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Microorganisms
Special Issues
Detection and Identification of Emerging and Re-Emerging Pathogens
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Detection and Identification of Emerging and Re-Emerging Pathogens

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1684

Special Issue Editors

Prof. Dr. Xing-Yi Ge

E-Mail Website
Guest Editor
Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China
Interests: virus discovery; viral diversity and evolution; coronavirus; emerging pathogens
Special Issues, Collections and Topics in MDPI journals
Dr. Ye Qiu

E-Mail Website
Guest Editor
Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China
Interests: enterovirus; virus–host interaction; pathogenic mechanism; antiviral
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The frequent emergence and re-emergence of viral epidemics have become a severe threat to public health worldwide. Among these, the prominent emerging pathogen SARS-CoV-2 has had a significant impact in recent years. Concurrently, various pathogens have emerged alongside or followed the COVID-19 epidemic, including both emerging and re-emerging pathogens, such as the mpox virus, dengue virus, adenovirus, enterovirus, and so on. The alternating epidemics and co-epidemics of pathogens, including new strains, mutants, and different serotypes, underscore the importance of enhancing the detection and identification of pathogens. Investigating the discovery, classification, and characterization of pathogens forms the foundation for understanding their prevalence, evolution, transmission, and pathogenicity, thereby providing etiological and epidemiological information for the prevention and control of related diseases.

This Special Issue focuses on the detection and identification of emerging and re-emerging pathogens, encompassing clinical pathogens, zoonotic pathogens, vector-borne pathogens, and more. It aims to enhance our understanding of the genomics, epidemiology, evolution, and pathogenicity of these pathogens, and contribute to their prevention.

Prof. Dr. Xing-Yi Ge
Dr. Ye Qiu
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

  • virus
  • pathogen discovery
  • genomic epidemiology
  • intra- and cross-species transmission
  • zoonosis
  • evolution and phylogeny

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

16 pages, 4165 KiB  
Article
Establishment of a Sensitive and Visual Detection Platform for Viable Salmonella in Wastewater That Combines Propidium Monoazide with Recombinase Polymerase Amplification—CRISPR/Cas12a System
by Jiayin Liang, Xintian Sui, Yan Xu, Xiangqun Zheng and Lu Tan
Microorganisms 2025, 13(5), 1166; https://doi.org/10.3390/microorganisms13051166 - 21 May 2025
Abstract
Urban sewage, aquaculture wastewater, and medical wastewater are significant reservoirs and transmission sources of Salmonella. Rapid detection of Salmonella is crucial for effectively reducing the risk of disease transmission and safeguarding public health. Differentiating viable Salmonella from inactivated cells presents significant challenges, [...] Read more.
Urban sewage, aquaculture wastewater, and medical wastewater are significant reservoirs and transmission sources of Salmonella. Rapid detection of Salmonella is crucial for effectively reducing the risk of disease transmission and safeguarding public health. Differentiating viable Salmonella from inactivated cells presents significant challenges, affecting the accurate assessment of pathogen risks. Moreover, current detection methods face several limitations, including lengthy detection periods, high costs, and limited applicability, underscoring the need for rapid, sensitive, and visual detection diagnostic approaches. In this study, we combined propidium monoazide (PMA) with recombinase polymerase amplification (RPA) and clustered regularly spaced short palindromic repeats (CRISPR)/Cas12a systems to develop a rapid detection system for viable Salmonella targeting the fimY gene. DNA of viable Salmonella was amplified and visually detected within 60 min and dead cells were effectively excluded. We assessed the specificity and sensitivity of the PMA-RPA-CRISPR/Cas12a assay. The results showed that the assay had a high level of specificity, with no reactions observed with other pathogens. The application of PMA has no effect on the sensitivity of RPA-CRISPR/Cas12a technology and the visibility of the fluorescence reporting system. We successfully detected viable Salmonella in wastewater with a minimum detection limit of 101 CFU/mL. In summary, the PMA-RPA-CRISPR/Cas12a system developed in this study allows for the rapid and visual detection of viable Salmonella in wastewater at concentrations as low as 101 CFU/mL. By integrating PMA with the RPA-CRISPR/Cas12a technology, this system offers valuable technical support for the efficient, sensitive, and clear detection of viable Salmonella in wastewater. Full article
(This article belongs to the Special Issue Detection and Identification of Emerging and Re-Emerging Pathogens)
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14 pages, 3567 KiB  
Article
Evolutionary Analysis and Antiviral Drug Prediction of Mpox Virus
by Zhong-Hao Lian, Chen-Hui Yang, Ye Qiu and Xing-Yi Ge
Microorganisms 2024, 12(11), 2239; https://doi.org/10.3390/microorganisms12112239 - 5 Nov 2024
Viewed by 1367
Abstract
The resurgence of mpox virus (MPXV) poses a significant challenge to global public health. Currently, there is a limited understanding of the evolutionary details of MPXV during its epidemics, and no specific drugs have been developed for it. Herein, analysis of mutations and [...] Read more.
The resurgence of mpox virus (MPXV) poses a significant challenge to global public health. Currently, there is a limited understanding of the evolutionary details of MPXV during its epidemics, and no specific drugs have been developed for it. Herein, analysis of mutations and positive selection sites (PSSs) within the MPXV genomes revealed 799 mutations and 40 PSSs. Visualization analysis indicated that these mutations and PSSs may affect protein structure. Additionally, a protein–protein interaction (PPI) network between human and MPXV was established, identifying 346 MPXV-interacting human proteins (MIHPs). An interaction network involving MIHPs and other viruses confirmed that these proteins can interact with various viruses that infect humans. Functional analysis of MIHPs suggested their enrichment in host immunity pathways. Lastly, two drugs targeting MIHPs and four compounds targeting MPXV proteins were screened as candidate antivirals against MPXV. These findings not only deepen our understanding of MPXV evolution but also aid in the development of anti-MPXV drugs. Full article
(This article belongs to the Special Issue Detection and Identification of Emerging and Re-Emerging Pathogens)
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