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Microorganisms
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The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic...
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The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic Infections and Antimicrobial Resistance

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 8175

Special Issue Editor

Dr. Joseph M. Blondeau

E-Mail Website
Guest Editor
1. Head, Department of Clinical Microbiology, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada
2. Provincial Lead, Clinical Microbiology, Saskatchewan Health Authority, Saskatoon, SK S7N 0W8, Canada
Interests: clinical microbiology; antimicrobial agents/resistance; one health

Special Issue Information

Dear Colleagues,

SARS CoV 2 or COVID-19 and the various variants of concern have dominated the world for the past 2 years and continue to do so. However, clinical microbiology has continued to evolve, with advances made in automated/semi-automated technology, multiplex testing assays, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF), new applications, advancements in “real time” susceptibility testing and the evolving role of whole genome sequencing. Total lab automation (TLA) is becoming more commonplace and seen as a solution to medical laboratory technologists and/or medical laboratory assistant shortages. Additionally, “emerging” pathogens and zoonotic transmission have challenged diagnostic laboratories more frequently in recent years to isolate and identify such pathogens, identify a potential source and relate the findings to the patient’s clinical condition. One Health is a catch-all phrase recognizing that human health is closely associated with animal and environmental health. The interrelationships with antimicrobial use in humans, animals and the environment require further collaborative investigation. In this Special Issue, we attempt to assemble a collection of manuscripts focusing on clinical microbiology in human and animal health, advances made in the detection and isolation of pathogens and reductions in turn-around-time to clinically important results. Additionally, we investigate what the future will look like with technological advances and the ongoing need for “traditional” microbiology.

This Special Issue, entitled " The Ongoing Renaissance in Clinical Microbiology Considering One Health, Zoonotic Infections and Antimicrobial Resistance", aims to present recent research on any aspect of clinical microbiology. Its focal points include, but are not limited to, the following:

  1. Clinical microbiology in humans;
  2. Clinical microbiology in animals;
  3. One Health;
  4. Antimicrobial susceptibility and resistance;
  5. Total lab automation.

Reviews, original research, and communications are welcome.

Dr. Joseph M. Blondeau
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. Microorganisms 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 2700 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 (4 papers)

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Research

14 pages, 957 KiB  
Article
Antibiotic Prescriptions in Critically Ill Patients with Bloodstream Infection Due to ESBL-Producing Enterobacteriaceae: Compliance with the French Guidelines for the Treatment of Infections with Third-Generation Cephalosporin-Resistant Enterobacteriaceae—A Multicentric Retrospective Cohort Study
by Camille Le Berre, Marion Houard, Anne Vachée, Hugues Georges, Frederic Wallet, Pierre Patoz, Patrick Herbecq, Saad Nseir, Pierre-Yves Delannoy and Agnès Meybeck
Microorganisms 2023, 11(11), 2676; https://doi.org/10.3390/microorganisms11112676 - 31 Oct 2023
Viewed by 849
Abstract
National and international guidelines were recently published regarding the treatment of Enterobacteriaceae resistant to third-generation cephalosporins infections. We aimed to assess the implementation of the French guidelines in critically ill patients suffering from extended-spectrum β-lactamase-producing Enterobacteriaceae bloodstream infection (ESBL-E BSI). We conducted a [...] Read more.
National and international guidelines were recently published regarding the treatment of Enterobacteriaceae resistant to third-generation cephalosporins infections. We aimed to assess the implementation of the French guidelines in critically ill patients suffering from extended-spectrum β-lactamase-producing Enterobacteriaceae bloodstream infection (ESBL-E BSI). We conducted a retrospective observational cohort study in the ICU of three French hospitals. Patients treated between 2018 and 2022 for ESBL-E BSI were included. The primary assessment criterion was the proportion of adequate empirical carbapenem prescriptions, defined as prescriptions consistent with the French guidelines. Among the 185 included patients, 175 received an empirical anti-biotherapy within 24 h of ESBL-E BSI onset, with a carbapenem for 100 of them. The proportion of carbapenem prescriptions consistent with the guidelines was 81%. Inconsistent prescriptions were due to a lack of prescriptions of a carbapenem, while it was recommended in 25% of cases. The only factor independently associated with adequate empirical carbapenem prescription was ESBL-E colonization (OR: 107.921 [9.303–1251.910], p = 0.0002). The initial empirical anti-biotherapy was found to be appropriate in 83/98 patients (85%) receiving anti-biotherapy in line with the guidelines and in 56/77 (73%) patients receiving inadequate anti-biotherapy (p = 0.06). Our results illustrate the willingness of intensivists to spare carbapenems. Promoting implementation of the guidelines could improve the proportion of initial appropriate anti-biotherapy in critically ill patients with ESBL-E BSI. Full article
(This article belongs to the Special Issue The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic Infections and Antimicrobial Resistance)
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15 pages, 648 KiB  
Article
Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors
by Eftychios Vittorakis, Mihaela Laura Vică, Calina Oana Zervaki, Evangelos Vittorakis, Sofia Maraki, Viktoria Eirini Mavromanolaki, Michael Ewald Schürger, Vlad Sever Neculicioiu, Evangelia Papadomanolaki, Theodoros Sinanis, Georgia Giannoulaki, Evangelia Xydaki, Serafeim G. Kastanakis and Lia Monica Junie
Microorganisms 2023, 11(4), 841; https://doi.org/10.3390/microorganisms11040841 - 25 Mar 2023
Cited by 4 | Viewed by 1886
Abstract
S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal [...] Read more.
S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020–2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections. Full article
(This article belongs to the Special Issue The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic Infections and Antimicrobial Resistance)
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35 pages, 1132 KiB  
Article
Targeted Therapy of Severe Infections Caused by Staphylococcus aureus in Critically Ill Adult Patients: A Multidisciplinary Proposal of Therapeutic Algorithms Based on Real-World Evidence
by Milo Gatti, Bruno Viaggi, Gian Maria Rossolini, Federico Pea and Pierluigi Viale
Microorganisms 2023, 11(2), 394; https://doi.org/10.3390/microorganisms11020394 - 3 Feb 2023
Cited by 2 | Viewed by 3180
Abstract
(1) Introduction: To develop evidence-based algorithms for targeted antibiotic therapy of infections caused by Staphylococcus aureus in critically ill adult patients. (2) Methods: A multidisciplinary team of four experts had several rounds of assessment for developing algorithms concerning targeted antimicrobial therapy of severe [...] Read more.
(1) Introduction: To develop evidence-based algorithms for targeted antibiotic therapy of infections caused by Staphylococcus aureus in critically ill adult patients. (2) Methods: A multidisciplinary team of four experts had several rounds of assessment for developing algorithms concerning targeted antimicrobial therapy of severe infections caused by Staphylococcus aureus in critically ill patients. The literature search was performed by a researcher on PubMed-MEDLINE (until August 2022) to provide evidence for supporting therapeutic choices. Quality and strength of evidence was established according to a hierarchical scale of the study design. Two different algorithms were created, one for methicillin-susceptible Staphylococcus aureus (MSSA) and the other for methicillin-resistant Staphylococcus aureus (MRSA). The therapeutic options were categorized for each different site of infection and were selected also on the basis of pharmacokinetic/pharmacodynamic features. (3) Results: Cefazolin or oxacillin were the agents proposed for all of the different types of severe MSSA infections. The proposed targeted therapies for severe MRSA infections were different according to the infection site: daptomycin plus fosfomycin or ceftaroline or ceftobiprole for bloodstream infections, infective endocarditis, and/or infections associated with intracardiac/intravascular devices; ceftaroline or ceftobiprole for community-acquired pneumonia; linezolid alone or plus fosfomycin for infection-related ventilator-associated complications or for central nervous system infections; daptomycin alone or plus clindamycin for necrotizing skin and soft tissue infections. (4) Conclusions: We are confident that targeted therapies based on scientific evidence and optimization of the pharmacokinetic/pharmacodynamic features of antibiotic monotherapy or combo therapy may represent valuable strategies for treating MSSA and MRSA infections. Full article
(This article belongs to the Special Issue The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic Infections and Antimicrobial Resistance)
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13 pages, 575 KiB  
Article
A 2-Year Retrospective Case Series on Isolates of the Emerging Pathogen Actinotignum schaalii from a Canadian Tertiary Care Hospital
by Pramath Kakodkar and Camille Hamula
Microorganisms 2022, 10(8), 1608; https://doi.org/10.3390/microorganisms10081608 - 9 Aug 2022
Cited by 1 | Viewed by 1588
Abstract
(1) Background: Actinotignum schaalii is an emerging, opportunistic pathogen often linked with UTIs but can extend beyond the urogenital system. Data on the clinical significance of A. schaalii are still emerging. (2) Methods: A retrospective review of A. schaalii isolates in a Canadian [...] Read more.
(1) Background: Actinotignum schaalii is an emerging, opportunistic pathogen often linked with UTIs but can extend beyond the urogenital system. Data on the clinical significance of A. schaalii are still emerging. (2) Methods: A retrospective review of A. schaalii isolates in a Canadian tertiary care hospital was conducted. The clinical data of patients that grew A. schaalii from January 2020 to 2022 were documented. Demographics, site, management, and microbiological parameters surrounding culture and sensitivities were recorded. (3) Results: A total of 43 cases of A. schaalii were identified. Actinotignum schaalii was primarily involved in UTIs (n = 17), abscesses (n = 9), bacteremia (n = 6), septic arthritis (n = 5), and ulcers (n = 5). A. schaalii had a slight predilection for polymicrobial infections (51.1%, n = 22 out of 43), with Aerococcus urinae (n = 5) being the most common coisolate. Susceptibility testing was only performed in two cases that showed sensitivity to beta-lactam antibiotics and resistance to metronidazole and ciprofloxacin. Amoxicillin–clavulanate (n = 5) is the most frequently prescribed antibiotic. (4) Conclusions: The non-urogenic clinical significance of A. schaalii remains undervalued. The management of A. schaalii infection is multimodal, consisting predominantly of antimicrobials and surgical procedures specific to the etiology. Clinicians should request sensitivities for A. schaalii so that appropriate antimicrobial coverage can be provided. Full article
(This article belongs to the Special Issue The Ongoing Renaissance in Clinical Microbiology considering One Health, Zoonotic Infections and Antimicrobial Resistance)
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