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Microorganisms
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Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition
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Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 11425

Special Issue Editor

Dr. Shengxi Chen

E-Mail Website
Guest Editor
Biodesign Institute, Arizona State University, Tempe, AZ, USA
Interests: cancers; viral infection; emerging pathogens; diagnosis; treatment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, entitled “Diagnosis, Characterization and Treatment of Emerging Pathogens”.

Emerging infectious diseases are perhaps the most rapidly spreading diseases. SARS-CoV-2 has infected 556 million people and caused more than 6 million deaths worldwide. To date, the effects of this virus are still resonating worldwide. Recently, the monkeypox virus emerged and spread to more than 30 countries over the course of about one month. Concurrently, many other pathogens have emerged, including malaria, Zika virus, dengue, Ebola, West Nile virus, and diarrheagenic E. coli, all of which threaten the health of billions of people worldwide. To help in the fight against these emerging infectious diseases, we aim to collect manuscripts focusing on emerging pathogens, including viruses, bacteria, protozoa, and fungi. 

The areas of interest could include, but are not limited to, the following:

  • Novel methods and strategies for the early detection of emerging pathogens;
  • The characterization of specific genes or protein targets for the detection or treatment of emerging pathogens;
  • Novel agents to inhibit emerging pathogens.

Dr. Shengxi Chen
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.

Keywords

  • emerging pathogens
  • detection
  • characterization treatment
  • infectious diseases
  • viruses
  • bacteria
  • protozoa
  • fungi

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Published Papers (8 papers)

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Research

Jump to: Review, Other

17 pages, 8730 KiB  
Article
Mycobacteria Exploit Host GPR84 to Dampen Pro-Inflammatory Responses and Promote Infection in Macrophages
by Reziya Wumaier, Ke Zhang, Jing Zhou, Zilu Wen, Zihan Chen, Geyang Luo, Hao Wang, Juliang Qin, Bing Du, Hua Ren, Yanzheng Song, Qian Gao and Bo Yan
Microorganisms 2025, 13(1), 110; https://doi.org/10.3390/microorganisms13010110 - 8 Jan 2025
Viewed by 1141
Abstract
Tuberculosis (TB) remains the major cause of mortality and morbidity, causing approximately 1.3 million deaths annually. As a highly successful pathogen, Mycobacterium tuberculosis (Mtb) has evolved numerous strategies to evade host immune responses, making it essential to understand the interactions between [...] Read more.
Tuberculosis (TB) remains the major cause of mortality and morbidity, causing approximately 1.3 million deaths annually. As a highly successful pathogen, Mycobacterium tuberculosis (Mtb) has evolved numerous strategies to evade host immune responses, making it essential to understand the interactions between Mtb and host cells. G-protein-coupled receptor 84 (GPR84), a member of the G-protein-coupled receptor family, contributes to the regulation of pro-inflammatory reactions and the migration of innate immune cells, such as macrophages. Its role in mycobacterial infection, however, has not yet been explored. We found that GPR84 is induced in whole blood samples from tuberculosis patients and Mycobacterium marinum (Mm)-infected macrophage models. Using a Mm-wasabi infection model in mouse tails, we found that GPR84 is an important determinant of the extent of tissue damage. Furthermore, from our studies in an in vitro macrophage Mm infection model, it appears that GPR84 inhibits pro-inflammatory cytokines expression and increases intracellular lipid droplet (LD) accumulation, thereby promoting intracellular bacterial survival. Our findings suggest that GPR84 could be a potential therapeutic target for host-directed anti-TB therapeutics. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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16 pages, 2594 KiB  
Article
Structural Characterization of Mycobacterium tuberculosis Encapsulin in Complex with Dye-Decolorizing Peroxide
by Bonnie J. Cuthbert, Xiaorui Chen, Kalistyn Burley, Gaëlle Batot, Heidi Contreras, Shandee Dixon and Celia W. Goulding
Microorganisms 2024, 12(12), 2465; https://doi.org/10.3390/microorganisms12122465 - 30 Nov 2024
Cited by 1 | Viewed by 1216
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the world’s deadliest infectious disease. Mtb uses a variety of mechanisms to evade the human host’s defenses and survive intracellularly. Mtb’s oxidative stress response enables Mtb to survive within activated macrophages, an environment with [...] Read more.
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the world’s deadliest infectious disease. Mtb uses a variety of mechanisms to evade the human host’s defenses and survive intracellularly. Mtb’s oxidative stress response enables Mtb to survive within activated macrophages, an environment with reactive oxygen species and low pH. Dye-decolorizing peroxidase (DyP), an enzyme involved in Mtb’s oxidative stress response, is encapsulated in a nanocompartment, encapsulin (Enc), and is important for Mtb’s survival in macrophages. Encs are homologs of viral capsids and encapsulate cargo proteins of diverse function, including those involved in iron storage and stress responses. DyP contains a targeting peptide (TP) at its C-terminus that recognizes and binds to the interior of the Enc nanocompartment. Here, we present the crystal structure of the Mtb-Enc•DyP complex and compare it to cryogenic-electron microscopy (cryo-EM) Mtb-Enc structures. Investigation into the canonical pores formed at symmetrical interfaces reveals that the five-fold pore for the Mtb-Enc crystal structure is strikingly different from that observed in cryo-EM structures. We also observe DyP-TP electron density within the Mtb-Enc shell. Finally, investigation into crystallographic small-molecule binding sites gives insight into potential novel avenues by which substrates could enter Mtb-Enc to react with Mtb-DyP. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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11 pages, 560 KiB  
Article
Performance Evaluation of NovaplexTM Multiplex Real-Time PCR Assay for Detection of Streptococcus agalactiae Serotypes
by Mallikarjun Handigund and Jaehyeon Lee
Microorganisms 2024, 12(10), 2043; https://doi.org/10.3390/microorganisms12102043 - 10 Oct 2024
Viewed by 1217
Abstract
Streptococcus agalactiae, or group B streptococcus (GBS), is a Gram-positive pathogen with an extended track record of colonization in the gastrointestinal and genitourinary tracts. GBS can induce disease in individuals across all age demographics, yet it predominantly triggers infections in neonates and [...] Read more.
Streptococcus agalactiae, or group B streptococcus (GBS), is a Gram-positive pathogen with an extended track record of colonization in the gastrointestinal and genitourinary tracts. GBS can induce disease in individuals across all age demographics, yet it predominantly triggers infections in neonates and the elderly. Identification of the serotype is vital for effective management of the disease as it provides critical information for clinicians on the cause of the disease. In this study, we evaluated the rapid, simple, and easy-to-adopt multiplex real-time PCR technique, NovaplexTM (NovaPCR). A total of 131 clinical isolates of different serotypes were tested using NovaPCR. Observations revealed that 129 isolates showed the same observations as LA and conventional mPCR. NovaPCR accurately identified serotypes IV and V, which were first classified as serotype Ia in the LA test and mPCR, and the difference between the traditional (LA test and mPCR) and NovaPCR methods is only 1.52%. Accurate serotype identification is helpful for monitoring the epidemics and achieving optimal clinical outcomes, and NovaPCR showed a reliable, fast, easy-to-interpret, and cost-efficient performance in GBS serotyping. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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11 pages, 1148 KiB  
Article
Pulmonary Tuberculosis Diagnosis Using an Intelligent Microscopy Scanner and Image Recognition Model for Improved Acid-Fast Bacilli Detection in Smears
by Wei-Chuan Chen, Chi-Chuan Chang and Yusen Eason Lin
Microorganisms 2024, 12(8), 1734; https://doi.org/10.3390/microorganisms12081734 - 22 Aug 2024
Cited by 1 | Viewed by 2383
Abstract
Microscopic examination of acid-fast mycobacterial bacilli (AFB) in sputum smears remains the most economical and readily available method for laboratory diagnosis of pulmonary tuberculosis (TB). However, this conventional approach is low in sensitivity and labor-intensive. An automated microscopy system incorporating artificial intelligence and [...] Read more.
Microscopic examination of acid-fast mycobacterial bacilli (AFB) in sputum smears remains the most economical and readily available method for laboratory diagnosis of pulmonary tuberculosis (TB). However, this conventional approach is low in sensitivity and labor-intensive. An automated microscopy system incorporating artificial intelligence and machine learning for AFB identification was evaluated. The study was conducted at an infectious disease hospital in Jiangsu Province, China, utilizing an intelligent microscope system. A total of 1000 sputum smears were included in the study, with the system capturing digital microscopic images and employing an image recognition model to automatically identify and classify AFBs. Referee technicians served as the gold standard for discrepant results. The automated system demonstrated an overall accuracy of 96.70% (967/1000), sensitivity of 91.94% (194/211), specificity of 97.97% (773/789), and negative predictive value (NPV) of 97.85% (773/790) at a prevalence of 21.1% (211/1000). Incorporating AI and machine learning into an automated microscopy system demonstrated the potential to enhance the sensitivity and efficiency of AFB detection in sputum smears compared to conventional manual microscopy. This approach holds promise for widespread application in TB diagnostics and potentially other fields requiring labor-intensive microscopic examination. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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12 pages, 1728 KiB  
Article
Emergence of Recombinant Subclade D3/Y in Coxsackievirus A6 Strains in Hand-Foot-and-Mouth Disease (HFMD) Outbreak in India, 2022
by Sanjaykumar Tikute, Pratik Deshmukh, Nutan Chavan, Anita Shete, Pooja Shinde, Pragya Yadav and Mallika Lavania
Microorganisms 2024, 12(3), 490; https://doi.org/10.3390/microorganisms12030490 - 28 Feb 2024
Cited by 2 | Viewed by 2144
Abstract
Coxsackievirus-A6 (CV-A6) is responsible for more severe dermatological manifestations compared to other enteroviruses such as CV-A10, CV-A16, and EV-A71, causing HFMD in children and adults. Between 2005 and 2007, the recombinant subclade D3/RF-A started to expand globally, and a CV-A6 pandemic started. The [...] Read more.
Coxsackievirus-A6 (CV-A6) is responsible for more severe dermatological manifestations compared to other enteroviruses such as CV-A10, CV-A16, and EV-A71, causing HFMD in children and adults. Between 2005 and 2007, the recombinant subclade D3/RF-A started to expand globally, and a CV-A6 pandemic started. The study aimed to conduct whole-genome sequencing (WGS) of an isolated CV-A6 strain from currently circulating HFMD cases from India in 2022. Gene-specific RT-PCR and sequencing were used to perform molecular characterization of the isolated virus. Confirmation of these isolates was also performed by transmission electron microscopy and WGS. Among eleven positive clinical enterovirus specimens, eight CV-A6 strains were successfully isolated in the RD cell line. Isolates confirmed the presence of the CV-A6 strain based on VP1 and VP2 gene-specific RT-PCR. Sequences of isolates were clustered and identified as the novel CV-A6 strain of the D3/Y sub-genotype in India. The studies revealed that the D3/Y sub-genotype is being introduced into Indian circulation. The predicted putative functional loops found in VP1 of CV-A6 showed that the nucleotide sequences of the amino acid were a remarkably conserved loop prediction compatible with neutralizing linear epitopes. Therefore, this strain represents a potential candidate for vaccine development and antiviral studies. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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Review

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22 pages, 361 KiB  
Review
Using In Vitro Models to Study the Interactions Between Environmental Exposures and Human Microbiota
by Qiwen Cheng and Shengxi Chen
Microorganisms 2025, 13(2), 247; https://doi.org/10.3390/microorganisms13020247 - 23 Jan 2025
Viewed by 892
Abstract
Research has demonstrated a close correlation between human microbiota and overall health, highlighting their intimate connection. Exposure to environmental factors, such as chemical contaminants and biological agents, has the potential to alter the composition and function of microbiota, thereby influencing health outcomes. Meanwhile, [...] Read more.
Research has demonstrated a close correlation between human microbiota and overall health, highlighting their intimate connection. Exposure to environmental factors, such as chemical contaminants and biological agents, has the potential to alter the composition and function of microbiota, thereby influencing health outcomes. Meanwhile, microbiota may contribute to host protection by degrading, or rendering harmless, exposures. Environmental exposures demonstrate significant diversity and dynamism; however, conventional methods for exposure–microbiota research, such as animal and epidemiological studies, are often both time-consuming and costly. Additionally, they may raise ethical concerns. This review aimed to examine the existing understanding of employing in vitro models to investigate the interactions between environmental exposures and human microbiota, particularly those located outside the large intestine. A comprehensive search was conducted across the Web of Science, PubMed, and Scopus databases, employing a range of keywords related to microbiota, exposures, and in vitro models. A total of 58 studies fulfilled the search criteria, revealing instances of microbial modulation of exposures and vice versa. It was observed that, although considerable research has been conducted on these interactions in vitro, there remains a pressing need for enhanced model designs and application contexts. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)

Other

Jump to: Research, Review

15 pages, 1000 KiB  
Systematic Review
Unraveling Pediatric Group A Streptococcus Meningitis: Lessons from Two Case Reports and a Systematic Review
by Lavinia Di Meglio, Maia De Luca, Laura Cursi, Lorenza Romani, Mara Pisani, Anna Maria Musolino, Stefania Mercadante, Venere Cortazzo, Gianluca Vrenna, Paola Bernaschi, Roberto Bianchi and Laura Lancella
Microorganisms 2025, 13(5), 1100; https://doi.org/10.3390/microorganisms13051100 - 9 May 2025
Viewed by 200
Abstract
Streptococcus pyogenes meningitis is a rare invasive disease, accounting for less than 2% of bacterial meningitis. We presented two case reports and conducted a systematic review using PUBMED, covering the database from its inception up to 31 December 2024, of pediatric cases of [...] Read more.
Streptococcus pyogenes meningitis is a rare invasive disease, accounting for less than 2% of bacterial meningitis. We presented two case reports and conducted a systematic review using PUBMED, covering the database from its inception up to 31 December 2024, of pediatric cases of Streptococcus pyogenes meningitis. Only case reports and case series were included. Differences in clinical and laboratory parameters were compared between uneventful course and complicated admissions. A total of 57 cases were included. The median age at diagnosis was 4 years. A primary infection focus outside the brain was identified in 61.39% of cases. S. pyogenes was identified from cerebrospinal fluid in 66.66% of cases and from blood in 15.79%. Septic shock occurred in 24.56% of cases, and 36.84% had brain anatomical anomalies. All patients received broad-spectrum empiric antibiotics, while protein-synthesis inhibitors were administered in 26.31% of cases. A total of 17% of patients died, and 28.07% experienced sequelae. The identification of S. pyogenes from blood and a Phoenix Sepsis Score ≥ 2 were significantly associated with a complicated clinical course. Our findings may offer useful insights for the clinical management of Streptococcus pyogenes meningitis. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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8 pages, 1239 KiB  
Case Report
First Case of Candida Auris Sepsis in Southern Italy: Antifungal Susceptibility and Genomic Characterisation of a Difficult-to-Treat Emerging Yeast
by Stefania Stolfa, Giuseppina Caggiano, Luigi Ronga, Lidia Dalfino, Francesca Centrone, Anna Sallustio, Davide Sacco, Adriana Mosca, Monica Stufano, Annalisa Saracino, Nicolo’ De Gennaro, Daniele Casulli, Nicola Netti, Savino Soldano, Maria Faggiano, Daniela Loconsole, Silvio Tafuri, Salvatore Grasso and Maria Chironna
Microorganisms 2024, 12(10), 1962; https://doi.org/10.3390/microorganisms12101962 - 27 Sep 2024
Viewed by 1388
Abstract
Candida auris is an emerging yeast considered a serious threat to global health. We report the first case of C. auris candidemia in Southern Italy, characterized using whole genome sequencing (WGS), and compared with a second strain isolated from a patient who presented [...] Read more.
Candida auris is an emerging yeast considered a serious threat to global health. We report the first case of C. auris candidemia in Southern Italy, characterized using whole genome sequencing (WGS), and compared with a second strain isolated from a patient who presented as C. auris-colonized following screening. The C. auris strain was isolated from clinical samples, identified via MALDI-TOF, and subjected to WGS. Antifungal susceptibility testing was performed using commercial broth microdilution plates, and resistance protein sequences were evaluated with TBLASTN-2.15.0. Following the initial C. auris isolation from patient A, active surveillance and environmental investigations were implemented for all ICU patients. Of the 26 ICU surfaces sampled, 46.1% tested positive for C. auris via real-time PCR. Screening identified a second patient (patient B) as C. auris-colonized. The phylogenetic characterization of strains from patients A and B, based on the D1/D2 region of the 28s rDNA and the internal transcribed spacer (ITS) region, showed high similarity with strains from Lebanon. SNP analysis revealed high clonality, assigning both strains to clade I, indicating a significant similarity with Lebanese strains. This case confirms the alarming spread of C. auris infections and highlights the need for stringent infection control measures to manage outbreaks. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)
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