of the unit-economics relative to traditional antigen or polymerase chain reaction-based diagnostics. This review summarizes recent advances with the potential to overcome existing translational barriers, describes the events in CRISPR-based detection of target molecules, and offers perspective on how multiple approaches can be combined to decrease the limit of detection without introducing pre-amplification. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
21 pages, 1118 KiB  
Review
Thinking Outside the Box: Utilizing Nontraditional Animal Models for COVID-19 Research
by Sachithra Gunasekara, Miruthula Tamil Selvan, Craig A. Miller and Jennifer M. Rudd
Int. J. Transl. Med. 2022, 2(1), 113-133; https://doi.org/10.3390/ijtm2010010 - 9 Mar 2022
Cited by 2 | Viewed by 4097
Abstract
The ongoing COVID-19 pandemic continues to affect the lives, wellbeing, and stability of communities worldwide. The race to save human lives is critical, and the development of useful translational animal models to elucidate disease pathogenesis and prevention, and to test therapeutic interventions, is [...] Read more.
The ongoing COVID-19 pandemic continues to affect the lives, wellbeing, and stability of communities worldwide. The race to save human lives is critical, and the development of useful translational animal models to elucidate disease pathogenesis and prevention, and to test therapeutic interventions, is essential to this response. However, significant limitations exist with the currently employed animal models that slow our ability to respond to the pandemic. Non-human primates serve as an excellent animal model for SARS-CoV-2 disease and interventions, but the availability of these animals is scarce, and few facilities are able to house and utilize this model. Adapted murine models are accessible and improving but lack natural hACE-2 receptors and are only moderate representatives of human COVID-19 disease, transmission, and immune responses. On the other hand, there are several animal species that are both naturally and experimentally infected, such as domestic cats, hamsters, ferrets, and mink. Several of these have proven animal-to-animal transmission and evidence of significant clinical and histopathologic disease that mimics acute COVID-19 in humans. Mobilizing these nontraditional animal models could have a crucial role in SARS-CoV-2 research efficiency and impact. This review focuses on what is known about these nontraditional animal models, including their immune responses to SARS-CoV-2 infection, evidence of clinical and histopathologic disease, transmission potential, and the practicality of each model in a research setting. Comparative insight into these animal models for COVID-19 can strengthen the efforts to mitigate this pandemic. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
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14 pages, 303 KiB  
Review
Asymptomatic Bacteriuria or Urinary Tract Infection? New and Old Biomarkers
by Francesca K Martino and Giacomo Novara
Int. J. Transl. Med. 2022, 2(1), 52-65; https://doi.org/10.3390/ijtm2010006 - 1 Feb 2022
Cited by 4 | Viewed by 3594
Abstract
Urinary tract infections (UTIs) are among the most common infective disease in the adult population. UTI diagnosis is based essentially on the presence of lower urinary tract symptoms (e.g., dysuria, urgency, and frequency) and the evidence of bacteriuria (by dipstick testing and/or urine [...] Read more.
Urinary tract infections (UTIs) are among the most common infective disease in the adult population. UTI diagnosis is based essentially on the presence of lower urinary tract symptoms (e.g., dysuria, urgency, and frequency) and the evidence of bacteriuria (by dipstick testing and/or urine culture). UTI diagnosis is not always easy because symptoms can be vague, or patient basal conditions can interfere negatively with the diagnostic process, whereas urine culture is still ongoing. In those cases, the differential diagnosis among UTIs and asymptomatic bacteriuria (ABU) may be challenging, while the clinician has to decide whether to start an antibiotic treatment shortly. The purpose of the present review is to analyze the biomarkers that could help in UTI diagnosis. Some biomarkers, such as procalcitonin, interleukin-6, neutrophil gelatinase-associated lipocalin, chemokines, lactoferrin, and bone morphogenetic protein-2, seem promising in UTI diagnosis, while other biomarkers failed to show any utility. Whereas a single biomarker was not enough, a combination of biomarkers could have more chances to help in the diagnosis. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
21 pages, 1650 KiB  
Review
Insights into the Function of Regulatory RNAs in Bacteria and Archaea
by Elahe Soltani-Fard, Sina Taghvimi, Zahra Abedi Kichi, Christian Weber, Zahra Shabaninejad, Mortaza Taheri-Anganeh, Seyyed Hossein Khatami, Pegah Mousavi, Ahmad Movahedpour and Lucia Natarelli
Int. J. Transl. Med. 2021, 1(3), 403-423; https://doi.org/10.3390/ijtm1030024 - 16 Dec 2021
Cited by 3 | Viewed by 3449
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that comprise about 80% of both mammals and prokaryotes genomes. Recent studies have identified a large number of small regulatory RNAs in Escherichia coli and other bacteria. In prokaryotes, RNA regulators are a diverse group of [...] Read more.
Non-coding RNAs (ncRNAs) are functional RNA molecules that comprise about 80% of both mammals and prokaryotes genomes. Recent studies have identified a large number of small regulatory RNAs in Escherichia coli and other bacteria. In prokaryotes, RNA regulators are a diverse group of molecules that modulate a wide range of physiological responses through a variety of mechanisms. Similar to eukaryotes, bacterial microRNAs are an important class of ncRNAs that play an important role in the development and secretion of proteins and in the regulation of gene expression. Similarly, riboswitches are cis-regulatory structured RNA elements capable of directly controlling the expression of downstream genes in response to small molecule ligands. As a result, riboswitches detect and respond to the availability of various metabolic changes within cells. The most extensive and most widely studied set of small RNA regulators act through base pairing with RNAs. These types of RNAs are vital for prokaryotic life, activating or suppressing important physiological processes by modifying transcription or translation. The majority of these small RNAs control responses to changes in environmental conditions. Finally, clustered regularly interspaced short palindromic repeat (CRISPR) RNAs, a newly discovered RNA regulator group, contains short regions of homology to bacteriophage and plasmid sequences that bacteria use to splice phage DNA as a defense mechanism. The detailed mechanism is still unknown but devoted to target homologous foreign DNAs. Here, we review the known mechanisms and roles of non-coding regulatory RNAs, with particular attention to riboswitches and their functions, briefly introducing translational applications of CRISPR RNAs in mammals. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
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Other

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9 pages, 930 KiB  
Tutorial
Python Programming in PyPI for Translational Medicine
by Yoshiyasu Takefuji
Int. J. Transl. Med. 2021, 1(3), 323-331; https://doi.org/10.3390/ijtm1030019 - 24 Nov 2021
Cited by 1 | Viewed by 3706
Abstract
This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers [...] Read more.
This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users. Full article
(This article belongs to the Special Issue Translational Aspects of Infectious Diseases: From Bench to Bedside)
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