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Infectious Diseases, New Approaches to Old Problems 2.0

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

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 16591

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Dr. Eva Torres-Sangiao

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Clinical Microbiology Laboratory, University Hospital Marqués de Valdecilla, Researh Institute IDIVAL, 39001 Santander, Spain
Interests: system biology; immunoproteome; infectious diseases; sexual transmission diseases; mass spectrometry
Special Issues, Collections and Topics in MDPI journals

Dr. Monica Cartelle Gestal

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Microbiology and Immunology Department, Louisiana State University Health Sciences Center, Shreveport, LA, USA
Interests: microbiology; infectious diseases; bordetella; vaccines
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Dr. Nelson C. Soares

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College of Pharmacy, Department of Medicinal Chemistry, Sharjah University, Sharjah, United Arab Emirates
Interests: proteomics; mass spectrometry; metabolomics; microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During recent years and till now, we have been living in a time of concern regarding not only COVID-19 but also “old-known” infections such as monkeypox. It is well-known that infectious diseases are one of the leading causes of death worldwide, and past as well as current efforts focus on their prevention and treatment, with the expectation of reducing their morbidity, mortality, and associated economic burden. One trait common to most pathogens is their ability to modulate, manipulate, and escape host immune responses. Therefore, immunomodulation approaches, such as adjuvants, therapies, and vaccines, appear to be the most compelling methods with which to enhance immune responses, and appear to be highly promising. Additionally, the concept of One Health has hallmarked the lack of prevention in control in other areas that have great implications for human health. Importantly, bacteria, along with viruses and parasites, are great hazards and a challenge to prevent as well as treat.

This aim of this Special Issue is to unite several fields of research to approach the problem from a One Health perspective. This Special Issue emerges as a result of the lack of strategies and solutions with which to overcome infectious diseases in the framework of technology and the interconnected world. It will also be a platform on which novel strategies for vaccine and therapeutic development will be provided, focusing on immunomodulation.

Dr. Eva Torres-Sangiao
Dr. Monica Cartelle Gestal
Dr. Nelson C Soares
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

infectious diseases
antibiotic resistance
vaccines and therapies
biomarkers and diagnosis
mass spectrometry
immunomodulation
inflammation
systems biology
metabolomics

Published Papers (8 papers)

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Research

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15 pages, 3943 KiB

Open AccessArticle

Adenoviral Vector Codifying for TNF as a Co-Adjuvant Therapy against Multi-Drug-Resistant Tuberculosis

by Sujhey Hernández-Bazán, Dulce Mata-Espinosa, Octavio Ramos-Espinosa, Vasti Lozano-Ordaz, Jorge Barrios-Payán, Fernando López-Casillas and Rogelio Hernández-Pando

Microorganisms 2023, 11(12), 2934; https://doi.org/10.3390/microorganisms11122934 - 07 Dec 2023

Viewed by 819

Abstract

Mycobacterium tuberculosis is the main causal agent of pulmonary tuberculosis (TB); the treatment of this disease is long and involves a mix of at least four different antibiotics that frequently lead to abandonment, favoring the surge of drug-resistant mycobacteria (MDR-TB), whose treatment becomes more aggressive, being longer and more toxic. Thus, the search for novel strategies for treatment that improves time or efficiency is of relevance. In this work, we used a murine model of pulmonary TB produced by the MDR-TB strain to test the efficiency of gene therapy with adenoviral vectors codifying TNF (AdTNF), a pro-inflammatory cytokine that has protective functions in TB by inducing apoptosis, granuloma formation and expression of other Th1-like cytokines. When compared to the control group that received an adenoviral vector that codifies for the green fluorescent protein (AdGFP), a single dose of AdTNF at the chronic active stage of the disease produced total survival, decreasing bacterial load and tissue damage (pneumonia), which correlated with an increase in cells expressing IFN-γ, iNOS and TNF in pneumonic areas and larger granulomas that efficiently contain and eliminate mycobacteria. Second-line antibiotic treatment against MDR-TB plus AdTNF gene therapy reduced bacterial load faster within a week of treatment compared to empty vector plus antibiotics or antibiotics alone, suggesting that AdTNF is a new potential type of treatment against MDR-TB that can shorten second-line chemotherapy but which requires further experimentation in other animal models (non-human primates) that develop a more similar disease to human pulmonary TB. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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16 pages, 1392 KiB

Open AccessArticle

CRISPR-Cas-Based Adaptive Immunity Mediates Phage Resistance in Periodontal Red Complex Pathogens

by Pradeep Kumar Yadalam, Deepavalli Arumuganainar, Raghavendra Vamsi Anegundi, Deepti Shrivastava, Sultan Abdulkareem Ali Alftaikhah, Haifa Ali Almutairi, Muhanad Ali Alobaida, Abdullah Ahmed Alkaberi and Kumar Chandan Srivastava

Microorganisms 2023, 11(8), 2060; https://doi.org/10.3390/microorganisms11082060 - 11 Aug 2023

Cited by 1 | Viewed by 1105

Abstract

Periodontal diseases are polymicrobial immune–inflammatory diseases that can severely destroy tooth-supporting structures. The critical bacteria responsible for this destruction include red complex bacteria such as Porphoromonas gingivalis, Tanerella forsythia and Treponema denticola. These organisms have developed adaptive immune mechanisms against bacteriophages/viruses, plasmids and transposons through clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas). The CRISPR-Cas system contributes to adaptive immunity, and this acquired genetic immune system of bacteria may contribute to moderating the microbiome of chronic periodontitis. The current research examined the role of the CRISPR-Cas system of red complex bacteria in the dysbiosis of oral bacteriophages in periodontitis. Whole-genome sequences of red complex bacteria were obtained and investigated for CRISPR using the CRISPR identification tool. Repeated spacer sequences were analyzed for homologous sequences in the bacteriophage genome and viromes using BLAST algorithms. The results of the BLAST spacer analysis for T. denticola spacers had a 100% score (e value with a bacillus phage), and the results for T. forsthyia and P. gingivalis had a 56% score with a pectophage and cellulophage (e value: 0.21), respectively. The machine learning model of the identified red complex CRISPR sequences predicts with area an under the curve (AUC) accuracy of 100 percent, indicating phage inhibition. These results infer that red complex bacteria could significantly inhibit viruses and phages with CRISPR immune sequences. Therefore, the role of viruses and bacteriophages in modulating sub-gingival bacterial growth in periodontitis is limited or questionable. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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15 pages, 3163 KiB

Open AccessArticle

Oral Myco- and Bacteriobiota and Yeast Infections in Mechanically Ventilated COVID-19 Patients

by Iwona Gregorczyk-Maga, Michal Kania, Beata Sulik-Tyszka, Magdalena Namysł, Anna Sepioło, Dorota Romaniszyn, Estera Jachowicz-Matczak and Jadwiga Wójkowska-Mach

Microorganisms 2023, 11(6), 1442; https://doi.org/10.3390/microorganisms11061442 - 30 May 2023

Viewed by 1135

Abstract

Critically ill COVID-19 patients requiring mechanical ventilation in the intensive care unit are at risk of developing invasive candidiasis. In this study we aimed to (1) characterize oral cultivable mycobiota of mechanically ventilated adult COVID-19 patients in an ICU setting by sampling four distinct oral niches in two fixed time points with regards to oral health status, (2) investigate Candida spp. infections in this population, and (3) compare oral mycobiota with selected bacteriobiota strains during the observation in the ICU. We recruited 56 adult COVID-19 patients who qualified for mechanical ventilation. Patients received either standard or extended oral care procedures with tooth brushing. Oral samples were taken first within 36 h and after 7 days of intubation. Yeast-like fungi were identified by MALDI/TOF mass spectrometry. Yeast infection cases were retrospectively analyzed. Candida spp. in oral sampling was identified in 80.4% and 75.7%, C. albicans in 57.1% and 61.1%, and non-albicans Candida species in 48.2% and 47.2% patients at baseline and follow-up, respectively. There were no differences in the overall CFU counts of Candida spp. species and individual Candida species in oral samples, both at baseline and follow-up. At baseline, a higher prevalence of Candida spp. was associated with a higher identification rate of Lactobacillus spp. (64.4% vs. 27.3%, p = 0.041). At follow-up, there was a borderline lower prevalence of Candida spp. in patients with Lactobacillus spp. identified (57.1% vs. 87.0%, p = 0.057). The incidence rate of candidiasis was 5.4% and the incidence density was 3.1/1000 pds. In conclusion, non-albicans Candida species in oral samples were identified in nearly half of patients. Oral health was moderately impaired. A high incidence of yeast infections, including invasive cases, in patients hospitalized in the ICU due to COVID-19 and requiring mechanical ventilation was noted. Severe COVID-19 and disease-specific interventions within the ICU possibly played a major role promoting Candida spp. infections. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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12 pages, 620 KiB

Open AccessArticle

Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study

by Edwin Kamau and Shangxin Yang

Microorganisms 2023, 11(5), 1259; https://doi.org/10.3390/microorganisms11051259 - 10 May 2023

Cited by 1 | Viewed by 1730

Abstract

With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software’s agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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18 pages, 6916 KiB

Open AccessArticle

HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut

by Lu Li, Xiaojie Zhao and Johnny J. He

Microorganisms 2023, 11(3), 799; https://doi.org/10.3390/microorganisms11030799 - 21 Mar 2023

Cited by 1 | Viewed by 1376

Abstract

The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial barrier integrity, which contribute to inflammation and immune activation. Our recent study shows that Tat expression and cocaine exposure result in changes of genome-wide DNA methylation and gene expression and lead to worsen the learning and memory impairments. In the current study, we extended the study to determine effects of Tat and cocaine on the gut microbiota composition. We found that both Tat expression and cocaine exposure increased Alteromonadaceae in 6-month-old female/male mice. In addition, we found that Tat, cocaine, or both increased Alteromonadaceae, Bacteroidaceae, Cyanobiaceae, Erysipelotrichaceae, and Muribaculaceae but decreased Clostridiales_vadinBB60_group, Desulfovibrionaceae, Helicobacteraceae, Lachnospiraceae, and Ruminococcaceae in 12-month-old female mice. Lastly, we analyzed changes of metabolic pathways and found that Tat decreased energy metabolism and nucleotide metabolism, and increased lipid metabolism and metabolism of other amino acids while cocaine increased lipid metabolism in 12-month-old female mice. These results demonstrated that Tat expression and cocaine exposure resulted in significant changes of the gut microbiota in an age- and sex-dependent manner and provide additional evidence to support the bidirectional gut–brain axis hypothesis. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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9 pages, 681 KiB

Open AccessCommunication

Mobile Phones: Reservoirs of Resistant Bacteria during the COVID-19 Pandemic in Abu Dhabi, United Arab Emirates

by Kawthar Kayed, Ghalia Khoder, Joviana Farhat and Rose Ghemrawi

Microorganisms 2023, 11(2), 523; https://doi.org/10.3390/microorganisms11020523 - 18 Feb 2023

Cited by 1 | Viewed by 5170

Abstract

Background: Mobile phones are excessively used even though microbes’ ability to survive on phone surfaces was confirmed. During the COVID-19 pandemic, heavy hygiene practices have been applied to mobile surfaces. Therefore, it is interesting to evaluate the emergence of antimicrobial-resistant bacteria on mobile phone surfaces. Methods: A random sampling technique was utilized on residents in Abu Dhabi, UAE between May and June 2021. A swab sample from each participant’s mobile phone was collected and transported to the microbiology laboratory for bacterial culture and antimicrobial susceptibility tests. Furthermore, a cross-sectional study was conducted via a self-administered questionnaire filled by participants. The questionnaire was used to collect sociodemographic data, phone frequency usage and cleaning methods. Results: One hundred two-sample swabs and data have been included in the study. The majority of participants (91.1%) reported cleaning their mobile phones with wipes and alcohol. However, 100% of participants had a mobile phone contaminated by bacteria such as S. aureus, E. coli, Coagulase-negative staphylococci, Micrococcus, Bacillus, Streptococcus, Citrobacter, Proteus, Enterococcus, klebsiella, Pseudomonas and Actinobacteria. Interestingly, most of these potentially pathogenic bacteria were found to be resistant to ampicillin, ceftazidime and cefotaxime. Conclusion: The continuous hand and mobile disinfectant have contributed to the emergence of resistant bacteria. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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Review

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23 pages, 2959 KiB

Open AccessReview

SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments

by Xinyi Wang, Jingwen Li, Hanshu Liu, Xinyu Hu, Zhicheng Lin and Nian Xiong

Microorganisms 2023, 11(3), 580; https://doi.org/10.3390/microorganisms11030580 - 24 Feb 2023

Cited by 1 | Viewed by 2123

Abstract

For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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Other

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10 pages, 1852 KiB

Open AccessBrief Report

Atypical Cutaneous Viral Infections Reveal an Inborn Error of Immunity in 8 Patients

by Assiya El Kettani, Fatima Ailal, Farida Marnissi, Fouzia Hali, Jalila El Bakkouri, Ibtihal Benhsaien, Tom Le Voyer, Mame Sokhna Guèye, Rémi Chevalier, Soumiya Chiheb, Khalid Zerouali, Emmanuelle Jouanguy, Jean-Laurent Casanova and Ahmed Aziz Bousfiha

Microorganisms 2023, 11(5), 1202; https://doi.org/10.3390/microorganisms11051202 - 04 May 2023

Cited by 3 | Viewed by 2385

Abstract

Unusual viral skin infections might be the first clinical manifestation in children with an inborn error of immunity (IEI). We performed a prospective study from 1 October 2017 to 30 September 2021, at the Department of Pediatric Infectious Diseases and Clinical Immunity of Ibn Rochd University Hospital-Casablanca. During this period, on 591 patients newly diagnosed with a probable IEI, eight of them (1.3%), from six independent families, had isolated or syndromic unusual viral skin infections, which were either profuse, chronic or recurrent infections, and resistant to any treatment. The median age of disease onset was nine years old and all patients were born from a first-degree consanguineous marriage. By combining clinical, immunological and genetic investigations, we identified GATA2 deficiency in one patient with recalcitrant profuse verrucous lesions and monocytopenia (1/8) and STK4 deficiency in two families with HPV lesions, either flat or common warts, and lymphopenia (2/8), as previously reported. We also identified COPA deficiency in twin sisters with chronic profuse Molluscum contagiosum lesions, pulmonary diseases and microcytic hypochromic anemia (2/8). Finally, we also found one patient with chronic profuse MC lesions and hyper IgE syndrome, (1/8) and two patients with either recalcitrant profuse verrucous lesions or recurrent post-herpetic erythema multiforme and a combined immunodeficiency (2/8) with no genetic defect identified yet. Raising clinicians awareness that infectious skin diseases might be the consequence of an inborn error of immunity would allow for optimized diagnosis, prevention and treatment of patients and their families. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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