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

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 62086

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Dr. Garyphallia Poulakou

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Guest Editor

3rd Department of Internal Medicine and Laboratory, School of Medicine, NKUA, Sotiria General Hospital, Athens, Greece
Interests: viral infections; emerging pathogens; infection control; antimicrobial resistance; antimicrobial stewardship; public health; medical education
Special Issues, Collections and Topics in MDPI journals

Dr. Nikolaos Spernovasilis

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Department of Infectious Diseases, German Oncology Center, 4108 Limassol, Cyprus
Interests: infection control; antimicrobial resistance; antimicrobial stewardship; refugee health; public health; medical education
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Emerging infectious diseases are defined as infections based upon whether they have recently appeared within a population or those whose incidence or geographic range is rapidly increasing or threatens to increase in the near future. They can be caused by a variety of pathogens, and existing examples include SARS virus, SARS-CoV-2, MERS virus, filoviruses, hemorrhagic fever viruses, dengue virus, chikungunya virus, West Nile virus, Zika virus, Borrelia burgdorferi, and Candida auris. Emerging infectious diseases can have a serious public health impact if not detected and contained while they are localized and manageable, as was the case with COVID-19 pandemic.

We are pleased to invite you to submit articles related to the epidemiology, diagnosis, treatment and control of emerging and re-emerging infectious diseases, focusing on recent advances in the aforementioned fields. Original research articles and reviews are welcome. Research areas may include (but not limited to) the following: new pathogen identification; diagnosis and detection; outbreak investigation and management; infection prevention and control; vaccination; education and training.

We look forward to receiving your contributions.

Dr. Garyphallia Poulakou
Dr. Nikolaos Spernovasilis
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

emerging infectious diseases
re-emerging infectious diseases
epidemic-prone diseases
infection prevention
infection control
outbreak management
preventive vaccines
health education

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 567 KiB

Open AccessEditorial

Emerging and Re-Emerging Infectious Diseases: Humankind’s Companions and Competitors

by Nikolaos Spernovasilis, Sotirios Tsiodras and Garyphallia Poulakou

Microorganisms 2022, 10(1), 98; https://doi.org/10.3390/microorganisms10010098 - 4 Jan 2022

Cited by 23 | Viewed by 10836

Abstract

Infectious disease outbreaks had a significant impact on shaping the societies and cultures throughout human history [...] Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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Research

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8 pages, 452 KiB

Open AccessArticle

Greek Remdesivir Cohort (GREC) Study: Effectiveness of Antiviral Drug Remdesivir in Hospitalized Patients with COVID-19 Pneumonia

by Vasilis Petrakis, Vasiliki Rapti, Karolina Akinosoglou, Constantinos Bonelis, Kalomoira Athanasiou, Vasiliki Dimakopoulou, Nikolaos K. Syrigos, Nikolaos Spernovasilis, Grigoris Trypsianis, Markos Marangos, Charalambos Gogos, Dimitrios Papazoglou, Periklis Panagopoulos and Garyfallia Poulakou

Microorganisms 2022, 10(10), 1949; https://doi.org/10.3390/microorganisms10101949 - 30 Sep 2022

Cited by 7 | Viewed by 2460

Abstract

In several randomized studies, remdesivir (RDV) has been reported to shorten the recovery period and improve clinical outcomes in COVID-19 patients, and thus, it is recommended as a standard of care. Nevertheless, controversial reports have been published. The aim of the present study is to evaluate the effectiveness of remdesivir in hospitalized patients with COVID-19 pneumonia at three Greek University Departments of Infectious Diseases with homogenous treatment protocols. From September 2020 to February 2021, we retrospectively analyzed adults hospitalized with confirmed SARS-CoV-2 infection and radiological findings of pneumonia, who received remdesivir once daily for five days. Exploratory end points were duration of hospitalization, time of intubation, and death. Overall, 551 patients were included in the study. The optimal cutoff point for the number of days needed after symptom initiation for drug administration associated with better clinical outcome was 7 days. Higher odds for discharge and lower for intubation were observed in patients with treatment initiation ≤7 days (p = 0.052 and p = 0.019, retrospectively) regardless of gender (p = 0.537), hypertension (p = 0.096), dyslipidemia (p = 0.221), diabetes mellitus (p = 0.306), and usage of immunomodulators (p = 0.408). Our study has demonstrated beneficial effects of early treatment with remdesivir (≤7 days from symptom onset) on rates of intubation and probability of discharge. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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19 pages, 25272 KiB

Open AccessArticle

Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization

by Lukas Zemaitis, Gediminas Alzbutas, Dovydas Gecys, Arnoldas Pautienius, Rasa Ugenskiene, Marius Sukys and Vaiva Lesauskaite

Microorganisms 2022, 10(7), 1356; https://doi.org/10.3390/microorganisms10071356 - 5 Jul 2022

Cited by 2 | Viewed by 1863

Abstract

Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April–May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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12 pages, 903 KiB

Open AccessArticle

Bloodstream Infections in a COVID-19 Non-ICU Department: Microbial Epidemiology, Resistance Profiles and Comparative Analysis of Risk Factors and Patients’ Outcome

by Efthymia Giannitsioti, Christina Louka, Vasiliki Mamali, Elisavet Kousouli, Lemonia Velentza, Vaia Papadouli, Georgios Loizos, Panagiotis Mavroudis, Georgios Kranidiotis, Nektaria Rekleiti, Alexandra Stamati, Ioannis Speggos, Ioannis Daniil, Panagiotis Kouvatsos, Chrysanthi Sidiropoulou, Garifallia Linardaki, Styliani Gerakari, Georgios Chrysos, Katina Themeli-Digalaki and Olympia Zarkotou

Microorganisms 2022, 10(7), 1314; https://doi.org/10.3390/microorganisms10071314 - 29 Jun 2022

Cited by 17 | Viewed by 2869

Abstract

Background: Bloodstream infections (BSI) caused by highly resistant pathogens in non-ICU COVID-19 departments pose important challenges. Methods: We performed a comparative analysis of incidence and microbial epidemiology of BSI in COVID-19 vs. non-COVID-19, non-ICU departments between 1 September 2020-31 October 2021. Risk factors for BSI and its impact on outcome were evaluated by a case-control study which included COVID-19 patients with/without BSI. Results: Forty out of 1985 COVID-19 patients developed BSI. The mean monthly incidence/100 admissions was 2.015 in COVID-19 and 1.742 in non-COVID-19 departments. Enterococcus and Candida isolates predominated in the COVID-19 group (p < 0.001 and p = 0.018, respectively). All Acinetobacter baumannii isolates were carbapenem-resistant (CR). In the COVID-19 group, 33.3% of Klebsiella pneumoniae was CR, 50% of Escherichia coli produced ESBL and 19% of Enterococcus spp. were VRE vs. 74.5%, 26.1% and 8.8% in the non-COVID-19 group, respectively. BSI was associated with prior hospitalization (p = 0.003), >2 comorbidities (p < 0.001), central venous catheter (p = 0.015), severe SARS-CoV-2 pneumonia and lack of COVID-19 vaccination (p < 0.001). In the multivariate regression model also including age and multiple comorbidities, only BSI was significantly associated with adverse in-hospital outcome [OR (CI95%): 21.47 (3.86–119.21), p < 0.001]. Conclusions: BSI complicates unvaccinated patients with severe SARS-CoV-2 pneumonia and increases mortality. BSI pathogens and resistance profiles differ among COVID-19/non-COVID-19 departments, suggesting various routes of pathogen acquisition. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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13 pages, 656 KiB

Open AccessArticle

Evaluation of the Kinetics of Antibody Response to COVID-19 Vaccine in Solid Organ Transplant Recipients: The Prospective Multicenter ORCHESTRA Cohort

by Maddalena Giannella, Elda Righi, Renato Pascale, Matteo Rinaldi, Natascia Caroccia, Chiara Gamberini, Zaira R. Palacios-Baena, Giulia Caponcello, Maria Cristina Morelli, Mariarosa Tamè, Marco Busutti, Giorgia Comai, Luciano Potena, Elena Salvaterra, Giuseppe Feltrin, Umberto Cillo, Gino Gerosa, Mara Cananzi, Salvatore Piano, Elisa Benetti, Patrizia Burra, Monica Loy, Lucrezia Furian, Gianluigi Zaza, Francesco Onorati, Amedeo Carraro, Fiorella Gastaldon, Maurizio Nordio, Samir Kumar-Singh, Mahsa Abedini, Paolo Boffetta, Jesús Rodríguez-Baño, Tiziana Lazzarotto, Pierluigi Viale, Evelina Tacconelli and on behalf of The ORCHESTRA Study Group Workpackage Show full author list Hide full author list

Microorganisms 2022, 10(5), 1021; https://doi.org/10.3390/microorganisms10051021 - 12 May 2022

Cited by 16 | Viewed by 3461

Abstract

Previous studies assessing the antibody response (AbR) to mRNA COVID-19 vaccines in solid organ transplant (SOT) recipients are limited by short follow-up, hampering the analysis of AbR kinetics. We present the ORCHESTRA SOT recipients cohort assessed for AbR at first dose (t0), second dose (t1), and within 3 ± 1 month (t2) after the first dose. We analyzed 1062 SOT patients (kidney, 63.7%; liver, 17.4%; heart, 16.7%; and lung, 2.5%) and 5045 health care workers (HCWs). The AbR rates in the SOTs and HCWs were 52.3% and 99.4%. The antibody levels were significantly higher in the HCWs than in the SOTs (p < 0.001). The kinetics showed an increase (p < 0.001) in antibody levels up to 76 days and a non-significant decrease after 118 days in the SOT recipients versus a decrease up to 76 days (p = 0.02) and a less pronounced decrease between 76 and 118 days (p = 0.04) in the HCWs. Upon multivariable analysis, liver transplant, ≥3 years from SOT, mRNA-1273, azathioprine, and longer time from t0 were associated with a positive AbR at t2. Older age, other comorbidities, mycophenolate, steroids, and impaired graft function were associated with lower AbR probability. Our results may be useful to optimize strategies of immune monitoring after COVID-19 vaccination and indications regarding timing for booster dosages calibrated on SOT patients’ characteristics. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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17 pages, 310 KiB

Open AccessArticle

COVID-19 and C. auris: A Case-Control Study from a Tertiary Care Center in Lebanon

by Fatima Allaw, Sara F. Haddad, Nabih Habib, Pamela Moukarzel, Nour Sabiha Naji, Zeina A. Kanafani, Ahmad Ibrahim, Nada Kara Zahreddine, Nikolaos Spernovasilis, Garyphallia Poulakou and Souha S. Kanj

Microorganisms 2022, 10(5), 1011; https://doi.org/10.3390/microorganisms10051011 - 11 May 2022

Cited by 15 | Viewed by 3453

Abstract

Many healthcare centers around the world have reported the surge of Candida auris (C. auris) outbreaks during the COVID-19 pandemic, especially among intensive care unit (ICU) patients. This is a retrospective study conducted at the American University of Beirut Medical Center (AUBMC) between 1 October 2020 and 15 June 2021, to identify risk factors for acquiring C. auris in patients with severe COVID-19 infection and to evaluate the impact of C. auris on mortality in patients admitted to the ICU during that period. Twenty-four non-COVID-19 (COV−) patients were admitted to ICUs at AUBMC during that period and acquired C. auris (C. auris+/COV−). Thirty-two patients admitted with severe COVID-19 (COV+) acquired C. auris (C. auris+/COV+), and 130 patients had severe COVID-19 without C. auris (C. auris−/COV+). Bivariable analysis between the groups of (C. auris+/COV+) and (C. auris−/COV+) showed that higher quick sequential organ failure assessment (qSOFA) score (p < 0.001), prolonged length of stay (LOS) (p = 0.02), and the presence of a urinary catheter (p = 0.015) or of a central venous catheter (CVC) (p = 0.01) were associated with positive culture for C. auris in patients with severe COVID-19. The multivariable analysis showed that prolonged LOS (p = 0.008) and a high qSOFA score (p < 0.001) were the only risk factors independently associated with positive culture for C. auris. Increased LOS (p = 0.02), high “Candida score” (p = 0.01), and septic shock (p < 0.001) were associated with increased mortality within 30 days of positive culture for C. auris. Antifungal therapy for at least 7 days (p = 0.03) appeared to decrease mortality within 30 days of positive culture for C. auris. Only septic shock was associated with increased mortality in patients with C. auris (p = 0.006) in the multivariable analysis. C. auris is an emerging pathogen that constitutes a threat to the healthcare sector. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

9 pages, 1475 KiB

Open AccessArticle

Evaluation of S1RBD-Specific IgG Antibody Responses following COVID-19 Vaccination in Healthcare Professionals in Cyprus: A Comparative Look between the Vaccines of Pfizer-BioNTech and AstraZeneca

by Elie Deeba, George Krashias, Astero Constantinou, Dana Koptides, Anastasia Lambrianides and Christina Christodoulou

Microorganisms 2022, 10(5), 967; https://doi.org/10.3390/microorganisms10050967 - 4 May 2022

Cited by 2 | Viewed by 2244

Abstract

There is an ongoing effort to report data on SARS-CoV-2 antibodies in different individuals. Ninety-seven healthcare workers were enrolled in this study (Pfizer’s BNT162b2, n = 52; and AstraZeneca’s ChAdOx1-S, n = 45) and S1RBD-specific IgG antibodies were analyzed over time. Both vaccines induced S1RBD-specific antibodies after the second dose. A significant increase in S1RBD-specific IgG median levels 3 weeks following the second dose was detected (BNT162b2, 118.0 BAU/mL to 2018.0 BAU/mL; ChAdOx1-S, 38.1 BAU/mL to 182.1 BAU/mL). At 3 months post the second dose, a significant decrease in S1RBD-specific IgG median levels was also evident (BNT162b2, 415.6 BAU/mL, ChAdOx1-S, 84.7 BAU/mL). The elimination rate of these antibodies was faster in BNT162b2- rather than ChAdOx1-S- vaccinated individuals. A booster dose induced a significant increase in the S1RBD-specific IgG median levels (BNT162b2, 1823.0 BAU/mL; ChAdOx1-S, 656.8 BAU/mL). This study is the first of its kind to characterize S1RBD-specific IgG antibody responses in vaccinated healthcare workers in Cyprus. While the positivity for S1RBD-specific antibodies was maintained 3 months after the second vaccine dose, the level of these antibodies waned over the same period, indicating the importance of a booster vaccination. The results herein could complement the public health policies regarding the immunization schedule for COVID-19. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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8 pages, 552 KiB

Open AccessArticle

Infections Caused by Moellerella wisconsensis: A Case Report and a Systematic Review of the Literature

by Daphnie Germanou, Nikolaos Spernovasilis, Anastasios Papadopoulos, Sofia Christodoulou and Aris P. Agouridis

Microorganisms 2022, 10(5), 892; https://doi.org/10.3390/microorganisms10050892 - 24 Apr 2022

Cited by 3 | Viewed by 4010

Abstract

Background: Moellerella wisconsensis, a member of the family of Enterobacteriaceae, although isolated widely in nature, rarely causes infections in humans. Herein, we report a case of isolation of M. wisconsensis from pigtail end culture, urine culture and blood culture in a 76-year-old patient. Objective: To systematically address all the relevant information regarding M. wisconsensis through literature. Methods: We searched PubMed and Scopus databases up to January 2022 and performed a qualitative synthesis of published articles reporting infection from M. wisconsensis in humans. Results: We identified 25 records on PubMed and 43 additional records on Scopus. After removing duplicates, we examined in detail 15 articles. Ten studies with a total of 17 cases were included in our systematic review. Nine studies described isolated case reports, while 1 study described 8 cases. The origin of the infection was the alimentary tract in 9 cases, gallbladder in 4 cases, peritoneal cavity in 2 cases, respiratory tract in 1 case and hemodialysis catheter insertion site in 1 case. In 3 of the aforementioned cases M. wisconsensis was also isolated in blood cultures. Conclusion: Physicians should be aware that M. wisconsensis can be present in multiple clinical specimens and that the antibiotic resistance profile of the isolates may pose significant challenges. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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Review

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16 pages, 1840 KiB

Open AccessReview

Lomentospora prolificans: An Emerging Opportunistic Fungal Pathogen

by Afroditi Konsoula, Constantinos Tsioutis, Ioulia Markaki, Michail Papadakis, Aris P. Agouridis and Nikolaos Spernovasilis

Microorganisms 2022, 10(7), 1317; https://doi.org/10.3390/microorganisms10071317 - 29 Jun 2022

Cited by 18 | Viewed by 3571

Abstract

Lomentospora prolificans is an emerging opportunistic pathogen that primarily affects immunocompromised individuals leading to disseminated disease with high mortality rates while also causing infections in healthy populations. Successful recovery from infection is difficult due to high rates of intrinsic resistance to antifungals. Rapid and readily available diagnostic methods, aggressive surgical debridement wherever appropriate, and effective and timely antifungal treatment are the pillars for successful management. Future research will need to clarify the environmental niche of the fungus, further investigate the pathophysiology of infection and define species-specific therapeutic targets. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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14 pages, 1483 KiB

Open AccessReview

SARS CoV-2-Induced Viral Sepsis: The Role of Gut Barrier Dysfunction

by Stelios F. Assimakopoulos, Gerasimos Eleftheriotis, Maria Lagadinou, Vassilios Karamouzos, Periklis Dousdampanis, Georgios Siakallis and Markos Marangos

Microorganisms 2022, 10(5), 1050; https://doi.org/10.3390/microorganisms10051050 - 19 May 2022

Cited by 20 | Viewed by 6517

Abstract

A considerable proportion of patients with severe COVID-19 meet Sepsis-3 criteria and share common pathophysiological mechanisms of multiorgan injury with bacterial sepsis, in absence of secondary bacterial infections, a process characterized as “viral sepsis”. The intestinal barrier exerts a central role in the pathophysiological sequence of events that lead from SARS-CoV-2 infection to severe systemic complications. Accumulating evidence suggests that SARS-CoV-2 disrupts the integrity of the biological, mechanical and immunological gut barrier. Specifically, microbiota diversity and beneficial bacteria population are reduced, concurrently with overgrowth of pathogenic bacteria (dysbiosis). Enterocytes’ tight junctions (TJs) are disrupted, and the apoptotic death of intestinal epithelial cells is increased leading to increased gut permeability. In addition, mucosal CD4(+) and CD8(+) T cells, Th17 cells, neutrophils, dendritic cells and macrophages are activated, and T-regulatory cells are decreased, thus promoting an overactivated immune response, which further injures the intestinal epithelium. This dysfunctional gut barrier in SARS-CoV-2 infection permits the escape of luminal bacteria, fungi and endotoxin to normally sterile extraintestinal sites and the systemic circulation. Pre-existing gut barrier dysfunction and endotoxemia in patients with comorbidities including cardiovascular disease, obesity, diabetes and immunosuppression predisposes to aggravated endotoxemia. Bacterial and endotoxin translocation promote the systemic inflammation and immune activation, which characterize the SARS-CoV-2 induced “viral sepsis” syndrome associated with multisystemic complications of severe COVID-19. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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Other

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28 pages, 3043 KiB

Open AccessSystematic Review

Cutaneous Complications of mRNA and AZD1222 COVID-19 Vaccines: A Worldwide Review

by George Kroumpouzos, Maria Eleni Paroikaki, Sara Yumeen, Shashank Bhargava and Eleftherios Mylonakis

Microorganisms 2022, 10(3), 624; https://doi.org/10.3390/microorganisms10030624 - 15 Mar 2022

Cited by 20 | Viewed by 17623

Abstract

Because of the increasing emergence of cutaneous reactions from COVID-19 vaccines worldwide, we investigated the published reports of these complications. We searched the PubMed, Google Scholar, and Scopus databases and the preprint server bioRxiv for articles on cutaneous complications linked to mRNA-1273 (Moderna), BNT162b2 (Pfizer–BioNTech), and AZD1222 (AstraZeneca–Oxford University) vaccines published until 30 September 2021. Eighty studies describing a total of 1415 reactions were included. Cutaneous reactions were more prevalent in females (81.6%). Delayed large local reactions were the most common complication (40.4%), followed by local injection site reactions (16.5%), zoster (9.5%), and urticarial eruptions (9.0%). Injection site and delayed large local reactions were predominantly caused by the mRNA-1273 vaccine (79.5% and 72.0%, respectively). BNT162b2 vaccination was more closely linked to distant reactions (50.1%) than mRNA-1273 (30.0%). Zoster was the most common distant reaction. Of reactions with adequate information for both vaccine doses, 58.3% occurred after the first dose only, 26.9% after the second dose only, and 14.8% after both doses. Overall, a large spectrum of cutaneous reaction patterns occurred following the COVID-19 vaccination. Most were mild and without long-term health implications. Therefore, the occurrence of such dermatologic complications does not contraindicate subsequent vaccination. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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