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Antibiotics
Special Issues
Diagnostics, Treatment and Prevention of Bacterial Infections
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Diagnostics, Treatment and Prevention of Bacterial Infections

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotic Therapy in Infectious Diseases".

Deadline for manuscript submissions: closed (1 August 2023) | Viewed by 13360

Special Issue Editors

Dr. Silvia Würstle

E-Mail Website
Guest Editor
1. Technical University of Munich, School of Medicine, Department of Internal Medicine II, 81675 Munich, Germany
2. Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
3. Yale Center for Phage Biology & Therapy, Yale University, New Haven, CT 06520, USA
Interests: infectious diseases in internal medicine; bacteriophages; antimicrobial resistance
Dr. Gail Stanley

E-Mail Website
Guest Editor
1. Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
2. Yale Center for Phage Biology and Therapy, Yale University, New Haven, CT 06520, USA
Interests: pulmonary disease; cystic fibrosis; antimicrobial resistance; bacteriophage therapy
Dr. Kathrin Rothe

E-Mail Website
Guest Editor
1. Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich, Germany
2. München Klinik gGmbH, Munich, Germany
Interests: antimicrobial resistance; microbiological diagnostics; antimicrobial therapy; bacterial infections; antibiotic stewardship; diagnostic stewardship

Special Issue Information

Dear Colleagues,

Managing bacterial diseases in humans is becoming increasingly challenging due to the rise of antibiotic resistance. Thus, translational science efforts addressing prevalent bacterial infections are of the utmost importance to fight this global threat to public health. To improve the diagnosis of bacterial infections, novel, rapid, and streamlined testing approaches, in context of diagnostic stewardship are required. Additionally, alternatives to conventional antibiotic treatment regimens based on the accurate investigation of the pathogen spectrum, antibiotic resistance patterns and global variations of these, as well as rapid initiation of targeted narrow-spectrum treatment can improve patient outcomes. Prevention strategies, including identification of infection reservoirs, understanding reservoir infection dynamics, close monitoring by means of human reservoir transmission, and practical disease control interventions could prevent pathogen spread in the future.

The focus of this Special Issue, is the development and application of translational science methods for the diagnosis, prevention, treatment, and containment of bacterial infections.

The following topics are addressed in this special issue on bacterial infections:

  • Experimental and applied microbiology
  • Epidemiological surveillance of bacterial infections and antibiotic resistance in target populations and infection reservoirs
  • Pathogen spectrum and antibiotic resistance patterns
  • Evolution of antimicrobial resistance
  • Diagnostics for managing bacterial infections and antibiotic resistance traits
  • Personalized therapy against bacterial infections
  • Novel antibacterial therapies and drug development
  • Bioavailability of antibacterial drugs
  • Monitoring and preventing transmission of bacteria and antibiotic resistant traits in healthcare settings
  • Prevention and isolation strategies against bacterial infections
  • Antimicrobial and diagnostic stewardship

We welcome the submission of research articles, case studies, clinical trials, short communications, and reviews.

Dr. Silvia Würstle
Dr. Gail Stanley
Dr. Kathrin Rothe
Guest Editors

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. Antibiotics 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 2900 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 resistance
  • microbiological diagnostics
  • antimicrobial therapy
  • infection control and prevention
  • bacterial infections

Published Papers (7 papers)

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Research

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12 pages, 1548 KiB  
Article
Risk Factors and Pathogens of Wound Infection in Burn Inpatients from East China
by Siqi Zhou, Shuzhen Xiao, Xuedong Wang, Xuefeng Wang and Lizhong Han
Antibiotics 2023, 12(9), 1432; https://doi.org/10.3390/antibiotics12091432 - 11 Sep 2023
Viewed by 1189
Abstract
Background: Infection is the predominant contributor to morbidity and mortality in burn patients, and burn wound infection (BWI) is the most common reason. The objective of this research was to analyze the incidence, factors and progression of BWI, in terms of events and [...] Read more.
Background: Infection is the predominant contributor to morbidity and mortality in burn patients, and burn wound infection (BWI) is the most common reason. The objective of this research was to analyze the incidence, factors and progression of BWI, in terms of events and bacteria. Methods: Clinical variables of all qualified patients admitted to burn wards were analyzed retrospectively in 2021 at a tertiary hospital in eastern China through univariate analysis and multivariate logistic regression. The Kaplan–Meier method was also used for plotting survival curves. Isolates and resistance data were evaluated to demonstrate the evolution of targeted antibiotics of strains from BWI. Results: A total of 580 (median age, 39.5 years (23–56 years); 372/580 (64.14%) male) patients were evaluated, 348 (60.0%) of whom experienced BWI. A variety of factors are associated with BWI. Multivariate logistic regression analysis showed that depth and area of burn and duration from burn to first hospitalization are independent risk factors for BWI. For BWI onset in these patients, 47.24% (274/580) occurred in the first week. The most frequently isolated causative organism was Staphylococcus aureus (15.7%) in patients with BWI. The duration of transition from Gram-positive strains (median 3 days, (2–7 days)) to Gram-negative (median 10 days, (4–17 days)) ones isolated from burn wound shrunk. Hospital length of stay was considered as a protective factor for BWI. Conclusion: The precise assessment of factors affecting BWI in burn patients enhances prompt and suitable management. Swab cultures for surveillance could be utilized to monitor the microbiological status of burn patients. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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10 pages, 249 KiB  
Article
Usefulness of Routine Laboratory Tests for Follow up of Patients Receiving Outpatient Parenteral Antimicrobial Therapy Run by Infectious Diseases Fellows
by Jared Frisby, Naureen Ali, Samson Niemotka and Getahun Abate
Antibiotics 2023, 12(2), 330; https://doi.org/10.3390/antibiotics12020330 - 04 Feb 2023
Cited by 2 | Viewed by 1293
Abstract
Background: The infectious disease society of America (IDSA) recommends routine laboratory tests for all patients receiving outpatient parenteral antimicrobial therapy (OPAT) to monitor for adverse events. There are no data to support how often patients should take monitoring laboratory tests. In addition, the [...] Read more.
Background: The infectious disease society of America (IDSA) recommends routine laboratory tests for all patients receiving outpatient parenteral antimicrobial therapy (OPAT) to monitor for adverse events. There are no data to support how often patients should take monitoring laboratory tests. In addition, the relevance of different laboratory tests commonly used for OPAT follow up is not clearly known. Methods: We conducted a retrospective observational cohort study over a 7-year study interval (1 January 2014 to 31 December 2021). Clinical data were obtained to identify the risk factors associated with abnormal laboratory tests and determine if abnormal laboratory tests led to antibiotic change or hospital readmission. Results: Two hundred and forty-six patients met the inclusion criteria for this study. In our multivariate analysis, the Charlson comorbidity index (CCI) of 0–4 (aOR 0.39, 95%Cl 0.18–0.86), the use of ceftriaxone without vancomycin (aOR 0.47, 95%Cl 0.24–0.91) and an OPAT duration of 2–4 weeks (aOR 0.47, 95%Cl 0.24–0.91) were associated with a lower risk of OPAT complications. A CCI of 5 or more (aOR 2.5, 95%Cl (1.1–5.7)) and an OPAT duration of 5 or more weeks (aOR 2.7, 95% Cl 1.3–5.6) were associated with a higher risk of OPAT complications. An abnormal complete metabolic panel or vancomycin levels, but not an abnormal complete blood count, were associated with antibiotic change or readmission. Conclusion: Patients with fewer comorbidities, ceftriaxone and short OPAT durations are at lower risk for OPAT complications. These patients could be followed with less frequent laboratory monitoring. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
9 pages, 724 KiB  
Article
A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study
by Silvia Würstle, Alexander Hapfelmeier, Siranush Karapetyan, Fabian Studen, Andriana Isaakidou, Tillman Schneider, Roland M. Schmid, Stefan von Delius, Felix Gundling, Julian Triebelhorn, Rainer Burgkart, Andreas Obermeier, Ulrich Mayr, Stephan Heller, Sebastian Rasch, Tobias Lahmer, Fabian Geisler, Benjamin Chan, Paul E. Turner, Kathrin Rothe, Christoph D. Spinner and Jochen Schneideradd Show full author list remove Hide full author list
Antibiotics 2022, 11(11), 1610; https://doi.org/10.3390/antibiotics11111610 - 12 Nov 2022
Cited by 1 | Viewed by 1626
Abstract
This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes [...] Read more.
This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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Review

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19 pages, 1227 KiB  
Review
Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives
by Ekaterina Avershina, Abdolrahman Khezri and Rafi Ahmad
Antibiotics 2023, 12(4), 781; https://doi.org/10.3390/antibiotics12040781 - 19 Apr 2023
Cited by 10 | Viewed by 2934
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread [...] Read more.
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic). Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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11 pages, 2045 KiB  
Review
Macrolide Resistance in Bordetella pertussis: Current Situation and Future Challenges
by Lauri Ivaska, Alex-Mikael Barkoff, Jussi Mertsola and Qiushui He
Antibiotics 2022, 11(11), 1570; https://doi.org/10.3390/antibiotics11111570 - 07 Nov 2022
Cited by 5 | Viewed by 2880
Abstract
Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis bacterium. The mainstay of treatment is macrolide antibiotics that reduce transmissibility, shorten the duration of symptoms and decrease mortality in infants. Recently, the macrolide resistance of B. pertussis has been reported globally [...] Read more.
Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis bacterium. The mainstay of treatment is macrolide antibiotics that reduce transmissibility, shorten the duration of symptoms and decrease mortality in infants. Recently, the macrolide resistance of B. pertussis has been reported globally but is especially widespread in mainland China. In this review, we aim to summarise the current understanding of the epidemiology, resistance mechanisms and clinical implications of B. pertussis macrolide resistance. Since the first appearance of macrolide-resistant B. pertussis in Arizona, USA, in 1994, only sporadic cases have been reported outside China. In certain parts of China, on the other hand, up to 70–100% of the recent clinical isolates have been found to be macrolide resistant. Reasons for macrolide resistance being centred upon China during the last decade can only be speculated on, but the dominant B. pertussis lineage is different between China and most of the high-income countries. It seems evident that efforts to increase awareness, guide molecular epidemiological surveillance and carry out systematic screening of B. pertussis positive samples for macrolide resistance should be implemented globally. In addition, practices to improve the clinical care of infants with pertussis caused by resistant strains should be studied vigorously. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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Other

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16 pages, 2674 KiB  
Systematic Review
Clinical Equivalence between Generic Versus Branded Antibiotics: Systematic Review and Meta-Analysis
by André Cotia, Haliton Alves Oliveira Junior, Jessica Y. Matuoka and Ícaro Boszczowski
Antibiotics 2023, 12(5), 935; https://doi.org/10.3390/antibiotics12050935 - 21 May 2023
Viewed by 1638
Abstract
Regulatory authorities authorize the clinical use of generic drugs (GD) based on bioequivalence studies, which consist of the evaluation of pharmacokinetics after a single dose in vitro or in healthy individuals. There are few data on clinical equivalence between generic and branded antibiotics. [...] Read more.
Regulatory authorities authorize the clinical use of generic drugs (GD) based on bioequivalence studies, which consist of the evaluation of pharmacokinetics after a single dose in vitro or in healthy individuals. There are few data on clinical equivalence between generic and branded antibiotics. Our aim was to synthesize and analyze the available evidence on the clinical efficacy and safety of generic antibiotics compared to their original formulations. A systematic review was performed on Medline (PubMed) and Embase and validated through Epistemonikos and Google Scholar. The last search was conducted on 30 June 2022. Meta-analyses of clinical cure and mortality outcomes were performed. One randomized clinical trial (RCT) and 10 non-randomized intervention studies were included. No differences in clinical cure were observed between groups in the meta-analysis (OR = 0.89, 95% CI [0.61–1.28]; I2 = 70%, p = 0.005). No difference was observed between groups when considering the use of carbapenems for overall mortality (OR = 0.99, 95% CI [0.63–1.55]; I2 = 78%) or death associated with infections (OR = 0.79, 95% CI [0.48–1.29], I2 = 67%). Most of the studies were observational, and the duration of follow-up, the characteristics of the participants, and the sites of infections were heterogeneous. Due to the uncertainty of the evidence, it is not possible to contraindicate the use of generics, which is an important strategy to expand access. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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10 pages, 946 KiB  
Brief Report
Transcriptome Mining to Identify Molecular Markers for the Diagnosis of Staphylococcus epidermidis Bloodstream Infections
by Susana Brás and Angela França
Antibiotics 2022, 11(11), 1596; https://doi.org/10.3390/antibiotics11111596 - 11 Nov 2022
Cited by 1 | Viewed by 1133
Abstract
Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate “true” infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in [...] Read more.
Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate “true” infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis. Full article
(This article belongs to the Special Issue Diagnostics, Treatment and Prevention of Bacterial Infections)
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