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Microorganisms
Special Issues
The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects
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The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects

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

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 16412

Special Issue Editors

Dr. Vincenzo Di Pilato

E-Mail Website
Guest Editor
Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
Interests: antimicrobial resistance; resistance mechanisms; genomic epidemiology of healthcare-associated infections; bacterial genomics; carbapenemase-producing Enterobacterales
Dr. Costas C. Papagiannitsis

E-Mail Website
Guest Editor
Department of Microbiology, Faculty of Medicine, University of Thessaly, Larissa, Greece
Interests: antimicrobial resistance; resistance mechanisms; carbapenemase; mobile genetic elements (MGEs); whole-genome sequencing (WGS)
Special Issues, Collections and Topics in MDPI journals
Dr. Daniele Roberto Giacobbe

E-Mail Website
Guest Editor
Department of Health Sciences (DISSAL), Università degli Studi di Genova, Genoa, Italy
Interests: antimicrobial resistance; carbapenem resistance; antimicrobial stewardship
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since December 2019, we have been facing a pandemic due to the spread of SARS-CoV-2 coronavirus, which is affecting millions of individuals and is characterized by high morbidity and mortality globally. Despite the proven importance of bacterial co-infections in determining the severity of respiratory diseases, they are still understudied and, at present, current knowledge on the microbiological and clinical characteristics of bacterial co-infections in patients with coronavirus disease 2019 (COVID-19) is scarce. Indeed, limited information is available on antimicrobial sensitivities, resistance mechanisms, and on the organisms that were identified, in addition to the type and duration of antimicrobial treatment.

This Special Issue of Microorganisms, “The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects”, is therefore dedicated to addressing these gaps in knowledge. It aims to bring together up-to-date information on all aspects concerning bacterial infections and the COVID-19 pandemic. Topics of particular interest include, but are not limited to, mechanisms of emergence and dissemination of antimicrobial resistance (with particular emphasis on newly introduced drugs) or virulence, biofilm-associated infections, molecular epidemiology of multidrug-resistant organisms and antimicrobial resistances, use of antibiotics in patients with COVID-19, and microbiological and clinical features of difficult-to-treat bacterial co-infections in patients with COVID-19.

Papers reporting on original research, comprehensive reviews providing a critical and constructive analysis of the existing literature, as well as short communications and case reports are welcomed. Manuscripts that only deal with clinical management/policy/healthcare will be considered for publication following an evaluation by the Guest Editors.

Dr. Vincenzo Di Pilato
Dr. Costas C. Papagiannitsis
Dr. Daniele Roberto Giacobbe
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. 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.

Keywords

  • COVID-19
  • bacterial infections
  • antimicrobial sensitivities
  • resistance mechanisms
  • molecular epidemiology
  • antimicrobial stewardship

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Published Papers (5 papers)

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Editorial

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2 pages, 185 KiB  
Editorial
Editorial of Special Issue “The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects”
by Vincenzo Di Pilato and Daniele Roberto Giacobbe
Microorganisms 2023, 11(4), 1009; https://doi.org/10.3390/microorganisms11041009 - 12 Apr 2023
Cited by 3 | Viewed by 1217
Abstract
The emergence in late 2019 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the pandemic coronavirus disease 2019 (COVID-19), posed significant health challenges worldwide [...] Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)

Research

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9 pages, 1969 KiB  
Article
Changes in Invasive Neisseria meningitidis and Haemophilus influenzae Infections in France during the COVID-19 Pandemic
by Ala-Eddine Deghmane and Muhamed-Kheir Taha
Microorganisms 2022, 10(5), 907; https://doi.org/10.3390/microorganisms10050907 - 26 Apr 2022
Cited by 25 | Viewed by 4733
Abstract
BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data [...] Read more.
BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data considering the current COVID-19 pandemic situation. Methods: The data of the national reference center for meningococci and Haemophilus influenzae in France were mined to examine the above aspects of invasive bacterial infection before (2018–2019) and after (2020–2021) the COVID-19 pandemic. Detailed epidemiological, clinical, and microbiological data were collected, and whole genome sequencing was carried out on meningococcal isolates (n = 1466). Results: In addition to the overall decline in the number of cases, various changes in age, sex, and phenotypes of isolates were also noted. As for N. meningitidis, more cases were observed in adults, as well as more invasive pneumopathies. Furthermore, fewer hyperinvasive meningococcal genotypes have circulated since COVID-19 emerged. The situation has been different for H. influenzae, as the number of invasive cases among adults decreased due to a reduction in non-typeable isolates. In contrast, cases due to serotypeable isolates, particularly serotypes a and b, increased in children <5 years-old. Conclusions: It is possible that measures implemented to stop COVID-19 may have reduced the circulation of N. meningitidis and H. influenzae isolates, but to a variable extent. This may be due to differences in circulation between these two species according to age groups. Vaccination schedules against these two species may have also influenced the evolution of these invasive bacterial infections since the emergence of the COVID-19 pandemic. Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)
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17 pages, 938 KiB  
Article
High Rates of Bacterial Pulmonary Co-Infections and Superinfections Identified by Multiplex PCR among Critically Ill COVID-19 Patients
by Regev Cohen, Frida Babushkin, Talya Finn, Keren Geller, Hanna Alexander, Candice Datnow, Martina Uda, Maurice Shapiro, Svetlana Paikin and Jonathan Lellouche
Microorganisms 2021, 9(12), 2483; https://doi.org/10.3390/microorganisms9122483 - 30 Nov 2021
Cited by 20 | Viewed by 2532
Abstract
Background: The role of bacterial co-infection and superinfection among critically ill COVID-19 patients remains unclear. The aim of this study was to assess the rates and characteristics of pulmonary infections, and associated outcomes of ventilated patients in our facility. Methods: This was a [...] Read more.
Background: The role of bacterial co-infection and superinfection among critically ill COVID-19 patients remains unclear. The aim of this study was to assess the rates and characteristics of pulmonary infections, and associated outcomes of ventilated patients in our facility. Methods: This was a retrospective study of ventilated COVID-19 patients between March 2020 and March 2021 that underwent BioFire®, FilmArray® Pneumonia Panel, testing. Community-acquired pneumonia (CAP) was defined when identified during the first 72 h of hospitalization, and ventilator-associated pneumonia (VAP) when later. Results: 148 FilmArray tests were obtained from 93 patients. With FilmArray, 17% of patients had CAP (16/93) and 68% had VAP (64/93). Patients with VAP were older than those with CAP or those with no infection (68.5 vs. 57–59 years), had longer length of stay and higher mortality (51% vs. 10%). The most commonly identified FilmArray target organisms were H. influenzae, S. pneumoniae, M. catarrhalis and E. cloacae for CAP and P. aeruginosa and S. aureus for VAP. FilmArray tests had high negative predictive values (99.6%) and lower positive predictive values (~60%). Conclusions: We found high rates of both CAP and VAP among the critically ill, caused by the typical and expected organisms for both conditions. VAP diagnosis was associated with poor patient outcomes. Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)
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9 pages, 799 KiB  
Article
Use of Sedatives and Neuromuscular-Blocking Agents in Mechanically Ventilated Patients with COVID-19 ARDS
by Amédée Ego, Lorenzo Peluso, Julie Gorham, Alberto Diosdado, Giovanni Restuccia, Jacques Creteur and Fabio Silvio Taccone
Microorganisms 2021, 9(11), 2393; https://doi.org/10.3390/microorganisms9112393 - 20 Nov 2021
Cited by 7 | Viewed by 2242
Abstract
Objectives: To assess differences in the use of analgesics, sedatives and neuromuscular-blocking agents (NMBA) in patients with acute respiratory distress syndrome (ARDS) due to COVID-19 or other conditions. Methods: Retrospective observational cohort study, single-center tertiary Intensive Care Unit. COVID-19 patients with ARDS (March–May [...] Read more.
Objectives: To assess differences in the use of analgesics, sedatives and neuromuscular-blocking agents (NMBA) in patients with acute respiratory distress syndrome (ARDS) due to COVID-19 or other conditions. Methods: Retrospective observational cohort study, single-center tertiary Intensive Care Unit. COVID-19 patients with ARDS (March–May 2020) and non-COVID ARDS patients (2017–2020) on mechanical ventilation and receiving sedation for at least 48 h. Results: A total of 39 patients met the inclusion criteria in each group, with similar demographics at baseline. COVID-19 patients had a longer duration of MV (median 22 (IQRs 16–29) vs. 9 (6–18) days; p < 0.01), of sedatives administration (18 (11–22) vs. 5 (4–9) days; p < 0.01) and NMBA therapy (12 (9–16) vs. 3 (2–7) days; p < 0.01). During the first 7 days of sedation, compared to non-COVID patients, COVID patients received more frequently a combination of multiple sedative drugs (76.9% vs. 28.2%; p < 0.01) and a higher NMBA regimen (cisatracurium: 3.0 (2.1–3.7) vs. 1.3 (0.9–1.9) mg/kg/day; p < 0.01). Conclusions: The duration and consumption of sedatives and NMBA was significantly increased in patients with COVID-19 related ARDS than in non-COVID ARDS. Different sedation strategies and protocols might be needed in COVID-19 patients with ARDS, with potential implications on long-term complications and drugs availability. Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)
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Other

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6 pages, 244 KiB  
Case Report
Hafnia alvei Pneumonia: A Rare Cause of Infection in a Patient with COVID-19
by Lucía Méndez, Jorge Ferreira and Cátia Caneiras
Microorganisms 2021, 9(11), 2369; https://doi.org/10.3390/microorganisms9112369 - 17 Nov 2021
Cited by 7 | Viewed by 4368
Abstract
Herein, we describe a case report of a critically ill patient, a 48-year-old man without comorbidities admitted to the hospital with a serious type 1 (hypoxemic) respiratory insufficiency and confirmed diagnosis of COVID-19. After 5 days with invasive mechanical ventilation, the patient developed [...] Read more.
Herein, we describe a case report of a critically ill patient, a 48-year-old man without comorbidities admitted to the hospital with a serious type 1 (hypoxemic) respiratory insufficiency and confirmed diagnosis of COVID-19. After 5 days with invasive mechanical ventilation, the patient developed a bacterial co-infection, namely a pneumonia by Hafnia alvei, requiring the last line of respiratory support: extracorporeal membrane oxygenation (ECMO). Subsequently, his clinical situation gradually stabilized, until he was discharged from the hospital on day 61, being accompanied in ambulatory consultation by the physical medicine and pulmonology department during the post-COVID-19 recovery. H. alvei is a Gram-negative bacterium that is rarely isolated from human specimens and is rarely considered to be pathogenic. However, COVID-19 disease can cause substantial organ dysfunction and can be associated with bacterial secondary infections which can favor the emergence of rare infectious diseases by uncommon microorganisms. Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)
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